CSC Spring School 2014 Quantum Chemistry Workshop Basics - Orca & Gabedit - Michael Patzschke University of Helsinki The Codes ● Orca – general purpose QC code – Free (download from http://cec.mpg.de/forum/) – Developed by F.Neese et al. in C++ – Precompiled binaries (no sources) ● Gabedit – Free (download from https://sites.google.com/site/allouchear/Home/gabedit/download) – Developed by A.-R. Allouche – Sources and Binaries available ● Both codes available for Mac, Linux & Windows – Good combination for research & teaching Learning Outcome ● Draw and import molecular structures ● Pre-optimization ● Creating input files using the GUI ● Writing simple input files ● Comparing QC methods (quality and timing) ● Running constraint optimizations ● Visualizing results – More on Friday using VMD Gabedit ● Assuming you have gabedit in your $PATH ● Open a terminal mkdir qc_lab cd qc_lab gabedit ● Have a look around ● Open the structur editor Editing Structures ● Press the pen tool to add atoms ● Press the periodic-table button to change the atom (C is standard) ● Press the button below that to toggle adding hydrogens ● Pre-optimizing self-drawn structures – Important for speedup of real calculation – Avoid for transition metals, lanthanides & actinides – Two methods available: MM or semiempirical calculations ● Press “M” button or right-click in drawing window – Choose “Molecular Mechanics” “Optimization” Editing Structures – Further Points ● Fragments can be used to draw structures ● Parts of the molecule can be selected ● Atoms and parts of the molecule can be removed ● And moved ● Structural parameters can be measured and changed ● Measurements can be shown or removed ● For Semiempirical methods: – Interface to Mopac, Orca & Firefly Drawing Formaldehyde ● Please try to draw formaldehyde – “Menu-Edit-Delete Molecule” – Add Carbon – Choose Oxygen from periodic table – Replace one hydrogen – Click on the bond to make double bond – Pre optimize using MM ● The result should look like this ● Close the drawing window (“Menu-Close”) (saving possible – not necessary here) Setting up an Orca calculation ● Gabedit generates input for different QC codes ● Choose Orca from the top menu ● The pop-up menu lets you set up the calculation ● Change “Job Type” to “Equilibrium Structure Search” ● Change “Type of method” to “Meta-GGA and hybrid meta GGA's” ● Change “Method” to “TPSS” ● Change “Type” to “def2 Ahlrichs basis sets” Setting up an Orca calculation ● “Basis” will change, leave that choice ● Press “Ok” Orca input files ● Inspect the generated input file # Lines are comments ! Lines contain keywords % Lines start key blocks end lines end key blocks * starts and ends the geometry block ● Comments can be inserted like this: ! Opt # this will be ignored # TPSS ● The “output” block is added by gabedit for visualisation, but not necessary ● The “geom” block is wrong, remove it Running Orca ● Input files can be saved (“File” menu) ● QC codes can be run by Gabedit – Set up run commands in “Settings”-“Preferences” on the “Commands” tab – Press cogwheels to start a job – Choose “Orca” – Press “Ok” – Click on “NoName.out” tab to see the output Interlude ● Congratulations, you have hopefully just run your Orca calculation ● A few considerations: – Gabedit is great for drawing simple structures – Good to remember basic input file structure – Excellent for visualizing results – The input file can be changed in gabedit – A simple editor might be easier to use ... ● We will visualize the results ● Then an editor will be used to set up some more advanced calculations Looking at results ● During a run you can – Look at the output file – Update it – Look at geometry convergence – Visualize MO's & Densities from the first step of the calculation – Get data from remote calculations ● After the calculation has finished, press the visualize button Visualizing Orbitals ● In the visualization window click “M” or right-click ● Choose “Orbitals” from the menu ● Choose “Orca output file” ● Read the “NoName.out” file ● An MO selection should appear – Select an orbital – The right part shows its participating AO's – Change cut-off value here – Click “Ok” Visualising Orbitals ● Orbitals are calculated in a cube – Select position here – Select size here – Select quality here – Standard choices are ok – Press “Ok” ● After the calculation is finished you can – Change the iso-value – 0.1 should be a good choice – Get a proposition for a certain size – Press “Ok” Other Things to Visualize ● Take a few moments to look around the menu (“M” or right-click”) ● Geometry optimizations can be visualized from the .trj files ● Choose “Animation” and load the .trj file ● Press “Play” ● A movie can be made for presentation purposes Orca Input Help ● Have the orca manual ready (532 pages including theory...) ● Have a look at “https://sites.google.com/site/orcainputlibrary/home” – a very good input library ● Under “http://cec.mpg.de/forum/” you can join the forum – Very active, fast help – Please read the manual and forum first! More Advanced Calculations ● Close gabedit (Press “File”-“Exit” from the main window) ● Open your input file using your favourite editor ● Edit it to look like this: ● Change the functional – For a list see next page ● Change the basis set – For a list see further down ● Save the input file under a new name ● Start orca by issuing at the prompt: “orca filename.inp > filename.out &” Orca List of DFT functionals ● Some functionals: ● Double hybrids are available (MP2 calculation will be performed!) ● DFT tries to use the RI approach automatically (NORI to witch of) ● Dispersion correction with keywords vdw10 or vdw10bj Basis Sets in Orca ● Many different basis sets available some examples: ● Ahlrich's good for DFT ● Dunning's good for CC ● Basis set can be changed for an element: %basis newgto Element "def2-TZVPP" # Specifying the basis set on "Element" end ● Or for a specific atom in the geometry section: H 0.0 0.0 1.0 newgto "def2-TZVP" end ● To try MP2 use the following line: !Opt RI-MP2 def2-TZVPP def2-TZVPP/J def2-TZVPP/C TightSCF RIJCOSX ● For test purposes here you might want to replace TZVPP by SVP You task ● Make a small table for the C-O bond length of formaldehyde and computational timings using two or three different methods and two or three different basis sets ● Run calculations, fill in the table and compare with experimental data SVP TZVPP QZVPP Exp. r(CO) = r(CO) = r(CO) = BP86 t= t= t= r(CO) = r(CO) = r(CO) = TPSS t= t= t= r(CO) = r(CO) = r(CO) = r(CO) = PBE0 t= t= t= 120,5 pm r(CO) = r(CO) = r(CO) = HF t= t= t= r(CO) = r(CO) = r(CO) = MP2 t= t= t= Remarks on task ● The table is a suggestion only ● To run HF simply do: ! Opt def2-SVP ● MP2 TZVPP took 2 min on my laptop, ● MP2 QZVPP could take too long Constraints ● Useful for optimisations: ● Freeze parts of the molecule during optimisation: ● Wildcards to freeze all bonds/angles/torsions to certain atoms ● Giving no value takes that value from the geometry section ● Just optimize hydrogens (good for crystal structures): Hydrogen Optimisation - Example ● Simple example: Constrained Scans - Example ● Scan energy along bond expansion, optimise all steps: ● Took 2 min on my laptop ● File filename.allxyz contains optimized geometries for all steps ● File filename.relaxscanact.dat contains energy data (visualize with e.g. gnuplot) Energy Extrapolation ● We would like to know energies at the basis set limit – Computationally not feasible – Extrapolation procedures exist for e.g. Dunning's and ANO basis sets – Orca uses for HF: – And for the correlation part: – Look at a simple example: ! RHF MP2 CCSD(T) Extrapolate(2/3,cc) TightSCF Conv Bohrs * int 0 1 O 0 0 0 0 0 0 H 1 0 0 1.81975 0 0 H 1 2 0 1.81975 105.237 0 * Visualising Without Gabedit ● Orca can produce molden input files ● After the calculation is finished, write at the prompt: orca_2mkl basename -molden ● Orca has an “interactive” program to produce cube files – Orbitals and densities are available – Excited state density differences possible – Different formats available ● Start at the prompt with: orca_plot filename.gbw -i MEP and Densities ● Use keyword “KeepDens” ● Mapped electrostatic potentials can be done with Gabedit – Warning: the faster methods don't work well – The slow method is very slow – Alternative: python script mep.py (get from: https://gist.github.com/mretegan/5501553) – Usage: python mep.py basename npoints – Basename: name of the files .gbw and .scfp (both needed) – Npoints number of points per side in the cube file – Scales as npoints^3... The End ● Have Fun Using Orca ● And thank you for your attention! .