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Diffusion lammps dc1278ee51e6

Merge remote branch 'lammps-ro/master' into lammps-icms
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Nov 5 2013, 13:37.

Description

Merge remote branch 'lammps-ro/master' into lammps-icms

Resolved Conflicts:
doc/Manual.txt
doc/Section_commands.txt
doc/Section_start.txt
doc/dump_image.txt
doc/dump_modify.txt
doc/write_dump.txt
src/USER-PHONON/fix_phonon.cpp
src/dump_movie.cpp
src/write_dump.cpp

Details

Committed
Axel Kohlmeyer <akohlmey@gmail.com>Nov 5 2013, 13:37
Pushed
jungeOct 6 2016, 16:49
Parents
rLAMMPS661c056cdb2e: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10965 f3b2605a-c512-4ea7…
rLAMMPS421454bb122f: Merge remote branch 'lammps-ro/master' into lammps-icms
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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSdc1278ee51e6: Merge remote branch 'lammps-ro/master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Nov 5 2013, 13:37

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Adoc/Eqs/fix_ti_rs_force.jpg
Adoc/Eqs/fix_ti_rs_force.tex
Adoc/Eqs/fix_ti_rs_function_1.jpg
Adoc/Eqs/fix_ti_rs_function_1.tex
Adoc/Eqs/fix_ti_rs_function_2.jpg
Adoc/Eqs/fix_ti_rs_function_2.tex
Adoc/Eqs/fix_ti_rs_function_3.jpg
Adoc/Eqs/fix_ti_rs_function_3.tex
Adoc/Eqs/fix_ti_spring_force.jpg
Adoc/Eqs/fix_ti_spring_force.tex
Adoc/Eqs/fix_ti_spring_function_1.jpg
Adoc/Eqs/fix_ti_spring_function_1.tex
Adoc/Eqs/fix_ti_spring_function_2.jpg
Adoc/Eqs/fix_ti_spring_function_2.tex
Mdoc/Eqs/pair_comb1.jpg
Mdoc/Eqs/pair_comb1.tex
Mdoc/Eqs/pair_comb2.jpg
Mdoc/Eqs/pair_comb2.tex
Mdoc/Manual.html
Mdoc/Manual.txt
Mdoc/Section_commands.html
Mdoc/Section_commands.txt
Mdoc/Section_start.html
Mdoc/Section_start.txt
Mdoc/compute_ti.html
Mdoc/compute_ti.txt
Mdoc/dump.html
Mdoc/dump.txt
Mdoc/dump_image.html
Mdoc/dump_image.txt
Mdoc/dump_modify.html
Mdoc/dump_modify.txt
Mdoc/fix_phonon.html
Mdoc/fix_phonon.txt
Adoc/fix_ti_rs.html
Adoc/fix_ti_rs.txt
Adoc/fix_ti_spring.html
Adoc/fix_ti_spring.txt
Mdoc/pair_comb.html
Mdoc/pair_comb.txt
Mdoc/write_dump.html
Mdoc/write_dump.txt
Mexamples/COUPLE/simple/simple.c
A(dir)examples/USER/misc/ti/
Aexamples/USER/misc/ti/in.ti_rs
Aexamples/USER/misc/ti/in.ti_spring
Aexamples/comb/data.comb3-OHCCu
Aexamples/comb/ffield.comb3
Aexamples/comb/in.comb3
Aexamples/comb/lib.comb3
Aexamples/comb/log.comb3.4Nov13.linux.1
Aexamples/comb/log.comb3.4Nov13.linux.4
Mpotentials/README
Apotentials/ffield.comb3
Apotentials/lib.comb3
Msrc/MANYBODY/fix_qeq_comb.cpp
Msrc/MANYBODY/fix_qeq_comb.h
Asrc/MANYBODY/pair_comb3.cpp
Asrc/MANYBODY/pair_comb3.h
Msrc/USER-MISC/README
Asrc/USER-MISC/fix_ti_rs.cpp
Asrc/USER-MISC/fix_ti_rs.h
Asrc/USER-MISC/fix_ti_spring.cpp
Asrc/USER-MISC/fix_ti_spring.h
Msrc/USER-PHONON/fix_phonon.cpp
Msrc/USER-PHONON/fix_phonon.h
Msrc/dump_cfg.cpp
Msrc/dump_cfg.h
Msrc/dump_custom.cpp
Msrc/dump_movie.cpp
Msrc/version.h
Msrc/write_dump.cpp
Mtools/amber2lmp/README
Mtools/amber2lmp/amber2lammps.py
A(dir)tools/moltemplate/common/amber/
Atools/moltemplate/common/amber/README.TXT
Atools/moltemplate/common/amber/amberparm2lt.sh
Atools/moltemplate/common/amber/amberparm_angle_to_lt.py
Atools/moltemplate/common/amber/amberparm_bond_to_lt.py
Atools/moltemplate/common/amber/amberparm_dihedral_to_lt.py
Atools/moltemplate/common/amber/amberparm_improper_to_lt.py
Atools/moltemplate/common/amber/amberparm_mass_to_lt.py
Atools/moltemplate/common/amber/amberparm_pair_to_lt.py
Atools/moltemplate/common/gaff.lt
Mtools/moltemplate/common/spce.lt
Vtools/moltemplate/common/{tip3p_1983.lt ← tip3p_attempts/tip3pcharmm.lt}
Vtools/moltemplate/common/{tip3p_2004.lt ← tip3p_attempts/tip3p2004.lt}
Dtools/moltemplate/common/tip3p_attempts
Dtools/moltemplate/common/tip3p_attempts/README.TXT
Vtools/moltemplate/common/{tip3p_attempts/tip3p2004.lt → tip3p_2004.lt}
Vtools/moltemplate/common/{tip3p_attempts/tip3pcharmm.lt → tip3p_1983.lt}
Dtools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization
Dtools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools
Dtools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf
Mtools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT
A(dir)tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README.TXT
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README_run.sh
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README_setup.sh
Ptools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
Copied from tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt
A(dir)tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/
Atools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg
A(dir)tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/1beadProtSci2010.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/1beadProtSci2010_variations.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/CGLipidBr2005.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/README.sh
V(dir)tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/ ← vesicle_PACKMOL/moltemplate_files/calc_table}
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V(dir)tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/ ← vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff}
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/system.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/table_int.dat
A(dir)tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/DLPC.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/DPPC.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/README.sh
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/protein.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step1_proteins.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step2_innerlayer.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step3_outerlayer.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/run.in.min
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/run.in.nvt
Dtools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README.TXT
