Diffusion lammps 81879899299d

Merge remote-tracking branch 'upstream/lammps-icms' into…
81879899299d
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Authored by Richard Berger <richard.berger@temple.edu> on Jul 14 2016, 17:58.

Description

Merge remote-tracking branch 'upstream/lammps-icms' into improved_python_interface

Details

Committed

Richard Berger <richard.berger@temple.edu>

Jul 14 2016, 17:58

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPSee0a8a9d37da: Update iPython interface usage example
rLAMMPScca89b7cb2dd: make fix wall/gran/omp compile again

Branches

Unknown

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Event Timeline

Richard Berger <richard.berger@temple.edu> committed rLAMMPS81879899299d: Merge remote-tracking branch 'upstream/lammps-icms' into… (authored by Richard Berger <richard.berger@temple.edu>).Jul 14 2016, 17:58

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
cca89b7cb2dd	Axel Kohlmeyer	make fix wall/gran/omp compile again	Jul 14 2016
8213a5d6e8e5	Axel Kohlmeyer	port changes to fix wall/gran to fix wall/gran/omp	Jul 14 2016
5d0a755ef7a0	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jul 14 2016
202057838606	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15307 f3b2605a-c512-4ea7…	Jul 14 2016
35bc617478ed	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15306 f3b2605a-c512-4ea7…	Jul 14 2016
53fbe4558aae	Axel Kohlmeyer	add proper bugfix for uninitialized data issue	Jul 14 2016
4b186656067a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15305 f3b2605a-c512-4ea7…	Jul 14 2016
5881c6da6f6c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15304 f3b2605a-c512-4ea7…	Jul 14 2016
320a6214f511	Axel Kohlmeyer	whitespace cleanup	Jul 14 2016
f538bd5fc85a	Axel Kohlmeyer	fix serious bug in molecule command, where flags were used uninitialized	Jul 14 2016
c1fb6c967e3d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15303 f3b2605a-c512-4ea7…	Jul 14 2016
6367c3700bd4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15302 f3b2605a-c512-4ea7…	Jul 14 2016
d7032bd8e992	Axel Kohlmeyer	Merge branch 'merge-pull-115' into lammps-icms	Jul 13 2016
6171c774aa49	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15301 f3b2605a-c512-4ea7…	Jul 13 2016
b3aeb43a93c4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15300 f3b2605a-c512-4ea7…	Jul 13 2016
020484f2547b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15299 f3b2605a-c512-4ea7…	Jul 13 2016
71fe537ebcdf	Tim Mattox	USER-DPD: move SSA data structures from Neighbor class to NeighList class This…	Jul 13 2016
1e59f6f1182d	Axel Kohlmeyer	update README file for QM/MM library	Jul 13 2016
f3047583bf19	Axel Kohlmeyer	include QM/MM lib folder makefile for intel compilers and MPI	Jul 13 2016
