Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z

A

access (module)
AccessType (class in access)
add() (build.Code method)
add_item() (method.Schedule method)
add_line() (build.Code method)
all_reduce() (in module mpi)
AllToAll (class in pairloop)
AllToAllNS (class in pairloop)
analyse() (in module kernel)
apply() (domain.BoundaryTypePeriodic method)
Array (class in host)
as_func() (state.BaseMDState method)
available_free_memory() (in module host)

B

barrier() (mpi.MDMPI method)
BaseDomainHalo (class in domain)
BaseMDSimulation (class in simulation)
BaseMDState (class in state)
BasePotential (class in potential)
boundary (domain.BaseDomainHalo attribute)
boundary_outer (domain.BaseDomainHalo attribute)
BoundaryTypePeriodic (class in domain)
broadcast_data_from() (data.ParticleDat method)
(state.BaseMDState method)
Buckingham (class in potential)
BuckinghamSymmetric (class in potential)
build (module)
build_lib() (in module build)

C

CartesianHaloSix (class in halo)
cell (module)
cell_array (domain.BaseDomainHalo attribute)
cell_contents_count (cell.CellList attribute)
cell_count (domain.BaseDomainHalo attribute)
cell_decompose() (domain.BaseDomainHalo method)
cell_edge_lengths (domain.BaseDomainHalo attribute)
cell_list (cell.CellList attribute)
cell_occupancy_counter() (cell.CellLayerSort method)
cell_occupancy_matrix (cell.CellLayerSort attribute)
cell_reverse_lookup (cell.CellList attribute)
cell_width (cell.CellList attribute)
CellLayerSort (class in cell)
CellList (class in cell)
CellSlice (class in halo)
check() (cell.CellList method)
check_file_existance() (in module build)
cleanup() (method.DrawParticles method)
close() (pio.pfprint method)
Code (class in build)
code (kernel.Kernel attribute)
comm (mpi.MDMPI attribute)
compressed (state.BaseMDState attribute)
Constant (class in kernel)
copy() (data.ParticleDat method)
count (method.Schedule attribute)
Cpp11MT19937 (class in kernel)
create() (cell.CellList method)
create_cart() (mpi.MDMPI method)
create_halo_pairs_slice_halo() (in module halo)
creation_timer (build.SharedLib attribute)
ctypes_data (host.Array attribute)
(host.Matrix attribute)
(host.PointerArray attribute)
ctypes_data_access() (data.ParticleDat method)
(host.Array method)
(host.Matrix method)
ctypes_data_post() (data.ParticleDat method)
(host.Array method)
(host.Matrix method)
ctypes_value (data.ScalarArray attribute)

D

data (data.ParticleDat attribute)
(host.Matrix attribute)
(module)
datdict() (potential.Buckingham method)
(potential.LennardJonesCounter method)
(potential.LennardJonesShifted method)
(potential.NULL static method)
decomposition (in module mpi)
determine_update_status() (method.ListUpdateController method)
dims (mpi.MDMPI attribute)
domain (cell.CellList attribute)
(module)
(state.BaseMDState attribute)
draw() (method.DrawParticles method)
DrawParticles (class in method)
dtype (host.Array attribute)
(host.Matrix attribute)
(host.PointerArray attribute)

E

end (host.Array attribute)
EnergyStore (class in method)
enum() (in module mpi)
evaluate() (method.RadialDistributionPeriodicNVE method)
(method.VelocityAutoCorrelation method)
exchange_cell_counts() (halo.CartesianHaloSix method)
execute() (build.SharedLib method)
(loop.ParticleLoop method)
(method.KineticEnergyTracker method)
(method.PotentialEnergyTracker method)
(pairloop.AllToAllNS method)
(pairloop.PairLoopNeighbourListNS method)
(pairloop.PairLoopRapaportHalo method)
execute_boundary_conditions() (method.ListUpdateController method)
execute_overhead_timer (build.SharedLib attribute)
execute_timer (build.SharedLib attribute)
extent (domain.BaseDomainHalo attribute)
extent_internal (domain.BaseDomainHalo attribute)

F

factor() (in module domain)
filter_on_domain_boundary() (state.BaseMDState method)
finalise() (method.ParticleTracker method)
forces_update() (simulation.BaseMDSimulation method)
fortran_comm (mpi.MDMPI attribute)

