Index

_

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

A

abspath() (in module halmd.utility) 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) acquire_mass() (halmd.observables.phase_space method) acquire_position() (halmd.observables.phase_space method) acquire_species() (halmd.observables.phase_space method) acquire_velocity() (halmd.observables.phase_space method)

add() (in module halmd.numeric) 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) add_scalar() (in module halmd.numeric) advance() (in module halmd.mdsim.clock) all (class in halmd.mdsim.particle_groups) argument_parser (class in halmd.utility.program_options) assert_close() (in module halmd.numeric) assert_kwarg() (in module halmd.utility) assert_type() (in module halmd.utility) author (halmd.io.readers.h5md attribute) aux_enable() (halmd.mdsim.particle method) axis (halmd.mdsim.geometries.cylinder attribute)

B

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

Boost_USE_STATIC_LIBS box (class in halmd.mdsim) built-in function define_args() main()

C

cell_occupancy (halmd.mdsim.neighbour attribute) center_of_mass() (halmd.observables.thermodynamics method) center_of_mass_velocity() (halmd.observables.thermodynamics method) centre (halmd.mdsim.geometries.cylinder attribute) (halmd.mdsim.geometries.sphere attribute) 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, [1] collision_rate (halmd.mdsim.integrators.verlet_nvt_andersen attribute) concat() (in module halmd.utility) connect() (halmd.observables.dynamics.stress_tensor_autocorrelation method) 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) cuboid (class in halmd.mdsim.geometries) CUDA_USE_STATIC_CUDA_RUNTIME CUDACC CUDAFLAGS custom (class in halmd.mdsim.potentials.pair) cutoff (halmd.mdsim.potentials.external.planar_wall attribute) CXX CXXFLAGS cylinder (class in halmd.mdsim.geometries)

D

Da (in module halmd.utility.constants) data (halmd.mdsim.particle attribute) debug() (halmd.io.log.logger method) (in module halmd.io.log) define_args() built-in function 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.external.harmonic attribute) (halmd.mdsim.potentials.external.planar_wall attribute) (halmd.mdsim.potentials.pair.custom attribute) (halmd.mdsim.potentials.pair.lennard_jones attribute) (halmd.mdsim.potentials.pair.mie attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute) diag() (in module halmd.numeric) dimension (halmd.mdsim.box attribute) (halmd.observables.phase_space.reader attribute) (halmd.observables.thermodynamics attribute) dirname() (in module halmd.utility) disconnect() (halmd.mdsim.binning method) (halmd.mdsim.forces.external method) (halmd.mdsim.forces.pair method) (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) (halmd.mdsim.integrators.euler method) (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.mdsim.integrators.verlet_nvt_hoover.writer method) (halmd.mdsim.max_displacement method) (halmd.mdsim.neighbour method) (halmd.mdsim.particle_groups.region method) (halmd.mdsim.particle_groups.region_species method) (halmd.mdsim.positions.lattice method) (halmd.mdsim.sorts.hilbert 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)

displacement (halmd.mdsim.neighbour attribute) distortion (halmd.mdsim.potentials.pair.morse attribute) divide() (in module halmd.numeric) divide_scalar() (in module halmd.numeric)

E

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

error_of_mean() (halmd.observables.utility.accumulator method) euler (class in halmd.mdsim.integrators) eV (in module halmd.utility.constants) exclude_sphere() (halmd.mdsim.positions.excluded_volume method) exclude_spheres() (halmd.mdsim.positions.excluded_volume method) excluded_volume (class in halmd.mdsim.positions) external (class in halmd.mdsim.forces)

F

finalize() (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_hoover method) find_comp() (in module halmd.numeric)

finish() (in module halmd.observables.sampler) fluctuating (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.id_range attribute) (halmd.mdsim.particle_groups.region attribute) (halmd.mdsim.particle_groups.region_species attribute) flush() (halmd.io.writers.h5md method)

G

generator() (in module halmd.random) get() (halmd.mdsim.particle method) global (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.id_range attribute) (halmd.mdsim.particle_groups.region attribute) (halmd.mdsim.particle_groups.region_species attribute)

gpu (in module halmd.utility.device) group (halmd.observables.phase_space attribute) (halmd.observables.thermodynamics attribute)

