Index

A

add_part() (micmec.pes.mmff.MicMecForceField method) AndersenThermostat (class in micmec.sampling.nvt)

angular_moment() (in module micmec.sampling.utils) angular_velocity() (in module micmec.sampling.utils)

B

BaseCellDOF (class in micmec.sampling.dof) BerendsenBarostat (class in micmec.sampling.npt) BerendsenThermostat (class in micmec.sampling.nvt)

build_input() (in module micmec.builder.builder_io) build_output() (in module micmec.builder.builder_io) build_system() (in module micmec.utils) build_type() (in module micmec.utils)

C

CartesianDOF (class in micmec.sampling.dof) CGOptimizer (class in micmec.sampling.opt) clean_momenta() (in module micmec.sampling.utils)

clear() (micmec.pes.mmff.ForcePart method) compute() (micmec.pes.mmff.ForcePart method) ConsErrTracker (class in micmec.sampling.verlet) CSVRThermostat (class in micmec.sampling.nvt)

D

Domain (class in micmec.pes.ext)

domain_lower() (in module micmec.sampling.utils) domain_symmetrize() (in module micmec.sampling.utils)

E

elastic_energy_nanocell() (in module micmec.pes.nanocell) (in module micmec.pes.nanocell_original) (in module micmec.pes.nanocell_thesis)

EPotContribStateItem (class in micmec.sampling.iterative)

F

ForcePart (class in micmec.pes.mmff) ForcePartMechanical (class in micmec.pes.mmff) from_file() (micmec.system.System class method)

from_hdf5() (micmec.system.System class method) FullCellDOF (class in micmec.sampling.dof) fun() (micmec.sampling.dof.BaseCellDOF method) (micmec.sampling.dof.CartesianDOF method)

G

get_cell0() (in module micmec.analysis.advanced) get_elasticity0() (in module micmec.analysis.advanced) get_mass() (in module micmec.analysis.advanced) get_ndof_baro() (in module micmec.sampling.utils) get_ndof_internal_md() (in module micmec.sampling.utils) get_random_vel() (in module micmec.sampling.utils) get_random_vel_press() (in module micmec.sampling.utils)

get_slice() (in module micmec.analysis.utils) get_time() (in module micmec.analysis.utils) GLEThermostat (class in micmec.sampling.nvt) grad_elastic_energy_nanocell() (in module micmec.pes.nanocell) (in module micmec.pes.nanocell_original) (in module micmec.pes.nanocell_thesis) gvecs (micmec.pes.ext.Domain property)

I

inertia_tensor() (in module micmec.sampling.utils)

L

LangevinBarostat (class in micmec.sampling.npt)

LangevinThermostat (class in micmec.sampling.nvt)

M

method (micmec.sampling.npt.BerendsenBarostat attribute) (micmec.sampling.npt.LangevinBarostat attribute) (micmec.sampling.npt.MTKBarostat attribute) (micmec.sampling.nvt.AndersenThermostat attribute) (micmec.sampling.nvt.BerendsenThermostat attribute) (micmec.sampling.nvt.CSVRThermostat attribute) (micmec.sampling.nvt.GLEThermostat attribute) (micmec.sampling.nvt.LangevinThermostat attribute) (micmec.sampling.nvt.NHCThermostat attribute) micmec.analysis.advanced module micmec.analysis.basic module micmec.analysis.tensor module micmec.analysis.utils module micmec.builder.builder_io module micmec.log module micmec.pes.ext module micmec.pes.mmff module micmec.pes.nanocell module micmec.pes.nanocell_original module micmec.pes.nanocell_thesis module micmec.pes.nanocell_utils module micmec.sampling.dof module micmec.sampling.iterative module micmec.sampling.npt module

micmec.sampling.nvt module micmec.sampling.opt module micmec.sampling.trajectory module micmec.sampling.utils module micmec.sampling.verlet module micmec.system module micmec.utils module MicMecForceField (class in micmec.pes.mmff) module micmec.analysis.advanced micmec.analysis.basic micmec.analysis.tensor micmec.analysis.utils micmec.builder.builder_io micmec.log micmec.pes.ext micmec.pes.mmff micmec.pes.nanocell micmec.pes.nanocell_original micmec.pes.nanocell_thesis micmec.pes.nanocell_utils micmec.sampling.dof micmec.sampling.iterative micmec.sampling.npt micmec.sampling.nvt micmec.sampling.opt micmec.sampling.trajectory micmec.sampling.utils micmec.sampling.verlet micmec.system micmec.utils MTKBarostat (class in micmec.sampling.npt)

N

ncelldof (micmec.sampling.dof.BaseCellDOF property) ncellvar (micmec.sampling.dof.BaseCellDOF property)

NHCThermostat (class in micmec.sampling.nvt) nvec (micmec.pes.ext.Domain property)

P

parameters (micmec.pes.ext.Domain property) plot_directional_young_modulus() (in module micmec.analysis.tensor) plot_domain_pars() (in module micmec.analysis.basic) plot_energies() (in module micmec.analysis.basic) plot_press_dist() (in module micmec.analysis.basic)

plot_pressure() (in module micmec.analysis.basic) plot_temp_dist() (in module micmec.analysis.basic) plot_temperature() (in module micmec.analysis.basic) plot_volume_dist() (in module micmec.analysis.basic) pretty_3x3x3x3_tensor() (in module micmec.analysis.tensor) pretty_6x6_matrix() (in module micmec.analysis.tensor)

Q

QNOptimizer (class in micmec.sampling.opt)

R

remove_angular_moment() (in module micmec.sampling.utils) remove_com_moment() (in module micmec.sampling.utils)

rigid_body_angular_velocities() (in module micmec.sampling.utils) rvecs (micmec.pes.ext.Domain property)

S

solve_trust_radius() (in module micmec.sampling.opt) stabilized_cholesky_decomp() (in module micmec.sampling.utils)

StrainCellDOF (class in micmec.sampling.dof) System (class in micmec.system)

T

TBCombination (class in micmec.sampling.npt) to_file() (micmec.system.System method)

to_hdf5() (micmec.system.System method) transform_lower_triangular() (in module micmec.sampling.utils)

U

update_pos() (micmec.pes.mmff.ForcePart method) (micmec.pes.mmff.MicMecForceField method)

update_rvecs() (micmec.pes.ext.Domain method) (micmec.pes.mmff.ForcePart method) (micmec.pes.mmff.MicMecForceField method)

V

VerletHook (class in micmec.sampling.verlet) VerletScreenLog (class in micmec.sampling.verlet)

voigt() (in module micmec.analysis.tensor) voigt_inv() (in module micmec.analysis.tensor) volume (micmec.pes.ext.Domain property)