PyRETIS
2.5.0
About
Installing
Getting started
Input file
Site
PyRETIS License (GNU Lesser General Public License v2.1+)
About PyRETIS
The PyRETIS team
To cite us:
User Guide
Introduction to PyRETIS and rare event methods
Obtaining and installing PyRETIS
Getting started with PyRETIS
Running PyRETIS
Input reference for sections
The PyRETIS application
The PyRETIS analysis application
PyRETIS exercises
Introduction to the PyRETIS library
Creating custom order parameters
Creating custom engines
PyRETIS units
Running LAMMPS with PyRETIS
Some common PyRETIS errors
The PyRETIS library
The PyRETIS package
Examples
Umbrella Sampling
Molecular dynamics examples
TIS in a 1D potential
RETIS in a 1D potential
RETIS in a 2D potential
Using C or FORTRAN
Molecular dynamics in PyRETIS with C or FORTRAN
Particle Swarm Optimization
Transport of methane in a sI hydrate
Breaking a bond with RETIS
Dissociation of Hydrogen with CP2K
Breaking a bond with RETIS and LAMMPS
Running a PyRETIS simulation with OpenMM
PyVisA: Visualization and Analysis of Path Sampling results
Compressor
Visualization
Developer Guide
Guidelines
Contributing to PyRETIS
Page
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
_
__call__() (pyretis.engines.internal.MDEngine method)
(pyretis.simulation.simulation_task.SimulationTask method)
__del__() (pyretis.engines.gromacs2.GromacsRunner method)
(pyretis.inout.fileio.FileIO method)
__enter__() (pyretis.engines.gromacs2.GromacsRunner method)
(pyretis.inout.fileio.FileIO method)
__eq__() (pyretis.core.particles.Particles method)
(pyretis.core.path.PathBase method)
(pyretis.core.system.System method)
__exit__() (pyretis.engines.gromacs2.GromacsRunner method)
(pyretis.inout.fileio.FileIO method)
__iadd__() (pyretis.core.path.PathBase method)
__init__() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
(pyretis.core.path.PathBase method)
(pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.properties.Property method)
(pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
(pyretis.core.random_gen.ReservoirSampler method)
(pyretis.core.system.System method)
(pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.gromacs2.GromacsEngine2 method)
(pyretis.engines.gromacs2.GromacsRunner method)
(pyretis.engines.internal.Langevin method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.internal.RandomWalk method)
(pyretis.engines.internal.VelocityVerlet method)
(pyretis.engines.internal.Verlet method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
(pyretis.forcefield.forcefield.ForceField method)
(pyretis.forcefield.potential.PotentialFunction method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCutnp method)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
(pyretis.forcefield.potentials.potentials.DoubleWell method)
(pyretis.forcefield.potentials.potentials.RectangularWell method)
(pyretis.inout.archive.PathStorage method)
(pyretis.inout.common.OutputBase method)
(pyretis.inout.fileio.FileIO method)
(pyretis.inout.formats.cp2k.SectionNode method)
(pyretis.inout.formats.cross.CrossFile method)
(pyretis.inout.formats.cross.CrossFormatter method)
(pyretis.inout.formats.energy.EnergyFile method)
(pyretis.inout.formats.energy.EnergyFormatter method)
(pyretis.inout.formats.energy.EnergyPathFile method)
(pyretis.inout.formats.energy.EnergyPathFormatter method)
(pyretis.inout.formats.formatter.OutputFormatter method)
(pyretis.inout.formats.order.OrderFile method)
(pyretis.inout.formats.order.OrderFormatter method)
(pyretis.inout.formats.order.OrderPathFile method)
(pyretis.inout.formats.order.OrderPathFormatter method)
(pyretis.inout.formats.path.PathExtFile method)
(pyretis.inout.formats.path.PathExtFormatter method)
(pyretis.inout.formats.path.PathIntFile method)
(pyretis.inout.formats.path.PathIntFormatter method)
(pyretis.inout.formats.pathensemble.PathEnsembleFile method)
(pyretis.inout.formats.pathensemble.PathEnsembleFormatter method)
(pyretis.inout.formats.snapshot.SnapshotFile method)
(pyretis.inout.formats.snapshot.SnapshotFormatter method)
(pyretis.inout.formats.txt_table.PathTableFormatter method)
(pyretis.inout.formats.txt_table.ThermoTableFormatter method)
(pyretis.inout.formats.txt_table.TxtTableFormatter method)
(pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
(pyretis.inout.simulationio.OutputTask method)
(pyretis.inout.simulationio.Task method)
(pyretis.orderparameter.orderangle.Angle method)
(pyretis.orderparameter.orderdihedral.Dihedral method)
(pyretis.orderparameter.orderparameter.CompositeOrderParameter method)
(pyretis.orderparameter.orderparameter.Distance method)
(pyretis.orderparameter.orderparameter.Distancevel method)
(pyretis.orderparameter.orderparameter.DistanceVelocity method)
(pyretis.orderparameter.orderparameter.OrderParameter method)
(pyretis.orderparameter.orderparameter.Position method)
(pyretis.orderparameter.orderparameter.PositionVelocity method)
(pyretis.orderparameter.orderparameter.Velocity method)
(pyretis.simulation.mc_simulation.UmbrellaWindowSimulation method)
(pyretis.simulation.md_simulation.SimulationMD method)
(pyretis.simulation.md_simulation.SimulationMDFlux method)
(pyretis.simulation.md_simulation.SimulationNVE method)
(pyretis.simulation.path_simulation.PathSimulation method)
(pyretis.simulation.path_simulation.SimulationRETIS method)
(pyretis.simulation.path_simulation.SimulationSingleTIS method)
(pyretis.simulation.simulation.Simulation method)
(pyretis.simulation.simulation_task.SimulationTask method)
(pyretis.visualization.orderparam_density.PathDensity method)
(pyretis.visualization.orderparam_density.PathVisualize method)
__iter__() (pyretis.core.particles.Particles method)
(pyretis.inout.fileio.FileIO method)
__ne__() (pyretis.core.path.PathBase method)
__next__() (pyretis.inout.fileio.FileIO method)
__str__() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
(pyretis.core.path.PathBase method)
(pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.properties.Property method)
(pyretis.core.system.System method)
(pyretis.engines.engine.EngineBase method)
(pyretis.forcefield.forcefield.ForceField method)
(pyretis.forcefield.potential.PotentialFunction method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.inout.archive.PathStorage method)
(pyretis.inout.archive.PathStorageTar method)
(pyretis.inout.common.OutputBase method)
(pyretis.inout.fileio.FileIO method)
(pyretis.inout.formats.formatter.OutputFormatter method)
(pyretis.inout.formats.txt_table.TxtTableFormatter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.simulationio.OutputTask method)
(pyretis.orderparameter.orderparameter.CompositeOrderParameter method)
(pyretis.orderparameter.orderparameter.OrderParameter method)
(pyretis.simulation.mc_simulation.UmbrellaWindowSimulation method)
(pyretis.simulation.md_simulation.SimulationMD method)
(pyretis.simulation.md_simulation.SimulationMDFlux method)
(pyretis.simulation.md_simulation.SimulationNVE method)
(pyretis.simulation.path_simulation.SimulationRETIS method)
(pyretis.simulation.path_simulation.SimulationSingleTIS method)
(pyretis.simulation.simulation.Simulation method)
(pyretis.simulation.simulation_task.SimulationTask method)
_abc_impl (pyretis.engines.external.ExternalMDEngine attribute)
_activate() (pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
_add_generate_vel() (in module pyretis.engines.lammps)
_add_node() (in module pyretis.inout.formats.cp2k)
_add_order_fix() (in module pyretis.engines.lammps)
_add_stopping_condition() (in module pyretis.engines.lammps)
_add_to_archive() (pyretis.inout.archive.PathStorageTar static method)
_add_traj_dump() (in module pyretis.engines.lammps)
_adjust_dof_according_to_box() (pyretis.core.system.System method)
_check_args() (in module pyretis.simulation.simulation_task)
