git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16052 f3b2605a-c512-4ea7-a41b-209d697bcdaa
sync with latest GHub bug fixes
2017-01-26 21:05:57 +00:00 · 2017-01-26 21:05:55 +00:00 · 2017-01-26 20:54:58 +00:00 · 2017-01-26 02:07:37 +00:00 · 2017-01-23 23:04:40 +00:00 · 2017-01-23 22:40:21 +00:00
302 changed files with 182 additions and 1113 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,34 +0,0 @@
-*~
-*.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
@ -1,5 +0,0 @@
-/html
-/LAMMPS.epub
-/LAMMPS.mobi
-/Manual.pdf
-/Developer.pdf
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1 +1,2 @@
+__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -1 +0,0 @@
-*.mod
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- a/examples/mscg/output_9Jan17/log.lammps
+++ b/examples/mscg/output_9Jan17/log.lammps
@ -0,0 +1,140 @@
+LAMMPS (4 Nov 2016)
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1000 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 7 7 7
+Memory usage per processor = 5.44227 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 0.695789 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 2.359 ns/day, 10.172 hours/ns, 27.307 timesteps/s
+92.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.6958     |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1a mscg range finder"
+TEST_1a mscg range finder
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Memory usage per processor = 5.44227 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 1.48638 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 1.104 ns/day, 21.731 hours/ns, 12.783 timesteps/s
+88.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.486      |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1b mscg force matching"
+TEST_1b mscg force matching
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:02
--- 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
@ -1 +0,0 @@
-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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // 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: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/kokkos/.gitignore
+++ b/lib/kokkos/.gitignore
@ -0,0 +1,8 @@
+# Standard ignores
+*~
+*.pyc
+\#*#
+.#*
+.*.swp
+.cproject
+.project
--- a/lib/kokkos/config/configure_compton_cpu.sh
+++ b/lib/kokkos/config/configure_compton_cpu.sh
--- a/lib/kokkos/config/configure_compton_mic.sh
+++ b/lib/kokkos/config/configure_compton_mic.sh
--- a/lib/kokkos/config/configure_kokkos.sh
+++ b/lib/kokkos/config/configure_kokkos.sh
--- a/lib/kokkos/config/configure_kokkos_nvidia.sh
+++ b/lib/kokkos/config/configure_kokkos_nvidia.sh
--- a/lib/kokkos/config/configure_shannon.sh
+++ b/lib/kokkos/config/configure_shannon.sh
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
--- a/lib/linalg/Makefile.mingw32-cross
+++ b/lib/linalg/Makefile.mingw32-cross
--- a/lib/linalg/Makefile.mingw64-cross
+++ b/lib/linalg/Makefile.mingw64-cross
--- a/lib/meam/.gitignore
+++ b/lib/meam/.gitignore
@ -1 +0,0 @@
-*.mod
--- a/lib/meam/Makefile.tbird
+++ b/lib/meam/Makefile.tbird
--- a/lib/meam/meam_data.F
+++ b/lib/meam/meam_data.F
--- a/lib/meam/meam_dens_final.F
+++ b/lib/meam/meam_dens_final.F
--- a/lib/meam/meam_dens_init.F
+++ b/lib/meam/meam_dens_init.F
--- a/lib/meam/meam_force.F
+++ b/lib/meam/meam_force.F
--- a/lib/meam/meam_setup_done.F
+++ b/lib/meam/meam_setup_done.F
--- a/lib/meam/meam_setup_global.F
+++ b/lib/meam/meam_setup_global.F
--- a/lib/meam/meam_setup_param.F
+++ b/lib/meam/meam_setup_param.F
--- a/lib/reax/Makefile.g95
+++ b/lib/reax/Makefile.g95
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.gfortran
--- a/python/.gitignore
+++ b/python/.gitignore
@ -1 +1,3 @@
-/build
+*.pyc
+__pycache__
+build
--- a/python/examples/pylammps/.gitignore
+++ b/python/examples/pylammps/.gitignore
@ -1 +0,0 @@
-*.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/Show More
+++ b/Show More