92e5aae7bb0e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15298 f3b2605a-c512-4ea7…	Jul 13 2016
53ebd8cfeb5a	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jul 13 2016
e58791e29d4b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15296 f3b2605a-c512-4ea7…	Jul 13 2016
e3e7d0280d06	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15295 f3b2605a-c512-4ea7…	Jul 13 2016
f9047919e8f2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15294 f3b2605a-c512-4ea7…	Jul 13 2016
070ca2614844	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15293 f3b2605a-c512-4ea7…	Jul 13 2016
5783c78f4462	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15292 f3b2605a-c512-4ea7…	Jul 13 2016
eec4d961c0c9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15291 f3b2605a-c512-4ea7…	Jul 13 2016
6ec2346ca0f0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15290 f3b2605a-c512-4ea7…	Jul 13 2016
c5aece5b435f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15289 f3b2605a-c512-4ea7…	Jul 13 2016
0ff512a6da4e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15288 f3b2605a-c512-4ea7…	Jul 13 2016
568c530bfe28	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15287 f3b2605a-c512-4ea7…	Jul 13 2016
3f802d97c9a2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15286 f3b2605a-c512-4ea7…	Jul 13 2016
1df9db5091da	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15285 f3b2605a-c512-4ea7…	Jul 13 2016
c7e4cf7d332b	Axel Kohlmeyer	Merge branch 'merge-qe-qmmm' into lammps-icms	Jul 12 2016
8067fedbdf95	Axel Kohlmeyer	update figures for dihedral spherical and general dihedrals. move the latter to…	Jul 12 2016
bbb642bfb724	Axel Kohlmeyer	more cleanup and bugifxes for fix qmmm. use proper indexing by atom tag.	Jul 12 2016
69194a748d14	Axel Kohlmeyer	fix bug in assigning covalent radii for qm/mm. cleanups. more message tags	Jul 12 2016
bf9e82105508	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15284 f3b2605a-c512-4ea7…	Jul 12 2016
afe07ccca651	Axel Kohlmeyer	Merge branch 'merge-dihedral-spherical' into lammps-icms	Jul 12 2016
9998d7f66dc8	Axel Kohlmeyer	integrate dihedral style spherical provided by andrew jewett	Jul 12 2016
dfbecf047fdd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15283 f3b2605a-c512-4ea7…	Jul 12 2016
cd2fe6f99765	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jul 12 2016
2812b100322b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15282 f3b2605a-c512-4ea7…	Jul 11 2016
c4529dc00a4d	Axel Kohlmeyer	Merge branch 'lammps-icms' into merge-qe-qmmm	Jul 10 2016
8363441a2804	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jul 10 2016
5ea854de2eae	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15280 f3b2605a-c512-4ea7…	Jul 9 2016
4484686077fa	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15279 f3b2605a-c512-4ea7…	Jul 9 2016
