Documentation 2024.1

General

Installation Manual

Installation of the Amsterdam Modeling Suite program package.

Tutorials

GUI-, Scripting- and Advanced tutorials for all programs.

Programs

AMS driver

The driver program of the Amsterdam Modeling Suite.

ADF (Amsterdam Density Functional)

A DFT engine particularly strong in understanding and predicting structure, reactivity, and spectra of molecules.

BAND

BAND is an atomic-orbital based DFT engine for periodic systems.

DFTB

DFTB (Density-Functional based Tight-Binding) is a fast approximate DFT engine.

ReaxFF

Reactive force field approach developed by Prof. Adri van Duin and coworkers.

MLPotential

Machine learning potentials (machine learning force fields).

ForceField

ForceField engine, including UFF.

GFNFF

GFNFF force field

Hybrid

Hybrid engine, for embedding and QM/MM calculations that combine multiple engines.

MOPAC

MOPAC is a general-purpose semiempirical molecular orbital package.

ASE engine

Use calculators from the Atomic Simulation Environment (ASE) with the AMS driver.

Quantum ESPRESSO as an AMS engine

Quantum ESPRESSO is a plane-wave-based DFT engine for periodic systems.

Utilities

Molecular dynamics trajectory analysis, conformer generation, …

GUI

The Graphical User Interface.

COSMO-RS

COSMO-RS (COnductor like Screening MOdel for Realistic Solvents) is a program for calculating thermodynamic properties of (mixed) fluids.

ParAMS

ParAMS is a GUI and Python toolkit for the parameterization of ReaxFF, DFTB, and machine learning potentials.

Kinetics

Microkinetics and Kinetic Monte Carlo

Workflows

ChemTrayZer2, OLED Workflows, Reactions Discovery, Simple Active Learning

Scripting

Scripting

Command-line tools and Python stack.

PLAMS

PLAMS (Python Library for Automating Molecular Simulation) is a collection of tools that aim at providing powerful, flexible and easily extendable Python interface to molecular modeling programs.

PISA

PISA (Python Input System for AMS) is a replacement/alternative for the PLAMS settings.input object for defining simulation input. It provides a collection of Python classes that allow for easy programmatic setup of text input, with modern features such as autocompletion and type hinting.

pyZacros

pyZacros is a Python interface to Zacros to simulate reactions on catalytic surfaces using kinetic Monte Carlo.

reactmap

reactmap is a python tool that maps atoms from reactants to products so as to minimize the number of required bond cleavages and formations.

ACErxn

ACErxn is a tool that generates reaction networks for given reactant/product pairs.

Third party software

References