Index

_

__eq() (halmd.observables.utility.wavevector method)

A

accumulator (class in halmd.observables.utility) acquire() (halmd.observables.dynamics.correlation method) (halmd.observables.dynamics.helfand_moment method) (halmd.observables.dynamics.intermediate_scattering_function method) (halmd.observables.dynamics.mean_quartic_displacement method) (halmd.observables.dynamics.mean_square_displacement method) (halmd.observables.dynamics.stress_tensor_autocorrelation method) (halmd.observables.dynamics.velocity_autocorrelation method) (halmd.observables.phase_space method) add_argument() (halmd.utility.program_options.argument_parser method) add_argument_group() (halmd.utility.program_options.argument_parser method) add_options() (in module halmd.observables.utility.semilog_grid) (in module halmd.observables.utility.wavevector)

all (class in halmd.mdsim.particle_groups) argument_parser (class in halmd.utility.program_options) assert_kwarg() (in module halmd.utility) assert_type() (in module halmd.utility) author (halmd.io.readers.h5md attribute)

B

binning (class in halmd.mdsim) blocking_scheme (class in halmd.observables.dynamics) blocking_scheme.correlation (class in halmd.observables.dynamics) boltzmann (class in halmd.mdsim.velocities)

BOOST_INCLUDEDIR BOOST_LIBRARYDIR Boost_USE_STATIC_LIBS box (class in halmd.mdsim)

C

cell_occupancy (halmd.mdsim.binning attribute) (halmd.mdsim.neighbour attribute) center_of_mass() (halmd.observables.thermodynamics method) center_of_mass_velocity() (halmd.observables.thermodynamics method) check() (in module halmd.io.readers.h5md) close() (halmd.io.readers.h5md method) close_console() (in module halmd.io.log) close_file() (in module halmd.io.log) CMAKE_BUILD_TYPE CMAKE_PREFIX_PATH coherent/intermediate scattering function collision_rate (halmd.mdsim.integrators.verlet_nvt_andersen attribute)

correlate() (halmd.observables.dynamics.correlation method) (halmd.observables.dynamics.helfand_moment method) (halmd.observables.dynamics.mean_quartic_displacement method) (halmd.observables.dynamics.mean_square_displacement method) (halmd.observables.dynamics.stress_tensor_autocorrelation method) (halmd.observables.dynamics.velocity_autocorrelation method) correlation (class in halmd.observables.dynamics) correlation.writer (class in halmd.observables.dynamics) count (halmd.observables.density_mode attribute) count() (halmd.observables.utility.accumulator method) creation_time (halmd.io.readers.h5md attribute) creator (halmd.io.readers.h5md attribute) creator_version (halmd.io.readers.h5md attribute) CUDA_INSTALL_PREFIX CXXFLAGS

D

debug() (halmd.io.log.logger method) (in module halmd.io.log) density() (halmd.observables.thermodynamics method) density_mode (class in halmd.observables) density_mode.writer (class in halmd.observables)

desc (halmd.observables.dynamics.correlation attribute) (halmd.observables.dynamics.helfand_moment attribute) (halmd.observables.dynamics.intermediate_scattering_function attribute) (halmd.observables.dynamics.mean_quartic_displacement attribute) (halmd.observables.dynamics.mean_square_displacement attribute) (halmd.observables.dynamics.stress_tensor_autocorrelation attribute) (halmd.observables.dynamics.velocity_autocorrelation attribute) (halmd.observables.utility.accumulator attribute) description (halmd.mdsim.potentials.lennard_jones attribute) (halmd.mdsim.potentials.lennard_jones_linear attribute) (halmd.mdsim.potentials.morse attribute) (halmd.mdsim.potentials.power_law attribute) dimension (halmd.mdsim.box attribute) (halmd.observables.phase_space.reader attribute) (halmd.observables.thermodynamics attribute) disconnect() (halmd.mdsim.binning method) (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.mdsim.max_displacement method) (halmd.mdsim.neighbour method) (halmd.mdsim.positions.lattice method) (halmd.observables.density_mode method) (halmd.observables.density_mode.writer method) (halmd.observables.dynamics.blocking_scheme method) (halmd.observables.dynamics.blocking_scheme.correlation method) (halmd.observables.dynamics.helfand_moment method) (halmd.observables.dynamics.intermediate_scattering_function method) (halmd.observables.phase_space method) (halmd.observables.phase_space.writer method) (halmd.observables.ssf method) (halmd.observables.ssf.writer method) (halmd.observables.thermodynamics method) (halmd.observables.utility.accumulator method) (in module halmd.utility.signal)