a33753ae6f46	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15278 f3b2605a-c512-4ea7…	Jul 9 2016
80b6719d686f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15277 f3b2605a-c512-4ea7…	Jul 9 2016
ee6f9b96211a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15276 f3b2605a-c512-4ea7…	Jul 9 2016

Changes (425)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		doc/html/Manual.html
M		doc/html/Section_commands.html
M		doc/html/Section_intro.html
A		doc/html/_images/offload_knc.png
A		doc/html/_images/user_intel.png
M		doc/html/_sources/Manual.txt
M		doc/html/_sources/Section_commands.txt
M		doc/html/_sources/Section_intro.txt
M		doc/html/_sources/accelerate_intel.txt
M		doc/html/_sources/compute_modify.txt
M		doc/html/_sources/compute_pe.txt
M		doc/html/_sources/compute_pe_atom.txt
M		doc/html/_sources/dihedral_table.txt
M		doc/html/_sources/fix_modify.txt
M		doc/html/_sources/fix_qeq_reax.txt
M		doc/html/_sources/fix_rx.txt
M		doc/html/_sources/fix_shardlow.txt
M		doc/html/_sources/fix_wall_gran.txt
M		doc/html/_sources/molecule.txt
M		doc/html/_sources/package.txt
M		doc/html/_sources/pair_dpd_fdt.txt
M		doc/html/_sources/pair_gran.txt
M		doc/html/_sources/pair_reax_c.txt
M		doc/html/_sources/thermo_style.txt
M		doc/html/_sources/timer.txt
M		doc/html/accelerate_intel.html
M		doc/html/compute_modify.html
M		doc/html/compute_pe.html
M		doc/html/compute_pe_atom.html
M		doc/html/dihedral_table.html
M		doc/html/fix_modify.html
M		doc/html/fix_orient.html
M		doc/html/fix_qeq_reax.html
M		doc/html/fix_rx.html
M		doc/html/fix_shardlow.html
M		doc/html/fix_wall_gran.html
M		doc/html/genindex.html
M		doc/html/molecule.html
M		doc/html/package.html
M		doc/html/pair_dpd_fdt.html
M		doc/html/pair_gran.html
M		doc/html/pair_reax_c.html
M		doc/html/searchindex.js
M		doc/html/thermo_style.html
M		doc/html/timer.html
D		doc/src/Eqs/dihedral_sign.jpg
A		doc/src/Eqs/dihedral_spherical.jpg
A		doc/src/Eqs/dihedral_spherical.tex
A		doc/src/JPG/dihedral_sign.jpg
A		doc/src/JPG/dihedral_spherical_angles.jpg
A		doc/src/JPG/offload_knc.png
A		doc/src/JPG/user_intel.png
M		doc/src/Manual.txt
M		doc/src/PDF/colvars-refman-lammps.pdf
M		doc/src/Section_commands.txt
M		doc/src/Section_intro.txt
M		doc/src/accelerate_intel.txt
M		doc/src/compute_modify.txt
M		doc/src/compute_pe.txt
M		doc/src/compute_pe_atom.txt
A		doc/src/dihedral_spherical.txt
M		doc/src/dihedral_style.txt
M		doc/src/dihedral_table.txt
M		doc/src/fix_addforce.txt
M		doc/src/fix_aveforce.txt
M		doc/src/fix_enforce2d.txt
M		doc/src/fix_freeze.txt
M		doc/src/fix_modify.txt
M		doc/src/fix_rx.txt
M		doc/src/fix_shake.txt
M		doc/src/fix_wall_gran.txt
M		doc/src/molecule.txt
M		doc/src/package.txt
M		doc/src/pair_gran.txt
M		examples/USER/dpd/dpdrx-shardlow/in.dpdrx
