CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
pyproject.toml
bash/README
bash/cfg2lmp.sh
bash/create_system_specific_input.sh
bash/diff2html.sh
bash/extract_thermo.sh
bash/gmx2pdb.sh
bash/gmx2pdb.sh.template
bash/gmx_genrestr.sh
bash/gmx_pdp2gro_solvate_em.sh
bash/gmx_solvate.sh
bash/lmp_16Mar18_moab.sh
bash/make_system_subdirs.sh
bash/pdb_packmol2gmx.sh
bash/renumber_png.sh
bash/replicate.sh
bash/select_indenter.sh
dat/indenter/AU_111_r_25.pdb
dat/indenter/AU_111_r_25.xyz
dat/indenter/AU_111_r_50.xyz
dat/indenter/README
dat/subst/coord/AU_111_12x7x2/AU_111_12x7x2.pdb
dat/subst/coord/AU_111_12x7x2/AU_111_12x7x2.xyz
dat/subst/coord/AU_111_51x30x21/lmp_fcc_AU_111.input
dat/subst/coord/AU_111_51x30x21/metadata.yaml
dat/subst/eam/20190406_series_6/010_initial_config.txt
dat/subst/eam/20190406_series_6/020_bulk_minimized_box_fixed.txt
dat/subst/eam/20190406_series_6/030_bulk_minimized_box_relaxed.txt
dat/subst/eam/20190406_series_6/040_slab_minimized_box_fixed.txt
dat/subst/eam/20190406_series_6/050_slab_minimized_box_relaxed.txt
dat/subst/eam/20190406_series_6/060_slab_nvt_20_ps_0_to_298_K_ramped_final.txt
dat/subst/eam/20190406_series_6/065_bulk_nvt_20_ps_0_to_298_K_ramped_final.txt
dat/subst/eam/20190406_series_6/070_slab_npt_200_ps_298_K_0_atm_cell_measures.txt
dat/subst/eam/20190406_series_6/070_slab_npt_200_ps_298_K_0_atm_final.txt
dat/subst/eam/20190406_series_6/070_slab_npt_200_ps_298_K_0_atm_total_rdf.txt
dat/subst/eam/20190406_series_6/070_slab_npt_200_ps_298_K_0_atm_total_rdf_3_col.txt
dat/subst/eam/20190406_series_6/075_bulk_npt_200_ps_298_K_0_atm_cell_measures.txt
dat/subst/eam/20190406_series_6/075_bulk_npt_200_ps_298_K_0_atm_final.txt
dat/subst/eam/20190406_series_6/075_bulk_npt_200_ps_298_K_0_atm_total_rdf.txt
dat/subst/eam/20190406_series_6/075_bulk_npt_200_ps_298_K_0_atm_total_rdf_3_col.txt
dat/subst/eam/20190412_series_8/010_equilibration_npt_bulk_0_atm_box.txt
dat/subst/eam/20190412_series_8/010_equilibration_npt_bulk_0_atm_fcc_rdf.txt
dat/subst/eam/20190412_series_8/010_equilibration_npt_bulk_0_atm_rdf.txt
dat/subst/eam/20190412_series_8/010_equilibration_npt_bulk_0_atm_thermo.out
dat/subst/eam/20190412_series_8/020_equilibration_npt_bulk_1_atm_box.txt
dat/subst/eam/20190412_series_8/020_equilibration_npt_bulk_1_atm_fcc_rdf.txt
dat/subst/eam/20190412_series_8/020_equilibration_npt_bulk_1_atm_rdf.txt
dat/subst/eam/20190412_series_8/020_equilibration_npt_bulk_1_atm_thermo.out
dat/subst/eam/20190412_series_8/030_equilibration_npt_slab_0_atm_box.txt
dat/subst/eam/20190412_series_8/030_equilibration_npt_slab_0_atm_fcc_rdf.txt
dat/subst/eam/20190412_series_8/030_equilibration_npt_slab_0_atm_rdf.txt
dat/subst/eam/20190412_series_8/030_equilibration_npt_slab_0_atm_thermo.out
dat/subst/eam/20190412_series_8/040_equilibration_npt_slab_1_atm_box.txt
dat/subst/eam/20190412_series_8/040_equilibration_npt_slab_1_atm_fcc_rdf.txt
dat/subst/eam/20190412_series_8/040_equilibration_npt_slab_1_atm_rdf.txt
dat/subst/eam/20190412_series_8/040_equilibration_npt_slab_1_atm_thermo.out
dat/subst/eam/20190424_series_9/substrate_AU_111_51x30x21_box.txt
dat/subst/eam/20190424_series_9/substrate_AU_111_51x30x21_fcc_rdf.txt
dat/subst/eam/20190424_series_9/substrate_AU_111_51x30x21_rdf.txt
dat/subst/eam/20190424_series_9/substrate_AU_111_51x30x21_thermo.out
dat/subst/eam/201905_dimer_ernergies/units_metal/dimer.in