_copy_attribute() (pyretis.core.particles.Particles method)
_copy_path() (pyretis.core.pathensemble.PathEnsembleExt static method)
_copyfile() (pyretis.engines.external.ExternalMDEngine static method)
_execute_grompp() (pyretis.engines.gromacs.GromacsEngine method)
_execute_grompp_and_mdrun() (pyretis.engines.gromacs.GromacsEngine method)
_execute_mdrun() (pyretis.engines.gromacs.GromacsEngine method)
_execute_mdrun_continue() (pyretis.engines.gromacs.GromacsEngine method)
_extend_and_execute_mdrun() (pyretis.engines.gromacs.GromacsEngine method)
_extend_gromacs() (pyretis.engines.gromacs.GromacsEngine method)
_extract_frame() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
_fill_up_tis_and_retis_settings() (in module pyretis.inout.settings)
_find_backup_files() (pyretis.engines.cp2k.CP2KEngine static method)
_format_with_vel() (pyretis.inout.formats.snapshot.SnapshotFormatter method)
_format_without_vel() (pyretis.inout.formats.snapshot.SnapshotFormatter method)
_grid_it_up() (in module pyretis.visualization.plotting)
_init_parameters() (pyretis.engines.internal.Langevin method)
_lj1 (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_lj2 (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_lj3 (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_lj4 (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_look_for_input_files() (pyretis.engines.external.ExternalMDEngine method)
_make_order_fix() (pyretis.engines.lammps.LAMMPSEngine method)
_modify_input() (pyretis.engines.external.ExternalMDEngine static method)
_move_path() (pyretis.core.pathensemble.PathEnsembleExt static method)
_movefile() (pyretis.engines.external.ExternalMDEngine static method)
_name_output() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
_offset (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_prepare_shooting_point() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
_print_figures_to_file() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
_propagate_from() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.gromacs2.GromacsEngine2 method)
(pyretis.engines.lammps.LAMMPSEngine method)
_rcut2 (pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
_read_configuration() (pyretis.engines.cp2k.CP2KEngine static method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
_read_input_settings() (pyretis.engines.external.ExternalMDEngine static method)
_remove_files() (pyretis.engines.external.ExternalMDEngine method)
_remove_gromacs_backup_files() (pyretis.engines.gromacs.GromacsEngine method)
_removefile() (pyretis.engines.external.ExternalMDEngine static method)
_reverse_velocities() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
A
add() (pyretis.core.properties.Property method)
add_child() (pyretis.inout.formats.cp2k.SectionNode method)
add_input_files() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
add_orderparameter() (pyretis.orderparameter.orderparameter.CompositeOrderParameter method)
add_particle() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
(pyretis.core.system.System method)
add_path_data() (pyretis.core.pathensemble.PathEnsemble method)
add_potential() (pyretis.forcefield.forcefield.ForceField method)
add_task() (pyretis.simulation.simulation.Simulation method)
add_to_lammps_input() (in module pyretis.engines.lammps)
add_to_path() (pyretis.engines.engine.EngineBase static method)
add_to_tar_file() (in module pyretis.inout.archive)
adjust_coordinate() (in module pyretis.inout.formats.snapshot)
adjust_dof() (pyretis.core.system.System method)
analyse_energies() (in module pyretis.analysis.energy_analysis)
analyse_file() (in module pyretis.inout.analysisio.analysisio)
analyse_flux() (in module pyretis.analysis.flux_analysis)
analyse_md_flux() (in module pyretis.analysis)
analyse_orderp() (in module pyretis.analysis.order_analysis)
analyse_path_ensemble() (in module pyretis.analysis.path_analysis)
analyse_path_ensemble_object() (in module pyretis.analysis.path_analysis)
Angle (class in pyretis.orderparameter.orderangle)
append() (pyretis.core.path.PathBase method)
(pyretis.core.random_gen.ReservoirSampler method)
apply_format() (in module pyretis.inout.formats.formatter)
(pyretis.inout.formats.energy.EnergyFormatter method)
archive_acc (pyretis.inout.archive.PathStorage attribute)
,
[1]
(pyretis.inout.archive.PathStorageTar attribute)
archive_name_from_status() (pyretis.inout.archive.PathStorage method)
archive_rej (pyretis.inout.archive.PathStorage attribute)
,
[1]
(pyretis.inout.archive.PathStorageTar attribute)
archive_traj (pyretis.inout.archive.PathStorage attribute)
,
[1]
args (pyretis.simulation.simulation_task.SimulationTask attribute)
atomic_kinetic_energy_tensor() (in module pyretis.core.particlefunctions)
B
backup (pyretis.inout.fileio.FileIO attribute)
(pyretis.inout.plotting.plotting.Plotter attribute)
bfs_convert() (in module pyretis.core.units)
big_fat_comparer() (in module pyretis.core.common)
block_error() (in module pyretis.analysis.analysis)
block_error_corr() (in module pyretis.analysis.analysis)
box (pyretis.core.system.System attribute)
bye_bye_world() (in module pyretis.bin.pyretisanalyse)
(in module pyretis.bin.pyretisrun)
bytes_read (pyretis.engines.gromacs2.GromacsRunner attribute)
C
calculate() (pyretis.orderparameter.orderangle.Angle method)
(pyretis.orderparameter.orderdihedral.Dihedral method)
(pyretis.orderparameter.orderparameter.CompositeOrderParameter method)
(pyretis.orderparameter.orderparameter.Distance method)
(pyretis.orderparameter.orderparameter.Distancevel method)
(pyretis.orderparameter.orderparameter.OrderParameter method)
(pyretis.orderparameter.orderparameter.Position method)
(pyretis.orderparameter.orderparameter.Velocity method)
calculate_beta() (pyretis.core.system.System method)
calculate_kinetic_energy() (in module pyretis.core.particlefunctions)
calculate_kinetic_energy_tensor() (in module pyretis.core.particlefunctions)
calculate_kinetic_temperature() (in module pyretis.core.particlefunctions)
calculate_linear_momentum() (in module pyretis.core.particlefunctions)
calculate_order() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.MDEngine static method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
calculate_pressure_from_temp() (in module pyretis.core.particlefunctions)
calculate_pressure_tensor() (in module pyretis.core.particlefunctions)
calculate_scalar_pressure() (in module pyretis.core.particlefunctions)
calculate_temperature() (pyretis.core.system.System method)
calculate_thermo() (in module pyretis.core.particlefunctions)
calculate_thermo_path() (in module pyretis.core.particlefunctions)
can_use_order_function() (pyretis.engines.engine.EngineBase class method)
check_interfaces() (pyretis.core.path.PathBase method)
check_parameters() (pyretis.forcefield.potential.PotentialFunction method)
(pyretis.forcefield.potentials.potentials.RectangularWell method)
check_poll() (pyretis.engines.gromacs2.GromacsRunner method)
check_python_version() (in module pyretis.inout.common)
check_settings() (in module pyretis.inout.setup.common)
check_Steps() (pyretis.visualization.orderparam_density.PathDensity method)
children (pyretis.inout.formats.cp2k.SectionNode attribute)
clean_dir() (in module pyretis.testing.helpers)
clean_up() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
close() (pyretis.engines.gromacs2.GromacsRunner method)
(pyretis.inout.fileio.FileIO method)
cmd (pyretis.engines.gromacs2.GromacsRunner attribute)
compare_and_cut() (pyretis.visualization.orderparam_density.PathDensity method)
compare_files() (in module pyretis.testing.compare)
compare_files_columns() (in module pyretis.testing.compare)
compare_files_lines() (in module pyretis.testing.compare)
compare_files_numerical() (in module pyretis.testing.compare)