V		examples/USER/hadress/H-AdResS/{HADRESS_Water → in.hadress_water}
V		examples/USER/hadress/H-AdResS/{in.hadress_water ← HADRESS_Water}
A		examples/USER/hadress/H-AdResS/log.hadress_water
V		examples/USER/hadress/Relaxation/{LongSetup → in.long_setup}
V		examples/USER/hadress/Relaxation/{in.long_setup ← LongSetup}
A		examples/USER/hadress/Relaxation/log.long_setup
M		examples/USER/hadress/Relaxation/molecule
M		examples/pour/in.pour
M		examples/pour/in.pour.2d
M		examples/pour/in.pour.2d.molecule
M		lib/README
M		lib/colvars/colvarbias.cpp
M		lib/colvars/colvarbias.h
M		lib/colvars/colvarbias_abf.cpp
M		lib/colvars/colvarbias_abf.h
M		lib/colvars/colvarbias_alb.cpp
M		lib/colvars/colvarbias_alb.h
M		lib/colvars/colvarbias_histogram.cpp
M		lib/colvars/colvarbias_histogram.h
M		lib/colvars/colvarbias_meta.cpp
M		lib/colvars/colvarbias_meta.h
M		lib/colvars/colvarbias_restraint.cpp
M		lib/colvars/colvarbias_restraint.h
M		lib/colvars/colvardeps.cpp
M		lib/colvars/colvardeps.h
M		lib/colvars/colvargrid.h
M		lib/colvars/colvarmodule.cpp
M		lib/colvars/colvarmodule.h
M		lib/colvars/colvarparse.cpp
M		lib/colvars/colvarparse.h
D		lib/cuda
D		lib/cuda/Makefile
D		lib/cuda/Makefile.common
D		lib/cuda/Makefile.cudalib
D		lib/cuda/Makefile.defaults
D		lib/cuda/Makefile.lammps
D		lib/cuda/README
D		lib/cuda/atom_vec_angle_cuda.cu
D		lib/cuda/atom_vec_angle_cuda_cu.h
D		lib/cuda/atom_vec_atomic_cuda.cu
D		lib/cuda/atom_vec_atomic_cuda_cu.h
D		lib/cuda/atom_vec_charge_cuda.cu
D		lib/cuda/atom_vec_charge_cuda_cu.h
D		lib/cuda/atom_vec_cuda.cu
D		lib/cuda/atom_vec_cuda_cu.h
D		lib/cuda/atom_vec_cuda_kernel.cu
D		lib/cuda/atom_vec_full_cuda.cu
D		lib/cuda/atom_vec_full_cuda_cu.h
D		lib/cuda/comm_cuda.cu
D		lib/cuda/comm_cuda_cu.h
D		lib/cuda/comm_cuda_kernel.cu
D		lib/cuda/compute_temp_cuda.cu
D		lib/cuda/compute_temp_cuda_cu.h
D		lib/cuda/compute_temp_cuda_kernel.cu
D		lib/cuda/compute_temp_partial_cuda.cu
D		lib/cuda/compute_temp_partial_cuda_cu.h
D		lib/cuda/compute_temp_partial_cuda_kernel.cu
D		lib/cuda/crm_cuda_utils.cu
D		lib/cuda/cuda.cu
D		lib/cuda/cuda_common.h
D		lib/cuda/cuda_cu.h
D		lib/cuda/cuda_data.cu
D		lib/cuda/cuda_data_cu.h
D		lib/cuda/cuda_data_kernel.cu
D		lib/cuda/cuda_kernel.cu
D		lib/cuda/cuda_pair.cu
D		lib/cuda/cuda_pair_cu.h
D		lib/cuda/cuda_pair_kernel.cu
D		lib/cuda/cuda_pair_virial_kernel_nc.cu
D		lib/cuda/cuda_precision.h
D		lib/cuda/cuda_shared.h
D		lib/cuda/cuda_wrapper.cu
D		lib/cuda/cuda_wrapper_cu.h
D		lib/cuda/cuda_wrapper_kernel.cu
D		lib/cuda/domain.cu
D		lib/cuda/domain_cu.h
D		lib/cuda/domain_kernel.cu
D		lib/cuda/fft3d_cuda.cu
D		lib/cuda/fft3d_cuda_cu.h
D		lib/cuda/fft3d_cuda_kernel.cu
D		lib/cuda/fix_addforce_cuda.cu
D		lib/cuda/fix_addforce_cuda_cu.h
D		lib/cuda/fix_addforce_cuda_kernel.cu
