Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
51072805199b
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Aug 6 2015, 06:51.

Description

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

Conflicts:
doc/Manual.html
doc/Manual.txt

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Aug 6 2015, 06:51

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPSe309f5f98d74: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13843 f3b2605a-c512-4ea7…
rLAMMPS444e9f3db214: import GPU library update from Trung

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS51072805199b: Merge remote-tracking branch 'lammps-ro/master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Aug 6 2015, 06:51

Merged Changes

Commit	Author	Details	Committed
e309f5f98d74	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13843 f3b2605a-c512-4ea7…	Aug 5 2015
901bb5d2dc55	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13841 f3b2605a-c512-4ea7…	Aug 5 2015
cefaee3342f5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13840 f3b2605a-c512-4ea7…	Aug 5 2015
b616d795109a	sjplimp	''	Aug 5 2015
fbfd916c6998	sjplimp	''	Aug 5 2015
e5beeb163b7a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13835 f3b2605a-c512-4ea7…	Aug 5 2015
7e1de6da045e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13834 f3b2605a-c512-4ea7…	Aug 4 2015
d7e358c35978	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13833 f3b2605a-c512-4ea7…	Aug 4 2015
318aefa19c70	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13832 f3b2605a-c512-4ea7…	Aug 4 2015
2f7344a02a6b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13831 f3b2605a-c512-4ea7…	Aug 4 2015
365d1190a2ca	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13830 f3b2605a-c512-4ea7…	Aug 4 2015
810a13413b28	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13827 f3b2605a-c512-4ea7…	Aug 4 2015
b0dec93ffb44	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13826 f3b2605a-c512-4ea7…	Aug 4 2015
57ed47000346	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13825 f3b2605a-c512-4ea7…	Aug 4 2015

