DMOL3 GUIDE MATERIALS STUDIO 8.0 Copyright Notice
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DMol3 1 Setting up a molecular dynamics calculation20 Introduction 1 Choosing an ensemble 21 Further Information 1 Defining the time step 21 Tasks in DMol3 2 Defining the thermostat control 21 Energy 3 Constraints during dynamics 21 Setting up the calculation 3 Setting up a transition state calculation 22 Dynamics 4 Which method to use? 22 Selecting the thermodynamic ensemble 4 Verifying a transition state 22 Defining the time step 4 Setting up a TS confirmation calculation 23 Controlling the thermostat 4 Setting up a work function calculation 23 Constraints during dynamics 4 Setting up an elastic constants calculation 24 Transition state searching 5 Parameters for the optimization 24 Transition state optimization 6 Setting up a reaction kinetics calculation 24 Transition state searching by synchronous Transition state search 25 transit methods 6 Hessian calculation 25 Verifying a transition state 7 Reaction rate calculation 25 Transition state searching via synchronous Setting up an electron transport calculation 25 transit methods 7 Requesting electronic and structural Input to a synchronous transit calculation 8 properties 26 Restarting a QST calculation 9 Setting up electron densities 27 Transition state searching via eigenvector Setting up electrostatics 27 following 9 Setting up vibrational frequencies 28 Calculation parameters 9 Setting up Raman intensities 28 Use of the Hessian 9 Setting up Fukui functions 28 Geometry optimization 9 Setting up molecular orbital analysis 29 Following a reaction path 10 Setting up a population analysis 29 Elastic constants 11 Setting up band structures 30 Reaction kinetics 11 Setting up density of states 30 Electron Transport 12 Setting up Fermi surfaces 31 Electrodes 12 Setting up COSMO Sigma profile Properties 13 calculation 31 Setting up DMol3 calculations 13 Setting up an optics calculation 31 Setting up electronic options 14 Manipulating files 32 Integration accuracy 14 Input files 32 SCF tolerance 14 Output files 33 k-points 14 Restarting a DMol3 calculation 33 Core treatment 14 Importing a Hessian file 35 Real space cutoff 15 Analyzing DMol3 results 35 Harris approximation 17 Updating structure 36 Solvation scheme 17 Displaying trajectory and chart data 37 Performance tips 18 Creating a trajectory and chart 37 Setting up k-points 18 Animating the trajectory 38 Setting up a geometry optimization 19 Chart Viewer point selection 38 Algorithms for the optimization 20 Visualizing volumetric data 38 Parameters for the optimization 20 Electron density 38 Electrostatic potential 39 Meta-GGA functionals 63 Fukui functions 40 Numerical basis sets 63 Molecular orbitals 40 Atomic basis sets are generated Field visualization 41 numerically 63 Visualizing Fermi surfaces 42 Advantages of numerically derived basis sets 63 Displaying population analysis results 42 Additional basis functions, including Displaying computed charges, spins, and polarization 63 bond orders 43 Numerical integration 65 Displaying band structure charts 43 Atomic and molecular integration grids 65 Displaying density of states charts 44 Integration points, atomic size, precision, Full density of states 45 and computational cost 65 Partial density of states 45 Atomic shells 66 Calculating elastic constants 46 Assuring consistent precision during Displaying the averaged potential chart for integration 66 work function calculations 46 Partition functions improve convergence Analyzing optical properties 47 and avoid nuclear cusps 66 Displaying Raman spectra 48 Pseudopotentials 67 Calculating reaction kinetics 48 Norm-conserving pseudopotentials 68 Displaying solvation properties 49 Evaluating the Coulombic potential Analyzing current and transmission numerically 69 properties 50 The model charge density 70 DMol3 jobs 51 Effect of angular truncation on precision Using DMol3 job control 51 of model charge density 70 Remote DMol3 jobs 51 The Coulombic potential 70 A sample DMol3 run 51 The total potential 70 Computational self-consistent field If a remote DMol3 job fails 53 procedure 70 Running DMol3 in standalone mode 54 Interpolating the numerical atomic bases DMol3 file formats 57 onto the molecular grid 70 DMol3 file formats - ARC 58 Constructing the initial molecular electron DMol3 file formats - BANDS 58 density 71 DMol3 file formats - CAR and MDF 58 Additional computational costs 71 DMol3 file formats - COSMO 58 Reducing the computational cost 71 DMol3 file formats - GRD 59 Damping and convergence 71 DMol3 file formats - HESSIAN 59 Efficiently calculating the electrostatic potential 71 DMol3 file formats - HESSWK 59 Effect of auxiliary density approximation DMol3 file formats - INPUT 60 on accuracy of calculated total energy 72 DMol3 file formats - OCCUP 60 SCF convergence acceleration by DIIS 72 DMol3 file formats - OUTMOL 60 Energy gradients 73 DMol3 file formats - PDOS_WEIGHTS 61 Predicting chemical structure 73 DMol3 file formats - TPVEC 61 First derivative of total energy with DMol3 file formats - TPDENSK 61 respect to change in nuclear position 73 Reaction Kinetics Study Table 61 Derivative of the basis function 74 Theory in DMol3 62 Derivation of other terms 74 Density functional theory (DFT) in DMol3 62 The final equation for the derivative of the Functionals in DMol3 62 energy 75 Local functionals 62 Computational costs 75 Nonlocal functionals 62 Potential problems 75 Hybrid functionals 62 Minimization algorithms; molecular DMol3 TS Optimization dialog 105 symmetry 75 DMol3 TS Confirmation dialog 105 Electronic excitations with TD-DFT 75 DMol3 Elastic Constants dialog 106 Predicting UV-Vis spectra 75 DMol3 Reaction Kinetics dialog 107 Computational costs 76 DMol3 Transport dialog 109 Accuracy of excitation energies and orbital Setup tab 110 overlap 77 Density Mixing 110 TD-DFT in combination with hybrid functionals in DMol3 77 Electrode 111 Molecular dynamics 77 DMol3 Transmission dialog 111 Ensembles 77 DMol3 Current/Voltage dialog 111 NVE ensemble 78 Electrodes tab 111 NVT dynamics 78 Electrostatics tab 112 Constraints 79 DMol3 Poisson Boundary Conditions dialog 112 Point group symmetry 80 Electronic tab 113 COSMO-solvation effects 80 DMol3 Electronic Options dialog 115 DMol3/COSMO 82 SCF tab 116 Determination of the cavity surface (or solvent-accessible surface) 83 k-points tab 117 Determination of non-electrostatic Orbital Cutoff tab 118 contributions to the free energy of Solvent tab 119 solvation 83 DFT-D tab 120 COSMO-SAC model 83 Properties tab 121 COSMO sigma profile 84 Band structure selection 122 Electric field gradients 84 Density of states selection 122 Thermodynamic calculations 86 DMol3 Density of States Options Enthalpy 86 dialog 123 Entropy 87 Electron density selection 124 Heat capacity 87 Electrostatics selection 125 Using the results 88 Frequency selection 125 Fitting atomic point charges to the Partial Hessian dialog 126 electrostatic potential (ESP) 88 Fukui function selection 127 Mulliken and Mayer bond orders 89 Optics selection 127 Hirshfeld charge analysis 90 DMol3 Optics Options dialog 128 Fukui functions 91 Orbitals selection 129 Raman spectra 92 Population analysis selection 129 Basis set superposition error 93 DMol3 Grid Parameters dialog 130 Converging SCF 93 Job Control tab 131 Challenging systems 94 DMol3 Job Control Options dialog 132 Checklist 94 DMol3 Job Files dialog 133 Dialogs in DMol3 96 DMol3 Analysis dialog 133 DMol3 Calculation dialog 96 Band structure selection 134 Setup tab 96 Current/Voltage selection 135 DMol3 Energy dialog 99 Density of states selection 136 DMol3 Geometry Optimization dialog 100 DMol3 DOS Analysis Options dialog 137 DMol3 Dynamics dialog 101 Elastic constants selection 138 Dynamics tab 102 Electron density selection 138 Thermostat tab 102 Energy evolution selection 139 DMol3 Transition State Search dialog 103 Fermi surface selection 139 Fukui function selection 140 Optics selection 141 DMol3 Optics Analysis Options dialog 141 Orbitals selection 142 Population analysis selection 143 Potentials selection 144 Raman spectrum selection 144 Reaction kinetics selection 145 Solvation properties selection 146 Choose COSMO File dialog 146 Structure selection 147 Thermodynamic properties selection 147 Transmission selection 148 DMol3 keywords 149 DMol3 References 150 DMol3
Introduction DMol3 allows you to model the electronic structure and energetics of molecules, solids, and surfaces using density functional theory (DFT). This produces highly accurate results, while keeping the computational cost fairly low for an ab initio method. You can study a broad range of systems using DMol3, including organic and inorganic molecules, molecular crystals, covalent solids, metallic solids, and surfaces of a material. With DMol3, you can predict structure, reaction energies, reaction barriers, thermodynamic properties, and optics and vibrational spectra. DMol3 uses DFT to produce highly accurate results, while keeping the computational cost fairly low for an ab initio method. You can learn more about how DMol3 works in the Theory in DMol3 section.
Note: DMol3 is suitable for molecules and 3D periodic solids, but will not work for 1D or 2D periodic structures. To model such systems, you must build a 3D structure with a vacuum between periodic copies.
Further Information For more information about the Materials Studio and other Accelrys software products, visit BIOVIA Support on the Web: https://community.accelrys.com/index.jspa
DMol3 | Page 1 Tasks in DMol3 The DMol3 module allows you to model the electronic structure and energetics of organic and inorganic molecules, molecular crystals, covalent solids, metallic solids, and infinite surfaces. DMol3 can currently perform several different tasks: n Single-point energy calculation n Geometry optimization n Molecular dynamics n Transition-state search n Transition-state optimization n Following a reaction path n Elastic constants calculations n Reaction kinetics calculations n Electron transport calculations Each of these calculations can be set up so that it generates specified chemical and physical properties. An additional task, known as a properties calculation, allows you to restart a completed job to compute additional properties that were not calculated as part of the original run. There are a number of steps involved in running a DMol3 calculation, which can be grouped as follows: n Structure definition: A 3D Atomistic document containing the system of interest must be specified. There are a number of ways to prepare a structure: n Molecules can be built using the sketching tools in the Materials Visualizer n Polymers can be constructed using the Polymer Builder in the Materials Visualizer n 3D periodic structures can be built using the tools available in the Materials Visualizer for building crystals n Nanostructures can be prepared using the tools available in the Nanostructure Builder in the Materials Visualizer n Existing structures can be modified using the Materials Visualizer sketching tools n Structures can be imported from an existing structure file In the case of a transition-state calculation, a 3D Atomistic Trajectory document containing a reaction sequence is required as the input document. You should define the structures of the reactants and the products in two separate 3D Atomistic documents via the methods listed above and then use the Reaction Preview tool to generate the trajectory.
Note: DMol3 can only be used to perform calculations on molecules and 3D periodic structures (crystals). Structures with 2D periodicity (surfaces) cannot be used in DMol3. n Calculation setup: Once a suitable 3D structure document has been defined, then it is necessary to select the type of calculation to be performed and set the associated parameters. For example, in the case of a transition-state search, these parameters include the search protocol and the convergence threshold. Finally, the server on which the calculation is to be run should be selected and the job initiated. n Analysis of the results: When the calculation is complete, the files related to that job are returned to the client and, where appropriate, displayed in the Project Explorer. The tools on the DMol3 Analysis dialog may be used to visualize the results of the calculation.
Page 2 | Materials Studio • DMol Guide To select a DMol3 task 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Select the Setup tab. 3. Select the required DMol3 task from the Task dropdown list. Energy The "total energy" of a molecule or crystal refers to the energy of a specific arrangement of atoms as calculated using Eq. DFT-8 or Eq. DFT-12. The zero of energy is taken to be the infinite separation of all electrons and nuclei, so the total energy is generally negative, corresponding to a bound state. This quantity should not be confused with the "binding energy", which is the energy required to separate the individual atoms. Both of these quantities appear in the DMol3 output file. The default unit of energy in DMol3 is the Hartree (Ha) or atomic unit (au), equivalent to 627.5 kcal/mol. By comparing total energies of different systems you can compute many properties of chemical significance such as: n heats of reaction n energy barriers n conformational energy differences n bond strengths n adsorption energies Setting up the calculation The energy computed by DMol3 for a particular molecular or crystalline geometry depends upon a number of computational parameters. When comparing energies, it is necessary that you use the same parameters for each system. When you set up a calculation using the DMol3 Calculation dialogs, Materials Studio selects reasonable defaults for you, so it is not absolutely necessary to choose new values for these parameters. 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. Open the Setup tab. 3. Set the Task to Energy. 4. Set the charge and spin state of the system. 5. Set the exchange-correlation functional. This specifies the DFT functional that will be used in the calculation. In general, LDA functionals provide quicker calculations, but GGA functional provide more reliable results. For any calculations involving comparison of energies, GGA functionals are recommended. 6. If a basis set superposition error (BSSE) calculation is required, click the More... to open the DMol3 Energy dialog and prepare the appropriate atom sets. 7. Select the electronic parameters for the calculation on the Electronic tab. The most important options are discussed in Setting up electronic options. 8. Set the basis set. This controls the number of atomic orbitals used to describe each molecular orbital. The numerical basis sets used in DMol3 provide a means of balancing the cost and accuracy of a calculation. 9. Select appropriate options on the Job Control tab. The most important option to specify is the Gateway location, or the name of the compute server. 10. Click the Run button.
Tasks in DMol3 | Page 3 Dynamics Molecular dynamics in DMol3 allows you to simulate how the atoms in a structure will move as a function of time under the influence of computed forces by solving Newton's classical equations of motion, modified, where appropriate, to take account of the effects of temperature on the system. Before performing a DMol3 molecular dynamics calculation, you should select a thermodynamic ensemble and set the associated parameters, specify the simulation time, and enter the temperature at which the simulation is to be carried out. Selecting the thermodynamic ensemble Integrating Newton's equations of motion allows you to explore the constant energy surface (NVE dynamics) of a system. However, most natural phenomena occur under conditions where a system exchanges heat with the environment. These conditions can be simulated using NVT ensembles (Gaussian, Nosé-Hoover, or (massive) generalized Gaussian moments). Defining the time step An important parameter in the integration algorithm is the time step. To make the best use of computation time, a large time step should be used. However, if the time step is too large, it may lead to instability and inaccuracy in the integration process. Typically, this is manifested as a systematic drift in the constant of motion, but it can also lead to the job failing unexpectedly due to a large energy deviation between steps. Controlling the thermostat A second important parameter for NVT ensembles is the definition of the thermostat mass or relaxation time step. For Nosé-type thermostats, this is done by defining a ratio between the thermostat mass and the desired kinetic energy of the system. For the two generalized Gaussian moments thermostats, this is done by defining a time scale, τ, which must be significantly larger than the time step. Constraints during dynamics DMol3 supports two types of constraints during molecular dynamics simulations via Materials Studio interface: n Internal coordinates can be fixed (distances, angles, and torsions) n Individual atom positions can be fixed
Page 4 | Materials Studio • DMol Guide To perform a molecular dynamics calculation 1. Either import the structure from a pre-existing file or construct a new system using the sketching tools or the tools for building crystals and nanostructures in the Materials Visualizer. 2. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 3. Select the Setup tab and choose Dynamics from the Task dropdown list. 4. Set the Quality of the calculation. 5. If you wish to customize any of the job settings, click he More... button to display the DMol3 Dynamics dialog and alter the parameters accordingly. 6. Select the exchange-correlation functional from the Functional dropdown lists. This specifies the DFT functional that will be used in the calculation. In general, LDA functionals produce faster calculations, but GGA functionals yield more reliable results. For any calculations involving comparison of energies, GGA functionals are recommended. 7. If you wish to carry out a spin-unrestricted calculation, check the Spin unrestricted checkbox, then either check the Use formal spin as initial checkbox or select a particular spin state that the calculation will be carried out on from the Multiplicity dropdown list. Specify the charge of the system. 8. Select the Electronic tab. Set the electronic parameters for the calculation. The most important options are discussed in the Setting up electronic options topic. 9. Select a basis set. This controls the number of atomic orbitals used to describe each molecular orbital. The numerical basis sets used in DMol3 provide a means of balancing the cost and accuracy of a calculation. 10. Select the Properties tab. If you wish to compute any additional properties of the system as part of the DMol3 run, check the appropriate checkboxes in the list and set the associated parameters as required. 11. Select the Job Control tab and choose a server on which to run the DMol3 job from the Gateway location dropdown list. If necessary, specify the Queue to which the job will be submitted. DMol3 will automatically assign a name to the job based on the name of the 3D structure document containing the system being studied. If you wish to specify an alternative name, uncheck the Automatic checkbox and enter the new name in the Job description text box. 12. Specify the number of cores on which to run the job in the Run in parallel on field. 13. Click the More... button to display the DMol3 Job Control Options dialog. Select the documents to be used for live updates and set the behavior of DMol3 on job completion. 14. Click the Run button. 15. If you wish, you can examine the intermediate results to ensure that the calculation parameters are reasonable. 16. After the job has finished, view the output files. You can then analyze the results.
Note: When starting an MD simulation a geometry optimization should be performed on a system studied, with the same parameters (basis set, functional etc.). If the system is not in its equilibrium geometry, large fluctuations and/or lack of MD convergence may be expected.
Transition state searching When a molecular or crystal structure is built, it usually needs to be refined to bring it to a stable geometry. The refinement process is known as optimization (or minimization) and is an iterative procedure in which the coordinates of the atoms are adjusted so that the energy of the structure is brought to a stationary point, i.e., one in which the forces on the atoms are zero. A transition state is a
Tasks in DMol3 | Page 5 stationary point that is an energy maximum in one direction (the direction of the reaction coordinate) and an energy minimum in all other directions. During the course of chemical reaction, the total energy naturally changes. Starting from the reactants, the energy increases to a maximum and then decreases to the energy of the products. The maximum energy along the reaction pathway is known as the activation energy; the structure corresponding to this energy is called the transition state. You can also perform an optimization to a transition state by setting the Task to TS Optimization or to TS Search. By performing geometry optimization you can predict barriers to chemical reactions and determine reaction pathways.
Note: When a transition state search is performed on a periodic system the unit cell is fixed. DMol3 offers two different methods for locating a transition state. Transition state optimization When you use the TS Optimization task, DMol3 starts from a reasonable guess for the transition state and performs a Newton-Raphson search on the potential energy surface. This uses techniques similar to a search for an energy minimum but searches instead for an energy maximum along one normal mode. Because this method follows one of the Hessian eigenvectors to an energy maximum, the method is often referred to as "eigenvector following" (EF). You must have a Hessian associated with the model in order to perform transition state optimization. Before proceeding, generate a Hessian by requesting a frequency calculation on the starting geometry. The transition state setup will automatically detect whether or not you have a Hessian, and it will not allow you to submit a transition state optimization without one. See the section on Transition state searching via eigenvector following for additional information. To perform a transition state optimization 1. Choose Modules | DMol3 | Calculation from the menu bar. 2. Open the Setup tab and set the Task to TS Optimization. 3. Select Vibrational Analysis from the Tools menu. This dialog is used to specify the vibrational frequencies and normal modes. Select the frequency of the normal mode that corresponds to the reaction coordinate by clicking on the frequency in the tabulated list. This mode is used by the transition state optimization to search for a maximum. 4. If desired, set additional options by selecting the More... button to bring up the DMol3 TS Optimization dialog. 5. Click the Run button. Transition state searching by synchronous transit methods Starting from reactants and products, the synchronous transit methods interpolate a reaction pathway to find a transition state. These methods alternate searching for an energy maximum with constrained searches for a minimum in order to refine the transition state to a high degree. See the section on Transition state searching via synchronous transit methods for background information.
Page 6 | Materials Studio • DMol Guide To perform a transition state search 1. Construct or import one model representing reactants and a second for products. 2. Determine the correspondence between atoms in the two documents using the Find Equivalent Atoms tool. The synchronous transit method works by performing a geometric interpolation between the atomic coordinates of the atoms in the reactants with the atoms in the products. In order to accomplish this, it is necessary that the program understand which atom matches to which. 3. Generate a trajectory that converts reactants into products using the Reaction Preview. You can animate this document to verify that the reactants are converted correctly to products. If you are satisfied with the match, proceed with the calculation. If not, use the Find Equivalent Atoms tool to edit the atom correspondence and try again. 4. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 5. Set the Task to TS Search on the Setup tab. 6. If desired, click the More... button to open the DMol3 Transition State Search dialog where you can set additional options (such as Optimize reactants and products). 7. Click the Run button.
Tip: For best results you should optimize the structures of the reactants and products before generating the trajectory in step 3. Verifying a transition state At the conclusion of a successful transition state calculation by either method, you will have a stationary point. It is more difficult to prove that the stationary point actually corresponds to a transition state. To do this, you must perform a vibrational analysis. A true transition state will have one imaginary vibrational frequency whose normal mode corresponds to the reaction coordinate; all other eigenvalues will be real. A structure with two or more imaginary frequencies is not a true transition state. In such cases, it will be possible to locate a lower energy barrier by following one of the modes.
Tip: You can request that a vibrational frequency calculation be performed automatically following a successful transition state optimization or transition state search. Simply select Frequency on the Properties tab. Transition state searching via synchronous transit methods Synchronous transit methods are used to find a transition state (TS) when reasonable structures for the reactants and products exist, but the location of the TS is unknown. You can perform this type of calculation by setting the Task to TS Search. Starting from reactants and products, the synchronous transit methods interpolate a reaction pathway to find a transition state. The Linear Synchronous Transit (LST) method performs a single interpolation to a maximum energy. The Quadratic Synchronous Transit (QST) method alternates searches for an energy maximum with constrained minimizations in order to refine the transition state to a high degree. The options available through DMol3 include:
Tasks in DMol3 | Page 7 n LST Maximum performs a single LST maximization, bracketing the maximum between the reactants and product. This is the quickest but least accurate of the options. The TS structure determined by this method generally requires further refinement. n LST/Optimization performs an LST maximization, followed by an energy minimization in directions conjugate to the reaction pathway. This yields a structure lower in energy and closer to the true TS than a simple LST. Minimization steps continue until an energy minimum is reached or the number of conjugate directions is exhausted. n Halgren-Lipscomb is a kind of limited LST/Optimization, and is designed to reproduce the algorithm popularized by Halgren and Lipscomb. After determining the LST maximum, this method performs a conjugate gradient minimization, but only in a single direction. n Complete LST/QST begins by performing an LST/Optimization calculation. The TS approximation obtained in that way is used to perform a QST maximization. From that point, another conjugate gradient minimization is performed. The cycle is repeated until a stationary point is located or the number of allowed QST steps is exhausted. This is considerably more accurate than the other methods, yielding results close to those obtainable using eigenvector following methods. Input to a synchronous transit calculation There are few parameters for these sorts of calculations, and they are discussed on the DMol3 Transition State Search - Setup topic. The synchronous transit calculations are always performed in Cartesian coordinates. There is no option to override this. Unlike other methods, the synchronous transit calculations require a trajectory rather than a single model. Follow this procedure to set up a calculation. To set up a synchronous transit calculation 1. Begin by constructing two separate documents, one for the reactants and a second for the products. 2. Determine the correspondence between atoms in the two documents using the Find Equivalent Atoms tool. The synchronous transit method performs a geometric interpolation between the atomic coordinates of the atoms in the reactants and the atoms in the products. In order to accomplish this, it is necessary that the program understand which atom matches to which. 3. Generate a trajectory that converts reactants into products using the Reaction Preview tool. You can animate this document to check that the reactants are converted correctly to products. If you are satisfied with the match, proceed with the calculation. If not, use the Find Equivalent Atoms tool to edit the atom correspondence and try again. 4. Using the document that was created by the Reaction Preview tool, select your options for the TS Search calculation and submit the DMol3 calculation by pressing the Run button.
Note: Problems may arise when the reactant and product structures have high symmetry but the transition state does not. In these cases, the interpolation procedure may be unable to break symmetry. It is recommended in such cases that you manually break the symmetry of the structure by a small amount.
For example, consider the HNC to CNH rearrangement. If the reactant and product are both perfectly linear, then interpolated geometries will always put the H colinear with C and N. Bending the HCN angle even by 0.1° solves this problem and allows the procedure to locate the correct transition state.
Page 8 | Materials Studio • DMol Guide Restarting a QST calculation One further option is available on the TS Search dialog: QST/Optimization. This option allows you to use the results of a DMol33 synchronous transit calculation as the starting point for a QST calculation. In this way, you can further refine the results of any of the four different types of calculations mentioned above. The result of any of these calculations is a trajectory document. Provided you have such a trajectory, simply use it as input to DMol3: open the document, select QST/Optimization on the DMol3 Transition State Search dialog, and submit the job to DMol3. In principle, this procedure may be repeated indefinitely; in practice, little refinement will be generated after the first five cycles of a QST. Transition state searching via eigenvector following Searching for a transition state (TS) by eigenvector following (EF) is similar to performing a geometry minimization. Many of the options are the same, and the setup dialogs are similar. Whereas the minimization will automatically choose from among several algorithms for the minimization, the TS optimization in DMol3 always uses a Newton-Raphson method. Like the minimization, the TS optimization can proceed in Cartesian, internal, or redundant internal coordinates. DMol3 chooses the most efficient method to perform the calculation. Starting from a reasonable guess for the TS, DMol3 performs a Newton-Raphson search on the potential energy surface. This searches for an energy maximum along one normal mode and a minimum along all other nodes. This method requires the presence of a Hessian matrix in order to compute the normal modes. Generate a Hessian by performing a frequency calculation on the starting geometry. Calculation parameters Perform an EF calculation by setting the Task to TS Optimization on the Setup tab of the DMol3 Calculation dialog. The most important setup parameter is Quality. The Quality control specifies how close to a minimum you want to get. As described in the DMol3 TS Optimization dialog topic, the quality setting controls the convergence thresholds for energy change, maximum force, and maximum geometry displacement between optimization cycles. The optimization will stop when at least two of these criteria are satisfied. Use of the Hessian If you have computed a Hessian using Materials Studio, it will be imported automatically when you open the job for analysis. To import a Hessian file from another calculation see the HESSIAN file format topic. Select the normal mode that the EF method will follow. This should be the mode corresponding most closely to the reaction coordinate. Generally, this will be the mode of the only imaginary frequency, or the imaginary frequency largest in magnitude. To specify the mode, use controls on the Vibrational Analysis dialog to compute the vibrational frequencies. On the tabulated list of frequencies, select the frequency you wish to follow by clicking on the row. The EF method will use the this mode when you start the calculation. Geometry optimization After a molecular or crystal structure is built, it usually needs to be refined to bring it to a stable geometry. The refinement process is known as optimization, and is an iterative procedure in which the coordinates of the atoms are adjusted so that the energy of the structure is brought to a stationary point, i.e., one in which the forces on the atoms are zero. You can request an energy minimization, a search for a relative minimum on the energy hypersurface. The geometry corresponding to this structure should have a close resemblance to an actual physical
Tasks in DMol3 | Page 9 structure of the system at equilibrium. You can also perform an optimization to a transition state. Searching for a transition state is covered elsewhere. In this section, "geometry optimization" is taken to mean "geometry minimization". To perform a geometry optimization (minimization) 1. Choose Modules | DMol3 | Calculation from the menu bar. 2. Open the Setup tab. 3. Set the Task to Geometry Optimization. 4. If desired, set additional options by selecting the More... button to bring up the DMol3 Geometry Optimization dialog. Normally, the default options will yield adequate results. 5. Click the Run button.
Tip: When high accuracy is required in geometry optimization, set the Quality to Fine on the Geometry Optimization dialog. In addition, it is recommended that you set both Integration accuracy and SCF tolerance to Fine on the Electronic tab.
Tip: Optimization using delocalized internals may fail if angles close to 180 degrees occur during optimization. In such cases, specify a value using the Opt_Bend_Lin keyword. This sets a threshold, in degrees, that limits the number of linear bends. The default value is 0.01, and can be increased significantly to improve the robustness of the optimization procedure.
Note: The Hessian file resulting from a DMol3 geometry optimization run should not be used to obtain the vibrational spectrum.
Following a reaction path The LST and QST tools locate a maximum energy structure along the reaction path, but this maximum may not, in fact, be the transition state that you are looking for. You can use the TS confirmation tool to confirm that the transition state found does indeed connect your presumed reactant and product. To perform a Transition State Confirmation 1. First perform a TS Search using LST or QST. The trajectory computed by this method is used as input to the TS Confirmation. Make sure this trajectory document is in focus when you set up the TS Confirmation. 2. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 3. Open the Setup tab. 4. Set the Task to TS Confirmation. 5. If desired, set additional options by selecting the More... button to bring up the DMol3 TS Confirmation dialog. Normally, the default options will yield adequate results. 6. Click the Run button. Users should be aware that TS Confirmation jobs can take a long time to complete. These jobs perform a series of geometry optimizations along the reaction pathway, requiring quite a lot of computer time.
Tip: At the end of the calculation, you can select any geometry on the reaction pathway using the chart/trajectory tools and perform subsequent calculations. In this way you could, for example, perform further geometry optimization on an interesting structure.
Page 10 | Materials Studio • DMol Guide Elastic constants In DMol3, the mechanisms responsible for optimizing the unit cells of periodic systems can also be used to calculate the mechanical properties (for example, the elastic constants) of these materials. This is achieved by obtaining the stress tensor of a given unit cell by applying finite displacement distortions. For each distortion, the energy is minimized using a standard geometry optimization procedure. The elastic constant tensor is then calculated from the energies corresponding to each finite displacement. The analysis section for elastic constants in DMol3 also calculates common mechanical properties that can be derived from the elastic constants tensor.
Note: Elastic constants should only be calculated on periodic structures with optimized lattice constants. Use Periodicity (Materials) and then Property Range Filter to assess and filter periodic data records.
Reaction kinetics Reaction rate coefficients can be estimated from transition state theory. Canonical transition state theory assumes that the energy distribution of the reacting species does not vary significantly from the Boltzmann distribution. This allows the rate coefficient to be calculated in terms of the canonical partition functions of the reactant(s) and transition state, the reaction threshold energy, and the heat of reaction. To calculate a reaction rate coefficient 1. Perform a TS Search using LST or QST. The 3D Atomistic Collection document generated will be used as input for the Reaction Kinetics task. You must ensure that it is in focus when you set up Reaction Kinetics.
Tip: LST/QST search often produces only an approximate transition state which should be optimized further. To make this step easier it is advisable to request frequency calculations at end of the successful transition state search (see DMol3 Properties for more details). 2. In order to calculate the correct rate coefficient, the Reaction Kinetics task needs to determine the type of reaction - whether it is an isomerization reaction, an association/dissociation reaction, or an exchange reaction. Reaction Kinetics does this by attempting to assign motion groups to the reactive fragments, however, if desired, motion groups on the reactant(s) and product(s) can be explicitly set using the Motion Groups dialog. 3. Select Modules | DMol3 | Calculation from the Materials Studio menu bar to open the DMol3 Calculation dialog. 4. On the Setup tab, choose Reaction Kinetics from the Task dropdown list. 5. Click the More... button to open the DMol3 Reaction Kinetics dialog and specify more advanced options if required. Normally, the default options will yield adequate results. 6. If the Optimize transition state checkbox is checked you should ensure a Hessian matrix is present.
Tip: You can check whether a Hessian matrix is available using the Vibrational Analysis dialog, this also allows you to inspect which eigenvectors will be followed during the transition state optimization phase of the Reaction Kinetics run. 7. Click the Run button.
Tasks in DMol3 | Page 11 When Reaction Kinetics calculation has successfully completed a new 3D Atomistic Collection document containing optimized structures of the reactant(s), product(s), and transition state with their Hessians and total energies will be generated. The Reaction kinetics analysis option in DMol3 can now be used to calculate and fit the reaction rate coefficient. Electron Transport The DMol3 Electron Transport task allows you to calculate electron transport properties, such as transmission and current, using non-equilibrium Green's function theory. For a structure to be valid for the transport task it must contain two electrodes. Electrodes and complete devices can be constructed using the Transport Device Builder tools. Note: The DMol3 Electron Transport task cannot be run under certain circumstances, if: n On the Setup tab of the DMol3 Calculation dialog: n Use method for DFT-D correction checkbox is checked n Functional is set to B3LYP or m-GGA option n Spin unrestricted checkbox is checked n Charge is set to any non-zero value n On the Electronic tab of the DMol3 Calculation dialog: n Core treatment is not set to DFT Semi-core Pseudopots when there is an element with Z > 20 n Use solvation model checkbox is checked n On the Properties tab of the DMol3 Calculation dialog, any of the following are selected: n Density of states n Electron density n Electrostatics n Frequency n Fukui function n Optics n Orbitals n Population analysis Electrodes Electrodes are represented by semi-periodic structures that are connected to a central region of the device. The electrode comprises two regions; a wire and a tip. The wire region is a repeat unit that will be used to define the semi-periodic part of the contact. The tip region defines a section of the electrode that is part of the central device region. When the electrode is translated or rotated using the editing tools the operation will apply to the atoms in both regions. The setup of electron transport calculations requires a buffer region between the electrode and device that has exactly the same periodically continued structure as the electrode. Materials Studio automatically determines the minimal necessary buffer size from the atomic radial cutoff and inserts these atoms into the entire system. This automatic insertion means that there will be more atoms in the electrode than shown in the visual displays. Nevertheless, it is still recommended that you should converge the size of their electrodes and add additional electrode atoms to the boundary region if possible.
Page 12 | Materials Studio • DMol Guide Properties Use the Properties tab on the DMol3 Calculation dialog to request that electronic or structural properties be calculated as part of the DMol3 run. You can view the results using the DMol3 Analysis dialog. Each time that you want to compute more properties, you must submit another DMol3 calculation. The properties that can be requested through the Properties tab are: n Electron densities n Electrostatics n Vibrational frequencies n Fukui functions n Molecular orbitals n Atomic populations n Band structure n Density of states (DOS) n Optics To include properties as part of your DMol3 calculation 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. Select the Properties tab. 3. Check the checkbox next to the desired property, for example Electron density. 4. In most cases, checking the checkbox will provide you with additional options. For example, checking the Electron density checkbox presents you with the option of computing any or all of the total density, deformation density, and spin density. Check the appropriate checkboxes to compute the desired properties. 5. Repeat for all desired properties. 6. Click the Run button. If you uncheck the checkbox next to one of the major property headings, then all the associated properties will become inaccessible. For example, if you uncheck the Electron density checkbox, then none of the three types of densities can be computed. Setting up DMol3 calculations The topics in this section describe how to set up DMol3 calculations of various types, as well as the ways in which the job control facility can be used. There are a number of options that are understood by DMol3 which are not currently accessible via the Materials Studio interface. Such options can be utilized by manually editing the DMol3 input files. Information about how to do this is also presented in this section. A convenient way to select DMol3 options is to specify the overall quality of calculations by using the Quality option on the Setup tab of the DMol3 Calculation dialog. Testing confirms that the overall accuracy of calculations, as measured by the total energy, depend on the choice of Quality option as follows: n Coarse - 1.0 × 10-4 Ha n Medium - 1.0 × 10-5 Ha n Fine - 1.0 × 10-6 Ha
Tasks in DMol3 | Page 13 Tip: Use the Coarse quality setting for qualitative and approximate calculations. The Medium and Fine settings are designed to produce accurate quantitative results.
