lammps-interface
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lammps-interface
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__dict__ (lammps_interface.CIFIO.CIF attribute)
(lammps_interface.create_cluster_v2.Cluster attribute)
(lammps_interface.create_cluster_v2.LammpsSimulation attribute)
(lammps_interface.ForceFields.ForceField attribute)
(lammps_interface.InputHandler.Options attribute)
(lammps_interface.lammps_main.LammpsSimulation attribute)
(lammps_interface.lammps_potentials.AnglePotential attribute)
(lammps_interface.lammps_potentials.AnglePotential.Charmm attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2 attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondAngle attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondBond attribute)
(lammps_interface.lammps_potentials.AnglePotential.Cosine attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineDelta attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosinePeriodic attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShift attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineSquared attribute)
(lammps_interface.lammps_potentials.AnglePotential.Dipole attribute)
(lammps_interface.lammps_potentials.AnglePotential.Fourier attribute)
(lammps_interface.lammps_potentials.AnglePotential.FourierSimple attribute)
(lammps_interface.lammps_potentials.AnglePotential.Harmonic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Quartic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Sdk attribute)
(lammps_interface.lammps_potentials.AnglePotential.Table attribute)
(lammps_interface.lammps_potentials.BondPotential attribute)
(lammps_interface.lammps_potentials.BondPotential.Class2 attribute)
(lammps_interface.lammps_potentials.BondPotential.Fene attribute)
(lammps_interface.lammps_potentials.BondPotential.FeneExpand attribute)
(lammps_interface.lammps_potentials.BondPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShift attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShiftCut attribute)
(lammps_interface.lammps_potentials.BondPotential.Morse attribute)
(lammps_interface.lammps_potentials.BondPotential.NonLinear attribute)
(lammps_interface.lammps_potentials.BondPotential.Quartic attribute)
(lammps_interface.lammps_potentials.BondPotential.Table attribute)
(lammps_interface.lammps_potentials.DihedralPotential attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Charmm attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleAngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.BondBond13 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.EndBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.MiddleBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Fourier attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Helix attribute)
(lammps_interface.lammps_potentials.DihedralPotential.MultiHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.nHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Opls attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Quadratic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Table attribute)
(lammps_interface.lammps_potentials.ImproperPotential attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2 attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2.AngleAngle attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cossq attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cvff attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Fourier attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Ring attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Umbrella attribute)
(lammps_interface.lammps_potentials.PairPotential attribute)
(lammps_interface.lammps_potentials.PairPotential.Buck attribute)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCut attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong attribute)
(lammps_interface.lammps_potentials.PairPotential.Table attribute)
(lammps_interface.structure_data.Cell attribute)
(lammps_interface.structure_data.MDMC_config attribute)
__iadd__() (lammps_interface.structure_data.MolecularGraph method)
__init__() (lammps_interface.CIFIO.CIF method)
(lammps_interface.create_cluster_v2.Cluster method)
(lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.InputHandler.Options method)
(lammps_interface.lammps_main.LammpsSimulation method)
(lammps_interface.lammps_potentials.AnglePotential.Charmm method)
(lammps_interface.lammps_potentials.AnglePotential.Class2 method)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondAngle method)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondBond method)
(lammps_interface.lammps_potentials.AnglePotential.Cosine method)
(lammps_interface.lammps_potentials.AnglePotential.CosineDelta method)
(lammps_interface.lammps_potentials.AnglePotential.CosinePeriodic method)
(lammps_interface.lammps_potentials.AnglePotential.CosineShift method)
(lammps_interface.lammps_potentials.AnglePotential.CosineShiftExp method)
(lammps_interface.lammps_potentials.AnglePotential.CosineSquared method)
(lammps_interface.lammps_potentials.AnglePotential.Dipole method)
(lammps_interface.lammps_potentials.AnglePotential.Fourier method)
(lammps_interface.lammps_potentials.AnglePotential.FourierSimple method)
(lammps_interface.lammps_potentials.AnglePotential.Harmonic method)
(lammps_interface.lammps_potentials.AnglePotential.Quartic method)
(lammps_interface.lammps_potentials.AnglePotential.Sdk method)
(lammps_interface.lammps_potentials.AnglePotential.Table method)
(lammps_interface.lammps_potentials.BondPotential.Class2 method)
(lammps_interface.lammps_potentials.BondPotential.Fene method)
(lammps_interface.lammps_potentials.BondPotential.FeneExpand method)
