diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/USER/tally/log.12Jun17.force.1
new file mode 100644
index 0000000000000000000000000000000000000000..98b3bad2457c44d328556eecf183f537be2b9b93
--- /dev/null
+++ b/examples/USER/tally/log.12Jun17.force.1
@@ -0,0 +1,177 @@
+LAMMPS (19 May 2017)
+
+units real
+atom_style full
+
+read_data data.spce
+ orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 4500 atoms
+ scanning bonds ...
+ 2 = max bonds/atom
+ scanning angles ...
+ 1 = max angles/atom
+ reading bonds ...
+ 3000 bonds
+ reading angles ...
+ 1500 angles
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+pair_style lj/cut/coul/long 12.0 12.0
+kspace_style pppm 1.0e-4
+
+pair_coeff 1 1 0.15535 3.166
+pair_coeff * 2 0.0000 0.0000
+
+bond_style harmonic
+angle_style harmonic
+dihedral_style none
+improper_style none
+
+bond_coeff 1 1000.00 1.000
+angle_coeff 1 100.0 109.47
+
+special_bonds lj/coul 0.0 0.0 1.0
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 2 = max # of special neighbors
+
+neighbor 2.0 bin
+
+fix 1 all shake 0.0001 20 0 b 1 a 1
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 1500 = # of frozen angles
+fix 2 all nvt temp 300.0 300.0 100.0
+
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 8000 3375
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 3e-06 on 1 procs for 0 steps with 4500 atoms
+
+
+group one molecule 1 2
+6 atoms in group one
+
+# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords
+
+# compute pairwise force between two molecules and everybody
+compute fpa one group/group all pair yes kspace no boundary no
+# tally pairwise force between two molecules and the all molecules
+compute c1 one force/tally all
+# tally the force of all with all (should be zero)
+compute c2 all force/tally all
+# collect per atom data. only reduce over the first group.
+compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
+compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
+# determine magnitude of force
+variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
+variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
+# round to 10**-10 absolute precision.
+variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
+variable all equal round(1e10*c_c2)*1e-10
+
+velocity all create 300 432567 dist uniform
+
+timestep 2.0
+
+# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
+thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
+thermo 10
+
+run 50
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 8000 3375
+WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
+WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute group/group, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 28.47 | 28.47 | 28.47 Mbytes
+Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
+ 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0
+ 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0
+ 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0
+ 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0
+ 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0
+ 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0
+Loop time of 13.9507 on 1 procs for 50 steps with 4500 atoms
+
+Performance: 0.619 ns/day, 38.752 hours/ns, 3.584 timesteps/s
+32.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 12.594 | 12.594 | 12.594 | 0.0 | 90.27
+Bond | 7.3e-05 | 7.3e-05 | 7.3e-05 | 0.0 | 0.00
+Kspace | 0.56296 | 0.56296 | 0.56296 | 0.0 | 4.04
+Neigh | 0.65858 | 0.65858 | 0.65858 | 0.0 | 4.72
+Comm | 0.019093 | 0.019093 | 0.019093 | 0.0 | 0.14
+Output | 0.055025 | 0.055025 | 0.055025 | 0.0 | 0.39
+Modify | 0.057276 | 0.057276 | 0.057276 | 0.0 | 0.41
+Other | | 0.004003 | | | 0.03
+
+Nlocal: 4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 21131 ave 21131 max 21131 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2601983
+Ave neighs/atom = 578.218
+Ave special neighs/atom = 2
+Neighbor list builds = 4
+Dangerous builds = 1
+
+Total wall time: 0:00:15
diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/USER/tally/log.12Jun17.force.4
new file mode 100644
index 0000000000000000000000000000000000000000..4238173fb60e3a5eb806da82101b0282c0185cac
--- /dev/null
+++ b/examples/USER/tally/log.12Jun17.force.4
@@ -0,0 +1,177 @@
+LAMMPS (19 May 2017)
+
+units real
+atom_style full
+
+read_data data.spce
+ orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 4500 atoms
+ scanning bonds ...
+ 2 = max bonds/atom
+ scanning angles ...
+ 1 = max angles/atom
+ reading bonds ...
+ 3000 bonds
+ reading angles ...
+ 1500 angles
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+pair_style lj/cut/coul/long 12.0 12.0
+kspace_style pppm 1.0e-4
+
+pair_coeff 1 1 0.15535 3.166
+pair_coeff * 2 0.0000 0.0000
+
+bond_style harmonic
+angle_style harmonic
+dihedral_style none
+improper_style none
+
+bond_coeff 1 1000.00 1.000
+angle_coeff 1 100.0 109.47
+
+special_bonds lj/coul 0.0 0.0 1.0
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 2 = max # of special neighbors
+
+neighbor 2.0 bin
+
+fix 1 all shake 0.0001 20 0 b 1 a 1
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 1500 = # of frozen angles
+fix 2 all nvt temp 300.0 300.0 100.0
+
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3380 960
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 4.5e-06 on 4 procs for 0 steps with 4500 atoms
+
+
+group one molecule 1 2
+6 atoms in group one
+
+# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords
+
+# compute pairwise force between two molecules and everybody
+compute fpa one group/group all pair yes kspace no boundary no
+# tally pairwise force between two molecules and the all molecules
+compute c1 one force/tally all
+# tally the force of all with all (should be zero)
+compute c2 all force/tally all
+# collect per atom data. only reduce over the first group.
+compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
+compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
+# determine magnitude of force
+variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
+variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
+# round to 10**-10 absolute precision.
+variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
+variable all equal round(1e10*c_c2)*1e-10
+
+velocity all create 300 432567 dist uniform
+
+timestep 2.0
+
+# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
+thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
+thermo 10
+
+run 50
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3380 960
+WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
+WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute group/group, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.59 | 11.6 Mbytes
+Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
+ 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0
+ 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0
+ 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0
+ 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0
+ 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0
+ 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0
+Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms
+
+Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s
+31.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5075 | 3.6114 | 3.7489 | 4.7 | 83.67
+Bond | 8.6e-05 | 0.00010525 | 0.000141 | 0.0 | 0.00
+Kspace | 0.2581 | 0.39489 | 0.49723 | 14.2 | 9.15
+Neigh | 0.19826 | 0.19888 | 0.19918 | 0.1 | 4.61
+Comm | 0.034639 | 0.037137 | 0.038938 | 0.9 | 0.86
+Output | 0.025465 | 0.025997 | 0.027558 | 0.6 | 0.60
+Modify | 0.044022 | 0.044175 | 0.044407 | 0.1 | 1.02
+Other | | 0.003593 | | | 0.08
+
+Nlocal: 1125 ave 1148 max 1097 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost: 12212.5 ave 12269 max 12162 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs: 650496 ave 675112 max 631353 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 2601983
+Ave neighs/atom = 578.218
+Ave special neighs/atom = 2
+Neighbor list builds = 4
+Dangerous builds = 1
+
+Total wall time: 0:00:04
diff --git a/examples/USER/tally/log.21Aug15.pe.1 b/examples/USER/tally/log.12Jun17.pe.1
similarity index 50%
rename from examples/USER/tally/log.21Aug15.pe.1
rename to examples/USER/tally/log.12Jun17.pe.1
index aea553003871b4fec713295409636c14f3afb446..8b0f7534144b7b00ad05ec59926250503934a0a9 100644
--- a/examples/USER/tally/log.21Aug15.pe.1
+++ b/examples/USER/tally/log.12Jun17.pe.1
@@ -1,5 +1,4 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
+LAMMPS (19 May 2017)
units real
atom_style full
@@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 8000 3375
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 1e-06 on 1 procs for 0 steps with 4500 atoms
+
+
group oxy type 1
1500 atoms in group oxy
group hyd type 2
@@ -88,6 +116,7 @@ thermo 10
run 50
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.218482
grid = 15 15 15
stencil order = 5
@@ -95,38 +124,49 @@ PPPM initialization ...
estimated relative force accuracy = 9.61968e-05
using double precision FFTs
3d grid and FFT values/proc = 8000 3375
-WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
-WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
+WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
+WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 17.381 Mbytes
-Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair
- 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827
- 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972
- 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572
- 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165
- 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345
- 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911
-
-Loop time of 4.31105 on 1 procs for 50 steps with 4500 atoms
-100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-Performance: 2.004 ns/day 11.975 hours/ns 11.598 timesteps/s
-
-MPI task timings breakdown:
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute group/group, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 29.08 | 29.08 | 29.08 Mbytes
+Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair
+ 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425
+ 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003
+ 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594
+ 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191
+ 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369
+ 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935
+Loop time of 15.3339 on 1 procs for 50 steps with 4500 atoms
+
+Performance: 0.563 ns/day, 42.594 hours/ns, 3.261 timesteps/s
+32.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.5071 | 3.5071 | 3.5071 | 0.0 | 81.35
-Bond | 0.00025034 | 0.00025034 | 0.00025034 | 0.0 | 0.01
-Kspace | 0.19991 | 0.19991 | 0.19991 | 0.0 | 4.64
-Neigh | 0.31459 | 0.31459 | 0.31459 | 0.0 | 7.30
-Comm | 0.010338 | 0.010338 | 0.010338 | 0.0 | 0.24
-Output | 0.24722 | 0.24722 | 0.24722 | 0.0 | 5.73
-Modify | 0.029466 | 0.029466 | 0.029466 | 0.0 | 0.68
-Other | | 0.002182 | | | 0.05
+Pair | 13.432 | 13.432 | 13.432 | 0.0 | 87.60
+Bond | 0.000365 | 0.000365 | 0.000365 | 0.0 | 0.00
+Kspace | 0.581 | 0.581 | 0.581 | 0.0 | 3.79
+Neigh | 0.66081 | 0.66081 | 0.66081 | 0.0 | 4.31
+Comm | 0.019908 | 0.019908 | 0.019908 | 0.0 | 0.13
+Output | 0.57731 | 0.57731 | 0.57731 | 0.0 | 3.76
+Modify | 0.058515 | 0.058515 | 0.058515 | 0.0 | 0.38
+Other | | 0.003889 | | | 0.03
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -135,10 +175,10 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 2601984
-Ave neighs/atom = 578.219
+Total # of neighbors = 2601983
+Ave neighs/atom = 578.218
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1
-Total wall time: 0:00:04
+Total wall time: 0:00:16
diff --git a/examples/USER/tally/log.21Aug15.pe.4 b/examples/USER/tally/log.12Jun17.pe.4
similarity index 50%
rename from examples/USER/tally/log.21Aug15.pe.4
rename to examples/USER/tally/log.12Jun17.pe.4
index 303af555ff2655073827812bfdeab7e737731b39..f684fabe01032051684737adf1241a6b0471a78a 100644
--- a/examples/USER/tally/log.21Aug15.pe.4
+++ b/examples/USER/tally/log.12Jun17.pe.4
@@ -1,5 +1,4 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
+LAMMPS (19 May 2017)
units real
atom_style full
@@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3380 960
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 1.75e-06 on 4 procs for 0 steps with 4500 atoms
+
+
group oxy type 1
1500 atoms in group oxy
group hyd type 2
@@ -88,6 +116,7 @@ thermo 10
run 50
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.218482
grid = 15 15 15
stencil order = 5
@@ -95,38 +124,49 @@ PPPM initialization ...