For structure optimizations, it is often best to use a Fine numerical integration grid for both Medium and Fine quality calculations. Setting up electronic options The electronic options control the details of the way that DMol3 solves the SCF equations. To set electronic options 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Select the Electronic tab. Most of the important parameters can be set using the controls on this tab. 3. Click the More... button to display the DMol3 Electronic Options dialog. This dialog allows finer control over some of the electronic parameters and offers additional settings. Integration accuracy The integration accuracy controls the precision with which Hamiltonian matrix elements are computed, as described in the Numerical integration topic. Generally, you should not need to change this parameter from the default. You could use a Coarse grid for performing fast calculations of limited accuracy. A Fine integration grid is recommended when you wish to converge geometry optimizations to high accuracy. To set the integration accuracy, choose Coarse, Medium, or Fine from the Integration accuracy dropdown list. SCF tolerance The SCF tolerance control specifies the accuracy to which the SCF equations are converged. Normally, the default accuracy of Medium is sufficient. When you need to converge a geometry optimization to high accuracy, then the Fine setting is recommended. k-points The k-point set control specifies the number of wave vectors used to describe the band structure of periodic systems. When studying large nonsymmetrical systems, it is often sufficient to use the so-called Γ-point. In other cases, the default setting should be adequate. To set the number of k-points choose Gamma, Coarse, Medium, or Fine from the k-point set dropdown list. For more details on controlling the number of k-points, see Setting up k-points. Core treatment The Core treatment parameter controls how electrons in the lowest lying atomic orbitals are treated. The default setting, All Electron, treats these in the same manner as valence electrons, and is appropriate for atoms up to about atomic number 36 (Kr). With heavier elements, relativistic effects become important in the core electrons. One method of incorporating these effects is to use the All Electron Relativistic option. As the name implies, the core electrons are still included in the calculation, but scalar relativistic effects are included (Koelling and Harmon, 1977; Douglas and Kroll, 1974). This yields a more accurate calculation, but increases the computational cost. An alternative to all-electron calculations is to use DFT Semi-core Pseudopots (DSPP; Delley, 2002) or Effective Core Potentials (ECP; Dolg et al., 1987; Bergner et al., 1993). These replace the effects of core
Page 14 | Materials Studio • DMol Guide electrons with a simple potential. Because the core electrons are dropped, the calculation is less computationally expensive, but because these core potentials include some degree of relativistic effects, they can be very useful approximations for heavier elements. You cannot restrict the use of ECPs or DSPPs to specific elements. Whenever you use either option, DMol3 examines a data file that contains the potentials. If DSPP or ECP data are found for an element, then the core electrons for that element are replaced; if the data are not found for an element, then all its electrons are retained. Currently, DSPPs and ECPs are provided beginning with element number 21, Sc. For example, in a system containing H, O, Al, Cu, and Au, if you opt to use ECPs or DSPPs, only the core electrons for Cu and Au will be replaced; H, O, and Al will be treated as in the all-electron case. When it is necessary to use one of these approximations, Accelrys recommends that you use DSPPs rather than ECPs. The former have been developed specifically for DMol3 calculations, whereas the latter are Hartree-Fock potentials. To set the type of core treatment, choose All Electron, Effective Core Potential, All Electron Relativistic, or DFT Semi-core Pseudopots from the Core treatment dropdown list. Real space cutoff In principle, when performing numerical integrations, the charge density and functionals must be integrated over all space. Because the density drops off quickly as the distance from an atomic nucleus increases, in practice, it is possible to limit the range of the integrations. This serves to reduce computation time with little impact on the accuracy of the results. This cutoff is actually applied to the generation of the numerical basis sets. A global real space cutoff is selected for every system as a maximum value of the cutoffs specific for every element of that system. Earlier versions of DMol3 applied the same default value for real space cutoffs to all systems.
Real space cutoffs for elements were optimized by considering total energies of atoms at various quality levels of DMol3 calculations. For every quality level, the chosen Cutoff_Element values lead to the atomic energies, which differ from the reference energy within the accuracy thresholds defined for the quality levels: n Coarse - 1.0 eV atom-1 n Medium - 0.3 eV atom-1 n Fine - 0.1 eV atom-1 The reference energy is assumed to be that calculated using the Fine quality setting and with a real space cutoff of 6.5 Å. The tables below specify Cutoff_Element values, in Å, for each quality level. Typically the cutoff values increase within a column and decrease within the row of the Periodic Table. The current implementation assumes the values for the lanthanides are the same as for La and those for the actinides are the same as for Ac.
Tasks in DMol3 | Page 15 Default Cutoff_Element values (Å) for Coarse quality calculations
H He 3.0 3.0 Li Be B C N O F Ne 3.6 3.3 3.1 3.0 3.0 3.0 3.0 3.0 Na Mg Al Si P S Cl Ar 3.8 3.7 3.5 3.5 3.4 3.3 3.3 3.2 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 4.2 4.2 4.0 3.9 3.7 3.6 3.5 3.5 3.4 3.4 3.4 3.4 3.5 3.5 3.4 3.3 3.3 3.3 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 4.3 4.4 4.2 4.0 3.8 3.7 3.6 3.6 3.4 3.4 3.4 3.5 3.6 3.6 3.6 3.6 3.5 3.4 Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn 4.5 4.6 4.3 4.0 3.8 3.7 3.7 3.6 3.4 3.4 3.4 3.5 3.7 3.7 3.7 3.7 3.6 3.6 Fr Ra Ac 4.6 4.7 4.5 Default Cutoff_Element values (Å) for Medium quality calculations
H He 3.0 3.0 Li Be B C N O F Ne 4.4 3.9 3.4 3.3 3.2 3.2 3.2 3.2 Na Mg Al Si P S Cl Ar 4.5 4.3 4.2 4.0 3.7 3.6 3.4 3.3 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 4.9 4.8 4.7 4.5 4.4 4.4 4.4 4.3 4.1 4.0 4.0 3.9 4.2 4.1 3.9 3.8 3.7 3.5 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 5.0 5.0 4.8 4.6 4.5 4.4 4.4 4.3 4.2 4.0 4.0 4.0 4.4 4.3 4.2 4.1 3.9 3.8 Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn 5.1 5.2 5.0 4.7 4.6 4.5 4.4 4.3 4.2 4.0 4.0 4.1 4.5 4.4 4.3 4.2 4.1 4.0 Fr Ra Ac 5.2 5.3 5.1
Page 16 | Materials Studio • DMol Guide Default Cutoff_Element values (Å) for Fine quality calculations
H He 3.1 3.0 Li Be B C N O F Ne 5.1 4.4 4.1 3.7 3.4 3.3 3.2 3.2 Na Mg Al Si P S Cl Ar 5.2 4.9 4.8 4.6 4.2 4.0 3.8 3.5 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 5.6 5.5 5.4 5.2 5.0 4.8 4.7 4.6 4.5 4.5 4.4 4.4 4.8 4.7 4.4 4.2 4.0 3.8 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 5.8 5.8 5.6 5.3 5.0 4.9 4.8 4.7 4.6 4.5 4.5 4.5 5.0 4.9 4.7 4.6 4.4 4.2 Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn 6.1 6.1 5.8 5.3 5.1 4.9 4.8 4.7 4.6 4.5 4.5 4.6 5.1 5.0 4.8 4.7 4.6 4.4 Fr Ra Ac 6.2 6.2 5.9 Increasing the Fine Cutoff_Element values rarely has an impact on the results. Reducing this value will significantly decrease the computation time for periodic systems, but has little effect on molecular calculations, except for extended polymer-type molecules. Generally, the absolute energy computed with a reduced cutoff will change a bit, while the relative energy (for example reactants-products) changes very little with cutoff. The smallest allowed value is 2.5 Å. These are the general rules, and there are exceptions, depending on the system choice and computation task. For example, anions may require larger cutoffs, while for the bulk solids, smaller cutoffs may be acceptable. You can specify a value for the cutoff in the Global orbital cutoff field on the Orbital Cutoff tab of the DMol3 Electronic Options dialog.
Note: Using too small or too large a cutoff may result in failure to converge during SCF or geometry optimization calculations. The smallest recommended values for the cutoff are those in the table of Coarse quality values. The largest value should not exceed 20 Å.
Harris approximation Normally, the evaluation of the energy requires the solution of the self-consistent DFT equations. This can take about a dozen iterations for an organic molecule and can take well over 100 iterations in the case of metallic systems with low lying virtual orbitals. The Harris approximation is an alternative to the iterative solution of the SCF DFT equations. In this procedure, the density from the first SCF iteration is used to compute the energy and forces on the atoms. This density, composed of the superimposed charge density from isolated atoms, is a remarkably good approximation when you need reasonable geometries. Although the method yields reasonable structures, the relative energies are not reliable (Harris, 1985). The Harris method is limited to closed-shell systems and LDA functionals. To activate this option, check the Harris approximation checkbox. Solvation scheme DMol3 allows you to simulate a solvent environment using the COSMO (conductor-like screening model) scheme. COSMO allows you to include the effects of a solvent in a DMol3 calculation. This is a continuum solvation model where the solute molecule forms a cavity within the dielectric continuum of
Tasks in DMol3 | Page 17 permittivity that represents the solvent. The charge distribution of the solute polarizes the dielectric medium. The response of the dielectric medium is described by the generation of screening (or polarization) charges on the cavity surface. It is frequently important to include solvent effects in a DFT calculation, since many properties are strongly influenced by the solvent medium. This includes heats of formation, heats of reaction, dipole moments, and other electronic properties. To simulate solvation in a DMol3 calculation, check the Use COSMO checkbox on the Solvent tab of the DMol3 Electronic Options dialog and select a solvent from the Solvent dropdown list. If you wish, you can specify the dielectric constant of the solvent in the Dielectric constant field. For all calculations using the COSMO solvation model a COSMO Sigma Profile plot, named
Page 18 | Materials Studio • DMol Guide Simple method for setting the k-points 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. Select the Electronic tab. 3. Choose the desired k-point set from dropdown list. This method creates either a Monkhorst-Pack set of the selected quality (Coarse, Medium, or Fine) or instructs DMol3 to use only one Γ-point (the origin in reciprocal space).
Note: Explicit selection of Γ-point sampling is not recommended. DMol3 will automatically use this option if the cell is very large in real space, so that the Brillouin zone is small and no sampling is required.
In all other cases, the Γ-point is the least representative of all Brillouin zone points and using it as the only sampling point can distort the results severely. Puska (2000) showed, for example, that there is a 1-2 eV error in the vacancy formation energy in silicon when the Γ-point is used for cells containing up to 128 atoms. Finer control over k-point sets can be exercised by using the k-points tab on the DMol3 Electronic Options dialog. This tab allows you to enter the actual Monkhorst-Pack mesh parameters by selecting the Custom grid parameters option. Materials Studio automatically optimizes the mesh parameters according to the point group symmetry of the 3D model. For example, in a cubic crystal the even mesh parameters, N, will generate the set with as many k-points as the one with the odd mesh parameters, N-1. Since the former set provides better sampling, it will be selected automatically when either Quality or k-point separation is used to define the k-point set. Custom grid parameters is the only option which allows you to specify a suboptimal mesh with odd divisions. The quality of the k-point sampling is particularly important for metallic systems, where rapid changes in electronic structure may occur along the energy band that crosses the Fermi level. Insulators or semiconductors, even when they are treated using variable occupation numbers for electronic states, are less sensitive to the quality of k-point sampling. The default settings used by DMol3 are designed to give accurate sampling for metallic systems. This means that you can get good results for insulators and semiconductors with a slightly less fine k-point mesh than the default.
Note: The total energy is not guaranteed to decrease as more k-points are added. Therefore, when carrying out convergence testing, you should strive to find a set such that further improvements to it do not alter the total energy beyond the tolerance level you require. However, the energy is not likely to converge smoothly and oscillations are to be expected. Setting up a geometry optimization When a molecular or crystal structure is built, it usually needs to be refined to bring it to a stable geometry. The refinement process is known as optimization, and is an iterative procedure in which the coordinates of the atoms are adjusted so that the energy of the structure is brought to a stationary point, i.e., one in which the forces on the atoms are zero. When you set the Task to Geometry Optimization on the Setup tab, you actually request an energy minimization, a search for a relative minimum on the energy hypersurface. The geometry corresponding to this structure should have a close resemblance to an actual physical structure.
Tasks in DMol3 | Page 19 You can also perform an optimization to a transition state by setting the Task to TS Optimization. See Transition state searching for additional information. By performing geometry optimization (minimizations) you can: n Predict the structure of molecules and crystals n Determine the optimum binding site of a molecule on a surface n Predict the lowest energy conformation or isomer to list just a few examples. Algorithms for the optimization DMol3 can use several different algorithms for performing the optimization. These include steepest descent, conjugate gradient, and Newton-Raphson methods. These are not under user control. DMol3 will choose the appropriate method automatically. Optimization can be performed using Cartesian coordinates, internal coordinates, or in redundant internal coordinates (using linear combinations of internals). These are also not under user control. Optimizations will use redundant internals whenever possible, since these are most efficient. If there is a problem with the internals, then the program will print a message and switch to Cartesian coordinates. Both the Cartesian and redundant internal optimization methods are available for both molecular and crystalline systems.
Note: DMol3 supports atom positions fixed in Cartesian space, and partial constraints on the x, y, or z components of Cartesian atom positions, but ignores constraints on fractional positions and lattice parameters. In addition, fixed interatomic distances, angles, and torsions are supported for nonperiodic structures only.
Parameters for the optimization The parameters that control the accuracy of an energy calculation are still relevant for a geometry optimization, since each step of the optimization requires an energy calculation. Other important parameters include: n Quality - controls how close to a minimum you want to get. The Quality setting controls the convergence thresholds for energy change, maximum force, and maximum geometry displacement between optimization cycles. The optimization will stop when at least two of these criteria are satisfied. If the calculated initial gradients are below the threshold, the optimization will successfully stop without making a single step and without comparing displacements and energies. n Use starting Hessian - whenever you have generated a Hessian (a matrix of second derivatives) you can use this to speed up the geometry optimization. Simply check the box on the DMol3 Geometry Optimization dialog. This box is accessible only if there is a valid Hessian matrix already associated with the document. For information on generating a Hessian, see the vibrational calculation section in the Properties topic. To import a Hessian file from a calculation see the topic on the Hessian file. Setting up a molecular dynamics calculation A DMol3 molecular dynamics calculation allows you to simulate how the atoms in a molecule will move as a function of time under the influence of forces arising from the effects of temperature on the system. In most cases, a molecular dynamics calculation should be preceded by geometry optimization. It may also be desirable to perform minimizations on several of the conformations that are generated during the dynamics run.
Page 20 | Materials Studio • DMol Guide Choosing an ensemble You can control the temperature of a DMol3 molecular dynamics calculation in order to simulate a system that exchanges heat with the environment. Under these conditions, the total energy of the system is no longer conserved and extended forms of molecular dynamics are required. You can simulate two different thermodynamics ensembles with a constant number of particles in DMol3. Ensemble Conditions Description NVE Constant The Newtonian equations of motion, which conserve the total energy, volume/constant are used. The temperature is allowed to vary. Energy is the constant of energy dynamics motion - it can fluctuate slightly, but there should be no systematic drift. NVT Constant The dynamics are modified to allow the system to exchange heat with volume/constant the environment at a controlled temperature. A range of thermostats temperature for scaling or controlling the temperature are available: dynamics n Gaussian n Simple Nosé-Hoover n Nosé-Hoover chain n Massive Nosé-Hoover n Generalized Gaussian moments n Massive generalized Gaussian moments
Defining the time step A key parameter in the integration algorithms is the integration time step. A common rule-of-thumb used to set the time step is that the highest frequency vibration should be sampled between 15 and 20 times in one cycle. For example, if the highest frequency is 20 THz, a typical optical mode frequency, a time step of 2.5-3.3 fs is appropriate (period = 1/frequency = 50 fs). In water, the stretching frequencies are around 110 THz, indicating that a time step of 0.45-0.6 fs is required. You will probably be able to use a time step that samples the motion as few as 10 times in a cycle. However, you must check your choice of time step by monitoring energy conservation in the NVE ensemble. A thermostat in the NVT ensemble can completely mask inadequate integration. Defining the thermostat control For NVT ensembles, it is important to define the thermostat control. For Nosé-Hoover thermostats, this is done using the Nosé Q ratio value. The generalized Gaussian moment thermostats use a relaxation time, τ, which defines a time scale over which the temperature control is implemented. For a stable molecular dynamics run, it is important to chose a relaxation time that is large enough, for example, at least between 10 and 100 times the size of the integration time step. Constraints during dynamics DMol3 dynamics respects atoms that have been fixed in Cartesian space, i.e., the x, y, and z coordinates of any atom that is fixed in all three planes using the controls on the Atom tab of the Edit Constraints dialog will remain constant during a calculation. Fixed atoms still contribute to the energy expression that is used to calculate the forces on atoms, so fixed atoms influence the motion of the movable atoms. DMol3 also allows you to define constraints in terms of the geometric relationship between atoms, i.e., by fixing distances, angles, and/or torsion angles using the controls on the Measurement tab of the Edit Constraints dialog.
Tasks in DMol3 | Page 21 Setting up a transition state calculation When a molecular or crystal structure is built, it usually needs to be refined to bring it to a stable geometry. The refinement process is known as optimization and is an iterative procedure in which the coordinates of the atoms are adjusted so that the energy of the structure is brought to a stationary point, i.e., one in which the forces on the atoms are zero. A transition state is a stationary point that is an energy maximum in one direction (the direction of the reaction coordinate) and an energy minimum in all other directions. During the course of chemical reaction, the total energy naturally changes. Starting from the reactants, the energy increases to a maximum and then decreases to the energy of the products. The maximum energy along the reaction pathway is known as the activation energy; the structure corresponding to this energy is called the transition state. You can perform an optimization to a transition state by setting the Task to TS Optimization or to TS Search. By performing geometry optimization (minimizations) you can predict barriers to chemical reactions and determine reaction pathways. DMol3 offers two different methods for locating a transition state. n Transition state optimization: Starting from a reasonable guess for the transition state, DMol3 performs a Newton-Raphson search on the potential energy surface. This uses techniques similar to a search for an energy minimum but searches instead for an energy maximum along one normal mode. Because this method follows one of the Hessian eigenvectors to an energy maximum, the method is often referred to as "eigenvector following" (EF). See the section on Transition state searching via eigenvector following for additional information. n Synchronous transit methods: Starting from reactants and products, the synchronous transit methods interpolate a reaction pathway to find a transition state. These methods alternate searching for an energy maximum with constrained searches for a minimum in order to refine the transition state. See the section on Transition state searching via synchronous transit methods for additional information. Which method to use? The synchronous transit methods are best employed when you know the product and reactant but do not have good guess for the transition state. The EF methods are best employed when have a reasonably good guess for the transition state, say from chemical intuition or another calculation. A "good guess" means one in which the atomic forces are less than about 0.02 Hartree/Å. The EF will generally yield a more accurate result, meaning one with smaller atomic forces. However, the EF is also considerably more expensive since it requires you generate a Hessian matrix before you can start the calculation. Verifying a transition state At the conclusion of a successful transition state calculation by either method, you will have a stationary point. It is more difficult to prove that the stationary point actually corresponds to a transition state. To do this, you must perform a vibrational analysis. A true transition state will have one imaginary eigenvalue whose vibrational mode corresponds to the reaction coordinate; all other eigenvalues will be real. A structure with two or more imaginary frequencies is not a true transition state: in such cases, it will be possible to locate a lower energy barrier by following one of the modes.
Tip: You can request that a vibrational frequency calculation be performed automatically following a successful transition state optimization or transition state search. Simply select Frequency on the Properties tab.
Page 22 | Materials Studio • DMol Guide Setting up a TS confirmation calculation The TS Confirmation tool verifies that a TS calculated by an LST or QST search connects the reactant and product as expected. See Following a reaction path for more details on the mechanics of this method. Materials Studio automatically determines the reactant, TS and product from the given LST or QST trajectory document. Select and display the trajectory file. On the Setup tab of the DMol3 Calculation dialog, change the Task to TS Confirmation. Click the More... button to display the DMol3 TS Confirmation dialog. Use the controls on this dialog to specify the convergence criteria for each individual geometry optimization (microiteration), and to specify the number of frames to use in the TS confirmation trajectory.
Note: That this is the upper limit for the number of frames. Structures that are too similar will be dropped during the calculation. The output of a TS confirmation calculation is another trajectory document. This one follows the Intrinsic Reaction Path (IRP) as discussed in Reaction pathways. Each successive refinement to the pathway is displayed as a graph in Materials Studio. Use the chart selection tools to choose any point on the graphs and display the corresponding geometry. In most cases, no minima will be found on the IRP other than your reactant and product. If so, the TS confirmation calculation verifies that the TS does connect your presumed reactant and product. On the other hand, any other minima located by the TS confirmation are the structures that are actually connected by the TS. These are identified with an asterisk (*). You should perform a geometry optimization to refine the geometry of these minima. Select the structures as described in the topic Displaying trajectory and chart data. You can generate a detailed map of the entire reaction by repeating TS Search and TS Confirmation for all minima on the IRP. Setting up a work function calculation The work function is the minimum energy (usually measured in electron Volts) required to remove an electron from a solid to a point immediately outside the solid surface (or the energy needed to move an electron from the Fermi energy level into a vacuum). This energy depends on the orientation of the crystal, different crystallographic surfaces have different work function values. The typical range of values of work function for all crystalline elements is from 2 to 6 eV, and the orientational dependence of the work function is of the order of 1 eV. A practical way of evaluating work function is to compare the values of the Fermi energy and that of the electrostatic potential in a vacuum away from the surface. DMol3 calculations for crystal surfaces are carried out on slabs with a region of vacuum. Effectively, an infinite array of 2D-periodic slabs of material is separated by wide vacuum spacings. DMol3 produces the Fermi energy for such systems, and the spatial distribution of the electrostatic potential. Materials Studio averages the electrostatic potential in the planes parallel to the surface. This approach allows the value of electrostatic potential in vacuum, and hence the work function, to be determined. The work function can have a large dependence on the crystal structure and surface orientation. It is recommended that the structure is carefully prepared before calculation of the work function, as described in the steps below. The recommended sequence of steps includes the geometry optimization of the bulk structure, preparation of the surface followed optionally by optimization of atomic coordinates in the surface and bulk layers. It is possible to perform work function calculations without this optimization, so that the effects of surface relaxation on the work function can be investigated. It is
Tasks in DMol3 | Page 23 reasonable to keep the structure of the middle of the slab as close to the perfect bulk structure as possible, for example by imposing fixed atom constraints on some inner atoms of the slab. It is important to have a fair representation of the bulk material, by including at least 8-10 Å of material in the slab calculation. It is equally important to provide enough vacuum between layers of materials so that the electrostatic interactions between two sides of a slab are negligible and electrostatic potential reaches its asymptotic value; there should be at least 30 Å of vacuum in the cell. To set up a work function calculation 1. Either import a structure of the bulk material from a pre-existing file or construct a new structure using the sketching and crystal building tools in the Materials Visualizer. 2. Geometry optimize the bulk structure using DMol3. 3. Cleave the required crystallographic surface using the Cleave Surface dialog so that the thickness provides a meaningful representation of the bulk. 4. Build a slab using the Build Vacuum Slab Crystal dialog, you should ensure that the distance between the surface and the end of the vacuum is great enough that there can be no potential interactions between the surface and the next layer. 5. Choose Modules | DMol3 | Calculation from the menu bar. 6. Select the Setup tab. 7. Choose the Geometry Optimization task. 8. Select a Functional from the dropdown list (see the theory section for more information on functionals). 9. On the Properties tab select and check the Electrostatics checkbox and ensure that the Electrostatic potential checkbox is checked. 10. Ensure that the Work function checkbox is checked. 11. Fix Cartesian atomic positions of some atoms in the middle of the slab using the Edit Constraints dialog, accessible from the Modify menu. 12. Click the Run button. 13. Follow the steps in the Displaying the averaged potential chart for work function calculations topic. The result of this procedure is a chart of the electrostatic potential as a function of position along the surface normal, with Fermi energy and the vacuum energy level marked as two horizontal lines. The work function value is reported in the chart caption. Setting up an elastic constants calculation The calculation of elastic constants enables you to predict some of the following properties: n mechanical hardness and strengths for crystals and polycrystalline materials n shear strength n Poisson ratio, which determines the change in the crystal's cross-sectional area perpendicular to an applied strain. Parameters for the optimization Most of the parameters involved in setting up geometry optimizations are also necessary for obtaining elastic constants. The additional Displacement step setting governs the absolute size of each finite displacement used in the distortions. Setting up a reaction kinetics calculation The reaction kinetics task enables you to predict the reaction rate coefficient of a chemical reaction. The algorithm is based on transition state theory and involves evaluation of the partition functions of
Page 24 | Materials Studio • DMol Guide reactant(s), product(s), and transition state. Calculation of a partition function involves obtaining the vibration spectra, this in turn is calculated from the Hessian matrix. The reaction rate calculation process has three main steps: 1. Transition state search 2. Calculation of the Hessians for all the reaction species 3. Calculation of the partition functions and reaction rates for forward and reverse reactions Transition state search Transition state search in DMol3 can be done using LST or QST formalism. To optimize the transition state further (using the eigenvector following method) it is necessary to request the calculation of frequencies following a successful transition state search - check the Frequency checkbox on the Properties tab of the DMol3 Calculation dialog. The result of the transition state search is a 3D Atomistic Collection Document containing reactant, product, and transition state structures. Hessian calculation To calculate the Hessians for all the reaction species you should use the Reaction kinetics task. Depending on the type of reaction (isomerization, association, dissociation, or exchange) the original reactant and product will be split into two structures if necessary and each structure will automatically be assigned a motion group.
Tip: Automatic determination of reaction species is disabled if you have defined motion group(s) for reactant and/or product - refer to the Motion Groups dialog topic for more information. If you define your own motion groups they must cover all the atoms in the reaction. For reactions which are split into multiple structures the Hessian calculations will be carried out for each structure individually. Reaction rate calculation Transition states can also be optimized via an eigenvector following procedure if the original transition state search included frequency calculations. For such an optimization the eigenvector with the largest imaginary frequency is chosen. If you want to select a different eigenvector to follow or inspect the spectrum you can use the Vibrational Analysis tool.
Note: The reaction rate coefficient can be calculated only if the transition state has exactly one imaginary frequency with its eigenvector along the reaction path. The 3D Atomistic Collection Document generated will contain all the necessary information to perform the reaction rate calculation itself. Setting up an electron transport calculation The electron transport task allows calculation of electron transport properties. The task requires the target structure to contain at least two electrodes.
Tasks in DMol3 | Page 25 To set up an electron transport calculation 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Select the Setup tab. 3. Select Electron Transport from the Task dropdown list. 4. Specify the Quality for the calculation. 5. Click the More... button to open the DMol3 Transport dialog. 6. Choose whether to Calculate transmission function or Calculate current/voltage characteristics. 7. Select the Electrodes tab and review the defined electrodes. 8. Select the Electrostatics tab and specify the Poisson solver settings. 9. Close the DMol3 Transport dialog. 10. Choose the Electronic tab of the DMol3 Calculation dialog. 11. Click the More... button to open the DMol3 Electronic Options dialog and adjust the settings as appropriate. 12. Click the Run button. Note: The DMol3 Electron Transport task cannot be run under certain circumstances, if: n On the Setup tab of the DMol3 Calculation dialog: n Use method for DFT-D correction checkbox is checked n Functional is set to B3LYP or m-GGA option n Spin unrestricted checkbox is checked n Charge is set to any non-zero value n On the Electronic tab of the DMol3 Calculation dialog: n Core treatment is not set to DFT Semi-core Pseudopots when there is an element with Z > 20 n Use solvation model checkbox is checked n On the Properties tab of the DMol3 Calculation dialog, any of the following are selected: n Density of states n Electron density n Electrostatics n Frequency n Fukui function n Optics n Orbitals n Population analysis Requesting electronic and structural properties It is possible to request electronic or structural properties through the Properties tab of the DMol3 Calculation dialog. These properties are computed as part of a calculation and viewed using the DMol3 Analysis dialog. Each time that you want to compute more properties, you must submit another DMol3 calculation. The properties that can be accessed through the Properties tab are:
Page 26 | Materials Studio • DMol Guide n Electron densities n Electrostatics n Vibrational frequencies n Raman intensities n Fukui functions n Molecular orbitals n Atomic populations n Band structure n Density of states (DOS) n Fermi surfaces n Sigma profile n Optics All properties are computed at the end of a calculation using the converged charge density at the final geometry. Setting up electron densities When you check the Electron density checkbox, you are presented with the option of creating 3D plots of three types of densities: n Total density - the self-consistent charge density computed via Eq. DFT-4. n Deformation density - the total density with the density of the isolated atoms subtracted. Positive regions indicate areas where bonds have formed. n Spin density - the difference between the charge density for alpha-spin and beta-spin electrons. Spin density computations are available only for spin-unrestricted calculations. All the densities will be rendered on a regular rectangular grid with 0.2 Å spacing. In the molecular case, the plots extend 2.0 Å beyond the molecule; in the periodic case, the plots fill the entire unit cell. Computation of electron densities is possible for molecules and for periodics.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Setting up electrostatics When you check the Electrostatics checkbox, you are presented with the option of displaying three types of electrostatic properties: n Electrostatic potential - produces a 3D rendering of the electrostatic (Coulomb) potential. This is rendered on a regular rectangular grid with 0.2 Å spacing. In the molecular case, the plots extend 2.0 Å beyond the molecule; in the periodic case, the plots fill the entire unit cell. Computation of electrostatic potential is possible for molecules and for periodics using the Γ-point and multiple k- points. n Electrostatic moments - produces a list of multipole moments from dipole through hexadecapole. This option is available only for molecules. These moments appear in the output file; open the .outmol file in Materials Studio to view the results. n Nuclear electric field gradients - computes fields that are an important component of the nuclear magnetic shift. The nuclear electric field gradients appear in the output file; open the .outmol file in Materials Studio to view the results.
Tasks in DMol3 | Page 27 Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Note: If Electrostatics are requested for a slab, DMol3 analysis can be used to calculate the work function.
Setting up vibrational frequencies When you check the Frequency checkbox, DMol3 will compute a Hessian and vibrational spectrum. You can visualize the vibrational spectrum and the results of the calculation by using the Vibrational Analysis dialog. The frequencies and corresponding intensities are also given in the .outmol file. Frequencies, including intensities, can be computed for any molecular or periodic system.
Note: For intensity calculations symmetry should not be used, ensure that the Use Symmetry checkbox on the Setup tab is unchecked. If symmetry is used only frequencies will be calculated and the results will not include any intensities. DMol3 computes the Hessian by finite differences of analytic first derivatives. This means that each atom in the system must be displaced in each Cartesian direction (including positive and negative directions). DMol3 uses point group symmetry to reduce the total number of displacements whenever possible. A good approximation to the Hessian can sometimes be obtained by limiting the number of atoms that are displaced. This is useful when you need a Hessian to search for a transition state, but only a few atoms are involved in the reaction coordinate. An especially important example of this is a molecule reacting on a surface, where the atoms in the second and third layers are not involved in the reaction. By default, all atoms are included in a Hessian calculation, To create a list of atoms that you want to move, select the atoms and use the Edit Sets dialog to create a set named HessianAtoms. Only when this set is present in the system will the Calculate partial Hessian checkbox become enabled. Checking this checkbox limits the Hessian calculation to only those atoms in the HessianAtoms set. Setting up Raman intensities Raman intensities are necessary for the prediction of Raman spectra during analysis. To generate Raman intensities 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. Select the Properties tab. 3. Check the Frequency option on the properties list. 4. Check the Calculate Raman intensities checkbox.
Note: For Raman intensity calculations symmetry will not be used, even if the Use Symmetry checkbox on the Setup tab is checked. This can cause convergence problems with certain some highly symmetric systems. If this happens, enabling thermal smearing can be used to accelerate the convergence.
Setting up Fukui functions Fukui functions provide information on chemical reactivity. When you check the Fukui function checkbox, you are presented with the option of creating 3D plots of three types of Fukui functions:
Page 28 | Materials Studio • DMol Guide n f(-) Electrophilic - computes the f- Fukui function, which reflects susceptibility to electrophilic attack. n f(+) Nucleophilic - computes the f+ Fukui function, which reflects susceptibility to nucleophilic attack. n f(0) Radical - computes the f0 Fukui function, which reflects susceptibility to attack by radicals. This is simply the average of f+ and f-. All the functions will be rendered on a regular rectangular grid with 0.2 Å spacing. In the molecular case, the plots extend 2.0 Å beyond the molecule; in the periodic case, the plots fill the entire unit cell. Computation of Fukui functions is possible for molecules and for periodics that use the Γ-point, but not for periodic structures with multiple k-points.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Note: Due to the algorithm used, Fukui calculations on highly symmetric or/and near-degenerate systems may exhibit difficulty converging to the ground state. If this happens, checking the Use symmetry checkbox on the Setup tab of the DMol3 Calculation dialog or enabling thermal smearing can accelerate the convergence.
Setting up molecular orbital analysis When you check the Orbitals checkbox, you are presented with the option of creating 3D plots of DFT molecular orbitals: n HOMO - produces a plot of the HOMO (highest occupied molecular orbital). n LUMO - produces a plot of the LUMO (lowest unoccupied molecular orbital). n Levels above and below the HOMO level - specifies additional orbitals above and below the HOMO level to be computed. For example, entering a value of 5 results in a total of 5 occupied and 5 virtual orbitals being computed, in addition to the HOMO. All the functions will be rendered on a regular rectangular grid with 0.2 Å spacing. In the molecular case, the plots extend 2.0 Å beyond the molecule; in the periodic case, the plots fill the entire unit cell. Computation of orbitals is possible for molecules and for periodics that use the Γ-point, but not for periodic structures with multiple k-points.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Setting up a population analysis When you check the Population analysis checkbox, you are presented with the option of performing several types of atomic population analysis:
Tasks in DMol3 | Page 29 n Mulliken analysis - produces charges based on the density matrix and atomic overlap matrix. This is the most common sort of charge analysis. See the Mulliken and Mayer bond orders topic for more details. Three different analysis options are available: n Atomic Charge - computes the total Mulliken charges on each atom, as in Eq. DMol3-62. n Orbital & Charge - computes the contribution to the atomic charge from each atomic orbital on each atom. n Overlap Matrix - computes the overlap population in each pair of atomic orbitals on different atoms, as in Eq. DFT-58. Whenever Mulliken bond orders are calculated, DMol3 will automatically compute Mayer bond orders as well. Mayer bond orders gives valences that are close to the classical values. Unlike Mulliken bond orders, Mayer quantities are less dependent on the basis set choice and are transferable, so they can be used to describe similar molecules. See the Mulliken and Mayer bond orders topic for more details.
Note: Bond orders can only be calculated for nonperiodic structures. Symmetry information should not be used when calculating bond orders, i.e., the Use symmetry checkbox on the Setup tab of the DMol3 Calculation dialog should be unchecked. n Hirshfeld analysis - produces partitioned charges that are defined relative to the deformation density, which is the difference between the molecular and the unrelaxed atomic charge densities. See the Hirshfeld charge analysis topic for more details. Three different analysis options are available: n Charge n Dipole n Quadrupole n ESP charges - produces atomic-centered charges that best reproduce the DFT Coulomb potential. This method is often used to derive charges to be used in forcefield calculations. See the Fitting atomic point charges to the electrostatic potential topic for more details. Setting up band structures When you check the Band structure checkbox, you are presented with options for controlling band structure calculations. Calculating band structure properties produces electronic energies along high symmetry directions in the Brillouin zone. The standard path for each lattice type is taken from Bradley and Cracknell (1972). The path can be modified using the Brillouin Zone Path dialog, accessed via the Path... button. The density of points along the path, which affects the appearance of the resulting chart, can be controlled by the selection for the k-point set dropdown list or the approximate k-point separation can be manually specified in the Separation text box, in Å-1, on the Properties tab of the DMol3 Calculation dialog. Conduction band states can be included by specifying a non-zero value in the Empty bands text box. Setting up density of states When you check the Density of states checkbox, you are presented with options for controlling density of states calculations. For periodic systems, calculating densities of states produces electronic energies on the Monkhorst- Pack mesh of k-points. The k-point set can be specified using the DMol3 Density of States Options dialog, accessed via the More... button. The quality of the k-points set is controlled by the k-point set dropdown list. Conduction band states can be included by specifying a non-zero value in the Empty bands text box. A partial density of states can be requested by checking the Calculate PDOS checkbox.
Page 30 | Materials Studio • DMol Guide Tip: To obtain representative density of states it is recommended to use a k-point set which is either the same or finer quality than the one used in the SCF calculations.
Setting up Fermi surfaces In order to generate Fermi surfaces for the structure resulting from a calculation density of states properties must be selected. To generate Fermi surfaces 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. Select the Properties tab. 3. Check the Density of states option on the properties list and set the appropriate DOS options. 4. Click the More... button to open the DMol3 Density of States Options dialog. 5. Click the Separation radio button and specify a value of 0.01 1/Å or less. This ensures that enough k- points are used for generating the Fermi surface data without requiring such fine settings for the rest of the calculation. Setting up COSMO Sigma profile calculation In order to generate Sigma profiles for the structure resulting from a calculation the Use solvation model electronic option must be selected. To generate Sigma profile chart 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. On the Electronic tab check the Use solvation model checkbox. 3. Click the More... button to open the DMol3 Electronic options dialog and, if required, set the appropriate solvent details on Solvent tab. At the end of the calculation, the Sigma profile chart will be generated automatically. Setting up an optics calculation In order to generate optical properties for the structure resulting from a calculation the type of optics to calculate must be selected.
Tasks in DMol3 | Page 31 To generate optics information 1. Choose Modules | DMol3 | Calculation from the Materials Studio menu bar. 2. On the Properties tab select and check the Optics checkbox. 3. Choose the type of optics from the Calculate dropdown list and the method of calculation from the Use dropdown list. 4. Check the Calculate polarizability checkbox if required and click the More... button to configure specific options on the DMol3 Optics Options dialog. 5. Check the Optimize geometry checkbox. Note: Geometry optimization of an excited state uses the original structure as the initial point. If the Task is set to Geometry Optimization and excited state optimization is requested, the results folder will contain two sets of geometry optimization results, both with the same initial point. The name of the results file for the excited state optimization has the form
Tip: If the job is not reaching convergence in the TD-DFT process, modifying the input file and adding tighter convergence criteria might help, as explained on the tddft_crit keyword page in the online help. Manipulating files DMol3 is a file-based application, all input and output is delivered in a mixture of text and binary files. This section describes some file handling issues which may arise, especially when the DMol3 server is run in a standalone mode and not via a gateway. Input files The DMol3 Job Files dialog allows you to save input files for subsequent manual editing or for running in standalone mode. To save input files 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Click the Files... button to open the DMol3 Job Files dialog. 3. Click the Save Files button.
