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General
Overview
What’s new in the AMS2019 driver?
Motivation and progress
Input, execution and output
System definition
System geometry
Additional system properties
Restoring a system from disk
Exploring the PES: Tasks
Single point calculations
Geometry optimization
Constrained optimization
Optimization methods
Quasi-Newton
FIRE
SCMGO
Conjugate gradients
Troubleshooting
Failure to converge
Restarting a geometry optimization
Transition state search
PES scan
Troubleshooting
Intrinsic Reaction Coordinate (IRC) Scan
Method details
Input
Output
Molecular dynamics
General
(Re-)Starting a simulation
Thermostats and barostats
Temperature and pressure regimes
Trajectory sampling and output
Molecule Gun: adding molecules during simulation
Removing molecules during simulation
The PLUMED library support in AMS
Collective Variable-driven HyperDynamics (CVHD)
Non-equilibrium MD (NEMD): heat exchange
Vibrational analysis
Full analysis
Mode selective analysis
Mode Scanning
Mode Refinement
Mode Tracking
Selecting modes
Grand Canonical Monte Carlo (GCMC)
General info
Method Details
Input
Output
PES point properties
Nuclear gradients and stress tensor
Hessian and normal modes of vibration
Thermodynamics (ideal gas)
Partial Vibrational Spectra (PVDOS)
Elastic tensor
Phonons
Numerical differentiation options
Engines
Available engines
External programs as engines
Toy engines
Technical topics
Input syntax
General remarks on input structure and parsing
Keys
Blocks
Units
Double parallelism
Running AMS on compute clusters
Python interface
Examples
Geometry optimization
Example: Simple geometry optimization
Example: Two-stage geometry optimization with initial Hessian
Example: Periodic lattice optimization under pressure
Example: Constrained optimizations
Transition state search
Example: TS search starting from initial Hessian
Example: PES scan and TS search for H2 on graphene
Intrinsic reaction coordinate (IRC)
Example: IRC for HCN
Example: TS and IRC for Claisen reaction
PES scan
Example: Linear transit
Example: 2D PES scan
Molecular dynamics
Example: Simple MD for H2
Example: MD for a box of water
Vibrational analysis
Example: Mode Refinement
Example: Mode Tracking
PES point properties
Example: Phonons for graphene
Example: Phonons with isotopes
Example: Elastic tensor
Appendices
Environment variables
Extended XYZ file format
Developer options
Required citations
General references
Feature references
Vibrational analysis
Mode tracking
Mode refinement
References
External programs and libraries
Keywords
Links to manual entries
Summary of all keywords
AMS
Documentation
/
AMS
/
AMS Manual 2019
AMS Manual 2019
ΒΆ
(PDF)
AMS
Manual
Table of Contents:
General
Overview
What’s new in the AMS2019 driver?
Motivation and progress
Input, execution and output
System definition
System geometry
Additional system properties
Restoring a system from disk
Exploring the PES: Tasks
Single point calculations
Geometry optimization
Transition state search
PES scan
Intrinsic Reaction Coordinate (IRC) Scan
Molecular dynamics
Vibrational analysis
Grand Canonical Monte Carlo (GCMC)
PES point properties
Nuclear gradients and stress tensor
Hessian and normal modes of vibration
Elastic tensor
Phonons
Numerical differentiation options
Engines
Available engines
External programs as engines
Toy engines
Technical topics
Input syntax
Double parallelism
Running AMS on compute clusters
Python interface
Examples
Geometry optimization
Transition state search
Intrinsic reaction coordinate (IRC)
PES scan
Molecular dynamics
Vibrational analysis
PES point properties
Appendices
Environment variables
Extended XYZ file format
Developer options
Required citations
General references
Feature references
References
External programs and libraries
Keywords
Links to manual entries
Summary of all keywords
Index