estimated relative force accuracy = 9.61968e-05
using double precision FFTs
3d grid and FFT values/proc = 3380 960
-WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
-WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
+WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
+WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 8.44413 Mbytes
-Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair
- 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827
- 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972
- 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572
- 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165
- 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345
- 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911
-
-Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms
-100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-Performance: 7.168 ns/day 3.348 hours/ns 41.482 timesteps/s
-
-MPI task timings breakdown:
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute group/group, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 11.86 | 11.87 | 11.88 Mbytes
+Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair
+ 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425
+ 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003
+ 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594
+ 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191
+ 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369
+ 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935
+Loop time of 2.32344 on 4 procs for 50 steps with 4500 atoms
+
+Performance: 3.719 ns/day, 6.454 hours/ns, 21.520 timesteps/s
+64.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94
-Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02
-Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43
-Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33
-Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48
-Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87
-Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80
-Other | | 0.001719 | | | 0.14
+Pair | 1.5561 | 1.8883 | 2.0327 | 14.1 | 81.27
+Bond | 8.8e-05 | 0.000116 | 0.000135 | 0.0 | 0.00
+Kspace | 0.094718 | 0.1933 | 0.26055 | 14.1 | 8.32
+Neigh | 0.085117 | 0.1073 | 0.1147 | 3.9 | 4.62
+Comm | 0.014156 | 0.017907 | 0.020005 | 1.8 | 0.77
+Output | 0.071634 | 0.090599 | 0.097665 | 3.6 | 3.90
+Modify | 0.019447 | 0.024101 | 0.026277 | 1.8 | 1.04
+Other | | 0.001804 | | | 0.08
Nlocal: 1125 ave 1148 max 1097 min
Histogram: 1 0 0 1 0 0 0 0 1 1
@@ -135,10 +175,10 @@ Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 650496 ave 675112 max 631353 min
Histogram: 1 0 0 1 1 0 0 0 0 1
-Total # of neighbors = 2601984
-Ave neighs/atom = 578.219
+Total # of neighbors = 2601983
+Ave neighs/atom = 578.218
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1
-Total wall time: 0:00:01
+Total wall time: 0:00:02
diff --git a/examples/USER/tally/log.21Aug15.stress.1 b/examples/USER/tally/log.12Jun17.stress.1
similarity index 56%
rename from examples/USER/tally/log.21Aug15.stress.1
rename to examples/USER/tally/log.12Jun17.stress.1
index c20b51559655d55f10d69024485f95f791214975..a76012487cca3c6d73f4331fc27f62165d326c8d 100644
--- a/examples/USER/tally/log.21Aug15.stress.1
+++ b/examples/USER/tally/log.12Jun17.stress.1
@@ -1,5 +1,4 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
+LAMMPS (19 May 2017)
units real
atom_style full
@@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 8000 3375
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 2e-06 on 1 procs for 0 steps with 4500 atoms
+
+
group one molecule 1 2
6 atoms in group one
@@ -79,6 +107,7 @@ thermo 10
run 50
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.218482
grid = 15 15 15
stencil order = 5
@@ -86,38 +115,32 @@ PPPM initialization ...