D		lib/cuda/fix_aveforce_cuda.cu
D		lib/cuda/fix_aveforce_cuda_cu.h
D		lib/cuda/fix_aveforce_cuda_kernel.cu
D		lib/cuda/fix_enforce2d_cuda.cu
D		lib/cuda/fix_enforce2d_cuda_cu.h
D		lib/cuda/fix_enforce2d_cuda_kernel.cu
D		lib/cuda/fix_freeze_cuda.cu
D		lib/cuda/fix_freeze_cuda_cu.h
D		lib/cuda/fix_freeze_cuda_kernel.cu
D		lib/cuda/fix_gravity_cuda.cu
D		lib/cuda/fix_gravity_cuda_cu.h
D		lib/cuda/fix_gravity_cuda_kernel.cu
D		lib/cuda/fix_nh_cuda.cu
D		lib/cuda/fix_nh_cuda_cu.h
D		lib/cuda/fix_nh_cuda_kernel.cu
D		lib/cuda/fix_nve_cuda.cu
D		lib/cuda/fix_nve_cuda_cu.h
D		lib/cuda/fix_nve_cuda_kernel.cu
D		lib/cuda/fix_set_force_cuda.cu
D		lib/cuda/fix_set_force_cuda_cu.h
D		lib/cuda/fix_set_force_cuda_kernel.cu
D		lib/cuda/fix_shake_cuda.cu
D		lib/cuda/fix_shake_cuda_cu.h
D		lib/cuda/fix_shake_cuda_kernel.cu
D		lib/cuda/fix_temp_berendsen_cuda.cu
D		lib/cuda/fix_temp_berendsen_cuda_cu.h
D		lib/cuda/fix_temp_berendsen_cuda_kernel.cu
D		lib/cuda/fix_temp_rescale_cuda.cu
D		lib/cuda/fix_temp_rescale_cuda_cu.h
D		lib/cuda/fix_temp_rescale_cuda_kernel.cu
D		lib/cuda/fix_temp_rescale_limit_cuda.cu
D		lib/cuda/fix_temp_rescale_limit_cuda_cu.h
D		lib/cuda/fix_temp_rescale_limit_cuda_kernel.cu
D		lib/cuda/fix_viscous_cuda.cu
D		lib/cuda/fix_viscous_cuda_cu.h
D		lib/cuda/fix_viscous_cuda_kernel.cu
D		lib/cuda/neighbor.cu
D		lib/cuda/neighbor_cu.h
D		lib/cuda/neighbor_kernel.cu
D		lib/cuda/pair_born_coul_long_cuda.cu
D		lib/cuda/pair_born_coul_long_cuda_cu.h
D		lib/cuda/pair_born_coul_long_cuda_kernel_nc.cu
D		lib/cuda/pair_buck_coul_cut_cuda.cu
D		lib/cuda/pair_buck_coul_cut_cuda_cu.h
D		lib/cuda/pair_buck_coul_long_cuda.cu
D		lib/cuda/pair_buck_coul_long_cuda_cu.h
D		lib/cuda/pair_buck_cuda.cu
D		lib/cuda/pair_buck_cuda_cu.h
D		lib/cuda/pair_buck_cuda_kernel_nc.cu
D		lib/cuda/pair_eam_cuda.cu
D		lib/cuda/pair_eam_cuda_cu.h
D		lib/cuda/pair_eam_cuda_kernel_nc.cu
D		lib/cuda/pair_gran_hooke_cuda.cu
D		lib/cuda/pair_gran_hooke_cuda_cu.h
D		lib/cuda/pair_gran_hooke_cuda_kernel_nc.cu
D		lib/cuda/pair_lj96_cut_cuda.cu
D		lib/cuda/pair_lj96_cut_cuda_cu.h
D		lib/cuda/pair_lj96_cut_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_charmm_coul_charmm_cuda.cu
D		lib/cuda/pair_lj_charmm_coul_charmm_cuda_cu.h
D		lib/cuda/pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda.cu
D		lib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda_cu.h
D		lib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_charmm_coul_long_cuda.cu
D		lib/cuda/pair_lj_charmm_coul_long_cuda_cu.h
D		lib/cuda/pair_lj_class2_coul_cut_cuda.cu
D		lib/cuda/pair_lj_class2_coul_cut_cuda_cu.h
D		lib/cuda/pair_lj_class2_coul_long_cuda.cu
D		lib/cuda/pair_lj_class2_coul_long_cuda_cu.h
D		lib/cuda/pair_lj_class2_cuda.cu
D		lib/cuda/pair_lj_class2_cuda_cu.h