H

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.geometries module halmd.mdsim.integrators module halmd.mdsim.particle_groups module halmd.mdsim.positions module halmd.mdsim.potentials module halmd.mdsim.potentials.external module halmd.mdsim.potentials.pair module halmd.mdsim.potentials.pair.adapters module halmd.mdsim.potentials.pair.adapters.modify module halmd.mdsim.potentials.pair.adapters.truncate module halmd.mdsim.potentials.pair.modified_lennard_jones module halmd.mdsim.sorts module

halmd.mdsim.velocities module halmd.numeric module halmd.observables module halmd.observables.dynamics module halmd.observables.sampler module halmd.observables.utility module halmd.random module halmd.utility module halmd.utility.constants module halmd.utility.device module halmd.utility.posix_signal module halmd.utility.profiler module halmd.utility.program_options module halmd.utility.program_options.argument_parser.action (class in halmd.utility.program_options) halmd.utility.signal module halmd.utility.timer_service module halmd.utility.version module HALMD_POTENTIALS HALMD_USE_STATIC_LIBS HALMD_VARIANT_FORCE_DSFUN HALMD_VARIANT_HILBERT_ALT_3D HALMD_VARIANT_HOST_SINGLE_PRECISION HALMD_VARIANT_VERLET_DSFUN HALMD_WITH_GPU harmonic (class in halmd.mdsim.potentials.external) HDF5_USE_STATIC_LIBS helfand_moment (class in halmd.observables.dynamics) helfand_moment.writer (class in halmd.observables.dynamics) hilbert (class in halmd.mdsim.sorts)

I

id_range (class in halmd.mdsim.particle_groups) index (halmd.mdsim.potentials.pair.power_law attribute) index_m (halmd.mdsim.potentials.pair.mie attribute) index_n (halmd.mdsim.potentials.pair.mie attribute) info() (halmd.io.log.logger method) (in module halmd.io.log) integrate() (halmd.mdsim.integrators.euler method) (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_boltzmann 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) internal_energy() (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.observables.thermodynamics method) interp() (in module halmd.utility) interval (halmd.mdsim.integrators.verlet_nvt_boltzmann attribute)

K

kB (in module halmd.utility.constants)

keys() (in module halmd.utility) kinetic_energy() (halmd.observables.thermodynamics method)

L

label (halmd.mdsim.particle attribute) (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.id_range attribute) (halmd.mdsim.particle_groups.region attribute) (halmd.mdsim.particle_groups.region_species 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) (halmd.mdsim.geometries.cuboid attribute) (halmd.mdsim.geometries.cylinder attribute) lennard_jones (class in halmd.mdsim.potentials.pair) loader() (in module halmd.utility.module) logger (class in halmd.io.log) lowest_corner (halmd.mdsim.geometries.cuboid attribute) lowest_corner() (halmd.mdsim.box method) LUA_USE_STATIC_LIBS

M

main() built-in function mass (halmd.mdsim.integrators.verlet_nvt_hoover attribute) mass() (halmd.observables.phase_space method) max() (in module halmd.numeric) max_displacement (class in halmd.mdsim) mdstep() (in module halmd.mdsim.core) 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) (halmd.mdsim.potentials.external.harmonic attribute) (halmd.mdsim.potentials.external.planar_wall attribute) (halmd.mdsim.potentials.pair.custom attribute) (halmd.mdsim.potentials.pair.lennard_jones attribute) (halmd.mdsim.potentials.pair.mie attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute) message() (halmd.io.log.logger method) (in module halmd.io.log) mie (class in halmd.mdsim.potentials.pair) min() (in module halmd.numeric) modify() (halmd.mdsim.potentials.pair.custom method) (halmd.mdsim.potentials.pair.lennard_jones method) (halmd.mdsim.potentials.pair.mie method) (halmd.mdsim.potentials.pair.morse method) (halmd.mdsim.potentials.pair.power_law method) module halmd halmd.io halmd.io.log halmd.io.readers halmd.io.writers halmd.mdsim halmd.mdsim.clock halmd.mdsim.core halmd.mdsim.forces halmd.mdsim.geometries halmd.mdsim.integrators halmd.mdsim.particle_groups halmd.mdsim.positions halmd.mdsim.potentials halmd.mdsim.potentials.external halmd.mdsim.potentials.pair halmd.mdsim.potentials.pair.adapters halmd.mdsim.potentials.pair.adapters.modify halmd.mdsim.potentials.pair.adapters.truncate halmd.mdsim.potentials.pair.modified_lennard_jones halmd.mdsim.sorts halmd.mdsim.velocities halmd.numeric halmd.observables halmd.observables.dynamics halmd.observables.sampler halmd.observables.utility halmd.random halmd.utility halmd.utility.constants halmd.utility.device halmd.utility.posix_signal halmd.utility.profiler halmd.utility.program_options halmd.utility.signal halmd.utility.timer_service halmd.utility.version

module (class in halmd.utility) morse (class in halmd.mdsim.potentials.pair) multi_index_to_offset() (in module halmd.numeric) multiply() (in module halmd.numeric) multiply_scalar() (in module halmd.numeric)

