Index

_

__version__ (in module porereax)

A

add_angle_sampling() (porereax.sample.Sample method) add_bond_density_sampling() (porereax.sample.Sample method) add_bond_length_sampling() (porereax.sample.Sample method) add_charge_sampling() (porereax.sample.Sample method) add_density_sampling() (porereax.sample.Sample method) add_image_dump() (porereax.simulate.Simulate method)

add_molecule_structure_sampling() (porereax.sample.Sample method) add_rdf_sampling() (porereax.sample.Sample method) add_reaction_sampling() (porereax.sample.Sample method) add_sim() (porereax.simulate.Simulate method) AngleSampler (class in porereax.angle) AtomSampler (class in porereax.meta_sampler) auto_freeze() (porereax.simulate.Simulate method)

B

BondDensitySampler (class in porereax.density) BondLengthSampler (class in porereax.bond_length)

BondSampler (class in porereax.meta_sampler) box_region() (in module porereax.regions)

C

ChargeSampler (class in porereax.charge)

D

DensitySampler (class in porereax.density)

E

entry (in module porereax.regions)

F

freeze_region() (porereax.simulate.Simulate method)

G

generate() (porereax.simulate.Simulate method) get_bonds() (porereax.meta_sampler.BondSampler method) get_data() (in module porereax.utils)

get_identifiers() (in module porereax.utils) get_mols() (porereax.meta_sampler.Sampler method) get_region_function() (in module porereax.regions) get_trajectory_data() (porereax.sample.Sample static method)

I

init_helper() (porereax.sample.Sample method)

init_samplers() (porereax.sample.Sample method) init_subprocess_sampler() (porereax.sample.Sample static method)

J

join_samplers() (porereax.angle.AngleSampler method) (porereax.bond_length.BondLengthSampler method) (porereax.charge.ChargeSampler method) (porereax.density.BondDensitySampler method) (porereax.density.DensitySampler method) (porereax.density.ReactionSampler method) (porereax.meta_sampler.Sampler method) (porereax.molecule_structure.MoleculeStructureSampler method) (porereax.rdf.RdfSampler method)

L

load_object() (in module porereax.utils)

load_yaml() (in module porereax.utils)

M

min_image_convention() (in module porereax.utils) min_image_midpoint() (in module porereax.utils) module porereax porereax.angle porereax.bond_length porereax.charge porereax.density porereax.meta_sampler porereax.molecule_structure porereax.plot porereax.rdf porereax.regions porereax.sample porereax.simulate porereax.utils

MoleculeStructureSampler (class in porereax.molecule_structure)

P

plot() (in module porereax.plot) pore_region() (in module porereax.regions) porereax module porereax.angle module porereax.bond_length module porereax.charge module porereax.density module porereax.meta_sampler module

porereax.molecule_structure module porereax.plot module porereax.rdf module porereax.regions module porereax.sample module porereax.simulate module porereax.utils module

R

RdfSampler (class in porereax.rdf) ReactionSampler (class in porereax.density)

read_pore_yml() (in module porereax.utils) Region (in module porereax.sample) reservoir_region() (in module porereax.regions)

S

Sample (class in porereax.sample) sample() (porereax.angle.AngleSampler method) (porereax.bond_length.BondLengthSampler method) (porereax.charge.ChargeSampler method) (porereax.density.BondDensitySampler method) (porereax.density.DensitySampler method) (porereax.density.ReactionSampler method) (porereax.meta_sampler.Sampler method) (porereax.molecule_structure.MoleculeStructureSampler method) (porereax.rdf.RdfSampler method) (porereax.sample.Sample method)

sample_helper() (porereax.sample.Sample method) Sampler (class in porereax.meta_sampler) save_object() (in module porereax.utils) (porereax.meta_sampler.Sampler method) set_force_field() (porereax.simulate.Simulate method) set_job_file() (porereax.simulate.Simulate method) Simulate (class in porereax.simulate)

W

wall_region() (in module porereax.regions)