E

edges (halmd.mdsim.box attribute) empty() (in module halmd.utility) epsilon (halmd.mdsim.potentials.lennard_jones attribute) (halmd.mdsim.potentials.lennard_jones_linear attribute) (halmd.mdsim.potentials.morse attribute) (halmd.mdsim.potentials.power_law attribute) error() (halmd.io.log.logger method) (in module halmd.io.log)

error_of_mean() (halmd.observables.utility.accumulator method) exclude_sphere() (halmd.mdsim.positions.excluded_volume method) exclude_spheres() (halmd.mdsim.positions.excluded_volume method) excluded_volume (class in halmd.mdsim.positions)

F

finalize() (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_hoover method) flush() (halmd.io.writers.h5md method)

from_range (class in halmd.mdsim.particle_groups)

G

generator() (in module halmd.random) get_en_pot() (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) get_hypervirial() (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) get_image() (halmd.mdsim.particle method) get_mass() (halmd.mdsim.particle method) get_net_force() (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) get_position() (halmd.mdsim.particle method)

get_reverse_tag() (halmd.mdsim.particle method) get_species() (halmd.mdsim.particle method) get_stress_pot() (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) get_tag() (halmd.mdsim.particle method) get_velocity() (halmd.mdsim.particle method) gpu (in module halmd.utility.device) group (halmd.observables.phase_space attribute) (halmd.observables.thermodynamics attribute)

H

h (halmd.mdsim.forces.trunc.local_r4 attribute) h5md (class in halmd.io.readers) (class in halmd.io.writers) halmd (module) halmd.io (module) halmd.io.log (module) halmd.io.readers (module) halmd.io.writers (module) halmd.mdsim (module) halmd.mdsim.clock (module) halmd.mdsim.core (module) halmd.mdsim.forces (module) halmd.mdsim.forces.trunc (module) halmd.mdsim.integrators (module) halmd.mdsim.particle_groups (module) halmd.mdsim.positions (module) halmd.mdsim.potentials (module) halmd.mdsim.velocities (module) halmd.observables (module) halmd.observables.dynamics (module) halmd.observables.sampler (module) halmd.observables.utility (module)

halmd.random (module) halmd.utility (module) halmd.utility.device (module) halmd.utility.posix_signal (module) halmd.utility.profiler (module) halmd.utility.program_options (module) halmd.utility.signal (module) halmd.utility.timer_service (module) halmd.utility.version (module) HALMD_BACKEND_EXECUTABLES HALMD_USE_STATIC_LIBS HALMD_VARIANT_CELL_SUMMATION_ORDER HALMD_VARIANT_FORCE_DSFUN HALMD_VARIANT_HILBERT_ALT_3D HALMD_VARIANT_HILBERT_ORDER HALMD_VARIANT_HOST_SINGLE_PRECISION HALMD_VARIANT_VERLET_DSFUN HDF5_USE_STATIC_LIBS helfand_moment (class in halmd.observables.dynamics) helfand_moment.writer (class in halmd.observables.dynamics) hypervirial() (halmd.observables.thermodynamics method)

I

incoherent/self-intermediate scattering function index (halmd.mdsim.potentials.power_law attribute) info() (halmd.io.log.logger method) (in module halmd.io.log) integrate() (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_hoover method)

intermediate_scattering_function (class in halmd.observables.dynamics) intermediate_scattering_function.writer (class in halmd.observables.dynamics) interval (halmd.mdsim.integrators.verlet_boltzmann attribute)

K

keys() (in module halmd.utility)

kinetic_energy() (halmd.observables.thermodynamics method)

L

label (halmd.mdsim.particle attribute) (halmd.observables.density_mode attribute) (halmd.observables.dynamics.intermediate_scattering_function attribute) (halmd.observables.ssf attribute) lattice (class in halmd.mdsim.positions) length (halmd.mdsim.box attribute) Lennard-Jones force Lennard-Jones potential lennard_jones (class in halmd.mdsim.potentials)

lennard_jones_linear (class in halmd.mdsim.potentials) loader() (in module halmd.utility.module) local_r4 (class in halmd.mdsim.forces.trunc) log() (halmd.mdsim.forces.trunc.local_r4 method) logger (class in halmd.io.log)