compare_pathensemble_files() (in module pyretis.testing.compare)
compare_traj_archive() (in module pyretis.testing.compare)
CompositeOrderParameter (class in pyretis.orderparameter.orderparameter)
compute_weight_ss() (in module pyretis.core.tis)
config (pyretis.core.particles.ParticlesExt attribute)
CONSTANTS (in module pyretis.core.units)
CONVERT (in module pyretis.core.units)
convert_bases() (in module pyretis.core.units)
copy() (pyretis.core.particles.Particles method)
(pyretis.core.path.PathBase method)
(pyretis.core.system.System method)
cp2k (pyretis.engines.cp2k.CP2KEngine attribute)
CP2KEngine (class in pyretis.engines.cp2k)
create_backup() (in module pyretis.inout.common)
create_box() (in module pyretis.core.box)
create_empty_ensembles() (in module pyretis.inout.common)
create_engine() (in module pyretis.inout.setup.common)
create_external() (in module pyretis.inout.setup.common)
create_force_field() (in module pyretis.inout.setup.createforcefield)
create_initial_positions() (in module pyretis.inout.setup.createsystem)
create_lammps_md_input() (in module pyretis.engines.lammps)
create_orderparameter() (in module pyretis.inout.setup.common)
create_output_tasks() (pyretis.simulation.path_simulation.PathSimulation method)
(pyretis.simulation.simulation.Simulation method)
create_plotter() (in module pyretis.inout.plotting)
create_potential() (in module pyretis.inout.setup.common)
create_potentials() (in module pyretis.inout.setup.createforcefield)
create_reports() (in module pyretis.bin.pyretisanalyse)
create_simulation() (in module pyretis.inout.setup.createsimulation)
create_system() (in module pyretis.inout.setup.createsystem)
create_system_ext() (in module pyretis.testing.systemhelp)
create_velocities() (in module pyretis.inout.setup.createsystem)
CROSS_FMT (pyretis.inout.formats.cross.CrossFormatter attribute)
CrossFile (class in pyretis.inout.formats.cross)
CrossFormatter (class in pyretis.inout.formats.cross)
crossing_counter() (in module pyretis.core.common)
crossing_finder() (in module pyretis.core.common)
cycle (pyretis.simulation.simulation.Simulation attribute)
D
data (pyretis.inout.formats.cp2k.SectionNode attribute)
data_keys (pyretis.inout.formats.snapshot.SnapshotFormatter attribute)
data_size (pyretis.engines.gromacs2.GromacsRunner attribute)
deepdish_data() (pyretis.visualization.orderparam_density.PathDensity method)
delete() (pyretis.core.path.PathBase method)
delta2 (pyretis.core.properties.Property attribute)
desc (pyretis.core.properties.Property attribute)
(pyretis.forcefield.forcefield.ForceField attribute)
(pyretis.forcefield.potential.PotentialFunction attribute)
description (pyretis.engines.engine.EngineBase attribute)
(pyretis.engines.external.ExternalMDEngine attribute)
(pyretis.engines.internal.MDEngine attribute)
(pyretis.orderparameter.orderparameter.OrderParameter attribute)
detect (pyretis.core.pathensemble.PathEnsemble attribute)
dfs_print() (in module pyretis.inout.formats.cp2k)
diff_matching() (in module pyretis.visualization.common)
Dihedral (class in pyretis.orderparameter.orderdihedral)
dim (pyretis.core.particles.Particles attribute)
(pyretis.forcefield.potential.PotentialFunction attribute)
(pyretis.orderparameter.orderparameter.Position attribute)
(pyretis.orderparameter.orderparameter.Velocity attribute)
DIMENSIONS (in module pyretis.core.units)
directories() (pyretis.core.pathensemble.PathEnsemble method)
Distance (class in pyretis.orderparameter.orderparameter)
Distancevel (class in pyretis.orderparameter.orderparameter)
DistanceVelocity (class in pyretis.orderparameter.orderparameter)
DoubleWell (class in pyretis.forcefield.potentials.potentials)
DoubleWellWCA (class in pyretis.forcefield.potentials.pairpotentials.wca)
draw_maxwellian_velocities() (pyretis.core.random_gen.RandomGeneratorBase method)
dump_config() (pyretis.engines.external.ExternalMDEngine method)
dump_frame() (pyretis.engines.external.ExternalMDEngine method)
dump_phasepoint() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
dump_to_file() (pyretis.core.properties.Property method)
dynamics (pyretis.engines.internal.MDEngine attribute)
E
edr_file (pyretis.engines.gromacs2.GromacsRunner attribute)
ekin (pyretis.core.particles.Particles attribute)
empty_list() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
empty_path() (pyretis.core.path.Path method)
(pyretis.core.path.PathBase method)
ENERGY_FMT (pyretis.inout.formats.energy.EnergyFormatter attribute)
energy_terms (pyretis.engines.gromacs.GromacsEngine attribute)
ENERGY_TERMS (pyretis.inout.formats.energy.EnergyFormatter attribute)
(pyretis.inout.formats.energy.EnergyPathFormatter attribute)
EnergyFile (class in pyretis.inout.formats.energy)
EnergyFormatter (class in pyretis.inout.formats.energy)
EnergyPathFile (class in pyretis.inout.formats.energy)
EnergyPathFormatter (class in pyretis.inout.formats.energy)
engine (pyretis.simulation.md_simulation.SimulationMD attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
engine_factory() (in module pyretis.engines)
engine_type (pyretis.engines.engine.EngineBase attribute)
,
[1]
(pyretis.engines.external.ExternalMDEngine attribute)
(pyretis.engines.internal.MDEngine attribute)
(pyretis.engines.openmm.OpenMMEngine attribute)
EngineBase (class in pyretis.engines.engine)
ensemble_name (pyretis.core.pathensemble.PathEnsemble attribute)
ensemble_name_simple (pyretis.core.pathensemble.PathEnsemble attribute)
ensemble_number (pyretis.core.pathensemble.PathEnsemble attribute)
entry_point() (in module pyretis.bin.pyretisanalyse)
(in module pyretis.bin.pyretisrun)
evaluate_force() (pyretis.core.system.System method)
(pyretis.forcefield.forcefield.ForceField method)
evaluate_potential() (pyretis.core.system.System method)
(pyretis.forcefield.forcefield.ForceField method)
evaluate_potential_and_force() (pyretis.core.system.System method)
(pyretis.forcefield.forcefield.ForceField method)
exe_dir (pyretis.engines.engine.EngineBase attribute)
(pyretis.engines.gromacs2.GromacsRunner attribute)
(pyretis.simulation.simulation.Simulation attribute)
exe_dir() (pyretis.engines.engine.EngineBase property)
execute() (pyretis.simulation.simulation_task.SimulationTask method)
execute_command() (pyretis.engines.external.ExternalMDEngine method)
execute_now() (pyretis.inout.simulationio.Task method)
execute_tasks() (pyretis.simulation.simulation.Simulation method)
ext (pyretis.engines.gromacs.GromacsEngine attribute)
ext_time (pyretis.engines.gromacs.GromacsEngine attribute)
extend_cycles() (pyretis.simulation.simulation.Simulation method)
extender() (in module pyretis.core.tis)
ExternalMDEngine (class in pyretis.engines.external)
extra (pyretis.orderparameter.orderparameter.CompositeOrderParameter attribute)
extra_files (pyretis.engines.cp2k.CP2KEngine attribute)
extra_setup() (pyretis.core.system.System method)
F
FILE_FLUSH (pyretis.inout.fileio.FileIO attribute)
,
[1]
file_mode (pyretis.inout.fileio.FileIO attribute)
fileh (pyretis.engines.gromacs2.GromacsRunner attribute)
(pyretis.inout.fileio.FileIO attribute)
FileIO (class in pyretis.inout.fileio)
filename (pyretis.inout.fileio.FileIO attribute)
first (pyretis.simulation.simulation_task.SimulationTask attribute)
first_step (pyretis.simulation.simulation.Simulation attribute)
first_write (pyretis.inout.common.OutputBase attribute)
fix_path_by_tis() (in module pyretis.initiation.initiate_kick)
flush() (pyretis.inout.fileio.FileIO method)
FMT (pyretis.inout.formats.path.PathExtFormatter attribute)
,
[1]
fmt (pyretis.inout.formats.snapshot.SnapshotFormatter attribute)
(pyretis.inout.formats.txt_table.TxtTableFormatter attribute)
fmt_vel (pyretis.inout.formats.snapshot.SnapshotFormatter attribute)
force (pyretis.core.particles.Particles attribute)
