MANIFEST.in
README
setup.py
MAST/__init__.py
MAST/_version.py
MAST.egg-info/PKG-INFO
MAST.egg-info/SOURCES.txt
MAST.egg-info/dependency_links.txt
MAST.egg-info/requires.txt
MAST.egg-info/top_level.txt
MAST/bin/__init__.py
MAST/bin/mast
MAST/bin/mast_diffusion_coefficient
MAST/bin/mast_finite_size_scaling_sizes
MAST/bin/mast_madelung_utility
MAST/controllers/__init__.py
MAST/controllers/mastinput.py
MAST/controllers/mastmon.py
MAST/controllers/modifyrecipe.py
MAST/data/__init__.py
MAST/doc/__init__.py
MAST/doc/run_sphinx_apidoc.py
MAST/examples/POSCAR.ga4as4
MAST/examples/README
MAST/examples/charged_defects_with_scaling.inp
MAST/examples/neb_int_and_sub_test.inp
MAST/examples/neb_with_phonons.inp
MAST/examples/neb_with_phonons_pathfinder.inp
MAST/examples/simple_optimization.inp
MAST/examples/testing_1.3
MAST/examples/u_ramping.inp
MAST/ingredients/__init__.py
MAST/ingredients/baseingredient.py
MAST/ingredients/chopingredient.py
MAST/ingredients/checker/__init__.py
MAST/ingredients/checker/basechecker.py
MAST/ingredients/checker/genericchecker.py
MAST/ingredients/checker/lammpschecker.py
MAST/ingredients/checker/lammpschecker_v1.py
MAST/ingredients/checker/phonchecker.py
MAST/ingredients/checker/structoptchecker.py
MAST/ingredients/checker/vaspchecker.py
MAST/ingredients/checker/vaspnebchecker.py
MAST/ingredients/errorhandler/__init__.py
MAST/ingredients/errorhandler/baseerror.py
MAST/ingredients/errorhandler/genericerror.py
MAST/ingredients/errorhandler/masterrorhandlers.py
MAST/ingredients/errorhandler/mastvasperrorhandlers.py
MAST/ingredients/errorhandler/phonerror.py
MAST/ingredients/errorhandler/vasperror.py
MAST/ingredients/errorhandler/vaspneberror.py
MAST/ingredients/pmgextend/__init__.py
MAST/ingredients/pmgextend/atom_index.py
MAST/ingredients/pmgextend/procar_parse_occ.py
MAST/ingredients/pmgextend/procar_parse_occ_spin.py
MAST/ingredients/pmgextend/structure_extensions.py
MAST/ingredients/programkeys/README
MAST/ingredients/programkeys/__init__.py
MAST/ingredients/programkeys/diff_allowed_keywords.py
MAST/ingredients/programkeys/lammps_allowed_keywords.py
MAST/ingredients/programkeys/madelung_allowed_keywords.py
MAST/ingredients/programkeys/phon_allowed_keywords.py
MAST/ingredients/programkeys/structopt_allowed_keywords.py
MAST/ingredients/programkeys/vasp_allowed_keywords.py
MAST/initialization/README_Archive
MAST/initialization/README_Control
MAST/initialization/README_Scratch
MAST/initialization/just_submitted
MAST/initialization/submitlist
MAST/parsers/__init__.py
MAST/parsers/indeploopinputparser.py
MAST/parsers/inputparser.py
MAST/parsers/inputpythoncreator.py
MAST/parsers/recipetemplateparser.py
MAST/recipe/__init__.py
MAST/recipe/recipeplan.py
MAST/recipe/recipesetup.py
MAST/recipe/recipeutility.py
MAST/structopt/Optimizer.py
MAST/structopt/StructOpt_User_Guide_v1.docx
MAST/structopt/__init__.py
MAST/structopt/crossover/CCP_Oct_Tet.py
MAST/structopt/crossover/__init__.py
MAST/structopt/crossover/clustbx.py
MAST/structopt/crossover/cxtp.py
MAST/structopt/crossover/cxtpa.py
MAST/structopt/crossover/cxtpc.py
MAST/structopt/crossover/newclus.py
MAST/structopt/crossover/randalloybox.py
MAST/structopt/crossover/rotct.py
