Index

_

__init__() (bicrystallography.bicrystallography method) (plastic_slip.dislocation_dipole method) (src.bicrystal.bicrystal method) (src.min_shuffle.min_shuffle method) (src.runLAMMPS.run_LAMMPS method)

A

atoms_minshuf (src.min_shuffle.min_shuffle attribute)

axis (bicrystallography.bicrystallography attribute) (src.bicrystal.bicrystal attribute)

B

bicrystal (class in src.bicrystal) bicrystallography module bicrystallography (class in bicrystallography)

box (src.bicrystal.bicrystal attribute) (src.min_shuffle.min_shuffle attribute) box_minshuf (src.min_shuffle.min_shuffle attribute) burgers_vec (src.runLAMMPS.run_LAMMPS attribute) burgers_vector (plastic_slip.dislocation_dipole attribute)

C

create_disconnection_containing_bicrystal() (src.bicrystal.bicrystal method)

create_fix_eco_orientationfile() (src.bicrystal.bicrystal method) create_flat_gb_bicrystal() (src.bicrystal.bicrystal method)

D

dislocation_dipole (class in plastic_slip) dislocation_distance (plastic_slip.dislocation_dipole attribute) dislocation_end (src.min_shuffle.min_shuffle attribute)

dislocation_points (plastic_slip.dislocation_dipole attribute) dislocation_start (src.min_shuffle.min_shuffle attribute) dislocation_vector (plastic_slip.dislocation_dipole attribute)

E

element (src.runLAMMPS.run_LAMMPS attribute)

F

final_atoms_transformed_region (src.min_shuffle.min_shuffle attribute) final_grain (src.min_shuffle.min_shuffle attribute)

find_gb_location() (in module IO) folder (src.runLAMMPS.run_LAMMPS attribute) format_input() (src.min_shuffle.min_shuffle method)

G

gb_data (src.bicrystal.bicrystal attribute) gb_info() (src.min_shuffle.min_shuffle method) gb_location (src.min_shuffle.min_shuffle attribute) gb_props() (bicrystallography.bicrystallography method) grain1 (src.bicrystal.bicrystal attribute) grain1_flatgb (src.bicrystal.bicrystal attribute) grain1_orientation (src.bicrystal.bicrystal attribute) grain2 (src.bicrystal.bicrystal attribute)

grain2_flatgb (src.bicrystal.bicrystal attribute) grain2_orientation (src.bicrystal.bicrystal attribute) grainA_posttransform (src.min_shuffle.min_shuffle attribute) grainA_pretransform (src.min_shuffle.min_shuffle attribute) grainB_posttransform (src.min_shuffle.min_shuffle attribute) grainB_pretransform (src.min_shuffle.min_shuffle attribute) gridsearch_output_folder (src.runLAMMPS.run_LAMMPS attribute) gridsearch_output_setting (src.runLAMMPS.run_LAMMPS attribute)

I

inclination (bicrystallography.bicrystallography attribute) (src.runLAMMPS.run_LAMMPS attribute) initial_atoms_transformed_region (src.min_shuffle.min_shuffle attribute)

initial_grain (src.min_shuffle.min_shuffle attribute) IO module

L

lammps_input_filename (src.runLAMMPS.run_LAMMPS attribute) lammps_location (src.runLAMMPS.run_LAMMPS attribute) lat_par (src.bicrystal.bicrystal attribute)

lat_Vec (src.bicrystal.bicrystal attribute) lattice_parameter (bicrystallography.bicrystallography attribute) (src.runLAMMPS.run_LAMMPS attribute) load_data() (src.min_shuffle.min_shuffle method)

M

min_shuffle (class in src.min_shuffle) misorientation (bicrystallography.bicrystallography attribute) (src.runLAMMPS.run_LAMMPS attribute) module bicrystallography IO plastic_slip src.bicrystal src.GBKineticsRunController src.min_shuffle src.runLAMMPS

mpi_location (src.runLAMMPS.run_LAMMPS attribute)

N

nCells (src.bicrystal.bicrystal attribute) neb_images (src.runLAMMPS.run_LAMMPS attribute)

neb_output_folder (src.runLAMMPS.run_LAMMPS attribute) non_periodic_direction_size (src.bicrystal.bicrystal attribute) number_of_images_provided (src.runLAMMPS.run_LAMMPS attribute)

O

ordered_write() (src.bicrystal.bicrystal method)

output_filename_gridsearch (src.runLAMMPS.run_LAMMPS attribute)

P

pbcdist() (src.min_shuffle.min_shuffle method) pbcwrap() (src.min_shuffle.min_shuffle method) period (plastic_slip.dislocation_dipole attribute) plastic_displacement() (plastic_slip.dislocation_dipole method) plastic_slip module

plot_min_shuffle_2d() (src.min_shuffle.min_shuffle static method) plot_min_shuffle_3d() (src.min_shuffle.min_shuffle static method) post_process_gridsearch_data() (src.runLAMMPS.run_LAMMPS method) post_process_neb_output() (src.runLAMMPS.run_LAMMPS method) potential (src.runLAMMPS.run_LAMMPS attribute)

R

read_gridsearch_results() (in module IO) read_LAMMPS_datafile() (in module IO) read_LAMMPS_dumpfile() (in module IO) read_neb_output_data() (in module IO) replicate() (src.min_shuffle.min_shuffle method) run() (src.min_shuffle.min_shuffle method)

run_grid_search() (src.runLAMMPS.run_LAMMPS method) run_LAMMPS (class in src.runLAMMPS) run_minimization() (src.runLAMMPS.run_LAMMPS method) run_neb_calc() (src.runLAMMPS.run_LAMMPS method) runGBkinetics() (in module src.GBKineticsRunController) runGridSearch() (in module src.GBKineticsRunController)

S

sigma (bicrystallography.bicrystallography attribute) (src.runLAMMPS.run_LAMMPS attribute) size_along_gb_period (src.runLAMMPS.run_LAMMPS attribute) size_along_period (src.bicrystal.bicrystal attribute) size_along_tilt_axis (src.bicrystal.bicrystal attribute) src.bicrystal module

src.GBKineticsRunController module src.min_shuffle module src.runLAMMPS module step_height (src.min_shuffle.min_shuffle attribute) (src.runLAMMPS.run_LAMMPS attribute)

T

types_minshuf (src.min_shuffle.min_shuffle attribute)

W

write() (src.bicrystal.bicrystal method) write_gridsearch_results() (in module IO) write_images() (src.min_shuffle.min_shuffle method) write_lammps_datafile() (in module IO)

write_lammps_gridsearch_input() (src.runLAMMPS.run_LAMMPS method) write_lammps_neb_input_script() (src.runLAMMPS.run_LAMMPS method) write_LAMMPSoutput_tstep() (in module IO) write_minimization_input() (src.runLAMMPS.run_LAMMPS method)