N

NA (in module halmd.utility.constants) neighbour (class in halmd.mdsim) norm_1() (in module halmd.numeric) norm_2() (in module halmd.numeric)

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

O

offset (halmd.mdsim.potentials.external.harmonic attribute) (halmd.mdsim.potentials.external.planar_wall attribute) offset_to_multi_index() (in module halmd.numeric) on_alrm() (in module halmd.utility.posix_signal) on_append_apply() (halmd.mdsim.forces.external method) (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) on_append_finalize() (in module halmd.mdsim.core) on_append_force() (halmd.mdsim.particle method) 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() (halmd.mdsim.particle method) 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) on_prepare() (in module halmd.observables.sampler)

on_prepend_apply() (halmd.mdsim.forces.external method) (halmd.mdsim.forces.pair_full method) (halmd.mdsim.forces.pair_trunc method) on_prepend_finalize() (in module halmd.mdsim.core) on_prepend_force() (halmd.mdsim.particle method) 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) order() (halmd.mdsim.sorts.hilbert method)

P

pair (class in halmd.mdsim.forces) pair_full (class in halmd.mdsim.forces) pair_trunc (class in halmd.mdsim.forces) param2 (halmd.mdsim.potentials.pair.custom attribute) param3 (halmd.mdsim.potentials.pair.custom attribute) parse_args() (halmd.utility.program_options.argument_parser method) particle (class in halmd.mdsim) (halmd.mdsim.binning attribute) (halmd.mdsim.max_displacement attribute) (halmd.mdsim.neighbour attribute) (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.id_range attribute) (halmd.mdsim.particle_groups.region attribute) (halmd.mdsim.particle_groups.region_species attribute) particle_number() (halmd.observables.thermodynamics method) path (halmd.io.readers.h5md attribute) (halmd.io.writers.h5md attribute) phase_space (class in halmd.observables)

phase_space.writer (class in halmd.observables) place_spheres() (halmd.mdsim.positions.excluded_volume method) planar_wall (class in halmd.mdsim.potentials.external) poll() (in module halmd.utility.posix_signal) position() (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.observables.phase_space method) potential (halmd.mdsim.forces.external attribute) (halmd.mdsim.forces.pair attribute) (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.pair) precision (halmd.mdsim.particle attribute) pressure() (halmd.observables.thermodynamics method) process() (in module halmd.utility.timer_service) prod() (in module halmd.numeric) profile() (in module halmd.utility.profiler) prologue() (in module halmd.utility.version)

R

r_cut (halmd.mdsim.binning attribute) (halmd.mdsim.potentials.pair.lennard_jones attribute) (halmd.mdsim.potentials.pair.mie attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute) r_cut_sigma (halmd.mdsim.potentials.pair.lennard_jones attribute) (halmd.mdsim.potentials.pair.mie attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute) r_min (halmd.mdsim.potentials.pair.morse attribute) r_min_sigma (halmd.mdsim.potentials.pair.morse attribute) r_skin (halmd.mdsim.binning attribute) (halmd.mdsim.neighbour attribute) radius (halmd.mdsim.geometries.cylinder attribute) (halmd.mdsim.geometries.sphere attribute) random_seed() (halmd.utility.program_options.halmd.utility.program_options.argument_parser.action method) rate (halmd.mdsim.integrators.verlet_nvt_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) region (class in halmd.mdsim.particle_groups) region_species (class in halmd.mdsim.particle_groups) repeat_element() (in module halmd.utility) 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) scalar_matrix() (in module halmd.numeric) scalar_vector() (in module halmd.numeric) seed() (in module halmd.random) semilog_grid (class in halmd.observables.utility) set() (halmd.mdsim.particle method) (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_mass() (halmd.mdsim.integrators.verlet_nvt_hoover method) set_temperature() (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_hoover method) set_timestep() (halmd.mdsim.integrators.euler method) (halmd.mdsim.integrators.verlet method) (halmd.mdsim.integrators.verlet_nvt_andersen method) (halmd.mdsim.integrators.verlet_nvt_boltzmann method) (halmd.mdsim.integrators.verlet_nvt_hoover method) (in module halmd.mdsim.clock) 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) shuffle() (in module halmd.random) sigma (halmd.mdsim.potentials.external.planar_wall attribute) (halmd.mdsim.potentials.pair.custom attribute) (halmd.mdsim.potentials.pair.lennard_jones attribute) (halmd.mdsim.potentials.pair.mie attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute)

