Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | U | W | Y | Z A add_electric_field() (in module mdcraft.openmm.system) add_image_charges() (in module mdcraft.openmm.system) add_slab_correction() (in module mdcraft.openmm.system) adjust_lightness() (in module mdcraft.plot.color) B biexp() (in module mdcraft.fit.exponential) C calculate_conductivity() (in module mdcraft.analysis.transport) (mdcraft.analysis.transport.Onsager method) calculate_coordination_numbers() (in module mdcraft.analysis.structure) (mdcraft.analysis.structure.RadialDistributionFunction method) calculate_electrophoretic_mobilities() (in module mdcraft.analysis.transport) (mdcraft.analysis.transport.Onsager method) calculate_pmf() (mdcraft.analysis.structure.RadialDistributionFunction method) calculate_potential_profile() (in module mdcraft.analysis.profile) calculate_potential_profiles() (mdcraft.analysis.profile.DensityProfile method) calculate_relative_permittivity() (in module mdcraft.analysis.electrostatics) (mdcraft.analysis.electrostatics.DipoleMoment method) calculate_relaxation_time() (in module mdcraft.analysis.polymer) calculate_relaxation_times() (mdcraft.analysis.polymer.EndToEndVector method) calculate_structure_factor() (in module mdcraft.analysis.structure) (mdcraft.analysis.structure.RadialDistributionFunction method) calculate_surface_charge_densities() (mdcraft.analysis.profile.DensityProfile method) calculate_surface_charge_density() (in module mdcraft.analysis.profile) calculate_transference_numbers() (in module mdcraft.analysis.transport) (mdcraft.analysis.transport.Onsager method) calculate_transport_coefficients() (in module mdcraft.analysis.transport) (mdcraft.analysis.transport.Onsager method) center_of_mass() (in module mdcraft.algorithm.molecule) close() (mdcraft.analysis.reader.LAMMPSDumpTrajectoryReader method) ConstantVolumeHeatCapacity (class in mdcraft.analysis.thermodynamics) convert_cell_representation() (in module mdcraft.algorithm.topology) correlation_fft() (in module mdcraft.algorithm.correlation) (in module mdcraft.analysis.polymer) correlation_shift() (in module mdcraft.algorithm.correlation) (in module mdcraft.analysis.polymer) cosine_column_sum() (in module mdcraft.analysis.structure) cosine_column_sum_inplace() (in module mdcraft.analysis.structure) coul_gauss() (in module mdcraft.openmm.pair) create_atoms() (in module mdcraft.algorithm.topology) (in module mdcraft.lammps.topology) (in module mdcraft.openmm.topology) D delta_fourier_transform_sum() (in module mdcraft.analysis.structure) DensityProfile (class in mdcraft.analysis.profile) depth_first_search() (in module mdcraft.algorithm.utility) describeNextReport() (mdcraft.openmm.reporter.NetCDFReporter method) DipoleMoment (class in mdcraft.analysis.electrostatics) dpd() (in module mdcraft.openmm.pair) DynamicAnalysisBase (class in mdcraft.analysis.base) E EndToEndVector (class in mdcraft.analysis.polymer) estimate_pressure_tensor() (in module mdcraft.openmm.system) exp() (in module mdcraft.fit.exponential) exp1() (in module mdcraft.fit.exponential) exp2() (in module mdcraft.fit.exponential) F fene() (in module mdcraft.openmm.bond) find_connected_nodes() (in module mdcraft.algorithm.utility) fourier() (in module mdcraft.fit.fourier) fourier1() (in module mdcraft.fit.fourier) fourier2() (in module mdcraft.fit.fourier) fourier3() (in module mdcraft.fit.fourier) fourier4() (in