Index

A

add_basis() (gpyumd.atoms.GpumdAtoms method) add_calc() (gpyumd.sim.StaticCalc method) add_group_method() (gpyumd.atoms.GpumdAtoms method) add_keyword() (gpyumd.sim.Run method)

add_potential() (gpyumd.sim.Potentials method) (gpyumd.sim.Simulation method) add_run() (gpyumd.sim.Simulation method) add_static_calc() (gpyumd.sim.Simulation method) autocorrelate() (in module gpyumd.math)

C

calc_gkma_kappa() (in module gpyumd.calc) calc_reduced_freq_info() (in module gpyumd.calc) calc_spectral_kappa() (in module gpyumd.calc) ChangeBox (class in gpyumd.keyword) clear_run() (gpyumd.sim.Run method) Compute (class in gpyumd.keyword) ComputeCohesive (class in gpyumd.keyword) ComputeDOS (class in gpyumd.keyword) ComputeElastic (class in gpyumd.keyword)

ComputeGKMA (class in gpyumd.keyword) ComputeHAC (class in gpyumd.keyword) ComputeHNEMA (class in gpyumd.keyword) ComputeHNEMD (class in gpyumd.keyword) ComputePhonon (class in gpyumd.keyword) ComputeSDC (class in gpyumd.keyword) ComputeSHC (class in gpyumd.keyword) copy_potentials() (gpyumd.sim.Potentials method) correlate() (in module gpyumd.math) create_simulation() (gpyumd.sim.Simulation method)

D

default_elastic (gpyumd.keyword.EnsembleNPT attribute) Deform (class in gpyumd.keyword) DumpEXYZ (class in gpyumd.keyword) DumpForce (class in gpyumd.keyword)

DumpNetCDF (class in gpyumd.keyword) DumpPosition (class in gpyumd.keyword) DumpRestart (class in gpyumd.keyword) DumpThermo (class in gpyumd.keyword) DumpVelocity (class in gpyumd.keyword)

E

EnsembleHeat (class in gpyumd.keyword) EnsembleNPT (class in gpyumd.keyword)

EnsembleNVE (class in gpyumd.keyword) EnsembleNVT (class in gpyumd.keyword)

F

finalize_types() (gpyumd.sim.Potentials method)

Fix (class in gpyumd.keyword)

G

general() (gpyumd.keyword.ChangeBox class method) get_dt_in_fs() (gpyumd.sim.Run method) get_entry() (gpyumd.keyword.Keyword method) get_entry_rel_path() (gpyumd.keyword.Potential method) get_group() (gpyumd.atoms.GroupByPosition method) get_output() (gpyumd.sim.Potentials method) (gpyumd.sim.Run method) (gpyumd.sim.StaticCalc method) GpumdAtoms (class in gpyumd.atoms) gpyumd.atoms module gpyumd.calc module gpyumd.io module

gpyumd.keyword module gpyumd.load module gpyumd.math module gpyumd.sim module group_by_position() (gpyumd.atoms.GpumdAtoms method) group_by_symbol() (gpyumd.atoms.GpumdAtoms method) group_methods (gpyumd.atoms.GpumdAtoms attribute) GroupByPosition (class in gpyumd.atoms) GroupBySymbol (class in gpyumd.atoms) GroupGeneric (class in gpyumd.atoms) GroupMethod (class in gpyumd.atoms)

I

isotropic() (gpyumd.keyword.EnsembleNPT class method)

K

Keyword (class in gpyumd.keyword)

L

load_compute() (in module gpyumd.load) load_dos() (in module gpyumd.load) load_force() (in module gpyumd.load) load_frequency_info() (in module gpyumd.load) load_hac() (in module gpyumd.load) load_heatmode() (in module gpyumd.load) load_kappa() (in module gpyumd.load) load_kappamode() (in module gpyumd.load)

load_omega2() (in module gpyumd.load) load_saved_heatmode() (in module gpyumd.load) load_saved_kappamode() (in module gpyumd.load) load_sdc() (in module gpyumd.load) load_shc() (in module gpyumd.load) load_thermo() (in module gpyumd.load) load_vac() (in module gpyumd.load) load_velocity() (in module gpyumd.load)

M

Minimize (class in gpyumd.keyword) module gpyumd.atoms gpyumd.calc gpyumd.io gpyumd.keyword gpyumd.load gpyumd.math gpyumd.sim

N

NeighborOff (class in gpyumd.keyword)

O

orthogonal() (gpyumd.keyword.EnsembleNPT class method)

P

Potential (class in gpyumd.keyword)

Potentials (class in gpyumd.sim) potentials (gpyumd.sim.Potentials attribute)

R

read_gpumd() (in module gpyumd.io) read_modal_analysis_file() (in module gpyumd.load) read_movie() (in module gpyumd.io)

repeat() (gpyumd.atoms.GpumdAtoms method) Run (class in gpyumd.sim) RunKeyword (class in gpyumd.keyword) running_ave() (in module gpyumd.math)

S

scale() (gpyumd.keyword.ChangeBox class method) set_cutoff() (gpyumd.atoms.GpumdAtoms method) set_directory() (gpyumd.sim.Simulation method) set_dt_in_fs() (gpyumd.sim.Run method) set_max_neighbors() (gpyumd.atoms.GpumdAtoms method) set_type_dict() (gpyumd.atoms.GpumdAtoms method)

set_types() (gpyumd.keyword.Potential method) Simulation (class in gpyumd.sim) sort_atoms() (gpyumd.atoms.GpumdAtoms method) StaticCalc (class in gpyumd.sim) stretch() (gpyumd.keyword.ChangeBox class method) supported_potentials (gpyumd.keyword.Potential attribute)

T

TimeStep (class in gpyumd.keyword)

triclinic() (gpyumd.keyword.EnsembleNPT class method)

U

update() (gpyumd.atoms.GroupByPosition method) (gpyumd.atoms.GroupBySymbol method) (gpyumd.atoms.GroupGeneric method) (gpyumd.atoms.GroupMethod method)

update_symbols() (gpyumd.keyword.Potential method)

V

valid_group_options() (gpyumd.keyword.Keyword method) validate_potentials() (gpyumd.sim.Simulation method)

validate_run() (gpyumd.sim.Run method) validate_runs() (gpyumd.sim.Simulation method) Velocity (class in gpyumd.keyword)

W

write_basis() (gpyumd.atoms.GpumdAtoms method) (in module gpyumd.io) write_gpumd() (gpyumd.atoms.GpumdAtoms method) (in module gpyumd.io)

write_kpoints() (gpyumd.atoms.GpumdAtoms method) (in module gpyumd.io)