Note: The Save Files button is enabled only if a suitable 3D model document is active. Only one input file,
Page 32 | Materials Studio • DMol Guide To edit the input file 1. Select the desired file in the Project Explorer. 2. Double-click to open the file in the text editor. 3. Make your changes - adding, deleting, or modifying input as desired. 4. Choose File | Save from the menu bar to save your changes.
Note: DMol3 input files use whitespace as the delimiting character, tabs are not supported. Input files can be run on a server after they have been edited. To run DMol3 using an existing set of input files 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Click the Files... button to open the DMol3 Job Files dialog. 3. Double-click on the input file. 4. Click the Run Files button.
Note: The Run Files button is enabled only if a suitable .input file is active. If your server does not support the gateway protocol, you may have to run DMol3 in standalone mode using the RunDMol3.sh or RunDMol3.bat files provided with the installation. In such circumstances, it is necessary to copy all the input files from the project folder to the appropriate directory on the server machine. You can find complete instructions for transferring files in Uploading data to the compute server. Output files Only one output file,
Note: If a job with File usage set to Memory fails, restart files will not be created.
Note: In order to restart a job, the output files from the previous run must be present in the project folder. If the files are present, their transfer to the server happens automatically whenever you launch a job.
Restarting with the SCF coefficients When a molecular DMol3 calculation completes, two files (
Tasks in DMol3 | Page 33 Explorer. Using these files to start a subsequent SCF calculation will reduce the number of iterations needed to reach convergence.
Note: The .tpdensk, and .tpotl files are binary, and can only be used on the platform on which it was created. So, the .tpdensk and .tpotl files can only be used to restart a run on the same platform. Whenever the .tpdensk and .tpotl files are present, they will be uploaded to the server, but they will not be read unless you instruct DMol3 to do so. To submit a DMol3 job that makes use of these files, perform the following steps: 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Open the results folder for the completed DMol3 job in the Project Explorer. 3. Open the .input file in the text editor by double-clicking on it. 4. Add the line scf_restart on anywhere in the input file. 5. Click the Files... button to open the DMol3 Job Files dialog. 6. Click the Run Files button. 7. If prompted to save the file, choose Yes. For periodic systems, the procedure is similar, but requires minor modifications. DMol3 does not save density and potential information at every SCF step, so if you expect to run a restart, an additional keyword needs to be added to the original DMol3 input file telling the program to save density and potential at each step. The keyword to add is save_density_each_it. The edited input file can then be used to restart the DMol3 periodic job. Restarting with the Hessian You can use a Hessian to restart a geometry minimization or TS search. When running through Materials Studio, it is not necessary to have an explicit .hessian file once a Hessian has been loaded into the model. You can obtain a starting Hessian from several sources as described in Importing a Hessian file. To use a Hessian in a geometry optimization or transition state optimization 1. Load the Hessian data. If you have generated a Hessian using Materials Studio, then the data are automatically loaded for you upon job completion. If you need to load a .hessian file generated outside Materials Studio, use the Edit | Insert From... command on the menu bar. 2. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 3. Set the Task to Geometry Optimization or TS Optimization. 4. If you are performing a geometry optimization, click the More... button to open the DMol3 Geometry Optimization dialog and check the Use starting Hessian checkbox. 5. If you are performing a TS optimization, a starting Hessian is required, so there is no option to specify this. 6. Click the Run button. Restarting a frequency calculation or Hessian evaluation DMol3 evaluates a Hessian by finite-difference of analytic gradients. This means that each atom in the system must be displaced in each Cartesian direction (including positive and negative directions). As each displacement is made, the gradient is written to a file called
Page 34 | Materials Studio • DMol Guide Note: If the frequency calculation that has been interrupted was a continuation of a Geometry Optimization task, then you must delete the .hessian file left behind in the job folder by the geometry optimization before you restart the run. Like the .tpdensk and .tpotl files, the .hesswk file is returned to the project folder, but hidden. Whenever the .hesswk file is present, it will be uploaded to the server, but it will not be read unless you instruct DMol3 to do so. To submit a DMol3 job that makes use of the .hesswk file 1. Choose Modules | DMol3 | Calculation from the menu bar to display the DMol3 Calculation dialog. 2. Open the results folder for the completed DMol3 job in the Project Explorer. 3. Open the .input file in the text editor by double-clicking on it. 4. Add the line vibration_restart on anywhere in the input file. 5. Click the Files... button to open the DMol3 Job Files dialog. 6. Click the Run Files button. 7. If prompted to save the file, choose Yes. Importing a Hessian file A Hessian file is required input for a transition state optimization and can also be used in a geometry minimization. There are several ways that you can create a Hessian and import it into your model. n Run a frequency calculation with VAMP or DMol3. At the end of jobs of this type a Hessian matrix is produced. If the job was run via the Materials Studio interface, the result will automatically be displayed in Materials Studio. n Run a geometry optimization with DMol3. This calculation uses an approximate Hessian matrix to find the minimum energy configuration. If the job is run through the Materials Studio interface, the result will automatically be displayed in Materials Studio. n Read in a Hessian matrix from an earlier calculation. You can import a Hessian from any earlier calculation if the file is in the correct format and uses the file extension ".hessian". This method is convenient if you have generated a Hessian matrix using another Accelrys product in standalone mode. To read a Hessian into your model: a. Make sure the desired molecule or solid is the active document. b. Choose Edit | Insert from... from the Materials Studio menu bar. The Insert Into Active Document dialog is displayed. c. Set the value of the file types dropdown list for the File name to Hessian Files (*.hessian;*.vres). d. Browse to the location of the Hessian file and click the Insert button. Hessian files produced by Materials Studio are marked as "hidden" files. To display any hidden files in the Insert Into Active Document dialog, you must remove the "hidden" attribute: n Browse to the file's location using the Windows Explorer. n Right-click on the file and select Properties from the shortcut menu. n Uncheck the checkbox labeled Hidden. The file should become visible in the Insert Into Active Document dialog. Analyzing DMol3 results DMol3 results become available for analysis on completion of the DMol3 run, once all the output files have been successfully downloaded to the results folder.
Tasks in DMol3 | Page 35 Select the results to be analyzed by opening the 3D structure document (.xsd) in the results folder. This allows all related DMol3 results to be analyzed.
Note: The structure is updated automatically on successful download of output files from a completed DMol3 job that was run using a gateway (the structure is not automatically updated if the DMol3 job was run in standalone mode).
The atoms in the updated structure document have an extra property, ServerAtomIndex, associated with them. This shows the atom sequence numbers as used in the DMol3 output files and can be seen by labeling atoms in the structure with the ServerAtomIndex property. (This property will be seen only in structures generated from DMol3 and other similar applications).
All other analysis functions require you to perform certain actions using the DMol3 Analysis dialog.
Tip: If you have calculated a Hessian matrix (i.e., by checking the Frequency checkbox on the Properties tab of the DMol3 Calculation dialog) as part of a DMol3 run, you can create a list of vibrational modes and view the spectrum for the structure using the Vibrational Analysis tool.
Vibrational intensities can only be obtained for nonperiodic systems. Without intensities, the displayed spectrum consists of points on the frequency axis only.
Note: The Hessian file resulting from a DMol3 geometry optimization run should not be used to obtain the vibrational spectrum. Updating structure Updating the atomic coordinates after geometry optimization, TS optimization, or TS search is the recommended first step in the analysis process. When a DMol3 job that was run through a gateway is completed, the output files are copied to the results folder and the structure is updated automatically. The procedure described below for updating the structure applies to jobs that were run in standalone mode. You can also use this procedure to return the view of a structure you've modified to its last saved form. The procedure also applies if you manually modified the final structure produced by DMol3, and you want to revert it back to the unmodified form.
Note: If the chemical composition (i.e., number of atomic species or number of each kind of atoms) has changed since Materials Studio saved the .xsd file in the results folder, you cannot update the structure. As a result of the update, the coordinates of the atoms are set to the values returned by the DMol3 run in the (hidden) .car file. To update the structure 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Structure from the list of properties. 3. Make sure that the 3D structure document you wish to be updated is the currently active document. 4. Click the Update button.
Page 36 | Materials Studio • DMol Guide An error message will be displayed if the .car structure file is incomplete or if the chemical composition of the model has been changed (i.e., atoms were added, removed, or modified). The Update button is disabled if the .car file is not present or if the current document cannot be updated. Displaying trajectory and chart data Depending on the type of calculation performed, a DMol3 run may produce a trajectory document and one or more chart documents. These documents have a special association with each other because each of the points on the graph corresponds to a frame in the trajectory. DMol3 produces a trajectory (.xtd) file whenever you run a geometry optimization, a TS optimization, or a TS search. In each case, a history of the optimization is returned in a file called seedname.xtd, where seedname is the name entered as the Job description on the Job Control tab. When you run a geometry or TS optimization, two chart documents are generated: n name Energies.xcd contains a plot of total energy vs. frame number for all steps of the calculation. n name Convergence.xcd contains three plots that describe the degree of convergence of the optimization as a function of frame number: n change in energy vs. frame number n maximum Cartesian force vs. frame number n maximum Cartesian step size vs. frame number Because these values span several orders of magnitude, the data are plotted on a log scale. 10 When you run a calculation with COSMO solvation a chart document is generated: n name Sigma prfile.xcd contains a plot of screening charge density vs. Sigma profile. When you run a TS search, a single chart containing a graph of energy vs. reaction coordinate for each step of the calculation, name TransitionState.xcd, is generated. This includes an individual graph for each LST or QST "uphill" cycle as well as a graph for each conjugate gradient minimization. See Transition state searching via synchronous transit methods for additional information on the meaning of these components of a TS search. Creating a trajectory and chart When you run DMol3 via the Materials Studio interface, the creation and display of these trajectories and charts are automatic. If you select Automatically view output on the DMol3 Job Control Options dialog, the graphs will be displayed automatically upon completion of the calculation. If you select Update graphs on the DMol3 Job Control Options dialog, these graphs will be displayed and updated with intermediate results throughout the course of the calculation. To create charts from output files generated by a standalone calculation 1. Download the files from the compute server to your PC using the procedure described in Running DMol3 in standalone mode. Be sure to retrieve the .car, .outmol, .arc, and .summ files. 2. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 3. Select Energy evolution from the list of properties. 4. Make sure that the .outmol file is the currently active document. 5. Click the Update button. If you have run the calculation through the Materials Studio interface, you can regenerate the chart documents by following a similar procedure.
Tasks in DMol3 | Page 37 1. Open either the .xsd or .outmol file and make it the currently active document. 2. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 3. Select Energy evolution on the DMol3 Analysis dialog. 4. Click the Update button. Animating the trajectory You can use the controls on the Animation toolbar to animate the trajectory, stepping through each of the frames of the document. If the chart is open during the animation, the point corresponding to the active frame becomes highlighted. Chart Viewer point selection Alternatively, you can use Chart Viewer point selection to display the trajectory frames of the points you select from the chart document. To display a trajectory frame for a point on a chart document
1. Click the Selection Mode button on the Chart Viewer toolbar to enter selection mode. 2. Making sure you have the corresponding trajectory document open, select a data point on the chart document. 3. The corresponding trajectory frame is displayed. 4. Drag the mouse over other data points on the chart document to display their corresponding trajectory frames. 5. If DMol3 generated a second chart document, its related data points will also be highlighted.
Tip: To make it easier to see the chart and trajectory documents, close all the other documents and then maximize the sizes of these two documents by selecting Window | Tile Vertically from the menu bar. Visualizing volumetric data Materials Studio allows you to visualize the spatial distribution of electron density, electrostatic potential, molecular orbitals, or Fukui functions calculated by DMol3. The relevant data from DMol3.grd files are used to add a field to the model. This field can be subsequently visualized in a variety of ways, for example direct field visualization, isosurfaces, or slices. Electron density Materials Studio uses the information generated by DMol3 to create a field that corresponds to the total electron density. When you analyze a spin-unrestricted calculation, you can also create a field for the spin density (the difference between the density of alpha and beta electrons). This field allows you to visualize the spatial distribution of the magnetic moment in a spin-unrestricted system. You can also create a field of the deformation density, the total density with the density of the isolated atoms subtracted. Regions of positive deformation density indicate the formation of bonds, while negative regions indicate electron loss.
Page 38 | Materials Studio • DMol Guide To create a density field 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Electron density from the list of properties. 3. Make sure that the desired 3D structure document (.xsd) is the currently active document. 4. Select the type of density you wish to display (total, deformation, or spin) from the Density field dropdown list. The choices are limited to those that you specified in the Electron density section on the Properties tab when you ran the calculation. 5. Optionally, check or uncheck the View isosurface on import checkbox. This is checked by default. 6. Click the Import button.
Tips: If you select View isosurface on import, you should see a 3D contour after the field has been imported. To change the value of the contour, open the Display Style dialog and select the Isosurface tab. If you do not see an isosurface, the default value is possibly outside of the range of the field values. Select the Isosurface tab and choose a different value. If you do not check the View isosurface on import checkbox, you will not see a volumetric data display. Use the Volume Visualization toolbar and Display Style dialog to control the display of the field data.
Tip: If the dipole slab correction has been applied in the calculation, the structure may have been modified by Materials Studio in order to place the center of the vacuum region in the center of the cell. In this case you can improve the display by using the Display Style dialog to change the lattice display style on the Lattice tab to In-Cell, for example. This change would improve the correspondence between the display of atoms and of fields.
Electrostatic potential Materials Studio uses the information generated by DMol3 to create a field that corresponds to the electrostatic, or Coulomb, potential. Positive regions correspond to electron-deficient areas and are subject to nucleophilic attack, negative regions correspond to electron-rich areas and are subject to electrophilic attack. To create an electrostatic potential field 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Potentials from the list of properties. 3. Make sure that the desired 3D structure document (.xsd) is the currently active document. 4. Select the type of potential you wish to display from the Potential field dropdown list. The choice is limited to electrostatic potential, and that only if you requested it in the Electrostatics section on the Properties tab. 5. Optionally, check or uncheck the View isosurface on import checkbox. This is unchecked by default. 6. Click the Import button. If you wish to use the potential to color an isosurface, see the Color and contour mapping topic.
Tasks in DMol3 | Page 39 Tips: If you select View isosurface on import, you should see a 3D contour after the field has been imported. To change the value of the contour, open the Display Style dialog and select the Isosurface tab. If you do not see an isosurface, the default value is possibly outside of the range of the field values. Select the Isosurface tab and choose a different value. If you do not check the View isosurface on import checkbox, you will not see a volumetric data display. Use the Volume Visualization toolbar and Display Style dialog to control the display of the field data.
Fukui functions Materials Studio uses the information generated by DMol3 to create a field that corresponds to the Fukui functions. There are three different functions that you can view: f(-) Electrophilic reflects susceptibility to electrophilic attack; f(+) Nucleophilic reflects susceptibility to nucleophilic attack; f(0) Radical reflects susceptibility to attack by radicals. Further information is available in the Fukui functions topic. To create a Fukui function field 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Fukui function from the list of properties. 3. Make sure that the desired 3D structure document (.xsd) is the currently active document. 4. Select the type of field you wish to display (f(+), f(-), or f(0)) from the Fukui field dropdown list. The choices are limited to those that you specified in the Fukui function section on the Properties tab when you ran the calculation. 5. Optionally, check or uncheck the View isosurface on import checkbox. This is unchecked by default. 6. Click the Import button. If you wish to use the potential to color an isosurface, see the Color and contour mapping topic.
Tips: If you select View isosurface on import, you should see a 3D contour after the field has been imported. To change the value of the contour, open the Display Style dialog and select the Isosurface tab. If you do not see an isosurface, the default value is possibly outside of the range of the field values. Select the Isosurface tab and choose a different value. If you do not check the View isosurface on import checkbox, you will not see a volumetric data display. Use the Volume Visualization toolbar and Display Style dialog to control the display of the field data.
Molecular orbitals Materials Studio uses the information generated by DMol3 to create a field that corresponds to any of the molecular orbitals in the system. The molecular orbitals are the single-particle wavefunctions constructed from linear combinations of atomic orbitals as discussed in the theory section. The highest occupied orbital (HOMO) and lowest unoccupied orbital (LUMO) are especially important in determining the chemical reactivity of a system. The Filter dropdown list allows you to control which orbitals have their information displayed in the table:
Page 40 | Materials Studio • DMol Guide n All displays data for all orbitals. n Available displays data only for orbitals that are available to create fields. n Spin up displays data only for alpha-spin orbitals. In the unrestricted case, this is the same as All. n Spin down displays data only for beta-spin orbitals. In the unrestricted case, no data are displayed. The orbital analysis table provides a list of eigenvalues and information about each orbital. The list of eigenvalues starts with the lowest core orbital and extends to include ten orbitals above the Fermi level (i.e., above the HOMO). If there are fewer than ten virtual orbitals in the list, it is because there are not that many in your particular system. The accompanying information includes: n Field contains Yes when field data have been computed and is blank otherwise. n N indicates the number of the orbital, with 1 corresponding to the lowest energy orbital. In an unrestricted calculation, the alpha- and beta-spin orbitals are numbered separately. n s indicates spin, + for alpha, - for beta. In a spin-restricted calculation, all orbitals are labeled as +. n Eigenvalue indicates the orbital eigenvalue in Hartree. n Type indicates the HOMO and LUMO. These labels appear in the appropriate row. To create a molecular orbital field 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Orbitals from the list of properties. 3. Make sure that the desired 3D structure document (.xsd) is the currently active document. 4. Select the row in the table corresponding to the orbital you wish to display. The choices are limited to those that you specified in the Orbitals section on the Properties tab when you ran the calculation. 5. Optionally, check or uncheck the View isosurface on import checkbox. This is checked by default. 6. Click the Import button.
Tips: If you select View isosurface on import, you should see a 3D contour after the field has been imported. To change the value of the contour, open the Display Style dialog and select the Isosurface tab. If you do not see an isosurface, the default value is possibly outside of the range of the field values. Select the Isosurface tab and choose a different value. If you do not check the View isosurface on import checkbox, you will not see a volumetric data display. Use the Volume Visualization toolbar and Display Style dialog to control the display of the field data.
Tip: The list of all eigenvalues is much longer than the list of those available to create fields. Set the Filter to Available to see only those orbitals that can be used to create fields.
Field visualization Materials Studio provides a number of tools for field visualization. They are accessed via the Volume Visualization toolbar and Field, Isosurface, and Slice tabs on the Display Style dialog. The Volume Visualization toolbar provides access to the Volumetric Selection dialog, which enables you to specify the field to be visualized and set visibility attributes for fields, slices, and isosurfaces. This toolbar also contains controls for creating new isosurfaces and slices, including the shortcuts for orienting the slice based on either the cell axes or the coordinates of selected atoms. The Color Maps dialog, which can also be accessed from the Volume Visualization toolbar, provides control over the
Tasks in DMol3 | Page 41 coloring of volumetric objects (it also provides useful shortcuts for determining the minimum and maximum values of the field). The Field tab of the Display Style dialog allows you to visualize the field directly using either the Dots or Volume display styles. The Isosurface tab of the Display Style dialog allows you to alter the visualization style of a selected isosurface, change its isovalue, or use another field for color mapping. The Slice tab of the Display Style dialog allows you to alter the visualization style of a selected slice.
Note: The volumetric visualization tabs on the Display Style dialog are displayed only if an object of the relevant type is present in the active document. If a field, isosurface, or slice is selected, for example by using the Volumetric Selection dialog, the volumetric visualization tabs that are not relevant to the selection will be removed from the Display Style dialog.
Tip: Field visualization in Materials Studio fully supports periodic display. You can use the Field tab on the Display Style dialog to change the range of a field to display more or less than one unit cell of a structure.
Note: The default settings for field visualization result in the fields being displayed over one unit cell of a structure. It might be helpful to use the "In-Cell" display mode for the lattice (accessed from the Lattice tab on the Display Style dialog) to make sure that the field is positioned around displayed atoms. Visualizing Fermi surfaces Fermi surfaces are generated from information from DMol3 calculations which is stored in the .bands output file. Fermi surfaces can be considered as the energy isosurfaces in reciprocal space.
Tip: The results under analysis must include density of states information generated during the calculation. Select Density of states on the Properties tab of the DMol3 Calculation dialog.
To ensure that the generated Fermi surface(s) are reliable you must use as many Density of states k- points as computational resources will allow when setting up the calculation. To create a Fermi surface 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Fermi surface from the list of properties. 3. Ensure that the 3D Atomistic document to be analyzed is the active document. 4. Select the Band for which to display the Fermi surface. 5. Click the Import button. To change the Fermi level used for the Fermi surface 1. Create a Fermi surface according to the steps above. 2. Open the Display Style dialog and select the Isosurface tab. 3. In the Generation section change the Isovalue. The Fermi surface will be updated appropriately. Displaying population analysis results A DMol3 calculation can compute atomic charges by Mulliken, Hirshfeld, and ESP-fitted charge analysis. In addition, spins can be computed using Mulliken or Hirshfeld analysis and both Mulliken and Mayer
Page 42 | Materials Studio • DMol Guide bond orders can be calculated. Mulliken analysis is one of the most common types of charge, spin, and bond order analysis. The spin density matrix and atomic overlap matrix are used to partition charges among the atoms. This method is, however, very sensitive to the choice of basis set. See the Mulliken and Mayer bond orders topic for more details. Hirshfeld charge and spin analysis is based on the deformation density, as described in the Hirshfeld charge analysis topic. This method is more stable with respect to the basis set than Mulliken charge analysis, but seems to generally underestimate the atomic charges. ESP-fitted charge analysis fits atom-centered charges to the DFT Coulomb potential, as described in Fitting atomic point charges to the electrostatic potential (ESP). Charges computed in this manner have frequently been used in subsequent forcefield calculations. Mayer bond order analysis gives valences that are close to the classical values. Unlike Mulliken bond orders, Mayer quantities are less dependent on the basis set choice and they are transferable, so they can be used to describe similar molecules. See the Mulliken and Mayer bond orders topic for more details. Displaying computed charges, spins, and bond orders To import and display computed atomic charges, spins, and bond orders, the output structure from the calculation (.xsd) and the DMol3 output file (.outmol) must be saved in a folder within the current project.
Note: If the calculation is to be a standalone job, you will need to save your .car file in .xsd format before you start. To update an output structure with charges, spins, and bond orders 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Population analysis from the list of properties. 3. Make sure that the 3D Atomistic document (.xsd) output from the DMol3 calculation is the currently active document. 4. Select the type of charges (Mulliken, Hirshfeld, or ESP), spins (Mulliken or Hirshfeld), or bond orders (Mayer or Mulliken) that you wish to apply from the respective dropdown lists. The choices are limited to those properties that you specified in the Population analysis section on the Properties tab when you ran the calculation. 5. Click the appropriate Assign button to import the charge, spin, or bond order data into the structure document. 6. Right-click in the 3D Atomistic document and select Label from the shortcut menu to display the Label dialog. Set the Object type to Atom, select Charge or Spin from the Properties list, and click the Apply button to display the charges or spins. 7. On the Label dialog, set the Object type to Bond, select BondOrder from the Properties list, and click the Apply button to display the bond orders. Once you have imported the charges, spins, and bond orders using the Assign charges to structure, Assign spins to structure, and Assign bond orders to structure buttons, you can export a .car file that contains these data. Displaying band structure charts Band structure charts show how electronic energies depend on the k-vector along high symmetry directions in the Brillouin zone. These charts provide a useful tool for qualitative analysis of the electronic structure of a material; for example, it is easy to identify the narrow bands of d and f states, as
Tasks in DMol3 | Page 43 opposed to the free electron-like bands that correspond to s and p electrons. It is also instructive to look for directions with relatively flat, dispersionless bands, as these directions are likely to contribute strongly to optical absorption, thus allowing the anisotropy of optical properties to be explained. The energy band gap is also easily deduced from the band structure plots, as it normally corresponds to the energy difference between two states at high symmetry points. To create a band structure chart 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Band structure from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) or corresponding output file (seedname.outmol) is the currently active document.
Note: If you are using an output file, make sure you select the output file from the main DMol3 run (seedname.outmol) rather than that from the band structure calculation (seedname_ BandStr.outmol). 4. Select the display style (Points or Lines) from the Graph style dropdown list. 5. Optionally, check the Show DOS checkbox and set the DOS options. 6. Click the View button. 7. A new chart document, seedname Band Structure.xcd, is created in the results folder.
Note: The lower energy limit for the band structure graph can be changed, if necessary, by modifying Plot_DOS keyword with a numeric argument. The default value is set to -1.0 a.u. Displaying density of states charts Density of states (DOS) and partial density of states (PDOS) charts give a quick, qualitative picture of the electronic structure of a material and, sometimes, can be related directly to experimental spectroscopic results.
Page 44 | Materials Studio • DMol Guide Full density of states To create a DOS chart 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Density of states from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) or corresponding output file (seedname.outmol) is the currently active document.
Note: If you are using an output file, make sure you select the output file from the main DMol3 run (seedname.outmol) rather than that from the density of states calculation (seedname_ DOS.outmol). 4. Select the Full radio button to display the total DOS. 5. For spin-polarized calculations, select the required DOS component from the DOS display dropdown list. 6. Optionally, click the More... button to open the DMol3 DOS Analysis Options dialog, where additional analysis options can be set.
Tip: The Interpolation integration method gives more accurate results than the Smearing method, although it is slightly slower.
Note: The Interpolation integration method is only available for calculations on periodic systems. 7. Click the View button. 8. A new chart document, seedname DOS.xcd, is created in the results folder.
Note: The lower energy limit for the density of states graph can be changed, if necessary, by modifying Plot_DOS keyword with a numeric argument. The default value is set to -1.0 a.u.
Partial density of states Materials Studio produces PDOS plots for certain angular momenta on selected atoms. The Sum curve represents the local density of states (LDOS) when one atom is selected. If more than one atom is selected, the contributions in each angular momentum channel from all selected atoms are added together. When no atoms are selected, the behavior is the same as if all atoms were selected.
Tasks in DMol3 | Page 45 To create a PDOS chart 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Density of states from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) or corresponding output file (seedname.outmol) is the currently active document.
Note: If you are using an output file, make sure you select the output file from the main DMol3 run (seedname.outmol) rather than that from the density of states calculation (seedname_ DOS.outmol). 4. Select the Partial radio button to display the partial DOS. 5. Check the appropriate checkboxes to select the required angular momentum components for the PDOS. 6. Select the atom or atoms in the model for which the PDOS is to be created. 7. For spin-polarized calculations, select the required DOS component from the DOS display dropdown list. 8. Optionally, click the More... button to open the DMol3 DOS Analysis Options dialog, where additional analysis options can be set.
Tip: The Interpolation integration method gives more accurate results than the Smearing method, although it is slightly slower.
Note: The Interpolation integration method is only available for calculations on periodic systems. 9. Click the View button. 10. A new chart document, seedname PDOS.xcd, is created in the results folder.
Tip: It is recommended that you rename this file to indicate the atoms on which it is based.
Note: The lower energy limit for the partial density of states graph can be changed, if necessary, by modifying Plot_DOS keyword with a numeric argument. The default value is set to -1.0 a.u. Calculating elastic constants Elastic constants are basic mechanical properties of periodic crystals. DMol3 provides calculation of pure elastic constants and compliance tensors and a variety of derived quantities such as bulk modulus, shear modulus, and their approximations for polycrystalline materials. To calculate elastic constants 1. Choose Modules | DMol3 | Analysis from the Materials Studio menu bar. 2. Select Elastic constants from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) or corresponding output file (seedname.outmol) is the currently active document. 4. Click the Calculate button. 5. A new text document, seedname Elastic Constants.txt, is created in the results folder. Displaying the averaged potential chart for work function calculations The DMol3 Analysis dialog can be used to generate plots of the change in electrostatic potential through a slab, which is related to the energy required to remove an electron from the bulk into the vacuum (the
Page 46 | Materials Studio • DMol Guide work function). The plots are created by averaging electrostatic potential in the planes perpendicular to the slab normal.
Note: Work functions can only be calculated for slabs for which electrostatics have been calculated during a DMol3 run and the Work function checkbox is checked. The electrostatic potential is reported along the fractional coordinate of the unit cell in the direction of the vacuum. The energy required to free an electron is greater at the layers and smaller between the layers, in the vacuum it is negligible. The Fermi level is reported on the work function chart. To create an averaged potential chart 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Potentials from the list of properties. 3. Make the 3D Atomistic document containing the 3D periodic slab the active document. 4. Select the Potential field from the dropdown list. 5. Optionally check the View isosurface on import checkbox. 6. Click the Import button. 7. A new chart document, seedname Potential Profile.xcd, is created in the results folder and becomes the active document. The selected potential field is imported into the 3D Atomistic document and may be displayed as an isosurface. Analyzing optical properties The DMol3 Analysis dialog can be used to generate plots of the optical absorption spectrum These plots are generated based on the excitation energies and oscillator strengths reported in the DMol3 .outmol file. DMol3 enables you to calculate the electronic states of the final output structure from a run. The Optics selection option on the DMol3 Analysis dialog allows you to view excitation data and to generate optical (UV-Vis) spectra in both chart and grid form. To view excitation data or create optical spectrum, you need to have the structure file (.xsd) and DMol3 output file in a folder in the Project Explorer. To create optical spectrum 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Optics from the list of properties. 3. Make sure that the 3D structure document you wish to be updated is the currently active document. 4. Optionally, select the required Units from the dropdown list. 5. Click the View spectrum button. To create optical grid 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Optics from the list of properties. 3. Make sure that the 3D structure document you wish to be updated is the currently active document. 4. Optionally, select the required Units from the dropdown list. 5. Click the View grid button.
Tasks in DMol3 | Page 47 Note: In order to calculate the optical excitations, you must request optics properties in the initial calculation.
Note: Oscillator strengths are available only for singlet state calculations. To analyze excited states optimization 1. Open the .outmol file corresponding to the excited state optimization. 2. Search for the first occurrence of the words Done calculating TDDFT forces. 3. The next three lines contain the excitation energy and the dissociation energy for the initial state of the geometry optimization. The value listed as Excitation energy corresponds to the photon absorption energy of the molecule in its initial state. 4. Search for the last occurrence of the words Done calculating TDDFT forces. 5. The next three lines contain the excitation energy and the dissociation energy for the final state of the geometry optimization. The value listed as Excitation energy corresponds to the photon emission energy of the molecule in its optimized configuration, which is the fluorescence energy. Displaying Raman spectra Raman intensities and activities are calculated in DMol3 by the finite differentiation technique. A number of separate gradient calculations are performed in the presence of varying electric fields in order to generate the polarizability tensor derivative which defines the Raman activity. You can only generate Raman spectra if the necessary intensities have been obtained during the calculation. To display a Raman spectrum 1. Choose Modules | DMol3 | Analysis from the menu bar to display the DMol3 Analysis dialog. 2. Select Raman spectrum from the list of options at the top of the dialog. 3. Make sure that the 3D Atomistic document (.xsd) output from the DMol3 calculation is the currently active document. 4. Select the Function of the mode to be calculated. 5. If the Function is set to Intensity set the Temperature. 6. Set the Smearing value to be used. 7. Select the Units for the X axis. 8. Specify whether to reverse the wavenumber and intensity axes. 9. Click the View button. 10. A new chart document, seedname Raman Spectrum.xcd, is created in the results folder. Calculating reaction kinetics Reaction kinetics are described in terms of reaction rate coefficients. The rate coefficients are evaluated in the transition state theory framework using information about the energies, geometries and vibrational frequencies of reactants, products and transition state. In order to achieve better agreement with experiment it might be advantageous to increase the reaction threshold value from the DFT calculated one, and also to scale calculated harmonic frequencies to account for DFT deficiency and for anharmonic effects. The threshold correction can be applied either on a basis of more accurate ab initio calculations, or based on the comparison of calculated and experimental rate coefficients. It appears that value in the region of 6-7 kcal/mol describes DFT error quite adequately.
Page 48 | Materials Studio • DMol Guide The recommended correction factors for DFT frequencies can be found at the NIST website (http://cccbdb.nist.gov/vibscalejust.asp) for a variety of exchange-correlation functionals. To calculate reaction kinetics 1. Choose Modules | DMol3 | Analysis from the Materials Studio menu bar. 2. Select Reaction kinetics from the list of properties. 3. Ensure that the desired 3D Atomistic collection document (seedname.xod) is the currently active document. 4. Specify the temperature range of interest. 5. Check the Apply tunneling correction checkbox if the reaction involves motion of light elements. 6. Optionally specify a Threshold correction and a Vibrational frequencies scaling factor. 7. Click the Calculate button. 8. A new study table document, seedname.std, is created in the results folder. Displaying solvation properties COSMO surfaces are generated from information from DMol3 calculations which is stored in the .cosmo output file. COSMO surfaces are generated from the point charges used in the DMol3 calculation and represent the cavity that excludes solvent and includes the solute. To create a COSMO surface 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Solvation properties from the list of properties. 3. Ensure that the 3D Atomistic document to be analyzed is the active document. 4. Select COSMO surface from the list of properties to show. 5. Click the Import button. To display COSMO charges 1. Choose Modules | DMol3 | Analysis from the menu bar to open the DMol3 Analysis dialog. 2. Select Solvation properties from the list of properties. 3. Ensure that the 3D Atomistic document to be analyzed is the active document. 4. Select COSMO point charges from the list of properties to show. 5. Click the Import button. To create a sigma chart 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Solvation properties from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) or corresponding output file (seedname.outmol) is the currently active document. 4. Check the View sigma chart on import checkbox. 5. Click the Import button. 6. A new chart document, seedname Sigma Profile.xcd, is created in the results folder.
Note: The sigma chart is automatically generated and imported at the end of any DMol3 calculation which includes solvent. Creating the sigma chart from the DMol3 Analysis dialog will generate a new copy of the same chart.
Tasks in DMol3 | Page 49 Analyzing current and transmission properties The transmission function provides an assessment of how electrons are transmitted between electrodes as a function of their energy. It is often fundamental to the understanding of other transport properties. The current/voltage chart shows how the current through an electrode depends on the applied potential. To perform current analysis 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Current from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) is the currently active document. 4. Click the View button. To perform transmission analysis 1. Choose Modules | DMol3 | Analysis from the menu bar. 2. Select Transmission from the list of properties. 3. Ensure that the desired 3D Atomistic document (seedname.xsd) is the currently active document. 4. Click the View button.
Page 50 | Materials Studio • DMol Guide DMol3 jobs The topics in this section cover controlling and running remote DMol3 jobs, running jobs in standalone mode, deviations from the generic remote job procedure, and potential reasons why DMol3 might fail. Using DMol3 job control Materials Studio can run DMol3 jobs as background processes on a server. The following tools are provided to setup and control the jobs: n Use the Job Control tab on the DMol3 Calculation dialog to select the gateway location and job parameters. n Use the Server Console to add new servers and to monitor multiple jobs. n Use the Job Explorer to monitor multiple jobs. For further information on using job control see the main job control and live updates help topics. Live updates can be requested on the DMol3 Job Control Options dialog. Remote DMol3 jobs DMol3 in Materials Studio uses a client-server architecture so you use your PC to control calculations of the total energy and electronic properties of a system, or geometry optimization running on a remote computer. This separation of the client user interface from the server system running calculations allows you to use a high performance supercomputer from your Windows desktop PC. It also allows you to use spare CPU cycles on other desktop PCs. DMol3 jobs are controlled by input files that are generated by Materials Studio when you start a job. DMol3 writes the results of the calculations in various output files which are loaded upon job completion into your Materials Studio project. DMol3 remote jobs run according to the standard sequence of processes described in A sample remote job run with the differences explained in the Sample DMol3 run help topic. A sample DMol3 run Whether you perform a single-point energy calculation, minimize a structure, run a molecular dynamics simulation, or perform a transition-state search, the sequence of steps that is executed to run a remote DMol3 job is always the same. When you click the Run button on the DMol3 Calculation dialog, the steps described in A sample remote job run happen with the following differences: For all calculations using the COSMO solvation model a COSMO Sigma Profile plot, named
DMol3 jobs | Page 51 n Update structure is checked: Materials Studio downloads a snapshot of the structure and modifies a copy of the original structure accordingly. n Update graphs is checked: Materials Studio creates a chart document called [seedname] Energies.xcd, showing the total energy versus optimization step, and another chart document called [seedname] Convergence.xcd, showing, on the logarithmic scale, the total energy change, the maximum displacement, and the maximum force versus optimization step. n Update textual results is checked: Materials Studio downloads a text file called Status.txt that contains a summary of the calculation performed (task, DFT functional, basis set, system charge and spin, etc.), the SCF iteration number, the number of completed optimization steps, the total energy, the total energy convergence (i.e., the change from the previous iteration), the maximum displacement, and the maximum force for the last completed optimization step. For Dynamics calculations, if n Update structure is checked: Materials Studio downloads a snapshot of the structure and modifies a copy of the original structure accordingly. n Update graphs is checked: Materials Studio creates a chart document called [seedname] Constant.xcd, showing the constant of motion versus simulation time, and another chart document called [seedname] Temperature.xcd, showing the temperature versus simulation time. n Update textual results is checked: Materials Studio downloads a text file called Status.txt that contains a summary of the calculation performed (task, DFT functional, basis set, system charge and spin, etc.), the number of completed dynamics steps, the temperature, and the constant of motion for the last completed optimization step. For TS Search calculations, if n Update structure is checked: Materials Studio downloads a snapshot of the structure and modifies a copy of the original structure accordingly. n Update graphs is selected: Materials Studio creates a chart document called [seedname] TransitionState.xcd, showing the total energy versus reaction coordinate. For each phase of the transition-state search, a separate graph is displayed within the chart document. n Update textual results is selected: Materials Studio downloads a text file called Status.txt that contains a summary of the calculation performed (task, DFT functional, basis set, system charge and spin, etc.), the SCF iteration number, the phase of the transition-state search currently being processed (whether for a maximum or relative minimum), the reaction path coordinate, the total energy, the total energy convergence (i.e., the change from the previous iteration), and the RMS displacement and RMS force for the last completed optimization step. For TS Optimization and TS Confirmation calculations, the behavior is the same as for a Geometry Optimization run. Once the job has finished, Materials Studio will transfer the output files back to your PC, where you can view and edit them, analyze the results, or use them for further calculations. Additional output files may be generated or modified depending on the type of calculation you performed.
