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Scripting
| https://www.scm.com/doc/Documentation/index.html |
|
Installation
| https://www.scm.com/doc/Installation/index.html |
| Windows | https://www.scm.com/doc/Installation/Windows_Quickstart_Guide.html |
| Linux | https://www.scm.com/doc/Installation/Linux_Quickstart_Guide.html |
| MacOS | https://www.scm.com/doc/Installation/MacOS_Quickstart_Guide.html |
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Package manager
Install optional components
| https://www.scm.com/doc/Installation/Optional_Components.html |
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Tutorials
| https://www.scm.com/doc/Tutorials/index.html |
| Getting started | https://www.scm.com/doc/Tutorials/GettingStarted/index.html |
| All tutorials | https://www.scm.com/doc/Tutorials/index.html |
|
AMS Driver
| https://www.scm.com/doc/AMS/index.html |
| Geometry and System | https://www.scm.com/doc/AMS/System.html |
| Geometry Optimization | https://www.scm.com/doc/AMS/Tasks/Geometry_Optimization.html |
| Molecular Dynamics | https://www.scm.com/doc/AMS/Tasks/Molecular_Dynamics.html |
| Nudged Elastic Band (NEB) | https://www.scm.com/doc/AMS/Tasks/NEB.html |
| PES Exploration | https://www.scm.com/doc/AMS/Tasks/PES_Exploration.html |
| PES Scan, Linear Transit | https://www.scm.com/doc/AMS/Tasks/PES_Scan.html |
| Transition State Search | https://www.scm.com/doc/AMS/Tasks/Transition_State_Search.html |
| Vibrational Spectroscopy | https://www.scm.com/doc/AMS/Vibrational_Spectroscopy.html |
|
Engines
| https://www.scm.com/doc/AMS/Engines.html |
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ADF
Molecular DFT
| https://www.scm.com/doc/ADF/index.html |
|
BAND
Periodic DFT
| https://www.scm.com/doc/BAND/index.html |
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DFTB
Semi-empirical
| https://www.scm.com/doc/DFTB/index.html |
|
ForceField
AMBER, UFF, APPLE&P...
| https://www.scm.com/doc/ForceField/index.html |
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GFNFF
Force field
| https://www.scm.com/doc/GFNFF/index.html |
|
Hybrid
QM/MM and mixed methods
| https://www.scm.com/doc/Hybrid/index.html |
|
ML Potential
Machine Learning potentials
| https://www.scm.com/doc/MLPotential/index.html |
|
MOPAC
Semi-empirical
| https://www.scm.com/doc/MOPAC/index.html |
|
Quantum ESPRESSO
Periodic DFT
| https://www.scm.com/doc/QuantumEspresso/index.html |
|
VASP
Periodic DFT
| https://www.scm.com/doc/VASP/index.html |
|
ReaxFF
Reactive force field
| https://www.scm.com/doc/ReaxFF/index.html |
|
ASE engine
Use any ASE calculator
| https://www.scm.com/doc/ASE/index.html |
|
Meso/Macro
| https://www.scm.com/doc/Documentation/index.html |
|
COSMO-RS
Thermodynamic properties of fluids
| https://www.scm.com/doc/COSMO-RS/index.html |
|
Bumblebee
OLED device modeling
| https://www.scm.com/doc/Bumblebee/index.html |
| Microkinetics | https://www.scm.com/doc/GUI/AMSkinetics.html |
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Zacros
Kinetic Monte Carlo
| https://www.scm.com/doc/GUI/AMSkinetics.html |
|
Tools
| https://www.scm.com/doc/Documentation/index.html |
|
GUI
Graphical User Interface
| https://www.scm.com/doc/GUI/index.html |
|
ParAMS
Parametrization tool
| https://www.scm.com/doc/params/index.html |
|
Simple Active Learning
On-the-fly training of ML
| https://www.scm.com/doc/Workflows/SimpleActiveLearning/SimpleActiveLearning.html |
|
OLED Deposition and Properties
Multiscale OLED modeling
| https://www.scm.com/doc/Workflows/OLEDWorkflows/OLEDWorkflows.html |
|
Reactions Discovery
Automatic reaction-discovery workflow
| https://www.scm.com/doc/Workflows/ReactionsDiscovery/ReactionsDiscovery.html |
|
ACE Reaction Network
Generation of reaction networks
| https://www.scm.com/doc/acerxn/index.html |
|
Conformers
Conformers generation
| https://www.scm.com/doc/AMS/Utilities/Conformers.html |
|
MD Trajectory Analysis
Analysis of MD trajectories
| https://www.scm.com/doc/AMS/Utilities/TrajectoryAnalysis.html |
|
ChemTraYzer2
Detect reactions from MD simulations
| https://www.scm.com/doc/Workflows/ChemTraYzer2/ChemTraYzer2.html |