force() (pyretis.core.system.System method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCutnp method)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
(pyretis.forcefield.potentials.potentials.DoubleWell method)
ForceField (class in pyretis.forcefield.forcefield)
forcefield (pyretis.core.system.System attribute)
format() (pyretis.inout.formats.cross.CrossFormatter method)
(pyretis.inout.formats.energy.EnergyFormatter method)
(pyretis.inout.formats.energy.EnergyPathFormatter method)
(pyretis.inout.formats.formatter.OutputFormatter method)
(pyretis.inout.formats.formatter.PyretisLogFormatter method)
(pyretis.inout.formats.order.OrderFormatter method)
(pyretis.inout.formats.order.OrderPathFormatter method)
(pyretis.inout.formats.path.PathExtFormatter method)
(pyretis.inout.formats.path.PathIntFormatter method)
(pyretis.inout.formats.pathensemble.PathEnsembleFormatter method)
(pyretis.inout.formats.snapshot.SnapshotFormatter method)
(pyretis.inout.formats.txt_table.PathTableFormatter method)
(pyretis.inout.formats.txt_table.TxtTableFormatter method)
format_data() (pyretis.inout.formats.order.OrderFormatter method)
format_snapshot() (pyretis.inout.formats.snapshot.SnapshotFormatter method)
format_xyz_data() (in module pyretis.inout.formats.xyz)
formatter (pyretis.inout.common.OutputBase attribute)
formatter_info() (pyretis.inout.archive.PathStorage method)
(pyretis.inout.common.OutputBase method)
formatters (pyretis.inout.archive.PathStorage attribute)
,
[1]
function (pyretis.simulation.simulation_task.SimulationTask attribute)
G
gamma (pyretis.engines.internal.Langevin attribute)
gen_surface() (in module pyretis.visualization.plotting)
generate_conversion_factors() (in module pyretis.core.units)
generate_initial_path_kick() (in module pyretis.initiation.initiate_kick)
generate_inverse() (in module pyretis.core.units)
generate_latex_table() (in module pyretis.inout.report.markup)
generate_lattice() (in module pyretis.tools.lattice)
generate_maxwellian_velocities() (pyretis.core.random_gen.RandomGeneratorBase method)
generate_pair_interactions() (in module pyretis.forcefield.potentials.pairpotentials.pairpotential)
generate_report() (in module pyretis.inout.report.report)
generate_report_mdflux() (in module pyretis.inout.report.report_md)
generate_report_retis() (in module pyretis.inout.report.report_path)
generate_report_tis() (in module pyretis.inout.report.report_path)
generate_report_tis_path() (in module pyretis.inout.report.report_path)
generate_rst_table() (in module pyretis.inout.report.markup)
generate_traj_names() (in module pyretis.inout.archive)
generate_velocities() (pyretis.core.system.System method)
generated (pyretis.core.path.PathBase attribute)
generic_factory() (in module pyretis.core.common)
get_acceptance_rate() (pyretis.core.pathensemble.PathEnsemble method)
get_accepted() (pyretis.core.pathensemble.PathEnsemble method)
get_all_parents() (pyretis.inout.formats.cp2k.SectionNode method)
get_boltzmann() (pyretis.core.system.System method)
get_data() (in module pyretis.engines.gromacs2)
get_dim() (pyretis.core.system.System method)
get_Edata() (pyretis.visualization.orderparam_density.PathVisualize method)
get_end_point() (pyretis.core.path.PathBase method)
get_energies() (pyretis.engines.gromacs.GromacsEngine method)
get_EOP() (pyretis.visualization.orderparam_density.PathDensity method)
get_file_mode() (in module pyretis.inout.simulationio)
get_force() (pyretis.core.particles.Particles method)
get_gromacs_frames() (pyretis.engines.gromacs2.GromacsRunner method)
get_initiation_method() (in module pyretis.initiation)
get_item() (pyretis.core.random_gen.ReservoirSampler method)
get_min_max() (in module pyretis.visualization.common)
get_move() (pyretis.core.path.PathBase method)
get_Odata() (pyretis.visualization.orderparam_density.PathVisualize method)
get_OP() (pyretis.visualization.orderparam_density.PathDensity method)
get_path_data() (pyretis.core.path.PathBase method)
get_paths() (pyretis.core.pathensemble.PathEnsemble method)
(pyretis.inout.formats.pathensemble.PathEnsembleFile method)
get_pos() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
get_report_name() (in module pyretis.bin.pyretisanalyse)
get_selection() (pyretis.core.particles.Particles method)
get_shooting_point() (pyretis.core.path.Path method)
(pyretis.core.path.PathBase method)
get_start_point() (pyretis.core.path.PathBase method)
get_startat() (in module pyretis.visualization.common)
get_state() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
get_task_type() (in module pyretis.inout.simulationio)
get_template() (in module pyretis.inout.report.report)
get_vel() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
gmx (pyretis.engines.gromacs.GromacsEngine attribute)
GromacsEngine (class in pyretis.engines.gromacs)
GromacsEngine2 (class in pyretis.engines.gromacs2)
GromacsRunner (class in pyretis.engines.gromacs2)
H
half_idt (pyretis.engines.internal.Verlet attribute)
half_timestep (pyretis.engines.internal.VelocityVerlet attribute)
HEADER (pyretis.inout.formats.energy.EnergyFormatter attribute)
(pyretis.inout.formats.energy.EnergyPathFormatter attribute)
header (pyretis.inout.formats.formatter.OutputFormatter attribute)
HEADER (pyretis.inout.formats.pathensemble.PathEnsembleFormatter attribute)
header() (pyretis.inout.formats.formatter.OutputFormatter property)
header_size (pyretis.engines.gromacs2.GromacsRunner attribute)
hello_pyvisa() (in module pyretis.visualization.common)
hello_world() (in module pyretis.bin.pyretisanalyse)
(in module pyretis.bin.pyretisrun)
high_friction (pyretis.engines.internal.Langevin attribute)
histogram() (in module pyretis.analysis.histogram)
histogram_and_avg() (in module pyretis.analysis.histogram)
I
imass (pyretis.core.particles.Particles attribute)
import_from() (in module pyretis.inout.setup.common)
index (pyretis.orderparameter.orderangle.Angle attribute)
(pyretis.orderparameter.orderdihedral.Dihedral attribute)
(pyretis.orderparameter.orderparameter.Distance attribute)
(pyretis.orderparameter.orderparameter.Distancevel attribute)
(pyretis.orderparameter.orderparameter.Position attribute)
(pyretis.orderparameter.orderparameter.Velocity attribute)
init_params (pyretis.engines.internal.Langevin attribute)
initial_positions_file() (in module pyretis.inout.setup.createsystem)
initial_positions_lattice() (in module pyretis.inout.setup.createsystem)
initiate() (pyretis.simulation.path_simulation.PathSimulation method)
initiate_instance() (in module pyretis.core.common)
initiate_kick() (in module pyretis.initiation.initiate_kick)
initiate_kick_max() (in module pyretis.initiation.initiate_kick)
initiate_kicki() (in module pyretis.initiation.initiate_kick)
initiate_load() (in module pyretis.initiation.initiate_load)
initiate_path_ensemble_kick() (in module pyretis.initiation.initiate_kick)
initiate_path_simulation() (in module pyretis.initiation)
initiate_restart() (in module pyretis.initiation.initiate_restart)
ino (pyretis.engines.gromacs2.GromacsRunner attribute)
input_files (pyretis.engines.gromacs.GromacsEngine attribute)
(pyretis.engines.lammps.LAMMPSEngine attribute)
input_path (pyretis.engines.cp2k.CP2KEngine attribute)
(pyretis.engines.gromacs.GromacsEngine attribute)
(pyretis.engines.lammps.LAMMPSEngine attribute)
inspect_function() (in module pyretis.core.common)
integrate() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.gromacs2.GromacsEngine2 method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
integration_step() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.Langevin method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.internal.RandomWalk method)
(pyretis.engines.internal.VelocityVerlet method)
(pyretis.engines.internal.Verlet method)
(pyretis.engines.openmm.OpenMMEngine method)
