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PDF Version of the AMS Driver Manual AMS Manual Amsterdam Modeling Suite 2021.1 www.scm.com May 21, 2021 CONTENTS 1 General 1 1.1 Overview.................................................1 1.2 What’s new in the AMS driver?.....................................1 1.2.1 New in AMS2021.1.......................................1 1.2.2 New in AMS2020.1.......................................1 1.2.3 New in AMS2019.3.......................................2 1.2.4 New in AMS2019.1.......................................3 1.3 Motivation and progress.........................................3 1.4 Input, execution and output.......................................4 2 Input, execution and output 7 2.1 Input...................................................7 2.1.1 Example.............................................7 2.1.2 Tasks..............................................8 2.1.3 Properties............................................8 2.1.4 General remarks on input structure and parsing........................9 2.1.5 Keys...............................................9 2.1.6 Blocks.............................................. 11 2.1.7 Including an external file.................................... 12 2.1.8 Units.............................................. 12 2.2 Execution................................................. 13 2.2.1 Shell script........................................... 13 2.2.2 Interactive input file....................................... 13 2.2.3 Running AMS on compute clusters............................... 14 2.3 Output.................................................. 16 2.3.1 Results directory........................................ 16 2.3.2 Logfile ams.log......................................... 16 2.3.3 Binary output files....................................... 16 2.3.4 Standard output......................................... 17 2.3.5 Optimized geometry in xyz format............................... 17 2.3.6 AMS environment variables.................................. 18 2.4 Driver level parallelism......................................... 18 2.5 Python interface............................................. 22 2.6 Pipe interface............................................... 22 2.6.1 AMSPipe protocol specification................................ 22 Low-level message encoding................................... 23 Return messages and error handling............................... 23 Methods............................................. 24 2.6.2 AMS as a pipe master...................................... 26 2.6.3 AMS as a pipe worker..................................... 27 i 3 Geometry, System definition 29 3.1 Geometry, Lattice............................................ 29 3.1.1 Modifying the geometry.................................... 31 3.2 Symmetry................................................ 33 3.3 Regions.................................................. 34 3.4 Charge, atomic masses, input bond orders................................ 35 3.5 Homogeneous electric field and multipole charges........................... 35 3.6 Load a System from file......................................... 37 3.7 Atom attributes.............................................. 38 3.8 Force field related extensions...................................... 38 3.8.1 Load charges for a forcefield into regions........................... 38 3.8.2 Load forcefield atom types................................... 39 4 Structure and Reactivity, Molecular Dynamics 41 4.1 Single point calculations......................................... 41 4.2 Bond energy calculations......................................... 41 4.2.1 Ground state energy....................................... 41 4.2.2 Formation energy........................................ 42 4.2.3 Atomization energies...................................... 42 4.2.4 Chemisorption energies..................................... 42 4.2.5 Atomic corrections....................................... 42 4.2.6 Open shell systems....................................... 43 4.2.7 Impurities............................................ 43 4.3 Geometry optimization.......................................... 43 4.3.1 Constrained optimization.................................... 46 Restraints............................................. 48 4.3.2 Optimization under pressure / external stress.......................... 48 4.3.3 Optimization methods..................................... 48 Quasi-Newton.......................................... 49 FIRE............................................... 52 SCMGO............................................. 54 Limited-memory BFGS..................................... 55 Conjugate gradients....................................... 56 4.3.4 Troubleshooting......................................... 56 Failure to converge........................................ 56 Restarting a geometry optimization............................... 57 4.4 Transition state search.......................................... 57 4.5 Linear Transit, PES scan......................................... 60 4.5.1 Troubleshooting......................................... 62 4.6 Nudged Elastic Band (NEB)....................................... 63 4.6.1 Input............................................... 64 4.6.2 Frozen atom constraints..................................... 69 4.6.3 Optimizations and convergence criteria............................ 69 4.6.4 Output.............................................. 70 4.6.5 Troubleshooting......................................... 70 4.7 Intrinsic Reaction Coordinate (IRC)................................... 70 4.7.1 Method details......................................... 71 4.7.2 Input............................................... 72 4.7.3 Output.............................................. 76 4.8 Excited state optimizations........................................ 76 4.9 Molecular dynamics........................................... 77 4.9.1 General............................................. 81 4.9.2 Constrained molecular dynamics................................ 82 4.9.3 (Re-)Starting a simulation................................... 83 ii 4.9.4 Thermostats and barostats................................... 84 Temperature and pressure regimes................................ 88 4.9.5 Trajectory sampling and output................................. 89 4.9.6 Lattice deformations (volume regimes)............................. 91 4.9.7 Molecule Gun: adding molecules during simulation...................... 94 4.9.8 Removing molecules during simulation............................ 98 4.9.9 Accelerated dynamics...................................... 101 The PLUMED library support in AMS............................. 101 Metadynamics for Conformer-Rotamer Ensemble Sampling (CREST-MTD).......... 102 Collective Variable-driven HyperDynamics (CVHD)...................... 103 Temperature Replica Exchange................................. 106 Bond Boost Method....................................... 108 Force bias Monte Carlo (fbMC)................................. 110 4.9.10 Non-equilibrium MD (NEMD)................................. 112 T-NEMD for thermoconductivity: heat exchange........................ 112 4.10 Grand Canonical Monte Carlo (GCMC)................................. 116 4.10.1 General info........................................... 116 4.10.2 Method Details......................................... 116 4.10.3 Input............................................... 118 4.10.4 Output.............................................. 123 4.11 Automated PES Exploration....................................... 124 4.11.1 Overview............................................ 125 4.11.2 Job selection and main options................................. 126 4.11.3 Results: the “Energy Landscape”................................ 128 Results on the text output..................................... 128 4.11.4 Continue a PES exploration from a previous calculation.................... 129 4.11.5 Structure comparison...................................... 130 4.11.6 Process Search job....................................... 132 Overview............................................. 132 Input options........................................... 132 4.11.7 Saddle Search job........................................ 133 Overview............................................. 133 Input options........................................... 133 4.11.8 Basin Hopping job....................................... 135 Overview............................................. 135 Input options........................................... 135 4.11.9 Landscape Refinement..................................... 137 4.11.10 Optimizer............................................ 137 4.11.11 Binding Sites.......................................... 138 Input options........................................... 139 4.11.12 References........................................... 141 5 Gradients, Hessian, Stress tensor, Elasticity 143 5.1 Nuclear gradients............................................. 143 5.2 Hessian.................................................. 144 5.3 PES point character........................................... 144 5.4 Thermodynamics, gas phase Gibbs free energy............................. 147 5.5 Stress tensor............................................... 147 5.6 Elastic tensor............................................... 148 5.7 Numerical differentiation options.................................... 150 6 Vibrational Spectroscopy 153 6.1 General.................................................
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