MAST/structopt/crossover/rotct_defect.py
MAST/structopt/crossover/rotct_rand.py
MAST/structopt/crossover/rotct_rand_clus.py
MAST/structopt/crossover/rotct_rand_defect.py
MAST/structopt/fingerprinting/__init__.py
MAST/structopt/fingerprinting/dirac.py
MAST/structopt/fingerprinting/fingerprint_dist.py
MAST/structopt/fingerprinting/get_fingerprint.py
MAST/structopt/fitness/__init__.py
MAST/structopt/fitness/chempotswap.py
MAST/structopt/fitness/enpafit.py
MAST/structopt/fitness/enthalpyfit.py
MAST/structopt/fitness/exponentialfit.py
MAST/structopt/fitness/formationenergy.py
MAST/structopt/fitness/sibias.py
MAST/structopt/fitness/sibias2.py
MAST/structopt/fitness/stem_cost.py
MAST/structopt/fitness/stem_cost_rotation.py
MAST/structopt/fitness/surfaceenergy.py
MAST/structopt/fitness/totalenfit.py
MAST/structopt/generate/Individual.py
MAST/structopt/generate/__init__.py
MAST/structopt/generate/gen_pop_box.py
MAST/structopt/generate/gen_pop_ellipsoid.py
MAST/structopt/generate/gen_pop_plate.py
MAST/structopt/generate/gen_pop_plate_old.py
MAST/structopt/generate/gen_pop_plate_v0.py
MAST/structopt/generate/gen_pop_sphere.py
MAST/structopt/generate/generate_dumbbells.py
MAST/structopt/generate/get_population.py
MAST/structopt/generate/get_restart_population.py
MAST/structopt/generate/rot_vec.py
MAST/structopt/generate/crystal/__init__.py
MAST/structopt/generate/crystal/get_crystal_indiv.py
MAST/structopt/generate/crystal/get_crystal_restart_indiv.py
MAST/structopt/generate/defect/__init__.py
MAST/structopt/generate/defect/gen_solid.py
MAST/structopt/generate/defect/generate_dumbbells.py
MAST/structopt/generate/defect/get_defect_indiv.py
MAST/structopt/generate/defect/get_defect_indiv_random.py
MAST/structopt/generate/defect/get_defect_restart_indiv.py
MAST/structopt/generate/surface/__init__.py
MAST/structopt/generate/surface/get_surface_indiv.py
MAST/structopt/generate/surface/get_surface_restart_indiv.py
MAST/structopt/inp_out/__init__.py
MAST/structopt/inp_out/loggerUtils.py
MAST/structopt/inp_out/read_Ltraj_file.py
MAST/structopt/inp_out/read_individual.py
MAST/structopt/inp_out/read_parameter_input.py
MAST/structopt/inp_out/read_xyz.py
MAST/structopt/inp_out/read_xyz_non_stem.py
MAST/structopt/inp_out/read_xyz_stem.py
MAST/structopt/inp_out/read_xyz_v0.py
MAST/structopt/inp_out/restart_output.py
MAST/structopt/inp_out/setup_output.py
MAST/structopt/inp_out/setup_par_output.py
MAST/structopt/inp_out/write_individual.py
MAST/structopt/inp_out/write_lammps_data.py
MAST/structopt/inp_out/write_optimizer.py
MAST/structopt/inp_out/write_parameters.py
MAST/structopt/inp_out/write_pop.py
MAST/structopt/inp_out/write_xyz.py
MAST/structopt/moves/__init__.py
MAST/structopt/moves/ase_minimization.py
MAST/structopt/moves/atoms_add.py
MAST/structopt/moves/atoms_remove.py
MAST/structopt/moves/atoms_remove_surf.py
MAST/structopt/moves/basin_hop_la.py
MAST/structopt/moves/basin_hop_permute.py
MAST/structopt/moves/basin_hop_ra_atoms.py
MAST/structopt/moves/basin_hop_rattle.py
MAST/structopt/moves/basin_hop_rotate.py
MAST/structopt/moves/cell_relax_lammps.py
MAST/structopt/moves/cell_shape.py
MAST/structopt/moves/fss_bcc.py
MAST/structopt/moves/lattice_alteration.py
