Merge branch 'integration' into new-master

2016-09-29 10:37:09 -04:00
parent 78a22be93f 596b260f5d
commit 5b2becd09b
185 changed files with 1073 additions and 34 deletions
--- a/.gitignore
+++ b/.gitignore
@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -0,0 +1 @@
+/html
--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1,2 +1 @@
-__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- a/examples/vashishta/InP.vashishta
+++ b/examples/vashishta/InP.vashishta
--- a/examples/vashishta/SiO.1990.vashishta
+++ b/examples/vashishta/SiO.1990.vashishta
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -0,0 +1 @@
+Makefile.lammps
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_globals.h
+++ b/lib/gpu/cudpp_mini/cudpp_globals.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan.h
@ -2,7 +2,7 @@
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan_manager.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan_manager.h
@ -2,7 +2,7 @@
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_radixsort.h
+++ b/lib/gpu/cudpp_mini/cudpp_radixsort.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_scan.h
+++ b/lib/gpu/cudpp_mini/cudpp_scan.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/sharedmem.h
+++ b/lib/gpu/cudpp_mini/sharedmem.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/meam/.gitignore
+++ b/lib/meam/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/python/.gitignore
+++ b/python/.gitignore
@ -1,3 +1 @@
-*.pyc
-__pycache__
-build
+/build
--- a/python/examples/ipython/.gitignore
+++ b/python/examples/ipython/.gitignore
@ -0,0 +1 @@
+*.orig
--- a/src/.gitignore
+++ b/src/.gitignore
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
--- a/src/ASPHERE/compute_temp_asphere.h
+++ b/src/ASPHERE/compute_temp_asphere.h
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
--- a/src/ASPHERE/fix_npt_asphere.h
+++ b/src/ASPHERE/fix_npt_asphere.h
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
--- a/src/ASPHERE/fix_nve_asphere.h
+++ b/src/ASPHERE/fix_nve_asphere.h
--- a/src/ASPHERE/fix_nve_asphere_noforce.h
+++ b/src/ASPHERE/fix_nve_asphere_noforce.h
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
--- a/src/ASPHERE/fix_nvt_asphere.h
+++ b/src/ASPHERE/fix_nvt_asphere.h
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
--- a/src/ASPHERE/pair_gayberne.h
+++ b/src/ASPHERE/pair_gayberne.h
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
--- a/src/ASPHERE/pair_resquared.h
+++ b/src/ASPHERE/pair_resquared.h
--- a/src/BODY/compute_temp_body.cpp
+++ b/src/BODY/compute_temp_body.cpp
--- a/src/BODY/compute_temp_body.h
+++ b/src/BODY/compute_temp_body.h
--- a/src/BODY/fix_npt_body.cpp
+++ b/src/BODY/fix_npt_body.cpp
--- a/src/BODY/fix_npt_body.h
+++ b/src/BODY/fix_npt_body.h
--- a/src/BODY/fix_nvt_body.cpp
+++ b/src/BODY/fix_nvt_body.cpp
--- a/src/BODY/fix_nvt_body.h
+++ b/src/BODY/fix_nvt_body.h
--- a/src/COLLOID/pair_brownian.cpp
+++ b/src/COLLOID/pair_brownian.cpp
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.h
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.h
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_long.h
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.h
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
--- a/src/DIPOLE/pair_lj_long_dipole_long.h
+++ b/src/DIPOLE/pair_lj_long_dipole_long.h
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.h
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.h
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.h
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.h
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
--- a/src/KOKKOS/angle_charmm_kokkos.h
+++ b/src/KOKKOS/angle_charmm_kokkos.h
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
--- a/src/KOKKOS/angle_harmonic_kokkos.h
+++ b/src/KOKKOS/angle_harmonic_kokkos.h
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
--- a/src/KOKKOS/bond_fene_kokkos.h
+++ b/src/KOKKOS/bond_fene_kokkos.h
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
--- a/src/KOKKOS/bond_harmonic_kokkos.h
+++ b/src/KOKKOS/bond_harmonic_kokkos.h
--- a/src/KOKKOS/compute_temp_kokkos.cpp
+++ b/src/KOKKOS/compute_temp_kokkos.cpp
--- a/src/KOKKOS/compute_temp_kokkos.h
+++ b/src/KOKKOS/compute_temp_kokkos.h
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
--- a/src/KOKKOS/dihedral_charmm_kokkos.h
+++ b/src/KOKKOS/dihedral_charmm_kokkos.h
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
--- a/src/KOKKOS/dihedral_opls_kokkos.h
+++ b/src/KOKKOS/dihedral_opls_kokkos.h
--- a/src/KOKKOS/fix_deform_kokkos.cpp
+++ b/src/KOKKOS/fix_deform_kokkos.cpp
--- a/src/KOKKOS/fix_deform_kokkos.h
+++ b/src/KOKKOS/fix_deform_kokkos.h
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
--- a/src/KOKKOS/fix_nh_kokkos.h
+++ b/src/KOKKOS/fix_nh_kokkos.h
--- a/src/KOKKOS/fix_nph_kokkos.cpp
+++ b/src/KOKKOS/fix_nph_kokkos.cpp
--- a/src/KOKKOS/fix_nph_kokkos.h
+++ b/src/KOKKOS/fix_nph_kokkos.h
--- a/src/KOKKOS/fix_npt_kokkos.cpp
+++ b/src/KOKKOS/fix_npt_kokkos.cpp
--- a/src/KOKKOS/fix_npt_kokkos.h
+++ b/src/KOKKOS/fix_npt_kokkos.h
--- a/src/KOKKOS/fix_nvt_kokkos.cpp
+++ b/src/KOKKOS/fix_nvt_kokkos.cpp
--- a/src/KOKKOS/fix_nvt_kokkos.h
+++ b/src/KOKKOS/fix_nvt_kokkos.h
--- a/src/KOKKOS/fix_setforce_kokkos.cpp
+++ b/src/KOKKOS/fix_setforce_kokkos.cpp
--- a/src/KOKKOS/fix_setforce_kokkos.h
+++ b/src/KOKKOS/fix_setforce_kokkos.h
--- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
--- a/src/KOKKOS/fix_wall_reflect_kokkos.h
+++ b/src/KOKKOS/fix_wall_reflect_kokkos.h
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
--- a/src/KOKKOS/improper_harmonic_kokkos.h
+++ b/src/KOKKOS/improper_harmonic_kokkos.h
--- a/src/KOKKOS/neigh_bond_kokkos.cpp
+++ b/src/KOKKOS/neigh_bond_kokkos.cpp
--- a/src/KOKKOS/neigh_bond_kokkos.h
+++ b/src/KOKKOS/neigh_bond_kokkos.h
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
--- a/src/KOKKOS/pair_buck_kokkos.h
+++ b/src/KOKKOS/pair_buck_kokkos.h
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
--- a/src/KOKKOS/pair_coul_dsf_kokkos.h
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.h
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
--- a/src/KOKKOS/pair_coul_wolf_kokkos.h
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.h
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
--- a/src/KOKKOS/pair_sw_kokkos.h
+++ b/src/KOKKOS/pair_sw_kokkos.h
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
--- a/Show More
+++ b/Show More