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General
Overview
What’s new in the AMS driver?
New in AMS2020.1
New in AMS2019.3
New in AMS2019.1
Motivation and progress
Input, execution and output
Input, execution and output
Input
Example
Tasks
Properties
General remarks on input structure and parsing
Keys
Blocks
Including an external file
Units
Execution
Shell script
Running AMS on compute clusters
Output
Results directory
Logfile ams.log
Binary output files
Standard output
AMS environment variables
Driver level parallelism
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
Geometry, System definition
Geometry, Lattice
Modifying the geometry
Symmetry
Regions
Charge, atomic masses, input bond orders
Homogeneous electric field and multipole charges
Load a System from file
Atom attributes
Force field related extensions
Load charges for a forcefield into regions
Load forcefield atom types
Structure and Reactivity, Molecular Dynamics
Single point calculations
Bond energy calculations
Ground state energy
Formation energy
Atomization energies
Chemisorption energies
Atomic corrections
Open shell systems
Impurities
Geometry optimization
Constrained optimization
Restraints
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
Linear Transit, PES scan
Troubleshooting
Nudged Elastic Band (NEB)
Input
Frozen atom constraints
Optimizations and convergence criteria
Output
Troubleshooting
Intrinsic Reaction Coordinate (IRC)
Method details
Input
Output
Excited state optimizations
Molecular dynamics
General
Constrained molecular dynamics
(Re-)Starting a simulation
Thermostats and barostats
Temperature and pressure regimes
Trajectory sampling and output
Lattice deformations (volume regimes)
Molecule Gun: adding molecules during simulation
Removing molecules during simulation
Accelerated dynamics
The PLUMED library support in AMS
Metadynamics for Conformer-Rotamer Ensemble Sampling (CREST-MTD)
Collective Variable-driven HyperDynamics (CVHD)
Temperature Replica Exchange
Bond Boost Method
Non-equilibrium MD (NEMD)
T-NEMD for thermoconductivity: heat exchange
Grand Canonical Monte Carlo (GCMC)
General info
Method Details
Input
Output
Gradients, Hessian, Stress tensor, Elasticity
Nuclear gradients
Hessian
PES point character
Thermodynamics, gas phase Gibbs free energy
Stress tensor
Elastic tensor
Numerical differentiation options
Vibrational Spectroscopy
General
Where are the results?
IR frequencies and normal modes
All vibrational Modes
Rescanning Imaginary modes
Symmetric Displacements
Mobile Block Hessian (MBH)
Mode Scanning
Theory
Input
Mode Refinement
Theory
Input
Mode Tracking
Theory
Input
Input: Tracking methods
Input: Selecting modes
Input: Convergence
Selecting modes
Thermodynamics (ideal gas)
Gibbs free energy change for a gas phase reaction
Moments of inertia
Partial Vibrational Spectra (PVDOS)
Phonons
(Resonance) Raman
Raman
Resonance Raman: excited-state finite lifetime
Resonance Raman: VG-FC
Theory
Input
VROA: (Resonance) vibrational Raman optical activity
Engine ADF
VCD: Vibrational Circular Dichroism
Atomic polar tensor (APT) model
Analytical VCD in ADF
Vibrationally resolved electronic spectra
AH-FC: Adiabatic Hessian Franck-Condon
FCF module: Franck-Condon Factors
Theory
Input
Result: TAPE61
FCF example absorption and fluorescence
FCF Example phosphorescence
VG-FC: Vertical Gradient Franck-Condon
Theory
Theory: Vibronic-Structure Tracking
Theory: Vibronic-Structure Refinement
Theory: Adiabatic excitation energy
Input: Vibronic-Structure all modes
Input: Vibronic-Structure Tracking
Input: Restarting VST
Input: Vibronic-Structure Refinement
Input: Excited State
Input: Producing the spectrum
Dipole moment, Polarizability, Bond orders
Charges, Dipole Moment, Polarizability
Bond orders & Molecule detection
Engines
Available engines
Summary of engine capabilities
External programs as engines
Toy engines
Engine add-ons
Dispersion corrections
Pressure
Non-isotropic external stress
Atom energies
Restraints
Utilities
ChemTraYzer
General information
Graphical user interface
Command line execution
Results
Trajectory Analysis
Radial Distribution Function (RDF)
Description
Options
Histogram
Autocorrelation Functions
Description
Options