Page 52 | Materials Studio • DMol Guide n For Energy runs, Materials Studio downloads all the DMol3 output files. n For Geometry Optimization runs, Materials Studio downloads all the DMol3 output files, updates the structure it has copied into the results folder to show the final geometry, and creates a trajectory file, [seedname].xtd, that contains the history of the optimization process. The trajectory file can be animated using the tools on the Animation toolbar. n For Dynamics runs, Materials Studio downloads all the DMol3 output files, updates the structure it has copied into the results folder to show the configuration at the beginning of the dynamics run, and creates a trajectory file, [seedname].xtd, that describes the molecular dynamics calculation. The trajectory file can be animated using the tools on the Animation toolbar. n For TS Search, TS Optimization, and TS Confirmation runs, the behavior is the same as for a Geometry Optimization run. The description given above is somewhat simplified, but provides a reasonable overview of a DMol3 run. If a remote DMol3 job fails Materials Studio checks most of the data and settings required to perform a DMol3 job prior to launch. If it cannot start the job, error messages are generated detailing the reasons. However, sometimes jobs may fail for reasons which cannot be checked prior to launch. In such cases, an error message giving more detailed information appears in the [seedname].outmol file produced by the job and, in some situations, in the job log window as well. Other files stored in the job directory on the server may also contain further clues. To view the server-side files, you can use the Remote View facility of the Job Explorer. Below is a list of the most common reasons for DMol3 jobs to fail. It may help you to identify and fix any problems you have with your remote DMol3 jobs. For generic reasons for remote job failures please consult the If a remote job fails help topic.
Tip: Select View | Project Log from the menu bar to see if any error or warning messages have been reported. Cannot start a DMol3 job Run button is grayed out n The active document is not a 3D Atomistic document. If something other than a 3D Atomistic document is the current document, a chart or text document, for example, then the Run button will be grayed out. To run the calculation, select an appropriate document. n The active document is 2D periodic. DMol3 can only operate on molecules and 3D periodic structures. To model a 2D structure, build a slab with a region of vacuum from the surface. n The active document does not contain a trajectory and you are trying to perform a transition-state search. To perform a transition-state search, you must first create a trajectory using the Reaction Preview tool. See Transition state searching via synchronous transit methods for additional information. Common reasons for a DMol3 job to fail to start Server-side problems
DMol3 jobs | Page 53 n Parallel DMol3 job fails with runtime input/output error message under Linux. Depending upon the options selected, DMol3 may use significant amounts of disk space to store scratch files. Scratch files are created by each node during the execution of a parallel DMol3 job. DMol3 uses the value of the environment variable GATEWAY_TMP as the location to be used to save these files; this variable is set by share/bin/ms_vars.sbd and can be changed using the gateway's web interface. You should ensure that the location that will be used on each node points to a file system with at least 1 GB of free space. Note that the ./tmp setting for GATEWAY_TMP corresponds to using the common file space on the head node, in the actual job directory, to store the temporary files. This setting can have a detrimental effect on the performance of Linux clusters. An additional problem may occur if the NFS mount of the head node file system is set up incorrectly on the nodes. This mount should be done in a synchronous mode using hard mounts, as detailed in Installing Materials Studio on Linux systems. n DMol3 job fails when B3LYP functional used. B3LYP calculations are very demanding in terms of memory use. The exact amount of memory required for a B3LYP calculation is not easy to estimate, but DMol3 will try to optimize the algorithm to fit within the requested limit. If the job fails, either try to allocate more memory (if available) or modify the job parameters (such as basis set size, atomic cutoff, or system size) to reduce the amount of memory required.
Tip: It is important to identify the reason for the failure of a DMol3 job before taking any action. In most cases, the error message will give a good indication of the reason for the failure. If the error message indicates that the job failed, but does not provide specific reasons, check the [seedname].outmol file produced by the job or check the project log.
Note: If a job with File usage set to Memory fails, restart files will not be created.
Running DMol3 in standalone mode The most convenient way of running DMol3 is through the Materials Studio interface, which performs all the preparatory tasks required to run a DMol3 job. However, in some circumstances, it may be necessary to run DMol3 in standalone mode with a set of input files prepared elsewhere. For example, you may wish to use results files from an earlier DMol3 calculation or you might want to run a calculation on a server that has not been configured as a gateway (i.e., a computer that does not communicate with your Materials Studio client). Generate the input files In order to run, DMol3 requires an .input file containing specifications for the calculation and a .car file containing the Cartesian coordinates of the atoms. Some calculations also require an .mdf or .arc file. You can create these files using a text editor, such as WordPad on Windows or vi on Linux. However, because the number of input files required is quite large and the information they contain quite complex, you should use Materials Studio to generate them for you. You can create the required files using the DMol3 Job Files dialog, see the Running jobs in standalone mode topic for further information. Transfer the input files to the server If you generated the input files manually using a text editor on the server machine, then no file transfer is required. However, if you generated the files on your PC using Materials Studio, you must transfer them to the server before you can start the calculation. If you are unable to access the hard drive on the server, you should use the File Transfer tool to transfer files from the client to the server.
Page 54 | Materials Studio • DMol Guide Execute the job To assist you in running DMol3 in standalone mode, a batch/shell file called RunDMol3 is supplied. It can be found in the directory in which the DMol3 executables are located, usually etc/DMol3/bin in the main Materials Studio directory. RunDMol3 scripts are used to start DMol3 jobs in standalone mode. RunDMol3.sh is provided for Linux servers, while RunDMol3.bat is provided for Windows servers. Usage: RunDMol3.sh [-h] [-nodelete] [-np number of cores] [-q queue name] seedname (Linux) or RunDMol3.bat [-h] [-nodelete] [-np number of cores] [-q queue name] seedname (Windows)
Argument Description -h Displays the help text. -nodelete Specifies whether job and scratch files created during DMol3 execution are deleted. When this option is used, all temporary and scratch files are retained on the server. If the option is not used, the script deletes these files upon the termination of the job. -np Specifies the number of cores on which to run DMol3. When this option is not specified a single core is used. number of cores The number of cores to use. -q Submits the job to the specified queue. queue name The name of the queue on which to run the job. seedname The seed used to identify the set of DMol3 input and output files. The input files should be present in the directory in which the DMol3 script is started. If you wish to calculate properties, you should execute the script for the main run first: RunDMol3.sh -nodelete seedname When that run is complete, you should make copies of the .car, .tpdensk and .tpotl files that will be used in all subsequent properties runs: cp seedname.car seedname_BandStr.car cp seedname.car seedname_DOS.car etc Specifically, one needs the following files for a DOS calculation: seedname_DOS.tpotl seedname_DOS.car seedname_DOS.kpoints (for periodic structures only) seedname_DOS.tpdensk (for periodic structures only) and the following files for a Band structure calculation: seedname_BandStr.tpotl seedname_BandStr.car
DMol3 jobs | Page 55 seedname_BandStr.kpoints (for periodic structures only) seedname_BandStr.tpdensk (for periodic structures only) When the appropriate copies have been made, execute RunDMol3 for each properties run: RunDMol3.sh -nodelete seedname_DOS RunDMol3.sh -nodelete seedname_BandStr These jobs can be run independently because they do not share input or output files. When running jobs on computers equipped with a queuing system it may be necessary to define certain environment variables which DMol3 is using: n DMOL_TMP - directory where DMol3 will store large temporary files during calculation. By default it is /var/tmp on Linux and C:\TEMP on Windows. n DMOL3_DATA - directory containing DMol3 runtime files, for example BASFILE, AREP, DSPP etc. The default location is share/Resources/Quantum/DMol3. Download the output files from the server When the DMol3 calculation is complete, you must transfer the output files back to your PC for analysis in Materials Studio. See Running jobs in standalone mode for further information. To transfer the output files back to your PC Transfer the following output files to the client PC either using copy and paste or the File Transfer tool: seedname.car seedname.mdf seedname.outmol seedname.tpdensk seedname.hessian seedname.hesswk seedname.arc seedname*.summ seedname*.grd seedname*.bands seedname*_pdos.weights If DOS or band structure calculations were performed, all above files with seedname_DOS and seedname_BandStr should also be copied. Not all of these files will necessarily be present in every case.
Tip: If you have transferred files into a Materials Studio project folder, but you cannot see them in the
Project Explorer, try using the Refresh button to update the Project Explorer.
Open the output files in Materials Studio Provided that you have transferred the correct files from the server to your PC and stored them in a folder in a Materials Studio project, you should be able to make use of the DMol3 analysis options described in the topic Analyzing DMol3 results. To view the final geometry Open the .xsd file, you should use the Structure section on the DMol3 Analysis dialog, click the Update button. See the Updating structure topic for more information.
Page 56 | Materials Studio • DMol Guide To create a chart of energy and/or gradients vs. geometry optimization Open the .xsd file, you should use the Energy evolution section on the DMol3 Analysis dialog, click the View button. See the Displaying trajectory and chart data topic for more information. To link the charts to a trajectory You can use the resulting trajectory and chart documents as described in the Displaying trajectory and chart data topic. To perform vibrational analysis 1. Open the .xsd file from the calculation by double-clicking on the file in the Project Explorer. 2. Load a .hessian file using the Insert Into Active Document dialog. 3. Navigate to and select the .hessian file you wish to load into the project. 4. Click the Insert button. 5. When a .hessian file has been associated with a structure, you can make use of the Vibrational Analysis dialog, which is accessed from the Tools menu. To perform charge, spin, and bond order analysis Open the .xsd file, you should use the Population analysis section on the DMol3 Analysis dialog, to display atomic charges, spins, and bond orders. See the Displaying population analysis results topic for further details. DMol3 file formats The DMol3 server program requires a number of different input files and produces a number of output files. The number and type of input files required and output files produced depend on the details of the DMol3 job to be performed. The table below summarizes information on the format and purpose of the major file types, and provides links to further information. File type Input or Output Brief description .input Input General input file .car * Input / Output Cartesian coordinates .mdf * Input Supplementary structure information .outmol Output Textual results of the calculation .hessian * Input / Output Hessian matrix .tpvec * Input / Output LCAO MO coefficients .tpdensk * Input / Output Charge density .hesswk * Input / Output Components of a finite-difference Hessian .arc * Input / Output Trajectory data .grd * Output Volumetric data .occup * Input / Output Orbital occupations .bands * Input / Output Eigenvalues .pdos_weights * Input / Output Weights required to calculate PDOS
DMol3 jobs | Page 57 File type Input or Output Brief description .cosmo * Output Solvent charges and COSMO details * These files are hidden by default, so they will not appear in the Materials Studio Project Explorer; these files are only visible in Windows Explorer if Windows on your machine is configured to show hidden files. DMol3 file formats - ARC DMol3 stores an optimization history of a calculation in the .arc file. When you run a geometry optimization, TS optimization, or TS search, each geometry and energy is written to the .arc file. This is returned to the Materials Studio client and may be used to analyze the trajectory of the optimization as described in Displaying trajectory and chart data. See the ARC file format topic for details of the .arc file. DMol3 file formats - BANDS The .bands file contains electronic eigenvalues for a DMol3 job. The data in this file are used for band structure plotting and optics, DOS, and PDOS calculations. The eigenvalues are given in atomic units. The k-points are specified using fractional coordinates, which are followed by the corresponding k-point weight.
Note: For nonperiodic systems, the number of k-points is specified as 0 in the .bands file. DMol3 file formats - CAR and MDF DMol3 reads data from the .car file. This file is generated by Materials Studio when you n launch a calculation n select Save Files from the Job Files dialog or n export a file using File | Export The data read include Cartesian coordinates, atom labels, and element types. Other data may be present in the .car file, but are ignored. At the end of a calculation, the coordinates in the .car file are updated by DMol3. When a .car file is created by Materials Studio an .mdf file is also written. DMol3 jobs do not require an .mdf file, but if one is present DMol3 reads the following from it: n Bonding information, used to construct internal coordinates for the optimizer. When no .mdf file exists, DMol3 generates bonds based on proximity of atoms. n The presence of any frozen atoms. If there is a set named "MDF_FIXED_ATOMS_SUBSET" then the Cartesian coordinates of these atoms will be held fixed. If this subset is not present, all atoms will be moved. Such a set is generated by Materials Studio whenever needed. n The presence of any partial Hessian atoms. If there is a subset named "HessianAtoms" in the .mdf file, then only these atoms will be perturbed during the finite-difference evaluation of the Hessian. If this subset is not present, all atoms will be moved. This information is ignored if you are not running a Hessian or frequency calculation or explicitly choose to use all atoms in the DMol3 frequency calculation. Such a set is generated by Materials Studio whenever needed. DMol3 file formats - COSMO When Use solvation model calculation is specified on the Electronics tab of the DMol3 Calculation dialog the results folder will contain a .cosmo file. This file contains information related to the solvent effect on a studied system.
Page 58 | Materials Studio • DMol Guide The first part of the file contains details of the solvent-related input. The data is taken either from specifications in the .input file or from internal DMol3 defaults. The second part of the file lists atomic centers and corresponding COSMO surface/charge parameters on a per-atom basis. The third part of the file lists output energies and properties calculated with the COSMO IBS formalism. COSMO-related energy components are listed in Hartree, eV, and kcal/mol. The last and largest part of the file contains a table with COSMO segment details. For each segment the position, charge, corresponding area, and potential are listed. The information in the $segment information part can be used for further analysis, for example calculating COSMO Sigma profiles. DMol3 file formats - GRD The .grd file stores 3D volumetric data. These files may be imported and used to create fields isosurfaces and 2D slices of volumetric data. See GRD file format for more detailed information on this file. DMol3 file formats - HESSIAN A DMol3 geometry optimization begins with an initial guess for the Hessian and updates it with each optimization step. After each step, the latest Hessian data are stored in the .hessian file. The final Hessian in a DMol3 vibrational frequency or Hessian evaluation is also saved in the .hessian file. You can use an existing .hessian file for the initial guess in a geometry optimization or a transition state optimization as described in Restarting a DMol3 calculation. See the HESSIAN file format topic for an explanation of the format of the .hessian file. DMol3 file formats - HESSWK When DMol3 performs a vibrational frequency or Hessian evaluation, it evaluates the Hessian by finite differences of gradients. This requires an evaluation of the forces for each possible Cartesian displacement of atoms in the molecule. The gradients for each displacement are stored in the .hesswk file. Once all the displacements have been performed, the data are consolidated into a .hessian file. If a Hessian calculation terminates before all the displacements have been performed, you can supply the .hesswk as input. DMol3 can read the data from a .hesswk and continue the job from the point of termination. This procedure is described in Restarting a DMol3 calculation. The format of the .hesswk file is explained in detail below: The file begins with one line for each atom in the file describing the integration mesh. Including this information ensures that a restarted calculation uses the same mesh. These lines are generated by the program; users should not alter them. Following this come the forces for each atom for each displaced geometry. Each section begins with three integers that indicate: n The number of the atom being moved (as numbered in the car file) n The direction of the displacement, 1=x, 2=y, 3=z n Whether the direction is in the positive or negative direction, 1 or 2, respectively. Following these integers is the step size in Bohr and the binding energy in Hartree. The next line contains the forces on each atom in Hartree per Bohr. The order of the atoms is the same as in the .car file. After the Cartesian forces appears the dipole moment in atomic units at the displaced geometry. The first list of forces is for the undisplaced geometry, and uses "0 0 0" as the integers to indicate that.
DMol3 jobs | Page 59 DMol3 file formats - INPUT The DMol3.input file supplies the parameters for a job including, for example, the type of calculation, charge, spin state, and convergence tolerances. The file consists of lines, keywords and options. A .input file is generated by Materials Studio when you launch a calculation or when you select Save Files from the DMol3 Job Files dialog. Job options selected through the interface appear as keywords in the resulting .input file. Under special circumstances you may wish to add manually certain keywords to an .input file that are not supported in the interface. The procedure is described in Manipulating files. The following rules govern keywords in the .input file: n Line width is 80 characters n Delimiting character is a space, tabs are not supported n Keywords may appear in any order n The keywords and values are case-insensitive n Only one keyword and its options may appear on a line n Keywords that do not appear in the .input file are set to their default values n Comment lines (those beginning with "#") and blank lines are ignored A typical .input file has the form: # Comment keyword_1 option_1 keyword_2 option_2 # Comment keyword_3 option_3 ... Keywords and options are fully described in DMol3 keywords in the online help. DMol3 file formats - OCCUP When Fixed is specified for the value of the Occupation keyword the occupations are read from the .occup file. The basic format of the occup file is: N oc od Representation in format (I5, 2f10.6,2x,a). n N (integer) indicates the number of orbitals having this occupation n oc (real) is the spin-up (alpha) orbital occupation number n od (real) is the spin-down (beta) orbital occupation n Representation is the symmetry symbol of the orbital occupation Terminate the occupation for each irreducible representation with a line containing N=0. DMol3 file formats - OUTMOL The .outmol file contains the numerical output of a DMol3 job in text format. The header describes the settings used and system specifications (unit cell vectors, atomic coordinates), followed by the calculation results.
Page 60 | Materials Studio • DMol Guide DMol3 file formats - PDOS_WEIGHTS The .pdos_weights file contains the weights that are required to generate partial densities of state (PDOS), based on the results of a DMol3 job. DMol3 file formats - TPVEC The .tpvec file holds the molecular orbital coefficients for a wavefunction. These are available for molecules and solids using the Γ-point. For solids using multiple k-points, the charge density is stored directly in the .tpdensk file. The .tpvec file is updated after each SCF iteration. At the end of a calculation, you can use the .tpvec file to supply an initial SCF guess to a subsequent calculation, thereby speeding convergence. The .tpvec file is in binary format and is not intended to be read outside of DMol3. The small code sample below illustrates how the data are stored: read (iunit) ms, (Vec(i),i=1,ms) if(nspin.gt.0) read (iunit) (Vecbeta(i),i=1,ms) read (iunit) (eig(i), elno(i) ,i=1,lx) where Vec is the MO coefficient for alpha spin (or for closed shells); Vecbeta is the coefficient for beta spin; eig is the eigenvalue in Hartree; and elno is the orbital occupation The MO coefficients are stored in Vec as a series of symmetry blocks. Say there are N irreducible representations, and representation i contains n orbitals, 1 ≤ i ≤ N. Then: i lx = Σ n if nspin=0 i lx = 2 × Σ n if nspin>0 i ms = Σ n 2 i nspin = 0 for restricted calculations and nspin > 0 for unrestricted calculations. DMol3 file formats - TPDENSK The .tpdensk file holds the charge density at each integration point for computations using multiple k- points. The .tpdensk file is updated after each SCF iteration. At the end of a calculation, you can use the .tpdensk file to supply an initial SCF guess to a follow-on calculation, thereby speeding convergence. The .tpdensk file is in binary format and is not intended to be read outside of DMol3. Reaction Kinetics Study Table The results of the reaction rate calculation are collected in a study table which contains three tabs: n Summary - contains a summary of the results, reporting the main parameters of the calculation, fit coefficients, and root-mean-square error (RMSE) which is calculated for ln(k(T)). If the fit parameters (also shown on the Graphs tab) produce too high n, or Ea becomes negative, the corresponding lines in the study table are highlighted in red. n Graphs - contains the temperature dependence of the reaction rates coefficients (k(T)) for forward and backward reactions together with equilibrium constants. It also contains results of the fit using Arrhenius form (see Kinetics constants theory) with temperature T = 298 K together with standard 0 Arrhenius form (n = 0, the temperature independent pre-exponential coefficient). n Partition Function - contains the calculated partition functions for reactant(s), product(s), and transition state.
DMol3 jobs | Page 61 Theory in DMol3 The following topics provide specifics about the theory behind DMol3. Density functional theory (DFT) in DMol3 This section provides information specific to the implementation of DFT in the DMol3 program. A general overview of DFT is provided elsewhere. The overview provides information on the concepts of charge density, DFT functionals, the SCF procedure, and band structures, which are generally applicable to any computational implementation of DFT. The application of dispersion corrections to DFT is also described. In contrast, this section provides background on aspects of DFT unique to DMol3. Functionals in DMol3 Local functionals The exchange-correlation energy is given by Eq. DFT-7. The specific local functionals provided in DMol3 are the VWN functional (Vosko et al., 1980) and PWC (Perdew and Wang, 1992). The default is PWC. Nonlocal functionals The so-called nonlocal or gradient-corrected functionals depend on dρ/dr as well as on ρ. This provides a considerable increase in the accuracy of predicted energies and structures, but with an additional cost. The NLSD functionals available in DMol3 include: Name Description Reference PW91 Perdew-Wang generalized-gradient approximation Perdew and Wang (1992) BP Becke exchange plus Perdew correlation Becke (1988), Perdew and Wang (1992) PBE Perdew-Burke-Ernzerhof correlation Perdew et al. (1996) RPBE Revised PBE functional by Hammer et al. Hammer et al. (1999) PBEsol PBE functional optimized for solids Perdew et al. (2008) HCTH Hamprecht, Cohen, Tozer and Handy functional Boese and Handy (2001) BLYP Becke exchange plus Lee-Yang-Parr correlation Becke (1988), Lee et al. (1988) BOP Becke One Parameter functional Tsuneda et al. (1999) VWN- BP functional with the local correlation replaced by Vosko et al. (1980), Becke (1988), Perdew BP the VWN functional. and Wang (1992) Hybrid functionals The B3LYP hybrid functional is provided in DMol3 (Becke, 1993, Stephens et al., 1994). Hybrid functionals attempt to improve the exchange-correlation energy functional by incorporating a portion of exact exchange from Hartree-Fock theory along with exchange and correlation contributions from other, mainly local, functionals with carefully chosen weights. The weights are obtained by fitting to experimental data. E HF E VWN Apart from the exact Hartree-Fock exchange term, x , B3LYP employs the local VWN ( c ) and LDA E LDA E LDA ( c ) correlation functionals as well as local LDA exchange ( x ). In addition, Becke's gradient ΔE B88 E LYP correction ( x ) to the exact exchange and LYP correlation functional ( c ) are used.
Page 62 | Materials Studio • DMol Guide Eq. B3LYP-1 B3 LYP HF LDA B88 LYP VWN EXC = aEx +(1−) aEx +∆ bEx + cEc +(1−) cEc Becke (1993) suggested a = 0.2, b = 0.72, and c = 0.81 based on fitting to heats of formation of small molecules. Meta-GGA functionals In addition to the generalized gradient (GGA) functionals which depend on the local density and its gradient, DMol3 can handle functionals that depend on the kinetic energy density:
1 2 τ(r ) = ∑occup ∇ ψ () r i i 2 i The following meta-GGA functionals are available: Name Description Reference M06-L Minnesota 2006 meta-GGA functional Zhao and Truhlar (2006) M11-L Minnesota 2011 meta-GGA functional Peverati and Truhlar (2012) Numerical basis sets The matrix elements needed to solve the SCF equations and compute the total energy are given by the expressions in Eq. DFT-15 and Eq. DFT-16. DMol3 uses numerical orbitals for the basis functions, each function corresponding to an atomic orbital (AO). This section describes in more detail how such orbitals are generated and used. Atomic basis sets are generated numerically The basis functions χ are given numerically as values on an atomic-centered spherical-polar mesh, μ rather than as analytical functions (i.e., Gaussian orbitals). The angular portion of each function is the appropriate spherical harmonic Ylm(θ,φ). The radial portion F(r) is obtained by solving the atomic DFT equations numerically. A reasonable level of accuracy is usually obtained by using about 300 radial points from the nucleus to an outer distance of 10 Bohr (~5.3 Å). Radial functions are stored as a set of cubic spline coefficients for each of the 300 sections, so that F(r) is actually piecewise analytic. This is an important consideration for generating analytic energy gradients. In addition to the basis sets, the - ∇ 2/ 2 terms required for evaluation of the kinetic energy are also stored as spline coefficients. Atomic basis sets are confined within a cutoff value, r , appropriate for a particular quality level of DMol3 c calculations. This is an important feature of the numerical basis set that can lead to much faster calculations, particularly for solid state systems. DMol3 uses a so-called soft confinement potential, which ensures the strict localization of the basis set within an r value, without discontinuous derivatives c at r . Geometry optimization is efficient, even with small cutoff values. c Advantages of numerically derived basis sets The use of the exact DFT spherical atomic orbitals has several advantages. For one, the molecule can be dissociated exactly to its constituent atoms (within the DFT context). Because of the quality of these orbitals, basis set superposition effects (Delley, 1990) are minimized and it is possible to obtain an excellent description, even for weak bonds. Additional basis functions, including polarization Greater variational freedom is obtained by providing larger basis sets. Generation of an entire second set of functions results in doubling the basis set size; this is referred to as a double-numerical (DN) set.
Theory in DMol3 | Page 63 This notation is used by analogy with Gaussian double-zeta (DZ) sets, but the N is used to emphasize the numerical nature of these orbitals. Additional basis functions, including polarization, are obtained by several procedures: n DFT atomic ion calculations n DFT excited-state atom calculations n Hydrogenic orbitals For first-row atoms, functions from +2 ions provide a reasonable double basis set. A hydrogenic 3D orbital obtained for a nucleus of Z = 5 provides a good polarization function for each of these atoms. A hydrogenic 2p function for Z = 1.3 is used for hydrogen. The use of various nuclear charges to generate polarization functions is analogous to the variation of zeta in Gaussian basis sets. For metals, 4p polarization functions are generated by solving the atomic equations for a 4s → 4p excited state. Basis set quality has been analyzed in detail by Delley (1990). The triple-numerical (TNP) set has been recently generated and validated by Delley (2006). The table below summarizes the basis sets used in the program. Basis Description Examples Name MIN Minimal basis. One AO for each occupied atomic H: 1s orbital. C: 1s 2s 2p Yields low accuracy but fast computation. Si: 1s 2s 2p 3s 3p DN Double Numerical. MIN + a second set of valence H: 1s 1s' AOs. C: 1s 2s 2p 2s' 2p' Improved accuracy over MIN. Si: 1s 2s 2p 3s 3p 3s' 3p' DND Double Numerical plus d-functions. Like DN with H: 1s 1s' a polarization d-function on all non-hydrogen C: 1s 2s 2p 2s' 2p' 3d atoms. Si: 1s 2s 2p 3s 3p 3s' 3p' 3d The default basis set, providing reasonable accuracy for modest computational cost. DNP Double Numerical plus polarization. Like DND H: 1s 1s' 2p including a polarization p-function on all C: 1s 2s 2p 2s' 2p' 3d hydrogen atoms. Si: 1s 2s 2p 3s 3p 3s' 3p' 3d Best accuracy, highest cost. Important for hydrogen bonding. TNP Triple Numerical plus polarization. Like DNP H: 1s 1s' 2p 1s" 2p' 3d including additional polarization functions on all O: 1s 2s 2p 2s' 2p' 3d 2s" 2p" 3p 4d atoms. S: 1s 2s 2p 2s' 2p' 3s 3p 3s' 3p' 3d 3s" 3p" Available only for H to Cl except He and Ne. 3d' 4d Best accuracy, highest cost.
Page 64 | Materials Studio • DMol Guide Basis Description Examples Name DNP+ Double Numerical plus polarization, with H: 1s 1s' 2p 1s" 2p' addition of diffuse functions. C: 1s 2s 2p 2s' 2p' 3d 1s' 2p" 3d' Good accuracy for cases requiring diffuse Si: 1s 2s 2p 3s 3p 3s' 3p' 3d 1s' 2p' 3d' functions, very high cost coming mostly from very large atomic cutoffs required for this set. Important for anions, excited state calculations and for cases where long-range effects are non- negligible. The bold components are the additional diffuse functions. Numerical integration Evaluation of the integrals in Eqs. DFT-15 and DFT-16 must be accomplished by a 3D numerical integration procedure, due to the nature of the basis functions. The matrix elements need to be approximated by the finite sums: Eq. DMol3-1
Eq. DMol3-2
The sums run over several numerical integration points ri. The term H ( ri) represents the value of the eff integrand of Eq. DFT-15 at point r and w(r ) represents a weight associated with each mesh point. i i Increasing the number of mesh points improves the numerical precision of the integral but also results in additional computational cost. Atomic and molecular integration grids Careful selection of a set of integration points is important for the quality of the calculation (Delley, 1990; Ellis and Painter, 1968; Boerrigter et al., 1988). In general, the grid used to generate the atomic basis set is not suitable for molecular calculations. The grid used for atomic basis sets can take advantage of spherical symmetry, which greatly simplifies matters. For molecules, it is necessary to be able to correctly handle the rapid oscillations of the molecular orbitals near the nuclei, and to avoid integration of the nuclei themselves because of the nuclear cusps (Delley, 1990). Integration points, atomic size, precision, and computational cost The integration points are generated in a spherical pattern around each atomic center. Radial points are typically taken from the nucleus to an outer distance of 5.5 Å (~10.4 Bohr). The number of radial points within this distance is designed to scale with increasing atomic number. For example, Fe requires more points than C. The typical number of radial points N for a nucleus of charge Z is: R Eq. DMol3-3
Theory in DMol3 | Page 65 This number may, of course, be manually adjusted to accommodate the required precision or allowed cost of a calculation. The spacing between points is logarithmic. Points are spaced more closely near the nucleus where oscillations in the wavefunction are more rapid. Atomic shells Angular integration points N are generated at each of the N radial points, creating a series of shells θ R around each nucleus. Angular points are selected by schemes designed to yield points ri and weights w (ri), which could yield exact angular integration for a spherical harmonic with a given value of l. Such quadrature schemes (Stroud, 1971; Lebedev, 1975 and 1977; Konyaev, 1979) are available for functions up to l = 41. Alternatively, a product-Gauss rule in cos θ and ϕ may be used for arbitrary values of l (Stroud, 1971). The product-Gauss methods use (l + 1) points on each shell, while the quadrature methods use more points. The scheme used in DMol3 provides the following numbers of points for each value of l:
l 5 7 11 17 23 29 35 41 N θ 14 26 50 110 194 302 434 590 Assuring consistent precision during integration In practice, few angular points are needed near the core or far from an atomic center, since the charge density is fairly homogeneous. By contrast, in the valence region around an atom the angular density varies quite a bit. Therefore, one would like to use as many points as practical to assure good precision; at the same time, one does not want to use more points than are necessary, as this increases the cost of the calculation. In DMol3 the number of angular points is "ramped-up" from a modest value near the nucleus to a maximum value in the valence region. Input may be used to fine tune the precise number of points, but a typical calculation will use about 1000 points per atom. Partition functions improve convergence and avoid nuclear cusps Partition functions are used to increase the convergence of the numerical integration and to avoid integrating over nuclear cusps (Delley, 1990; Hirshfeld, 1977; Becke, 1988). A partition function ρ is α defined as: Eq. DMol3-4
where α is an atom index and g (r - R ) is a function that typically is large for small r - R and small for α α α large r - R (i.e., larger near the nucleus). Integrals are rewritten using partition functions as: α Eq. DMol3-5
which is further reduced to a sum over 3D integration points: Eq. DMol3-6
In practice, the partition functions are combined with the integration weights w(ri) to simplify the computation. The default choice for a partition function is:
Page 66 | Materials Studio • DMol Guide Eq. DMol3-7
where r = |ri - R |, r = 0.5, and ρ is the atomic charge density for atom α. Other options for partition α 0 a functions are available in DMol3 but are not recommended. Evaluation of the exchange-correlation energy, E , may be accomplished by numerical integration of the xc expression in Eq. DFT-7. Matrix elements of the exchange-correlation potential are evaluated by inserting the expression for μ from Eq. DFT-11 into Eq. DFT-17 in place of H . xc eff This requires numerical evaluation of the charge density ρ(r) at many points in space (i.e., εxc and μxc are tabulated numerically). This restriction actually applies to most density function methods, even if analytical basis functions are used (Andzelm et al., 1989; Versluis and Ziegler, 1988). The use of numerical basis functions facilitates this process, since all required quantities are already available on a grid of adequate numerical precision. An alternative approach (Baerends et al., 1973) is to fit the charge density to an analytic multipolar expansion via a least-squares fitting procedure. This simplifies the evaluation of εxc and μxc, but still requires the use of a numerical grid for the least-squares fitting. Pseudopotentials Pseudopotentials reduce computational effort by replacing some basis functions with a simplified analytic or numerical form. The matrix elements over these functions need to be computed only once and are excluded from the self-consistent field procedure. Consider a molecule or solid as a collection of valence electrons and ion cores. The ion cores contain nuclei and tightly bound core electrons. The valence electron wavefunctions are orthogonal to core- electron wavefunctions. All-electron DFT methods treat core and valence electrons on an equal footing. In the pseudopotential approach ion cores are considered to be frozen. This means that properties of molecules or solids are calculated on the assumption that the ion cores are not involved in chemical bonding and do not change as a result of structural modifications. The pseudopotential approximation replaces core electrons and the strong Coulomb potential by a weaker pseudopotential that acts on a set of pseudo wavefunctions. Matrix elements of this potential can be computed efficiently. Pseudo wavefunctions ideally should have no nodes inside the core regions and thus they may be represented by a small number of functions. Traditionally, pseudopotentials are constructed so as to reproduce faithfully the scattering properties of the full ionic potential. The phase shift produced by the ionic core is different for each angular momentum component (s, p, d, etc.) of the valence wavefunction. Thus, the scattering from the pseudopotential must be angular momentum dependent. The most general form for a pseudopotential is: V = Σ |lm> Vl
Theory in DMol3 | Page 67 1. DSPP: The Density functional Semi-core PseudoPotentials were generated by fitting all-electron relativistic DFT results. Thus the DSPPs have been specifically designed to reproduce accurate DMol3 calculations. These potentials have a nonlocal contribution for each channel up to l =2, as well as a nonlocal contribution to account for higher channels. The potentials are norm conserving. 2. ECP: The Effective Core Potentials (Dolg et al. 1987, Bergner et al. 1993) are best used in Hartree-Fock calculations. DSPP is now the preferred method for DFT calculations. 3. Scalar relativity: These potentials do not replace core electrons; instead they supplement the core potentials with approximate relativistic effects. Such effects are important for heavier elements, and are certainly required starting with the second row of transition metals (element 39, Yttrium). Using these potentials yields the most accurate results, though at the highest cost. The DSPP also include relativistic effects. You cannot restrict the use of ECPs or DSPPs to specific elements. Whenever you use either option, DMol3 examines a data file that contains the potentials. If DSPP or ECP data are found for an element, then the core electrons for that element are replaced; if the data are not found for an element, then all its electrons are retained. Currently, DSPPs and ECPs are provided beginning with element number 21, Sc. For example, in a system containing H, O, Al, Cu, and Au, if you opt to use ECPs or DSPPs, only the core electrons for Cu and Au will be replaced; H, O, and Al will be treated as in the all-electron case. Norm-conserving pseudopotentials The main requirement of the pseudopotential approach is that it reproduces the valence charge density associated with chemical bonds. It has been shown (Hamann et al., 1979) that for pseudo and all- electron wavefunctions to be identical beyond the core radius, R , it is necessary for the integrals of c squared amplitudes of the two functions be the same. This is equivalent to requiring norm-conservation from pseudo wavefunctions, i.e. that each of them should carry exactly one electron. This condition ensures that the scattering properties of the pseudopotential are reproduced correctly.