MAST/structopt/moves/lattice_alteration_crystal.py
MAST/structopt/moves/lattice_alteration_group.py
MAST/structopt/moves/lattice_alteration_nn.py
MAST/structopt/moves/lattice_alteration_rdrd.py
MAST/structopt/moves/lattice_alteration_small.py
MAST/structopt/moves/move_la.py
MAST/structopt/moves/pea_rd_mutation.py
MAST/structopt/moves/permutation.py
MAST/structopt/moves/permutation_bulk.py
MAST/structopt/moves/permutation_crystal.py
MAST/structopt/moves/permutation_crystal_multi.py
MAST/structopt/moves/quench.py
MAST/structopt/moves/quench1.py
MAST/structopt/moves/random_replacement.py
MAST/structopt/moves/rattle.py
MAST/structopt/moves/rotation.py
MAST/structopt/moves/rotation_bk.py
MAST/structopt/moves/rotation_geo.py
MAST/structopt/moves/scale_size.py
MAST/structopt/moves/stem_add.py
MAST/structopt/moves/stem_mutation.py
MAST/structopt/moves/stem_remove.py
MAST/structopt/moves/stem_shift.py
MAST/structopt/moves/swap.py
MAST/structopt/moves/swap_cluster.py
MAST/structopt/moves/swap_int.py
MAST/structopt/moves/swap_int_local.py
MAST/structopt/moves/swap_species.py
MAST/structopt/moves/swap_species_pea.py
MAST/structopt/moves/swap_vacancy.py
MAST/structopt/moves/zp_rotation.py
MAST/structopt/moves/zp_rotation_fixed.py
MAST/structopt/post_processing/__init__.py
MAST/structopt/post_processing/finite_size_scale.py
MAST/structopt/post_processing/get_lattice_concentration.py
MAST/structopt/post_processing/read_genealogy.py
MAST/structopt/post_processing/read_ouput.py
MAST/structopt/post_processing/view.py
MAST/structopt/predator/__init__.py
MAST/structopt/predator/adapting.py
MAST/structopt/predator/energy_cluster.py
MAST/structopt/predator/fingerprint_niche.py
MAST/structopt/predator/fitpred.py
MAST/structopt/predator/fitpred_bests.py
MAST/structopt/predator/fitpred_new.py
MAST/structopt/predator/mutation_dups.py
MAST/structopt/predator/mutation_dups_adapt_stem.py
MAST/structopt/predator/mutation_dups_energy.py
MAST/structopt/predator/mutation_dups_quench.py
MAST/structopt/predator/mutation_dups_zp.py
MAST/structopt/selection/__init__.py
MAST/structopt/selection/best.py
MAST/structopt/selection/cost.py
MAST/structopt/selection/fuss.py
MAST/structopt/selection/fuss1.py
MAST/structopt/selection/fuss1r.py
MAST/structopt/selection/fuss2.py
MAST/structopt/selection/fussf.py
MAST/structopt/selection/fussr.py
MAST/structopt/selection/metropolis.py
MAST/structopt/selection/multitournament.py
MAST/structopt/selection/random_pick.py
MAST/structopt/selection/rank.py
MAST/structopt/selection/tournament.py
MAST/structopt/selection/tournament1.py
MAST/structopt/selection/tournament2.py
MAST/structopt/switches/__init__.py
MAST/structopt/switches/crossover_switch.py
MAST/structopt/switches/fitness_switch.py
MAST/structopt/switches/lambdacommamu.py
MAST/structopt/switches/moves_switch.py
MAST/structopt/switches/predator_switch.py
MAST/structopt/switches/selection_switch.py
MAST/structopt/tools/BestInds.py
MAST/structopt/tools/StemCalc.py
MAST/structopt/tools/__init__.py
MAST/structopt/tools/calc_dist.py
MAST/structopt/tools/check_atomlist_concentration.py
MAST/structopt/tools/check_cell_type.py
MAST/structopt/tools/convert_time.py
MAST/structopt/tools/eval_energy.py