(lammps_interface.lammps_potentials.BondPotential.Harmonic method)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShift method)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShiftCut method)
(lammps_interface.lammps_potentials.BondPotential.Morse method)
(lammps_interface.lammps_potentials.BondPotential.NonLinear method)
(lammps_interface.lammps_potentials.BondPotential.Quartic method)
(lammps_interface.lammps_potentials.BondPotential.Table method)
(lammps_interface.lammps_potentials.DihedralPotential.Charmm method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2 method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleAngleTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.BondBond13 method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.EndBondTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.MiddleBondTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.CosineShiftExp method)
(lammps_interface.lammps_potentials.DihedralPotential.Fourier method)
(lammps_interface.lammps_potentials.DihedralPotential.Harmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.Helix method)
(lammps_interface.lammps_potentials.DihedralPotential.MultiHarmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.nHarmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.Opls method)
(lammps_interface.lammps_potentials.DihedralPotential.Quadratic method)
(lammps_interface.lammps_potentials.DihedralPotential.Table method)
(lammps_interface.lammps_potentials.ImproperPotential.Class2 method)
(lammps_interface.lammps_potentials.ImproperPotential.Class2.AngleAngle method)
(lammps_interface.lammps_potentials.ImproperPotential.Cossq method)
(lammps_interface.lammps_potentials.ImproperPotential.Cvff method)
(lammps_interface.lammps_potentials.ImproperPotential.Fourier method)
(lammps_interface.lammps_potentials.ImproperPotential.Harmonic method)
(lammps_interface.lammps_potentials.ImproperPotential.Ring method)
(lammps_interface.lammps_potentials.ImproperPotential.Umbrella method)
(lammps_interface.lammps_potentials.PairPotential.Buck method)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse method)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCut method)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong method)
(lammps_interface.lammps_potentials.PairPotential.Table method)
(lammps_interface.Molecules.EPM2_CO2 method)
(lammps_interface.Molecules.TIP4P_Water method)
(lammps_interface.Molecules.TIP5P_Water method)
(lammps_interface.structure_data.Cell method)
(lammps_interface.structure_data.MDMC_config method)
(lammps_interface.structure_data.MolecularGraph method)
__metaclass__ (lammps_interface.ForceFields.ForceField attribute)
__module__ (lammps_interface.CIFIO.CIF attribute)
(lammps_interface.create_cluster_v2.Cluster attribute)
(lammps_interface.create_cluster_v2.LammpsSimulation attribute)
(lammps_interface.ForceFields.BTW_FF attribute)
(lammps_interface.ForceFields.Dreiding attribute)
(lammps_interface.ForceFields.Dubbeldam attribute)
(lammps_interface.ForceFields.EPM2_CO2 attribute)
(lammps_interface.ForceFields.FMOFCu attribute)
(lammps_interface.ForceFields.ForceField attribute)
(lammps_interface.ForceFields.MOF_FF attribute)
(lammps_interface.ForceFields.OverwriteFF attribute)
(lammps_interface.ForceFields.SPC_E attribute)
(lammps_interface.ForceFields.TIP3P attribute)
(lammps_interface.ForceFields.TIP4P attribute)
(lammps_interface.ForceFields.TIP5P attribute)
(lammps_interface.ForceFields.UFF attribute)
(lammps_interface.ForceFields.UFF4MOF attribute)
(lammps_interface.ForceFields.UserFF attribute)
(lammps_interface.InputHandler.Options attribute)
(lammps_interface.lammps_main.LammpsSimulation attribute)
(lammps_interface.lammps_potentials.AnglePotential attribute)
(lammps_interface.lammps_potentials.AnglePotential.Charmm attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2 attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondAngle attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondBond attribute)
(lammps_interface.lammps_potentials.AnglePotential.Cosine attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineDelta attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosinePeriodic attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShift attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineSquared attribute)
(lammps_interface.lammps_potentials.AnglePotential.Dipole attribute)
(lammps_interface.lammps_potentials.AnglePotential.Fourier attribute)
(lammps_interface.lammps_potentials.AnglePotential.FourierSimple attribute)
(lammps_interface.lammps_potentials.AnglePotential.Harmonic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Quartic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Sdk attribute)
(lammps_interface.lammps_potentials.AnglePotential.Table attribute)
(lammps_interface.lammps_potentials.BondPotential attribute)
(lammps_interface.lammps_potentials.BondPotential.Class2 attribute)
(lammps_interface.lammps_potentials.BondPotential.Fene attribute)
(lammps_interface.lammps_potentials.BondPotential.FeneExpand attribute)
(lammps_interface.lammps_potentials.BondPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShift attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShiftCut attribute)
(lammps_interface.lammps_potentials.BondPotential.Morse attribute)
(lammps_interface.lammps_potentials.BondPotential.NonLinear attribute)
(lammps_interface.lammps_potentials.BondPotential.Quartic attribute)
(lammps_interface.lammps_potentials.BondPotential.Table attribute)
(lammps_interface.lammps_potentials.DihedralPotential attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Charmm attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleAngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.BondBond13 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.EndBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.MiddleBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Fourier attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Helix attribute)