estimated relative force accuracy = 9.61968e-05
using double precision FFTs
3d grid and FFT values/proc = 8000 3375
-WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
-WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- master list distance cutoff = 14
- ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 24.631 Mbytes
-Step press spa press one ref
- 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
- 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
- 20 23338.149 23338.149 23338.149 -2034283 -2034283
- 30 25946.4 25946.4 25946.4 -2002817 -2002817
- 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
- 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
-
-Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms
-100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s
-
-MPI task timings breakdown:
+WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
+WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
+Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
+Step c_press v_spa v_press v_one v_ref
+ 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7
+ 10 23665.129 23665.129 23665.129 -2096059 -2096059
+ 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1
+ 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3
+ 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7
+ 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5
+Loop time of 14.2089 on 1 procs for 50 steps with 4500 atoms
+
+Performance: 0.608 ns/day, 39.469 hours/ns, 3.519 timesteps/s
+32.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69
-Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04
-Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38
-Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68
-Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24
-Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20
-Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72
-Other | | 0.002368 | | | 0.06
+Pair | 12.983 | 12.983 | 12.983 | 0.0 | 91.37
+Bond | 0.002788 | 0.002788 | 0.002788 | 0.0 | 0.02
+Kspace | 0.62745 | 0.62745 | 0.62745 | 0.0 | 4.42
+Neigh | 0.49839 | 0.49839 | 0.49839 | 0.0 | 3.51
+Comm | 0.018597 | 0.018597 | 0.018597 | 0.0 | 0.13
+Output | 0.015852 | 0.015852 | 0.015852 | 0.0 | 0.11
+Modify | 0.058415 | 0.058415 | 0.058415 | 0.0 | 0.41
+Other | | 0.004126 | | | 0.03
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -132,4 +155,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
-Total wall time: 0:00:04
+Total wall time: 0:00:15
diff --git a/examples/USER/tally/log.21Aug15.stress.4 b/examples/USER/tally/log.12Jun17.stress.4
similarity index 55%
rename from examples/USER/tally/log.21Aug15.stress.4
rename to examples/USER/tally/log.12Jun17.stress.4
index c681960c99d4759c302907fbb07791281d6c48d9..37bb60f013ee2b589a569a11a65139b6cc0a3f10 100644
--- a/examples/USER/tally/log.21Aug15.stress.4
+++ b/examples/USER/tally/log.12Jun17.stress.4
@@ -1,5 +1,4 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
+LAMMPS (19 May 2017)
units real
atom_style full
@@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
+# make certain that shake constraints are satisfied
+run 0 post no
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.218482
+ grid = 15 15 15
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0319435
+ estimated relative force accuracy = 9.61968e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 3380 960
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16692.358 0 -16692.358 -1289.8319
+Loop time of 4e-06 on 4 procs for 0 steps with 4500 atoms
+
+
group one molecule 1 2
6 atoms in group one
@@ -79,6 +107,7 @@ thermo 10
run 50
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.218482
grid = 15 15 15
stencil order = 5
@@ -86,44 +115,38 @@ PPPM initialization ...
estimated relative force accuracy = 9.61968e-05
using double precision FFTs
3d grid and FFT values/proc = 3380 960
-WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
-WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- master list distance cutoff = 14
- ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 12.0691 Mbytes
-Step press spa press one ref
- 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
- 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
- 20 23338.149 23338.149 23338.149 -2034283 -2034283
- 30 25946.4 25946.4 25946.4 -2002817 -2002817
- 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
- 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
-
-Loop time of 1.17266 on 4 procs for 50 steps with 4500 atoms
-100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-Performance: 7.368 ns/day 3.257 hours/ns 42.638 timesteps/s
-
-MPI task timings breakdown:
+WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
+WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
+Per MPI rank memory allocation (min/avg/max) = 15.25 | 15.26 | 15.27 Mbytes
+Step c_press v_spa v_press v_one v_ref
+ 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7
+ 10 23665.129 23665.129 23665.129 -2096059 -2096059
+ 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1
+ 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3
+ 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7
+ 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5
+Loop time of 4.32017 on 4 procs for 50 steps with 4500 atoms
+
+Performance: 2.000 ns/day, 12.000 hours/ns, 11.574 timesteps/s
+31.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.89832 | 0.93222 | 0.98611 | 3.4 | 79.50
-Bond | 0.00081754 | 0.00096095 | 0.0011327 | 0.4 | 0.08
-Kspace | 0.068058 | 0.12154 | 0.15522 | 9.4 | 10.36
-Neigh | 0.065756 | 0.065785 | 0.065824 | 0.0 | 5.61
-Comm | 0.017489 | 0.017982 | 0.018623 | 0.4 | 1.53
-Output | 0.010985 | 0.011017 | 0.011111 | 0.1 | 0.94
-Modify | 0.021429 | 0.021491 | 0.021551 | 0.0 | 1.83
-Other | | 0.001671 | | | 0.14
+Pair | 3.5816 | 3.6917 | 3.839 | 4.9 | 85.45
+Bond | 0.001579 | 0.0016563 | 0.001709 | 0.1 | 0.04
+Kspace | 0.22505 | 0.3716 | 0.48023 | 15.3 | 8.60
+Neigh | 0.14558 | 0.14568 | 0.14575 | 0.0 | 3.37
+Comm | 0.032009 | 0.03441 | 0.036274 | 0.8 | 0.80
+Output | 0.02253 | 0.023115 | 0.024844 | 0.7 | 0.54
+Modify | 0.046954 | 0.047086 | 0.047132 | 0.0 | 1.09
+Other | | 0.004935 | | | 0.11
Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 12263.5 ave 12300 max 12219 min
Histogram: 1 0 1 0 0 0 0 0 0 2
-Neighs: 650438 ave 678786 max 626279 min
+Neighs: 650438 ave 678787 max 626279 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 2601750
@@ -132,4 +155,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:04
diff --git a/examples/USER/tally/log.21Aug15.force.1 b/examples/USER/tally/log.21Aug15.force.1
deleted file mode 100644
index 8e7bdb9520deef2758c2a556edb69f5483e1604d..0000000000000000000000000000000000000000
--- a/examples/USER/tally/log.21Aug15.force.1
+++ /dev/null
@@ -1,136 +0,0 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
-
-units real
-atom_style full
-
-read_data data.spce
- orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 4500 atoms
- scanning bonds ...
- 2 = max bonds/atom
- scanning angles ...
- 1 = max angles/atom
- reading bonds ...
- 3000 bonds
- reading angles ...
