Index

_

_atoms (ASEWrappers.atomic_structure.AtomicStructure attribute)

_label (ASEWrappers.atomic_structure.AtomicStructure attribute)

A

a1ToM1() (in module Utils.unitConversions) a2ToM2() (in module Utils.unitConversions) a3ToM3() (in module Utils.unitConversions) addArguments() (Utils.inputParser.InputParser method) append() (ASEWrappers.DataContainer.DataTrajectory method) appendStress() (MDClasses.StretchRun method) ASEWrappers module ASEWrappers.atomic_structure module ASEWrappers.contextManager module

ASEWrappers.DataContainer module ASEWrappers.integrator module ASEWrappers.potential module atomicMassTokg() (in module Utils.unitConversions) AtomicStructure (class in ASEWrappers.atomic_structure) attach() (ASEWrappers.integrator.Integrator method) auToGPascal() (in module Utils.unitConversions) auToPascal() (in module Utils.unitConversions)

B

BerendsenNPTIntegrator (class in ASEWrappers.integrator)

C

calcMaxRc() (in module Utils.LJRegistry) calculateCMatrix() (in module Utils.stretchFunctions) CalculateDelta module calculateModuli() (QuantityCalculator.QuantityCalculator static method) cell (ASEWrappers.atomic_structure.AtomicStructure property) cellpar (ASEWrappers.atomic_structure.AtomicStructure property) checkDistances() (PreProcessing.PreProcessing method) checkInternalPressureStable() (Utils.equilibriumCondition.EquilibriumCondition static method) checkLattice() (PreProcessing.PreProcessing method) checkStable() (Utils.equilibriumCondition.EquilibriumCondition static method) clearData() (ASEWrappers.integrator.Integrator method)

cohesive_energy() (ASEWrappers.atomic_structure.AtomicStructure method) COLORS (Utils.logger.CustomFormatter attribute) CommitAndClose() (in module MDStoreUtils) computeBulkModulus() (QuantityCalculator.QuantityCalculator static method) computeDebyeTemperature() (QuantityCalculator.QuantityCalculator static method) computeLindemannIndex() (QuantityCalculator.QuantityCalculator static method) computeMSD() (ASEWrappers.atomic_structure.AtomicStructure method) computeNearestNeighbour() (ASEWrappers.atomic_structure.AtomicStructure method) computeSelfDiffusionCoefficient() (QuantityCalculator.QuantityCalculator static method) computeSpecificHeatNVT() (QuantityCalculator.QuantityCalculator static method) configuration (DBClasses.MDDefectInfos attribute) createSimulationList() (PreProcessing.PreProcessing method) CustomFormatter (class in Utils.logger)

D

DataTrajectory (class in ASEWrappers.DataContainer) DBClasses module defect (DBClasses.MDDelta attribute) (DBClasses.MDScreenResult attribute) defect_index (DBClasses.MDAbadParameters attribute) defect_name (DBClasses.MDDefectCell attribute) (DBClasses.MDDefectInfos attribute)

defect_structure (DBClasses.MDDefectCell attribute) defect_type (DBClasses.MDDefectInfos attribute) delta (DBClasses.MDDelta attribute) (DBClasses.MDScreenResult attribute) depth (DBClasses.MDAbadParameters attribute) dopant (DBClasses.MDDelta attribute) (DBClasses.MDScreenResult attribute)

E

EMTPotential (class in ASEWrappers.potential) ensemble (ASEWrappers.integrator.BerendsenNPTIntegrator property) (ASEWrappers.integrator.Integrator property) (ASEWrappers.integrator.IsotropicMTKNPTIntegrator property) (ASEWrappers.integrator.LangevinIntegrator property) (ASEWrappers.integrator.VelocityVerletIntegrator property)

EquilibriumCondition (class in Utils.equilibriumCondition) EquilibriumRun (class in MDClasses) evToJ() (in module Utils.unitConversions) expansion_factor (DBClasses.MDAbadParameters attribute)

F

fitter() (in module Utils.numerics) (in module Utils.plotting) flattenDict() (in module Utils.plotting)

forces (ASEWrappers.atomic_structure.AtomicStructure property) format() (Utils.logger.CustomFormatter method) Frame (class in ASEWrappers.DataContainer) fromFile() (ASEWrappers.atomic_structure.AtomicStructure class method)

G

get_all_distances (ASEWrappers.atomic_structure.AtomicStructure property) get_atomic_numbers (ASEWrappers.atomic_structure.AtomicStructure property) get_cell (ASEWrappers.atomic_structure.AtomicStructure property) get_defect_cif() (in module Utils.exportCifs) getAllDefectKeys() (in module MDDefectUtils) getASEPotentialCalculator() (ASEWrappers.potential.EMTPotential method) (ASEWrappers.potential.LennardJonesPotential method) (ASEWrappers.potential.MACEPotential method) (ASEWrappers.potential.Potential method)

getAtoms() (ASEWrappers.atomic_structure.AtomicStructure method) getDelta() (in module MDDefectUtils) getDopant() (in module CalculateDelta) getIntegrator() (PreProcessing.PreProcessing method) getMDDelta() (in module MDDefectUtils) getMDKeys() (in module MDDefectUtils) getPotential() (PreProcessing.PreProcessing method) getRunResult module GPascalToAu() (in module Utils.unitConversions)

H

hartreePerbohr3ToJPerM3() (in module Utils.unitConversions) host (DBClasses.MDDelta attribute) (DBClasses.MDScreenResult attribute)

host_name (DBClasses.MDDefectCell attribute) (DBClasses.MDDefectInfos attribute) HTP module