D		lib/cuda/pair_lj_class2_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_cut_coul_cut_cuda.cu
D		lib/cuda/pair_lj_cut_coul_cut_cuda_cu.h
D		lib/cuda/pair_lj_cut_coul_debye_cuda.cu
D		lib/cuda/pair_lj_cut_coul_debye_cuda_cu.h
D		lib/cuda/pair_lj_cut_coul_long_cuda.cu
D		lib/cuda/pair_lj_cut_coul_long_cuda_cu.h
D		lib/cuda/pair_lj_cut_cuda.cu
D		lib/cuda/pair_lj_cut_cuda_cu.h
D		lib/cuda/pair_lj_cut_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_cut_experimental_cuda.cu
D		lib/cuda/pair_lj_cut_experimental_cuda_cu.h
D		lib/cuda/pair_lj_expand_cuda.cu
D		lib/cuda/pair_lj_expand_cuda_cu.h
D		lib/cuda/pair_lj_expand_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_gromacs_coul_gromacs_cuda.cu
D		lib/cuda/pair_lj_gromacs_coul_gromacs_cuda_cu.h
D		lib/cuda/pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_gromacs_cuda.cu
D		lib/cuda/pair_lj_gromacs_cuda_cu.h
D		lib/cuda/pair_lj_gromacs_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_sdk_coul_cut_cuda.cu
D		lib/cuda/pair_lj_sdk_coul_cut_cuda_cu.h
D		lib/cuda/pair_lj_sdk_coul_debye_cuda.cu
D		lib/cuda/pair_lj_sdk_coul_debye_cuda_cu.h
D		lib/cuda/pair_lj_sdk_coul_long_cuda.cu
D		lib/cuda/pair_lj_sdk_coul_long_cuda_cu.h
D		lib/cuda/pair_lj_sdk_cuda.cu
D		lib/cuda/pair_lj_sdk_cuda_cu.h
D		lib/cuda/pair_lj_sdk_cuda_kernel_nc.cu
D		lib/cuda/pair_lj_smooth_cuda.cu
D		lib/cuda/pair_lj_smooth_cuda_cu.h
D		lib/cuda/pair_lj_smooth_cuda_kernel_nc.cu
D		lib/cuda/pair_manybody_const.h
D		lib/cuda/pair_morse_coul_long_cuda.cu
D		lib/cuda/pair_morse_coul_long_cuda_cu.h
D		lib/cuda/pair_morse_coul_long_cuda_kernel_nc.cu
D		lib/cuda/pair_morse_cuda.cu
D		lib/cuda/pair_morse_cuda_cu.h
D		lib/cuda/pair_morse_cuda_kernel_nc.cu
D		lib/cuda/pair_sw_cuda.cu
D		lib/cuda/pair_sw_cuda_cu.h
D		lib/cuda/pair_sw_cuda_kernel_nc.cu
D		lib/cuda/pair_tersoff_cuda.cu
D		lib/cuda/pair_tersoff_cuda_cu.h
D		lib/cuda/pair_tersoff_cuda_kernel_nc.cu
D		lib/cuda/pair_virial_compute_cu.h
D		lib/cuda/pppm_cuda.cu
D		lib/cuda/pppm_cuda_cu.h
D		lib/cuda/pppm_cuda_kernel.cu
A		lib/gpu/Makefile.shannon
M		lib/gpu/lal_base_three.cpp
M		lib/gpu/lal_tersoff.cpp
M		lib/gpu/lal_tersoff.cu
M		lib/gpu/lal_tersoff_mod.cpp
M		lib/gpu/lal_tersoff_mod.cu
M		lib/gpu/lal_tersoff_zbl.cpp
M		lib/gpu/lal_tersoff_zbl.cu
A		lib/qmmm/Makefile.ifort
M		lib/qmmm/README
A	(dir)	lib/qmmm/example-ec/
A		lib/qmmm/example-ec/README
A	(dir)	lib/qmmm/example-ec/mm-master/
P		lib/qmmm/example-ec/mm-master/data.water Copied from lib/qmmm/example1/mm-master/data.water
P		lib/qmmm/example-ec/mm-master/water.in Copied from lib/qmmm/example1/mm-master/water.in
A	(dir)	lib/qmmm/example-ec/mm-slave/
A		lib/qmmm/example-ec/mm-slave/data.single_water
P		lib/qmmm/example-ec/mm-slave/water_single.in Copied from lib/qmmm/example1/mm-slave/water_single.in
A	(dir)	lib/qmmm/example-ec/qm-pw/