MAST/structopt/tools/eval_energy2.py
MAST/structopt/tools/eval_energy_non_stem.py
MAST/structopt/tools/eval_energy_stem.py
MAST/structopt/tools/find_defects.py
MAST/structopt/tools/find_top_layer.py
MAST/structopt/tools/get_best.py
MAST/structopt/tools/lammps.py
MAST/structopt/tools/lammps_non_stem.py
MAST/structopt/tools/lammps_v0.py
MAST/structopt/tools/position_average.py
MAST/structopt/tools/rattle.py
MAST/structopt/tools/remove_duplicates.py
MAST/structopt/tools/setup_calculator.py
MAST/structopt/tools/setup_fixed_region_calculator.py
MAST/structopt/tools/shift_atoms.py
MAST/structopt_stem/Optimizer.py
MAST/structopt_stem/STEM_run.py
MAST/structopt_stem/__init__.py
MAST/structopt_stem/crossover/CCP_Oct_Tet.py
MAST/structopt_stem/crossover/__init__.py
MAST/structopt_stem/crossover/clustbx.py
MAST/structopt_stem/crossover/cxtp.py
MAST/structopt_stem/crossover/cxtpa.py
MAST/structopt_stem/crossover/cxtpc.py
MAST/structopt_stem/crossover/newclus.py
MAST/structopt_stem/crossover/randalloybox.py
MAST/structopt_stem/crossover/rotct.py
MAST/structopt_stem/crossover/rotct_defect.py
MAST/structopt_stem/crossover/rotct_rand.py
MAST/structopt_stem/crossover/rotct_rand_clus.py
MAST/structopt_stem/crossover/rotct_rand_defect.py
MAST/structopt_stem/fingerprinting/__init__.py
MAST/structopt_stem/fingerprinting/dirac.py
MAST/structopt_stem/fingerprinting/fingerprint_dist.py
MAST/structopt_stem/fingerprinting/get_fingerprint.py
MAST/structopt_stem/fitness/__init__.py
MAST/structopt_stem/fitness/chempotswap.py
MAST/structopt_stem/fitness/enpafit.py
MAST/structopt_stem/fitness/enthalpyfit.py
MAST/structopt_stem/fitness/exponentialfit.py
MAST/structopt_stem/fitness/formationenergy.py
MAST/structopt_stem/fitness/sibias.py
MAST/structopt_stem/fitness/sibias2.py
MAST/structopt_stem/fitness/stem_cost.py
MAST/structopt_stem/fitness/stem_cost_rotation.py
MAST/structopt_stem/fitness/surfaceenergy.py
MAST/structopt_stem/fitness/totalenfit.py
MAST/structopt_stem/generate/Individual.py
MAST/structopt_stem/generate/__init__.py
MAST/structopt_stem/generate/gen_pop_box.py
MAST/structopt_stem/generate/gen_pop_ellipsoid.py
MAST/structopt_stem/generate/gen_pop_plate.py
MAST/structopt_stem/generate/gen_pop_plate_v0.py
MAST/structopt_stem/generate/gen_pop_sphere.py
MAST/structopt_stem/generate/generate_dumbbells.py
MAST/structopt_stem/generate/get_population.py
MAST/structopt_stem/generate/get_restart_population.py
MAST/structopt_stem/generate/rot_vec.py
MAST/structopt_stem/generate/crystal/__init__.py
MAST/structopt_stem/generate/crystal/get_crystal_indiv.py
MAST/structopt_stem/generate/crystal/get_crystal_restart_indiv.py
MAST/structopt_stem/generate/defect/__init__.py
MAST/structopt_stem/generate/defect/gen_solid.py
MAST/structopt_stem/generate/defect/generate_dumbbells.py
MAST/structopt_stem/generate/defect/get_defect_indiv.py
MAST/structopt_stem/generate/defect/get_defect_indiv_random.py
MAST/structopt_stem/generate/defect/get_defect_restart_indiv.py
MAST/structopt_stem/generate/surface/__init__.py
MAST/structopt_stem/generate/surface/get_surface_indiv.py
MAST/structopt_stem/generate/surface/get_surface_restart_indiv.py
MAST/structopt_stem/inp_out/__init__.py