I

InputParser (class in Utils.inputParser) Integrator (class in ASEWrappers.integrator) integrator (MDClasses.MDBase attribute)

internal_pressure (ASEWrappers.atomic_structure.AtomicStructure property) interstitial (DBClasses.MDDefectInfos attribute) IsotropicMTKNPTIntegrator (class in ASEWrappers.integrator)

J

jToEv() (in module Utils.unitConversions)

K

key (DBClasses.MDAbadParameters attribute) (DBClasses.MDDefectCell attribute) (DBClasses.MDDefectInfos attribute) (DBClasses.MDDelta attribute) (DBClasses.MDScreenResult attribute)

keys (ASEWrappers.DataContainer.Frame property) kgToAtomicMass() (in module Utils.unitConversions) kinetic_energy (ASEWrappers.atomic_structure.AtomicStructure property)

L

label (ASEWrappers.atomic_structure.AtomicStructure property) LangevinIntegrator (class in ASEWrappers.integrator) lattice_constant (ASEWrappers.atomic_structure.AtomicStructure property) (DBClasses.MDAbadParameters attribute)

LennardJonesPotential (class in ASEWrappers.potential) LJParams() (in module Utils.LJRegistry) loggerSetup() (in module Utils.logger)

M

m2ToA2() (in module Utils.unitConversions) m3ToA3() (in module Utils.unitConversions) MACEPotential (class in ASEWrappers.potential) main() (in module HTP) (in module MolecularDynamics) masses (ASEWrappers.atomic_structure.AtomicStructure property) MDAbadParameters (class in DBClasses) MDBase (class in MDClasses) MDClasses module MDDefectCell (class in DBClasses) MDDefectInfos (class in DBClasses) MDDefectUtils module MDDelta (class in DBClasses) MDManager module MDManager (class in MDManager) MDScreenResult (class in DBClasses) MDStoreUtils module module ASEWrappers ASEWrappers.atomic_structure ASEWrappers.contextManager ASEWrappers.DataContainer ASEWrappers.integrator ASEWrappers.potential CalculateDelta DBClasses getRunResult HTP MDClasses MDDefectUtils MDManager MDStoreUtils MolecularDynamics PreProcessing QuantityCalculator SimulationInput Utils Utils.equilibriumCondition Utils.exportCifs Utils.inputParser Utils.LJRegistry Utils.logger Utils.numerics Utils.plotting Utils.stretchFunctions Utils.unitConversions Visualizer

MolecularDynamics module mToA() (in module Utils.unitConversions)

N

nearestNeighborsMean() (QuantityCalculator.QuantityCalculator static method) notDoneDelta() (in module MDDefectUtils)

notDoneMDRuns() (in module MDDefectUtils) numericalDerivative() (in module Utils.numerics) (in module Utils.plotting)

P

parseList() (Utils.inputParser.InputParser method) pascalToAu() (in module Utils.unitConversions) plot() (in module Utils.plotting) positions (ASEWrappers.atomic_structure.AtomicStructure property) potential (ASEWrappers.atomic_structure.AtomicStructure property)

Potential (class in ASEWrappers.potential) potential_energy (ASEWrappers.atomic_structure.AtomicStructure property) PreProcessing module PreProcessing (class in PreProcessing)

Q

QuantityCalculator module

QuantityCalculator (class in QuantityCalculator)

R

readAtomicStructure() (PreProcessing.PreProcessing method) readSettings() (PreProcessing.PreProcessing method) RESET (Utils.logger.CustomFormatter attribute) run() (ASEWrappers.integrator.Integrator method) (MDClasses.EquilibriumRun method) (MDClasses.SampleRun method) (MDClasses.StretchRun method) (MDManager.MDManager method)

run_type (MDClasses.MDBase attribute)

S

sample_data (MDClasses.MDBase attribute) SampleRun (class in MDClasses) sanityCheckAtomicStructure() (PreProcessing.PreProcessing method) sanityCheckSettings() (PreProcessing.PreProcessing method) saveMDAbadParameters() (in module MDStoreUtils) saveMDDefectCell() (in module MDStoreUtils) saveMDScreenResult() (in module MDStoreUtils) secondOrderNumericalDerivative() (in module Utils.stretchFunctions) selfDiffusionCoeffAuToSI() (in module Utils.unitConversions) setVelocitiesMB() (ASEWrappers.atomic_structure.AtomicStructure method) SimulationInput module

SimulationSettings (class in SimulationInput) SingleMetavarHelpFormatter (class in Utils.inputParser) sortRealignAndFilter() (in module Utils.numerics) (in module Utils.plotting) specificHeatAuToSI() (in module Utils.unitConversions) storeTxtFile() (ASEWrappers.DataContainer.DataTrajectory method) stress (ASEWrappers.atomic_structure.AtomicStructure property) StretchRun (class in MDClasses) substitutional (DBClasses.MDDefectInfos attribute) suppress_cpp_output() (in module ASEWrappers.contextManager) symbols (ASEWrappers.atomic_structure.AtomicStructure property)

T

temperature (ASEWrappers.atomic_structure.AtomicStructure property)

total_energy (ASEWrappers.atomic_structure.AtomicStructure property)

U

Utils module Utils.equilibriumCondition module Utils.exportCifs module Utils.inputParser module Utils.LJRegistry module

Utils.logger module Utils.numerics module Utils.plotting module Utils.stretchFunctions module Utils.unitConversions module

V

vacancy (DBClasses.MDDefectInfos attribute) vals (ASEWrappers.DataContainer.Frame property) velocities (ASEWrappers.atomic_structure.AtomicStructure property) VelocityVerletIntegrator (class in ASEWrappers.integrator)

visualize() (Visualizer.Visualizer method) Visualizer module Visualizer (class in Visualizer) volume (ASEWrappers.atomic_structure.AtomicStructure property)