G

gather_data_on() (data.ParticleDat method)
(state.BaseMDState method)
get_boundary_cell_contents_count() (halo.CartesianHaloSix method)
get_boundary_cell_groups() (halo.CartesianHaloSix method)
get_boundary_cells() (domain.BaseDomainHalo method)
get_cell_to_particle_map() (state.BaseMDState method)
get_cpp_arguments_ast() (kernel.Cpp11MT19937 method)
(kernel.Module method)
get_cpp_headers_ast() (kernel.Cpp11MT19937 method)
(kernel.Module method)
get_cpp_post_loop_code_ast() (kernel.Cpp11MT19937 method)
(kernel.Module method)
get_cpp_pre_loop_code_ast() (kernel.Cpp11MT19937 method)
(kernel.Module method)
get_data_map() (potential.Buckingham method)
(potential.LennardJonesShifted method)
(potential.VLennardJonesNoU method)
get_dir_counts() (halo.CartesianHaloSix method)
get_domain() (state.BaseMDState method)
get_extent() (simulation.PosInitDLPOLYConfig method)
(simulation.PosInitLatticeNRho method)
(simulation.PosInitLatticeNRhoRand method)
(simulation.PosInitOneParticleInABox method)
(simulation.PosInitTwoParticlesInABox method)
get_first_cell_is_halo_symbol() (in module pairloop)
get_first_index_symbol() (in module pairloop)
get_halo_cell_groups() (halo.CartesianHaloSix method)
get_kinetic_energy_array() (method.KineticEnergyTracker method)
get_move_send_recv_ranks() (mpi.MDMPI method)
get_npart_local_func() (state.BaseMDState method)
get_position_dat() (state.BaseMDState method)
get_position_shifts() (halo.CartesianHaloSix method)
get_potential_energy_array() (method.PotentialEnergyTracker method)
get_python_parameters() (kernel.Cpp11MT19937 method)
(kernel.Module method)
get_recv_ranks() (halo.CartesianHaloSix method)
get_second_cell_is_halo_symbol() (in module pairloop)
get_second_index_symbol() (in module pairloop)
get_send_ranks() (halo.CartesianHaloSix method)
get_setup_parameters() (cell.CellList method)
get_shift() (domain.BaseDomainHalo method)
get_type_map_symbol() (in module pairloop)
group_by_cell() (cell.GroupByCell method)
GroupByCell (class in cell)

H

halo (module)
halo_exchange() (data.ParticleDat method)
halo_start (data.ParticleDat attribute)
halo_start_reset() (data.ParticleDat method)
halo_start_set() (data.ParticleDat method)
halo_start_shift() (data.ParticleDat method)
halo_update() (cell.NeighbourListHaloAware method)
halo_version_id (cell.CellList attribute)
halos (domain.BaseDomainHalo attribute)
Header (class in kernel)
headers (kernel.Kernel attribute)
hexdigest() (kernel.Kernel method)
host (module)

I

INC (in module access)
inc_version() (host.Array method)
(host.Matrix method)
increment_step_count() (method.ListUpdateController method)
incremented (access.AccessType attribute)
index (kernel.Reduction attribute)
integrate() (method.IntegratorVelocityVerlet method)
(method.VelocityVerlet method)
integrate_thermostat() (method.VelocityVerletAnderson method)
IntegratorRange (class in method)
IntegratorVelocityVerlet (class in method)
invalidate_lists (state.BaseMDState attribute)

K

Kernel (class in kernel)
kernel (module)
(potential.Buckingham attribute)
(potential.BuckinghamSymmetric attribute)
(potential.LennardJones attribute)
(potential.LennardJonesCounter attribute)
(potential.LennardJonesShifted attribute)
(potential.NULL attribute)
(potential.NoVLennardJones attribute)
(potential.TestPotential1 attribute)
(potential.TestPotential2 attribute)
(potential.TestPotential3 attribute)
(potential.TestPotential4 attribute)
(potential.TestPotential4p attribute)
(potential.VLennardJones attribute)
(potential.VLennardJones2 attribute)
(potential.VLennardJonesNoU attribute)
kinetic_energy_update() (simulation.BaseMDSimulation method)
KineticEnergyTracker (class in method)

L

LennardJones (class in potential)
LennardJonesCounter (class in potential)
LennardJonesShifted (class in potential)
ListUpdateController (class in method)
load() (in module build)
load_library_exception() (in module build)
loop (module)
loop_unroll() (in module build)