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README_run.sh
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README_setup.sh
Ptools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt
Deleted after being copied to multiple locations:
tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt
Dtools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images
Dtools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg
Dtools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010_variations.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/CGLipidBr2005.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/README.sh
V(dir)tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL/moltemplate_files/calc_table/ → vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table}
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V(dir)tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/ → vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff}
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/system.lt
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/table_int.dat
Dtools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/DLPC.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/DPPC.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/README.sh
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/protein.xyz
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step1_proteins.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step2_innerlayer.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step3_outerlayer.inp
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/run.in.min
Vtools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/run.in.nvt
Mtools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
Mtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
Dtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt
Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt
Mtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
Dtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue
Dtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt
Mtools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
Dtools/moltemplate/examples/CG_misc/translocation/images/for_visualization
Dtools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools
Dtools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf
Atools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg
Atools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg
Atools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg
Mtools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
A(dir)tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/
A(dir)tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
Vtools/moltemplate/examples/{all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane ← CG_biomolecules/vesicle_PACKMOL}/README_visualize.txt
A(dir)tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg
A(dir)tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
Atools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
Ptools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
Ptools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
Mtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_lammps.sh → README_step3_run_lammps.sh}
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_ltemplify.sh → README_step1_run_ltemplify.sh}
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_moltemplate.sh → README_step2_run_moltemplate.sh}
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step1_run_ltemplify.sh ← README_run_ltemplify.sh}
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step2_run_moltemplate.sh ← README_run_moltemplate.sh}
Vtools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step3_run_lammps.sh ← README_run_lammps.sh}
Mtools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
Mtools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt
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Mtools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
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Ptools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
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Mtools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt
Atools/moltemplate/src/bonds_by_type.py
Atools/moltemplate/src/dump2data.py
Mtools/moltemplate/src/ltemplify.py
Mtools/moltemplate/src/lttree.py
Mtools/moltemplate/src/lttree_check.py
Mtools/moltemplate/src/lttree_styles.py
Mtools/moltemplate/src/moltemplate.sh
Ptools/moltemplate/src/nbody_Impropers.py
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tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py
tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py
tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py
A(dir)tools/moltemplate/src/nbody_alternate_symmetry/
Atools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
Atools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILnoswap.py
Ptools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py
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Ptools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py
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Atools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLnoswap.py
Atools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIK.py
Atools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIKL.py
Ptools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py
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Mtools/moltemplate/src/nbody_by_type.py
Ptools/moltemplate/src/nbody_by_type_lib.py
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Ptools/moltemplate/src/nbody_by_type_lib_old.py
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Mtools/moltemplate/src/pdbsort.py
Mtools/moltemplate/src/postprocess_input_script.py
Atools/moltemplate/src/raw2data.py
Mtools/moltemplate/src/ttree.py
Mtools/moltemplate/src/ttree_lex.py
Mtools/msi2lmp/README
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