size (halmd.mdsim.particle_groups.all attribute) (halmd.mdsim.particle_groups.id_range attribute) (halmd.mdsim.particle_groups.region attribute) (halmd.mdsim.particle_groups.region_species attribute) slab (halmd.mdsim.positions.lattice attribute) smoothing (halmd.mdsim.potentials.external.planar_wall attribute) sorted() (in module halmd.utility) species() (halmd.observables.phase_space method) sphere (class in halmd.mdsim.geometries) ssf (class in halmd.observables) ssf.writer (class in halmd.observables) start() (in module halmd.observables.sampler) step (in module halmd.mdsim.clock) stiffness (halmd.mdsim.potentials.external.harmonic attribute) stress_tensor() (halmd.observables.thermodynamics method) stress_tensor_autocorrelation (class in halmd.observables.dynamics) stress_tensor_autocorrelation.writer (class in halmd.observables.dynamics) substitute_date_time() (halmd.utility.program_options.halmd.utility.program_options.argument_parser.action method) substitute_environment() (halmd.utility.program_options.halmd.utility.program_options.argument_parser.action method) subtract() (in module halmd.numeric) subtract_scalar() (in module halmd.numeric) sum() (halmd.observables.utility.accumulator method) (in module halmd.numeric) surface_normal (halmd.mdsim.potentials.external.planar_wall attribute)

T

table_shallow_copy() (in module halmd.utility) temperature (halmd.mdsim.integrators.verlet_nvt_andersen attribute) (halmd.mdsim.integrators.verlet_nvt_boltzmann 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) timestep (halmd.mdsim.integrators.euler attribute) (halmd.mdsim.integrators.verlet attribute) (halmd.mdsim.integrators.verlet_nvt_andersen attribute) (halmd.mdsim.integrators.verlet_nvt_boltzmann attribute) (halmd.mdsim.integrators.verlet_nvt_hoover attribute) (in module halmd.mdsim.clock)

to_particle() (halmd.mdsim.particle_groups.id_range method) (halmd.mdsim.particle_groups.region method) (halmd.mdsim.particle_groups.region_species method) total_force() (halmd.observables.thermodynamics method) trace() (halmd.io.log.logger method) (in module halmd.io.log) trans() (in module halmd.numeric) truncate() (halmd.mdsim.potentials.pair.custom method) (halmd.mdsim.potentials.pair.lennard_jones method) (halmd.mdsim.potentials.pair.mie method) (halmd.mdsim.potentials.pair.morse method) (halmd.mdsim.potentials.pair.power_law method)

V

value (in module halmd.observables.utility.semilog_grid) value() (halmd.observables.utility.wavevector method) variance() (halmd.observables.utility.accumulator method) velocity() (halmd.mdsim.integrators.verlet_nvt_hoover method) (halmd.observables.phase_space method) velocity_autocorrelation (class in halmd.observables.dynamics) velocity_autocorrelation.writer (class in halmd.observables.dynamics) verlet (class in halmd.mdsim.integrators) verlet_nvt_andersen (class in halmd.mdsim.integrators) verlet_nvt_boltzmann (class in halmd.mdsim.integrators)

verlet_nvt_hoover (class in halmd.mdsim.integrators) verlet_nvt_hoover.writer (class in halmd.mdsim.integrators) version (halmd.io.readers.h5md attribute) version() (in module halmd.io.writers.h5md) virial() (halmd.observables.thermodynamics method) volume (halmd.mdsim.box attribute) (halmd.mdsim.geometries.cuboid attribute) (halmd.mdsim.geometries.cylinder attribute) (halmd.mdsim.geometries.sphere attribute) volume() (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)

wetting (halmd.mdsim.potentials.external.planar_wall attribute) writer() (halmd.io.writers.h5md method) (halmd.mdsim.box method) (halmd.observables.thermodynamics method) (halmd.observables.utility.accumulator method)