Page 68 | Materials Studio • DMol Guide Figure 1. Schematic representation of the all-electron and pseudo wavefunctions and potentials The typical method for generating pseudopotentials is as follows. All-electron calculations are carried out for an isolated atom in a chosen electronic configuration (not necessarily in the ground state). This provides valence electron eigenvalues and valence electron wavefunctions for the atom (shown as ψ in Figure 1). A parameterized form for the ionic pseudopotential (or the pseudo wavefunction) is chosen. The parameters are then adjusted, so that a pseudoatom calculation with the same exchange- correlation potential as the all-electron atom gives pseudo wavefunctions, ψ (Figure 1), that match the ps valence wavefunctions outside some cutoff radius, R , and pseudoeigenvalues that are equal to the c valence eigenvalues. This procedure involves direct inversion of the radial Kohn-Sham equation in the case when the pseudo wavefunction, and not the pseudopotential itself, is parameterized. If each wavefunction, pseudo and all-electron, is normalized to one, then the norm-conservation constraint is automatically satisfied as a result of matching the wavefunctions outside R . c Evaluating the Coulombic potential numerically The Coulombic potential is evaluated by solving the Poisson equation for the charge density: Eq. DMol3-8 rather than by explicitly evaluating the Coulombic term as: Eq. DMol3-9
Theory in DMol3 | Page 69 In the this approach, the Poisson equation is solved in a completely numerical (non-basis set) approach (Delley, 1990). This provides greater numerical precision, since the evaluation of V is essentially exact e once the form of ρ(r) has been specified. Such a method requires specification of an analytic form of ρ(r), as discussed above. However, rather than use a least-squares fitting procedure, a projection scheme is used. The charge density is first partitioned into atomic densities and then decomposed into multipolar components. Appropriate partition functions can ensure that such an expansion is rapidly convergent. The model charge density The density obtained in this way is called the model density. The term ρ lm |r - R | gives the model a α density for the multipolar component lm on atom α for a shell at |r - R | distance from the nucleus: α Eq. DMol3-10
Note that the partition function p used for decomposition of the density is in general not the same as α that used to improve the numerical integration in Eq. DMol3-6. The total model density is obtained from the summation over all ρ lm: a Eq. DMol3-11
Effect of angular truncation on precision of model charge density The total model charge density is, in general, not equal to the orbital density ρ because of angular truncations. However, the flexibility of this model charge density is superior to that obtained with fitting procedures. The degree of angular truncation can be specified as an input parameter. Typically, a value of l one greater than that in the atomic basis provides sufficient precision; for example, the use of l = 3 truncation when p functions are present in the basis or l = 2 truncation if only p functions are used. The Coulombic potential The Coulombic potential for each component is calculated using the Green's function of the Laplacian (Delley, 1990): Eq. DMol3-12
The total potential The total potential is given by: Eq. DMol3-13
Computational self-consistent field procedure Interpolating the numerical atomic bases onto the molecular grid Before the self-consistent field (SCF) procedure can be used, a step is required that is analogous to the evaluation of integrals over atomic orbitals, such as in Hartree-Fock methods. This is the interpolation of
Page 70 | Materials Studio • DMol Guide the numerical atomic basis set onto the molecular grid. Neglecting symmetry and any frozen-core approximations, this step requires a computational effort on the order of N × P for N atomic orbitals and P integration points. The basis set is controlled by the user, the number of points typically being on the order of 1000 points per atom. The overlap matrix (Eq. DFT-16) and the constant portion of the effective Hamiltonian (Eq. DFT-15) (kinetic and nuclear attraction terms) are constructed at this time, and each requires N × (N + 1) × P operations. The interpolated values can be stored externally and read as they are required. Alternatively, these data can be generated as needed, obviating the need for storage. This is termed a direct SCF procedure, by analogy with the direct Hartree-Fock method (Almlöf et al., 1982). Constructing the initial molecular electron density In practice, it is more convenient to skip choosing an initial C and constructing an initial set of ϕi, and iμ to begin instead with an initial ρ constructed from the superposition of atomic densities (quantities that are readily constructed from the numerical atomic basis set). In the SCF procedure, reconstruction of the new density requires a computational effort on the order of N × N x P, where N is the number of o o occupied orbitals. Additional computational costs Once ρ(r) is known, evaluation of the exchange-correlation potential μ requires only P operations. xc Construction of the Coulombic potential requires only P × M effort, where M is the number of multipolar functions. M is typically on the order of 9 functions atom-1 (l = 2) or 16 functions atom-1 (l = 3). Neither of these steps is especially time consuming. Construction of the Hamiltonian matrix elements (Eq. DFT-14) is among the most time-consuming steps, requiring N × (N + 1) × P operations each iteration. Solution of the secular equation is also time consuming, requiring N3 operations. This can be reduced by solving only for the eigenvectors corresponding to occupied orbitals to N2 × N . o Reducing the computational cost For large systems, the computational cost does not necessarily grow as rapidly as implied by the above comments. Since the atomic basis functions have a finite extent (~10 Bohr), only a limited number of points contribute to each matrix element and P eventually converges to a constant. In addition, construction of the density and the secular matrix can be accomplished using sparse matrix multiplier routines, further reducing the computational cost. Damping and convergence Construction of a new density follows solution of the secular equation. Damping is usually required to ensure smooth convergence. In the current method, simple damping is possible: Eq. DMol3-14 where d is the damping factor, ρ is the density that was used to construct the secular matrix, ρ is old new the density constructed from the new MO coefficients without damping, and ρ is the density that is actually used in the next iteration. An interpolation/extrapolation scheme is available. This technique constructs an effective vector from ρ to ρ for the current iteration and for the previous iteration. old new The effective vectors are generally skew vectors. The point of closest approach between ρ and ρ is old new used to extrapolate the actual density for the next iteration. Efficiently calculating the electrostatic potential The equations of density functional theory include an electrostatic potential arising from the negatively charged electron density. For more efficient calculations, the potential is found by solving the Poisson
Theory in DMol3 | Page 71 equation rather than by the equivalent approach of four-center direct integrals. Using the Poisson equation requires an auxiliary density representation ρ~, which is a function rather than the sum of squares of a function. ρ~ differs from ρ (Eq. DFT-4): Eq. DMol3-15
Effect of auxiliary density approximation on accuracy of calculated total energy To minimize the impact of this difference a total-energy formula is used that is second-order in δρ (Delley et al., 1983; Delley, 1990; Delley, 1991). The default starting density in DMol3 is the sum of the spherical atom densities. The total energy calculated in the first SCF cycle is thus the so-called Harris approximation (Harris, 1985). The atomic dissociation energy in the first cycle is usually overestimated, since the electrostatic error term for the total energy: Eq. DMol3-16
is negative definite. The less important second-order term for local density functionals is positive definite, which leads to a slight overestimation of the total energy during the SCF iterations. The complete total-energy formula, correct to the second order in δρ, is now: Eq. DMol3-17
where are the densities for spin alpha and beta, respectively; n are the occupations of orbitals with the iσ orbital and spin labels i, σ; εi is the corresponding eigenvalue, which has been calculated using the σ static V~e and exchange-correlation potential μ~xc arising from the spin densities ρ~ and E is the σ σ xc exchange-correlation functional (local or nonlocal). SCF convergence acceleration by DIIS A method based on the direct inversion of the iterative subspace (or DIIS) technique developed by Pulay (1982) has been implemented in DMol3 as a mechanism to speed up SCF convergence. The method rests on the suitable definition of an error vector that is zero when convergence is achieved and on performing a linear combination of a set of error vectors sampled along iterations that produces a new error vector with minimal norm. The DIIS method is much more powerful if one allows for a slightly larger dimension of iterative subspace. The default dimension currently adopted in DMol3 is 6. The error vector for the DIIS procedure is defined as the difference between the input and output charge densities: Eq. DMol3-18
The final model density is a linear combination of the densities at each SCF iteration i:
Page 72 | Materials Studio • DMol Guide Eq. DMol3-19
with the constraint that:
The C coefficients are calculated by minimizing the norm: i Eq. DMol3-20
Where:
For spin-unrestricted calculations, the error vectors obtained from the total density (sum of densities for electrons of spin alpha and spin beta) and the spin density (difference of densities for electrons of spin alpha and spin beta) are combined. In practice, the spin density error vector is appended to the total density error vector. Inversion of the DIIS linear equation system is achieved by means of a singular value decomposition. This is necessary for dealing with singularities caused by linear dependencies between error vectors. Energy gradients Predicting chemical structure The ability to evaluate the derivative of the total energy with respect to geometric changes is critical for the study of chemical systems. Without the first derivatives, a laborious point-by-point procedure is required, which is taxing to both computer and human resources. The availability of analytic energy derivatives for Hartree-Fock (Pulay, 1969), CI (Brooks et al., 1980), and MBPT (Pople et al., 1979) theories (to name just a few) has made these remarkably successful methods for predicting chemical structures. The energy gradient formulas for the Hartree-Fock-Slater method were first derived by Satako (1981) and later implemented practically using Slater basis sets (Versluis and Ziegler, 1988). Others have used Gaussian basis sets to compute derivatives of the DFT energy (Andzelm et al., 1989). First derivative of total energy with respect to change in nuclear position The derivative of the total energy in Eq. DFT-12 with respect to a nuclear perturbation in direction a (x, y, or z) of atom α may be written as: Eq. DMol3-21
where the derivative density is defined as: Eq. DMol3-22
Theory in DMol3 | Page 73 with: Eq. DMol3-23
Derivative of the basis function The derivative of the basis function χm with respect to the perturbation a can be computed analytically because of the representation of the numerical basis sets. The angular portion of χm is a spherical harmonic function, which is analytic and easily differentiated. The radial portion is represented by several cubic splines, each of which is also differentiable. Derivation of other terms The derivatives of the eigenvalues can be obtained from Eq. DFT-10. Multiplying by ϕi and integrating gives an expression for εi: Eq. DMol3-24
Differentiating and rearranging yields: Eq. DMol3-25
The terms in Eqs. DMol3-25 and DMol3-29 involving Z represent the Hellmann-Feynman force α (Hellmann, 1937; Feynman, 1939), which gives the derivative in the absence of any orbital relaxation. Substituting Eq. DMol3-25 into Eq. DMol3-21 yields: Eq. DMol3-26
Where Ea is the Hellmann-Feynman term. Now (Andzelm et al., 1989): t Eq. DMol3-27
and recalling the definition in Eq. DFT-11: Eq. DMol3-28
Page 74 | Materials Studio • DMol Guide The final equation for the derivative of the energy Therefore, the terms in Eq. DMol3-26 involving εxc cancel. In addition, if Eq. DMol3-9 is used to construct the charge density, then the last two terms in Eq. DMol3-26 also cancel, leaving: Eq. DMol3-29
which is formally the same as the equation derived by other researchers (Andzelm et al., 1989; Versluis and Ziegler, 1988). In practice, however, it is necessary to compute both ρVa/2 and ρaV/2, because the model density from Eq. DMol3-11 is not exactly equal to the numerical charge density computed from Eq. DFT-4. Computational costs The time required to evaluate all 3N first derivatives for an N-atom system is typically the same as the time required for 3-4 SCF iterations. If convergence is achieved in, say, 10-12 iterations, then 25-30% additional time is required to evaluate the derivatives. Others have obtained similar results (Versluis and Ziegler, 1988). Potential problems Because of numerical precision, two potential problems have been observed in evaluating gradients. First, the energy minimum does not correspond exactly to the point with zero derivative (Versluis and Ziegler, 1988). The gradients are typically about 10-4 at the energy minimum. A second important point is that the sum of the gradients is not always zero, as it must be for translational invariance. The sum can be as high as 10-3 if the calculation is very poor. Increasing the quality of the integration mesh and the number of multipolar functions in the model density can reduce this to about 3.0 × 10-5. This magnitude of error seems to be permissible for geometry optimizations: the error introduced in the geometry is typically on the order of 0.001 Å. Only for very flat potential energy surfaces should this be a problem. Minimization algorithms; molecular symmetry Currently, the geometry is optimized using both Cartesian and internal coordinates. When the geometry is optimized under conditions of symmetry, only forces that maintain molecular symmetry are evaluated, resulting in considerable time savings. Even in the absence of symmetry, certain forces can be omitted from the calculation, resulting in faster calculations. For example, for a substrate adsorbed on a metal cluster, it is possible to compute gradients for the substrate only and perform no optimization on the metal. Electronic excitations with TD-DFT Predicting UV-Vis spectra Predicting visible and near-visible UV spectra involves calculations of excitations between discrete electronic levels in a system. These excitation energies indicate the location of absorption peaks in the spectrum, whereas the peak intensities are evaluated by calculating transition dipole moments between the states involved in the given excitation. The most common means of calculating the excitation energies in the DFT formalism is the Time- Dependent DFT method (TD-DFT). This method has been developed by Runge et al. as an extension of the standard, time-independent DFT and implemented in DMol3 by Delley (Delley, 2010). The time-dependent analog of the Hohenberg-Kohn theorem shows that, for a given initial wavefunction, there is a unique mapping between the time-dependent external potential of a system
Theory in DMol3 | Page 75 and its time-dependent density. This analogy allows the most significant limitation of conventional DFT to be overcome, which is its inability to describe electronic excitations. Excited states in time- independent DFT are not properly described and this shortcoming restricts the use of "conventional" DFT to properties such as optical absorption and emission, polarizabilities, and higher order nonlinear effects. Similar to time-independent DFT the new formalism reduces the many-electron problem to a self- consistent single-particle equation (Vasiliev et al, 2002) : Eq. DMol3-21
which generates time-dependent density: Eq. DMol3-22
The most convenient way to express these equations is to use the linear response method. The linear response function describes how the electron density changes with changes in external potential. This function describes the response of the charge density to a potential that couples to the charge density of the system. Because of this, the response function has poles at the excitation energies of the system, meaning that the induced density also has these poles. This method can be used when the external field is small (it does not change the ground state) and is therefore treated as perturbation. By the nature of being linear in perturbation, the first order response properties will depend only on the ground state density and are therefore easily obtained. The response of the Kohn-Sham density matrix can be obtained by introducing a time-dependent perturbation Eq. DMol3-23 which is used as a basis for further calculation of the excited state energies as poles of the response function evaluated with respect to the unperturbed charge densities (linear approximation). The linear response of the density matrix expressed in frequency space (through Fourier transformation) δP (ω) is σ defined as: Eq. DMol3-24
and is dependent on the difference of occupation numbers λ , difference of eigenvalues ω - ω and σ σ (frequency dependent) SCF response δν scf. σ Computational costs The response matrix can be, in general, very large in the order of N *N , where N is the number of orb orb orb orbitals used in calculation. Diagonalization of such a large matrix is a difficult task but all its eigenvalues are rarely needed. The most physically significant are the lowest solutions or lowest energy excitations and these can be calculated iteratively using, for example, the Davidson iterative process (Davidson, 1975).
Page 76 | Materials Studio • DMol Guide Accuracy of excitation energies and orbital overlap There exists a clear correlation between excitation energy errors and the degree of spatial overlap between the occupied and virtual orbitals involved in an excitation. The errors increase as the amount of overlap reduces. A simple diagnostic test for judging the reliability of a given excitation is; if the overlap is less than 0.4 the excitation is likely to be in very significant error (Peach et al., 2008). This quantity is not unique and its diagnostic value is qualitative rather than quantitative. However, it captures the essential physics of the problem and is useful in practical calculations. The DMol3 output file contains the value of overlap for every excitation to assist with the evaluation of potential TD-DFT errors. TD-DFT in combination with hybrid functionals in DMol3 The DMol3 implementation of time-dependent density functional theory only considers the exchange- correlation functionals which can be defined with the keyword tddft_xc. In particular, the exchange- correlation functional in TD-DFT does not take into account any non-local effects of hybrid functionals. It is not recommended to use a hybrid functional, such B3LYP, if you intend to run an optical property calculation after the main ground state calculation. Molecular dynamics Molecular dynamics (MD) involves the stepwise integration of Newton's equations from a given starting point. It is the most natural method of performing equilibrium statistical-mechanical calculations via simulation. Molecular dynamics in total energy DFT schemes is implemented in essentially the same way as in conventional forcefield-based methods. The main difference is that the atomic forces are derived by solving DFT equations rather than from empirical potentials of interatomic interactions. Electrons are kept on the Born-Oppenheimer surface by means of explicit electronic structure optimization after each MD step. A side effect of this is that evaluation of force and energy from first principles is always the most computationally expensive part of ab initio MD. As a result, the efficiency of the MD step itself has no impact on the speed of the calculation. MD in DMol3 is based on the velocity Verlet algorithm for integration of the equation of motion. The implemented algorithm performs the Yoshida-Suzuki multiple-step numerical integration of varying quality, depending on the choice of interpolation parameter (Y. Liu, 2000, M. Suzuki, 1991, H. Yoshida, 1990). Ensembles Integrating Newton's equations of motion allows you to explore the constant energy surface of a system. However, most natural phenomena occur under conditions where the system is exposed to external pressure and/or exchanges heat with the environment. Under these conditions, the total energy of the system is no longer conserved and extended forms of molecular dynamics are required. Several methods are available for controlling temperature. Depending on which state variables - the energy, E, enthalpy, H (i.e., E + PV), number of particles, N, pressure, P, stress, S, temperature, T, and volume, V - are kept fixed, different statistical ensembles can be generated. A variety of structural, energetic, and dynamic properties can then be calculated from the averages or the fluctuations of these quantities over the ensemble generated. Both isothermal (where heat is exchanged with a temperature bath to maintain a constant thermodynamic temperature) and adiabatic (where no heat exchange occurs) ensembles are available: n Constant energy, constant volume (NVE) n Constant temperature, constant volume (NVT)
Theory in DMol3 | Page 77 NVE ensemble The constant energy, constant volume ensemble (NVE), also known as the microcanonical ensemble, is obtained by solving the standard Newton equation without any temperature and pressure control. Energy is conserved when this (adiabatic) ensemble is generated. However, because of rounding and truncation errors during the integration process, there is always a slight fluctuation, or drift, in energy. True constant energy conditions (i.e., without temperature control) are not recommended for the equilibration phase of the simulation because, without the energy flow facilitated by temperature control, the desired temperature cannot be achieved. However, during the data collection phase, if you are interested in exploring the constant energy surface of the conformational space or if, for some other reason, you do not want the perturbation introduced by temperature bath coupling, this is a useful ensemble. NVT dynamics The Nosé thermostat (Nosé, 1984) generates deterministic dynamics, with the temperature controlled by a fictitious additional coordinate, s, added to the Lagrangian of the system. The thermostat employs a feedback loop between the instantaneous kinetic energy and the required temperature. The rate of feedback is determined by the mass parameter, Q. This parameter should be chosen so that the natural oscillation frequency of the Nosé coordinate is close to the characteristic frequency of the actual system. The mass parameter is related to the thermostat relaxation time by: Eq. DMol3-30 Q = g(k T/τ2) B where g is the number of degrees of freedom (usually 3N - 3, where N is the number of atoms), k is B Boltzmann's constant, T is the thermostat temperature, and τ is the relaxation time. An improvement on the standard Nosé thermostat (or Nosé-Hoover thermostat) is the Nosé-Hoover chain method, described in detail by Tuckerman et al. (2001). In this method, the kinetic energy fluctuations of the thermostat variable are controlled by coupling it to another thermostat variable. The kinetic energy fluctuations of the second thermostat are, in turn, controlled by coupling to a third thermostat, and so on, to form a chain of M thermostats. This new coupling (the Nosé-Hoover 'chain' thermostatting mechanism) leads to a more general canonical dynamics method. Several other thermostat options are also implemented in DMol3: n Massive Nosé-Hoover chain This method is a generalization of the Nosé-Hoover (NH) method where each degree of freedom is coupled to its own independent NH thermostat. The bath particle itself is the subject of an equation of motion that is simply a function of the kinetic energy of the system and the desired temperature. n Gaussian thermostat One way to define a temperature is to apply Gauss' principle of non-holonomic constraints. In the non-holonomic case (when the final state of the system is path dependent) the constraints are given by the function g(r, v, t) = 0. The constraint is non-holonomic because it includes velocities. The constant temperature constraint is nonlinear and has the form (Windikis and Delley, 2003): Eq. DMol3-31
where N are the degrees of freedom, k is the Boltzmann constant, and T is the desired f B set temperature. Applying Gauss' principle yields:
Page 78 | Materials Studio • DMol Guide Eq. DMol3-32
To derive the Gaussian equation of motion with these constraints, m a is substituted with F = ξm v . i i i i i The resulting equation is then solved for the time derivative of the friction coefficient, ξ, which yields: Eq. DMol3-33
The conserved energy in this formalism then becomes: Eq. DMol3-34
n Generalized Gaussian moments thermostat The Generalized Gaussian moments (GGM) thermostat is based on controlling the fluctuations of an arbitrary number of moments of the multidimensional Gaussian momentum distribution function (Tuckerman et al., 2000). In this approach, one thermostat is coupled to all degrees of freedom, just as for a Nosé-Hoover chain. The GGM thermostat is explicitly reversible, which means that Newton's equations of motion possess the symmetry of time reversibility. This method produces dynamics with well-defined conserved quantities. This thermostat is controlled by a characteristic time scale, τ, which governs the size and speed of thermostat (and temperature) fluctuations. For a stable thermostat run, τ must be significantly larger than the molecular dynamics time step, with a recommended ratio of 10 to 100. n Massive generalized Gaussian moments thermostat This method is a generalization of the GGM method where each degree of freedom is coupled to its own independent GGM thermostat. This technique forces the canonical distribution of the kinetic energy over the degrees of freedom and, hence, produces rapid equilibration. This thermostat is also governed by a time scale, τ, which must be significantly (for example, 10-100 times) larger than the molecular dynamics time step. The thermostat implementation in DMol3 is described in detail by Windikis and Delley (2003). Constraints DMol3 can be used to perform MD simulations with structural constraints. The examination of slower modes in a system (for example, torsional conformation interconversion) necessitates relatively long simulation times because the upper limit of the MD time step is determined by the presence of fast modes (for example bond stretching and bond-angle vibrations). Hence, a large number of short time steps is required. Substantial improvement in the efficiency of MD simulations can be achieved by freezing the fast structural modes through constraint of the appropriate degrees of freedom. DMol3 supports two types of constraints during molecular dynamics simulations through Materials Studio interface:
Theory in DMol3 | Page 79 n Internal coordinates can be fixed (distances, angles, and torsions) n Individual atom positions can be fixed Point group symmetry DMol3 supports most of the chemically important symmetry point groups. If you select an unsupported point group system, DMol3 automatically switches to the highest order subgroup. The supported groups are:
Cs Ci
C2 C2v C2h D2 D2h D2D
C3v D3 D3h D3D
C4v D4 D4h D4d
C5v D5 D5h D5d
C6v D6 D6h D6d
Td O Oh I Ih The C , C , and S groups are not supported. Neither are the rotational groups C∞ and D∞ , n nh 2n v h however, such systems can be computed in C and D , respectively, without significant loss in 6v 6h efficiency. COSMO-solvation effects DMol3 includes certain COSMO controls, which allow for the treatment of solvation effects. The COnductor-like Screening MOdel (COSMO; Klamt and Schüürmann, 1993; Delley, 2006) is a continuum solvation model (CSM; Tomasi and Persico, 1994) in which the solute molecule forms a cavity within the dielectric continuum of permittivity, ε, that represents the solvent:
Page 80 | Materials Studio • DMol Guide The charge distribution of the solute polarizes the dielectric medium. The response of the dielectric medium is described by the generation of screening (or polarization) charges on the cavity surface. In contrast to other implementations of CSMs, COSMO does not require solution of the rather complicated boundary conditions for a dielectric in order to obtain screening charges, but instead calculates the screening charges using a much simpler boundary condition for a conductor. These charges are then scaled by a factor, f(ε) = (ε - 1) / (ε + 1/2), to obtain a good approximation for the screening charges in a dielectric medium. The deviations of this COSMO approximation from the exact solution are small. For strong dielectrics like water, they are less than 1%, while for nonpolar solvents with ε ~ 2, they may reach 10% of the total screening effects. However, for weak dielectrics, screening effects are small, and the absolute error therefore amounts to less than 1 kcal/mol. Altogether, COSMO is a considerable simplification of the CSM approach without significant loss of accuracy. Because of this simplification, COSMO allows for a more efficient implementation of the CSM into quantum chemical programs and for accurate calculation of gradients, which allows geometry optimization of the solute within the dielectric continuum. The screening charges are determined from the boundary condition of vanishing potential on the surface of a conductor. If q is defined as a vector of the screening charges on the surface of the cavity, and Q = ρ + Z for the total solute charges such as electron density, ρ, and nuclear charges, Z, then the vector of potentials, V , on the surface is V = BQ + Aq = V + V , where BQ is the potential arising tot tot sol pol from the solute charges, Q, and Aq is the potential arising from surface charges, q. B and A are Coulomb matrices. For a conductor, the relation V = 0 must hold, which defines the screening charges as: tot
Theory in DMol3 | Page 81 Eq. DMol3-35
For further details of the COSMO theory, see Klamt and Schüürmann (1993). COSMO provides the electrostatic contribution to the free energy of solvation. In addition, there are non-electrostatic contributions to the total free energy of solvation that describe the dispersion interactions and cavity formation effects. DMol3/COSMO The COSMO electrostatic energy is analogous in form to the DMol3 electrostatic energy, with the Coulombic operator replaced by the dielectric operator D = BA-1B. From Eq. DMol3-17: Eq. DMol3-36
where ρ~ represents the auxiliary density, which is introduced to solve the Poisson equation for the electrostatic potential of the solute. This total energy is minimized, resulting in the Kohn-Sham equations for the molecular orbitals. The Kohn-Sham Hamiltonian now includes an electrostatic COSMO potential: Eq. DMol3-37
This potential is present in every SCF cycle. This direct incorporation of the solvent effects within the SCF procedure is a major computational advantage of the COSMO scheme. Since the DMol3/COSMO orbitals are obtained using the variational scheme, accurate analytic gradients with respect to the coordinates of the solute atoms can be derived. The complete theory is presented in Klamt and Schüürmann (1993) and Andzelm et al. (1995). The gradients include the forces between the solute charges, Q, and the screening charges, q. To summarize, a DMol3/COSMO calculation begins with the construction of the cavity surface. The screening charges are then evaluated using Eq. DMol3-35 and the initial solute charges, Q. This allows for calculation of the electrostatic COSMO potential. The process is repeated until DMol3 SCF convergence is achieved. The final total energy includes the DMol3/COSMO electrostatic energy (Eq. DMol3-36). If geometry optimization is requested, DMol3/COSMO gradients are evaluated and the new geometry is calculated. The next optimization cycle begins with reconstruction of the cavity surface and the process continues until the DMol3 optimization convergence criteria are met. The DMol3/COSMO method has been tested extensively (Klamt and Schüürmann, 1993; Andzelm et al., 1995). The results depend mainly on the choice of the van der Waals radii used to evaluate the cavity surface. The other parameters defining the cavity surface (see below) are less important. Of course, solvation energies depend on the choice of DMol3 parameters, such as the type of DFT functional, the basis set, and integration grid. Results obtained so far (Andzelm et al., 1995) suggest that the DMol3/COSMO model can predict solvation energies for neutral solutes with an accuracy of about 2 kcal/mol. Recently, the DMol3/COSMO method has been generalized to the periodic boundary cases (Delley, 2006). In this case, all the screening charge is localized at the cavity surface. This is achieved with the use of Lagrange constraints with a new integration scheme based on a larger number of integration mesh points (Delley, 1996).
Page 82 | Materials Studio • DMol Guide Determination of the cavity surface (or solvent-accessible surface) The surface is obtained as a superimposition of spheres centered at the atoms, discarding all parts lying on the interior part of the surface (Klamt and Schüürmann, 1993). The spheres are represented by a discrete set of points, the so-called basic points. Eliminating the parts of the spheres that lie within the interior part of the molecule thus amounts to eliminating the basic grid points that lie in the interior of the molecule. The radii of the spheres are determined as the sum of the van der Waals radii of the atoms of the molecule and of the probe radius. The surviving basic grid points are then scaled to lie on the surface generated by the spheres of van der Waals radii alone. The basic points are then collected into segments, which are also represented as discrete points on the surface. The screening charges are located at the segment points. Determination of non-electrostatic contributions to the free energy of solvation The free energy of solvation is calculated as: Eq. DMol3-38 where Eo is the total DMol3 energy of the molecule in vacuo, E is the total DMol3/COSMO energy of the molecule in solvent, and ΔG is the non-electrostatic contribution due to dispersion and non-electrostatic cavity formation effects. The non-electrostatic contributions to the free energy of solvation are estimated from a linear interpolation of the free energies of hydration for linear-chain alkanes as a function of surface area: Eq. DMol3-39
In the present implementation, the VWN potential, DNP basis set, and fine integration grid of DMol3 were used to calculate energies of methane and octane (C ). The experimental values of the free energy 2h of solvation are 1.9 and 2.9 kcal/mol for methane and octane, respectively (Ben-Naim and Marcus, 1984). The calculated surface areas, using the default COSMO parameters, were 38.4 and 104.1 Å2 for methane and octane, respectively. The following values of A and B were used: n A = 1.67274 (kcal/mol) n B = 0.02052 (kcal/mol Å2) The best A and B values to use depend on the choice of DMol3 and COSMO input parameters. Tests (Andzelm et al., 1995) indicate that selection of other parameters, such as the nonlocal BP potential and the van der Waals radii of atoms, can influence ΔG by as much as 0.5 kcal/mol. nonelectrostatic COSMO-SAC model The most popular methods of COSMO-based prediction of activity coefficients and thermodynamic properties are COSMO-RS (conductor-like model for real solvents, Klamt et al., 1998) and COSMO-SAC (COSMO segment activity coefficient). COSMO-SAC model has been proposed by Lin and Sandler (2002) and further enhanced by Lin et al. (2004). Subsequent improvements resulted in COSMO-SAC 2007 (Wang et al., 2007), COSMO-SAC 2010 (Hsieh et al., 2010), and COSMO-SAC 2013 (Xiong et al., 2014) models. In all of these methods molecules are treated as a collection of surface segments. A solute molecule is moved from a vacuum to a perfect conductor, where the interaction energies between segments are determined from a COSMO calculation, that is, a solvation calculation for the molecule in the conductor. Then the solute is transferred from the perfect conductor to the real solvent, and for this process the
Theory in DMol3 | Page 83 chemical potential of each segment is self-consistently determined from statistical mechanics. The chemical potential of each molecule is then obtained by summing the contributions of the individual segments. In this way, thermodynamic properties of liquids are predicted in an a priori manner (Xiong et al., 2014). These models enable calculation of activity coefficients, vapor pressures, heats of vaporization, and phase equilibria for both pure fluid and liquid mixtures. Calculations based on COSMO-SAC models require .cosmo files produced by DMol3, and those files must be generated with specific COSMO settings that include high density of surface segments and that correspond to a conductor dielectric constant. COSMO sigma profile The sigma profile shows the amount of surface area for a given COSMO charge density. This profile is represented as the probability distribution of a molecular surface segment having a specific charge density. This is obtained by averaging surface charge densities from the .cosmo file and finding an effective surface charge density on a standard surface fragment: Eq. DMol3-25
where n (σ) is the number of segments with a discretized surface charge density σ, A is the total cavity i i surface area, and A (σ) is the total surface area of all of the segments with a particular density σ. i The default number of segments is 110 for all non-hydrogen atoms and 50 for hydrogen atoms. Electric field gradients The electric field gradient at a nucleus provides information about the electronic environment of that atom. The property can be probed experimentally by measuring NMR line widths for molecular species that contain NMR-active isotopes with a nuclear quadrupole moment where the quadrupolar relaxation mechanism determines the observed line width. The fact that electric field gradients are a function of the chemical environment is also exploited in NQR (zero-field NMR, or commonly, nuclear quadrupole resonance) scanning to detect explosives (C&E News, 1996). The electric field gradient at a nucleus may be obtained by differentiating the electric field around the molecule. It is, however, more practical to evaluate this as the second derivative of the electrostatic potential, V: Eq. DMol3-40
where R is the position at which the derivative is evaluated, Q is the electric field gradient, V is the 0 electrostatic potential, R is a general position vector, and a and b are x, y, or z. The electric field vector, F, at a given position is related to the first derivative:
Page 84 | Materials Studio • DMol Guide Eq. DMol3-41
The trace of Q defined as above yields (Poisson equation): Eq. DMol3-42 where ρ is the charge density. Q can be transformed into a traceless tensor Q' (or matrix) via: Eq. DMol3-43
In DMol3, the tensor Q is computed through expanding the electrostatic potential into a Taylor series with respect to each of the nuclei (if symmetry is imposed, only the symmetry-unique nuclei are visited). The matrix Q then appears as the coefficient of the second-order term in the Taylor expansion: Eq. DMol3-44
The energy of an electrostatic quadrupole moment embedded in an electrostatic potential is determined by the electric field gradient at the position of the quadrupole. This interaction contributes to the NMR line width (as further outlined below). A complete quantitative description of this interaction is actually more complex than what is presented above and is captured by the so-called Sternheimer factor (Sternheimer, 1966). The electric field gradient at a quadrupolar nucleus (spin I > 1/2) within a molecule determines the NMR longitudinal relaxation rate, 1/T , or the line width, W /2, (this assumes that the quadrupolar relaxation 1 1 mechanism dominates): Eq. DMol3-45
Note: Miyake et al. (1996) use a different formula, in which ε enters into the equation as (1 + ε2)/3. In Eq. DMol3-45, I is the nuclear spin quantum number (for example, I = 1 for 14N, I = 5/2 for 17O, I = 3/2 for 33S, I = 7/2 for 45Sc); χ is the nuclear quadrupolar coupling constant, which is given by e2Q q /h, zz where q is the largest principal component of the EFG tensor, q; ε is the asymmetry parameter, given zz by |q - q |/q . xx yy zz The x, y, and z axes are chosen such that |ε| < 1. Since ε enters into the relaxation time as ε2, the sign of ε is not important and may be dropped (Bagno and Scorrano, 1996). t is the rotational correlation time and can be estimated from the Debye-Stokes-Einstein formula as t = c c V η/(kT), where V is the hydrodynamic volume (= 4 (π/3) R3, where R is the hydrodynamic radius) and m m η is the solution viscosity.
