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General
Overview
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
SCMGO
FIRE
Conjugate gradients
Troubleshooting
Failure to converge
Restarting a geometry optimization
Transition state search
PES scan
Troubleshooting
Molecular dynamics
General
(Re-)Starting a simulation
Thermostats and barostats
Temperature and pressure regimes
Trajectory sampling and output
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
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
PES scan
Example: Linear transit
Example: 2D PES scan
Molecular dynamics
Example: Simple MD for H2
Example: MD for a box of water
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
References
External programs and libraries
Keywords
Links to manual entries
Summary of all keywords
AMS
Documentation
/
AMS
/
AMS Manual 2018
AMS Manual 2018
ΒΆ
(PDF)
AMS
Manual
Table of Contents:
General
Overview
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
Molecular dynamics
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
PES scan
Molecular dynamics
PES point properties
Appendices
Environment variables
Extended XYZ file format
Developer options
Required citations
References
External programs and libraries
Keywords
Links to manual entries
Summary of all keywords
Index