(lammps_interface.lammps_potentials.DihedralPotential.MultiHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.nHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Opls attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Quadratic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Table attribute)
(lammps_interface.lammps_potentials.ImproperPotential attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2 attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2.AngleAngle attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cossq attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cvff attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Fourier attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Ring attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Umbrella attribute)
(lammps_interface.lammps_potentials.PairPotential attribute)
(lammps_interface.lammps_potentials.PairPotential.Buck attribute)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCut attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong attribute)
(lammps_interface.lammps_potentials.PairPotential.Table attribute)
(lammps_interface.Molecules.CO2 attribute)
(lammps_interface.Molecules.EPM2_CO2 attribute)
(lammps_interface.Molecules.Molecule attribute)
(lammps_interface.Molecules.TIP4P_Water attribute)
(lammps_interface.Molecules.TIP5P_Water attribute)
(lammps_interface.Molecules.Water attribute)
(lammps_interface.structure_data.Cell attribute)
(lammps_interface.structure_data.MDMC_config attribute)
(lammps_interface.structure_data.MolecularGraph attribute)
__or__() (lammps_interface.structure_data.MolecularGraph method)
__repr__() (lammps_interface.lammps_potentials.PairPotential.Buck method)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse method)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCut method)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong method)
(lammps_interface.lammps_potentials.PairPotential.Table method)
__str__() (lammps_interface.CIFIO.CIF method)
(lammps_interface.lammps_potentials.AnglePotential.Charmm method)
(lammps_interface.lammps_potentials.AnglePotential.Class2 method)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondAngle method)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondBond method)
(lammps_interface.lammps_potentials.AnglePotential.Cosine method)
(lammps_interface.lammps_potentials.AnglePotential.CosineDelta method)
(lammps_interface.lammps_potentials.AnglePotential.CosinePeriodic method)
(lammps_interface.lammps_potentials.AnglePotential.CosineShift method)
(lammps_interface.lammps_potentials.AnglePotential.CosineShiftExp method)
(lammps_interface.lammps_potentials.AnglePotential.CosineSquared method)
(lammps_interface.lammps_potentials.AnglePotential.Dipole method)
(lammps_interface.lammps_potentials.AnglePotential.Fourier method)
(lammps_interface.lammps_potentials.AnglePotential.FourierSimple method)
(lammps_interface.lammps_potentials.AnglePotential.Harmonic method)
(lammps_interface.lammps_potentials.AnglePotential.Quartic method)
(lammps_interface.lammps_potentials.AnglePotential.Sdk method)
(lammps_interface.lammps_potentials.BondPotential.Class2 method)
(lammps_interface.lammps_potentials.BondPotential.Fene method)
(lammps_interface.lammps_potentials.BondPotential.FeneExpand method)
(lammps_interface.lammps_potentials.BondPotential.Harmonic method)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShift method)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShiftCut method)
(lammps_interface.lammps_potentials.BondPotential.Morse method)
(lammps_interface.lammps_potentials.BondPotential.NonLinear method)
(lammps_interface.lammps_potentials.BondPotential.Quartic method)
(lammps_interface.lammps_potentials.DihedralPotential.Charmm method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2 method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleAngleTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.BondBond13 method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.EndBondTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.MiddleBondTorsion method)
(lammps_interface.lammps_potentials.DihedralPotential.CosineShiftExp method)
(lammps_interface.lammps_potentials.DihedralPotential.Fourier method)
(lammps_interface.lammps_potentials.DihedralPotential.Harmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.Helix method)
(lammps_interface.lammps_potentials.DihedralPotential.MultiHarmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.nHarmonic method)
(lammps_interface.lammps_potentials.DihedralPotential.Opls method)
(lammps_interface.lammps_potentials.DihedralPotential.Quadratic method)
(lammps_interface.lammps_potentials.ImproperPotential.Class2 method)
(lammps_interface.lammps_potentials.ImproperPotential.Class2.AngleAngle method)
(lammps_interface.lammps_potentials.ImproperPotential.Cossq method)
(lammps_interface.lammps_potentials.ImproperPotential.Cvff method)
(lammps_interface.lammps_potentials.ImproperPotential.Fourier method)
(lammps_interface.lammps_potentials.ImproperPotential.Harmonic method)
(lammps_interface.lammps_potentials.ImproperPotential.Ring method)
(lammps_interface.lammps_potentials.ImproperPotential.Umbrella method)
(lammps_interface.lammps_potentials.PairPotential.Buck method)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse method)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCut method)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong method)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong method)