module mdcraft.fit.fourier) fourier5() (in module mdcraft.fit.fourier) fourier6() (in module mdcraft.fit.fourier) fourier7() (in module mdcraft.fit.fourier) fourier8() (in module mdcraft.fit.fourier) G gauss() (in module mdcraft.fit.gaussian) (in module mdcraft.openmm.pair) gauss1() (in module mdcraft.fit.gaussian) gauss2() (in module mdcraft.fit.gaussian) gauss3() (in module mdcraft.fit.gaussian) gauss4() (in module mdcraft.fit.gaussian) gauss5() (in module mdcraft.fit.gaussian) gauss6() (in module mdcraft.fit.gaussian) gauss7() (in module mdcraft.fit.gaussian) gauss8() (in module mdcraft.fit.gaussian) generate_spherical_wavevectors() (in module mdcraft.analysis.structure) get_cell_representation() (in module mdcraft.algorithm.topology) get_closest_factors() (in module mdcraft.algorithm.utility) get_dimensions() (mdcraft.openmm.file.NetCDFFile method) get_forces() (mdcraft.openmm.file.NetCDFFile method) get_lj_scale_factors() (in module mdcraft.algorithm.unit) (in module mdcraft.openmm.unit) get_num_atoms() (mdcraft.openmm.file.NetCDFFile method) get_num_frames() (mdcraft.openmm.file.NetCDFFile method) get_positions() (mdcraft.openmm.file.NetCDFFile method) get_scale_factors() (in module mdcraft.algorithm.unit) (in module mdcraft.openmm.unit) get_subset() (in module mdcraft.openmm.topology) get_supported_backends() (mdcraft.analysis.base.DynamicAnalysisBase class method) (mdcraft.analysis.base.NumbaAnalysisBase class method) (mdcraft.analysis.base.ParallelAnalysisBase class method) (mdcraft.analysis.base.SerialAnalysisBase class method) (mdcraft.analysis.electrostatics.DipoleMoment class method) (mdcraft.analysis.polymer.EndToEndVector class method) (mdcraft.analysis.polymer.Gyradius class method) (mdcraft.analysis.polymer.SingleChainStructureFactor class method) (mdcraft.analysis.profile.DensityProfile class method) (mdcraft.analysis.structure.IntermediateScatteringFunction class method) (mdcraft.analysis.structure.RadialDistributionFunction class method) (mdcraft.analysis.structure.StructureFactor class method) (mdcraft.analysis.transport.Onsager class method) get_times() (mdcraft.openmm.file.NetCDFFile method) get_velocities() (mdcraft.openmm.file.NetCDFFile method) Gyradius (class in mdcraft.analysis.polymer) H Hash (class in mdcraft.analysis.base) I IntermediateScatteringFunction (class in mdcraft.analysis.structure) is_lower_triangular() (in module mdcraft.algorithm.utility) is_unitless() (in module mdcraft.algorithm.unit) L LAMMPSDumpTrajectoryReader (class in mdcraft.analysis.reader) lj_coul() (in module mdcraft.openmm.pair) ljts() (in module mdcraft.openmm.pair) M mdcraft module mdcraft.algorithm module mdcraft.algorithm.accelerated module mdcraft.algorithm.correlation module mdcraft.algorithm.molecule module mdcraft.algorithm.topology module mdcraft.algorithm.unit module mdcraft.algorithm.utility module mdcraft.analysis module mdcraft.analysis.base module mdcraft.analysis.electrostatics module mdcraft.analysis.polymer module mdcraft.analysis.profile module mdcraft.analysis.reader module mdcraft.analysis.structure module mdcraft.analysis.thermodynamics module mdcraft.analysis.transport module mdcraft.fit module mdcraft.fit.distribution module mdcraft.fit.exponential module mdcraft.fit.fourier module mdcraft.fit.gaussian module mdcraft.fit.polynomial module mdcraft.fit.power module mdcraft.lammps module mdcraft.lammps.topology module