MAST/structopt_stem/inp_out/loggerUtils.py
MAST/structopt_stem/inp_out/read_Ltraj_file.py
MAST/structopt_stem/inp_out/read_individual.py
MAST/structopt_stem/inp_out/read_parameter_input.py
MAST/structopt_stem/inp_out/read_xyz.py
MAST/structopt_stem/inp_out/read_xyz_v0.py
MAST/structopt_stem/inp_out/restart_output.py
MAST/structopt_stem/inp_out/setup_output.py
MAST/structopt_stem/inp_out/setup_par_output.py
MAST/structopt_stem/inp_out/write_individual.py
MAST/structopt_stem/inp_out/write_lammps_data.py
MAST/structopt_stem/inp_out/write_optimizer.py
MAST/structopt_stem/inp_out/write_parameters.py
MAST/structopt_stem/inp_out/write_pop.py
MAST/structopt_stem/inp_out/write_xyz.py
MAST/structopt_stem/moves/__init__.py
MAST/structopt_stem/moves/ase_minimization.py
MAST/structopt_stem/moves/atoms_add.py
MAST/structopt_stem/moves/atoms_remove.py
MAST/structopt_stem/moves/atoms_remove_surf.py
MAST/structopt_stem/moves/basin_hop_la.py
MAST/structopt_stem/moves/basin_hop_permute.py
MAST/structopt_stem/moves/basin_hop_ra_atoms.py
MAST/structopt_stem/moves/basin_hop_rattle.py
MAST/structopt_stem/moves/basin_hop_rotate.py
MAST/structopt_stem/moves/cell_relax_lammps.py
MAST/structopt_stem/moves/cell_shape.py
MAST/structopt_stem/moves/fss_bcc.py
MAST/structopt_stem/moves/lattice_alteration.py
MAST/structopt_stem/moves/lattice_alteration_crystal.py
MAST/structopt_stem/moves/lattice_alteration_group.py
MAST/structopt_stem/moves/lattice_alteration_nn.py
MAST/structopt_stem/moves/lattice_alteration_rdrd.py
MAST/structopt_stem/moves/lattice_alteration_small.py
MAST/structopt_stem/moves/move_la.py
MAST/structopt_stem/moves/pea_rd_mutation.py
MAST/structopt_stem/moves/permutation.py
MAST/structopt_stem/moves/permutation_bulk.py
MAST/structopt_stem/moves/permutation_crystal.py
MAST/structopt_stem/moves/permutation_crystal_multi.py
MAST/structopt_stem/moves/quench.py
MAST/structopt_stem/moves/quench1.py
MAST/structopt_stem/moves/random_replacement.py
MAST/structopt_stem/moves/rattle.py
MAST/structopt_stem/moves/rotation.py
MAST/structopt_stem/moves/rotation_bk.py
MAST/structopt_stem/moves/rotation_geo.py
MAST/structopt_stem/moves/scale_size.py
MAST/structopt_stem/moves/stem_add.py
MAST/structopt_stem/moves/stem_mutation.py
MAST/structopt_stem/moves/stem_remove.py
MAST/structopt_stem/moves/stem_shift.py
MAST/structopt_stem/moves/swap.py
MAST/structopt_stem/moves/swap_cluster.py
MAST/structopt_stem/moves/swap_int.py
MAST/structopt_stem/moves/swap_int_local.py
MAST/structopt_stem/moves/swap_species.py
MAST/structopt_stem/moves/swap_species_pea.py
MAST/structopt_stem/moves/swap_vacancy.py
MAST/structopt_stem/moves/zp_rotation.py
MAST/structopt_stem/moves/zp_rotation_fixed.py
MAST/structopt_stem/post_processing/__init__.py
MAST/structopt_stem/post_processing/finite_size_scale.py
MAST/structopt_stem/post_processing/get_lattice_concentration.py
MAST/structopt_stem/post_processing/read_genealogy.py
MAST/structopt_stem/post_processing/read_ouput.py
MAST/structopt_stem/post_processing/view.py
MAST/structopt_stem/predator/__init__.py
MAST/structopt_stem/predator/adapting.py
MAST/structopt_stem/predator/energy_cluster.py
MAST/structopt_stem/predator/fingerprint_niche.py
MAST/structopt_stem/predator/fitpred.py