Theory in DMol3 | Page 85 The hydrodynamic volume can be estimated from (Noggle and Schirmer, 1971): Eq. DMol3-46
where M is the molecular weight, ρ is the solute density, and N is Avogadro's number. a The EFG in atomic units can be converted to SI units with the conversion factor: Eq. DMol3-47
Nuclear quadrupole moments, Q, are listed as areas, where εQ is the maximum expectation value of the zz traceless tensor element: 1 b = 100 fm2 = 10-28 m2 For example: n 14N Q = 2.01 fm2 n 17O Q = -2.558 fm2 n 33S Q = -6.78 fm2 n 45Sc Q = -22 fm2 (Q < 0: oblate, Q > 0: prolate) Quadrupole interaction energy tensor: Eq. DMol3-48
Thermodynamic calculations The results of a vibrational analysis or Hessian evaluation can be used to compute enthalpy (H), entropy (S), free energy (G), and heat capacity at constant pressure (C ) as functions of temperature. The DMol3 p total energy yields the total electronic energy at 0 K. The various translational, rotational, and vibrational components are used to compute H, S, G, and C at finite temperatures as discussed below. p When you perform a vibrational analysis with DMol3, these results appear in the .outmol file. You can create a chart of the result using the thermodynamic analysis tools. You can control the temperatures at which the properties are evaluated using the keyword thermo_range in the input deck. The formulas below are based on work by Hirano, 1993. In each case, two expressions are provided for rotational contributions: one for linear and one for nonlinear systems. Enthalpy The enthalpy correction, H, in the ideal gas approximation is given by: H(T) = E (T) + E (T) + E (T) + RT vib rot trans where the subscripts stand for vibrational, rotational, and translational contributions, respectively, and R is the ideal gas constant. The contributions are given by:
Page 86 | Materials Studio • DMol Guide Eq. DMol3-51 3 Etra = RT 2
Erot( linear ) = RT 3 Erot( nonlinear ) = RT 2 R 1 R hυiexp(− hυ i / kT ) Evib = ∑i hυi + ∑i k 2 k [1 − exp(−hυi / kT )] Where: k is Boltzmann's constant h is Planck's constant ν i are the individual vibrational frequencies Entropy The contributions to the entropy, S, are given by: Eq. DMol3-52
where w is the molecular weight, I is the moment of inertia about axis x, σ is the symmetry number, and x the other quantities are as described above. Heat capacity For nonperiodic systems, DMol3 calculates the heat capacity at constant pressure, C , based on the p ideal gas for the translational and rotational terms. Its contributions are given by the formulas below. The subscript p has been dropped from these equations. Eq. DMol3-53
Theory in DMol3 | Page 87 For solids, the only applicable term is the vibrational contribution C , which corresponds to the heat vib capacity at constant volume, C . In the output, DMol3 specifies explicitly whether C or , C has been v p v calculated. Using the results The DMol3 .outmol file or the thermodynamic analysis chart provides the corrections for H, S, and G for finite temperature. The SCF energy computed by DMol3 is the total electronic energy at 0 K. You can estimate ΔH or ΔG for a chemical reaction using the quantities from the table. To compute the ΔE of a reaction, you add up the DMol3 total energies for the reactants and the energies for the products. The energy of reaction is simply E - E . To compute ΔH(T), simply add the product reactant computed enthalpy to the electronic energy of each component. Remember that total energies are reported in Hartree/atom and the thermodynamic results are in kcal/mol (1 Hartree/atom = 627.5 kcal/mol). The table below provides a hypothetical example. Thermodynamics for A + B = C A B C C - (A + B) Energy -62.20 Hartree -15.50 Hartree -77.99 Hartree -181.98 kcal/mol Enthalpy 298.15 K kcal/mol 98.2 50.1 150.55 -179.73 Fitting atomic point charges to the electrostatic potential (ESP) Atomic multipole properties are often used to obtain the electrostatic parameters of classical forcefields. One of the most common approaches is to determine the atomic multipole properties by fitting them so as to reproduce the molecular electrostatic potential (ESP) (Singh and Kollman, 1984). Numerous applications of ESP-fitted charges in simulations of biochemical systems prove the usefulness of this technique (Bakalarski et al., 1996; Bayly et al., 1993; Merz, 1992). The ESP-derived charges can reproduce the intermolecular interaction properties of molecules well with a simple two-body additive potential. The ESP is generated in the space of a molecule and can be calculated from the positions of the atomic nuclei, α, and the electron density, ρ: Eq. DMol3-54
where w is the integration weight at point i, V(r ) is the Coulomb potential at point i, and q is the fitted i i α charge on atom α. The total molecular charge is conserved, using a Lagrange multiplier. The grid points i in Eq. DMol3-54 are selected based on the following criteria: Eq. DMol3-55 where R int and R ext are the internal and external radii of the atomic α shells, and depend on the atom α α type. To make the results less sensitive to the selection of the grid, the concept of a layer border was introduced. The weights, w , change smoothly across the border layer, as is evident from the following i formula:
Page 88 | Materials Studio • DMol Guide Eq. DMol3-56
where w int and w ext are the partial weights calculated with respect to all ESP centers in the system: iα iα Eq. DMol3-57
Eq. DMol3-58
where ΔR is the "diffusion" width of the layer border. Thus, the w change smoothly from 0 to 1 in the region R int - ΔR, R int + ΔR and from 1 to 0 across the i α α external radii R ext - ΔR, R ext + ΔR. α α The final set of linear equations is solved via the Gauss elimination technique to determine the point charges. The accuracy of the fit can be evaluated by calculating the rms deviation as follows: Eq. DMol3-59
It is quite common to obtain a rrms error of 20% for uncharged molecules, which can amount to a few kcal/mol of rms error obtained by using the fitted potential. Mulliken and Mayer bond orders The concept of bond order and valence indices is well established in chemistry. It allows for interpretation and deeper understanding of the results of DMol3 calculations using ideas familiar to chemists. First, a density matrix must be defined, or as it is sometimes called, a charge-density bond-order matrix. If ϕ is a molecular orbital and C are the SCF expansion coefficients, then: iμ Eq. DMol3-60
and matrix P and a set of atomic orbitals completely specify the charge density (Eq. DMol3-22). μν The trace of matrix P and the overlap S is equal to the total number of electrons in the molecule: Eq. DMol3-61
Theory in DMol3 | Page 89 Summing (PS) contributions over all μ ∈ A, ν ∈ B , where A and B are centers, P can be obtained, μν AB which can be interpreted as the number of electrons associated with the bond A-B. This is the so-called Mulliken population analysis (Mulliken, 1955). The net charge associated with the atom is then given by: Eq. DMol3-62
where Z is the charge on the atomic nucleus A. A Mayer (1986) defined the following quantities. n Bond order between atoms A and B: Eq. DMol3-63
where Pα, Pβ are the density matrices for spin α and β. n Actual total valence of atom A in the molecule: Eq. DMol3-64
n Actual free valence of atom A in the molecule: Eq. DMol3-65
where PS = Pα - Pβ. The Mayer bond orders and valence indices have several useful properties: 1. The values of bond orders are close to the corresponding classical values. This means that the double bond in H CO would have a C-O Mayer bond order close to 2.0. 2 2. The total valence indicates how many single bonds are associated with the atom. For example, in the methane molecule, the C atom would have a total valence close to 4.0. 3. The free valence index is zero for closed-shell systems. For open-shell radicals, it is a measure of the reactivity. The free valence index indicates whether free electrons are available for bonding on a particular atom. 4. Unlike Mulliken bond orders, Mayer quantities are less dependent on the basis set choice and they are transferable, so they can be used to describe similar molecules. 5. For similar molecules, the trends in Mayer quantities can be correlated well with electronic and geometrical changes due to substituents. Hirshfeld charge analysis Hirshfeld partitioned charges (Hirshfeld, 1977) are defined relative to the deformation density. The deformation density is the difference between the molecular and the unrelaxed atomic charge densities:
Page 90 | Materials Studio • DMol Guide Eq. DMol3-66
where ρ(r) is the molecular charge density and ρ (r - R ) is the density of the free atom α located at α α coordinates R . Using the deformation density, the effective atomic charges, dipoles, and quadrupole α are defined as (Delley, 1986): Eq. DMol3-67
Eq. DMol3-68
Eq. DMol3-69
The weight function W (r) is defined as the fraction of the atomic density from atom α at coordinate r: α Eq. DMol3-70
Fukui functions The chemical potential, chemical hardness and softness, and reactivity indices have been used by a number of workers to assess a priori the reactivity of chemical species from their intrinsic electronic properties. Various methods have included atomic charge computation, free valency, spin populations, and the Laplacian of the charge density, among others. Perhaps one of the most successful and best known methods is the frontier orbital theory of Fukui. Developed further by Parr and Yang (1989), the method relates the reactivity of a molecule with respect to electrophilic and nucleophilic attack to the charge density. These so-called Fukui functions (FFs) are a qualitative way of measuring and displaying the reactivity of regions of a molecule. Specifically, the FF measures the sensitivity of the charge density, ρ(r), with respect to the loss or gain of electrons via the expressions: Eq. DMol3-71
The expression f+(r) measures changes in the density when the molecule gains electrons and, hence, corresponds to reactivity with respect to nucleophilic attack. Conversely, f-(r) corresponds to reactivity with respect to electrophilic attack (loss of electrons). The FF for radical attack, f0(r), is simply the average of these two.
Theory in DMol3 | Page 91 Using the finite difference approximation shown above, the charge densities are converged to self- consistency for the neutral molecule, the cation, and the anion. The FFs are computed using the finite difference approximation and the self-consistent charge densities for the neutral molecule, the cation, and the anion. They may be may be viewed using the volumetric analysis tools. Generally, users will obtain the must useful information by mapping the FF onto an isodensity surface rather than by viewing isosurfaces of the FFs themselves. More quantitative predictions can be obtained from the condensed FF for an atom k: Eq. DMol3-72 f- = q - q cation k k k f+ = q anion - q k k k In this case, the q are atomic-centered charges that are computed in some reasonable manner, such as k from a Mulliken population analysis or from a numerical integration procedure such as a Hirshfeld analysis. This procedure effectively assigns the 3D FF to specific atoms, just like a charge analysis tries to assign charge density to atoms. In conventional FF computations, a value of 1.0 is used for ΔN, i.e., one full electron is removed or added for the calculation of the charge density of the ions. DMol3 can use fractional charges for this purpose. This yields faster SCF convergence and results closer to the limit of ΔN=0. A value of 0.1 is recommended. Raman spectra Raman spectroscopy is used to study the vibrational, rotational, and other low-frequency modes in a system. It is based on the Raman effect of inelastic scattering of monochromatic light. This interaction with vibrations results in the energy of incident photons being shifted up or down. The energy shift is defined by the vibrational frequency and the proportion of the inelastically scattered light is defined by the spatial derivatives of the macroscopic polarization, technical details are described by Porezag and Pederson (Porezag et al.). Spatial derivatives of the polarization are calculated in DMol3 based on finite difference calculation of the polarizability tensor derivatives with respect to the normal mode coordinates. There are two ways of calculating these derivatives: displacing normal modes and evaluating vibrational frequencies or displacing the electric field and calculating gradient. Due to the high cost of vibrational frequency calculations (also evaluated using finite displacements) the DMol3 implementation calculates the polarizability derivatives by 19 gradient evaluations at specified values of external electric field. Additionally, after calculating Raman activities, DMol3 can display corresponding Raman cross sections (intensity) for the Stokes component of the ith mode for a given experiment incident light frequency and temperature using the following expression: Eq. DMol3-23
Where ν is the frequency of scattered light, c is the speed of light, h is Planck constant, n is the Bose- s i Einstein statistical factor, and IRam is the Raman activity of the given mode. Since ν can be obtained from the frequency of incident light ν , i.e. ν = (ν - ν ), Raman intensities can s 0 s 0 i be calculated in experimental conditions T and ν . 0 Note: It is important to remember that Raman intensities are effectively third order derivatives, so to obtain reasonable results very accurate calculations are required.
Page 92 | Materials Studio • DMol Guide Basis set superposition error Basis set superposition error (BSSE) is the effect of lowering of the total energy when the electrons of each atom spread into the space defined by the basis functions provided by the other atoms due to an incomplete basis set. This effect is well pronounced when using Gaussian basis sets but for numerical basis sets, as used in DMol3, it can be neglected in most cases (Inada et al, 2008). However, high quality calculations involving weakly interacting moieties should include the BSSE correction when determining potential energy surfaces and interaction energy. DMol3 calculates the BSSE correction by means of counterpoise method. The counterpoise method, in a system AB consisting of subsystems A and B, is defined as a difference in energies of both subsystems in the full system basis set, E[A;AB], E[B;AB], and the subsystems alone, E [A] and E[B], (van Duijneveldt et al, 1994:)
To allow DMol3 to calculate the BSSE correction, two sets of atoms need to be created, defining interacting subsystems. These selections must be mutually exclusive and span the whole system. In order to help with the selection, DMol3 allows you to define the first set and it will automatically consider the rest of the 3D Document the second set. In addition, you should ensure that the charges on your BSSE sets are correct on the DMol3 Energy dialog.
Note: The BSSE correction calculation is enabled for nonperiodic systems only and for Energy task.
Converging SCF In general, the Kohn-Sham equations of density functional theory are solved iteratively using the SCF procedure outlined in the DFT theory topic. A reasonable guess of wavefunction coefficients is used as a starting point, the resulting density and potential are calculated, and then the Schrödinger equation is solved before obtaining a new density from the updated wavefunction coefficients. Repeating this procedure should, in principle, lead to convergence. In practice however, it is numerically unstable to use the density result from one iteration to calculate the potential of the next iteration directly. To resolve this difficulty, the initial and the updated charge and spin densities are mixed, such that the actual self-consistent density is approached slowly but in a numerical stable procedure. Moreover, the density guess for one iteration is likely to overshoot considerably in the initial stages of the SCF cycle. The mixing algorithm tends to dampen the overshoot. The important parameters for successfully achieving convergence consist of the charge and spin mixing factors and the number of histories from which new guesses are calculated. In addition, it is possible to dampen long-range density fluctuations using a charge density preconditioner. The default settings provided for these parameters are chosen to give good convergence in 90% of all systems and usually should not need to be changed. However, if a calculation takes more than 30-40 SCF cycles to converge it can be useful to check whether small adjustments to the mixing factors can improve the situation or whether the checklist provided below can help convergence.
Note: Decreasing the mixing factors often improves numerical stability and therefore convergence performance.
Note: A poor choice of parameters can lead to a significant increase in the computational cost of any calculation.
Theory in DMol3 | Page 93 Challenging systems For problematic systems there are some changes to settings that can improve the convergence behavior: n Surface slab models, particularly when they involve polar and/or metallic surfaces with adsorbates. Issues can arise from interactions between periodic images of the same surface. This can be resolved by adding a dipole slab correction on the SCF tab of the DMol3 Electronic Options dialog. n Systems with spatially separate but degenerate states (such as surface states in a thick-slab or multicenter organometallic molecules). Use the checklist, with a focus on the charge density preconditioner. n Spin frustrated systems or molecules/atoms with highly degenerate half-occupied states (for example. half-filled d-shells, transition metal clusters). Check whether it is sensible to break some of the existing symmetries and investigate the effects of smearing (SCF tab of the DMol3 Electronic Options dialog). n Inappropriate charge states Review the Charge setting on the Setup tab of the DMol3 Calculation dialog. n Anions To address problems with anions increase the orbital cutoff, grid, and basis accuracies (Orbital Cutoff tab of the DMol3 Electronic Options dialog, Setup tab of the DMol3 Calculation dialog). n Solid systems may cause problems in cases of incomplete Brillouin sampling. Check whether an increase in the quality of the k-point grid helps (k-points tab of the DMol3 Electronic Options dialog). n A calculation that stops converging at a certain threshold might require more accurate matrix element to achieve better numerics. Increase the Integration accuracy to Fine (Electronic tab of the DMol3 Calculation dialog). In difficult cases the convergence behavior of the SCF cycle should always be examined. If it is steadily decreasing but just a little slow, an increase of the number of iterations will definitely help while a small change of the mixing parameters in either direction could lead to quicker convergence. Checklist For systems with problematic convergence use the following steps to make improvements: n Check your model for physical consistency. In particular, make sure that all of the following have physically correct and intended settings: spin, charge, symmetry, metal, smearing, dipole slab correction (Setup tab of the DMol3 Calculation dialog, SCF tab of the DMol3 Electronic Options dialog). n Decrease the density mixing Charge and Spin settings to about 0.1 and increase the Max. SCF cycles to 100 or more. Optionally, increase the DIIS size (SCF tab of the DMol3 Electronic Options dialog). n For large systems (more than 50 atoms) turn on the charge density preconditioner (SCF tab of the DMol3 Electronic Options dialog). n Unless it is already Fine, increase the Integration accuracy of the grid and the k-point set if applicable (Electronic tab of the DMol3 Calculation dialog). n Further decrease the density mixing Charge and Spin settings to about 0.05 or even 0.01. However, this should be employed only as an emergency measure and should not be necessary for physically sensible problems (SCF tab of the DMol3 Electronic Options dialog). n For geometry optimizations or dynamics which fail to converge only on the second (or subsequent) geometry steps, add the Reset_SCF keyword to the .input file.
Page 94 | Materials Studio • DMol Guide n Should all of these fail, you might wish to change the mixing scheme from the default Pulay mixer and explore other options. However, this should really be taken as the ultimate last resort as the Pulay mixer generally outperforms the other schemes implemented in DMol3 (keyword SCF_DIIS).
Theory in DMol3 | Page 95 Dialogs in DMol3 The following topics and their subtopics describe the DMol3 dialogs: n DMol3 Calculation dialog n DMol3 Analysis dialog Use the Save settings... option to save the current dialog settings. DMol3 Calculation dialog The DMol3 Calculation dialog allows you to set up and display the parameters for a calculation. The DMol3 Calculation dialog contains the following tabs: n Setup: Allows you to choose the type and quality of calculation that DMol3 will perform, along with other basic input options, such as the basis set, DFT functional, spin state, and total charge. n Electronic: Allows you to set the parameters that control the details of the energy evaluation, including the integration accuracy and the SCF convergence. n Properties: Allows you to select the properties that will be computed by DMol3. These include volumetric visualizations (such as charge density and molecular orbitals) and electronic properties. n Job Control: Allows you to specify job settings for the DMol3 calculation.
Tip: See the Performance tips topic for ways to optimize DMol3 calculations. Run: Runs a job using the settings specified. The results are placed in a subfolder of the current Materials Studio project directory. Run | Copy Script: Converts the current settings to a script and copies the script to the clipboard. Refer to the Generating scripts topic for more information on using sections of scripts generated from a dialog. Files...: Provides access to the DMol3 Job Files dialog which allows you to save input files for a DMol3 calculation without running the job, or to run a job using an existing set of input files. This functionality is provided for users who need to run the DMol3 server program in standalone mode, or who wish to edit the DMol3 input files in order to gain access to features not supported by the DMol3 interface. Help: Displays the Help topic for the current tab. Access methods
Menu Modules | DMol3 | Calculation Toolbar | Calculation
Setup tab The Setup tab allows you to choose the type and quality of calculation that DMol3 will perform, along with other basic input options, such as the basis set, DFT functional, spin state, and total charge. Task: Select the type of calculation that you wish to perform from the dropdown list. Available options are:
Page 96 | Materials Studio • DMol Guide n Energy - performs a single-point energy calculation n Geometry Optimization - searches for a minimum energy structure n Dynamics - performs a molecular dynamics calculation n TS Search - searches for a transition state using linear synchronous transit (LST) and quadratic synchronous transit (QST) methods n TS Optimization - searches for a transition state using eigenvector-following methods n TS Confirmation - produces a refined reaction path based on an LST or QST search n Elastic Constants - performs an elastic constants calculation n Reaction Kinetics - calculates rate coefficients for a reaction whose transition state is known n Electron Transport - calculates electron transport properties, such as transmission and current More...: Provides access to further options for the selected task. Quality: Set the overall quality for the DMol3 calculation. This quality affects the basis set, k-point, and SCF convergence criteria, plus the convergence criteria for relevant tasks. Available options are: n Coarse n Medium n Fine These three levels offer progressively more accuracy at the expense of longer calculation times.
Tip: Use the Coarse quality setting for a quick assessment of the calculation, then progress to a higher quality level to obtain more accurate results. The Quality setting affects all relevant task parameters that control the precision of the simulation. If any parameter is set by the user to a value different from that specified by the overall quality level, the Quality is displayed as Customized. Functional: Select the type of DFT exchange-correlation potential to be used in the calculation. Choose the class of functional from the first dropdown list, then select the specific functional from the second dropdown list. n LDA: local functionals n PWC: Perdew and Wang, 1992 n VWN: Vosko et al., 1980 n GGA: gradient-corrected functionals n PW91: Perdew and Wang, 1992 n BP: Becke, 1988; Perdew and Wang, 1992 n PBE: Perdew et al., 1996 n BLYP: Becke, 1988; Lee et al., 1988 n BOP: Tsuneda et al., 1999 n VWN-BP: Vosko et al., 1980; Becke, 1988; Perdew and Wang, 1992 n RPBE: Hammer et al., 1999 n HCTH: Boese and Handy, 2001 n PBEsol: Perdew et al., 2008 n B3LYP: hybrid functional: Becke, 1993; Stephens et al., 1994 n m-GGA: meta-GGA functionals n M06-L: Zhao and Truhlar, 2006 n M11-L: Peverati and Truhlar, 2012
Dialogs in DMol3 | Page 97 Note: The B3LYP and meta-GGA functionals are not available for periodic systems. Use method for DFT-D correction: When checked, the selected method will be used for dispersion corrections. Available options are: n TS for GGA (PBE and BLYP) and B3LYP n Grimme for GGA (PBE and BLYP) and B3LYP n OBS for GGA (PW91) and LDA
Note: The option selected will automatically update the Use custom DFT-D parameters setting on the DFT-D tab of the DMol3 Electronic Options dialog. Spin unrestricted: When checked, indicates that the calculation will be performed using different orbitals for different spins. This is known as a 'spin-unrestricted' or 'spin-polarized' calculation. If unchecked, the calculation uses the same orbitals for alpha and beta spins. This is known as a 'spin- restricted' or 'non-spin-polarized' calculation. Default = unchecked. Use formal spin as initial: When checked, indicates that the initial value for the number of unpaired electrons for each atom will be taken from the formal spin introduced for each atom. This starting value will be subsequently optimized during the calculation. Default = checked.
Note: This option is enabled only if the Spin unrestricted checkbox is checked. Metal: When checked this indicates that the system is metallic and requires thermal smearing and a dense sampling of the Brillouin zone. When unchecked the k-point separations used by default are coarser and the smearing is not used. Default = unchecked.
Note: This option applies only to periodic systems. Use symmetry: When checked, indicates that symmetry information should be used in the calculation. Molecular dynamics simulations or calculations involving transition-state searching or confirmation cannot use symmetry information. Default = checked.
Note: Due to the DMol3 server-enforced symmetry snap, the total energy and other properties obtained in the DMol3 calculation may differ very slightly between Use symmetry set to on and off. This numerical effect may be noticeable in highly symmetric molecular systems.
Note: The Use symmetry checkbox is not available when Functional is set to B3LYP or when Task is set to Dynamics, TS Search, TS Confirmation, Reaction Kinetics or Electron Transport. In these cases, symmetry will not be used. Multiplicity: Select the multiplicity from the dropdown list to perform a calculation on a specific spin state. Available options are:
Page 98 | Materials Studio • DMol Guide n Auto n Singlet n Doublet n Triplet n Quartet n Quintet n Sextet n Septet n Octet When Auto is selected, DMol3 will attempt to determine the ground spin state by performing a spin- unrestricted calculation.
Note: This option is enabled only if the Spin unrestricted checkbox is checked and the Use formal spin as initial checkbox is unchecked.
Note: There is one limitation to specifying the spin state: it is not possible to force DMol3 to perform an unrestricted singlet calculation. If you check the Spin unrestricted checkbox and set the Multiplicity to Singlet, the results will be the same as if you used the Auto setting.
Note: In the case of a periodic system, the multiplicity refers to the spin state of the electrons in a single unit cell. Charge: Specify the total charge on the molecule or unit cell.
Note: DMol3 can operate using fractional charges, but non-integer charges can only be specified by manually editing the DMol3 input file.
Access methods
Menu Modules | DMol3 | Calculation | Setup Toolbar | Calculation | Setup
DMol3 Energy dialog The DMol3 Energy dialog allows you to define the atoms used in the basis set superposition error (BSSE) calculation and request this calculation. Calculate BSSE correction: Enables DMol3 to run a multi-stage counterpoise correction calculation. This involves calculations of separate subsystems alone and in presence of the other subsystem's basis functions. Add selected atoms to BSSE_1 set: Selected atoms are treated as one of two subsystems involved in the BSSE calculation.
Note: This button is enabled only if the BSSE sets are not yet defined and a subset of atoms is selected in the document.
Dialogs in DMol3 | Page 99 Note: The BSSE correction calculation is enabled for nonperiodic systems and for the Energy task only. Select atoms in BSSE_1 set: Highlights atoms belonging to the first subsystem. BSSE_1 set charge: Sets the charge for BSSE set 1. Select atoms in BSSE_2 set: Highlights atoms belonging to the second subsystem. BSSE_2 set charge: Sets the charge for BSSE set 2.
Note: The charges on both BSSE sets need to sum exactly to the total charge specified on the Setup tab of the DMol3 Calculation dialog. This is automatically enforced when the set charges are specified. If the total Charge is changed, the BSSE set charges will not be updated and you will not be able to start a calculation until they are adjusted such that their sum equals the total charge. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 Geometry Optimization dialog The DMol3 Geometry Optimization dialog allows you to set up and display the parameters that control the simulation in a DMol3 Geometry Optimization task. Quality: Set the geometry optimization convergence thresholds for energy change, maximum force, and maximum displacement between optimization cycles. The optimization will stop when the energy convergence is satisfied, along with either the displacement or gradient criteria. If the calculated initial gradients are below the threshold, the optimization will successfully stop without making a single step and without comparing displacements and energies. Three sets of convergence thresholds are available: n Coarse n Medium n Fine The values of the convergence thresholds in each set are given in the table below: Value Coarse Medium Fine Energy (Hartree) 1 × 10-4 2 × 10-5 1 × 10-5 Max. force (Hartree Å-1) 0.02 0.004 0.002 Max. displacement (Å) 0.05 0.005 0.005 Alternatively, thresholds can be specified independently for Energy, Max. force, and Max. displacement. If you enter your own values for any of these settings, the Quality is displayed as Customized on both the DMol3 Geometry Optimization dialog and the Setup tab of the DMol3 Calculation dialog. Energy: Specify the convergence threshold for the maximum energy change, in Hartree, during the geometry optimization.
Page 100 | Materials Studio • DMol Guide Max. force: Specify the convergence threshold for the maximum force, in Hartree Å-1, during the geometry optimization. Max. displacement: Specify the convergence threshold for the maximum displacement, in Å, during the geometry optimization. Max. iterations: Specify the maximum number of geometry optimization cycles. If this number of cycles is reached, then the calculation will stop, even if the convergence criteria are not satisfied.
Note: These convergence tolerances and the Max. iterations settings are only applied to the atomic coordinate optimization in the unit cell. Max. step size: Specify the maximum allowed change of any Cartesian coordinate. Geometric displacements are truncated such that they are less than this value. This prevents the optimizer from taking unreasonable steps.
Note: The default optimizer in DMol3 uses delocalized internal coordinates, the maximum Cartesian step size is not directly applicable to this method. You should reduce the value of Max. step size if you observe that the actual displacements during minimization are too large and cause large energy changes. Use starting Hessian: When checked, indicates that the Hessian associated with the current model will be used as the initial Hessian in the new calculation. If unchecked, the minimization will start without a Hessian. You can obtain a starting Hessian from several sources, as described in Importing a Hessian file.
Note: It is not possible to use a starting Hessian for geometry optimization in DMol3 when symmetry is activated. Optimize cell: When checked, indicates that the cell parameters will be optimized during the geometry optimization, in addition to the atomic coordinates. Default = unchecked.
Note: This option is enabled only if the currently active document contains a periodic structure. If this is disabled or unchecked then Optimization cycles and Displacement step are not available.
Note: Unit cell optimization requires many small changes in the cell vectors and a local optimization for each of the displacements. Optimization cycles: Determines the number of cell optimization steps. Displacement step: The magnitude of the cell vector displacements. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 Dynamics dialog The DMol3 Dynamics dialog allows you to set up and display the parameters that control the simulation in a DMol3 Dynamics task.
Dialogs in DMol3 | Page 101 The DMol3 Dynamics dialog contains the following tabs: n Dynamics: Allows you to specify the main parameters for a molecular dynamics calculation, including choice of ensemble, temperature, and the length of the run. n Thermostat: Allows you to specify the parameters that control the dynamics algorithm, including the temperature control method and associated settings. Help: Displays the Help topic for the current tab. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
Dynamics tab The Dynamics tab allows you to specify the main parameters for a molecular dynamics calculation, including choice of ensemble, temperature, and the length of the run. Ensemble: Select a thermodynamic ensemble to be used for the dynamics calculation. Available options are: n NVE (default) - dynamics at fixed volume and constant energy n NVT - dynamics at fixed volume with a thermostat to maintain a constant temperature Temperature: Specify the target temperature, in K, for the simulation. For the NVE ensemble, the initial random velocities of the atoms are scaled to this temperature. Default = 300.0 K. Time step: Specify the time, in fs, for each dynamics step. This value also determines the Total simulation time. Default = 1.0 fs. Total simulation time: Specify the total time, in ps, that the dynamics simulation will run for. This value also determines the Number of steps. Default = 1.0 ps. Number of steps: Specify the number of dynamics steps to be carried out. This value also determines the Total simulation time. Default = 1000. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Dynamics Toolbar | Calculation | Setup | More... | Dynamics
Thermostat tab The Thermostat tab allows you to specify the parameters that control the NVT dynamics algorithm, including the temperature control method and associated settings.
Note: This tab is enabled only if the NVT ensemble is selected on the Dynamics tab. Thermostat: Select the algorithm to be used to control the temperature of an NVT simulation. Available options are:
Page 102 | Materials Studio • DMol Guide n Gaussian n Simple NH - simple Nosé-Hoover n NH Chain - Nosé-Hoover chain n Massive NH - massive Nosé-Hoover n GGM - generalized Gaussian moments n Massive GGM (default) - massive generalized Gaussian moments Nosé Q ratio: Specify the value to be used to scale the fictitious mass, Q, of a Nosé-Hoover thermostat. A larger Q ratio implies decreased damping of temperature fluctuations. Default = 2.0.
Note: This control is disabled if the Gaussian, GGM, or Massive GGM Thermostat is selected. Chain length: Specify the length of the thermostat chain to be used with the Nosé-Hoover chain, massive Nosé-Hoover, and generalized Gaussian moments methods. Default = 2.
Note: This control is disabled if the Gaussian or Simple NH Thermostat is selected. Relaxation time: Specify the thermostat relaxation time for the generalized Gaussian moments method as a multiple of the time step. Default = 10.0.
Note: This control is disabled if the Gaussian, Simple NH, NH Chain, or Massive NH Thermostat is selected. Yoshida parameter: Specify the time step parameter for integration accuracy of the Nosé and generalized Gaussian moments methods. Available options are: n 1 n 3 (default) n 5 n 7 n 25
Note: This control is disabled if the Gaussian Thermostat is selected.
Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Thermostat Toolbar | Calculation | Setup | More... | Thermostat
DMol3 Transition State Search dialog The DMol3 Transition State Search dialog allows you to set up and display the parameters that control the simulation in a DMol3 TS Search task.
Note: A transition state search requires a frame-based document (for example, an .arc file or .xtd file) as input. So, even though you can set options on this dialog, you will not be able to start a job until you supply an appropriate file.
Note: When a transition state search is performed on a periodic system the unit cell is fixed.
Dialogs in DMol3 | Page 103 Note: A QST calculation estimates the actual transition state from the currently selected frame in the .xtd document. If this is identical to the product or reactant, it will select the penultimate frame as a transition state estimate. The reactants are taken from the first frame of the trajectory, and the products from the last frame of the trajectory. If you select a QST calculation, the next-to-the-last frame is used for the QST mid-point. The .arc files generated by any of these transition state searches may be used as input to a QST. In such situations DMol3 uses the first and last frames for the reactant and product, respectively, and puts the best guess for the transition state in the next-to-the-last frame. Search protocol: Select the type of synchronous transit that will be performed. Available options are: n LST Maximum - performs a single LST maximization, bracketing the maximum between the reactants and product. n Halgren-Lipscomb - performs an LST maximization, followed by a single line search minimization. n LST/Optimization - performs an LST maximization, followed by a full conjugate gradient minimization. n Complete LST/QST (default) - performs an LST, followed by repeated conjugate gradient minimizations and QST maximizations until a transition state has been located. n QST / Optimization - starting from a QST, performs repeated maximizations and conjugate gradient minimizations until a transition state has been located. Quality: Sets the geometry optimization convergence thresholds for the rms forces on the atoms. Convergence thresholds for Quality settings: Quality RMS Force (Hartree/Å) Coarse 0.02 Medium 0.01 Fine 0.002 Customized User specified Altering the value of any threshold is allowed and results in the Quality being set to Customized. RMS convergence: Specifies the value at which convergence is considered to take place, in terms of the RMS of the gradients. Max. number QST steps: Sets the maximum number of allowed QST maximization cycles. Optimize reactants and products: Specifies that the input structure for the reactant and product in a TS search calculation should be optimized to a local minimum. Selecting this allows the TS search to start from a "raw" trajectory, where the reactant and product structures have not already been optimized.
Note: This choice may lead to reactant and product structures deviating substantially from the input structures, so it is recommended that you carefully check the final path. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
Page 104 | Materials Studio • DMol Guide DMol3 TS Optimization dialog The DMol3 TS Optimization dialog allows you to set up and display the parameters that control the simulation in a DMol3 TS Optimization task.
Note: Since a transition state optimization requires a starting Hessian, even though you can set options on this dialog, you will not be able to start an optimization until you associate a Hessian matrix with the current structure. Quality: Sets the geometry optimization convergence thresholds for Energy change, Max. force, and Max. displacement between optimization cycles. The optimization will stop when the energy convergence is satisfied, along with either the displacement or gradient criteria. Convergence thresholds for Quality settings: Quality Energy (Hartree) Force (Hartree/Å) Displacement (Å) Coarse 1 × 10-4 0.02 0.05 Medium 2 × 10-5 0.004 0.005 Fine 1 × 10-5 0.002 0.005 Customized User defined User defined User defined Altering the value of any threshold is allowed and results in the Quality being set to Customized. Energy: Specify the convergence threshold for the maximum energy change, in Ha, during the geometry optimization. Max. force: Specify the convergence threshold for the maximum force, in Ha/Å, during the geometry optimization. Max. displacement: Specify the convergence threshold for the maximum displacement, in Å, during the geometry optimization. Max. iterations: Sets the maximum number of geometry optimization cycles. If the number of cycles is reached, then the calculation will stop even if the convergence criteria are not satisfied. Max. step size: Sets the maximum allowed change in any Cartesian coordinate. Geometric displacements are truncated such that they are less than this value. This prevents the optimizer from taking unreasonable steps. The transition state optimizer will follow a particular normal mode of the Hessian to the transition state. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 TS Confirmation dialog The DMol3 TS Confirmation dialog allows you to set up and display the parameters that control the simulation in a DMol3 TS Confirmation task.
Dialogs in DMol3 | Page 105 Quality: Sets the geometry optimization convergence thresholds for Energy change, Max. force, and Max. displacement between optimization cycles. The optimization will stop when the energy convergence is satisfied along with either the displacement or gradient criteria. Convergence thresholds for Quality settings: Quality Energy (Hartree) Force (Hartree/Å) Displacement (Å) Extra-coarse 10-2 0.1 0.1 Coarse 10-4 0.02 0.05 Medium 2 × 10-5 0.004 0.005 Fine 10-5 0.002 0.005 Customized User defined User defined User defined Altering the value of any threshold is allowed and results in the Quality being set to Customized. Energy: Specify the convergence threshold for the maximum energy change, in Hartree, during the transition state confirmation. Max. force: Specify the convergence threshold for the maximum force, in Hartree Å-1, during the transition state confirmation. Max. displacement: Specify the convergence threshold for the maximum displacement, in Å, during the transition state confirmation. Path quality: Specifies the gradation of the path, by setting the maximum number of images to generate. Max. images: The number of intermediate NEB images used during the transition state confirmation. Quality Max. images Coarse 6 Medium 10 Fine 20 Customized User defined Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 Elastic Constants dialog The DMol3 Elastic Constants dialog allows you to set up and display the parameters that control the simulation in a DMol3 Elastic Constants task. Displacement step: Specifies the finite displacement step used to set up the cell distortions necessary to calculate the elastic constants. Default = 0.05 Å. Quality: Set the geometry optimization convergence thresholds for energy change, maximum force, and maximum displacement between optimization cycles. The optimization will stop when the energy
Page 106 | Materials Studio • DMol Guide convergence is satisfied, along with either the displacement or gradient criteria. If the calculated initial gradients are below the threshold, the optimization will successfully stop without making a single step and without comparing displacements and energies. Three sets of convergence thresholds are available: n Coarse n Medium n Fine The values of the convergence thresholds in each set are given in the table below: Value Coarse Medium Fine Energy (Hartree) 1 × 10-4 2 × 10-5 1 × 10-5 Max. force (Hartree Å-1) 0.02 0.004 0.002 Max. displacement (Å) 0.05 0.005 0.005 Alternatively, thresholds can be specified independently for Energy, Max. force, and Max. displacement. If you enter your own values for any of these settings, the Quality is displayed as Customized on both the DMol3 Geometry Optimization dialog and the Setup tab of the DMol3 Calculation dialog. Energy: Specify the convergence threshold for the maximum energy change, in Hartree, during the geometry optimization. Max. force: Specify the convergence threshold for the maximum force, in Hartree Å-1, during the geometry optimization. Max. displacement: Specify the convergence threshold for the maximum displacement, in Å, during the geometry optimization. Max. iterations: Specify the maximum number of geometry optimization cycles. If this number of cycles is reached, then the calculation will stop, even if the convergence criteria are not satisfied. Max. step size: Specify the maximum allowed change of any Cartesian coordinate. Geometric displacements are truncated such that they are less than this value. This prevents the optimizer from taking unreasonable steps.
Note: The default optimizer in DMol3 uses delocalized internal coordinates, the maximum Cartesian step size is not directly applicable to this method. You should reduce the value of Max. step size if you observe that the actual displacements during minimization are too large and cause large energy changes. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 Reaction Kinetics dialog The DMol3 Reaction Kinetics dialog allows you to set up and display the parameters that control the simulation in a DMol3 Reaction Kinetics task.
Dialogs in DMol3 | Page 107 Optimize transition state: Perform a transition state optimization before calculation of the Hessian and total energy for the transition state.
Note: Transition state optimization can only be performed if the Hessian of the transition state is available. Reuse Hessian for reactants and products: When checked, if any reactant or product structure already has a Hessian imported no additional geometry optimization or Hessian calculation will be performed for that structure. Use coarse-grained parallelization: When checked, coarse-grained parallelization is used for the numerical displacement frequency calculation. Geometrical displacement calculations necessary for generating the system Hessian matrix are evenly split over all available computational nodes. Each displacement is then run in a serial mode and the final Hessian elements are gathered at the end of the calculation. This is the preferred method for larger systems with many vibrational modes and a non- trivial number of computational nodes. When unchecked, numerical displacements are calculated sequentially, each in a parallel DMol3 process. This might be advantageous for smaller systems with fewer normal modes or for machines with a limited number of computational nodes. By default the Hessian is evaluated using a 2-point difference of analytic forces. You can change this by modifying the Vibration_Steps keyword in the input file. See the DMol3 Job Files topic for information on how to modify the input file. Quality: Set the geometry and transition state optimization convergence thresholds for energy change, maximum force, and maximum displacement between optimization cycles. The optimization will stop when the energy convergence is satisfied, along with either the displacement or gradient criteria. If the calculated initial gradients are below the threshold, the optimization will successfully stop without making a single step and without comparing displacements and energies. Three sets of convergence thresholds are available: n Coarse n Medium n Fine The values of the convergence thresholds in each set are given in the table below: Value Coarse Medium Fine Energy (Hartree) 1 × 10-4 2 × 10-5 1 × 10-5 Max. force (Hartree Å-1) 0.02 0.004 0.002 Max. displacement (Å) 0.05 0.005 0.005 Alternatively, thresholds can be specified independently for Energy, Max. force, and Max. displacement. If you enter your own values for any of these settings, the Quality is displayed as Customized on both the DMol3 Reaction Kinetics dialog and the Setup tab of the DMol3 Calculation dialog. Energy: Specify the convergence threshold for the maximum energy change, in Hartree, during the geometry optimization. Max. force: Specify the convergence threshold for the maximum force, in Hartree Å-1, during the geometry optimization.