|
Utilities
Various utility tools
| https://www.scm.com/doc/AMS/Utilities/TOC.html |
|
Scripting
| https://www.scm.com/doc/Scripting/index.html |
|
Python Scripting Examples
Examples for Python scripting
| https://www.scm.com/doc/PythonExamples/index.html |
|
PLAMS
Python Library for Automating Molecular Simulations
| https://www.scm.com/doc/plams/index.html |
|
amspython
Python stack shipped with AMS
| https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html |
|
pyCRS
Python Scripting with COSMO-RS
| https://www.scm.com/doc/COSMO-RS/Python_Scripting_with_COSMO-RS.html |
|
SCM Base Library
Python library with core modules
| https://www.scm.com/doc/Scripting/LibBase/LibBase.html |
|
reactmap
Atom mapping between reactants and products
| https://www.scm.com/doc/reactmap/index.html |
| Command-line tools | https://www.scm.com/doc/Scripting/Commandline_Tools/Commandline_Tools.html |
| ASE calculator | https://www.scm.com/doc/plams/interfaces/amscalculator.html |
|
pyZacros
Python Library Zacros (Kinetic Monte Carlo)
| https://www.scm.com/doc/pyzacros/index.html |
| AMS2026.1 | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html |
| Other versions | https://www.scm.com/downloads/documentation-previous-versions/ |
|
Scripting | https://www.scm.com/doc/Scripting/index.html |
| Getting Started | https://www.scm.com/doc/Scripting/GettingStarted.html |
| amspython: Python Stack | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html |
| Amsterdam Modeling PySuite | https://www.scm.com/doc/Scripting/amsterdam-modeling-pysuite.html |
| Command-Line Tools | https://www.scm.com/doc/Scripting/Commandline_Tools/Commandline_Tools.html |
| AMSprep: generate (multiple) ADF jobs | https://www.scm.com/doc/Scripting/Commandline_Tools/AMSprep.html |
| Tutorial: Generate structures for substituent effects screening | https://www.scm.com/doc/Scripting/Commandline_Tools/AMSprepTutorial.html |
| AMSreport: generate reports | https://www.scm.com/doc/Scripting/Commandline_Tools/AMSreport.html |
| KF command line utilities | https://www.scm.com/doc/Scripting/Commandline_Tools/KF_command_line_utilities.html |
| Chemical System | https://www.scm.com/doc/Scripting/ChemicalSystem/ChemicalSystem.html |
| Overview | https://www.scm.com/doc/Scripting/ChemicalSystem/Overview.html |
| Read, write, file formats | https://www.scm.com/doc/Scripting/ChemicalSystem/FileFormats.html |
| Atoms, Bonds, Elements, Electrostatic Embedding | https://www.scm.com/doc/Scripting/ChemicalSystem/AtomsBondsElements.html |
| Atoms | https://www.scm.com/doc/Scripting/ChemicalSystem/Atoms.html |
| Bonds | https://www.scm.com/doc/Scripting/ChemicalSystem/Bonds.html |
| Elements | https://www.scm.com/doc/Scripting/ChemicalSystem/Elements.html |
| Electrostatic Embedding | https://www.scm.com/doc/Scripting/ChemicalSystem/ElectrostaticEmbedding.html |
| Lattice, Periodic Boundary Conditions | https://www.scm.com/doc/Scripting/ChemicalSystem/Lattice.html |
| Charge, mass, formula | https://www.scm.com/doc/Scripting/ChemicalSystem/Properties.html |
| Combine and split | https://www.scm.com/doc/Scripting/ChemicalSystem/CombineSplit.html |
| Geometry Manipulation | https://www.scm.com/doc/Scripting/ChemicalSystem/GeometryManipulation.html |
| Comparison of systems | https://www.scm.com/doc/Scripting/ChemicalSystem/Comparison.html |
| Regions | https://www.scm.com/doc/Scripting/ChemicalSystem/Regions.html |
| Select atoms | https://www.scm.com/doc/Scripting/ChemicalSystem/Selection.html |
| ASE, RDKit and PLAMS | https://www.scm.com/doc/Scripting/ChemicalSystem/ConversionPython.html |
| GUI and notebook integration | https://www.scm.com/doc/Scripting/ChemicalSystem/GUINotebook.html |
| ChemicalSystem Complete API | https://www.scm.com/doc/Scripting/ChemicalSystem/API.html |
| SCM Base Library | https://www.scm.com/doc/Scripting/LibBase/LibBase.html |
| Units | https://www.scm.com/doc/Scripting/LibBase/Units.html |
| Input File | https://www.scm.com/doc/Scripting/LibBase/InputFile.html |
| KFFile | https://www.scm.com/doc/Scripting/LibBase/KFFile.html |