- 1500 angles
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-pair_style lj/cut/coul/long 12.0 12.0
-kspace_style pppm 1.0e-4
-
-pair_coeff 1 1 0.15535 3.166
-pair_coeff * 2 0.0000 0.0000
-
-bond_style harmonic
-angle_style harmonic
-dihedral_style none
-improper_style none
-
-bond_coeff 1 1000.00 1.000
-angle_coeff 1 100.0 109.47
-
-special_bonds lj/coul 0.0 0.0 1.0
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 2 = max # of special neighbors
-
-neighbor 2.0 bin
-
-fix 1 all shake 0.0001 20 0 b 1 a 1
- 0 = # of size 2 clusters
- 0 = # of size 3 clusters
- 0 = # of size 4 clusters
- 1500 = # of frozen angles
-fix 2 all nvt temp 300.0 300.0 100.0
-
-group one molecule 1 2
-6 atoms in group one
-
-# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
-
-# compute pairwise force between two molecules and everybody
-compute fpa one group/group all pair yes kspace no boundary no
-# tally pairwise force between two molecules and the all molecules
-compute c1 one force/tally all
-# tally the force of all with all (should be zero)
-compute c2 all force/tally all
-# collect per atom data. only reduce over the first group.
-compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
-compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
-# determine magnitude of force
-variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
-variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
-# round to 10**-10 absolute precision.
-variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
-
-velocity all create 300 432567 dist uniform
-
-timestep 2.0
-
-# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
-thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2
-thermo 10
-
-run 50
-PPPM initialization ...
- G vector (1/distance) = 0.218482
- grid = 15 15 15
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0319435
- estimated relative force accuracy = 9.61968e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 8000 3375
-WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
-WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
-Neighbor list info ...
- 2 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- master list distance cutoff = 14
- ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 16.7648 Mbytes
-Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
- 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
- 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
- 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
- 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
- 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
- 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
-
-Loop time of 4.11825 on 1 procs for 50 steps with 4500 atoms
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-Performance: 2.098 ns/day 11.440 hours/ns 12.141 timesteps/s
-
-MPI task timings breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 3.5286 | 3.5286 | 3.5286 | 0.0 | 85.68
-Bond | 6.1274e-05 | 6.1274e-05 | 6.1274e-05 | 0.0 | 0.00
-Kspace | 0.1937 | 0.1937 | 0.1937 | 0.0 | 4.70
-Neigh | 0.31454 | 0.31454 | 0.31454 | 0.0 | 7.64
-Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.25
-Output | 0.039355 | 0.039355 | 0.039355 | 0.0 | 0.96
-Modify | 0.029273 | 0.029273 | 0.029273 | 0.0 | 0.71
-Other | | 0.002351 | | | 0.06
-
-Nlocal: 4500 ave 4500 max 4500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 21131 ave 21131 max 21131 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2601984
-Ave neighs/atom = 578.219
-Ave special neighs/atom = 2
-Neighbor list builds = 4
-Dangerous builds = 1
-
-Total wall time: 0:00:04
diff --git a/examples/USER/tally/log.21Aug15.force.4 b/examples/USER/tally/log.21Aug15.force.4
deleted file mode 100644
index 17cbc50f02fba59ef993419f88e91428ac824653..0000000000000000000000000000000000000000
--- a/examples/USER/tally/log.21Aug15.force.4
+++ /dev/null
@@ -1,136 +0,0 @@
-LAMMPS (21 Aug 2015-ICMS)
- using 1 OpenMP thread(s) per MPI task
-
-units real
-atom_style full
-
-read_data data.spce
- orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
- 2 by 2 by 1 MPI processor grid
- reading atoms ...
- 4500 atoms
- scanning bonds ...
- 2 = max bonds/atom
- scanning angles ...
- 1 = max angles/atom
- reading bonds ...
- 3000 bonds
- reading angles ...
- 1500 angles
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-pair_style lj/cut/coul/long 12.0 12.0
-kspace_style pppm 1.0e-4
-
-pair_coeff 1 1 0.15535 3.166
-pair_coeff * 2 0.0000 0.0000
-
-bond_style harmonic
-angle_style harmonic
-dihedral_style none
-improper_style none
-
-bond_coeff 1 1000.00 1.000
-angle_coeff 1 100.0 109.47
-
-special_bonds lj/coul 0.0 0.0 1.0
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 2 = max # of special neighbors
-
-neighbor 2.0 bin
-
-fix 1 all shake 0.0001 20 0 b 1 a 1
- 0 = # of size 2 clusters
- 0 = # of size 3 clusters
- 0 = # of size 4 clusters
- 1500 = # of frozen angles
-fix 2 all nvt temp 300.0 300.0 100.0
-
-group one molecule 1 2
-6 atoms in group one
-
-# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
-
-# compute pairwise force between two molecules and everybody
-compute fpa one group/group all pair yes kspace no boundary no
-# tally pairwise force between two molecules and the all molecules
-compute c1 one force/tally all
-# tally the force of all with all (should be zero)
-compute c2 all force/tally all
-# collect per atom data. only reduce over the first group.
-compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
-compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
-# determine magnitude of force
-variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
-variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
-# round to 10**-10 absolute precision.
-variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
-
-velocity all create 300 432567 dist uniform
-
-timestep 2.0
-
-# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
-thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2
-thermo 10
-
-run 50
-PPPM initialization ...