A	(dir)	lib/qmmm/example-ec/qm-pw/pseudo/
A		lib/qmmm/example-ec/qm-pw/pseudo/H.blyp-vbc.UPF
P		lib/qmmm/example-ec/qm-pw/pseudo/H.pbe-van_ak.UPF Copied from lib/qmmm/example1/qm-pw/pseudo/H.pbe-van_ak.UPF
A		lib/qmmm/example-ec/qm-pw/pseudo/O.blyp-mt.UPF
P		lib/qmmm/example-ec/qm-pw/pseudo/O.pbe-van_bm.UPF Copied from lib/qmmm/example1/qm-pw/pseudo/O.pbe-van_bm.UPF
P		lib/qmmm/example-ec/qm-pw/water.in Copied from lib/qmmm/example1/qm-pw/water.in
P		lib/qmmm/example-ec/qmmm.inp Copied from lib/qmmm/example1/qmmm.inp
A	(dir)	lib/qmmm/example-mc/
A		lib/qmmm/example-mc/README
V	(dir)	lib/qmmm/{example-mc/mm-master/ ← example1/mm-master}
V		lib/qmmm/{example-mc ← example1}/mm-master/data.water
V		lib/qmmm/{example-mc ← example1}/mm-master/water.in
V	(dir)	lib/qmmm/{example-mc/mm-slave/ ← example1/mm-slave}
V		lib/qmmm/{example-mc ← example1}/mm-slave/data.single_water
V		lib/qmmm/{example-mc ← example1}/mm-slave/water_single.in
V	(dir)	lib/qmmm/{example-mc/qm-pw/ ← example1/qm-pw}
V	(dir)	lib/qmmm/{example-mc/qm-pw/pseudo/ ← example1/qm-pw/pseudo}
V		lib/qmmm/{example-mc ← example1}/qm-pw/pseudo/H.pbe-van_ak.UPF
V		lib/qmmm/{example-mc ← example1}/qm-pw/pseudo/O.pbe-van_bm.UPF
V		lib/qmmm/{example-mc ← example1}/qm-pw/water.in
V		lib/qmmm/{example-mc ← example1}/qmmm.inp
D		lib/qmmm/example1
V	(dir)	lib/qmmm/{example1/mm-master/ → example-mc/mm-master}
P		lib/qmmm/example1/mm-master/data.water Deleted after being copied to multiple locations: lib/qmmm/example-ec/mm-master/data.water lib/qmmm/example-mc/mm-master/data.water
P		lib/qmmm/example1/mm-master/water.in Deleted after being copied to multiple locations: lib/qmmm/example-ec/mm-master/water.in lib/qmmm/example-mc/mm-master/water.in
V	(dir)	lib/qmmm/{example1/mm-slave/ → example-mc/mm-slave}
V		lib/qmmm/{example1 → example-mc}/mm-slave/data.single_water
P		lib/qmmm/example1/mm-slave/water_single.in Deleted after being copied to multiple locations: lib/qmmm/example-ec/mm-slave/water_single.in lib/qmmm/example-mc/mm-slave/water_single.in
V	(dir)	lib/qmmm/{example1/qm-pw/ → example-mc/qm-pw}
V	(dir)	lib/qmmm/{example1/qm-pw/pseudo/ → example-mc/qm-pw/pseudo}
P		lib/qmmm/example1/qm-pw/pseudo/H.pbe-van_ak.UPF Deleted after being copied to multiple locations: lib/qmmm/example-ec/qm-pw/pseudo/H.pbe-van_ak.UPF lib/qmmm/example-mc/qm-pw/pseudo/H.pbe-van_ak.UPF
P		lib/qmmm/example1/qm-pw/pseudo/O.pbe-van_bm.UPF Deleted after being copied to multiple locations: lib/qmmm/example-ec/qm-pw/pseudo/O.pbe-van_bm.UPF lib/qmmm/example-mc/qm-pw/pseudo/O.pbe-van_bm.UPF
P		lib/qmmm/example1/qm-pw/water.in Deleted after being copied to multiple locations: lib/qmmm/example-ec/qm-pw/water.in lib/qmmm/example-mc/qm-pw/water.in
