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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
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AMS
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Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
X
|
Y
A
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
D
Developer options
DFTB
Double parallelism
E
Elastic properties
Elastic tensor
Engine input
Engine output files
Engines
Environment variables
External engines
F
FIRE (geometry optimizer)
Fixed atoms
Forces
Fractional coordinates
G
Geometry constraints
Geometry convergence
Geometry optimization
Geometry optimization methods
Geometry relaxation
H
Hessian
I
Infrared spectroscopy
Initial Hessian
Input file syntax
Interface to external programs
IR spectrum
Isotopes
J
Job name
L
Lattice optimization
Lattice Vectors
Lattice vibrations
Lennard-Jones potential
Linear Transit
M
Molecular dynamics
Molecular dynamics checkpoint
Molecular vibrations
MOPAC
N
Normal modes of vibration
Nuclear gradients
P
PES point properties
PES Scan
Phonons
PLAMS
Pressure (geometry optimization)
(molecular dynamics)
Python
Q
Quasi-Newton (geometry optimizer)
R
ReaxFF
Restart (Geometry)
(molecular dynamics)
Results directory
Run types
S
Scan coordinate
SCM_TMPDIR
SCMGO (geometry optimizer)
Scratch directory
Scripting
Shear modulus
Single point calculation
Starting directory
Stress tensor
Structure relaxation
Super Cell
T
Task farming
Tasks
Temperature (molecular dynamics)
Temporary directory
Thermostat
Trajectory sampling
Transition state search
Two-level parallelism
U
UFF
V
Vibrations
X
XYZ file format
Y
Young modulus