integration_step_inertia() (pyretis.engines.internal.Langevin method)
integration_step_overdamped() (pyretis.engines.internal.Langevin method)
interfaces (pyretis.core.pathensemble.PathEnsemble attribute)
(pyretis.simulation.md_simulation.SimulationMDFlux attribute)
invert_dt() (pyretis.engines.internal.MDEngine method)
is_finished() (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation method)
(pyretis.simulation.simulation.Simulation method)
items (pyretis.core.random_gen.ReservoirSampler attribute)
K
kick_across_middle() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
kinetic_energy() (in module pyretis.core.particlefunctions)
kinetic_temperature() (in module pyretis.core.particlefunctions)
kwargs (pyretis.simulation.simulation_task.SimulationTask attribute)
L
LAMMPSEngine (class in pyretis.engines.lammps)
Langevin (class in pyretis.engines.internal)
last_flush (pyretis.inout.fileio.FileIO attribute)
last_path (pyretis.core.pathensemble.PathEnsemble attribute)
latexify_number() (in module pyretis.inout.report.markup)
leftside_prev (pyretis.simulation.md_simulation.SimulationMDFlux attribute)
length (pyretis.core.random_gen.ReservoirSampler attribute)
length() (pyretis.core.path.PathBase property)
level (pyretis.inout.formats.cp2k.SectionNode attribute)
list_superfluous() (pyretis.core.pathensemble.PathEnsembleExt method)
lmp (pyretis.engines.lammps.LAMMPSEngine attribute)
load() (pyretis.inout.fileio.FileIO method)
(pyretis.inout.formats.energy.EnergyFormatter method)
(pyretis.inout.formats.formatter.OutputFormatter method)
(pyretis.inout.formats.order.OrderFormatter method)
(pyretis.inout.formats.path.PathIntFormatter method)
(pyretis.inout.formats.pathensemble.PathEnsembleFormatter method)
(pyretis.inout.formats.snapshot.SnapshotFormatter method)
load_dd() (pyretis.visualization.orderparam_density.PathVisualize method)
load_pickle() (pyretis.visualization.orderparam_density.PathVisualize method)
load_restart_info() (pyretis.core.particles.Particles method)
(pyretis.core.path.Path method)
(pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.pathensemble.PathEnsembleExt method)
(pyretis.core.system.System method)
(pyretis.simulation.md_simulation.SimulationMDFlux method)
(pyretis.simulation.simulation.Simulation method)
M
main() (in module pyretis.bin.pyretisanalyse)
(in module pyretis.bin.pyretisrun)
make_dirs() (in module pyretis.inout.common)
make_path() (in module pyretis.core.tis)
make_retis_step() (in module pyretis.core.retis)
make_tis_step() (in module pyretis.core.tis)
make_tis_step_ensemble() (in module pyretis.core.tis)
mass (pyretis.core.particles.Particles attribute)
match_all_histograms() (in module pyretis.analysis.histogram)
match_probabilities() (in module pyretis.analysis.path_analysis)
mathexify_number() (in module pyretis.inout.report.markup)
max_displace_step() (in module pyretis.core.montecarlo)
maxdx (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
maxlen (pyretis.core.path.PathBase attribute)
maxpath (pyretis.core.pathensemble.PathEnsemble attribute)
maxwarn (pyretis.engines.gromacs.GromacsEngine attribute)
MDEngine (class in pyretis.engines.internal)
mdrun (pyretis.engines.gromacs.GromacsEngine attribute)
mdrun_c (pyretis.engines.gromacs.GromacsEngine attribute)
mean (pyretis.core.properties.Property attribute)
metropolis_accept_reject() (in module pyretis.core.montecarlo)
min_max() (pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
mincycle (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
mixing_parameters() (in module pyretis.forcefield.potentials.pairpotentials.pairpotential)
MockRandomGenerator (class in pyretis.core.random_gen)
modify_velocities() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.engine.EngineBase method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.internal.MDEngine static method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
move_path_to_generated() (pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.pathensemble.PathEnsembleExt method)
MplPlotter (class in pyretis.inout.plotting.mpl_plotting)
multivariate_normal() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
N
name (pyretis.core.particles.Particles attribute)
(pyretis.inout.formats.formatter.OutputFormatter attribute)
(pyretis.inout.simulationio.OutputTask attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
(pyretis.simulation.path_simulation.SimulationRETIS attribute)
(pyretis.simulation.path_simulation.SimulationSingleTIS attribute)
needs_order (pyretis.engines.engine.EngineBase attribute)
,
[1]
(pyretis.engines.lammps.LAMMPSEngine attribute)
normal() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
npart (pyretis.core.particles.Particles attribute)
nstats (pyretis.core.pathensemble.PathEnsemble attribute)
null_move() (in module pyretis.core.retis)
nval (pyretis.core.properties.Property attribute)
O
open() (pyretis.inout.fileio.FileIO method)
open_file_read() (pyretis.inout.fileio.FileIO method)
open_file_write() (pyretis.inout.fileio.FileIO method)
OpenMMEngine (class in pyretis.engines.openmm)
order (pyretis.core.system.System attribute)
order_factory() (in module pyretis.orderparameter)
ORDER_FMT (pyretis.inout.formats.order.OrderFormatter attribute)
order_function (pyretis.simulation.md_simulation.SimulationMD attribute)
OrderFile (class in pyretis.inout.formats.order)
OrderFormatter (class in pyretis.inout.formats.order)
ordermax (pyretis.core.path.PathBase attribute)
ordermax() (pyretis.core.path.PathBase property)
ordermin (pyretis.core.path.PathBase attribute)
ordermin() (pyretis.core.path.PathBase property)
OrderParameter (class in pyretis.orderparameter.orderparameter)
OrderPathFile (class in pyretis.inout.formats.order)
OrderPathFormatter (class in pyretis.inout.formats.order)
out_dir (pyretis.inout.plotting.plotting.Plotter attribute)
out_dir_fmt (pyretis.inout.archive.PathStorage attribute)
,
[1]
out_fmt (pyretis.inout.plotting.mpl_plotting.MplPlotter attribute)
(pyretis.inout.plotting.txt_plotting.TxtPlotter attribute)
output() (pyretis.inout.archive.PathStorage method)
(pyretis.inout.archive.PathStorageTar method)
(pyretis.inout.common.OutputBase method)
(pyretis.inout.fileio.FileIO method)
(pyretis.inout.simulationio.OutputTask method)
output_energy() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
output_flux() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
output_matched_probability() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
output_orderp() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
output_path() (pyretis.inout.plotting.mpl_plotting.MplPlotter method)
(pyretis.inout.plotting.plotting.Plotter method)
(pyretis.inout.plotting.txt_plotting.TxtPlotter method)
output_path_files() (pyretis.inout.archive.PathStorage method)
OUTPUT_TASKS (in module pyretis.inout.simulationio)
OutputBase (class in pyretis.inout.common)
OutputFormatter (class in pyretis.inout.formats.formatter)
OutputTask (class in pyretis.inout.simulationio)
overlap (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
P
PairLennardJonesCut (class in pyretis.forcefield.potentials.pairpotentials.lennardjones)
PairLennardJonesCutnp (class in pyretis.forcefield.potentials.pairpotentials.lennardjones)
pairs() (pyretis.core.particles.Particles method)
param_high (pyretis.engines.internal.Langevin attribute)
param_iner (pyretis.engines.internal.Langevin attribute)
params (pyretis.forcefield.forcefield.ForceField attribute)
(pyretis.forcefield.potential.PotentialFunction attribute)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut attribute)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA attribute)
(pyretis.forcefield.potentials.potentials.DoubleWell attribute)
(pyretis.forcefield.potentials.potentials.RectangularWell attribute)