M

mass (halmd.mdsim.integrators.verlet_nvt_hoover attribute) mass() (halmd.observables.phase_space method) max_displacement (class in halmd.mdsim) mdstep() (in module halmd.mdsim.core) mean kinetic energy per particle mean potential energy per particle mean quartic displacement mean squared displacement mean total energy per particle

mean() (halmd.observables.utility.accumulator method) mean_mass() (halmd.observables.thermodynamics method) mean_quartic_displacement (class in halmd.observables.dynamics) mean_quartic_displacement.writer (class in halmd.observables.dynamics) mean_square_displacement (class in halmd.observables.dynamics) mean_square_displacement.writer (class in halmd.observables.dynamics) memory (halmd.mdsim.particle attribute) module (class in halmd.utility) morse (class in halmd.mdsim.potentials)

N

neighbour (class in halmd.mdsim) nparticle (halmd.mdsim.particle attribute) (halmd.observables.phase_space.reader attribute) nparticle() (halmd.observables.thermodynamics method)

nspecies (halmd.mdsim.particle attribute) (halmd.observables.phase_space.reader attribute) NVCCFLAGS

O

on_alrm() (in module halmd.utility.posix_signal) on_append_finalize() (in module halmd.mdsim.core) on_append_force() (in module halmd.mdsim.core) on_append_integrate() (in module halmd.mdsim.core) on_append_profile() (in module halmd.utility.profiler) on_cont() (in module halmd.utility.posix_signal) on_finalize() (in module halmd.mdsim.core) on_finish() (in module halmd.observables.sampler) on_force() (in module halmd.mdsim.core) on_hup() (in module halmd.utility.posix_signal) on_int() (in module halmd.utility.posix_signal) on_integrate() (in module halmd.mdsim.core) on_periodic() (in module halmd.utility.timer_service), [1] on_prepend_finalize() (in module halmd.mdsim.core) on_prepend_force() (in module halmd.mdsim.core)

on_prepend_integrate() (in module halmd.mdsim.core) on_prepend_profile() (in module halmd.utility.profiler) on_profile() (in module halmd.utility.profiler) on_sample() (in module halmd.observables.sampler) on_set_timestep() (in module halmd.mdsim.clock) on_start() (in module halmd.observables.sampler) on_term() (in module halmd.utility.posix_signal) on_tstp() (in module halmd.utility.posix_signal) on_ttin() (in module halmd.utility.posix_signal) on_ttou() (in module halmd.utility.posix_signal) on_usr1() (in module halmd.utility.posix_signal) on_usr2() (in module halmd.utility.posix_signal) open_console() (in module halmd.io.log) open_file() (in module halmd.io.log) origin (halmd.mdsim.box attribute)

P

pair_full (class in halmd.mdsim.forces) pair_trunc (class in halmd.mdsim.forces) parse_args() (halmd.utility.program_options.argument_parser method) particle (class in halmd.mdsim) (halmd.mdsim.neighbour attribute) (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.from_range attribute) particle velocities path (halmd.io.readers.h5md attribute) (halmd.io.writers.h5md attribute) periodically extended particle coordinates phase_space (class in halmd.observables) phase_space.writer (class in halmd.observables) place_spheres() (halmd.mdsim.positions.excluded_volume method)

poll() (in module halmd.utility.posix_signal) position() (halmd.observables.phase_space method) potential (halmd.mdsim.forces.pair_full attribute) (halmd.mdsim.forces.pair_trunc attribute) potential_energy() (halmd.observables.thermodynamics method) power_law (class in halmd.mdsim.potentials) pressure() (halmd.observables.thermodynamics method) process() (in module halmd.utility.timer_service) profile() (in module halmd.utility.profiler) prologue() (in module halmd.utility.version)

R

r_cut (halmd.mdsim.binning attribute) (halmd.mdsim.potentials.lennard_jones attribute) (halmd.mdsim.potentials.lennard_jones_linear attribute) (halmd.mdsim.potentials.morse attribute) (halmd.mdsim.potentials.power_law attribute) r_cut_sigma (halmd.mdsim.potentials.lennard_jones attribute) (halmd.mdsim.potentials.lennard_jones_linear attribute) (halmd.mdsim.potentials.morse attribute) (halmd.mdsim.potentials.power_law attribute) r_min_sigma (halmd.mdsim.potentials.morse attribute) r_skin (halmd.mdsim.binning attribute) (halmd.mdsim.neighbour attribute) rate (halmd.mdsim.integrators.verlet_boltzmann attribute) read_at_step() (halmd.observables.phase_space.reader method) read_at_time() (halmd.observables.phase_space.reader method) reader (class in halmd.observables.phase_space) reader() (halmd.io.readers.h5md method) (in module halmd.mdsim.box)

rescale_velocity() (halmd.mdsim.particle method) rescale_velocity_group() (halmd.mdsim.particle method) reset() (halmd.observables.utility.accumulator method) resonance_frequency (halmd.mdsim.integrators.verlet_nvt_hoover attribute) reverse() (in module halmd.utility) root (halmd.io.readers.h5md attribute) (halmd.io.writers.h5md attribute) run() (in module halmd.observables.sampler) runtime_estimate (class in halmd.observables)