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M		doc/Manual.html
M		doc/Manual.txt
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A		doc/USER/smd/SMD_user_guide.pdf
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A		doc/compute_smd_contact_radius.txt
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A		doc/compute_smd_damage.txt
A		doc/compute_smd_hourglass_error.html
A		doc/compute_smd_hourglass_error.txt
A		doc/compute_smd_internal_energy.html
A		doc/compute_smd_internal_energy.txt
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A		doc/doc2/USER/atc/man_kernel_function.html
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A		doc/doc2/USER/atc/man_write_restart.html
A	(dir)	doc/doc2/USER/smd/
A		doc/doc2/USER/smd/SMD_user_guide.pdf
A	(dir)	doc/doc2/USER/sph/
A		doc/doc2/USER/sph/SPH_LAMMPS_userguide.pdf
M		doc/doc2/atom_style.html
A		doc/doc2/compute_smd_contact_radius.html
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A		doc/doc2/compute_smd_hourglass_error.html
A		doc/doc2/compute_smd_internal_energy.html
A		doc/doc2/compute_smd_plastic_strain.html
A		doc/doc2/compute_smd_plastic_strain_rate.html
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A		doc/doc2/compute_smd_tlsph_shape.html
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A		doc/doc2/compute_smd_ulsph_num_neighs.html
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A		doc/doc2/compute_smd_ulsph_strain_rate.html
A		doc/doc2/compute_smd_ulsph_stress.html
A		doc/doc2/compute_smd_vol.html
M		doc/doc2/fix_gcmc.html
A		doc/doc2/fix_smd_adjust_dt.html
A		doc/doc2/fix_smd_integrate_tlsph.html
A		doc/doc2/fix_smd_integrate_ulsph.html
A		doc/doc2/fix_smd_move_triangulated_surface.html
A		doc/doc2/fix_smd_setvel.html
A		doc/doc2/fix_smd_tlsph_reference_configuration.html
A		doc/doc2/fix_smd_wall_surface.html
A		doc/doc2/pair_smd_hertz.html
A		doc/doc2/pair_smd_tlsph.html
A		doc/doc2/pair_smd_triangulated_surface.html
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M		doc/doc2/prd.html
M		doc/doc2/read_data.html
M		doc/doc2/set.html
M		doc/fix_gcmc.html
A		doc/fix_smd.rst
A		doc/fix_smd_adjust_dt.html
A		doc/fix_smd_adjust_dt.txt
A		doc/fix_smd_integrate_tlsph.html
A		doc/fix_smd_integrate_tlsph.txt
A		doc/fix_smd_integrate_ulsph.html
A		doc/fix_smd_integrate_ulsph.txt
A		doc/fix_smd_move_triangulated_surface.html
A		doc/fix_smd_move_triangulated_surface.txt
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A		doc/fix_smd_setvel.txt
A		doc/fix_smd_tlsph_reference_configuration.html
V		{doc/fix_smd_tlsph_reference_configuration.txt ← tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/log.lammps}
A		doc/fix_smd_wall_surface.html
A		doc/fix_smd_wall_surface.txt
M		doc/genindex.html
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A		doc/pair_smd_hertz.txt
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A		doc/pair_smd_tlsph.txt
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A		doc/pair_smd_triangulated_surface.txt
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A		doc/pair_smd_ulsph.txt
M		doc/prd.html
M		doc/prd.txt
M		doc/read_data.html
M		doc/read_data.txt
M		doc/searchindex.js
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M		doc/set.txt
A	(dir)	examples/USER/smd/
A		examples/USER/smd/README
A	(dir)	examples/USER/smd/aluminum_strip_pull/
A		examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp
A	(dir)	examples/USER/smd/fluid_structure_interaction/
A		examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
A	(dir)	examples/USER/smd/funnel_flow/
A		examples/USER/smd/funnel_flow/boundary.stl
A		examples/USER/smd/funnel_flow/funnel_flow.lmp
A	(dir)	examples/USER/smd/rubber_rings_3d/
A		examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp
A		examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data
A	(dir)	examples/USER/smd/rubber_strip_pull/
A		examples/USER/smd/rubber_strip_pull/plot.gpl
A		examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp
M		lib/README
M		src/Makefile
M		src/PERI/pair_peri_ves.cpp
M		src/REPLICA/prd.cpp
A	(dir)	src/USER-SMD/
A		src/USER-SMD/Install.sh
A		src/USER-SMD/README
A		src/USER-SMD/atom_vec_smd.cpp
A		src/USER-SMD/atom_vec_smd.h
A		src/USER-SMD/compute_smd_contact_radius.cpp
A		src/USER-SMD/compute_smd_contact_radius.h
A		src/USER-SMD/compute_smd_damage.cpp
A		src/USER-SMD/compute_smd_damage.h
A		src/USER-SMD/compute_smd_hourglass_error.cpp
A		src/USER-SMD/compute_smd_hourglass_error.h
A		src/USER-SMD/compute_smd_internal_energy.cpp
A		src/USER-SMD/compute_smd_internal_energy.h
A		src/USER-SMD/compute_smd_plastic_strain.cpp
A		src/USER-SMD/compute_smd_plastic_strain.h
A		src/USER-SMD/compute_smd_plastic_strain_rate.cpp
A		src/USER-SMD/compute_smd_plastic_strain_rate.h
A		src/USER-SMD/compute_smd_rho.cpp
A		src/USER-SMD/compute_smd_rho.h
A		src/USER-SMD/compute_smd_tlsph_defgrad.cpp
A		src/USER-SMD/compute_smd_tlsph_defgrad.h
A		src/USER-SMD/compute_smd_tlsph_dt.cpp
A		src/USER-SMD/compute_smd_tlsph_dt.h
A		src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
A		src/USER-SMD/compute_smd_tlsph_num_neighs.h
A		src/USER-SMD/compute_smd_tlsph_shape.cpp
A		src/USER-SMD/compute_smd_tlsph_shape.h
A		src/USER-SMD/compute_smd_tlsph_strain.cpp
A		src/USER-SMD/compute_smd_tlsph_strain.h
A		src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
A		src/USER-SMD/compute_smd_tlsph_strain_rate.h
A		src/USER-SMD/compute_smd_tlsph_stress.cpp
A		src/USER-SMD/compute_smd_tlsph_stress.h
A		src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
A		src/USER-SMD/compute_smd_triangle_mesh_vertices.h
A		src/USER-SMD/compute_smd_ulsph_effm.cpp
A		src/USER-SMD/compute_smd_ulsph_effm.h
A		src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
A		src/USER-SMD/compute_smd_ulsph_num_neighs.h
A		src/USER-SMD/compute_smd_ulsph_strain.cpp
A		src/USER-SMD/compute_smd_ulsph_strain.h
A		src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
A		src/USER-SMD/compute_smd_ulsph_strain_rate.h
A		src/USER-SMD/compute_smd_ulsph_stress.cpp
A		src/USER-SMD/compute_smd_ulsph_stress.h
A		src/USER-SMD/compute_smd_vol.cpp
A		src/USER-SMD/compute_smd_vol.h
A		src/USER-SMD/fix_smd_adjust_dt.cpp
A		src/USER-SMD/fix_smd_adjust_dt.h
A		src/USER-SMD/fix_smd_integrate_tlsph.cpp
A		src/USER-SMD/fix_smd_integrate_tlsph.h
A		src/USER-SMD/fix_smd_integrate_ulsph.cpp
A		src/USER-SMD/fix_smd_integrate_ulsph.h
A		src/USER-SMD/fix_smd_move_triangulated_surface.cpp
A		src/USER-SMD/fix_smd_move_triangulated_surface.h
A		src/USER-SMD/fix_smd_setvel.cpp
A		src/USER-SMD/fix_smd_setvel.h
A		src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
A		src/USER-SMD/fix_smd_tlsph_reference_configuration.h