| AKFReader | https://www.scm.com/doc/Scripting/AKF/AKF.html |
| FlexMD | https://www.scm.com/doc/Scripting/FlexMD/FlexMD.html |
| Basic philosophy and intended usage | https://www.scm.com/doc/Scripting/FlexMD/Basic_philosophy_and_intended_usage.html |
| FlexMD functionality summary | https://www.scm.com/doc/Scripting/FlexMD/FlexMD_functionality_summary.html |
| Introduction | https://www.scm.com/doc/Scripting/FlexMD/Introduction.html |
| Molecular Dynamics | https://www.scm.com/doc/Scripting/FlexMD/Molecular_Dynamics.html |
| Multi-scale Molecular Dynamics | https://www.scm.com/doc/Scripting/FlexMD/Multi-scale_Molecular_Dynamics.html |
| Biased Molecular Dynamics | https://www.scm.com/doc/Scripting/FlexMD/Biased_Molecular_Dynamics.html |
| Working with FlexMD | https://www.scm.com/doc/Scripting/FlexMD/Working_with_FlexMD.html |
| Creating a molecule object | https://www.scm.com/doc/Scripting/FlexMD/Creating_a_molecule_object.html |
| Creating a ForceJob | https://www.scm.com/doc/Scripting/FlexMD/Creating_a_ForceJob.html |
| Creating and running the MD job | https://www.scm.com/doc/Scripting/FlexMD/Creating_and_running_the_MD_job.html |
| Required Citations | https://www.scm.com/doc/Scripting/FlexMD/Required_citations.html |
| References | https://www.scm.com/doc/Scripting/FlexMD/References.html |
| AuToGraFS | https://www.scm.com/doc/Scripting/AuToGraFS/AuToGraFS.html |
| General AuToGraFS Scripting concepts | https://www.scm.com/doc/Scripting/AuToGraFS/General_AuToGraFS_concepts.html |
| AuToGraFS Examples | https://www.scm.com/doc/Scripting/AuToGraFS/AuToGraFS_Examples.html |
| General | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#general |
| Python packages available in amspython | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#python-packages-available-in-amspython |
| Installing new modules in the AMS Python Stack | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#installing-new-modules-in-the-ams-python-stack |
| Running JupyterLab (Jupyter Notebooks) | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#running-jupyterlab-jupyter-notebooks |
| Run Jupyter notebooks through VS Code | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#run-jupyter-notebooks-through-vs-code |
| Method 1: Use an existing Jupyter server in VS Code | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#method-1-use-an-existing-jupyter-server-in-vs-code |
| Method 2: Create a conda environment that runs amspython | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#method-2-create-a-conda-environment-that-runs-amspython |
| Execute a notebook from the command-line | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#execute-a-notebook-from-the-command-line |
| Jupyter frequently asked questions | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#jupyter-frequently-asked-questions |
| Select kernel | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#select-kernel |
| Notebook is not trusted | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#notebook-is-not-trusted |
| — Logging error — | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#logging-error |
| Python virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#python-virtual-environment |
| Default Python virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#default-python-virtual-environment |
| Virtual environments for different AMS versions | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#virtual-environments-for-different-ams-versions |
| Changing the location of the Python virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#changing-the-location-of-the-python-virtual-environment |
| Disabling the virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#disabling-the-virtual-environment |
| Uninstalling the virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#uninstalling-the-virtual-environment |
| Reinstalling the virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#reinstalling-the-virtual-environment |
| Useful commands | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#useful-commands |