parent (pyretis.inout.formats.cp2k.SectionNode attribute)
parents (pyretis.inout.formats.cp2k.SectionNode attribute)
parse() (pyretis.inout.formats.cross.CrossFormatter static method)
(pyretis.inout.formats.formatter.OutputFormatter static method)
(pyretis.inout.formats.path.PathExtFormatter static method)
(pyretis.inout.formats.path.PathIntFormatter static method)
(pyretis.inout.formats.pathensemble.PathEnsembleFormatter static method)
(pyretis.inout.formats.snapshot.SnapshotFormatter static method)
parse_settings_file() (in module pyretis.inout.settings)
particle_type (pyretis.core.particles.Particles attribute)
(pyretis.core.particles.ParticlesExt attribute)
Particles (class in pyretis.core.particles)
particles (pyretis.core.system.System attribute)
ParticlesExt (class in pyretis.core.particles)
paste_paths() (in module pyretis.core.path)
Path (class in pyretis.core.path)
path_ensemble (pyretis.simulation.path_simulation.SimulationSingleTIS attribute)
path_ensembles (pyretis.simulation.path_simulation.PathSimulation attribute)
PATH_FMT (pyretis.inout.formats.pathensemble.PathEnsembleFormatter attribute)
PathBase (class in pyretis.core.path)
PathDensity (class in pyretis.visualization.orderparam_density)
PathEnsemble (class in pyretis.core.pathensemble)
PathEnsembleExt (class in pyretis.core.pathensemble)
PathEnsembleFile (class in pyretis.inout.formats.pathensemble)
PathEnsembleFormatter (class in pyretis.inout.formats.pathensemble)
PathExtFile (class in pyretis.inout.formats.path)
PathExtFormatter (class in pyretis.inout.formats.path)
PathIntFile (class in pyretis.inout.formats.path)
PathIntFormatter (class in pyretis.inout.formats.path)
paths (pyretis.core.pathensemble.PathEnsemble attribute)
PathSimulation (class in pyretis.simulation.path_simulation)
PathStorage (class in pyretis.inout.archive)
PathStorageTar (class in pyretis.inout.archive)
PathTableFormatter (class in pyretis.inout.formats.txt_table)
PathVisualize (class in pyretis.visualization.orderparam_density)
periodic (pyretis.orderparameter.orderangle.Angle attribute)
(pyretis.orderparameter.orderdihedral.Dihedral attribute)
(pyretis.orderparameter.orderparameter.Distance attribute)
(pyretis.orderparameter.orderparameter.Distancevel attribute)
(pyretis.orderparameter.orderparameter.Position attribute)
phasepoints (pyretis.core.path.PathBase attribute)
pickle_data() (pyretis.visualization.orderparam_density.PathDensity method)
plot_int_plane() (in module pyretis.visualization.plotting)
plot_regline() (in module pyretis.visualization.plotting)
Plotter (class in pyretis.inout.plotting.plotting)
plotter_type (pyretis.inout.plotting.plotting.Plotter attribute)
pos (pyretis.core.particles.Particles attribute)
Position (class in pyretis.orderparameter.orderparameter)
PositionVelocity (class in pyretis.orderparameter.orderparameter)
post_setup (pyretis.core.system.System attribute)
potential (pyretis.forcefield.forcefield.ForceField attribute)
potential() (pyretis.core.system.System method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCutnp method)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
(pyretis.forcefield.potentials.potentials.DoubleWell method)
(pyretis.forcefield.potentials.potentials.RectangularWell method)
potential_and_force() (pyretis.core.system.System method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCutnp method)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
(pyretis.forcefield.potentials.potentials.DoubleWell method)
potential_factory() (in module pyretis.forcefield.factory)
PotentialFunction (class in pyretis.forcefield.potential)
previous_pos (pyretis.engines.internal.Verlet attribute)
print_header (pyretis.inout.formats.formatter.OutputFormatter attribute)
print_potentials() (pyretis.forcefield.forcefield.ForceField method)
print_table() (in module pyretis.core.units)
print_to_screen() (in module pyretis.inout.screen)
propagate() (pyretis.engines.engine.EngineBase method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.internal.MDEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.engines.openmm.OpenMMEngine method)
Property (class in pyretis.core.properties)
ptype (pyretis.core.particles.Particles attribute)
pyretis.analysis (module)
pyretis.analysis.analysis (module)
pyretis.analysis.energy_analysis (module)
pyretis.analysis.flux_analysis (module)
pyretis.analysis.histogram (module)
pyretis.analysis.order_analysis (module)
pyretis.analysis.path_analysis (module)
pyretis.bin.pyretisanalyse (module)
pyretis.bin.pyretisrun (module)
pyretis.core (module)
pyretis.core.box (module)
pyretis.core.common (module)
pyretis.core.montecarlo (module)
pyretis.core.particlefunctions (module)
pyretis.core.particles (module)
pyretis.core.path (module)
pyretis.core.pathensemble (module)
pyretis.core.properties (module)
pyretis.core.random_gen (module)
pyretis.core.retis (module)
pyretis.core.system (module)
pyretis.core.tis (module)
pyretis.core.units (module)
pyretis.engines (module)
pyretis.engines.cp2k (module)
pyretis.engines.engine (module)
pyretis.engines.external (module)
pyretis.engines.gromacs (module)
pyretis.engines.gromacs2 (module)
pyretis.engines.internal (module)
pyretis.engines.lammps (module)
pyretis.engines.openmm (module)
pyretis.forcefield (module)
pyretis.forcefield.factory (module)
pyretis.forcefield.forcefield (module)
pyretis.forcefield.potential (module)
pyretis.forcefield.potentials (module)
pyretis.forcefield.potentials.pairpotentials (module)
pyretis.forcefield.potentials.pairpotentials.lennardjones (module)
pyretis.forcefield.potentials.pairpotentials.pairpotential (module)
pyretis.forcefield.potentials.pairpotentials.wca (module)
pyretis.forcefield.potentials.potentials (module)
pyretis.info (module)
pyretis.initiation (module)
pyretis.initiation.initiate_kick (module)
pyretis.initiation.initiate_load (module)
pyretis.initiation.initiate_restart (module)
pyretis.inout (module)
pyretis.inout.analysisio (module)
pyretis.inout.analysisio.analysisio (module)
pyretis.inout.archive (module)
pyretis.inout.common (module)
pyretis.inout.fileio (module)
pyretis.inout.formats (module)
pyretis.inout.formats.cp2k (module)
pyretis.inout.formats.cross (module)
pyretis.inout.formats.energy (module)
pyretis.inout.formats.formatter (module)
pyretis.inout.formats.gromacs (module)
pyretis.inout.formats.order (module)
pyretis.inout.formats.path (module)
pyretis.inout.formats.pathensemble (module)
pyretis.inout.formats.snapshot (module)
pyretis.inout.formats.txt_table (module)
pyretis.inout.formats.xyz (module)
pyretis.inout.plotting (module)
pyretis.inout.plotting.mpl_plotting (module)
pyretis.inout.plotting.plotting (module)
pyretis.inout.plotting.txt_plotting (module)
pyretis.inout.report (module)
pyretis.inout.report.markup (module)
pyretis.inout.report.report (module)
pyretis.inout.report.report_md (module)
pyretis.inout.report.report_path (module)
pyretis.inout.restart (module)
pyretis.inout.screen (module)
pyretis.inout.settings (module)
pyretis.inout.setup (module)
pyretis.inout.setup.common (module)
pyretis.inout.setup.createforcefield (module)
pyretis.inout.setup.createsimulation (module)
pyretis.inout.setup.createsystem (module)
pyretis.inout.simulationio (module)
pyretis.orderparameter (module)
pyretis.orderparameter.orderangle (module)
pyretis.orderparameter.orderdihedral (module)
pyretis.orderparameter.orderparameter (module)
pyretis.simulation (module)
pyretis.simulation.mc_simulation (module)
pyretis.simulation.md_simulation (module)
pyretis.simulation.path_simulation (module)
pyretis.simulation.simulation (module)
pyretis.simulation.simulation_task (module)
pyretis.testing (module)
pyretis.testing.compare (module)
pyretis.testing.helpers (module)
pyretis.testing.systemhelp (module)
pyretis.tools (module)
