All Examples

Title	Tags
2D Reaction Schematics from PLAMS Molecules	Technical Visualization Reaction equations
Active Learning: Committee Uncertainties and ReactionBoost for a Gasphase Reaction	MLPotential Active Learning ParAMS M3GNet ReactionBoost Committee Models
Active Learning: Conformer Training with CREST	MLPotential Active Learning ParAMS M3GNet Conformers CREST
Active Learning: Continue with a New System	MLPotential Active Learning ParAMS M3GNet Transfer Learning
Active Learning: Li-Vacancy Diffusion NEB in LiTiS2	MLPotential Active Learning ParAMS M3GNet NEB Diffusion
Active Learning: Liquid Water Properties	MLPotential Active Learning ParAMS M3GNet Molecular Dynamics Water
Active Learning: Ru/H Part 1, Initial Reference Scans	MLPotential Active Learning ParAMS M3GNet Surface Chemistry PES Scan
Active Learning: Ru/H Part 2, Surface PES Scans	MLPotential Active Learning ParAMS M3GNet Surface Chemistry PES Scan
Active Learning: Ru/H Part 3, Gas Snapshots	MLPotential Active Learning ParAMS M3GNet Surface Chemistry Molecular Dynamics
Active Learning: Ru/H Part 4, Initial Training	MLPotential Active Learning ParAMS M3GNet Surface Chemistry
Active Learning: Ru/H Part 5, Molecule-Gun MD	MLPotential Active Learning ParAMS M3GNet Surface Chemistry Molecular Dynamics
Active Learning: Single-Molecule Comparison to M3GNet-UP-2022	MLPotential Active Learning ParAMS M3GNet Benchmark
Active Learning: Single-Molecule Production Simulation	MLPotential Active Learning ParAMS M3GNet Geometry Optimization
Active Learning: Single-Molecule Results	MLPotential Active Learning ParAMS M3GNet Analysis
Active Learning: Single-Molecule Setup and Run	MLPotential Active Learning ParAMS M3GNet Molecular Dynamics
ADF and COSMO-RS Workflow	COSMO-RS ADF Property prediction Solubility pyCRS
ADF Fragment Analysis Recipe	ADF Bonding Analysis EDA
Automated Transition-State Workflow for a Diels-Alder Addition	DFTB Transition State Search Catalysis Molecular Dynamics
Balancing Reaction Equations from Formulas and Structures	Technical Reaction equations ChemicalSystem
BAND Fragment Analysis Recipe	BAND Bonding Analysis EDA
Band structure with BAND (HSE06, DFT+U)	BAND Materials Science Band structure Hybrid functional
Band structure with DFTB (SCC-DFTB, GFN1-xTB)	DFTB Materials Science Band structure
Band structure with Quantum ESPRESSO (PBE)	Quantum ESPRESSO Materials Science Band structure
Basic MD Trajectory Analysis with PLAMS	Molecular Dynamics Analysis Trajectory analysis
Benchmarking ML Potentials for Hydrocarbon Isomerization Energies	MLPotential M3GNet MACE Benchmark
Benchmarking Reaction Energies across AMS Engines	ADF BAND DFTB Benchmark Reaction energy
Benchmarking Reaction Energies across Basis Sets	ADF Benchmark Reaction energy Basis sets
Breaking bonds in a ring molecule and modifying distances for NEB	Building structures Technical DFTB NEB
BSSE correction for H2O on ZnO(10-10)	BAND BSSE Adsorption Surfaces Materials Science
Building Packed Systems with Packmol	Building structures Molecular Dynamics Packmol
Building Surfaces and Slabs	ChemicalSystem Building structures Surfaces Materials Science
Charge Transfer Integrals with ADF	ADF Fragment calculations Technical
Charged Systems with the AMS ASE Calculator	ADF ASE calculator Technical
ChemicalSystem: Getting Started With AMS System Blocks	Getting Started Technical ChemicalSystem AMS system
Complete guide to storing and converting PLAMS Molecules between Python libraries and file formats	Technical pymatgen ChemicalSystem ASE
Composing AMS Input Blocks with PLAMS Settings	Technical Settings AMS input
Conformer Generation for Multiple Molecules	GFNFF Conformers
Conformer Generation, Rescoring, and Filtering	GFNFF DFTB Conformers
Constrained Geometry Optimization with AMSWorker	ForceField Geometry Optimization Technical
Convert Between ParAMS and ASE Formats	ParAMS Technical ASE Data conversion
Convert from XYZ/OUTCAR to RKF	Trajectory analysis Molecular Dynamics Technical
Convert RKF Trajectory to DCD Format	Trajectory analysis Molecular Dynamics Technical
Correlation Plots for Computed Results	Analysis Plotting Benchmark
COSMO-RS Conformer Workflows for Acetic Acid	COSMO-RS Conformers
Diffusion Coefficient Supercell Dependence	Molecular Dynamics Diffusion Lennard-Jones MSD Finite-size effects