P		lib/qmmm/example1/qmmm.inp Deleted after being copied to multiple locations: lib/qmmm/example-ec/qmmm.inp lib/qmmm/example-mc/qmmm.inp
M		lib/qmmm/pwqmmm.c
M		src/.gitignore
M		src/BODY/body_nparticle.h
M		src/CLASS2/dihedral_class2.cpp
M		src/GRANULAR/fix_wall_gran.cpp
M		src/GRANULAR/fix_wall_gran.h
M		src/GRANULAR/pair_gran_hertz_history.cpp
M		src/GRANULAR/pair_gran_hooke_history.cpp
M		src/MC/fix_atom_swap.cpp
M		src/Makefile
M		src/RIGID/fix_shake.cpp
M		src/RIGID/fix_shake.h
M		src/USER-DPD/fix_eos_table_rx.cpp
M		src/USER-DPD/fix_eos_table_rx.h
M		src/USER-DPD/fix_rx.cpp
M		src/USER-DPD/fix_rx.h
M		src/USER-DPD/fix_shardlow.cpp
M		src/USER-DPD/fix_shardlow.h
M		src/USER-DPD/pair_exp6_rx.cpp
M		src/USER-DPD/pair_exp6_rx.h
M		src/USER-DPD/pair_multi_lucy_rx.cpp
M		src/USER-DPD/pair_multi_lucy_rx.h
M		src/USER-DPD/pair_table_rx.cpp
M		src/USER-DPD/pair_table_rx.h
M		src/USER-HADRESS/pair_lj_cut_hars_at.cpp
M		src/USER-INTEL/Install.sh
M		src/USER-INTEL/README
M		src/USER-INTEL/TEST/README
M		src/USER-INTEL/TEST/in.intel.rhodo
M		src/USER-INTEL/dihedral_charmm_intel.cpp
M		src/USER-INTEL/fix_intel.cpp
M		src/USER-INTEL/fix_intel.h
M		src/USER-INTEL/intel_simd.h
M		src/USER-INTEL/pair_buck_coul_long_intel.cpp
M		src/USER-INTEL/pair_buck_coul_long_intel.h
M		src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
M		src/USER-INTEL/pair_lj_charmm_coul_long_intel.h
M		src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
M		src/USER-INTEL/pair_lj_cut_coul_long_intel.h
M		src/USER-INTEL/pppm_intel.cpp
M		src/USER-INTEL/pppm_intel.h
A		src/USER-INTEL/verlet_lrt_intel.cpp
A		src/USER-INTEL/verlet_lrt_intel.h
A		src/USER-MISC/dihedral_spherical.cpp
A		src/USER-MISC/dihedral_spherical.h
M		src/USER-OMP/fix_wall_gran_omp.cpp
M		src/USER-OMP/pair_gran_hertz_history_omp.cpp
M		src/USER-OMP/pair_gran_hertz_history_omp.h
M		src/USER-OMP/pair_gran_hooke_history_omp.cpp
M		src/USER-OMP/pair_gran_hooke_history_omp.h
M		src/USER-QMMM/fix_qmmm.cpp
M		src/USER-QMMM/fix_qmmm.h
M		src/angle.cpp
M		src/atom_vec_body.cpp
M		src/atom_vec_line.cpp
M		src/atom_vec_tri.cpp
M		src/compute.cpp
M		src/compute.h
M		src/compute_pe.cpp
M		src/compute_pe.h
M		src/compute_pe_atom.cpp
M		src/compute_pe_atom.h
M		src/dihedral.cpp
M		src/domain.cpp
M		src/fix.cpp
M		src/fix.h
M		src/fix_shear_history.cpp
M		src/fix_shear_history.h
M		src/fix_store.cpp
M		src/improper.cpp
M		src/integrate.h
M		src/modify.cpp
M		src/modify.h
M		src/molecule.cpp
M		src/my_pool_chunk.h
M		src/neigh_derive.cpp
M		src/neigh_gran.cpp
M		src/neigh_list.cpp
M		src/neigh_list.h
M		src/neigh_request.cpp
M		src/neigh_request.h
M		src/neigh_shardlow.cpp
M		src/neighbor.cpp
M		src/neighbor.h
M		src/pair.cpp
M		src/pair.h
M		src/pair_coul_wolf.cpp
M		src/pair_hybrid.cpp
M		src/read_data.cpp
M		src/respa.cpp
M		src/version.h
M		src/write_data.cpp