mdcraft.openmm module mdcraft.openmm.bond module mdcraft.openmm.file module mdcraft.openmm.pair module mdcraft.openmm.reporter module mdcraft.openmm.system module mdcraft.openmm.topology module mdcraft.openmm.unit module mdcraft.openmm.utility module mdcraft.plot module mdcraft.plot.axis module mdcraft.plot.color module mdcraft.plot.rcparam module module mdcraft mdcraft.algorithm mdcraft.algorithm.accelerated mdcraft.algorithm.correlation mdcraft.algorithm.molecule mdcraft.algorithm.topology mdcraft.algorithm.unit mdcraft.algorithm.utility mdcraft.analysis mdcraft.analysis.base mdcraft.analysis.electrostatics mdcraft.analysis.polymer mdcraft.analysis.profile mdcraft.analysis.reader mdcraft.analysis.structure mdcraft.analysis.thermodynamics mdcraft.analysis.transport mdcraft.fit mdcraft.fit.distribution mdcraft.fit.exponential mdcraft.fit.fourier mdcraft.fit.gaussian mdcraft.fit.polynomial mdcraft.fit.power mdcraft.lammps mdcraft.lammps.topology mdcraft.openmm mdcraft.openmm.bond mdcraft.openmm.file mdcraft.openmm.pair mdcraft.openmm.reporter mdcraft.openmm.system mdcraft.openmm.topology mdcraft.openmm.unit mdcraft.openmm.utility mdcraft.plot mdcraft.plot.axis mdcraft.plot.color mdcraft.plot.rcparam msd_fft() (in module mdcraft.algorithm.correlation) (in module mdcraft.analysis.transport) msd_shift() (in module mdcraft.algorithm.correlation) (in module mdcraft.analysis.transport) N NetCDFFile (class in mdcraft.openmm.file) NetCDFReporter (class in mdcraft.openmm.reporter) numba_cosine_sum() (in module mdcraft.analysis.structure) numba_cross_pythagorean_trigonometric_identity() (in module mdcraft.analysis.structure) numba_delta_fourier_transform() (in module mdcraft.analysis.structure) numba_dot() (in module mdcraft.algorithm.accelerated) numba_histogram() (in module mdcraft.algorithm.accelerated) numba_histogram_bin_edges() (in module mdcraft.algorithm.accelerated) numba_inner() (in module mdcraft.algorithm.accelerated) numba_inner_parallel() (in module mdcraft.algorithm.accelerated) numba_pythagorean_trigonometric_identity() (in module mdcraft.analysis.structure) numba_sine_sum() (in module mdcraft.analysis.structure) NumbaAnalysisBase (class in mdcraft.analysis.base) O Onsager (class in mdcraft.analysis.transport) optimize_pme() (in module mdcraft.openmm.utility) P ParallelAnalysisBase (class in mdcraft.analysis.base) parallelizable (mdcraft.analysis.base.DynamicAnalysisBase property) (mdcraft.analysis.base.NumbaAnalysisBase property) (mdcraft.analysis.base.ParallelAnalysisBase property) (mdcraft.analysis.base.SerialAnalysisBase property) (mdcraft.analysis.electrostatics.DipoleMoment property) (mdcraft.analysis.polymer.EndToEndVector property) (mdcraft.analysis.polymer.Gyradius property) (mdcraft.analysis.polymer.SingleChainStructureFactor property) (mdcraft.analysis.profile.DensityProfile property) (mdcraft.analysis.structure.IntermediateScatteringFunction property) (mdcraft.analysis.structure.RadialDistributionFunction property) (mdcraft.analysis.structure.StructureFactor property) (mdcraft.analysis.transport.Onsager property) poly() (in module mdcraft.fit.polynomial) poly1() (in module mdcraft.fit.polynomial) poly2() (in module mdcraft.fit.polynomial) poly3() (in module mdcraft.fit.polynomial) poly4() (in module mdcraft.fit.polynomial) poly5() (in module mdcraft.fit.polynomial) poly6() (in module mdcraft.fit.polynomial) poly7() (in module