A		src/USER-SMD/fix_smd_wall_surface.cpp
A		src/USER-SMD/fix_smd_wall_surface.h
A		src/USER-SMD/pair_smd_hertz.cpp
A		src/USER-SMD/pair_smd_hertz.h
A		src/USER-SMD/pair_smd_tlsph.cpp
A		src/USER-SMD/pair_smd_tlsph.h
A		src/USER-SMD/pair_smd_triangulated_surface.cpp
A		src/USER-SMD/pair_smd_triangulated_surface.h
A		src/USER-SMD/pair_smd_ulsph.cpp
A		src/USER-SMD/pair_smd_ulsph.h
A		src/USER-SMD/smd_kernels.h
A		src/USER-SMD/smd_material_models.cpp
A		src/USER-SMD/smd_material_models.h
A		src/USER-SMD/smd_math.h
M		src/atom.cpp
M		src/atom.h
M		src/set.cpp
M		src/version.h
M		tools/moltemplate/common/graphene.lt
P		tools/moltemplate/common/spce.lt Copied to multiple locations: tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt
P		tools/moltemplate/common/watmw.lt Copied to tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/watmw.lt
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.min
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh
V		{tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/log.lammps → doc/fix_smd_tlsph_reference_configuration.txt}
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
A		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT
V		tools/moltemplate/{examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator → src}/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.nvt
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
P		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt Copied from tools/moltemplate/common/spce.lt
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT
D		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py
M		tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/README_run.sh
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/graphene.lt
P		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt Copied from tools/moltemplate/common/spce.lt
P		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/watmw.lt Copied from tools/moltemplate/common/watmw.lt
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.nvt
M		tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh
P		tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh Copied from tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt
P		tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh Copied to tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt
M		tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh
A	(dir)	tools/moltemplate/examples/coarse_grained_examples/membrane+protein/
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/README.TXT
A		tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/README_run.sh
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/README_setup.sh
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/README_visualize.txt
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein/images/ ← membrane+protein_Brannigan2005+Bellesia2010/images}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/images/membrane+protein_t=0ps_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/images/membrane+protein_t=0ps_no_pbc_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/images/membrane+protein_t=0ps_top_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/images/membrane+protein_t=5000ps_LR.jpg
A	(dir)	tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010_variations.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/CGLipidBr2005.lt
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein/moltemplate_files/calc_table/ ← membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/ ← membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
A		tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/moltemplate_files/table_int.dat
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/run.in.min
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/run.in.npt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein ← membrane+protein_Brannigan2005+Bellesia2010}/run.in.nvt
D		tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/README.TXT
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/README_run.sh
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/README_setup.sh
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/README_visualize.txt
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010/images/ → membrane+protein/images}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/images/membrane+protein_t=0ps_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/images/membrane+protein_t=0ps_no_pbc_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/images/membrane+protein_t=0ps_top_LR.jpg
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/images/membrane+protein_t=5000ps_LR.jpg
D		tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/1beadProtSci2010.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/1beadProtSci2010_variations.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/CGLipidBr2005.lt
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/ → membrane+protein/moltemplate_files/calc_table}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V	(dir)	tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/ → membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff}
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
D		tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/moltemplate_files/table_int.dat
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/run.in.min
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/run.in.npt
V		tools/moltemplate/examples/coarse_grained_examples/{membrane+protein_Brannigan2005+Bellesia2010 → membrane+protein}/run.in.nvt
M		tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt
M		tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh
A		tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT
M		tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh
M		tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
M		tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
M		tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min
M		tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh
D		tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in
M		tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
M		tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT
M		tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT
M		tools/moltemplate/moltemplate_manual.pdf
M		tools/moltemplate/src/dump2data.py
M		tools/moltemplate/src/ltemplify.py
M		tools/moltemplate/src/moltemplate.sh
V		tools/moltemplate/{src ← examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator}/oplsaa_moltemplate.py
A	(dir)	tools/smd/
A		tools/smd/Makefile
A		tools/smd/dump2vtk_tris.cpp