SourceCode

• ASEWrappers package
  • Submodules
  • ASEWrappers.DataContainer module
    • DataTrajectory
      • DataTrajectory.append()
      • DataTrajectory.storeTxtFile()
    • Frame
      • Frame.keys
      • Frame.vals
  • ASEWrappers.atomic_structure module
    • AtomicStructure
      • AtomicStructure._atoms
      • AtomicStructure._label
      • AtomicStructure.cell
      • AtomicStructure.cellpar
      • AtomicStructure.cohesive_energy()
      • AtomicStructure.computeMSD()
      • AtomicStructure.computeNearestNeighbour()
      • AtomicStructure.forces
      • AtomicStructure.fromFile()
      • AtomicStructure.getAtoms()
      • AtomicStructure.get_all_distances
      • AtomicStructure.get_atomic_numbers
      • AtomicStructure.get_cell
      • AtomicStructure.internal_pressure
      • AtomicStructure.kinetic_energy
      • AtomicStructure.label
      • AtomicStructure.lattice_constant
      • AtomicStructure.masses
      • AtomicStructure.positions
      • AtomicStructure.potential
      • AtomicStructure.potential_energy
      • AtomicStructure.setVelocitiesMB()
      • AtomicStructure.stress
      • AtomicStructure.symbols
      • AtomicStructure.temperature
      • AtomicStructure.total_energy
      • AtomicStructure.velocities
      • AtomicStructure.volume
  • ASEWrappers.contextManager module
    • suppress_cpp_output()
  • ASEWrappers.integrator module
    • BerendsenNPTIntegrator
      • BerendsenNPTIntegrator.ensemble
    • Integrator
      • Integrator.attach()
      • Integrator.clearData()
      • Integrator.ensemble
      • Integrator.run()
    • IsotropicMTKNPTIntegrator
      • IsotropicMTKNPTIntegrator.ensemble
    • LangevinIntegrator
      • LangevinIntegrator.ensemble
    • VelocityVerletIntegrator
      • VelocityVerletIntegrator.ensemble
  • ASEWrappers.potential module
    • EMTPotential
      • EMTPotential.getASEPotentialCalculator()
    • LennardJonesPotential
      • LennardJonesPotential.getASEPotentialCalculator()
    • MACEPotential
      • MACEPotential.getASEPotentialCalculator()
    • Potential
      • Potential.getASEPotentialCalculator()
  • Module contents
• CalculateDelta module
  • getDopant()
• DBClasses module
  • MDAbadParameters
    • MDAbadParameters.key
    • MDAbadParameters.depth
    • MDAbadParameters.expansion_factor
    • MDAbadParameters.defect_index
    • MDAbadParameters.lattice_constant
  • MDDefectCell
    • MDDefectCell.host_name
    • MDDefectCell.defect_structure
    • MDDefectCell.defect_name
    • MDDefectCell.key
  • MDDefectInfos
    • MDDefectInfos.key
    • MDDefectInfos.host_name
    • MDDefectInfos.defect_name
    • MDDefectInfos.defect_type
    • MDDefectInfos.configuration
    • MDDefectInfos.vacancy
    • MDDefectInfos.substitutional
    • MDDefectInfos.interstitial
  • MDDelta
    • MDDelta.host
    • MDDelta.dopant
    • MDDelta.defect
    • MDDelta.key
    • MDDelta.delta
  • MDScreenResult
    • MDScreenResult.host
    • MDScreenResult.dopant
    • MDScreenResult.defect
    • MDScreenResult.key
    • MDScreenResult.delta
• HTP module
  • main()
• MDClasses module
  • EquilibriumRun
    • EquilibriumRun.run()
  • MDBase
    • MDBase.integrator
    • MDBase.sample_data
    • MDBase.run_type
  • SampleRun
    • SampleRun.run()
  • StretchRun
    • StretchRun.appendStress()
    • StretchRun.run()
• MDDefectUtils module
  • getAllDefectKeys()
  • getDelta()
  • getMDDelta()
  • getMDKeys()
  • notDoneDelta()
  • notDoneMDRuns()
• MDManager module
  • MDManager
    • MDManager.run()
• MDStoreUtils module
  • CommitAndClose()
  • saveMDAbadParameters()
  • saveMDDefectCell()
  • saveMDScreenResult()
• MolecularDynamics module
  • main()
• PostProcessing module
• PreProcessing module
  • PreProcessing
    • PreProcessing.checkDistances()
    • PreProcessing.checkLattice()
    • PreProcessing.createSimulationList()
    • PreProcessing.getIntegrator()
    • PreProcessing.getPotential()
    • PreProcessing.readAtomicStructure()
    • PreProcessing.readSettings()
    • PreProcessing.sanityCheckAtomicStructure()
    • PreProcessing.sanityCheckSettings()
• QuantityCalculator module
  • QuantityCalculator
    • QuantityCalculator.calculateModuli()
    • QuantityCalculator.computeBulkModulus()
    • QuantityCalculator.computeDebyeTemperature()
    • QuantityCalculator.computeLindemannIndex()
    • QuantityCalculator.computeSelfDiffusionCoefficient()
    • QuantityCalculator.computeSpecificHeatNVT()
    • QuantityCalculator.nearestNeighborsMean()
• SimulationInput module
  • SimulationSettings
• Utils package
  • Submodules
  • Utils.LJRegistry module
    • LJParams()
    • calcMaxRc()
  • Utils.equilibriumCondition module
    • EquilibriumCondition
      • EquilibriumCondition.checkInternalPressureStable()
      • EquilibriumCondition.checkStable()
  • Utils.exportCifs module
    • get_defect_cif()
  • Utils.inputParser module
    • InputParser
      • InputParser.addArguments()
      • InputParser.parseList()
    • SingleMetavarHelpFormatter
  • Utils.logger module
    • CustomFormatter
      • CustomFormatter.COLORS
      • CustomFormatter.RESET
      • CustomFormatter.format()
    • loggerSetup()
  • Utils.numerics module
    • fitter()
    • numericalDerivative()
    • sortRealignAndFilter()
  • Utils.plotting module
    • fitter()
    • flattenDict()
    • numericalDerivative()
    • plot()
    • sortRealignAndFilter()
  • Utils.stretchFunctions module
    • calculateCMatrix()
    • secondOrderNumericalDerivative()
  • Utils.unitConversions module
    • GPascalToAu()
    • a1ToM1()
    • a2ToM2()
    • a3ToM3()
    • atomicMassTokg()
    • auToGPascal()
    • auToPascal()
    • evToJ()
    • hartreePerbohr3ToJPerM3()
    • jToEv()
    • kgToAtomicMass()
    • m2ToA2()
    • m3ToA3()
    • mToA()
    • pascalToAu()
    • selfDiffusionCoeffAuToSI()
    • specificHeatAuToSI()
  • Module contents
• Visualizer module
  • Visualizer
    • Visualizer.visualize()
• getRunResult module