Diffusion Coefficient Temperature Dependence	Molecular Dynamics Diffusion Lennard-Jones MSD Parallel jobs
Engine ASE with Import and File Calculators	ASE engine Technical
Extract Frames from an AMS Trajectory with PLAMS	Molecular Dynamics Trajectory analysis Technical
Franck-Condon Vibronic DOS with ADF	ADF Franck-Condon Vibrational spectroscopy DOS Spectroscopy
Gasphase IR spectrum from Molecular Dynamics	GFNFF Spectroscopy IR spectrum Molecular Dynamics
Generating COSMO-RS Compounds from XYZ Files and SMILES	COSMO-RS ADF Conformers
Getting Started: Geometry Optimization of Water	DFTB Getting Started Geometry Optimization Vibrational Analysis
H-H Spin-Spin Coupling with ADF	ADF NMR Spectroscopy
Helium Dimer Dissociation Curve with ADF	ADF Potential energy surface
Hybrid engine UseLowestEnergy	ADF PES Scan Technical
Hydrogen Bonds from MD	Molecular Dynamics Analysis Hydrogen bonds Trajectory analysis Spectroscopy FlexMD
i-PI Path Integral MD with AMS	ASE Molecular Dynamics Path integral Technical
Import Training Data with ResultsImporter	ParAMS Technical Reference data
In-cell adsorption energies with ReaxFF	ReaxFF Adsorption Surfaces Materials Science
IR Spectrum of an H2O Dimer from MD	Molecular Dynamics IR spectrum DFTB Technical Spectroscopy
Logging and Job Log Files in PLAMS	Technical Logging Workflow automation
M3GNet Custom Model	MLPotential ParAMS M3GNet Geometry Optimization
M3GNet Universal Potential: M3GNet-UP-2022	MLPotential M3GNet Geometry Optimization
ML Training with PES Scans and Geometry Optimizations	ParAMS MLPotential M3GNet PES Scan
Molecular Dynamics and Sampling	Molecular Dynamics
Molecular Dynamics with Python	Molecular Dynamics ForceField UFF NVE NVT NPT
Molecule and Bond Counts from Reactive MD	Molecular Dynamics Trajectory analysis ReaxFF Technical
Molecule Tools for Inspection and Manipulation	Technical Building structures Visualization
NBO Analysis with ADF and PLAMS	ADF Bonding Analysis
NEB for Li diffusion in layered LiTiS2 (M3GNet)	MLPotential Materials Science M3GNet NEB Diffusion
Nudged Elastic Band (NEB) for gasphase reaction with DFTB	DFTB NEB Catalysis
ParAMS for DFTB: Silicon Band Structure	ParAMS DFTB BAND Materials Science Band structure
PLUMED Biasing in AMS Molecular Dynamics	ReaxFF Molecular Dynamics PLUMED Biasing
Property Prediction from SMILES with pyCRS	COSMO-RS Property prediction pyCRS
Python Examples	:render-only: :category: programs :category: application_areas
Quantum ESPRESSO IR and Raman spectra for BeO	Quantum ESPRESSO Materials Science IR spectrum Raman Spectroscopy
Quantum ESPRESSO phonon band structure and DOS for BeO	Quantum ESPRESSO Materials Science Phonons DOS Thermodynamics
Quick Comparison	ChemicalSystem PLAMS Technical
Reaction Discovery with ReaxFF	ReaxFF Reaction discovery Molecular Dynamics
Reaction Paths and Reactivity	NEB Transition State
ReaxFF Density Equilibration	Molecular Dynamics ReaxFF Density NVT NPT
Reduction and Oxidation Potentials	ADF Redox Technical Batteries
Reorganization Energy Recipe	ADF Reaction energy
Reuse ForceField Parameters From Previous Calculations	ForceField Technical Workflow automation
Run a ParAMSJob for Lennard-Jones	ParAMS Getting Started Lennard-Jones
Running Many PLAMS Jobs in Parallel	Technical Parallelization Workflow automation
Screening Molecules for Promising Electronic Excitations	ADF DFTB Excitations
Set Up ParAMSJob Settings	ParAMS Technical Settings
Simulating XRD Patterns from a CIF Structure	Materials Science XRD ASE
Substituting Functional Groups in Molecules	Technical Building structures Visualization
Summarizing PLAMS Jobs with JobAnalysis	Technical Analysis Workflow automation
Surface Energy with ReaxFF	ReaxFF Materials Science Surface energy Surfaces
Train an M3GNet Potential with ParAMS	ParAMS MLPotential M3GNet
Transition State: Initial guess from PESScan	DFTB PES Scan Transition State Search
Tuning the Range Separation Parameter in ADF	ADF XC functionals Technical
Using AMS as an ASE Calculator	ASE calculator Technical Geometry Optimization
VASP geometry optimization with PLAMS	VASP ChemicalSystem Geometry Optimization External engines
Viscosity from MD with the Green-Kubo Formalism	Molecular Dynamics Analysis Viscosity
Visualizing Structures with PLAMS	Technical Visualization Molecular Dynamics