M

MassInitIdentical (class in simulation)
MassInitTwoAlternating (class in simulation)
Matrix (class in host)
max (data.ScalarArray attribute)
max() (data.ParticleDat method)
max_npart (data.ParticleDat attribute)
md5() (in module build)
MDMPI (class in mpi)
mean (data.ScalarArray attribute)
method (module)
min (data.ScalarArray attribute)
mode (access.AccessType attribute)
Module (class in kernel)
move_to_neighbour() (state.BaseMDState method)
mpi (module)
mpi_decompose() (domain.BaseDomainHalo method)

N

name (data.ParticleDat attribute)
(data.ScalarArray attribute)
(data.TypedDat attribute)
(kernel.Kernel attribute)
ncol (host.Matrix attribute)
ncomp (data.ParticleDat attribute)
(host.Array attribute)
(host.PointerArray attribute)
neighbour_matrix (cell.NeighbourListLayerBased attribute)
NeighbourList (class in cell)
NeighbourListHaloAware (class in cell)
NeighbourListLayerBased (class in cell)
NeighbourListNonN3 (class in cell)
NeighbourListPairIndices (class in cell)
NeighbourListv2 (class in cell)
NeighbourMatrix (class in cell)
next() (method.IntegratorRange method)
norm_linf() (data.ParticleDat method)
norm_vec() (method.DrawParticles method)
NoVLennardJones (class in potential)
npart (state.BaseMDState attribute)
npart_local (data.ParticleDat attribute)
(state.BaseMDState attribute)
npart_local_halo (data.ParticleDat attribute)
npart_total (data.ParticleDat attribute)
nproc (mpi.MDMPI attribute)
nrow (host.Matrix attribute)
NULL (class in potential)
null_matrix() (in module host)
num_layers (cell.CellLayerSort attribute)
num_neighbours_per_atom (cell.NeighbourListLayerBased attribute)
num_particles (cell.CellList attribute)

O

offset (cell.CellList attribute)
operator (kernel.Reduction attribute)

P

pairloop (module)
PairLoopNeighbourList (class in pairloop)
PairLoopNeighbourListNS (class in pairloop)
PairLoopRapaportHalo (class in pairloop)
particle_layers (cell.CellLayerSort attribute)
ParticleDat (class in data)
ParticleLoop (class in loop)
ParticleTracker (class in method)
PercentagePrinter (class in method)
periodic_mod() (in module simulation)
periods (mpi.MDMPI attribute)
pfactor() (in module domain)
pfprint (class in pio)
pio (module)
plot() (method.EnergyStore method)
(method.RadialDistributionPeriodicNVE method)
(method.VelocityAutoCorrelation method)
pointer (kernel.Reduction attribute)
pointer_offset() (in module host)
PointerArray (class in host)
PosInitDLPOLYConfig (class in simulation)
PosInitLatticeNRho (class in simulation)
PosInitLatticeNRhoRand (class in simulation)
PosInitOneParticleInABox (class in simulation)
PosInitTwoParticlesInABox (class in simulation)
post_halo_exchange() (cell.CellList method)
post_update() (method.ListUpdateController method)
potential (module)
(simulation.BaseMDSimulation attribute)
PotentialEnergyTracker (class in method)
pprint() (in module pio)
(pio.pfprint method)
pre_update() (method.ListUpdateController method)
prepare_halo_sort() (cell.CellList method)
print_str() (mpi.MDMPI method)
pwrite() (pio.pfprint method)

Q

query_boundary_exist (mpi.MDMPI attribute)
query_halo_exist (mpi.MDMPI attribute)

R

R (in module access)
RadialDistributionPeriodicNVE (class in method)
rank (mpi.MDMPI attribute)
raw_write() (method.RadialDistributionPeriodicNVE method)
rc (potential.LennardJonesShifted attribute)
(potential.NULL attribute)
read (access.AccessType attribute)
realloc() (host.Array method)
(host.Matrix method)
Reduction (class in kernel)
reduction_variable_lookup() (kernel.Kernel method)
remove_particles() (data.ParticleDat method)
replace() (kernel.Constant method)
reset() (method.RadialDistributionPeriodicNVE method)
(simulation.MassInitIdentical method)
(simulation.MassInitTwoAlternating method)
(simulation.PosInitDLPOLYConfig method)
(simulation.PosInitLatticeNRho method)
(simulation.PosInitLatticeNRhoRand method)
(simulation.PosInitOneParticleInABox method)
(simulation.PosInitTwoParticlesInABox method)
(simulation.VelInitDLPOLYConfig method)
(simulation.VelInitMaxwellBoltzmannDist method)
(simulation.VelInitNormDist method)
(simulation.VelInitOneParticleInABox method)
(simulation.VelInitPosBased method)
(simulation.VelInitTwoParticlesInABox method)
reset_callbacks() (cell.CellList method)
reset_cell_list() (in module cell)
reset_halos() (in module halo)
reset_mpi() (in module mpi)
resize() (data.ParticleDat method)
(data.ScalarArray method)
Restrict() (in module loop)
(in module pairloop)
rn (potential.NULL attribute)
rprint() (in module pio)
runtime (module)
RW (in module access)