(lammps_interface.lammps_potentials.PairPotential.Table method)
__weakref__ (lammps_interface.CIFIO.CIF attribute)
(lammps_interface.create_cluster_v2.Cluster attribute)
(lammps_interface.create_cluster_v2.LammpsSimulation attribute)
(lammps_interface.ForceFields.ForceField attribute)
(lammps_interface.InputHandler.Options attribute)
(lammps_interface.lammps_main.LammpsSimulation attribute)
(lammps_interface.lammps_potentials.AnglePotential attribute)
(lammps_interface.lammps_potentials.AnglePotential.Charmm attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2 attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondAngle attribute)
(lammps_interface.lammps_potentials.AnglePotential.Class2.BondBond attribute)
(lammps_interface.lammps_potentials.AnglePotential.Cosine attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineDelta attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosinePeriodic attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShift attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.AnglePotential.CosineSquared attribute)
(lammps_interface.lammps_potentials.AnglePotential.Dipole attribute)
(lammps_interface.lammps_potentials.AnglePotential.Fourier attribute)
(lammps_interface.lammps_potentials.AnglePotential.FourierSimple attribute)
(lammps_interface.lammps_potentials.AnglePotential.Harmonic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Quartic attribute)
(lammps_interface.lammps_potentials.AnglePotential.Sdk attribute)
(lammps_interface.lammps_potentials.AnglePotential.Table attribute)
(lammps_interface.lammps_potentials.BondPotential attribute)
(lammps_interface.lammps_potentials.BondPotential.Class2 attribute)
(lammps_interface.lammps_potentials.BondPotential.Fene attribute)
(lammps_interface.lammps_potentials.BondPotential.FeneExpand attribute)
(lammps_interface.lammps_potentials.BondPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShift attribute)
(lammps_interface.lammps_potentials.BondPotential.HarmonicShiftCut attribute)
(lammps_interface.lammps_potentials.BondPotential.Morse attribute)
(lammps_interface.lammps_potentials.BondPotential.NonLinear attribute)
(lammps_interface.lammps_potentials.BondPotential.Quartic attribute)
(lammps_interface.lammps_potentials.BondPotential.Table attribute)
(lammps_interface.lammps_potentials.DihedralPotential attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Charmm attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleAngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.AngleTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.BondBond13 attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.EndBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Class2.MiddleBondTorsion attribute)
(lammps_interface.lammps_potentials.DihedralPotential.CosineShiftExp attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Fourier attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Helix attribute)
(lammps_interface.lammps_potentials.DihedralPotential.MultiHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.nHarmonic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Opls attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Quadratic attribute)
(lammps_interface.lammps_potentials.DihedralPotential.Table attribute)
(lammps_interface.lammps_potentials.ImproperPotential attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2 attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Class2.AngleAngle attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cossq attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Cvff attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Fourier attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Harmonic attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Ring attribute)
(lammps_interface.lammps_potentials.ImproperPotential.Umbrella attribute)
(lammps_interface.lammps_potentials.PairPotential attribute)
(lammps_interface.lammps_potentials.PairPotential.Buck attribute)
(lammps_interface.lammps_potentials.PairPotential.BuckCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.HbondDreidingMorse attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCharmmCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCut attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutCoulLong attribute)
(lammps_interface.lammps_potentials.PairPotential.LjCutTip4pLong attribute)
(lammps_interface.lammps_potentials.PairPotential.Table attribute)
(lammps_interface.structure_data.Cell attribute)
(lammps_interface.structure_data.MDMC_config attribute)
_Cell__mkcell() (lammps_interface.structure_data.Cell method)
_Cell__mklammps() (lammps_interface.structure_data.Cell method)
_Cell__mkparam() (lammps_interface.structure_data.Cell method)
_set_attr() (lammps_interface.InputHandler.Options method)
_type_() (lammps_interface.Molecules.Molecule property)
A
a() (lammps_interface.structure_data.Cell property)
add_atomic_node() (lammps_interface.structure_data.MolecularGraph method)
add_bond_edge() (lammps_interface.structure_data.MolecularGraph method)
add_co2_model() (lammps_interface.lammps_main.LammpsSimulation method)
add_data() (lammps_interface.CIFIO.CIF method)
add_distance_matrix() (in module lammps_interface.mof_sbus)
add_water_model() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
alpha() (lammps_interface.structure_data.Cell property)
angle_term() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.ForceField method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
(lammps_interface.ForceFields.UserFF method)
AnglePotential (class in lammps_interface.lammps_potentials)
AnglePotential.Charmm (class in lammps_interface.lammps_potentials)
AnglePotential.Class2 (class in lammps_interface.lammps_potentials)
