Index

A

Angle (class in mdcraft.core)

are_entities_inside_box() (in module mdcraft.lib.cell) Atom (class in mdcraft.core)

B

BaseReader (class in mdcraft.io.base) BaseTopologyReader (class in mdcraft.io.base) BaseTopologyWriter (class in mdcraft.io.base) BaseTrajectoryReader (class in mdcraft.io.base)

BaseTrajectoryWriter (class in mdcraft.io.base) BaseWriter (class in mdcraft.io.base) Bond (class in mdcraft.core) build_neighbor_list() (in module mdcraft.lib.neighbor)

C

Chain (class in mdcraft.core) close() (mdcraft.io.base.BaseReader method) (mdcraft.io.base.BaseTopologyReader method) (mdcraft.io.base.BaseTopologyWriter method) (mdcraft.io.base.BaseTrajectoryReader method) (mdcraft.io.base.BaseTrajectoryWriter method) (mdcraft.io.base.BaseWriter method) (mdcraft.io.reader.CompositeReader method) (mdcraft.io.reader.LAMMPSDataReader method) (mdcraft.io.reader.LAMMPSDumpReader method) (mdcraft.io.reader.NetCDFReader method) (mdcraft.io.writer.NetCDFWriter method)

CompositeReader (class in mdcraft.io.reader) convert_cell_representation() (in module mdcraft.lib.cell) correlation() (in module mdcraft.lib.correlation) count_leading_zeros() (in module mdcraft.lib.bit)

D

Dihedral (class in mdcraft.core) dimensions (mdcraft.core.Topology property) (mdcraft.core.TrajectoryFrame property) (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property)

dt (mdcraft.core.Trajectory property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property)

F

ForceField (class in mdcraft.core)

forces (mdcraft.core.TrajectoryFrame property) frame (mdcraft.core.TrajectoryFrame property)

G

get_dimensions() (mdcraft.io.reader.NetCDFReader method) get_extra_variables() (mdcraft.io.reader.NetCDFReader method) get_forces() (mdcraft.io.reader.NetCDFReader method) get_frames() (mdcraft.core.Trajectory method) (mdcraft.core.TrajectorySubset method)

get_positions() (mdcraft.io.reader.NetCDFReader method) get_times() (mdcraft.io.reader.NetCDFReader method) get_velocities() (mdcraft.io.reader.NetCDFReader method)

I

ids (mdcraft.core.TrajectoryFrame property)

is_cell_orthogonal() (in module mdcraft.lib.cell)

L

LAMMPSDataReader (class in mdcraft.io.reader)

LAMMPSDumpReader (class in mdcraft.io.reader)

M

mdcraft module mdcraft.analysis module mdcraft.analysis.base module mdcraft.core module mdcraft.io module mdcraft.io.base module mdcraft.io.reader module mdcraft.io.writer module mdcraft.lib module mdcraft.lib.bit module mdcraft.lib.cell module

mdcraft.lib.correlation module mdcraft.lib.neighbor module mdcraft.lib.unit module module mdcraft mdcraft.analysis mdcraft.analysis.base mdcraft.core mdcraft.io mdcraft.io.base mdcraft.io.reader mdcraft.io.writer mdcraft.lib mdcraft.lib.bit mdcraft.lib.cell mdcraft.lib.correlation mdcraft.lib.neighbor mdcraft.lib.unit Molecule (class in mdcraft.core) msd() (in module mdcraft.lib.correlation)

N

n_angle_types (mdcraft.io.reader.LAMMPSDataReader property) n_angles (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_atom_types (mdcraft.io.reader.LAMMPSDataReader property) n_atoms (mdcraft.core.Topology property) (mdcraft.core.Trajectory property) (mdcraft.core.TrajectoryFrame property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDataReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property) n_bodies (mdcraft.io.reader.LAMMPSDataReader property) n_bond_types (mdcraft.io.reader.LAMMPSDataReader property) n_bonds (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_chains (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_dihedral_types (mdcraft.io.reader.LAMMPSDataReader property) n_dihedrals (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property)

n_ellipsoids (mdcraft.io.reader.LAMMPSDataReader property) n_entities (mdcraft.io.reader.LAMMPSDumpReader property) n_frames (mdcraft.core.Trajectory property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property) n_grids (mdcraft.io.reader.LAMMPSDumpReader property) n_improper_dihedral_types (mdcraft.io.reader.LAMMPSDataReader property) n_improper_dihedrals (mdcraft.io.reader.LAMMPSDataReader property) n_lines (mdcraft.io.reader.LAMMPSDataReader property) n_molecules (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_residues (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_segments (mdcraft.io.base.BaseTopologyReader property) (mdcraft.io.reader.LAMMPSDataReader property) n_triangles (mdcraft.io.reader.LAMMPSDataReader property) NetCDFReader (class in mdcraft.io.reader) NetCDFWriter (class in mdcraft.io.writer)

O

open() (mdcraft.io.base.BaseReader method) (mdcraft.io.base.BaseTopologyReader method) (mdcraft.io.base.BaseTopologyWriter method) (mdcraft.io.base.BaseTrajectoryReader method) (mdcraft.io.base.BaseTrajectoryWriter method) (mdcraft.io.base.BaseWriter method) (mdcraft.io.reader.CompositeReader method) (mdcraft.io.reader.LAMMPSDataReader method) (mdcraft.io.reader.LAMMPSDumpReader method) (mdcraft.io.reader.NetCDFReader method) (mdcraft.io.writer.NetCDFWriter method)

P

positions (mdcraft.core.TrajectoryFrame property)

R

read_frames() (mdcraft.io.base.BaseTrajectoryReader method) (mdcraft.io.reader.CompositeReader method) (mdcraft.io.reader.LAMMPSDumpReader method) (mdcraft.io.reader.NetCDFReader method)

reduce_box_vectors() (in module mdcraft.lib.cell) Residue (class in mdcraft.core)

S

scale_coordinates() (in module mdcraft.lib.cell) Segment (class in mdcraft.core)

strip_unit() (in module mdcraft.lib.unit) System (class in mdcraft.core)

T

time (mdcraft.core.TrajectoryFrame property) time_step (mdcraft.core.Trajectory property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property) times (mdcraft.core.Trajectory property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property)

timestep (mdcraft.core.TrajectoryFrame property) timesteps (mdcraft.core.Trajectory property) (mdcraft.core.TrajectorySubset property) (mdcraft.io.base.BaseTrajectoryReader property) (mdcraft.io.reader.CompositeReader property) (mdcraft.io.reader.LAMMPSDumpReader property) (mdcraft.io.reader.NetCDFReader property) Topology (class in mdcraft.core) Trajectory (class in mdcraft.core) TrajectoryFrame (class in mdcraft.core) TrajectorySubset (class in mdcraft.core)

V

velocities (mdcraft.core.TrajectoryFrame property)

W

wrap_coordinates() (in module mdcraft.lib.cell)