| Documentation | https://www.scm.com/doc/Documentation/index.html |
| Scripting | https://www.scm.com/doc/Scripting/index.html |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#amspython-python-stack |
| Python Examples | https://www.scm.com/doc/PythonExamples/index.html |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#general |
| Enthought Python Distribution | https://www.enthought.com/ |
| Getting Started | https://www.scm.com/doc/Scripting/GettingStarted.html#gettingstarted |
| Useful commands | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#usefulcommands |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#python-packages-available-in-amspython |
| PLAMS | https://www.scm.com/doc/plams/index.html |
| pyCRS | https://www.scm.com/doc/COSMO-RS/Python_Scripting_with_COSMO-RS.html |
| input-classes | https://www.scm.com/doc/pisa/index.html |
| SCM Base Library | https://www.scm.com/doc/Scripting/LibBase/LibBase.html#libbase |
| AKFReader | https://www.scm.com/doc/Scripting/AKF/AKF.html#akf-python |
| external calculators with AMS | https://www.scm.com/doc/ASE/index.html |
| AMS as an ASE calculator | https://www.scm.com/doc/plams/interfaces/amscalculator.html |
| pyZacros | https://www.scm.com/doc/pyzacros/index.html |
| FlexMD | https://www.scm.com/doc/Scripting/FlexMD/FlexMD.html#flexmd |
| AuToGraFS | https://www.scm.com/doc/Scripting/AuToGraFS/AuToGraFS.html#autografs |
| package manager | https://www.scm.com/doc/Installation/Optional_Components.html |
| Jupyter lab | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#jupyter |
| PyADF | https://github.com/chjacob-tubs/pyadf-releases |
| tcutility | https://theochem-vu.github.io/TCutility/ |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#installing-new-modules-in-the-ams-python-stack |
| PyPI | https://pypi.python.org/pypi |
| virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#virtualenvironment |
| virtual environment | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#virtualenvironment |
| package
manager | https://www.scm.com/doc/Installation/Optional_Components.html |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#running-jupyterlab-jupyter-notebooks |
| Run Jobs with Jupyter Notebooks | https://www.scm.com/doc/Tutorials/GettingStarted/JupyterLab/JupyterLab.html |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#run-jupyter-notebooks-through-vs-code |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#method-1-use-an-existing-jupyter-server-in-vs-code |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#method-2-create-a-conda-environment-that-runs-amspython |
| Get started with conda or mamba | https://www.scm.com/doc/ASE/python_environments.html#get-started-with-conda-or-mamba |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#execute-a-notebook-from-the-command-line |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#jupyter-frequently-asked-questions |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#select-kernel |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#notebook-is-not-trusted |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#logging-error |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#python-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#default-python-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#virtual-environments-for-different-ams-versions |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#changing-the-location-of-the-python-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#disabling-the-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#uninstalling-the-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#reinstalling-the-virtual-environment |
| ¶ | https://www.scm.com/doc/Scripting/Python_Stack/Python_Stack.html#useful-commands |
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PreviousGetting Started
| https://www.scm.com/doc/Scripting/GettingStarted.html |
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Amsterdam Modeling PySuite
| https://www.scm.com/doc/Scripting/amsterdam-modeling-pysuite.html |
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