dat/subst/eam/201905_dimer_ernergies/units_metal/dimer.lammps
dat/subst/eam/201905_dimer_ernergies/units_metal/dimer.lammpstrj
dat/subst/eam/201905_dimer_ernergies/units_metal/thermo.out
dat/subst/eam/201905_dimer_ernergies/units_metal_shifted/dimer.in
dat/subst/eam/201905_dimer_ernergies/units_metal_shifted/dimer.lammps
dat/subst/eam/201905_dimer_ernergies/units_metal_shifted/dimer.lammpstrj
dat/subst/eam/201905_dimer_ernergies/units_metal_shifted/thermo.out
dat/subst/eam/201905_dimer_ernergies/units_real/dimer.in
dat/subst/eam/201905_dimer_ernergies/units_real/dimer.lammps
dat/subst/eam/201905_dimer_ernergies/units_real/dimer.lammpstrj
dat/subst/eam/201905_dimer_ernergies/units_real/thermo.out
dat/subst/eam/201905_dimer_ernergies/units_real_inexact/dimer.in
dat/subst/eam/201905_dimer_ernergies/units_real_inexact/dimer.lammps
dat/subst/eam/201905_dimer_ernergies/units_real_inexact/dimer.lammpstrj
dat/subst/eam/201905_dimer_ernergies/units_real_inexact/thermo.out
dat/subst/eam/201905_dimer_ernergies/units_real_shifted/dimer.in
dat/subst/eam/201905_dimer_ernergies/units_real_shifted/dimer.lammps
dat/subst/eam/201905_dimer_ernergies/units_real_shifted/dimer.lammpstrj
dat/subst/eam/201905_dimer_ernergies/units_real_shifted/thermo.out
dat/sys/CTAB_on_AU_111.h5
dat/sys/CTAB_on_AU_111.json
dat/sys/CTAB_on_AU_111.pkl
dat/sys/SDS_on_AU_111.pkl
dat/sys/SDS_on_AU_111_extension.pkl
dat/sys/surfactant_on_AU_111.json
dat/sys/surfactant_on_AU_111.pkl
ff/Au-Grochola-JCP05-units-real.eam.alloy
ff/CTAB_in_H2O_on_AU_coeff.input
ff/CTAB_in_H2O_on_AU_coeff_bonded.input
ff/CTAB_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_charmmfsh.input
ff/CTAB_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_charmmfsh_nonbonded.input
ff/CTAB_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_long.input
ff/CTAB_in_H2O_on_AU_coeff_nonbonded.input
ff/CTAB_in_H2O_on_AU_masses.input
ff/CTAB_name2res.yaml
ff/CTAB_name2type.yaml
ff/CTAB_type2name.yaml
ff/README.md
ff/SDS_in_H2O_on_AU_coeff.input
ff/SDS_in_H2O_on_AU_coeff_bonded.input
ff/SDS_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_charmmfsh.input
ff/SDS_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_charmmfsh_nonbonded.input
ff/SDS_in_H2O_on_AU_coeff_hybrid_lj_charmmfsw_coul_long.input
ff/SDS_in_H2O_on_AU_coeff_nonbonded.input
ff/SDS_in_H2O_on_AU_masses.input
ff/SDS_name2res.yaml
ff/SDS_name2type.yaml
ff/SDS_type2name.yaml
ff/par_all36_lipid_extended_stripped.prm
ff/top_all36_lipid_extended_stripped.rtf
gmx_input/README
gmx_input/gro/au_cell_P1_111.gro
gmx_input/itp/AUM.itp
gmx_input/itp/NA.itp
gmx_input/itp/README
gmx_input/itp/SDS.itp
gmx_input/itp/tip3p.itp
gmx_input/mdp/README
gmx_input/mdp/em.mdp
gmx_input/mdp/em_solvated.mdp
gmx_input/mdp/ionize.mdp
gmx_input/mdp/npt.mdp
gmx_input/mdp/npt_z_only.mdp
gmx_input/mdp/nvt.mdp
gmx_input/mdp/pull.mdp.template
gmx_input/mdp/relax.mdp
gmx_input/mdp/relax_z_only.mdp
gmx_input/top/README
gmx_input/top/sys.top.template
ipynb/20250303_project_overview.ipynb
ipynb/20250303_project_overview.py
jlhpy/__init__.py
jlhpy/version.py
jlhpy.egg-info/PKG-INFO
jlhpy.egg-info/SOURCES.txt
jlhpy.egg-info/dependency_links.txt
jlhpy.egg-info/requires.txt
jlhpy.egg-info/top_level.txt
jlhpy/utilities/__init__.py
jlhpy/utilities/generate_pack_sphere_packmol_template_context.py