pyretis.tools.lattice (module)
pyretis.tools.recalculate_order (module)
pyretis.version (module)
pyretis.visualization (module)
pyretis.visualization.common (module)
pyretis.visualization.orderparam_density (module)
pyretis.visualization.plotting (module)
PyretisLogFormatter (class in pyretis.inout.formats.formatter)
R
rand() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
random_integers() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
RandomGenerator (class in pyretis.core.random_gen)
RandomGeneratorBase (class in pyretis.core.random_gen)
RandomWalk (class in pyretis.engines.internal)
read_box_data() (in module pyretis.inout.formats.cp2k)
read_conversions() (in module pyretis.core.units)
read_cp2k_box() (in module pyretis.inout.formats.cp2k)
read_cp2k_energy() (in module pyretis.inout.formats.cp2k)
read_cp2k_input() (in module pyretis.inout.formats.cp2k)
read_cp2k_restart() (in module pyretis.inout.formats.cp2k)
read_energies() (pyretis.engines.lammps.LAMMPSEngine method)
read_files() (in module pyretis.testing.compare)
read_gromacs_file() (in module pyretis.inout.formats.gromacs)
read_gromacs_gro_file() (in module pyretis.inout.formats.gromacs)
read_gromos96_file() (in module pyretis.inout.formats.gromacs)
read_lammps_input() (in module pyretis.engines.lammps)
read_lammps_log() (in module pyretis.engines.lammps)
read_order_parameters() (pyretis.engines.lammps.LAMMPSEngine method)
read_remaining_trr() (in module pyretis.engines.gromacs2)
read_restart_file() (in module pyretis.inout.restart)
read_snapshots() (pyretis.inout.formats.path.PathIntFormatter method)
read_some_lines() (in module pyretis.inout.fileio)
read_trr_data() (in module pyretis.inout.formats.gromacs)
read_trr_file() (in module pyretis.inout.formats.gromacs)
read_trr_header() (in module pyretis.inout.formats.gromacs)
read_txt_snapshots() (in module pyretis.inout.formats.snapshot)
read_xvg_file() (in module pyretis.inout.formats.gromacs)
read_xyz_file() (in module pyretis.inout.formats.xyz)
recalculate_from_frame() (in module pyretis.tools.recalculate_order)
recalculate_from_trj() (in module pyretis.tools.recalculate_order)
recalculate_from_xyz() (in module pyretis.tools.recalculate_order)
recalculate_order() (in module pyretis.tools.recalculate_order)
RectangularWell (class in pyretis.forcefield.potentials.potentials)
remove_nan() (in module pyretis.visualization.orderparam_density)
remove_node() (in module pyretis.inout.formats.cp2k)
remove_potential() (pyretis.forcefield.forcefield.ForceField method)
rename_energies() (pyretis.engines.gromacs.GromacsEngine static method)
render_report() (in module pyretis.inout.report.report)
reopen_file() (in module pyretis.engines.gromacs2)
required_settings (pyretis.simulation.path_simulation.PathSimulation attribute)
,
[1]
(pyretis.simulation.path_simulation.SimulationRETIS attribute)
(pyretis.simulation.path_simulation.SimulationSingleTIS attribute)
rescale_velocities() (pyretis.core.system.System method)
reservoir (pyretis.core.random_gen.ReservoirSampler attribute)
ReservoirSampler (class in pyretis.core.random_gen)
reset_data() (pyretis.core.pathensemble.PathEnsemble method)
reset_momentum() (in module pyretis.core.particlefunctions)
restart_freq (pyretis.simulation.simulation.Simulation attribute)
restart_info() (pyretis.core.particles.Particles method)
(pyretis.core.path.Path method)
(pyretis.core.path.PathBase method)
(pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.system.System method)
(pyretis.simulation.md_simulation.SimulationMDFlux method)
(pyretis.simulation.path_simulation.PathSimulation method)
(pyretis.simulation.simulation.Simulation method)
result (pyretis.inout.simulationio.OutputTask attribute)
(pyretis.simulation.simulation_task.SimulationTask attribute)
result() (pyretis.simulation.simulation_task.SimulationTask property)
ret_idx (pyretis.core.random_gen.ReservoirSampler attribute)
retis_flux() (in module pyretis.analysis.path_analysis)
retis_moves() (in module pyretis.core.retis)
retis_rate() (in module pyretis.analysis.path_analysis)
retis_swap() (in module pyretis.core.retis)
retis_swap_zero() (in module pyretis.core.retis)
retis_tis_moves() (in module pyretis.core.retis)
reverse() (pyretis.core.path.PathBase method)
reverse_velocities() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
(pyretis.core.path.PathBase static method)
reverse_xyz_file() (in module pyretis.inout.formats.xyz)
rgen (pyretis.core.path.PathBase attribute)
(pyretis.core.random_gen.RandomGenerator attribute)
(pyretis.core.random_gen.ReservoirSampler attribute)
(pyretis.engines.cp2k.CP2KEngine attribute)
(pyretis.engines.internal.Langevin attribute)
(pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
row_fmt (pyretis.inout.formats.txt_table.TxtTableFormatter attribute)
run() (pyretis.simulation.md_simulation.SimulationMD method)
(pyretis.simulation.md_simulation.SimulationMDFlux method)
(pyretis.simulation.simulation.Simulation method)
run_analysis_files() (in module pyretis.inout.analysisio.analysisio)
run_cp2k() (pyretis.engines.cp2k.CP2KEngine method)
run_first() (pyretis.simulation.simulation_task.SimulationTask method)
run_generic_simulation() (in module pyretis.bin.pyretisrun)
run_lammps() (pyretis.engines.lammps.LAMMPSEngine method)
run_md_flux_simulation() (in module pyretis.bin.pyretisrun)
run_md_simulation() (in module pyretis.bin.pyretisrun)
run_retis_simulation() (in module pyretis.bin.pyretisrun)
run_tis_simulation() (in module pyretis.bin.pyretisrun)
run_tis_single_simulation() (in module pyretis.bin.pyretisrun)
running (pyretis.engines.gromacs2.GromacsRunner attribute)
running_average() (in module pyretis.analysis.analysis)
S
ScreenOutput (class in pyretis.inout.screen)
search_for_files() (in module pyretis.testing.helpers)
SectionNode (class in pyretis.inout.formats.cp2k)
seed (pyretis.core.random_gen.RandomGenerator attribute)
(pyretis.core.random_gen.RandomGeneratorBase attribute)
select_and_trim_a_segment() (in module pyretis.core.common)
select_energy_terms() (pyretis.engines.gromacs.GromacsEngine static method)
select_shoot() (in module pyretis.core.tis)
select_thermo_function() (pyretis.engines.internal.MDEngine method)
set_force() (pyretis.core.particles.Particles method)
set_initial_positions() (pyretis.engines.internal.Verlet method)
set_move() (pyretis.core.path.PathBase method)
set_parameters() (pyretis.forcefield.potential.PotentialFunction method)
(pyretis.forcefield.potentials.pairpotentials.lennardjones.PairLennardJonesCut method)
(pyretis.forcefield.potentials.pairpotentials.wca.DoubleWellWCA method)
set_parents() (in module pyretis.inout.formats.cp2k)
set_pos() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
set_state() (pyretis.core.random_gen.MockRandomGenerator method)
(pyretis.core.random_gen.RandomGenerator method)
(pyretis.core.random_gen.RandomGeneratorBase method)
set_up_box() (in module pyretis.inout.setup.createsystem)
set_up_output() (pyretis.simulation.simulation.Simulation method)
set_up_simulation() (in module pyretis.bin.pyretisrun)
set_vel() (pyretis.core.particles.Particles method)
(pyretis.core.particles.ParticlesExt method)
settings (pyretis.inout.formats.cp2k.SectionNode attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
shift_data() (in module pyretis.visualization.common)
shoot() (in module pyretis.core.tis)
simplify_ensemble_name() (in module pyretis.inout.common)
Simulation (class in pyretis.simulation.simulation)
simulation (pyretis.engines.openmm.OpenMMEngine attribute)
simulation_output (pyretis.simulation.md_simulation.SimulationMD attribute)
(pyretis.simulation.md_simulation.SimulationMDFlux attribute)
(pyretis.simulation.md_simulation.SimulationNVE attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
(pyretis.simulation.path_simulation.SimulationRETIS attribute)
