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General
Overview
What’s new in the AMS2019 driver?
New in AMS2019.3
New in AMS2019.1
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 under pressure / external stress
Optimization methods
Quasi-Newton
FIRE
SCMGO
Limited-memory BFGS
Conjugate gradients
Troubleshooting
Failure to converge
Restarting a geometry optimization
Transition state search
PES scan
Troubleshooting
Nudged Elastic Band (NEB)
Input
Frozen atom constraints
Optimizations and convergence criteria
Output
Troubleshooting
Intrinsic Reaction Coordinate (IRC) Scan
Method details
Input
Output
Molecular dynamics
General
Constrained molecular dynamics
(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
Temperature Replica Exchange
Vibrational analysis
All vibrational modes
Vibrational Analysis Tools
Mode Selective Analysis
Vibrationally resolved electronic spectra
VG-FC Resonance Raman
Selecting modes
Overview of input options
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)
PES point character
Elastic tensor
Phonons
Numerical differentiation options
Other Properties
Engines
Available engines
External programs as engines
Toy engines
Engine add-ons
Dispersion corrections
Pressure
Non-isotropic external stress
Technical topics
Input syntax
General remarks on input structure and parsing
Keys
Blocks
Units
Driver level parallelism
Running AMS on compute clusters
Python interface
Pipe interface
AMSPipe protocol specification
Low-level message encoding
Return messages and error handling
Methods
AMS as a pipe master
AMS as a pipe worker
Utilities
Trajectory Analysis
Radial Distribution
Description
Options
Histogram
Examples
Geometry optimization
Example: Simple geometry optimization
Example: Two-stage geometry optimization with initial Hessian
Example: Periodic lattice optimization under pressure
Example: Phase Transition Due To External Nonuniform Stress
Example: Boron nitride optimization under external stress
Example: Graphene optimization under external stress
Example: Constrained optimizations
Transition state search
Example: TS search starting from initial Hessian
Example: PES scan and TS search for H2 on graphene
Nudged Elastic Band (NEB)
Nudged Elastic Band (NEB) Examples
HCN isomerization reaction with NEB
H2 dissociation on graphene
Running multiple NEB calculations using PLAMS
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
Example: Vibronic-Structure Tracking
PES point properties
Example: Phonons for graphene
Example: Phonons with isotopes
Example: User-defined Brillouin zone for phonon dispersion
Example: Elastic tensor
Pipe interface
Example: ASE calculator as a pipe worker
Example: AMS as a pipe worker
Appendices
Environment variables
Extended XYZ file format
Developer options
Required citations
General references
Feature references
Vibrational analysis
Mode tracking
Mode refinement
Keywords
Links to manual entries
Summary of all keywords
AMS
Documentation
/
AMS
/
AMS Manual 2019.3
AMS Manual 2019.3
¶
(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
Nudged Elastic Band (NEB)
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
PES point character
Elastic tensor
Phonons
Numerical differentiation options
Other Properties
Engines
Available engines
External programs as engines
Toy engines
Engine add-ons
Technical topics
Input syntax
Driver level parallelism
Running AMS on compute clusters
Python interface
Pipe interface
Utilities
Trajectory Analysis
Examples
Geometry optimization
Transition state search
Nudged Elastic Band (NEB)
Intrinsic reaction coordinate (IRC)
PES scan
Molecular dynamics
Vibrational analysis
PES point properties
Pipe interface
Appendices
Environment variables
Extended XYZ file format
Developer options
Required citations
General references
Feature references
Keywords
Links to manual entries
Summary of all keywords
Index