jlhpy/utilities/analysis/__init__.py
jlhpy/utilities/analysis/count_components.py
jlhpy/utilities/analysis/forces.py
jlhpy/utilities/analysis/map_distances_and_frames.py
jlhpy/utilities/analysis/mpi_msd.py
jlhpy/utilities/analysis/mpi_rdf.py
jlhpy/utilities/analysis/msd.py
jlhpy/utilities/analysis/rdf.py
jlhpy/utilities/geometry/__init__.py
jlhpy/utilities/geometry/bounding_box.py
jlhpy/utilities/geometry/bounding_sphere.py
jlhpy/utilities/geometry/morphology.py
jlhpy/utilities/geometry/simulation_box.py
jlhpy/utilities/mpi/__init__.py
jlhpy/utilities/mpi/launcher.py
jlhpy/utilities/prep/__init__.py
jlhpy/utilities/prep/convert.py
jlhpy/utilities/prep/create_fcc_111.py
jlhpy/utilities/prep/merge.py
jlhpy/utilities/prep/random.py
jlhpy/utilities/prep/segids.py
jlhpy/utilities/prep/unwrap.py
jlhpy/utilities/templates/__init__.py
jlhpy/utilities/templates/cylindrical_packing.py
jlhpy/utilities/templates/flat_packing.py
jlhpy/utilities/templates/spherical_packing.py
jlhpy/utilities/vis/__init__.py
jlhpy/utilities/vis/plot_side_views_with_boxes.py
jlhpy/utilities/vis/plot_side_views_with_spheres.py
jlhpy/utilities/wf/__init__.py
jlhpy/utilities/wf/file_config.py
jlhpy/utilities/wf/grep.txt
jlhpy/utilities/wf/hpc_config.py
jlhpy/utilities/wf/mappings.py
jlhpy/utilities/wf/phys_config.py
jlhpy/utilities/wf/sub_wf_as_leaf_compact.txt
jlhpy/utilities/wf/sub_wf_as_root_compact.txt
jlhpy/utilities/wf/sub_wf_concept.txt
jlhpy/utilities/wf/sub_wf_independent_compact.txt
jlhpy/utilities/wf/utils.py
jlhpy/utilities/wf/workflow_generator.py
jlhpy/utilities/wf/building_blocks/__init__.py
jlhpy/utilities/wf/building_blocks/sub_wf_count_components.py
jlhpy/utilities/wf/building_blocks/sub_wf_gromacs_analysis.py
jlhpy/utilities/wf/building_blocks/sub_wf_gromacs_vis.py
jlhpy/utilities/wf/building_blocks/sub_wf_lammps_analysis.py
jlhpy/utilities/wf/building_blocks/sub_wf_lammps_run.py
jlhpy/utilities/wf/building_blocks/sub_wf_packmol_pdb_cleanup.py
jlhpy/utilities/wf/building_blocks/sub_wf_surfactant_molecule_measures.py
jlhpy/utilities/wf/building_blocks/sub_wf_vmd_pdb_cleanup.py
jlhpy/utilities/wf/building_blocks/gmx/__init__.py
jlhpy/utilities/wf/building_blocks/gmx/chain_wf_gromacs.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_em_solvated.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_npt.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_nvt.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_prep.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_prep_wo_box_dimensions.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_relax.py
jlhpy/utilities/wf/building_blocks/gmx/sub_wf_gromacs_solvate.py
jlhpy/utilities/wf/building_blocks/lmp/__init__.py
jlhpy/utilities/wf/flat_packing/chain_wf_flat_substrate_passivation.py
jlhpy/utilities/wf/flat_packing/sub_wf_005_format_conversion.py
jlhpy/utilities/wf/flat_packing/sub_wf_010_flat_substrate_measures.py
jlhpy/utilities/wf/flat_packing/sub_wf_030_packing.py
jlhpy/utilities/wf/flat_packing/sub_wf_035_pdb_cleanup.py
jlhpy/utilities/wf/flat_packing/sub_wf_040_box_measures.py
jlhpy/utilities/wf/mixin/__init__.py
jlhpy/utilities/wf/mixin/mixin_wf_storage.py
jlhpy/utilities/wf/packing/README.md
jlhpy/utilities/wf/packing/__init__.py
jlhpy/utilities/wf/packing/chain_wf_spherical_indenter_passivation.py
jlhpy/utilities/wf/packing/sub_wf_010_indenter_bounding_sphere.py
