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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
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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
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E
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F
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G
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H
|
I
|
J
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
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U
|
V
|
X
|
Y
A
Add Molecules (molecular dynamics)
ADF
AMS input file
ams.rkf
AMS_JOBNAME
AMS_RESULTSDIR
AMS_SWITCH_LOGFILE_AND_STDOUT
Applications
Atomic Masses
Available engines
B
BAND
Barostats
Block contraints
Bulk modulus
C
Cell optimization
Charge
Compute clusters
Conjugate gradients (geometry optimizer)
Constrained optimization
Constraints
CVHD
D
Developer options
DFTB
Double parallelism
E
eHEX method (NEMD)
Elastic properties
Elastic tensor
Engine input
Engine output files
Engines
Enthalpy
Entropy
Environment variables
examples
External engines
F
FIRE (geometry optimizer)
Fixed atoms
Forces
Fractional coordinates
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
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
Lattice optimization
Lattice Vectors
Lattice vibrations
Lennard-Jones potential
Linear Transit
M
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
NEMD
Normal modes of vibration
Nuclear gradients
P
Partial Vibrational Density of States
Partial Vibrational Spectra
PES point properties
PES Scan
Phonons
PLAMS
PLUMED library
Pressure (geometry optimization)
(molecular dynamics)
PVDOS
Python
Q
Quasi-Newton (geometry optimizer)
R
ReaxFF
Remove molecules (molecular dynamics)
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
V
Vibrational analysis
Vibrations
X
XYZ file format
Y
Young modulus