Index

_

__eq() (halmd.mdsim.particle method) (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) 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_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) advance() (in module halmd.mdsim.clock) 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) aux_enable() (halmd.mdsim.particle method)

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)

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.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) 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 cutoff (halmd.mdsim.potentials.external.planar_wall attribute) CXX CXXFLAGS

D

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.lennard_jones attribute) (halmd.mdsim.potentials.pair.modified_lennard_jones 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) 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)

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.modified_lennard_jones 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) 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.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.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), [1] 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.modified_lennard_jones attribute) index_n (halmd.mdsim.potentials.pair.modified_lennard_jones 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

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) 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.lennard_jones attribute) (halmd.mdsim.potentials.pair.modified_lennard_jones attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute)

min() (in module halmd.numeric) modified_lennard_jones (class in halmd.mdsim.potentials.pair) modify() (halmd.mdsim.potentials.pair.lennard_jones method) (halmd.mdsim.potentials.pair.modified_lennard_jones method) (halmd.mdsim.potentials.pair.morse method) (halmd.mdsim.potentials.pair.power_law method) module (class in halmd.utility) morse (class in halmd.mdsim.potentials.pair) multi_index_to_offset() (in module halmd.numeric)

N

neighbour (class in halmd.mdsim) 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), [1] 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) 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.modified_lennard_jones 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.modified_lennard_jones attribute) (halmd.mdsim.potentials.pair.morse attribute) (halmd.mdsim.potentials.pair.power_law attribute) r_min_sigma (halmd.mdsim.potentials.pair.morse attribute) r_skin (halmd.mdsim.binning attribute) (halmd.mdsim.neighbour attribute) radius (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) 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.lennard_jones attribute) (halmd.mdsim.potentials.pair.modified_lennard_jones 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) sum() (halmd.observables.utility.accumulator method) (in module halmd.numeric) surface_normal (halmd.mdsim.potentials.external.planar_wall attribute)

T

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.lennard_jones method) (halmd.mdsim.potentials.pair.modified_lennard_jones 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)

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)