AnglePotential.Class2.BondAngle (class in lammps_interface.lammps_potentials)
AnglePotential.Class2.BondBond (class in lammps_interface.lammps_potentials)
AnglePotential.Cosine (class in lammps_interface.lammps_potentials)
AnglePotential.CosineDelta (class in lammps_interface.lammps_potentials)
AnglePotential.CosinePeriodic (class in lammps_interface.lammps_potentials)
AnglePotential.CosineShift (class in lammps_interface.lammps_potentials)
AnglePotential.CosineShiftExp (class in lammps_interface.lammps_potentials)
AnglePotential.CosineSquared (class in lammps_interface.lammps_potentials)
AnglePotential.Dipole (class in lammps_interface.lammps_potentials)
AnglePotential.Fourier (class in lammps_interface.lammps_potentials)
AnglePotential.FourierSimple (class in lammps_interface.lammps_potentials)
AnglePotential.Harmonic (class in lammps_interface.lammps_potentials)
AnglePotential.Quartic (class in lammps_interface.lammps_potentials)
AnglePotential.Sdk (class in lammps_interface.lammps_potentials)
AnglePotential.Table (class in lammps_interface.lammps_potentials)
approximate_positions() (lammps_interface.Molecules.CO2 method)
(lammps_interface.Molecules.Water method)
assign_force_fields() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
assign_molecule_ids() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
atom_site_constraints() (lammps_interface.CIFIO.CIF static method)
atom_site_description() (lammps_interface.CIFIO.CIF static method)
atom_site_fract_x() (lammps_interface.CIFIO.CIF static method)
atom_site_fract_y() (lammps_interface.CIFIO.CIF static method)
atom_site_fract_z() (lammps_interface.CIFIO.CIF static method)
atom_site_fragment() (lammps_interface.CIFIO.CIF static method)
atom_site_label() (lammps_interface.CIFIO.CIF static method)
atom_site_type_symbol() (lammps_interface.CIFIO.CIF static method)
atom_type_partial_charge() (lammps_interface.CIFIO.CIF static method)
atomic_node_sanity_check() (lammps_interface.structure_data.MolecularGraph method)
B
b() (lammps_interface.structure_data.Cell property)
beta() (lammps_interface.structure_data.Cell property)
bond_term() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.ForceField method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
(lammps_interface.ForceFields.UserFF method)
BondPotential (class in lammps_interface.lammps_potentials)
BondPotential.Class2 (class in lammps_interface.lammps_potentials)
BondPotential.Fene (class in lammps_interface.lammps_potentials)
BondPotential.FeneExpand (class in lammps_interface.lammps_potentials)
BondPotential.Harmonic (class in lammps_interface.lammps_potentials)
BondPotential.HarmonicShift (class in lammps_interface.lammps_potentials)
BondPotential.HarmonicShiftCut (class in lammps_interface.lammps_potentials)
BondPotential.Morse (class in lammps_interface.lammps_potentials)
BondPotential.NonLinear (class in lammps_interface.lammps_potentials)
BondPotential.Quartic (class in lammps_interface.lammps_potentials)
BondPotential.Table (class in lammps_interface.lammps_potentials)
BTW_FF (class in lammps_interface.ForceFields)
build_supercell() (lammps_interface.structure_data.MolecularGraph method)
C
c() (lammps_interface.structure_data.Cell property)
cap_1D_organic() (lammps_interface.create_cluster_v2.Cluster method)
cap_3D_organic() (lammps_interface.create_cluster_v2.Cluster method)
cap_by_material() (lammps_interface.create_cluster_v2.Cluster method)
cap_primary_cluster() (lammps_interface.create_cluster_v2.Cluster method)
cap_zeolite() (lammps_interface.create_cluster_v2.Cluster method)
cap_zeolite_v2() (lammps_interface.create_cluster_v2.Cluster method)
cart_dist() (lammps_interface.create_cluster_v2.Cluster method)
ccdc_geom_bond_type() (lammps_interface.CIFIO.CIF static method)
Cell (class in lammps_interface.structure_data)
cell() (lammps_interface.structure_data.Cell property)
cell_angle_alpha() (lammps_interface.CIFIO.CIF static method)
cell_angle_beta() (lammps_interface.CIFIO.CIF static method)
cell_angle_gamma() (lammps_interface.CIFIO.CIF static method)
cell_length_a() (lammps_interface.CIFIO.CIF static method)
cell_length_b() (lammps_interface.CIFIO.CIF static method)
cell_length_c() (lammps_interface.CIFIO.CIF static method)
CIF (class in lammps_interface.CIFIO)
clean() (in module lammps_interface.structure_data)
Cluster (class in lammps_interface.create_cluster_v2)
CO2 (class in lammps_interface.Molecules)
compute_all_angles() (lammps_interface.Molecules.Molecule method)
compute_angle_between() (lammps_interface.structure_data.MolecularGraph method)
compute_angle_terms() (lammps_interface.ForceFields.ForceField method)
compute_angles() (lammps_interface.structure_data.MolecularGraph method)
compute_atomic_pair_terms() (lammps_interface.ForceFields.ForceField method)
compute_bond_image_flag() (lammps_interface.structure_data.MolecularGraph method)
compute_bond_terms() (lammps_interface.ForceFields.ForceField method)
compute_bond_typing() (lammps_interface.structure_data.MolecularGraph method)
compute_bonding() (lammps_interface.structure_data.MolecularGraph method)
compute_cartesian_coordinates() (lammps_interface.structure_data.MolecularGraph method)
compute_cluster_box_size() (lammps_interface.create_cluster_v2.LammpsSimulation method)
compute_cluster_in_disgraph() (lammps_interface.create_cluster_v2.Cluster method)
compute_cluster_in_tree() (lammps_interface.create_cluster_v2.Cluster method)
compute_dihedral_between() (lammps_interface.structure_data.MolecularGraph method)
compute_dihedral_terms() (lammps_interface.ForceFields.ForceField method)
compute_dihedrals() (lammps_interface.structure_data.MolecularGraph method)
compute_force_field_terms() (lammps_interface.ForceFields.ForceField method)
(lammps_interface.ForceFields.UserFF method)
