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Diffusion lammps 66f676054ed6

Merge branch 'lammps-icms' into lammps-colvars
66f676054ed6
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 23 2012, 14:23.

Description

Merge branch 'lammps-icms' into lammps-colvars

Details

Committed
Axel Kohlmeyer <akohlmey@gmail.com>Oct 23 2012, 14:23
Pushed
jungeOct 6 2016, 16:49
Parents
rLAMMPS1af5a6d629b4: Merge branch 'master' into lammps-icms
rLAMMPSe8aaeba77e0a: update colvars library to Oct 03 2012 version
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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS66f676054ed6: Merge branch 'lammps-icms' into lammps-colvars (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 23 2012, 14:23

Merged Changes

CommitAuthorDetailsCommitted
1af5a6d629b4Axel Kohlmeyer
Merge branch 'master' into lammps-icms 
Oct 23 2012
68415eae0e7asjplimp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8990 f3b2605a-c512-4ea7… 
Oct 22 2012
5f377d2d450dsjplimp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8989 f3b2605a-c512-4ea7… 
Oct 22 2012
d028daec9273sjplimp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8988 f3b2605a-c512-4ea7… 
Oct 22 2012
be1593f66e1bsjplimp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8987 f3b2605a-c512-4ea7… 
Oct 22 2012

Changes (103)

Path
Mexamples/COUPLE/fortran2/LAMMPS.F90
Msrc/version.h
Mtools/moltemplate/README.TXT
Atools/moltemplate/common/graphene.lt
Dtools/moltemplate/common/same_files_with_comments
Dtools/moltemplate/common/same_files_with_comments/trappe1998_with_comments.lt
Dtools/moltemplate/common/same_files_with_comments/watmw_with_comments.lt
Mtools/moltemplate/common/spce.lt
A(dir)tools/moltemplate/common/tip3p_attempts/
Atools/moltemplate/common/tip3p_attempts/README.TXT
Atools/moltemplate/common/tip3p_attempts/tip3p2004.lt
Atools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt
Dtools/moltemplate/doc
Vtools/moltemplate/{doc → }/moltemplate_manual.pdf
Mtools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt
Mtools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt
Mtools/moltemplate/examples/CG_misc/translocation/run.in.npt
Mtools/moltemplate/examples/CG_misc/translocation/run.in.nvt
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/README.TXT
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/README_run.sh
Ptools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_setup.sh
Deleted after being copied to multiple locations:
tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh
tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/README_visualize.txt
V(dir)tools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/ → read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization}
V(dir)tools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/ → read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools}
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/moltemplate_files/README.sh
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Bonds
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Bonds.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings.template
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/tmp_atom_coords.dat
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/ttree_assignments.txt
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples/waterSPCE_from_PDBfile → nanotube+water}/moltemplate_files/spce.lt
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.data
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.coords
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.init
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.settings
Dtools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/run.in.min
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/run.in.npt
Vtools/moltemplate/examples/all_atom_examples/{convert_PDB_to_LT_examples → read_PDB_file_examples}/waterSPCE_from_PDBfile/run.in.nvt
A(dir)tools/moltemplate/examples/all_atom_examples/nanotube+water/
Atools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT
Ptools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh
Copied from tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_setup.sh
Atools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualise.txt
A(dir)tools/moltemplate/examples/all_atom_examples/nanotube+water/images/
A(dir)tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/
A(dir)tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/graphene_unit_cell.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg
Atools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg
A(dir)tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
Vtools/moltemplate/examples/all_atom_examples/{nanotube+water ← convert_PDB_to_LT_examples/waterSPCE_from_PDBfile}/moltemplate_files/spce.lt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
Atools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
A(dir)tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/
A(dir)tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/README.TXT
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/README_run.sh
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/README_setup.sh
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/README_visualize.txt
V(dir)tools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/ ← convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization}
V(dir)tools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/ ← convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools}
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf
A(dir)tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/moltemplate_files/README.sh
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
Ptools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
Atools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/run.in.min
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/run.in.npt
Vtools/moltemplate/examples/all_atom_examples/{read_PDB_file_examples ← convert_PDB_to_LT_examples}/waterSPCE_from_PDBfile/run.in.nvt
Ptools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
Copied to tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
Vtools/moltemplate/{ ← doc}/moltemplate_manual.pdf
Mtools/moltemplate/src/lttree.py
Mtools/moltemplate/src/moltemplate.sh
Mtools/moltemplate/src/ttree.py
Mtools/moltemplate/src/ttree_lex.py

rLAMMPS66f676054ed6

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examples/COUPLE/fortran2/LAMMPS.F90

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src/version.h

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tools/moltemplate/README.TXT

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tools/moltemplate/common/graphene.lt

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tools/moltemplate/doc

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tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt

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tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT

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tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf

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tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh

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tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt

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tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt

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tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.min

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt

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tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt

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tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt

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tools/moltemplate/moltemplate_manual.pdf

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tools/moltemplate/src/lttree.py

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tools/moltemplate/src/moltemplate.sh

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tools/moltemplate/src/ttree.py

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tools/moltemplate/src/ttree_lex.py

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