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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
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AMS
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Index
Index
A
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B
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C
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D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
X
|
Y
A
Add Molecules (molecular dynamics)
Add-ons
ADF
Adiabatic Hessian Franck-Condon
AMS input file
ams.rkf
AMS_JOBNAME
AMS_RESULTSDIR
AMS_SWITCH_LOGFILE_AND_STDOUT
AMSPipe
Applications
Atomic Masses
Available engines
B
BAND
Barostats
Block constraints
Bond orders
Bulk modulus
C
Cell optimization
Charge
Compute clusters
Conjugate gradients (geometry optimizer)
Constrained optimization
Constraints
CVHD
D
D3 Dispersion add-on
D4 Dispersion add-on
D5 Dispersion add-on
Developer options
DFTB
Dipole moment
Double parallelism
Driver level parallelism
E
eHEX method (NEMD)
Elastic properties
Elastic tensor
Engine add-ons
Engine input
Engine output files
Engines
Enthalpy
Entropy
Environment variables
examples
External engines
F
FCF
FIRE (geometry optimizer)
Fixed atoms
Forces
Fractional coordinates
Franck-Condon factors
G
GCMC
Geometry constraints
Geometry convergence
Geometry optimization
Geometry optimization methods
Geometry relaxation
Gibbs free energy
Grand Canonical Monte Carlo
H
Heat Capacity
Heat exchange (molecular dynamics)
Hessian
HEX method (NEMD)
I
Independent Mode Displaced Harmonic Oscillator
,
[1]
Infrared spectroscopy
Initial Hessian
Input file syntax
Intensity Tracking
Interface to external programs
Internal Energy
Intrinsic Reaction Coordinate
IR spectrum
IRC
Isotopes
J
Job name
L
L-BFGS (geometry optimizer)
Lattice optimization
Lattice Vectors
Lattice vibrations
Lennard-Jones potential
Linear Transit
M
MD Trajectory Analysis
MEP
Minimum Energy Profile
Mode Refinement
Mode Tracking
,
[1]
Molecular dynamics
Molecular dynamics checkpoint
Molecular vibrations
Molecule Gun (molecular dynamics)
Moments of Inertia
MOPAC
N
NEB
NEMD
non-isotropic stress
Normal modes of vibration
Nuclear gradients
Nudged Elastic Band
P
Partial Vibrational Density of States
Partial Vibrational Spectra
PES point characterization
PES point properties
PES Scan
Phonons
Pipe interface
Pipe protocol
PLAMS
PLUMED library
Pressure
(molecular dynamics)
PVDOS
Python
Q
Quasi-Newton (geometry optimizer)
R
Radial Distribution Function
ReaxFF
Remove molecules (molecular dynamics)
Resonance Raman
Restart (Geometry)
(molecular dynamics)
Results directory
Run types
S
Scan coordinate
ScanFreq
SCM_TMPDIR
SCMGO (geometry optimizer)
Scratch directory
Scripting
Shear modulus
Single point calculation
Starting directory
Stress tensor
Structure relaxation
Super Cell
T
T-NEMD
Task farming
Tasks
Temperature (molecular dynamics)
Temporary directory
Thermodynamics
Thermostat
Trajectory sampling
Transition state search
Two-level parallelism
U
UFF
Utilities
V
Vertical Gradient Franck-Condon
Vibrational analysis
vibrationally resolved electronic spectra
Vibrations
Vibronic Coupling
Vibronic-Structure excited state
X
XYZ file format
Y
Young modulus