compute_improper_dihedrals() (lammps_interface.structure_data.MolecularGraph method)
compute_improper_terms() (lammps_interface.ForceFields.ForceField method)
compute_init_typing() (lammps_interface.structure_data.MolecularGraph method)
compute_midpoint_vector() (lammps_interface.Molecules.Water method)
compute_min_img_distances() (lammps_interface.structure_data.MolecularGraph method)
compute_molecules() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
compute_orthogonal_vector() (lammps_interface.Molecules.Water method)
compute_primary_cluster() (lammps_interface.create_cluster_v2.Cluster method)
compute_required_caps() (lammps_interface.create_cluster_v2.Cluster method)
compute_simulation_size() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
compute_topology_information() (lammps_interface.structure_data.MolecularGraph method)
construct_data_file() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
construct_input_file() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
coplanar() (lammps_interface.structure_data.MolecularGraph method)
correspondence_graph() (lammps_interface.structure_data.MolecularGraph method)
count_angles() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.structure_data.MolecularGraph method)
count_dihedrals() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.structure_data.MolecularGraph method)
count_impropers() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.structure_data.MolecularGraph method)
create_cluster_around_point() (lammps_interface.create_cluster_v2.Cluster method)
create_cluster_around_point_v2() (lammps_interface.create_cluster_v2.Cluster method)
create_cluster_around_point_v3() (lammps_interface.create_cluster_v2.Cluster method)
crystal_system() (lammps_interface.structure_data.Cell property)
cut_cappable_bonds() (lammps_interface.create_cluster_v2.Cluster method)
cut_molecule() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
cxtd_comp_cap() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_continuous() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_convert_to_orig() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_from_undirected() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_num_keep() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_secondary_graph() (lammps_interface.create_cluster_v2.Cluster method)
cxtd_comp_to_keep() (lammps_interface.create_cluster_v2.Cluster method)
D
debug_edges_to_cut() (lammps_interface.create_cluster_v2.Cluster method)
define_styles() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
del_parenth() (in module lammps_interface.structure_data)
detect_clusters() (lammps_interface.structure_data.MolecularGraph method)
detect_ff_terms() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
dihedral_term() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.ForceField method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
(lammps_interface.ForceFields.UserFF method)
DihedralPotential (class in lammps_interface.lammps_potentials)
DihedralPotential.Charmm (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2 (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2.AngleAngleTorsion (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2.AngleTorsion (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2.BondBond13 (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2.EndBondTorsion (class in lammps_interface.lammps_potentials)
DihedralPotential.Class2.MiddleBondTorsion (class in lammps_interface.lammps_potentials)
DihedralPotential.CosineShiftExp (class in lammps_interface.lammps_potentials)
DihedralPotential.Fourier (class in lammps_interface.lammps_potentials)
DihedralPotential.Harmonic (class in lammps_interface.lammps_potentials)
DihedralPotential.Helix (class in lammps_interface.lammps_potentials)
DihedralPotential.MultiHarmonic (class in lammps_interface.lammps_potentials)
DihedralPotential.nHarmonic (class in lammps_interface.lammps_potentials)
DihedralPotential.Opls (class in lammps_interface.lammps_potentials)
DihedralPotential.Quadratic (class in lammps_interface.lammps_potentials)
DihedralPotential.Table (class in lammps_interface.lammps_potentials)
disconnect_1D_building_blocks() (lammps_interface.create_cluster_v2.Cluster method)
disconnect_external_building_blocks() (lammps_interface.create_cluster_v2.Cluster method)
DOD (lammps_interface.Molecules.TIP5P_Water attribute)
Dreiding (class in lammps_interface.ForceFields)
Dubbeldam (class in lammps_interface.ForceFields)
dummy() (lammps_interface.Molecules.TIP4P_Water property)
(lammps_interface.Molecules.TIP5P_Water property)
E
edges_iter2() (lammps_interface.structure_data.MolecularGraph method)
EPM2_CO2 (class in lammps_interface.ForceFields)
(class in lammps_interface.Molecules)
F
fixcount() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
FMOFCu (class in lammps_interface.ForceFields)
ForceField (class in lammps_interface.ForceFields)
fractional() (lammps_interface.structure_data.MolecularGraph method)
from_CIF() (in module lammps_interface.structure_data)
G
gamma() (lammps_interface.structure_data.Cell property)
general_label() (lammps_interface.CIFIO.CIF static method)
geom_bond_atom_site_label_1() (lammps_interface.CIFIO.CIF static method)
geom_bond_atom_site_label_2() (lammps_interface.CIFIO.CIF static method)
geom_bond_distance() (lammps_interface.CIFIO.CIF static method)
geom_bond_site_symmetry_2() (lammps_interface.CIFIO.CIF static method)
get_BFS_tree() (lammps_interface.create_cluster_v2.Cluster method)
get_cell() (lammps_interface.structure_data.Cell method)
get_cell_inverse() (lammps_interface.structure_data.Cell method)
get_element_label() (lammps_interface.CIFIO.CIF method)
get_non_loop_block() (lammps_interface.CIFIO.CIF method)