MAST/structopt_stem/predator/fitpred_bests.py
MAST/structopt_stem/predator/fitpred_new.py
MAST/structopt_stem/predator/mutation_dups.py
MAST/structopt_stem/predator/mutation_dups_adapt_stem.py
MAST/structopt_stem/predator/mutation_dups_energy.py
MAST/structopt_stem/predator/mutation_dups_quench.py
MAST/structopt_stem/predator/mutation_dups_zp.py
MAST/structopt_stem/selection/__init__.py
MAST/structopt_stem/selection/best.py
MAST/structopt_stem/selection/cost.py
MAST/structopt_stem/selection/fuss.py
MAST/structopt_stem/selection/fuss1.py
MAST/structopt_stem/selection/fuss1r.py
MAST/structopt_stem/selection/fuss2.py
MAST/structopt_stem/selection/fussf.py
MAST/structopt_stem/selection/fussr.py
MAST/structopt_stem/selection/metropolis.py
MAST/structopt_stem/selection/multitournament.py
MAST/structopt_stem/selection/random_pick.py
MAST/structopt_stem/selection/rank.py
MAST/structopt_stem/selection/tournament.py
MAST/structopt_stem/selection/tournament1.py
MAST/structopt_stem/selection/tournament2.py
MAST/structopt_stem/switches/__init__.py
MAST/structopt_stem/switches/crossover_switch.py
MAST/structopt_stem/switches/fitness_switch.py
MAST/structopt_stem/switches/lambdacommamu.py
MAST/structopt_stem/switches/moves_switch.py
MAST/structopt_stem/switches/predator_switch.py
MAST/structopt_stem/switches/selection_switch.py
MAST/structopt_stem/tools/BestInds.py
MAST/structopt_stem/tools/StemCalc.py
MAST/structopt_stem/tools/__init__.py
MAST/structopt_stem/tools/calc_dist.py
MAST/structopt_stem/tools/check_atomlist_concentration.py
MAST/structopt_stem/tools/check_cell_type.py
MAST/structopt_stem/tools/convert_time.py
MAST/structopt_stem/tools/eval_energy.py
MAST/structopt_stem/tools/eval_energy2.py
MAST/structopt_stem/tools/find_defects.py
MAST/structopt_stem/tools/find_top_layer.py
MAST/structopt_stem/tools/get_best.py
MAST/structopt_stem/tools/lammps.py
MAST/structopt_stem/tools/lammps_v0.py
MAST/structopt_stem/tools/position_average.py
MAST/structopt_stem/tools/rattle.py
MAST/structopt_stem/tools/remove_duplicates.py
MAST/structopt_stem/tools/setup_calculator.py
MAST/structopt_stem/tools/setup_fixed_region_calculator.py
MAST/structopt_stem/tools/shift_atoms.py
MAST/submit/__init__.py
MAST/submit/queue_commands.py
MAST/submit/runmast.py
MAST/submit/script_commands.py
MAST/submit/platforms/__init__.py
MAST/submit/platforms/aci/__init__.py
MAST/submit/platforms/aci/mastmon_submit.sh
MAST/submit/platforms/aci/queue_commands.py
MAST/submit/platforms/aci/submit_template.sh
MAST/submit/platforms/bardeen/__init__.py
MAST/submit/platforms/bardeen/mastmon_submit.sh
MAST/submit/platforms/bardeen/queue_commands.py
MAST/submit/platforms/bardeen/submit_template.sh
MAST/submit/platforms/chtc/__init__.py
MAST/submit/platforms/chtc/comparescratch.py
MAST/submit/platforms/chtc/comparescratch_2.py
MAST/submit/platforms/chtc/comparescratch_orig.py
MAST/submit/platforms/chtc/install_mast_on_epd.sh
MAST/submit/platforms/chtc/mast_on_headnode
MAST/submit/platforms/chtc/mastmon_submit.sh
MAST/submit/platforms/chtc/post_mast
MAST/submit/platforms/chtc/post_mast_2
MAST/submit/platforms/chtc/post_mast_gluster
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