Index

_

_add_distribution() (mdse.md.simulationmanager.SimulationManager method)

A

attach_output() (mdse.rm.runmanager.RunManager method)

C

calc_isobaric_enthalpy() (mdse.md.resultMD.ResultMD method) calc_isobaric_specific_heat() (in module mdse.cli.cli) (mdse.md.resultMD.ResultMD method) calc_isochoric_heat_capacity_per_atom() (mdse.md.resultMD.ResultMD method) calc_lindemann() (in module mdse.cli.cli) (mdse.md.resultMD.ResultMD method)

calc_msd() (in module mdse.cli.cli) (mdse.md.resultMD.ResultMD method) calc_self_diff() (in module mdse.cli.cli) (mdse.md.resultMD.ResultMD method) create_crystal() (mdse.md.simulationmanager.SimulationManager method), [1] crystal (mdse.md.simulationmanager.SimulationManager attribute)

E

estimate_average_a() (mdse.md.resultMD.ResultMD method)

estimate_nearest_neighbor_distance() (mdse.md.resultMD.ResultMD method) expand_parameter() (in module mdse.parser.parse_yml)

F

from_file() (mdse.md.resultMD.ResultMD class method)

M

main() (in module mdse.cli.cli) main_read() (in module mdse.parser.parse_yml) md_simulations (mdse.rm.runmanager.RunManager attribute) mdse module mdse.cli module mdse.cli.cli module mdse.logging module mdse.logging.logging_config module mdse.md module mdse.md.list_molecules module mdse.md.resultMD module mdse.md.simulationmanager module

mdse.parser module mdse.parser.parse_yml module mdse.rm module mdse.rm.runmanager module module mdse mdse.cli mdse.cli.cli mdse.logging mdse.logging.logging_config mdse.md mdse.md.list_molecules mdse.md.resultMD mdse.md.simulationmanager mdse.parser mdse.parser.parse_yml mdse.rm mdse.rm.runmanager

O

outputs (mdse.rm.runmanager.RunManager attribute)

P

print_energy() (mdse.md.simulationmanager.SimulationManager method), [1]

R

read_yaml_simulations() (in module mdse.parser.parse_yml) remove_all_traj() (in module mdse.cli.cli) ResultMD (class in mdse.md.resultMD)

run_npt_simulations() (mdse.rm.runmanager.RunManager method) run_nve_simulations() (mdse.rm.runmanager.RunManager method) run_nvt_simulations() (mdse.rm.runmanager.RunManager method) RunManager (class in mdse.rm.runmanager)

S

setup_logging() (in module mdse.logging.logging_config) simulate() (in module mdse.cli.cli) simulate_npt() (mdse.md.simulationmanager.SimulationManager method)

simulate_nve() (mdse.md.simulationmanager.SimulationManager method) simulate_nvt() (mdse.md.simulationmanager.SimulationManager method) SimulationManager (class in mdse.md.simulationmanager)

U

unnest_simulation_parameters() (in module mdse.parser.parse_yml)

V

view_crystal() (in module mdse.cli.cli)

view_super_crystal() (mdse.md.simulationmanager.SimulationManager method), [1] visualize_msd() (mdse.md.resultMD.ResultMD method)

W

write_results() (mdse.rm.runmanager.RunManager method)