get_nth_heirarcy_BFS_tree() (lammps_interface.create_cluster_v2.Cluster method)
get_params() (lammps_interface.structure_data.Cell method)
get_start_and_kept_nodes() (lammps_interface.create_cluster_v2.Cluster method)
get_time() (in module lammps_interface.CIFIO)
(lammps_interface.CIFIO.CIF method)
git_revision_hash() (in module lammps_interface.InputHandler)
groups() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
H
H_coord() (lammps_interface.Molecules.Water property)
hbond_pot() (lammps_interface.ForceFields.Dreiding method)
HOH (lammps_interface.Molecules.TIP4P_Water attribute)
(lammps_interface.Molecules.TIP5P_Water attribute)
I
identify_1D_building_blocks() (lammps_interface.create_cluster_v2.Cluster method)
identify_all_truncations() (lammps_interface.create_cluster_v2.Cluster method)
identify_mat_type() (lammps_interface.create_cluster_v2.Cluster method)
img_offset() (lammps_interface.structure_data.MolecularGraph method)
improper_term() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.ForceField method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
(lammps_interface.ForceFields.UserFF method)
ImproperPotential (class in lammps_interface.lammps_potentials)
ImproperPotential.Class2 (class in lammps_interface.lammps_potentials)
ImproperPotential.Class2.AngleAngle (class in lammps_interface.lammps_potentials)
ImproperPotential.Cossq (class in lammps_interface.lammps_potentials)
ImproperPotential.Cvff (class in lammps_interface.lammps_potentials)
ImproperPotential.Fourier (class in lammps_interface.lammps_potentials)
ImproperPotential.Harmonic (class in lammps_interface.lammps_potentials)
ImproperPotential.Ring (class in lammps_interface.lammps_potentials)
ImproperPotential.Umbrella (class in lammps_interface.lammps_potentials)
in_cell() (lammps_interface.structure_data.MolecularGraph method)
increment_graph_sizes() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
insert_block_order() (lammps_interface.CIFIO.CIF method)
insert_graph() (lammps_interface.ForceFields.FMOFCu method)
inverse() (lammps_interface.structure_data.Cell property)
iterative_BFS_tree_structure() (lammps_interface.create_cluster_v2.Cluster method)
L
label() (lammps_interface.CIFIO.CIF static method)
lammps_interface (module)
lammps_interface.atomic (module)
lammps_interface.BTW (module)
lammps_interface.ccdc (module)
lammps_interface.CIFIO (module)
lammps_interface.create_cluster_v2 (module)
lammps_interface.dreiding (module)
lammps_interface.Dubbeldam (module)
lammps_interface.ForceFields (module)
lammps_interface.gas_models (module)
lammps_interface.generic_raspa (module)
lammps_interface.InputHandler (module)
lammps_interface.lammps_main (module)
lammps_interface.lammps_potentials (module)
lammps_interface.mof_sbus (module)
lammps_interface.MOFFF (module)
lammps_interface.Molecules (module)
lammps_interface.structure_data (module)
lammps_interface.uff (module)
lammps_interface.uff4mof (module)
lammps_interface.uff_nonbonded (module)
lammps_interface.water_models (module)
LammpsSimulation (class in lammps_interface.create_cluster_v2)
(class in lammps_interface.lammps_main)
lx() (lammps_interface.structure_data.Cell property)
ly() (lammps_interface.structure_data.Cell property)
lz() (lammps_interface.structure_data.Cell property)
M
main() (in module lammps_interface.create_cluster_v2)
(in module lammps_interface.lammps_main)
map_pair_unique_bond() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
map_quadruplet_unique_dihedral() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
map_quadruplet_unique_improper() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
map_triplet_unique_angle() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
map_user_to_unique_atom() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
MDMC_config (class in lammps_interface.structure_data)
merge_graphs() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
min_img() (lammps_interface.structure_data.MolecularGraph method)
min_img_distance() (lammps_interface.structure_data.MolecularGraph method)
minimum_supercell() (lammps_interface.structure_data.Cell method)
minimum_width() (lammps_interface.structure_data.Cell property)
mod_to_UC() (lammps_interface.structure_data.Cell method)
modify_structure_w_hydrogens() (lammps_interface.create_cluster_v2.Cluster method)
MOF_FF (class in lammps_interface.ForceFields)
MolecularGraph (class in lammps_interface.structure_data)
Molecule (class in lammps_interface.Molecules)
molecule_template() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
N
node_dict_factory (lammps_interface.structure_data.MolecularGraph attribute)
nodes_iter2() (lammps_interface.structure_data.MolecularGraph method)
nodes_that_DNE_in_origraph() (lammps_interface.create_cluster_v2.Cluster method)
nodes_w_2plus_parents() (lammps_interface.create_cluster_v2.Cluster method)
O
O_coord() (lammps_interface.Molecules.CO2 property)
Options (class in lammps_interface.InputHandler)
orthogonal_transformation() (lammps_interface.structure_data.Cell method)
overwrite_force_field_terms() (lammps_interface.ForceFields.UserFF method)
OverwriteFF (class in lammps_interface.ForceFields)
P
pair_coul_term() (lammps_interface.ForceFields.MOF_FF method)
pair_terms() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
PairPotential (class in lammps_interface.lammps_potentials)
PairPotential.Buck (class in lammps_interface.lammps_potentials)
PairPotential.BuckCoulLong (class in lammps_interface.lammps_potentials)
PairPotential.HbondDreidingMorse (class in lammps_interface.lammps_potentials)
PairPotential.LjCharmmCoulLong (class in lammps_interface.lammps_potentials)
PairPotential.LjCut (class in lammps_interface.lammps_potentials)
PairPotential.LjCutCoulLong (class in lammps_interface.lammps_potentials)