Diffusion Coefficient
VCD Analysis: VCDtools
General Theory
General Coupled Oscillator Analysis
Available options
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
Example: Lattice deformations in MD
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
Extended XYZ file format
Developer options
Symmetry
Schönfliess symbols and symmetry labels
Molecular orientation requirements
Required citations
General references
Feature references
Frequencies, IR Intensities, Raman, VCD
External programs and Libraries
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
|
D
|
E
|
F
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G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
X
|
Y
|
Z
A
Add molecules (molecular dynamics)
Add-ons
ADF
Adiabatic Hessian Franck-Condon
AMS input file
ams.log
ams.rkf
AMS_JOBNAME
AMS_RESULTSDIR
AMS_SWITCH_LOGFILE_AND_STDOUT
AMSPipe
Applications
APT
Atom energies
Atomic charges
Atomic masses
Atomic polar tensor
Autocorrelation function
Available engines
B
BAND
Barostats
Binary output files
Block constraints
Block normal modes
Bond Boost method
Bond energy calculation
Bond orders
Bulk modulus
C
Cell optimization
Charge
Compute clusters
Conjugate gradients (geometry optimizer)
Constrained optimization
Constraints
CREST metadynamics
CVHD
D
D3 dispersion add-on
D4 dispersion add-on
D5 dispersion add-on
Developer options
DFTB
Diffusion coefficient
Dipole moment
Double group symmetry
Double parallelism
Driver level parallelism
E
eHEX method (NEMD)
Elastic properties
Elastic tensor
Electric field
Engine add-ons
Engine input
Engine output files
Engines
Enthalpy
Entropy
Environment variables
Examples
Excited state optimizations
External engines
F
FCF
FCF module
FIRE (geometry optimizer)
Fixed atoms
Fluorescence
Forces
Fractional coordinates
Franck-Condon factors
,
[1]
Free rotor interpolation corrections
G
GCMC
Geometry
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)
Histogram (molecular dynamics)
I
Imaginary modes
IMDHO
Independent mode displaced harmonic oscillator
Initial Hessian
Input file syntax
Input for AMS
Interface to external programs
Internal energy
Intrinsic reaction coordinate
IR frequencies
IRC
Irreducible representation
Isotopes
J
Job name
L
L-BFGS (geometry optimizer)
Lattice
Lattice constraints
Lattice deformations
Lattice optimization
Lattice vectors
Lattice vibrations
Lennard-Jones potential
Linear transit
Logfile ams.log
M
MBH
MD
MD trajectory analysis
MEP
Minimum energy profile
MLPotential
Mobile block Hessian
Mode intensity tracking
Mode refinement
Mode scanning
Mode selecting
Mode tracking
Molecular dynamics
Molecular dynamics checkpoint
Molecule detection
Molecule gun (molecular dynamics)
Moments of inertia
MOPAC
N
NEB
NEMD
Non-isotropic stress
Normal modes
Nuclear gradients
Nudged elastic band
O
Output files
Output of AMS
P
Partial vibrational density of states
Partial vibrational spectra
PES point characterization
PES point properties
PES scan
Phonons
Phosphorescence
Pipe interface
Pipe protocol
PLAMS
PLUMED library
Point charges
Polarizability
Pressure
(molecular dynamics)
Properties
PVDOS
Python
Q
Quasi-Newton (geometry optimizer)
R
Radial distribution function
Raman
Raman-active vibrations
RDF
ReaxFF
Regions
Remove molecules (molecular dynamics)
Required citations
Resonance Raman
Resonance VROA
Restart (geometry)
(molecular dynamics)
Restraints
Results directory
,
[1]
Run types
Running AMS
S
Scan coordinate
ScanFreq
Schönflies symbol
SCM_TMPDIR
SCMGO (geometry optimizer)
Scratch directory
Scripting
Shear modulus
Single point calculation
Starting directory
Strain constraints
Stress tensor
Structure relaxation
Subspecies
Super cell
Symmetric displacements
Symmetrization
Symmetry
,
[1]
Symmetry label
T
T-NEMD
Task farming
Tasks
,
[1]
Temperature (molecular dynamics)
Temporary directory
Thermodynamics
Thermostat
Trajectory sampling
Transition state search
Two-level parallelism
U
UFF
Utilities
V
VCD
VCDtools module
Vertical gradient Franck-Condon
VG-FC
Vibrational circular dichroism
Vibrational Raman optical activity
Vibrational spectroscopy
Vibrationally resolved electronic spectra
Vibronic-structure excited state
Volume regimes
VROA
X
XYZ file format
Y
Young modulus
Z
Z-matrix