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Table of contents
Introduction
What is PLAMS
What can be done with PLAMS
Simple example
What PLAMS is
not
About this documentation
Getting started
Library contents
Installing PLAMS
Updating PLAMS
Running PLAMS
Defaults file
The launch script
Working folder location
Passing variables
Importing past jobs
Restarting failed script
Multiple input scripts
Components overview
Settings
Tree-like structure
Dot notation
Case sensitivity
Global settings
API
Jobs
Preparing a job
Contents of job settings
Default settings
Running a job
Name conflicts
Prerun and postrun methods
Preview mode
Job API
Single jobs
Subclassing SingleJob
Multijobs
Using MultiJob
Results
Files in the job folder
Synchronization of parallel job executions
Examples
Cleaning job folder
Cleaning for multijobs
API
Job runners
Local job runner
Remote job runner
Job manager
Rerun prevention
Pickling
Restarting scripts
API
Public functions
Logging
Binding decorators
Molecule
Molecule
Atom labeling
Atom
Bond
RDKit interface
ASE interface
Utilities
Periodic Table
Units
Geometry tools
File format conversion tools
Trajectories
XYZ trajectory files
XYZ history files
RKF trajectory files
RKF history files
DCD trajectory files
Interfaces
Amsterdam Modeling Suite
AMS driver and engines
Preparing input
Preparing runscript
Molecule handling
AMSJob API
AMSResults API
AMS worker
AMSWorker API
AMSWorkerResults API
AMSWorkerPool API
Analysis tools: Densf, FCF, analysis
KF files
COSMO-RS
Settings
Settings with multiple compound
ADF and CRSJob
COSMO-RS Parameters
Data analyses and plotting
API
ADF (pre-2020 version)
Preparing input
Preparing runscript
API
ReaxFF (pre-2019 version)
Other programs
CP2K
Settings
Molecule parsing
Loading jobs
Molecule loading
API
Crystal
Preparing a calculation
Molecule parsing
Results extraction
Example
API
DFTB+
Preparing a calculation
Results extraction
Example
API
Dirac
Preparing a calculation
Results extraction
API
MOPAC (standalone program)
Preparing input
API
ORCA
API
RASPA
Input
Molecule parsing
Loading jobs
API
Examples
Examples
Helium dimer dissociation curve
Geometry optimization of water
Many jobs in parallel
Benchmark accuracy of basis sets
Reaction energies with many different engines
Workflow: filtering molecules based on excitation energies
Charge transfer integrals with ADF
Tuning the range separation
Oxidation Potential
Pre-made recipes
ADF and COSMO-RS workflow
ADF fragment job
Reorganization Energy
NBO with ADF
Numerical gradients
Numerical Hessian
ReaxFF molecule gun
Global Minimum Search
Vibrational analysis with ASE
Example
API
Cookbook
Settings and input
Create an input block with an header
Create an empty input block
Convert an AMS text input into an AMS job
Convert an AMS text input into settings object
Convert an AMS .run file into an AMS job
Specify paths to files in the input
Restart from a previous job
Molecules
Generate a molecule from a SMILES string
Load all files in a folder as molecules
Counting rings
Extracting Results
Directly from Functions
Examples: Total Energy and Final Structure
AMSResults API Functions
From the RKF Interface
Finding Section/Variable Pairs
From Python Directories
KFBrowser
From molecular dynamics trajectories
General MD properties
Molecules from trajectories
Accessing Old Jobs
Binding Native PLAMS Jobs
Binding old RKF Files
Parallelization
Citations
PLAMS
Documentation
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PLAMS
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