PairPotential.LjCutTip4pLong (class in lammps_interface.lammps_potentials)
PairPotential.Table (class in lammps_interface.lammps_potentials)
params() (lammps_interface.structure_data.Cell property)
parse_sym_flag_for_directionality() (lammps_interface.create_cluster_v2.Cluster method)
parse_user_input() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
preliminary_truncate_BFS_tree() (lammps_interface.create_cluster_v2.Cluster method)
R
RCO (lammps_interface.Molecules.EPM2_CO2 attribute)
Rdum (lammps_interface.Molecules.TIP4P_Water attribute)
(lammps_interface.Molecules.TIP5P_Water attribute)
read() (lammps_interface.CIFIO.CIF method)
read_xyz_center() (in module lammps_interface.create_cluster_v2)
recurse_bonds_to_end() (lammps_interface.structure_data.MolecularGraph method)
recurse_linear_chains() (lammps_interface.structure_data.MolecularGraph method)
redefine_lattice() (lammps_interface.structure_data.MolecularGraph method)
reorder_labels() (lammps_interface.structure_data.MolecularGraph method)
ROH (lammps_interface.Molecules.TIP4P_Water attribute)
(lammps_interface.Molecules.TIP5P_Water attribute)
rotation_from_vectors() (lammps_interface.Molecules.Molecule method)
rotation_matrix() (lammps_interface.Molecules.Molecule method)
run_command_line_options() (lammps_interface.InputHandler.Options method)
S
set_cell() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
(lammps_interface.structure_data.Cell method)
set_graph() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
set_MDMC_config() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
set_params() (lammps_interface.structure_data.Cell method)
show() (lammps_interface.structure_data.MolecularGraph method)
sorted_edge_list() (lammps_interface.structure_data.MolecularGraph method)
sorted_node_list() (lammps_interface.structure_data.MolecularGraph method)
SPC_E (class in lammps_interface.ForceFields)
special_commands() (lammps_interface.ForceFields.BTW_FF method)
(lammps_interface.ForceFields.Dreiding method)
(lammps_interface.ForceFields.Dubbeldam method)
(lammps_interface.ForceFields.EPM2_CO2 method)
(lammps_interface.ForceFields.FMOFCu method)
(lammps_interface.ForceFields.MOF_FF method)
(lammps_interface.ForceFields.SPC_E method)
(lammps_interface.ForceFields.TIP3P method)
(lammps_interface.ForceFields.TIP4P method)
(lammps_interface.ForceFields.TIP5P method)
(lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
split_graph() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
store_original_size() (lammps_interface.structure_data.MolecularGraph method)
str() (lammps_interface.Molecules.Molecule method)
subgraph() (lammps_interface.structure_data.MolecularGraph method)
T
TIP3P (class in lammps_interface.ForceFields)
TIP4P (class in lammps_interface.ForceFields)
TIP4P_Water (class in lammps_interface.Molecules)
TIP5P (class in lammps_interface.ForceFields)
TIP5P_Water (class in lammps_interface.Molecules)
truncate_all() (lammps_interface.create_cluster_v2.Cluster method)
truncation_criteria() (lammps_interface.create_cluster_v2.Cluster method)
U
UFF (class in lammps_interface.ForceFields)
UFF4MOF (class in lammps_interface.ForceFields)
uff_angle_type() (lammps_interface.ForceFields.UFF method)
(lammps_interface.ForceFields.UFF4MOF method)
unique_angles() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.lammps_main.LammpsSimulation method)
unique_atoms() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.lammps_main.LammpsSimulation method)
unique_bonds() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.lammps_main.LammpsSimulation method)
unique_dihedrals() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.lammps_main.LammpsSimulation method)
unique_impropers() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.ForceFields.UserFF method)
(lammps_interface.lammps_main.LammpsSimulation method)
unique_pair_terms() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
unwrap_node_coordinates() (lammps_interface.structure_data.MolecularGraph method)
update_num_keep() (lammps_interface.create_cluster_v2.Cluster method)
update_supercell() (lammps_interface.structure_data.Cell method)
update_symflag() (lammps_interface.structure_data.MolecularGraph method)
UserFF (class in lammps_interface.ForceFields)
V
van_der_waals_pairs() (lammps_interface.ForceFields.UserFF method)
visualize_n_levels_of_tree() (lammps_interface.create_cluster_v2.Cluster method)
volume() (lammps_interface.structure_data.Cell property)
W
Water (class in lammps_interface.Molecules)
write_CIF() (in module lammps_interface.structure_data)
write_cluster_to_host_xyz_v2() (lammps_interface.create_cluster_v2.Cluster method)
write_cluster_to_xyz() (lammps_interface.create_cluster_v2.Cluster method)
write_cluster_to_xyz_host_guest_v2() (lammps_interface.create_cluster_v2.Cluster method)
write_cutoff() (lammps_interface.create_cluster_v2.Cluster method)
write_lammps_files() (lammps_interface.create_cluster_v2.LammpsSimulation method)
(lammps_interface.lammps_main.LammpsSimulation method)
write_LSDALTON() (lammps_interface.create_cluster_v2.Cluster method)
write_map_from_cluster_xyz_to_unique_types() (lammps_interface.create_cluster_v2.Cluster method)
write_map_from_MOLECULE_to_unique_types() (lammps_interface.create_cluster_v2.Cluster method)
write_missing_uniques() (lammps_interface.ForceFields.OverwriteFF method)
(lammps_interface.ForceFields.UserFF method)
write_PDB() (in module lammps_interface.structure_data)
write_RASPA_CIF() (in module lammps_interface.structure_data)
write_RASPA_sim_files() (in module lammps_interface.structure_data)
X
xy() (lammps_interface.structure_data.Cell property)
xz() (lammps_interface.structure_data.Cell property)
Y
yz() (lammps_interface.structure_data.Cell property)
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