- G vector (1/distance) = 0.218482
- grid = 15 15 15
- stencil order = 5
- estimated absolute RMS force accuracy = 0.0319435
- estimated relative force accuracy = 9.61968e-05
- using double precision FFTs
- 3d grid and FFT values/proc = 3380 960
-WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
-WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75)
-Neighbor list info ...
- 2 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- master list distance cutoff = 14
- ghost atom cutoff = 14
- binsize = 7 -> bins = 6 6 6
-Memory usage per processor = 8.16441 Mbytes
-Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
- 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
- 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
- 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
- 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
- 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
- 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
-
-Loop time of 1.13658 on 4 procs for 50 steps with 4500 atoms
-100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-Performance: 7.602 ns/day 3.157 hours/ns 43.991 timesteps/s
-
-MPI task timings breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38
-Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00
-Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25
-Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56
-Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59
-Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21
-Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86
-Other | | 0.001656 | | | 0.15
-
-Nlocal: 1125 ave 1148 max 1097 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost: 12212.5 ave 12269 max 12162 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs: 650496 ave 675112 max 631353 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 2601984
-Ave neighs/atom = 578.219
-Ave special neighs/atom = 2
-Neighbor list builds = 4
-Dangerous builds = 1
-
-Total wall time: 0:00:01
diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp
index e97a1c751c323e4482d14477c1b76f75a448c2eb..cb7e3a4f23e54d1086b53bad14fba071c31e3dad 100644
--- a/src/USER-TALLY/compute_force_tally.cpp
+++ b/src/USER-TALLY/compute_force_tally.cpp
@@ -44,8 +44,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
peflag = 1; // we need Pair::ev_tally() to be run
- did_compute = 0;
- invoked_peratom = invoked_scalar = -1;
+ did_setup = invoked_peratom = invoked_scalar = -1;
nmax = -1;
fatom = NULL;
vector = new double[size_peratom_cols];
@@ -69,55 +68,50 @@ void ComputeForceTally::init()
else
force->pair->add_tally_callback(this);
- if (force->pair->single_enable == 0 || force->pair->manybody_flag)
- error->warning(FLERR,"Compute force/tally used with incompatible pair style");
+ if (comm->me == 0) {
+ if (force->pair->single_enable == 0 || force->pair->manybody_flag)
+ error->warning(FLERR,"Compute force/tally used with incompatible pair style");
- if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
- || force->improper || force->kspace))
- error->warning(FLERR,"Compute force/tally only called from pair style");
-
- did_compute = -1;
+ if (force->bond || force->angle || force->dihedral
+ || force->improper || force->kspace)
+ error->warning(FLERR,"Compute force/tally only called from pair style");
+ }
+ did_setup = -1;
}
-
/* ---------------------------------------------------------------------- */
-void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton,
- double, double, double fpair,
- double dx, double dy, double dz)
+
+void ComputeForceTally::pair_setup_callback(int, int)
{
const int ntotal = atom->nlocal + atom->nghost;
- const int * const mask = atom->mask;
- // do setup work that needs to be done only once per timestep
+ // grow per-atom storage, if needed
- if (did_compute != update->ntimestep) {
- did_compute = update->ntimestep;
+ if (atom->nmax > nmax) {
+ memory->destroy(fatom);
+ nmax = atom->nmax;
+ memory->create(fatom,nmax,size_peratom_cols,"force/tally:fatom");
+ array_atom = fatom;
+ }
- // grow local force array if necessary
- // needs to be atom->nmax in length
+ // clear storage
- if (atom->nmax > nmax) {
- memory->destroy(fatom);
- nmax = atom->nmax;
- memory->create(fatom,nmax,size_peratom_cols,"force/tally:fatom");
- array_atom = fatom;
- }
+ for (int i=0; i < ntotal; ++i)
+ for (int j=0; j < size_peratom_cols; ++j)
+ fatom[i][j] = 0.0;
- // clear storage as needed
+ for (int i=0; i < size_peratom_cols; ++i)
+ vector[i] = ftotal[i] = 0.0;
- if (newton) {
- for (int i=0; i < ntotal; ++i)
- for (int j=0; j < size_peratom_cols; ++j)
- fatom[i][j] = 0.0;
- } else {
- for (int i=0; i < atom->nlocal; ++i)
- for (int j=0; j < size_peratom_cols; ++j)
- fatom[i][j] = 0.0;
- }
+ did_setup = update->ntimestep;
+}
- for (int i=0; i < size_peratom_cols; ++i)
- vector[i] = ftotal[i] = 0.0;
- }
+/* ---------------------------------------------------------------------- */
+void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton,
+ double, double, double fpair,
+ double dx, double dy, double dz)
+{
+ const int * const mask = atom->mask;
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