mdcraft.fit.polynomial) poly8() (in module mdcraft.fit.polynomial) poly9() (in module mdcraft.fit.polynomial) power() (in module mdcraft.fit.power) power1() (in module mdcraft.fit.power) power2() (in module mdcraft.fit.power) psf_trigonometric() (in module mdcraft.analysis.structure) R radial_fourier_transform() (in module mdcraft.analysis.structure) radial_histogram() (in module mdcraft.analysis.structure) RadialDistributionFunction (class in mdcraft.analysis.structure) radius_of_gyration() (in module mdcraft.algorithm.molecule) rebin() (in module mdcraft.algorithm.utility) reduce_box_vectors() (in module mdcraft.algorithm.topology) register_particles() (in module mdcraft.openmm.system) replicate() (in module mdcraft.algorithm.utility) report() (mdcraft.openmm.reporter.NetCDFReporter method) run() (mdcraft.analysis.base.DynamicAnalysisBase method) (mdcraft.analysis.base.NumbaAnalysisBase method) (mdcraft.analysis.base.ParallelAnalysisBase method) (mdcraft.analysis.base.SerialAnalysisBase method) (mdcraft.analysis.electrostatics.DipoleMoment method) (mdcraft.analysis.polymer.EndToEndVector method) (mdcraft.analysis.polymer.Gyradius method) (mdcraft.analysis.polymer.SingleChainStructureFactor method) (mdcraft.analysis.profile.DensityProfile method) (mdcraft.analysis.structure.IntermediateScatteringFunction method) (mdcraft.analysis.structure.RadialDistributionFunction method) (mdcraft.analysis.structure.StructureFactor method) (mdcraft.analysis.thermodynamics.ConstantVolumeHeatCapacity method) (mdcraft.analysis.transport.Onsager method) S save() (mdcraft.analysis.base.DynamicAnalysisBase method) (mdcraft.analysis.base.NumbaAnalysisBase method) (mdcraft.analysis.base.ParallelAnalysisBase method) (mdcraft.analysis.base.SerialAnalysisBase method) (mdcraft.analysis.electrostatics.DipoleMoment method) (mdcraft.analysis.polymer.EndToEndVector method) (mdcraft.analysis.polymer.Gyradius method) (mdcraft.analysis.polymer.SingleChainStructureFactor method) (mdcraft.analysis.profile.DensityProfile method) (mdcraft.analysis.structure.IntermediateScatteringFunction method) (mdcraft.analysis.structure.RadialDistributionFunction method) (mdcraft.analysis.structure.StructureFactor method) (mdcraft.analysis.transport.Onsager method) SerialAnalysisBase (class in mdcraft.analysis.base) set_up_tabular_legend() (in module mdcraft.plot.axis) sine_column_sum() (in module mdcraft.analysis.structure) sine_column_sum_inplace() (in module mdcraft.analysis.structure) SingleChainStructureFactor (class in mdcraft.analysis.polymer) solvation() (in module mdcraft.openmm.pair) ssf_trigonometric() (in module mdcraft.analysis.structure) stretched_exp() (in module mdcraft.fit.exponential) strip_unit() (in module mdcraft.algorithm.unit) StructureFactor (class in mdcraft.analysis.structure) U unwrap() (in module mdcraft.algorithm.topology) unwrap_edge() (in module mdcraft.algorithm.topology) update() (in module mdcraft.plot.rcparam) W wca() (in module mdcraft.openmm.pair) weibull() (in module mdcraft.fit.distribution) wrap() (in module mdcraft.algorithm.topology) write_data() (in module mdcraft.lammps.topology) write_file() (mdcraft.openmm.file.NetCDFFile method) write_header() (mdcraft.openmm.file.NetCDFFile method) write_model() (mdcraft.openmm.file.NetCDFFile method) Y yukawa() (in module mdcraft.openmm.pair) Z zeroth_order_hankel_transform() (in module mdcraft.analysis.structure)