(pyretis.simulation.path_simulation.SimulationSingleTIS attribute)
(pyretis.simulation.simulation.Simulation attribute)
,
[1]
simulation_type (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
(pyretis.simulation.md_simulation.SimulationMD attribute)
(pyretis.simulation.md_simulation.SimulationMDFlux attribute)
(pyretis.simulation.md_simulation.SimulationNVE attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
(pyretis.simulation.path_simulation.SimulationRETIS attribute)
(pyretis.simulation.path_simulation.SimulationSingleTIS attribute)
(pyretis.simulation.simulation.Simulation attribute)
,
[1]
SimulationMD (class in pyretis.simulation.md_simulation)
SimulationMDFlux (class in pyretis.simulation.md_simulation)
SimulationNVE (class in pyretis.simulation.md_simulation)
SimulationRETIS (class in pyretis.simulation.path_simulation)
SimulationSingleTIS (class in pyretis.simulation.path_simulation)
SimulationTask (class in pyretis.simulation.simulation_task)
skip_trr_data() (in module pyretis.inout.formats.gromacs)
SLEEP (pyretis.engines.gromacs2.GromacsRunner attribute)
,
[1]
snapshot_to_system() (pyretis.engines.engine.EngineBase static method)
SnapshotFile (class in pyretis.inout.formats.snapshot)
SnapshotFormatter (class in pyretis.inout.formats.snapshot)
soft_exit() (pyretis.simulation.simulation.Simulation method)
soft_exit_ignore() (in module pyretis.bin.pyretisrun)
sorting() (pyretis.core.path.PathBase method)
ss_wt_acceptance() (in module pyretis.core.tis)
start() (pyretis.engines.gromacs2.GromacsRunner method)
startcycle (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
status (pyretis.core.path.PathBase attribute)
step() (pyretis.engines.cp2k.CP2KEngine method)
(pyretis.engines.external.ExternalMDEngine method)
(pyretis.engines.gromacs.GromacsEngine method)
(pyretis.engines.lammps.LAMMPSEngine method)
(pyretis.simulation.md_simulation.SimulationNVE method)
(pyretis.simulation.path_simulation.SimulationRETIS method)
(pyretis.simulation.path_simulation.SimulationSingleTIS method)
(pyretis.simulation.simulation.Simulation method)
stone_skipping() (in module pyretis.core.tis)
stop() (pyretis.engines.gromacs2.GromacsRunner method)
stop_read (pyretis.engines.gromacs2.GromacsRunner attribute)
store_path() (pyretis.core.pathensemble.PathEnsemble method)
(pyretis.core.pathensemble.PathEnsembleExt method)
store_simulation_settings() (in module pyretis.bin.pyretisrun)
style (pyretis.inout.plotting.mpl_plotting.MplPlotter attribute)
subcycles (pyretis.engines.cp2k.CP2KEngine attribute)
(pyretis.engines.external.ExternalMDEngine attribute)
subcyles (pyretis.engines.openmm.OpenMMEngine attribute)
success() (pyretis.core.path.PathBase method)
System (class in pyretis.core.system)
system (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
(pyretis.simulation.md_simulation.SimulationMD attribute)
(pyretis.simulation.path_simulation.PathSimulation attribute)
(pyretis.simulation.simulation.Simulation attribute)
system_to_lammps() (in module pyretis.engines.lammps)
T
target (pyretis.inout.archive.PathStorage attribute)
,
[1]
(pyretis.inout.common.OutputBase attribute)
,
[1]
(pyretis.inout.fileio.FileIO attribute)
(pyretis.inout.screen.ScreenOutput attribute)
(pyretis.inout.simulationio.OutputTask attribute)
Task (class in pyretis.inout.simulationio)
task_dict() (pyretis.inout.simulationio.OutputTask method)
(pyretis.inout.simulationio.Task method)
(pyretis.simulation.simulation_task.SimulationTask method)
task_from_settings() (in module pyretis.inout.simulationio)
tasks (pyretis.simulation.simulation.Simulation attribute)
temperature (pyretis.core.system.System attribute)
ThermoTableFormatter (class in pyretis.inout.formats.txt_table)
time_origin (pyretis.core.path.PathBase attribute)
time_reversal() (in module pyretis.core.tis)
timestep (pyretis.engines.cp2k.CP2KEngine attribute)
(pyretis.engines.external.ExternalMDEngine attribute)
(pyretis.engines.internal.MDEngine attribute)
(pyretis.engines.internal.RandomWalk attribute)
timestepsq (pyretis.engines.internal.Verlet attribute)
title (pyretis.inout.formats.cp2k.SectionNode attribute)
(pyretis.inout.formats.txt_table.TxtTableFormatter attribute)
top (pyretis.core.particles.ParticlesExt attribute)
trim_path_between_interfaces() (in module pyretis.core.common)
trr_file (pyretis.engines.gromacs2.GromacsRunner attribute)
trr_frame_to_g96() (in module pyretis.inout.formats.gromacs)
try_data_shift() (in module pyretis.visualization.common)
txt_save_columns() (in module pyretis.inout.formats.txt_table)
TxtPlotter (class in pyretis.inout.plotting.txt_plotting)
TxtTableFormatter (class in pyretis.inout.formats.txt_table)
U
umbrella (pyretis.simulation.mc_simulation.UmbrellaWindowSimulation attribute)
UmbrellaWindowSimulation (class in pyretis.simulation.mc_simulation)
UNIT_SYSTEMS (in module pyretis.core.units)
UNITS (in module pyretis.core.units)
units (pyretis.core.system.System attribute)
update_box() (pyretis.core.system.System method)
update_cp2k_input() (in module pyretis.inout.formats.cp2k)
update_directories() (pyretis.core.pathensemble.PathEnsemble method)
update_energies() (pyretis.core.path.PathBase method)
update_mean_and_variance() (pyretis.core.properties.Property method)
update_node() (in module pyretis.inout.formats.cp2k)
update_potential_parameters() (pyretis.forcefield.forcefield.ForceField method)
use_tqdm() (in module pyretis.bin.pyretisrun)
V
val (pyretis.core.properties.Property attribute)
variables (pyretis.inout.formats.txt_table.TxtTableFormatter attribute)
variance (pyretis.core.properties.Property attribute)
vel (pyretis.core.particles.Particles attribute)
vel_rev (pyretis.core.particles.ParticlesExt attribute)
Velocity (class in pyretis.orderparameter.orderparameter)
velocity_dependent (pyretis.orderparameter.orderparameter.OrderParameter attribute)
VelocityVerlet (class in pyretis.engines.internal)
Verlet (class in pyretis.engines.internal)
virial (pyretis.core.particles.Particles attribute)
vpot (pyretis.core.particles.Particles attribute)
W
walk_dirs() (pyretis.visualization.orderparam_density.PathDensity method)
web_throwing() (in module pyretis.core.tis)
weight (pyretis.core.path.PathBase attribute)
when (pyretis.inout.simulationio.OutputTask attribute)
(pyretis.inout.simulationio.Task attribute)
(pyretis.simulation.simulation_task.SimulationTask attribute)
when() (pyretis.inout.simulationio.Task property)
write() (pyretis.inout.archive.PathStorage method)
(pyretis.inout.common.OutputBase method)
(pyretis.inout.fileio.FileIO method)
(pyretis.inout.screen.ScreenOutput method)
write_conversions() (in module pyretis.core.units)
write_file() (in module pyretis.bin.pyretisanalyse)
write_for_continue() (in module pyretis.engines.cp2k)
write_for_genvel() (in module pyretis.engines.cp2k)
write_for_integrate() (in module pyretis.engines.cp2k)
write_for_step_vel() (in module pyretis.engines.cp2k)
write_gromacs_gro_file() (in module pyretis.inout.formats.gromacs)
write_gromos96_file() (in module pyretis.inout.formats.gromacs)
write_path_ensemble_restart() (in module pyretis.inout.restart)
write_restart() (pyretis.simulation.path_simulation.PathSimulation method)
(pyretis.simulation.simulation.Simulation method)
write_restart_file() (in module pyretis.inout.restart)
write_settings_file() (in module pyretis.inout.settings)
write_traceback() (in module pyretis.bin.pyretisanalyse)
write_trr_frame() (in module pyretis.inout.formats.gromacs)
write_vel (pyretis.inout.formats.snapshot.SnapshotFormatter attribute)
write_xyz_file() (in module pyretis.inout.formats.xyz)
write_xyz_trajectory() (in module pyretis.inout.formats.xyz)
writer (pyretis.inout.simulationio.OutputTask attribute)
X
xyz_merge() (in module pyretis.inout.formats.xyz)