@@ -181,7 +175,8 @@ void ComputeForceTally::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeForceTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
- if ((did_compute != invoked_scalar) || (update->eflag_global != invoked_scalar))
+ if ((did_setup != invoked_scalar)
+ || (update->eflag_global != invoked_scalar))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated forces across procs
@@ -197,7 +192,8 @@ double ComputeForceTally::compute_scalar()
void ComputeForceTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
- if ((did_compute != invoked_peratom) || (update->eflag_global != invoked_peratom))
+ if ((did_setup != invoked_peratom)
+ || (update->eflag_global != invoked_peratom))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
@@ -205,6 +201,7 @@ void ComputeForceTally::compute_peratom()
if (force->newton_pair) {
comm->reverse_comm_compute(this);
+ // clear out ghost atom data after it has been collected to local atoms
const int nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; ++i)
for (int j = 0; j < size_peratom_cols; ++j)
diff --git a/src/USER-TALLY/compute_force_tally.h b/src/USER-TALLY/compute_force_tally.h
index 0f7bc35a6d7ab774e3ef7574abb64bcf66fbdc6d..ae2f06a096f0516e513c0102693b0338039c3961 100644
--- a/src/USER-TALLY/compute_force_tally.h
+++ b/src/USER-TALLY/compute_force_tally.h
@@ -39,12 +39,12 @@ class ComputeForceTally : public Compute {
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
+ void pair_setup_callback(int, int);
void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double);
-
private:
- bigint did_compute;
+ bigint did_setup;
int nmax,igroup2,groupbit2;
double **fatom;
double ftotal[3];
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index 48cad538d5e09d5f9e32eff23ce3cbf02fc43afd..65f57b7678096e5a066f3710a54f2c4f70faedd3 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -43,12 +43,13 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
size_vector = 6;
peflag = 1; // we need Pair::ev_tally() to be run
- did_compute = 0;
+ did_setup = 0;
invoked_peratom = invoked_scalar = -1;
nmax = -1;
stress = NULL;
eatom = NULL;
vector = new double[size_vector];
+ heatj = new double[size_vector];
}
/* ---------------------------------------------------------------------- */
@@ -56,6 +57,9 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
ComputeHeatFluxTally::~ComputeHeatFluxTally()
{
if (force && force->pair) force->pair->del_tally_callback(this);
+ memory->destroy(stress);
+ memory->destroy(eatom);
+ delete[] heatj;
delete[] vector;
}
@@ -68,70 +72,56 @@ void ComputeHeatFluxTally::init()
else
force->pair->add_tally_callback(this);
- if (force->pair->single_enable == 0 || force->pair->manybody_flag)
- error->warning(FLERR,"Compute heat/flux/tally used with incompatible pair style");
+ if (comm->me == 0) {
+ if (force->pair->single_enable == 0 || force->pair->manybody_flag)
+ error->warning(FLERR,"Compute heat/flux/tally used with incompatible pair style");
- if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
- || force->improper || force->kspace))
- error->warning(FLERR,"Compute heat/flux/tally only called from pair style");
-
- did_compute = -1;
+ if (force->bond || force->angle || force->dihedral
+ || force->improper || force->kspace)
+ error->warning(FLERR,"Compute heat/flux/tally only called from pair style");
+ }
+ did_setup = -1;
}
-
/* ---------------------------------------------------------------------- */
-void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int newton,
- double evdwl, double ecoul, double fpair,
- double dx, double dy, double dz)
+void ComputeHeatFluxTally::pair_setup_callback(int, int)
{
const int ntotal = atom->nlocal + atom->nghost;
- const int * const mask = atom->mask;
- // do setup work that needs to be done only once per timestep
+ // grow per-atom storage, if needed
- if (did_compute != update->ntimestep) {
- did_compute = update->ntimestep;
+ if (atom->nmax > nmax) {
+ memory->destroy(stress);
+ memory->destroy(eatom);
+ nmax = atom->nmax;
+ memory->create(stress,nmax,6,"heat/flux/tally:stress");
+ memory->create(eatom,nmax,"heat/flux/tally:eatom");
+ }
- // grow local stress and eatom arrays if necessary
- // needs to be atom->nmax in length
+ // clear storage
- if (atom->nmax > nmax) {
- memory->destroy(stress);
- nmax = atom->nmax;
- memory->create(stress,nmax,6,"heat/flux/tally:stress");
+ for (int i=0; i < ntotal; ++i) {
+ eatom[i] = 0.0;
+ stress[i][0] = 0.0;
+ stress[i][1] = 0.0;
+ stress[i][2] = 0.0;
+ stress[i][3] = 0.0;
+ stress[i][4] = 0.0;
+ stress[i][5] = 0.0;
+ }
- memory->destroy(eatom);
- nmax = atom->nmax;
- memory->create(eatom,nmax,"heat/flux/tally:eatom");
- }
+ for (int i=0; i < size_vector; ++i)
+ vector[i] = heatj[i] = 0.0;
- // clear storage as needed
-
- if (newton) {
- for (int i=0; i < ntotal; ++i) {
- eatom[i] = 0.0;
- stress[i][0] = 0.0;
- stress[i][1] = 0.0;
- stress[i][2] = 0.0;
- stress[i][3] = 0.0;
- stress[i][4] = 0.0;
- stress[i][5] = 0.0;
- }
- } else {
- for (int i=0; i < atom->nlocal; ++i) {
- eatom[i] = 0.0;
- stress[i][0] = 0.0;
- stress[i][1] = 0.0;
- stress[i][2] = 0.0;
- stress[i][3] = 0.0;
- stress[i][4] = 0.0;