S

sample() (halmd.observables.utility.accumulator method) (in module halmd.observables.sampler) sampler (halmd.observables.ssf attribute) seed() (in module halmd.random) semilog_grid (class in halmd.observables.utility) set() (halmd.mdsim.positions.lattice method) (halmd.mdsim.velocities.boltzmann method) (halmd.observables.phase_space method) set_defaults() (halmd.utility.program_options.argument_parser method) set_image() (halmd.mdsim.particle method) set_mass() (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.mdsim.particle method) set_position() (halmd.mdsim.particle method) set_reverse_tag() (halmd.mdsim.particle method) set_species() (halmd.mdsim.particle method) set_tag() (halmd.mdsim.particle method) set_temperature() (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_hoover method) set_timestep() (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_hoover method) (in module halmd.mdsim.clock) set_velocity() (halmd.mdsim.particle method) shift_rescale_velocity() (halmd.mdsim.particle method) shift_rescale_velocity_group() (halmd.mdsim.particle method) shift_velocity() (halmd.mdsim.particle method)

shift_velocity_group() (halmd.mdsim.particle method) shifted, truncated Lennard-Jones potential sigma (halmd.mdsim.potentials.lennard_jones attribute) (halmd.mdsim.potentials.lennard_jones_linear attribute) (halmd.mdsim.potentials.morse attribute) (halmd.mdsim.potentials.power_law attribute) size (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.from_range attribute) slab (halmd.mdsim.positions.lattice attribute) Soft power-law force Soft power-law potential sorted() (in module halmd.utility) species() (halmd.observables.phase_space method) squared self-intermediate scattering function ssf (class in halmd.observables) ssf.writer (class in halmd.observables) step (in module halmd.mdsim.clock) stress_tensor() (halmd.observables.thermodynamics method) stress_tensor_autocorrelation (class in halmd.observables.dynamics) stress_tensor_autocorrelation.writer (class in halmd.observables.dynamics) sum() (halmd.observables.utility.accumulator method)

T

temperature (halmd.mdsim.integrators.verlet_boltzmann attribute) (halmd.mdsim.integrators.verlet_nvt_andersen attribute) (halmd.mdsim.integrators.verlet_nvt_hoover attribute) (halmd.mdsim.velocities.boltzmann attribute) temperature() (halmd.observables.thermodynamics method) thermodynamics (class in halmd.observables) time (in module halmd.mdsim.clock)

time of trajectory snapshots timestep (halmd.mdsim.integrators.verlet attribute) (halmd.mdsim.integrators.verlet_boltzmann attribute) (halmd.mdsim.integrators.verlet_nvt_andersen attribute) (halmd.mdsim.integrators.verlet_nvt_hoover attribute) (in module halmd.mdsim.clock) total_energy() (halmd.observables.thermodynamics method) trace() (halmd.io.log.logger method) (in module halmd.io.log)

U

unit of energy unit of length

unit of time

V

value (in module halmd.observables.utility.semilog_grid) value() (halmd.observables.utility.wavevector method) variance() (halmd.observables.utility.accumulator method) velocity auto-correlation function velocity center of mass velocity() (halmd.observables.phase_space method) velocity-Verlet algorithm velocity_autocorrelation (class in halmd.observables.dynamics) velocity_autocorrelation.writer (class in halmd.observables.dynamics)

verlet (class in halmd.mdsim.integrators) verlet_boltzmann (class in halmd.mdsim.integrators) verlet_nvt_andersen (class in halmd.mdsim.integrators) verlet_nvt_hoover (class in halmd.mdsim.integrators) version (halmd.io.readers.h5md attribute) version() (in module halmd.io.writers.h5md) virial pressure virial stress virial() (halmd.observables.thermodynamics method)

W

wait() (in module halmd.utility.posix_signal) warning() (halmd.io.log.logger method) (in module halmd.io.log) wavenumber() (halmd.observables.utility.wavevector method)

wavevector (class in halmd.observables.utility) (halmd.observables.density_mode attribute) writer() (halmd.io.writers.h5md method) (halmd.mdsim.box method) (halmd.observables.thermodynamics method) (halmd.observables.utility.accumulator method)