jlhpy/utilities/wf/packing/sub_wf_020_surfactant_molecule_measures.py
jlhpy/utilities/wf/packing/sub_wf_030_packing_constraint_spheres.py
jlhpy/utilities/wf/packing/sub_wf_040_spherical_surfactant_packing.py
jlhpy/utilities/wf/packing/sub_wf_110_gromacs_prep.py
jlhpy/utilities/wf/packing/sub_wf_120_gromacs_em.py
jlhpy/utilities/wf/packing/sub_wf_130_gromacs_pull_prep.py
jlhpy/utilities/wf/packing/sub_wf_140_gromacs_pull.py
jlhpy/utilities/wf/packing/sub_wf_150_gromacs_solvate.py
jlhpy/utilities/wf/packing/sub_wf_160_gromacs_em_solvated.py
jlhpy/utilities/wf/packing/sub_wf_170_gromacs_nvt.py
jlhpy/utilities/wf/packing/sub_wf_180_gromacs_npt.py
jlhpy/utilities/wf/packing/sub_wf_190_gromacs_relax.py
jlhpy/utilities/wf/packing/sub_wf_195_gromacs_relax_recover.py
jlhpy/utilities/wf/probe_on_substrate/README.md
jlhpy/utilities/wf/probe_on_substrate/__init__.py
jlhpy/utilities/wf/probe_on_substrate/chain_wf_probe_on_substrate_insertion.py
jlhpy/utilities/wf/probe_on_substrate/chain_wf_probe_on_substrate_lateral_sliding.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_010_merge.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_020_gmx2lmp.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_030_split_datafile.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_040_lammps_minimization.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_050_lammps_equilibration_nvt.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_060_lammps_equilibration_npt.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_070_lammps_equilibration_dpd.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_110_lammps_probe_normal_approach.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_120_probe_analysis.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_150_lammps_trajectory_frame_extraction.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_160_foreach_push_stub.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_170_wrap_join_datafile.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_190_lammps_equilibration_dpd.py
jlhpy/utilities/wf/probe_on_substrate/sub_wf_210_lammps_probe_lateral_sliding.py
jlhpy/utilities/wf/substrate/chain_wf_fcc_substrate_creation.py
jlhpy/utilities/wf/substrate/sub_wf_010_create_fcc_111_substrate.py
jlhpy/utilities/wf/substrate/sub_wf_020_lammps_fixed_box_minimization.py
jlhpy/utilities/wf/substrate/sub_wf_030_lammps_relaxed_box_minimization.py
jlhpy/utilities/wf/substrate/sub_wf_040_lammps_equilibration_nvt.py
jlhpy/utilities/wf/substrate/sub_wf_050_lammps_equilibration_npt.py
lmp_input/colvars.inp
lmp_input/lmp_align.input
lmp_input/lmp_convert_xyz.input
lmp_input/lmp_delete_nonSubst.input
lmp_input/lmp_delete_subst.input
lmp_input/lmp_equilibration_npt.input
lmp_input/lmp_equilibration_nvt.input
lmp_input/lmp_header.input
lmp_input/lmp_minimal_header.input
lmp_input/lmp_minimization.input
lmp_input/lmp_production.input
lmp_input/lmp_split_datafile.input
lmp_input/exchange_substrate/README.md
lmp_input/exchange_substrate/lmp_delete_subst.input
lmp_input/exchange_substrate/lmp_merge.input
lmp_input/exchange_substrate/lmp_scale_solution_to_substrate.input
lmp_input/exchange_substrate/lmp_shift_solution_to_zero_z.input
lmp_input/exchange_substrate/lmp_shift_surface_to_zero_z.input
lmp_input/exchange_substrate/lmp_snapshot.input
lmp_input/prepare_substrate/lmp_fcc_AU_111.input