Page 108 | Materials Studio • DMol Guide Max. displacement: Specify the convergence threshold for the maximum displacement, in Å, during the geometry optimization. Max. iterations: Specify the maximum number of geometry optimization cycles. If this number of cycles is reached, then the calculation will stop, even if the convergence criteria are not satisfied. Max. step size: Specify the maximum allowed change of any Cartesian coordinate. Geometric displacements are truncated such that they are less than this value. This prevents the optimizer from taking unreasonable steps.
Note: The default optimizer in DMol3 uses delocalized internal coordinates, the maximum Cartesian step size is not directly applicable to this method. You should reduce the value of Max. step size if you observe that the actual displacements during minimization are too large and cause large energy changes. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
DMol3 Transport dialog The DMol3 Transport dialog allows you to setup and display parameters relating to the DMol3 Transport task. It contains the following tabs: n Setup: Allows you to choose the type of calculation that will be performed. It also allows you to select a number of transport specific properties to be computed as part of the DMol3 calculation. n Electrodes: Allows you to set parameters related to the electrodes. n Electrostatics: Allows you to specify settings for the Poisson solver. Help: Displays the Help topic for the current tab. Note: The DMol3 Electron Transport task cannot be run under certain circumstances, if:
Dialogs in DMol3 | Page 109 n On the Setup tab of the DMol3 Calculation dialog: n Use method for DFT-D correction checkbox is checked n Functional is set to B3LYP or m-GGA option n Spin unrestricted checkbox is checked n Charge is set to any non-zero value n On the Electronic tab of the DMol3 Calculation dialog: n Core treatment is not set to DFT Semi-core Pseudopots when there is an element with Z > 20 n Use solvation model checkbox is checked n On the Properties tab of the DMol3 Calculation dialog, any of the following are selected: n Density of states n Electron density n Electrostatics n Frequency n Fukui function n Optics n Orbitals n Population analysis
Access methods
Menu Modules | DMol3 | Calculation | Setup | More... Toolbar | Calculation | Setup | More...
Setup tab The Setup tab allows you to choose the type of calculation that will be performed. It also allows you to select a number of transport specific properties to be computed as part of the DMol3 calculation. Calculate transmission function: When checked, this indicates that the transmission function will be computed as part of the calculation. More...: Provides access to the DMol3 Transmission dialog, which allows you access to further options for the transmission property. Calculate current/voltage characteristics: When checked, this indicates that current/voltage data will be computed as part of the calculation. More...: Provides access to the DMol3 Current/Voltage dialog, which allows you to access to further options for the current/voltage property. Density Mixing Mixing amplitude: Specify the value, to use in mixing the charge density matrix between the current and previous iterations. For example, a value of 0.02 will construct a charge density using 2 % from the current iteration and 98 % from the previous iterations.
Page 110 | Materials Studio • DMol Guide Electrode Number of k-points: The number of k-points along the electrode that will be used calculate the electrodes' Hamiltonians. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Setup Toolbar | Calculation | Setup | More... | Setup
DMol3 Transmission dialog The DMol3 Transmission dialog allows you to set options controlling the calculation of the transmission function. From: Specifies the beginning of the energy range for the transmission function. To: Specifies the end of the energy range for the transmission function. Steps: The number of energy points for which the transmission function will be evaluated. Transmission pairs: Lists the available electrode pairs for the current document. A checked electrode pair will have the transmission function between the two electrodes calculated. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Setup | More... Toolbar | Calculation | Setup | More... | Setup | More...
DMol3 Current/Voltage dialog The DMol3 Current/Voltage dialog allows to you define the parameters for the current/voltage calculation. Current through: Select the electrode through which the current will be calculated. Vary potential for: Select the electrode for which the potential will be varied. From: Specifies the beginning of the potential range. To: Specifies the end of the potential range. Steps: Specifies the number of potential points for which the current will be computed.
Note: If the number of Steps is one, the current will be calculated at a single voltage corresponding to the From value. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Setup | More... Toolbar | Calculation | Setup | More... | Setup | More...
Electrodes tab The Electrodes tab allows you to set parameters related to the electrodes.
Dialogs in DMol3 | Page 111 Electrode Name: The name to be used for the electrode. When the name is changed on this dialog any other settings that depends on the name of the electrode will be updated.
Note: If the name of the electrode is changed, using the Properties Explorer or an Undo/Redo action, any settings that depend on the name will be lost. The affected settings are: transmission pair selections, electrode potential values, and current and voltage electrode selections. Potential (V): Determines the potential of the electrode. Direction (XYZ): Shows the direction of the electrode. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Electrodes Toolbar | Calculation | Setup | More... | Electrodes
Electrostatics tab The Electrostatics tab allows you to specify settings for the Poisson solver. Buffer length: Specifies the buffer length added to the sides of a minimum box containing the device structure, in Å. Max. grid spacing: Sets the maximum grid spacing used for the Poisson grid. Use default boundary conditions: If checked default boundary conditions will be applied. The default is to use the Dirichlet condition on any box face containing one or more electrodes and Neumann conditions on any other surface. More...: Provides access to the DMol3 Poisson Boundary Conditions dialog, which allows you to specify non-default boundary conditions for the Poisson solver.
Note: This is enabled only if the Use default boundary conditions checkbox is unchecked.
Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Electrostatics Toolbar | Calculation | Setup | More... | Electrostatics
DMol3 Poisson Boundary Conditions dialog The DMol3 Poisson Boundary Conditions dialog allows you to specify non-default boundary conditions for the Poisson solver. X , X , Y , Y , Z , Z : Defines the boundary conditions for the six faces of the box used by min max min max min max the Poisson solver. For numerical reasons it is not possible to use Neumann conditions on all boundaries. Options for these are: n Neumann (default for box faces with no electrodes) n Dirichlet (default for box faces with electrodes) Electrode boundary: n Global (default) - Applies the selected boundary condition to the entire face of each box n Circle - Applies the Dirichlet boundary condition to a circular cross section around each electrode. n Square - Applies the Dirichlet boundary condition to a square cross section around each electrode.
Page 112 | Materials Studio • DMol Guide Electrode buffer: The length of the buffer applied to each electrode boundary region. Default = 3 Å. Set default boundary conditions: Sets the values on the dialog to the default boundary conditions.
Note: When changing to a new document or modifying an existing document the Poisson boundary conditions are not automatically updated for the system in focus. To use the default settings click the Set default boundary conditions button or check the Use default boundary conditions checkbox on the Electrostatics tab of the DMol3 Transport dialog. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Setup | More... | Electrostatics | More... Toolbar | Calculation | Setup | More... | Electrostatics | More...
Electronic tab The Electronic tab allows you to set the parameters associated with the electronic Hamiltonian. Integration accuracy: Specifies the precision used in the numerical integration of the Hamiltonian. Available options are: n Coarse n Medium n Fine The Medium option uses about 1000 grid points for each atom in the calculation. SCF tolerance: Specifies the threshold used to determine whether an SCF has converged. Options and associated convergence thresholds are: n Coarse = 10-4 n Medium = 10-5 n Fine = 10-6 A Customized option is also available. The parameters which control this option can be accessed using the More... button. k-point set: Defines the number of integration points that will be used to integrate the wavefunction in reciprocal space. Available options are: n Gamma - a single point n Coarse n Medium n Fine More detailed control is available on the DMol3 Electronic Options dialog.
Note: k-point control is active only for periodic systems. Core treatment: Four types of treatments of core electrons are available in DMol3:
Dialogs in DMol3 | Page 113 n All Electron (default) - provides no special treatment of cores. All electrons are included in the calculation. n Effective Core Potentials (ECP) - replaces core electrons by a single effective potential, reducing the computational cost. ECPs introduce some degree of relativistic correction into the core. n All Electron Relativistic - includes all electrons explicitly and introduces some relativistic effects into the core. This is the most accurate and also the most computationally expensive of the options. n DFT Semi-core Pseudopots (DSPP) - replaces core electrons by a single effective potential, reducing the computational cost. DSPPs introduce some degree of relativistic correction into the core. These are DFT-based potentials. For additional details on the use of ECPs in DMol3 see Core treatment under Setting up electronic options.
Note: Effective Core Potentials and DFT Semi-core Pseudopots are not available for the meta- GGA exchange correlation functionals. Basis set: Specifies the atomic orbital basis set that will be used in the calculation. Available options are: n MIN n DN n DND n DNP n TNP n DNP+ For more information on basis sets, see Numerical basis sets. Basis file: Specifies the version of the basis set file to use: n 3.5 n 4.4
Notes: n Selection of a Basis file is not available when Basis set is set to TNP as this has its own custom basis file. n Selection of a Basis file is not available when Basis set is set to DNP+ as this set is available only with version 4.4. n Selection of the DNP+ set requires very large orbital cutoff. Short cutoffs may lead to errors arising from squeezed diffuse tails approximations. n Basis set quality has been analyzed in detail by Delley (1990). n Version 4.4 of the basis set is the newly optimized set delivering slightly improved heats of formation. The set is described in Delley, 2006. n Version 3.5 is the original basis set file, the default. Orbital cutoff quality: Specifies the finite range cutoff of the atomic basis set. The orbital cutoff quality determines the size of the finite range cutoff, and is dependent on the Orbital cutoff scheme. Available options are: n Coarse n Medium n Fine
Page 114 | Materials Studio • DMol Guide A Customized option is also available. The parameters which control this option can be accessed using the More... button. The atomic orbitals are taken to be zero at this distance from their atomic center. Decreasing the cutoff reduces the computational time required for a calculation but introduces large approximations. The cutoff value must lie between 3.25 and 20 Å.
Note: Using too small or too large a cutoff may result in failure to converge during SCF or geometry optimization calculations. The smallest recommended values for cutoff are those in the table of coarse quality values. The largest value should not exceed 20 Å. Harris approximation: When checked specifies the Harris non-self-consistent approximation be used in the calculation. This greatly reduces the computational time required but also reduces the accuracy of the calculation. The Harris approximation is available only for spin-restricted calculations using LDA functionals without solvent effect. Use solvation model: When checked specifies that the COSMO solvation model will be used, further details can be set on the Solvent tab of the DMol3 Electronic Options dialog. When a solvation model is used the Harris Approximation is unavailable. Default = unchecked. For all calculations using the COSMO solvation model a COSMO Sigma Profile plot, named
Menu Modules | DMol3 | Calculation | Electronic Toolbar | Calculation | Electronic
DMol3 Electronic Options dialog The DMol3 Electronic Options dialog allows you more detailed control over parameters associated with the electronic Hamiltonian. The DMol3 Electronic Options dialog contains the following tabs: n SCF: Allows you to set the parameters that control the electronic minimization. n k-points: Allows you more detailed control over the k-point set to be used in the calculation. n Orbital Cutoff: Allows you to set more detailed parameters that control the atomic orbital cutoffs. n Solvent: Allows you to set up a simulated solvent environment for the calculation. n DFT-D: Provides access to the parameters for van der Waals dispersion correction calculations.
Note: Solvent environment calculations are available only for non-Harris runs. Help: Displays the Help topic for the current tab. Access methods
Menu Modules | DMol3 | Calculation | Electronic | More... Toolbar | Calculation | Electronic | More...
Dialogs in DMol3 | Page 115 SCF tab The SCF tab allows you to set the parameters that control the electronic minimization. SCF tolerance: Specify the threshold for SCF density convergence. The SCF procedure is considered converged to a minimum when the largest (in magnitude) component of the DIIS density error matrix is less than this value. This will override the SCF tolerance setting specified on the Electronic tab, changing the setting to Customized. Max. SCF cycles: Specify the maximum number of SCF iterations allowed for an energy calculation. If the SCF does not converge after the specified number of iterations, the calculation will be terminated. Multipolar expansion: Specify the maximum angular momentum function used in the multipolar representation of the charge density. Available options are: n Monopole n Dipole n Quadrupole n Octupole n Hexadecapole Charge: Specify the value, f, used in mixing the charge density between the current and previous iterations. Allowed values are 0.0 < f ≤ 1.0. For example, a value of 0.2 would construct a charge density using 20% of the current density and 80% from the previous iterations. Spin: Specify the value used in mixing the spin density between the current and previous iterations. Allowed values = 0.0 to 1.0. Use DIIS: When checked, indicates that the DIIS (direct inversion in an iterative subspace) will be used to speed up SCF convergence. DIIS size: Specify the maximum size of the subspace for the DIIS procedure. If the SCF does not converge with the default number of histories, increasing this value can sometimes lead to significantly improved SCF convergence. It is not recommended to use fewer than 4 histories. Allowed values = 1 to 10. Use preconditioner: When checked, indicates that the charge density preconditioner is turned on, this dampens charge density oscillations between successive SCF cycles. This can speed up convergence, particularly for large systems or for surface or interface calculations. q0: Specify the reference wave vector for damping the charge density oscillations, in inverse Bohr. Allowed values = 0.5 to 20.
Note: The q0 control is only enabled when the Use preconditioner checkbox is checked. Use smearing: When checked, indicates that thermal smearing will be applied to the orbital occupation to speed up convergence. Smearing: Specify the value, in Hartree, of the smearing parameter.
Note: The Smearing control is only enabled when the Use smearing checkbox is checked.
Note: A potential way to improve convergence for coarse k-point sets without introducing thermal smearing is to switch off the tetrahedra integration algorithm with the defeat_tetrahedra keyword. Apply dipole slab correction: When checked, adds an external potential to the vacuum region of the slab. This potential cancels the non-zero dipole moment of the cell due to polar adsorbates in slabs (or
Page 116 | Materials Studio • DMol Guide adsorbates on only one side of the slab). This correction is particularly helpful for workfunction calculations.
Note: The dipole slab correction is applied only for vacuum slabs, which must be at least 8 Å thick. For a calculation with insufficient vacuum, the dipole correction will be ignored.
Note: The dipole slab correction requires P1 symmetry. If your slab has symmetry other than P1, you will be prompted to convert the symmetry to P1 before you can continue.
Note: The dipole slab correction in DMol3 requires that the center of the vacuum coincides with the center of the unit cell. Materials Studio will shift the geometry accordingly prior to the calculation to enforce the correct vacuum center.
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Menu Modules | DMol3 | Calculation | Electronic | More... | SCF Toolbar | Calculation | Electronic | More... | SCF k-points tab The k-points tab allows you more detailed control over the k-point set to be used in the calculation. The Monkhorst-Pack k-point grid to be used in the calculation can be specified in several ways. For cubic cells and for the C direction of hexagonal cells the even and odd grids for the Monkhorst-Pack scheme give the same number of k-points. However, the even grid provides better sampling and will always be used automatically under these conditions. This ensures that a good grid with k-point separation at (or less than) the specified target can be achieved more economically. As a consequence, such lattices may have much finer separations than requested as odd grids have been excluded - even though they would have been closer to the specified separation - and the better even grids have been taken in preference. Gamma point only: When selected, indicates that a single k-point at (0,0,0) will be used for the density of states calculation. Quality: When selected, indicates that the k-point grid will be generated using a k-point separation appropriate to the specified quality level. Select the desired quality level from the dropdown list. Available options are: n Coarse n Medium n Fine The k-point separations associated with the three Quality settings depend on whether the Metal checkbox on the Setup tab is checked and are as follows: k-point separation (Å-1) Quality Metal checked Metal unchecked Coarse 0.07 0.1 Medium 0.05 0.08 Fine 0.04 0.07
Dialogs in DMol3 | Page 117 Separation: When selected, indicates that the k-point grid will be generated according to the specified k- point separation. Specify the k-point separation, in Å-1, in the associated text box.
Note: When the Separation option is selected, the Monkhorst-Pack parameters are derived to give the specified separation between neighboring grid points. Custom grid parameters: When selected, indicates that the k-point grid will be generated using the Monkhorst-Pack grid parameters and the origin shift in fractional reciprocal space coordinates specified in the Grid parameters and Origin shift text boxes, respectively. Grid parameters: Specify the Monkhorst-Pack grid parameters in each of the lattice directions. Actual spacing: Displays the k-point separation, in Å-1, resulting from the currently specified Monkhorst-Pack grid parameters in each of the lattice directions. Origin shift: Specify the offset of the Monkhorst-Pack grid in fractional reciprocal space coordinates.
Note: The Grid parameters and Origin shift controls are enabled only if the Custom grid parameters option is selected. Display points...: Displays the number and fractional coordinates of the reciprocal space mesh points that would be generated using the currently specified parameters.
Note: The actual set of k-points that will be used in the calculations may be altered if the symmetry of the system changes.
Access methods
Menu Modules | DMol3 | Calculation | Electronic | More... | k-points Toolbar | Calculation | Electronic | More... | k-points
Orbital Cutoff tab The Orbital Cutoff tab allows you to set more detailed parameters that control the atomic orbital cutoffs. Orbital cutoff scheme: Specify how the orbital cutoff values are to be determined. Available options are: n Global - determines the value of the cutoff based on either the selected Quality setting or a specified Custom cutoff value n Use current - uses the values of the OrbitalCutoffRadius property assigned to the atoms
Note: If you select the Use current option, you must assign an OrbitalCutoffRadius value to all the atoms in the structure. The calculation will fail if any atoms have undefined OrbitalCutoffRadius values. If the Global orbital cutoff scheme is to be used in the calculation, it can be specified in one of two ways: Quality: When selected, indicates that a global orbital cutoff appropriate to the specified quality level will be used. Select the desired quality level from the dropdown list. Available options are: n Coarse n Medium n Fine
Page 118 | Materials Studio • DMol Guide The exact value of the global orbital cutoff used will depend upon the elements present in the structure being studied.
Note: The Quality global setting is not appropriate for studying reactions between compounds containing different atoms. The actual numerical value of the atomic cutoff radius depends on atoms present in the system and can therefore vary between products and reactants making the results unpredictable. In such cases it is advised to use a constant, custom value for the global cutoff. Custom: When selected, indicates that the value specified in the Global orbital cutoff text box will be used. This will override the Orbital cutoff quality setting specified on the Electronic tab, changing the setting to Customized.
Note: The Quality and Custom controls are enabled only if the Global option is selected from the Orbital cutoff scheme dropdown list. Global orbital cutoff: Specify a value, in Å, for the global orbital cutoff.
Note: The Global orbital cutoff control is enabled only if the Custom option is selected for the global orbital cutoff scheme. Assign: Assigns the OrbitalCutoffRadius property to the selected atoms in the current structure (or all the atoms if none are selected), using the specified Global orbital cutoff parameter. Such assigned values can then be used in conjunction with the Use current orbital cutoff scheme.
Note: The Assign button is enabled only if the Global option is selected from the Orbital cutoff scheme dropdown list. The global real space cutoff is selected for every system as the maximum value from all the cutoffs specific to each element in that system. Cutoff_global = max(Cutoff_elementI) I ⊂ Elements of a system The following DMol3 keywords may be written into the output file: n Cutoff_Global n Cutoff_Element n Cutoff_Atom Access methods
Menu Modules | DMol3 | Calculation | Electronic | More... | Orbital Cutoff Toolbar | Calculation | Electronic | More... | Orbital Cutoff
Solvent tab The Solvent tab allows you to set up a simulated solvent environment for the calculation. Use COSMO: When checked, indicates that the conductor-like screening model (COSMO) will be used to simulate a solvent environment for the calculation. For all calculations using the COSMO solvation model a COSMO Sigma Profile plot, named
Dialogs in DMol3 | Page 119 Solvent: Select a solvent from the dropdown list to be used as the solvent environment for the calculation. Available options are: n Acetone n Acetonitrile n Benzene n Carbon tetrachloride n Chloroform n Diethyl ether n Dimethyl sulfoxide n Ethanol n Methanol n Methylene chloride n n-hexane n n-hexadecane n Nitrobenzene n Pyridine n Water When a solvent is selected, the Dielectric constant field is automatically updated with the appropriate value.
Note: If the Dielectric constant parameter is set to a value different to that dictated by the selected solvent, the Solvent is displayed as Customized. Dielectric constant: Specify a value for the solvent dielectric constant. This parameter is automatically updated to the appropriate value when a solvent is selected from the Solvent dropdown list, however, you can enter your own custom value if you wish.
Note: The Solvent and Dielectric constant controls are enabled only if the Use COSMO checkbox is checked.
Access methods
Menu Modules | DMol3 | Calculation | Electronic | More... | Solvent Toolbar | Calculation | Electronic | More... | Solvent
DFT-D tab The DFT-D tab allows you to set up customized parameters for van der Waals dispersion corrections. This can involve the definition of DFT-D corrections for exchange functionals that are not usually supported, the definition of support for additional elements, or changing existing parameters. Use custom DFT-D parameters: Specify whether to use custom DFT-D parameters. When this checkbox is checked, select the van der Waals scheme to use from the dropdown list, options are: n TS n Grimme n OBS
Page 120 | Materials Studio • DMol Guide Note: The option selected will automatically update the Use method for DFT-D correction setting on the Setup tab of the DMol3 Calculation dialog.
Atomic parameters This table allows you to edit the dispersion correction parameters for each of the atomic species. The type and number of parameters depend on the DFT-D scheme selected, please refer to the original literature for the meaning and usage of each parameter. The units are eV for energies and Å for lengths. The available columns are: Element: Denotes the element to be edited. C6 (eV Å6): Available for TS and Grimme schemes. R0 (Å): Available for TS and Grimme schemes. alpha (Å3): Available for TS and OBS schemes. I (eV): Available for the OBS scheme. Rvdw (Å): Available for the OBS scheme.
Note: Only the elements in the currently active document are listed in the Atomic parameters table .
Note: Each scheme includes a radius (R0 for TS and Grimme, Rvdw for OBS) that must be non-zero for each of the active elements.
Scheme parameters Scheme parameters are dimensionless numbers that define the functional form of each scheme. Please refer to the original literature to for the meaning and usage of each parameter. Depending on the van der Waals scheme selected for the custom DFT-D parameters setting, the Scheme parameters that can be specified are: n TS: sR, d n Grimme: s6, d n OBS: lambda, n
Note: The default values for these parameters depend on the exchange correlation functional selected on the Setup tab of the DMol3 Calculation dialog.
Note: Both scheme parameters must be non-zero for the calculations to start and for input files to be written. Reset All: Restores the default settings for each element in the grid. Access methods
Menu Modules | DMol3 | Calculation | Electronic | More... | DFT-D Toolbar | Calculation | Electronic | More... | DFT-D
Properties tab The Properties tab allows you to select the properties that will be computed as part of a DMol3 calculation.
Dialogs in DMol3 | Page 121 Choose the properties you wish to compute by checking the appropriate checkboxes in the list. Selection of certain properties activates additional Electron density options. Access methods
Menu Modules | DMol3 | Calculation | Properties Toolbar | Calculation | Properties
Band structure selection Checking the Band structure checkbox on the Properties tab displays options for controlling the band structure calculation. Empty bands: Specify the number of empty bands (in addition to occupied bands) to be included in the band structure calculation. k-point set: Specify the quality of the k-point set for the band structure calculation. Each quality corresponds to a particular approximate separation between consecutive k-points on the reciprocal space path. Quality k-point separation (Å-1) Coarse 0.04 Medium 0.025 Fine 0.015 Separation: Specify the approximate separation between k-points in Å-1. The default depends on the selected k-point set. Path...: Provides access to the Brillouin Zone Path dialog, which allows you to set the reciprocal space path for the band structure calculation. Access methods
Menu Modules | DMol3 | Calculation | Properties | Band structure Toolbar | Calculation | Properties | Band structure
Density of states selection Checking the Density of states checkbox on the Properties tab displays options for controlling the density of states calculation. Empty bands: Specify the number of empty bands (in addition to occupied bands) to be included in the density of states calculation. k-point set: Specify the quality of the k-point set for the density of states calculation. Each quality corresponds to a particular separation between neighboring k-points in the Monkhorst-Pack grid. Calculate PDOS: When checked, indicates that the information required to generate partial and local densities of states will also be calculated. More...: Gives access to the DMol3 Density of States Options dialog, which provides options for controlling the k-point set specification.
Page 122 | Materials Studio • DMol Guide Note: The k-point set dropdown list and the More... button are disabled for calculations on nonperiodic systems.
Tip: Calculations requesting Density of states properties will also provide information for the generation of Fermi surfaces.
Note: The default calculated range of the DOS plot for a periodic system is between -1.0 and 1.0 Ha. This range can be modified by editing the Plot_DOS keyword in the input file. DOS plots for nonperiodic structures include all calculated orbitals. For molecules and periodic systems with only a Gamma point, the entire density of states is shown including the core levels.
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Menu Modules | DMol3 | Calculation | Properties | Density of states Toolbar | Calculation | Properties | Density of states
DMol3 Density of States Options dialog The DMol3 Density of States Options dialog allows you to specify the k-point set used for density of states calculations. The Monkhorst-Pack k-point grid to be used in the calculation can be specified in one of four ways: Gamma point only: When selected, indicates that a single k-point at (0,0,0) will be used for the density of states calculation. Quality: When selected, indicates that the k-point grid will be generated using a k-point separation appropriate to the specified quality level. Select the desired quality level from the dropdown list. Available options are: n Coarse n Medium n Fine The k-point separations associated with the three Quality settings are as follows: Quality k-point separation (Å-1) Coarse 0.07 Medium 0.05 Fine 0.04 Separation: When selected, indicates that the k-point grid will be generated according to the specified k- point separation. Specify the k-point separation, in Å-1, in the associated text box.
Note: When the Separation option is selected, the Monkhorst-Pack parameters are derived to give the specified separation between neighboring grid points.
Tip: Calculations requesting Density of states properties will also provide information for the generation of Fermi surfaces. In order to generate accurate Fermi surfaces the Separation option should be selected and a value of 0.01 1/Å or less specified.
Dialogs in DMol3 | Page 123 Custom grid parameters: When selected, indicates that the k-point grid will be generated using the Monkhorst-Pack grid parameters and the origin shift in fractional reciprocal space coordinates specified in the Grid parameters and Origin shift text boxes, respectively. Grid parameters: Specify the Monkhorst-Pack grid parameters in each of the lattice directions. Actual spacing: Displays the k-point separation, in Å-1, resulting from the currently specified Monkhorst-Pack grid parameters in each of the lattice directions. Origin shift: Specify the offset of the Monkhorst-Pack grid in fractional reciprocal space coordinates.
Note: The Grid parameters and Origin shift controls are enabled only if the Custom grid parameters option is selected. Display points...: Displays the number and fractional coordinates of the reciprocal space mesh points that would be generated using the currently specified parameters.
Note: The actual set of k-points that will be used in the calculations may be altered if the symmetry of the system changes. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Properties | Density of states | More... Toolbar | Calculation | Properties | Density of states | More...
Electron density selection Choosing Electron density on the Properties tab displays options for computing several different types of charge density. Each type of density is returned as a set of volumetric data in a .grd file. Total density: When checked, indicates that the total electronic charge density will be computed. Deformation density: When checked, indicates that the total density with the density of the isolated atoms subtracted will be computed. Spin density: When checked, indicates that the difference between the charge density for alpha-spin and beta-spin electrons will be computed.
Note: The Spin density option is enabled only if the Spin unrestricted checkbox is checked on the Setup tab. Grid...: Provides access to the DMol3 Grid Parameters dialog, which allows you to set the resolution and extents of the grid used to calculate the volumetric properties of the orbitals.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Access methods
Menu Modules | DMol3 | Calculation | Properties | Electron density Toolbar | Calculation | Properties | Electron density
Page 124 | Materials Studio • DMol Guide Electrostatics selection Choosing Electrostatics on the Properties tab displays options for computing several different properties related to the electrostatics of the input structure. Electrostatic potential: When checked, indicates that the total electrostatic potential will be computed and returned as a set of volumetric data in a .grd file. Electrostatic moments: When checked, indicates that the dipole moment of a molecule will be computed.
Note: For a periodic system, these moments are undefined. Nuclear electric field gradients: When checked, indicates that nuclear electric field gradient, an important component of the nuclear magnetic shift, will be computed. Work function: When checked, indicates that work function calculations will be performed. The energy required to remove an electron from the bulk into the vacuum as a function of the slab distance will be calculated.
Note: This calculation is enabled for slabs only. When doing a workfunction calculation, you should activate the dipole slab corrections.
Note: This calculation will yield a slightly different total energy as a result of a different charge compensation algorithm, other properties are not affected. Grid...: Provides access to the DMol3 Grid Parameters dialog, which allows you to set the resolution and extents of the grid used to calculate the volumetric properties of the orbitals.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Access methods
Menu Modules | DMol3 | Calculation | Properties | Electrostatics Toolbar | Calculation | Properties | Electrostatics
Frequency selection Choosing Frequency on the Properties tab displays options for computing a Hessian which is used for vibrational frequencies of the model. The results can be used to generate a starting Hessian for a geometry optimization. The Hessian elements are computed by displacing each atom in the model and computing a gradient vector, this builds a complete second derivative matrix. By default all atoms are displaced in this procedure. Calculate Raman intensities: When checked Raman intensities for the vibrational modes will be calculated.
Note: The Calculate Raman intensities option is only available for calculations on nonperiodic systems.
Dialogs in DMol3 | Page 125 Use coarse-grained parallelization: When checked the coarse-grained parallelization is used for the numerical displacement frequency calculation. Geometrical displacement calculations necessary for generating the system Hessian matrix are evenly split over all available computational nodes. Each displacement is then run in a serial mode and the final Hessian elements is gathered at the end of the calculation. This is the preferred method for larger systems with a lot of vibrational modes and a non- trivial number of computational nodes. When unchecked, the numerical displacements are calculated sequentially, each displacement run in a parallel DMol3 process. This might be advantageous for smaller systems with fewer normal modes or for machines with a limited number of computational nodes.
Note: Coarse-grained parallelization requests will be ignored by the DMol3 server if B3LYP functional is used, if Raman intensities are requested, or if the requested number of cores is incompatible with the number of required displacements. In these circumstances coarse-grained parallelization is either not implemented or inefficient. Calculate partial Hessian: When checked only the atoms belonging to the HessianAtoms set are used to generate the Hessian. When unchecked, the HessianAtoms set is not used for calculation of the Hessian and the Hessian is built from the displacement of all atoms. By default the Hessian is evaluated using a 2-point difference of analytic forces. Users can change this by modifying the keyword Vibration_Steps in the input file. See the DMol3 Job Files topic for information on how to modify the input file. More...: Opens the Partial Hessian dialog, which provides options for creating and selecting sets of atoms for use in Hessian calculations. Access methods
Menu Modules | DMol3 | Calculation | Properties | Frequency Toolbar | Calculation | Properties | Frequency
Partial Hessian dialog The Partial Hessian dialog allows you to specify and view atoms used in partial Hessian frequency calculations. Add selected atoms to HessianAtoms set: Creates a set of atoms called HessianAtoms using the currently selected atoms in the active 3D Atomistic document. If a set named HessianAtoms has already been defined for the active document, any of the selected atoms that are not already members of the set will be added to it. To calculate the Hessian for only the atoms in HessianAtoms set you must check the Calculate partial Hessian checkbox. Select atoms in HessianAtoms set: Selects the atoms in the HessianAtoms set. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Properties | Frequency | More... Toolbar | Calculation | Properties | Frequency | More...
Menu Modules | DFTB+ | Calculation | Properties | Frequency | More... Toolbar | Calculation | Properties | Frequency | More...
Page 126 | Materials Studio • DMol Guide Fukui function selection Choosing Fukui function on the Properties tab displays options for computing the Fukui index for chemical reactivity. Each type of Fukui function is returned as a set of volumetric data in a .grd file. f(+) Nucleophilic: When checked, indicates that the f+ Fukui function, which reflects susceptibility to nucleophilic attack, will be computed. f(-) Electrophilic: When checked, indicates that the f- Fukui function, which reflects susceptibility to electrophilic attack, will be computed. f(0) Radical: When checked, indicates that the f0 Fukui function, which reflects susceptibility to attack by radicals will be computed. This is simply the average of f+ and f-. Grid...: Provides access to the DMol3 Grid Parameters dialog, which allows you to set the resolution and extents of the grid used to calculate the volumetric properties of the orbitals.
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Access methods
Menu Modules | DMol3 | Calculation | Properties | Fukui function Toolbar | Calculation | Properties | Fukui function
Optics selection Choosing Optics on the Properties tab displays options for computing optical properties for the structure using time-dependent density functional theory (TD-DFT). Calculate: Specifies the number of lowest states to be included in the calculation of optical properties and the type of states. Options are: n Singlet n Triplet
Note: Optics calculations can only be performed on nonperiodic systems or 3D periodics with the Gamma k-point only.
Note: Oscillator strengths are available only for singlet state calculations. Use: Specifies the TD-DFT method to use for calculating the optical properties, options are: n ALDA (default) - calculates TD-DFT excitations using the ALDA kernel with exchange-correlation terms included. n ALDAx - calculates TD-DFT excitations using a modified ALDA kernel with the exchange term only. n RPA - no exchange-correlation response, only electrostatic response included. More...: Opens the DMol3 Optics Options dialog, which provides options for controlling the polarizability and frequency. Optimize geometry for: Specify the excited state whose geometry should be optimized. Default = 1 (that is, the first excited state). The optimized structure for the specified state will be saved in the
Dialogs in DMol3 | Page 127 n S is a singlet state n T is a triplet state n E is a spin unrestricted state n
Note: The excited state's geometry can only be optimized for nonperiodic systems. Calculate polarizability: When checked, indicates that linear polarizability will also be calculated. This sum-over-states calculation requires all available excitations to be computed and prevents selection of the number of lowest states to calculate.
Note: Polarizabilities are calculated by a sum-over-states expression. This calculation can take a very long time and requires significantly more memory than the default optics calculation.
Note: Polarizabilities calculations can only be performed on nonperiodic systems.
Access methods
Menu Modules | DMol3 | Calculation | Properties | Optics Toolbar | Calculation | Properties | Optics
DMol3 Optics Options dialog The DMol3 Optics Options dialog allows you to specify options for polarizability calculations. Results of these calculations can be found by inspecting the job's .outmol file. Calculate hyperpolarizabilities: When checked, indicates that hyperpolarizabilities will also be calculated. Calculate frequency dependent properties: When checked, indicates that processes which depend on frequency will also be calculated. When the Calculate hyperpolarizabilities checkbox is checked, the available processes include: n frequency dependent linear polarizability n second harmonic generation (SHG) n optical rectification (OR) n electro-optic Pockels effect (EOPE) n third harmonic generation (THG) n dc-induced second harmonic generation (dc-SHG) n intensity dependent refractive index (IDRI) n electro-optic Kerr effect (EOKE) When the Calculate hyperpolarizabilities checkbox is unchecked only the frequency dependent linear polarizability is calculated. Incident light: The wavelength of the incoming light to apply to the processes (in nm).
Note: The default value of 514.5 nm corresponds to the standard Ar laser. Other popular wavelengths for laser spectrometers include 632.8 nm (He-Ne), 785 nm (diode), and 1064 nm (Nd:YAG). Help: Displays the Help topic in a browser.
Page 128 | Materials Studio • DMol Guide Access methods
Menu Modules | DMol3 | Calculation | Properties | Optics | More... Toolbar | Calculation | Properties | Optics | More...
Orbitals selection Choosing Orbitals on the Properties tab displays options for computing molecular orbitals for volumetric rendering. HOMO: When checked, indicates that the highest occupied molecular orbital is selected for rendering. LUMO: When checked, indicates that the lowest unoccupied molecular orbital is selected for rendering. Grid...: Provides access to the DMol3 Grid Parameters dialog, which allows you to set the resolution and extents of the grid used to calculate the volumetric properties of the orbitals. Extra levels above/below the Fermi level: Specify additional orbitals above the LUMO and below the HOMO level to be computed. Entering a value in this text box means that the specified number of occupied and virtual orbitals will be computed in addition to HOMO/LUMO, if chosen. For example, entering a value of 5 when HOMO and LUMO checkboxes are checked, results in 5 occupied and 5 virtual orbitals being computed, in addition to the HOMO and LUMO (a total of 12 orbitals).
Tip: The default resolution of the grid is 0.2 Å. You can also modify this by editing the input files and adding the keyword Grid.
Access methods
Menu Modules | DMol3 | Calculation | Properties | Orbitals Toolbar | Calculation | Properties | Orbitals
Population analysis selection Choosing Population analysis on the Properties tab displays options for computing various sorts of atomic population analyses. Mulliken analysis: Select the type of Mulliken population analysis to be performed from the dropdown list. Available options are: n None - turns off Mulliken analysis n Atomic Charge - computes the total Mulliken charge on each atom n Orbital & Charge - computes the contribution to the atomic charge from each atomic orbital on each atom n Overlap Matrix - computes the overlap population in each pair of atomic orbitals on different atoms Whenever Mulliken bond orders are calculated, DMol3 will automatically compute Mayer bond orders as well.
