PLAMS: Python Library for Automating Molecular Simulations
**********************************************************

Getting Started[image]

New to PLAMS? Take a look at this guide to learn how to install, set
up, and start using PLAMS.

Examples[image]

Explore these practical examples demonstrating PLAMS functionality,
and a wide range of use cases with AMS.

Amsterdam Modeling Suite[image]

Check out this user guide for detailed documentation on how to set up
and run AMS calculations.

Components (Settings, Job, ...)[image]

Find the detailed API reference for core PLAMS components.


Table of contents
^^^^^^^^^^^^^^^^^

* Getting Started

  * Overview

  * Quick Start

  * Installation Guide

  * What's new in PLAMS for AMS2026?

    * Added

    * Changed

    * Fixed

    * Deprecated

  * What's new in PLAMS for AMS2025?

    * Added

    * Changed

    * Fixed

    * Deprecated

    * Removed

  * What's new in PLAMS for AMS2024?

  * What's new in PLAMS for AMS2023?

* Examples

* Amsterdam Modeling Suite

  * AMS driver and engines

    * Preparing input

    * Preparing runscript

    * Molecule handling

    * AMSJob API

    * AMSResults API

    * Other functions

  * AMS worker

    * AMSWorker API

    * AMSWorkerResults API

    * AMSWorkerPool API

  * ASE Calculator for AMS

    * Introduction

    * AMS settings

    * AMS standalone and worker mode

    * Technical

    * AMSCalculator API

  * Quick jobs

    * "preoptimize()"

    * "refine_density()"

    * "refine_lattice()"

    * "shakemd()"

  * Analysis tools: Densf, FCF, analysis

    * "FCFJob"

    * "DensfJob"

    * "AMSAnalysisJob"

  * KF files

    * "KFFile"

    * "KFReader"

    * "KFHistory"

  * COSMO-RS

    * Settings

    * Settings with multiple compounds

    * ADF and CRSJob

    * COSMO-RS Parameters

    * Data analyses and plotting

    * API

  * ParAMS, Simple Active Learning

  * Conformers

    * ConformersJob

  * Recipes

    * COSMO-RS Compound

    * COSMO-RS Conformers

    * MD Jobs

    * ADF Fragment

    * BAND Fragment

    * Reorganization Energy

    * ADFNBO

    * pyAHFCDOS

    * ADFVibronicDOS

  * Reactions Discovery

  * Zacros

* Components (Settings, Job, ...)

  * Settings

    * Tree-like structure

    * Dot notation

    * Case sensitivity

    * API

    * Global settings

  * Jobs

    * Preparing a job

    * Running a job

    * Job API

    * Single jobs

    * Multijobs

  * Results

    * Files in the job folder

    * Synchronization of parallel job executions

    * Cleaning job folder

    * API

  * Job runners

    * Local job runner

    * Remote job runner

  * Job manager

    * Rerun prevention

    * Pickling

    * Restarting scripts

    * API

  * Public functions

    * "init()"

    * "finish()"

    * "jobs_in_directory()"

    * "load()"

    * "load_all()"

    * "read_molecules()"

    * "read_all_molecules_in_xyz_file()"

    * Logging

    * Binding decorators

  * Molecule

    * Molecule

    * Atom

    * Bond

    * RDKit interface

    * ASE interface

    * Packmol interface

  * Utilities

    * Periodic Table

    * Units

    * Geometry tools

    * File format conversion tools

    * Reaction energies

    * Plotting tools

    * Postprocess results

  * Trajectories

    * XYZ trajectory files

    * RKF trajectory files

    * DCD trajectory files

    * Trajectory class

  * Job Analysis

    * Adding Jobs

    * Adding Analysis Fields

    * Modifying Analysis

    * Extracting Analysis

    * API

  * View

    * API

* Cookbook

  * init and finish

    * Get the workdir created by plams.init

    * Load job results from a PLAMS workdir

  * Settings and input

    * Create an input block with a header

    * Create an empty input block

    * Create an input block with repeating keys

    * Repeating input block

    * Create a "free" 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

    * Generate a liquid or gas mixture

    * Write an ams.rkf-like trajectory

    * Convert a trajectory to ams.rkf with bond guessing

    * Pre-optimize a molecule

    * Counting rings

  * Extracting Results

    * Directly from Functions

    * From the RKF Interface

    * Finding Section/Variable Pairs

    * From molecular dynamics trajectories

  * Accessing Old Jobs

    * Binding Native PLAMS Jobs

    * Binding old RKF Files

  * Parallelization

    * Parallel job execution

    * PLAMS scripts under Slurm

* Citations

* 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

  * ORCA

    * Settings

    * Loading jobs

    * API

  * RASPA

    * Input

    * Molecule parsing

    * Loading jobs

    * API

  * VASP

    * Results

    * API

  * Serenity

    * Serenity calculation

    * ADF interface

    * API

* FAQ