S

ScalarArray (class in data)
scale() (data.ScalarArray method)
scatter_data_from() (state.BaseMDState method)
Schedule (class in method)
schedule (method.Schedule attribute)
set_extent() (domain.BaseDomainHalo method)
set_periods() (mpi.MDMPI method)
set_state() (domain.BoundaryTypePeriodic method)
set_timestep() (method.ListUpdateController method)
set_v0() (method.VelocityAutoCorrelation method)
set_val() (data.ParticleDat method)
setup() (cell.CellLayerSort method)
(cell.CellList method)
(cell.GroupByCell method)
(cell.NeighbourList method)
(cell.NeighbourListHaloAware method)
(cell.NeighbourListLayerBased method)
(cell.NeighbourListNonN3 method)
(cell.NeighbourListPairIndices method)
(cell.NeighbourListv2 method)
(cell.NeighbourMatrix method)
setup_callback_on_update() (cell.CellList method)
setup_pre_update() (cell.CellList method)
setup_update_tracking() (cell.CellList method)
SharedLib (class in build)
shift() (mpi.MDMPI method)
simple_lib_creator() (in module build)
simulation (module)
size (host.Array attribute)
(host.Matrix attribute)
sort() (cell.CellList method)
sort_halo_cells() (cell.CellList method)
source_write() (in module build)
State (class in state)
state (module)
(simulation.BaseMDSimulation attribute)
static_args (kernel.Kernel attribute)
string (build.Code attribute)
sum (data.ScalarArray attribute)

T

TestPotential1 (class in potential)
TestPotential2 (class in potential)
TestPotential3 (class in potential)
TestPotential4 (class in potential)
TestPotential4p (class in potential)
tick() (method.PercentagePrinter method)
(method.Schedule method)
timer1 (method.VelocityVerlet attribute)
timer2 (method.VelocityVerlet attribute)
top (mpi.MDMPI attribute)
total_num_particles (cell.CellList attribute)
trigger_update() (cell.CellList method)
TypedDat (class in data)

U

update() (cell.CellLayerSort method)
(cell.NeighbourList method)
(cell.NeighbourListHaloAware method)
(cell.NeighbourListLayerBased method)
(cell.NeighbourListNonN3 method)
(cell.NeighbourListPairIndices method)
(cell.NeighbourMatrix method)
(method.EnergyStore method)

V

variable (kernel.Reduction attribute)
VelInitDLPOLYConfig (class in simulation)
VelInitMaxwellBoltzmannDist (class in simulation)
VelInitNormDist (class in simulation)
VelInitOneParticleInABox (class in simulation)
VelInitPosBased (class in simulation)
VelInitTwoParticlesInABox (class in simulation)
VelocityAutoCorrelation (class in method)
VelocityVerlet (class in method)
VelocityVerletAnderson (class in method)
version (host.Array attribute)
(host.Matrix attribute)
version_id (cell.CellLayerSort attribute)
(cell.CellList attribute)
(cell.NeighbourList attribute)
(cell.NeighbourListHaloAware attribute)
(cell.NeighbourListLayerBased attribute)
(cell.NeighbourListPairIndices attribute)
(cell.NeighbourMatrix attribute)
VLennardJones (class in potential)
VLennardJones2 (class in potential)
VLennardJonesNoU (class in potential)
volume (domain.BaseDomainHalo attribute)

W

W (in module access)
write (access.AccessType attribute)
write() (method.ParticleTracker method)
(method.WriteTrajectoryXYZ method)
WriteTrajectoryXYZ (class in method)

Z

zero() (data.ParticleDat method)
(host.Array method)
(host.Matrix method)