lmp_input/prepare_substrate/lmp_heat_nve.input
lmp_input/template/lmp.input.template
lmp_input/template/lmp_convert_xyz.input.template
lmp_input/template/lmp_header.input.template
lmp_input/template/lmp_minimization.input.template
lmp_input/template/lmp_production.input.template
lmp_input/template/lmp_split_datafile.input.template
nco/forcesMinMax.nco
nco/selectByAtomType.nco
nco/selectByAtomType.sh
nco/sortByAtomID.nco
packmol/flat.inp.template
packmol/sphere.inp.template
pdb/1_BR.pdb
pdb/1_CTAB.pdb
pdb/1_NA.pdb
pdb/1_SDS.pdb
pdb/au_cell_P1_111.pdb
projects/2025-05-16/2020-07-29-sds-on-au-111-indenter-passivation_final_configs.json
projects/2025-05-16/2020-07-29-sds-on-au-111-indenter-passivation_steps.xlsx
projects/2025-05-16/2020-07-29-sds-on-au-111-indenter-passivation_uuids.xlsx
projects/2025-05-16/2020-12-14-sds-on-au-111-substrate-passivation_final_configs.json
projects/2025-05-16/2020-12-14-sds-on-au-111-substrate-passivation_steps.xlsx
projects/2025-05-16/2020-12-14-sds-on-au-111-substrate-passivation_uuids.xlsx
projects/2025-05-16/2020-12-23-sds-on-au-111-probe-and-substrate-conversion_final_configs.json
projects/2025-05-16/2020-12-23-sds-on-au-111-probe-and-substrate-conversion_steps.xlsx
projects/2025-05-16/2020-12-23-sds-on-au-111-probe-and-substrate-conversion_uuids.xlsx
projects/2025-05-16/2021-01-28-sds-on-au-111-probe-and-substrate-approach_final_configs.json
projects/2025-05-16/2021-01-28-sds-on-au-111-probe-and-substrate-approach_steps.xlsx
projects/2025-05-16/2021-01-28-sds-on-au-111-probe-and-substrate-approach_uuids.xlsx
projects/2025-05-16/2021-01-31-sds-on-au-111-probe-on-substrate-lateral-sliding_analysis.json
projects/2025-05-16/2021-01-31-sds-on-au-111-probe-on-substrate-lateral-sliding_steps.xlsx
projects/2025-05-16/2021-01-31-sds-on-au-111-probe-on-substrate-lateral-sliding_uuids.xlsx
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_LAMMPSEquilibrationDPD.json
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_LAMMPSProbeNormalApproach.json
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_ProbeAnalysis.json
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_final_configs.json
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_steps.xlsx
projects/2025-05-16/2021-02-05-sds-on-au-111-probe-and-substrate-approach_uuids.xlsx
projects/2025-05-16/2021-10-06-sds-on-au-111-substrate-passivation_final_configs.json
projects/2025-05-16/2021-10-06-sds-on-au-111-substrate-passivation_final_configs_monolayer_only.json
projects/2025-05-16/2021-10-06-sds-on-au-111-substrate-passivation_steps.xlsx
projects/2025-05-16/2021-10-06-sds-on-au-111-substrate-passivation_uuids.xlsx
projects/2025-05-16/2021-10-07-sds-on-au-111-probe-and-substrate-merge-and-approach_LAMMPSEquilibrationDPD.json
projects/2025-05-16/2021-10-07-sds-on-au-111-probe-and-substrate-merge-and-approach_LAMMPSProbeNormalApproach.json
projects/2025-05-16/2021-10-07-sds-on-au-111-probe-and-substrate-merge-and-approach_analysis.json
projects/2025-05-16/2021-10-07-sds-on-au-111-probe-and-substrate-merge-and-approach_steps.xlsx
projects/2025-05-16/2021-10-07-sds-on-au-111-probe-and-substrate-merge-and-approach_uuids.xlsx
projects/2025-05-16/2021-12-09-sds-on-au-111-probe-and-substrate-approach-frame-extraction_final_config.json
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