Note: Bond orders can only be calculated for nonperiodic structures. Symmetry information should not be used when calculating bond orders, i.e., the Use symmetry checkbox on the Setup tab should be unchecked. Hirshfeld analysis: Select the degree of Hirshfeld analysis to be performed from the dropdown list. Available options are:
Dialogs in DMol3 | Page 129 n None - turns off Hirshfeld analysis n Charge n Dipole n Quadrupole ESP charges: When checked, indicates that atomic-centered charges that best reproduce the DFT Coulomb potential will be computed as part of the DMol3 run. Access methods
Menu Modules | DMol3 | Calculation | Properties | Population analysis Toolbar | Calculation | Properties | Population analysis
DMol3 Grid Parameters dialog The DMol3 Grid Parameters dialog allows you to set the resolution and extents of the grid used to calculate the volumetric properties of the orbitals. Grid resolution: Specifies the resolution of the grid. Available values are: n Coarse - 0.4 Å grid interval n Medium - 0.25 Å grid interval n Fine - 0.15 Å grid interval Grid interval: Alternatively, specifies a user-defined value for the grid spacing. Setting this parameter to a value other than one of those listed above will cause the Grid resolution to be set to Customized.
Tip: A smaller grid interval (i.e., finer resolution) produces a higher quality grid, but is more costly to compute and display. Border: Specifies the size of the border to impose about the molecular extents when creating the volumetric grid.
Note: The values set in this dialog will be used for the computation of all volumetric properties, regardless of where the dialog was accessed from. Help: Displays the Help topic in a browser.
Page 130 | Materials Studio • DMol Guide Access methods
Menu Modules | DMol3 | Calculation | Properties | Electron density | Grid... Modules | DMol3 | Calculation | Properties | Electrostatics | Grid... Modules | DMol3 | Calculation | Properties | Fukui | Grid... Modules | DMol3 | Calculation | Properties | Orbitals | Grid... Toolbar | Calculation | Properties | Electron density | Grid...
| Calculation | Properties | Electrostatics | Grid...
| Calculation | Properties | Fukui | Grid...
| Calculation | Properties | Orbitals | Grid...
Job Control tab DMol3 calculations run in the background on a server through the gateway. The Job Control tab allows you to select a server for the DMol3 calculation and to control some aspects of how the calculation will be performed.
Note: The options specified on the Job Control tab only apply to new jobs. They do not affect jobs that are already running. Gateway location: Select a server for the DMol3 calculation from the list of available server machines. You can add servers to the list using the Server Console. Queue: Specify the queue to which the job will be submitted. Select the desired queue from the dropdown list, which displays the available queues on the chosen gateway. See Working with queues for additional details. Job description: Specify the name to be used to identify the job. A default job description is automatically assigned. An alternative description can be chosen by unchecking the Automatic checkbox and entering the new name in the Job description text box. Automatic: When checked, indicates that a job description will be selected automatically. Default = checked. Run in parallel on: Indicates that the job will be run on the selected gateway using the specified number of computer cores. The text to the right of the Run in parallel on control indicates the maximum number of cores available on the selected gateway. Max. memory: Specify the runtime memory per core, in MB, available to DMol3. Default = 2048 MB. File usage: Specify where to store temporary files and how often to write restart information. Available options are: n Smart - Keep as much data in memory as possible, but write out restart information after each completed geometry step. Data that does not fit into the memory allowance specified above will still be written to disk. n Memory - Maximize memory use, write restart information only at the end of a job. Large arrays are temporarily paged to disk. If a job fails with this setting, restart files will not be created. n Disk - Keep all data on disk, including restart information.
Dialogs in DMol3 | Page 131 More...: Provides access to the DMol3 Job Control Options dialog, which allows you to set additional options associated with monitoring and controlling the results of a DMol3 job. Access methods
Menu Modules | DMol3 | Calculation | Job Control Toolbar | Calculation | Job Control
DMol3 Job Control Options dialog The DMol3 Job Control Options dialog allows you to set the options associated with monitoring and controlling the results of a DMol3 calculation on a gateway. Update structure: When checked, indicates that intermediate results will be used to update the displayed structure as the job progresses. Default = unchecked. Update graphs: When checked, indicates that intermediate results will be used to update the displayed graphs as the job progresses. Default = checked. Two graphs are created for a geometry optimization or transition state optimization: n total energy vs. optimization cycle n change of energy, maximum force, plus maximum displacement vs. optimization cycle. The forces and displacements reported in this graph are computed in Cartesian coordinates. For a transition state search using a synchronous transit method, the document contains multiple graphs. There will be a graph of energy vs. reaction coordinate for each linear or quadratic reaction pathway, as well as for each conjugate gradient minimization. Together, these graphs show how the estimate for the transition state is gradually refined. Any of these graphs may be used to animate the history of a geometry optimization or transition state search. See Displaying trajectory and chart data for more information. Update textual results: When checked, indicates that intermediate results will be used to update textual results files as the job progresses. Default = checked.
Tip: Intermediate updates are useful shortly after initiating a job to assess if it is progressing as expected. Update every: Specify the time interval, in seconds, between requests for intermediate updates.
Note: The rate at which new results appear is limited by the time it takes for the server to perform a single iteration step of the chosen task. This may be significantly longer than the chosen update interval. Retain server files: When checked, indicates that the folder on the server containing the job files will be retained after the job is complete. Default = unchecked. If this checkbox is left unchecked, the job files on the server will be deleted. Regardless of whether it is checked or unchecked, copies of the results files will always be retrieved from the server, placed in the associated project on the local machine, and displayed in the Project Explorer. Automatically view output: When checked, automatically opens the job's output files when the calculation is complete. Files opened may include a structure document and an output file. Default = checked.
Page 132 | Materials Studio • DMol Guide Notify on job completion: When checked, indicates that a dialog will be displayed when the job is complete. Default = checked.
Tip: If you run several short jobs in one session, you may find it useful to stop the automatic display of job completion notices and results files. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Job Control | More... Toolbar | Calculation | Job Control | More...
DMol3 Job Files dialog The DMol3 Job Files dialog allows you to save input files for a DMol3 calculation without running the job, or to run a job using an existing set of input files. This functionality is provided for users who need to run the DMol3 server program in standalone mode, or who wish to edit the DMol3 input files in order to gain access to features not supported by the DMol3 interface. Save Files: Saves the input files required to run the DMol3 job on the server but does not submit the job.
Note: The Save Files button is enabled only when the active document is a 3D model document. The input files are placed in a subfolder of the current Materials Studio project directory and the primary DMol3 input file is displayed in the Materials Visualizer. Run Files: Runs a DMol3 job using an existing set of input files.
Note: The Run Files button is enabled only when the current document is a DMol3 input file. The job is submitted using the settings specified on the DMol3 Job Control tab. The results files are placed in a subfolder of the current Materials Studio project directory. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Calculation | Files... Toolbar | Calculation | Files...
DMol3 Analysis dialog Use the Analysis tools to analyze the results of a DMol3 calculation. The DMol3 Analysis dialog can be accessed from the Modules toolbar and the Modules menu. To use any of the Analysis features, you must first perform a DMol3 calculation. When the results are returned, open the 3D structure file (.xsd) in the Project Explorer and double-click on Analysis. The analysis applies to the active document. The types of analysis that can be performed include:
Dialogs in DMol3 | Page 133 n display of band structure plots n display of density of states plots n display of current/voltage plots n calculate elastic constants n display of electron density plots, including the charge, spin, and deformation densities n animation of the geometry optimization history for a geometry minimization or a transition state search n visualization of Fermi surfaces n display of Fukui function plots for electropositive, electronegative, or radical reactivity n display of optical spectra n display of orbital eigenvalues and plotting of molecular orbitals in three dimensions n display of the computed atomic populations from Mulliken, Hirshfeld, or electrostatic potential analysis n display of electrostatic potential plots n display a study table containing rate coefficients n display of Raman spectra n display of solvation properties n display of thermodynamic properties n display of transmission plots n calculation of vibrational spectra and animation of normal modes of vibrations Help: Displays the Help topic for the currently selected analysis. Access methods
Menu Modules | DMol3 | Analysis Toolbar | Analysis
Band structure selection Select the Band structure option on the DMol3 Analysis dialog to display the Band structure dialog. These controls specify the DMol3 band structure calculation results file to be used and the type of band structure chart to be generated. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Energy units: Specify the energy units to be used for the dispersion graph. Available options are: n eV n Ha Scissors: Specify the scissors operator to be used in plotting the band structure. The scissors operator is only applied for insulating systems, which have a clear separation between valence band and conduction band states. It is ignored for metallic systems. Graph style: Specify the style to be used for the band structure graph. Available options are: n Points n Line
Page 134 | Materials Studio • DMol Guide Show DOS: When checked, indicates that a density of states from the specified results file will be displayed, together with the band structure graph. Full DOS: When selected, indicates that the total density of states will be displayed. Partial: When selected, indicates that the partial density of states (PDOS) will be displayed. The angular momenta to be included in the PDOS display can be controlled using the s, p, d, f, and Sum checkboxes.
Note: When the appropriate structure document is active and atoms are selected, the contribution to the density of states from the selected atoms will be plotted. Otherwise, the contribution from all atoms is considered. Display DOS: Specify which spin components should be plotted in the density of states graph. For a spin-polarized calculation, the supported options are: n Total - contributions from both spin-up and spin-down eigenstates are summed. n Alpha - contributions from spin-up eigenstates only. n Beta - contributions from spin-down eigenstates only. n Alpha and Beta - contributions from both spin-up and spin-down eigenstates are displayed in a butterfly plot. n Spin - difference between contributions from spin-up and spin-down eigenstates is displayed. n Total and Spin When a non-spin-polarized DMol3 calculation is analyzed, only the Total option is available. Function: Specify whether to plot the untreated DOS or the integrated density of states (the number of states). More...: Provides access to the DMol3 DOS Analysis Options dialog, which allows the parameters controlling the density of states integration method to be specified.
Note: The Full, Partial, DOS display, and More... options are enabled only if the Show DOS checkbox is checked. View: Displays the band structure using the options specified. Access methods
Menu Modules | DMol3 | Analysis | Band structure Toolbar | Analysis | Band structure
Current/Voltage selection The following options are available when Current/Voltage is selected from the list of properties. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. View: Displays the current/voltage chart.
Dialogs in DMol3 | Page 135 Access methods
Menu Modules | DMol3 | Analysis | Current/Voltage Toolbar | Analysis | Current/Voltage
Density of states selection Select the Density of states option on the DMol3 Analysis dialog to display the Density of states dialog. These controls specify the DMol3 density of states calculation results file to be used and the type of density of states chart to be generated. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Energy units: Specify the energy units to be used for the density of states graph. Available options are: n eV n Ha Full DOS: When selected, indicates that the total density of states will be displayed. Partial: When selected, indicates that the partial density of states (PDOS) will be displayed. The angular momenta to be included in the PDOS display can be controlled using the s, p, d, f, and Sum checkboxes.
Note: When the appropriate structure document is active and atoms are selected, the contribution to the density of states from the selected atoms will be plotted. Otherwise, the contribution from all atoms is considered. Display DOS: Specify which spin components should be plotted in the density of states graph. For a spin-polarized calculation, the supported options are: n Total - contributions from both spin-up and spin-down eigenstates are summed. n Alpha - contributions from spin-up eigenstates only. n Beta - contributions from spin-down eigenstates only. n Alpha and Beta - contributions from both spin-up and spin-down eigenstates are displayed in a butterfly plot. n Spin - difference between contributions from spin-up and spin-down eigenstates is displayed. n Total and Spin When a non-spin-polarized DMol3 calculation is analyzed, only the Total option is available. Function: Specify whether to plot the untreated DOS or the integrated density of states (the number of states). Scissors: Specify the scissors operator to be used in plotting the density of states. The scissors operator is only applied for insulating systems, which have a clear separation between valence band and conduction band states. It is ignored for metallic systems. More...: Provides access to the DMol3 DOS Analysis Options dialog, which allows the parameters controlling the density of states integration method to be specified. View: Displays the density of states using the options specified.
Page 136 | Materials Studio • DMol Guide Access methods
Menu Modules | DMol3 | Analysis | Density of states Toolbar | Analysis | Density of states
DMol3 DOS Analysis Options dialog The DMol3 DOS Analysis Options dialog allows you to specify the parameters controlling the density of states integration method. Integration method: Select the method to be used for integrating the density of states results from the dropdown list. Supported methods are: n Smearing - Gaussian broadening is applied to the eigenvalues obtained from the DMol3 calculation. n Interpolation - eigenvalues (and partial weights for a partial density of states) from the DMol3 calculation are interpolated onto a finer k-point grid. The Interpolation method provides an improved representation of the density of states. However, it can only be used when eigenvalues are available on a Monkhorst-Pack grid with 3 or more points in each direction. The k-point set for density of states calculations can be specified on the Density of states - Properties tab on the DMol3 Calculation dialog. If the Interpolation method cannot be used for the selected results, it will be absent from the dropdown list.
Note: The Interpolation integration method is only available for calculations on periodic systems. Smearing width: Specify the Gaussian broadening to be used.
Note: This option is enabled only if the Smearing integration method is selected. Accuracy level: Specify the quality of the interpolation to be used. Available options are: n Coarse - Interpolates onto a k-point grid of about 50 × 50 × 50. n Medium - Interpolates onto a k-point grid of about 100 × 100 × 100. n Fine - Interpolates onto a k-point grid of about 200 × 200 × 200. Instrument broadening: Specify an additional broadening to be applied to the interpolated density of states.
Note: The Accuracy level and Instrument broadening options are enabled only if the Interpolation integration method is selected. Number of points per: Specify number of points per 1 eV or per 1 Ha energy range. Use high settings to generate charts that remain smooth after a zoom-in operation. OK: Updates the settings with any changes and closes the dialog. Cancel: Closes the dialog without updating any settings. Help: Displays the Help topic in a browser.
Dialogs in DMol3 | Page 137 Access methods
Menu Modules | DMol3 | Analysis | Density of states | More... Modules | DMol3 | Analysis | Band structure | More... Toolbar | Analysis | Density of states | More...
| Analysis | Band structure | More...
Elastic constants selection Select the Elastic constants option on the DMol3 Analysis dialog to display the Elastic constants dialog. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Calculate: Calculates the tensors of the elastic constants and the compliances, the bulk modulus, compressibility, Young modulus, Poisson ratio, and Lame constants for the selected run and writes the results to a new text document, seedname Elastic Constants.txt, in the results folder. Access methods
Menu Modules | DMol3 | Analysis | Elastic constants Toolbar | Analysis | Elastic constants
Electron density selection Select the Electron density option on the DMol3 Analysis dialog to display the Electron density dialog. These controls specify the DMol3 density calculation results file to be used and the type of density field to be calculated. The calculation is performed on the active structure file (.xsd file). Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Density field: Controls which type of density will be plotted. Select from the available density types in the dropdown list. Possible options include: n charge density n spin density n deformation density Only choices that were computed as part of a DMol3 job will appear. If you do not see a particular choice, it is because it has not been computed. Perform another calculation, specifying the desired choice to obtain the density. See the Properties tab and Electron density selection help topics for information on setting up such a calculation. View isosurface on import: Controls how the volumetric data is displayed. If this item is checked, a 3D isosurface is created when the Import button is pressed. The default value of the surface is: n charge density: 0.2 electrons/Å3 for crystals, and 0.017 electrons/Å3 for molecules n spin density: 10% of the maximum n deformation density: 10% of the maximum If this box is not checked, the volumetric data are imported as a 3D field.
Page 138 | Materials Studio • DMol Guide Once you have imported the data, refine the display using the volume visualization controls. Import: Loads the desired volumetric density data into the active document. Access methods
Menu Modules | DMol3 | Analysis | Electron density Toolbar | Analysis | Electron density
Energy evolution selection Use the Energy evolution option on the DMol3 Analysis dialog to display the optimization history of a DMol3 geometry optimization. The structure file (.xsd file) used in the geometry optimization must be open in the Materials Visualizer to perform the energy evolution procedure. For calculations using the COSMO solvent model, a COSMO Sigma Profile chart can be generated. Two charts are created during a geometry optimization or transition state optimization: n total energy vs. optimization cycle, and n change of energy, maximum force, plus maximum displacement vs. optimization cycle. The forces and displacements reported in these charts are in Cartesian coordinates. For a transition state search using a synchronous transit method, the chart document will contain multiple charts. There will be a chart of energy vs. reaction coordinate for each linear or quadratic reaction pathway, as well as for each conjugate gradient minimization. Together, these charts show how the estimate for the transition state is gradually refined. These charts are the same as would be generated by selecting Update graphs in the DMol3 Job Control Options dialog. Charts generated using Energy evolution can be generated whether or not you chose Update graphs in the original calculation.
Note: Each time you select Update graphs the existing chart documents are rewritten, and any changes or annotations you have made to the charts will be lost. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. View: Generates the chart documents as described above. Access methods
Menu Modules | DMol3 | Analysis | Energy evolution Toolbar | Analysis | Energy evolution
Fermi surface selection The following options are available when Fermi surface is selected from the list of properties. Results file: Select the DMol3 results file from which the optical properties information will be taken. When more than one set of results is available, use the button to browse the current directory and appropriate subdirectories for results files. Filter: Choose how to filter the available Fermi surfaces, options are: n All - all Fermi surfaces are available.
Dialogs in DMol3 | Page 139 Show only bands crossing Fermi level: When checked only the bands which traverse the Fermi level will be listed in the table below. n Band - the index of the band in this row n Spin - the spin for this band n From - lowest value of the energy for the band (in eV) n To - highest value of the energy for the band (in eV) Import: Imports the selected Fermi surface from the DMol3 results file into the current structure document.
Tip: In order to generate Fermi surfaces the calculation must have requested Density of states properties.
Access methods
Menu Modules | DMol3 | Analysis | Fermi surface Toolbar | Analysis | Fermi surface
Fukui function selection Select the Fukui function option on the DMol3 Analysis dialog to display the Fukui function dialog. These controls specify the Fukui function to be plotted. The plot is based on the specified .outmol results file and the active .xsd structure file. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Fukui field: Controls which type of Fukui function will be plotted. Select from the available Fukui functions in the dropdown list. Possible options include: n Electrophilic, f(-): the reactivity with respect to electrophilic attack n Nucleophilic, f(+): the reactivity with respect to nucleophilic attack n Radical, f(0): the reactivity with respect to radical attack In each case, greater values indicate a greater susceptibility to attack. Only choices that were computed as part of a DMol3 job will appear. If you do not see a particular choice, it is because it has not been computed. Perform another calculation, specifying the desired choice to obtain the function. See the Properties tab and Fukui function selection help topics for information on setting up such a calculation. View isosurface on import: Controls how the volumetric data is displayed. If this item is checked, a 3D isosurface is created when the Import button is pressed. The default value of the surface is 10% of the maximum for all types of Fukui functions. If this box is not checked, the volumetric data are imported as a 3D field. Once you have imported the data, refine the display by using the volume visualization controls. Assign Fukui charges: Imports the selected charges into the active structure document and assigns partial charges to each atom for the function selected as the Fukui field. Select the type of charges that you wish to import from the dropdown list. Available options are: n Mulliken n Hirshfeld
Page 140 | Materials Studio • DMol Guide Import: Loads the desired volumetric density data into the active document. Access methods
Menu Modules | DMol3 | Analysis | Fukui function Toolbar | Analysis | Fukui function
Optics selection Select the Optics option on the DMol3 Analysis dialog to display the Optics dialog. This provides controls for generating spectra, based on the specified .outmol results file and the active .xsd structure file. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. View spectrum: Generates a chart document containing the predicted optical spectrum for the structure being studied. The spectrum takes the form of a plot of oscillator strength in arbitrary units against wavelength expressed in nm. View grid: Generates a study table document containing a list of wavelengths (in nm) and peak oscillator strengths (in arbitrary units) for the allowed excitations used to generate the optical spectrum.
Note: Oscillator strengths are available only for singlet state calculations.
Note: Excited states calculated with unrestricted reference are a mixture of singlets and triplets. Comparing spin-restricted and spin-unrestricted results requires the results of spin-restricted calculations for singlet and triplet states. Units: Specify the frequency units used for the display of optical properties, options are: n eV n cm-1 n nm (default) More...: Provides access to the DMol3 Optics Analysis Options dialog. Access methods
Menu Modules | DMol3 | Analysis | Optics Toolbar | Analysis | Optics
DMol3 Optics Analysis Options dialog The DMol3 Optics Analysis Options dialog allows you to specify the parameters controlling the optics calculation method. Broadening method: Select the method to be used for calculating the optical spectrum from the dropdown list. Supported methods are: n Gaussian - Gaussian broadening is applied to the eigenvalues obtained from the DMol3 calculation. n Lorentzian n None Smearing width: Specify the Gaussian broadening to be used.
Dialogs in DMol3 | Page 141 Note: This option is enabled only if the Gaussian integration method is selected. FWHM parameter: Specify the full width at half maximum, in nm, for the Lorentzian smoothing function. Range = 0.1 - 100 nm. Default = 20 nm.
Note: This option is enabled only if the Lorentzian integration method is selected. Reverse wavelength axis: When checked, indicates that the values on the X axis will decrease from left to right. Reverse intensity axis: When checked, indicates that the values on the Y axis will decrease from bottom to top. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Analysis | Optics | More... | Analysis | Optics | More...
Orbitals selection Select the Orbitals option on the DMol3 Analysis dialog to display the Orbitals dialog. This dialog displays a list of orbital eigenvalues for a system and provides controls for generating 3D volumetric images of the orbitals. The calculation is based on the specified .outmol results file and the active .xsd structure file.
Note: The Orbitals analysis applies only to molecular systems and to periodic structures that use the Γ-point. Calculations using multiple k-points cannot be analyzed in this way. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Filter: Controls which orbitals are displayed in the table. Options include: n All: Displays eigenvalues for all the orbitals that were printed in the DMol3 output file. This includes all of the occupied orbitals and the first ten virtual orbitals. n Available: Displays only the eigenvalues associated with orbitals that are available for volumetric rendering. Only orbitals that were computed as part of a DMol3 job will appear. If the list of available orbitals is empty, perform another calculation, specifying the desired orbitals on the Properties tab. n Spin up: Displays only eigenvalues from alpha-spin (spin up) orbitals. If the calculation is closed-shell, this filter displays all orbitals. n Spin down: Displays only eigenvalues from beta-spin (spin down) orbitals. If the calculation is closed- shell, this filter displays no orbitals. The table displays molecular orbital eigenvalues along with information about them. The column headings provide the following information:
Page 142 | Materials Studio • DMol Guide n Field: If Yes, the orbital has volumetric data associated with it. These are the orbitals that can be displayed. n N: Indicates the orbital number starting from 1 for the lowest energy orbital. n s: Indicates the spin of the orbital. For spin-restricted calculations, all orbitals are labeled +. For spin- unrestricted calculations, alpha-spin orbitals are labeled + and beta-spin orbitals are labeled -. n Eigenvalue: Indicates the eigenvalue of each orbital in Hartree. n Type: Indicates the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Only orbitals whose data were computed as part of a DMol3 job will be available for rendering. If you do not see a Yes in the Field of a particular orbital, it is because it has not been computed. Perform another calculation, specifying the desired orbital. See the Properties tab and Orbitals selection help topics for information on setting up such a calculation. View isosurface on import: Controls how the volumetric data is displayed. If this item is checked, a 3D isosurface is created when the Import button is pressed. The default is two isosurfaces at values ±0.03. If this box is not checked, the volumetric data are imported as a 3D field. Once you have imported the data, refine the display using the volume visualization controls. Import: Loads the desired molecular orbital data into the active document for volumetric display. Access methods
Menu Modules | DMol3 | Analysis | Orbitals Toolbar | Analysis | Orbitals
Population analysis selection Select the Population analysis option on the DMol3 Analysis dialog to display the Population analysis dialog. These controls import atomic charges and bond orders and assign them to the active structure file (.xsd). Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Assign charges to structure: Imports the selected charges into the active structure document and assigns partial charges to each atom. Select the type of charges that you wish to import from the dropdown list. Available options are: n Mulliken n Hirshfeld n ESP Assign spins to structure: Imports the selected spins into the active structure document and assigns partial spins to each atom. Select the type of spins that you wish to import from the dropdown list. Available options are: n Mulliken n Hirshfeld Assign bond orders to structure: Imports the selected bond orders into the active structure document and assigns them to each bond. Select the type of bond orders that you wish to import from the dropdown list. Available options are:
Dialogs in DMol3 | Page 143 n Mayer n Mulliken
Note: The import options above are available only when the appropriate types of charges, spins, and bond orders have been generated as part of the DMol3 calculation.
Tip: You can see the charges, spins, and bond orders in the active structure document by labeling the atoms and bonds according to their charge, spin, or order.
Access methods
Menu Modules | DMol3 | Analysis | Population analysis Toolbar | Analysis | Population analysis
Potentials selection Select the Potentials option on the DMol3 Analysis dialog to display the Potentials dialog. These controls specify the type of potential field to be generated. The volumetric image calculation is based on the specified .outmol results file and the active .xsd structure file. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Potential field: Controls which type of potential will be plotted. The only option available is Electrostatic potential (Coulomb). Only choices that were computed as part of a DMol3 job will appear. If you do not see a particular choice, it is because it has not been computed. Perform another calculation, specifying the desired choice to obtain the function. See the Properties tab and Electrostatics selection help topics for information on setting up such a calculation. View isosurface on import: Controls how the volumetric data is displayed. If this item is checked, a 3D isosurface is created when the Import button is pressed. The default value of the surface is ±10 kcal/mol (0.016 au). If this box is not checked, the volumetric data are imported as a 3D field. Once you have imported the data, refine the display using the volume visualization controls. Import: Loads the desired molecular orbital data into the active document for volumetric display. If the structure is a slab with a region of vacuum and the Work function checkbox was checked, a Chart document, named
Menu Modules | DMol3 | Analysis | Potentials Toolbar | Analysis | Potentials
Raman spectrum selection The following options are available when Raman spectrum is selected from the list of properties.
Page 144 | Materials Studio • DMol Guide Results file: Select the DMol3 results file from which the Hessian will be taken. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Function: Specify whether to calculate the Intensity or the Activity of the vibrational mode. Temperature: If the intensity of the vibrational mode is being calculated set the temperature in Kelvin. Incident light: If the intensity of the vibrational mode is being calculated specify the wavelength of the incident light in nm. The default value of 514.5 nm corresponds to a standard Ar laser. Other popular wavelengths for laser Raman spectrometers include 632.8 nm (He-Ne), 785 nm (diode), and 1064 nm (Nd:YAG). Smearing: Specify the type of broadening (Gaussian or Lorentzian) and width to be used. Default Lorentzian broadening with width = 20.0 cm-1. Units: Specify the units for the X axis of the spectrum, options are: n meV n THz n cm-1 Reverse wavenumber axis: When checked, indicates that the values on the X axis will decrease from right to left. Reverse intensity axis: When checked, indicates that the values on the Y axis will decrease from bottom to top. Once a Hessian has been imported, vibrational mode frequencies and, if ATP tensors were calculated, absorption intensities can be displayed in the form of a list of values or graphically as a vibrational spectrum using the Vibrational Analysis tool. View: Displays the selected Raman spectrum. Access methods
Menu Modules | DMol3 | Analysis | Raman spectrum Toolbar | Analysis | Raman spectrum Reaction kinetics selection Select the Reaction kinetics option on the DMol3 Analysis dialog to display the Reaction kinetics dialog. Results file: Indicates the collection document containing the reaction ingredients. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer.
Note: Reaction kinetics calculation can be performed only if the collection document contains well- defined reaction ingredients: the reactant(s), the product(s), and the transition state. All the structures must have Hessians and total energy calculated. Reactant(s) and product(s) systems must be in the ground state - that is all the eigenfrequencies must be real and non-negative.The transition state must be a valid saddle point with one and only one imaginary frequency for which eigenvectors represent the reaction path. From: To: Specify the temperature range for the output of the calculated rate coefficient. Apply tunneling correction: When checked, indicates that the reaction rate coefficient will be calculated taking into account the tunneling correction.
Dialogs in DMol3 | Page 145 Threshold correction: Specify the value to be added to the DFT reaction threshold. This correction compensates for the underestimation of reaction barriers at the DFT level of theory. Vibrational frequencies scaling: Specify the value of the scaling coefficient to be applied to calculated vibrational frequencies before evaluation of vibrational partition functions. Calculate: Calculate and display a study table containing rate coefficients for the forward and reverse reactions. Access methods
Menu Modules | DMol3 | Analysis | Reaction kinetics Toolbar | Analysis | Reaction kinetics
Solvation properties selection Select the Solvation properties option on the DMol3 Analysis dialog to display the options for displaying COSMO properties. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Import: Controls which type of solvation field will be displayed and loads the desired volumetric density data into the active document. Available options are: n COSMO surface (default) - displays the surface created from COSMO charges. n COSMO point charges - displays points corresponding to COSMO charges. View sigma chart on import: Controls how the volumetric data is displayed. If this item is checked, a 3D isosurface is created when the Import button is clicked. Once you have imported the data, refine the display using the volume visualization controls.
Note: Both the COSMO surface and points can have the COSMO potential mapped onto them. They can be displayed using the volume visualization controls.
Access methods
Menu Modules | DMol3 | Analysis | Solvation properties Toolbar | Analysis | Solvation properties
Choose COSMO File dialog The Choose COSMO File dialog allows you to import COSMO solvent files from the current project or from local and network locations. Select a solvent file you would like to import from the project document chooser. The selected file will be displayed in the Solvent 1 or Solvent 2 dropdown list for the Solvation properties selection of the DMol3 Analysis dialog.
Note: The document chooser will only show COSMO files (.cosmo). Import...: Provides access to a file browser which enables you to navigate to and select COSMO solvent files from local or network locations. The selected file will be imported into the current project and
Page 146 | Materials Studio • DMol Guide displayed in the Solvent 1 or Solvent 2 dropdown list for the Solvation properties selection on the DMol3 Analysis dialog. Help: Displays the Help topic in a browser. Access methods
Menu Modules | DMol3 | Analysis | Solvation properties| Browse... Toolbar | Analysis | Solvation properties | Browse...
Structure selection Pressing the Update button on the Structure dialog restores the view of the active 3D model document based on the data in the last-saved version of the file. If you have made modifications to a structure on screen, use the Update button to restore the geometry to that saved in the file. If you have manually edited and saved the output file (.outmol), pressing the Update button causes Materials Studio to reload the structure, which you can then use for analysis.
Note: Every DMol3 calculation generates a structure containing the final geometry. For most types of calculation the final geometry will be different from the initial geometry. If an energy calculation is performed the final geometry is the same as the initial geometry, unless the structure is snapped to symmetry, in which case the final geometry will be only slightly different from the initial geometry. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. Update: Updates the structure of the active document with the geometry contained in the .outmol file. The Update button also reimports the Hessian into the model, if one exists. Access methods
Menu Modules | DMol3 | Analysis | Structure Toolbar | Analysis | Structure
Thermodynamic properties selection Whenever a DMol3 calculation includes a vibrational analysis, you can compute and display thermodynamic properties as a function of temperature. These include the enthalpy, entropy, free energy, and heat capacity. The method of computation is described in Thermodynamic calculations. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. View: Generates and displays a chart of the enthalpy, entropy, free energy, and heat capacity as a function of temperature. Access methods
Menu Modules | DMol3 | Analysis | Thermodynamic properties Toolbar | Analysis | Thermodynamic properties
Dialogs in DMol3 | Page 147 Transmission selection The following options are available when Transmission is selected from the list of properties. Results file: Indicates the DMol3 output file associated with this calculation. This field displays the name of the active document. You can change the active document by clicking on the desired document window or by double-clicking on the document name in the Project Explorer. View: Displays the transmission function. Access methods
Menu Modules | DMol3 | Analysis | Transmission Toolbar | Analysis | Transmission
Page 148 | Materials Studio • DMol Guide DMol3 keywords This section documents all keywords that are recognized by DMol3, including many that are not accessible from the DMol3 setup dialog. Commands are listed in alphabetical order on the Contents tab.
Tip: For information on DMol3 keywords, please refer to the Materials Studio Online Help.
The .input file The .input file is a simplified command input file that consists of keywords followed by values (real, integer, or character). These keywords and their values specify flags for the calculation, such as the type of basis set or the maximum number of self-consistent iterations to be employed. Using the .input file to run DMol3 in standalone mode is outlined in Running DMol3 in standalone mode. Format for documenting DMol3 standalone commands The keyword topics provide detailed descriptions of each of the commands available in the standalone version. For each command, documentation is divided into subsections. Conventions used in documenting the commands are described below, along with a short description of the intent of each subsection. The Syntax subsection begins with the command syntax presented in as generic a form as possible. Several type style conventions are used to distinguish different kinds of words. For example: command_keyword [value_keyword, ..., value_number, ...] Words (or letters) in bold and not italicized indicate the names of keywords that must be typed as shown.
Note: Keywords must be typed as shown, but are case-insensitive. They may be typed in lower-, upper-, or mixed case.
Note: Keyword options must be separated by spaces. Tab characters are not supported. A hash mark (#) at the beginning of a line indicates a comment line. It can also be used to temporarily comment-out a command. Words in bold italics indicate options that must be replaced with appropriate text, as indicated in the table of allowed values that follows the syntax line for each command. The values appropriate to each keyword are also listed and may be (as appropriate) numbers or enumerated constants: n Numbers can be represented in integer, floating-point, or exponential form. DMol3 converts the number to the appropriate form, depending on the context. n Mutually exclusive options are represented by enumerated constants identified by names The names of enumerated constants must not be enclosed in quotation marks. Optional item(s) are enclosed in round brackets( ), and, if there is more than one, the items are separated by commas. Ellipses (...) indicate that a kind of item may be repeated. The brackets, commas, and ellipses themselves are used for documentation only and should not be included in the real command.
DMol3 keywords | Page 149 DMol3 References A list of published papers describing calculations using DMol3 can be found on the Materials Studio website: http://accelrys.com/products/materials-studio/publication-references/dmol3-references/. Ackland, G. J. "Embrittlement and the Bistable Crystal Structure of Zirconium Hydride", Phys. Rev. Lett., 80, 2233-2236 (1998). Allis, D. G.; Prokhorova, D. A., Korter, T. M. J. Phys. Chem. A, 110, 1951 (2006). Almlöf, J.; Faegri., K, Jr.; Korsell, K. J. Comput. Chem., 3, 385 (1982). Andzelm, J.; Kölmel, Ch.; Klamt, A. "Incorporation of solvent effects into the density functional calculations of molecular energies and geometries", J. Chem. Phys., 103, 9312-9320 (1995). Andzelm, J.; Wimmer, E.; Salahub, D. R. "Spin density functional approach to the chemistry of transition metal clusters: Gaussian-type orbital implementation", in The Challenge of d- and f-Electrons: Theory and Computation, Salahub, D. R.; Zerner, M. C., Eds., ACS Symp. Ser., ser. 394 (1989). Auckenthaler, T.; Blum, V.; Bungartz, H.-J.; Huckle, T.; Johanni, R.; Krämer, L.; Lang, B.; Lederer, H.; Willems, P. R.; "Parallel solution of partial symmetrix eigenvalue problems from electronic structure calculations", Parallel Computing, 37, 783-794 (2011). Baerends, E. J.; Ellis, D. E.; Ros, P. Chem. Phys., 2, 41 (1973). Bagno, A.; Scorrano, G. J. Phys. Chem., 100, 1545 (1996). Bakalarski, G.; Grochowski, P.; Kwiatkowski, J. S.; Lesyng, B.; Leszczynski, J. "Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory", Chem. Phys., 204, 301- 311 (1996). Baker, J. "An algorithm for the location of transition states", J. Comput. Chem., 7, 385 (1986). Baker, J. "Geometry optimization in Cartesian coordinates: Constrained optimization", J. Comput. Chem., 13, 240 (1992). Baker, J. "Techniques for geometry optimization: A comparison of Cartesian and natural internal coordinates", J. Comput. Chem., 14, 1085 (1993). Baker, J.; Bergeron, D. "Constrained optimization in Cartesian coordinates", J. Comput. Chem., 14, 1339 (1993). Baker, J.; Hehre, W. J. "Geometry optimization in Cartesian coordinates: The end of the Z-matrix?", J. Comput. Chem., 12, 606 (1991). Banerjee, A.; Adams, N.; Simons, J.; Shepard, R. "Search for stationary points on surfaces", J. Phys. Chem., 89, 52 (1985). Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. "A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model", J. Phys. Chem., 97, 10269- 10280 (1993). Becke, A. D. J. Chem. Phys., 88, 2547 (1988). Becke, A. D. J. Chem. Phys., 84, 4524 (1986). Becke, A. D. "Density-functional thermochemistry. III. The role of exact exchange", J. Chem. Phys., 98, 5648-5652 (1993). Ben-Naim, A.; Marcus, Y. "Solvation thermodynamics of nonionic solutes", J. Chem. Phys., 81, 2016 (1984). Bengtsson, L. Phys. Rev. B, 59, 12301 (1999). Bergner, A.; Dolg, M.; Kuechle, W.; Stoll, H.; Preuss, H. Mol. Phys., 80, 1431 (1993).
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