- stress[i][5] = 0.0;
- }
- }
+ did_setup = update->ntimestep;
+}
- for (int i=0; i < size_vector; ++i)
- vector[i] = heatj[i] = 0.0;
- }
+/* ---------------------------------------------------------------------- */
+void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int newton,
+ double evdwl, double ecoul, double fpair,
+ double dx, double dy, double dz)
+{
+ const int * const mask = atom->mask;
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
@@ -210,7 +200,7 @@ void ComputeHeatFluxTally::unpack_reverse_comm(int n, int *list, double *buf)
void ComputeHeatFluxTally::compute_vector()
{
invoked_vector = update->ntimestep;
- if ((did_compute != invoked_vector) || (update->eflag_global != invoked_vector))
+ if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
@@ -243,6 +233,7 @@ void ComputeHeatFluxTally::compute_vector()
const double pfactor = 0.5 * force->mvv2e;
double **v = atom->v;
double *mass = atom->mass;
+ double *rmass = atom->rmass;
int *type = atom->type;
double jc[3] = {0.0,0.0,0.0};
@@ -250,17 +241,21 @@ void ComputeHeatFluxTally::compute_vector()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- double ke_i = pfactor * mass[type[i]] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
- jc[0] += (ke_i + eatom[i]) * v[i][0];
- jc[1] += (ke_i + eatom[i]) * v[i][1];
- jc[2] += (ke_i + eatom[i]) * v[i][2];
- jv[0] += stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
- stress[i][4]*v[i][2];
- jv[1] += stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
- stress[i][5]*v[i][2];
- jv[2] += stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
- stress[i][2]*v[i][2];
+ const double * const vi = v[i];
+ const double * const si = stress[i];
+ double ke_i;
+
+ if (rmass) ke_i = pfactor * rmass[i];
+ else ke_i *= pfactor * mass[type[i]];
+ ke_i *= (vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2]);
+ ke_i += eatom[i];
+
+ jc[0] += ke_i*vi[0];
+ jc[1] += ke_i*vi[1];
+ jc[2] += ke_i*vi[2];
+ jv[0] += si[0]*vi[0] + si[3]*vi[1] + si[4]*vi[2];
+ jv[1] += si[3]*vi[0] + si[1]*vi[1] + si[5]*vi[2];
+ jv[2] += si[4]*vi[0] + si[5]*vi[1] + si[2]*vi[2];
}
}
diff --git a/src/USER-TALLY/compute_heat_flux_tally.h b/src/USER-TALLY/compute_heat_flux_tally.h
index 8c6671cf1e59c04fa7ca25e765021233e41d135b..4158b2e29d9b16c04e93186b387eab0b2082d6c1 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.h
+++ b/src/USER-TALLY/compute_heat_flux_tally.h
@@ -38,15 +38,16 @@ class ComputeHeatFluxTally : public Compute {
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
+ void pair_setup_callback(int, int);
void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double);
private:
- bigint did_compute;
+ bigint did_setup;
int nmax,igroup2,groupbit2;
double **stress,*eatom;
- double heatj[6];
+ double *heatj;
};
}
diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp
index a30f2d6b9a9c9bc0d8edf509059a5f054abc0b49..25a172b7f81eb6cd68a75fcb520c401bb89ec1de 100644
--- a/src/USER-TALLY/compute_pe_mol_tally.cpp
+++ b/src/USER-TALLY/compute_pe_mol_tally.cpp
@@ -42,7 +42,7 @@ ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
peflag = 1; // we need Pair::ev_tally() to be run
- did_compute = invoked_vector = -1;
+ did_setup = invoked_vector = -1;
vector = new double[size_vector];
}
@@ -66,16 +66,24 @@ void ComputePEMolTally::init()
if (atom->molecule_flag == 0)
error->all(FLERR,"Compute pe/mol/tally requires molecule IDs");
- if (force->pair->single_enable == 0 || force->pair->manybody_flag)
- error->warning(FLERR,"Compute pe/mol/tally used with incompatible pair style");
+ if (comm->me == 0) {
+ if (force->pair->single_enable == 0 || force->pair->manybody_flag)
+ error->warning(FLERR,"Compute pe/mol/tally used with incompatible pair style");
- if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
- || force->improper || force->kspace))
- error->warning(FLERR,"Compute pe/mol/tally only called from pair style");
-
- did_compute = -1;
+ if (force->bond || force->angle || force->dihedral
+ || force->improper || force->kspace)
+ error->warning(FLERR,"Compute pe/mol/tally only called from pair style");
+ }
+ did_setup = -1;
}
+/* ---------------------------------------------------------------------- */
+
+void ComputePEMolTally::pair_setup_callback(int, int)
+{
+ etotal[0] = etotal[1] = etotal[2] = etotal[3] = 0.0;
+ did_setup = update->ntimestep;
+}
/* ---------------------------------------------------------------------- */
void ComputePEMolTally::pair_tally_callback(int i, int j, int nlocal, int newton,
@@ -85,14 +93,6 @@ void ComputePEMolTally::pair_tally_callback(int i, int j, int nlocal, int newton
const int * const mask = atom->mask;
const tagint * const molid = atom->molecule;
- // do setup work that needs to be done only once per timestep
-
- if (did_compute != update->ntimestep) {
- did_compute = update->ntimestep;
-
- etotal[0] = etotal[1] = etotal[2] = etotal[3] = 0.0;
- }
-
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ){
@@ -119,7 +119,7 @@ void ComputePEMolTally::pair_tally_callback(int i, int j, int nlocal, int newton
void ComputePEMolTally::compute_vector()
{
invoked_vector = update->ntimestep;
- if ((did_compute != invoked_vector) || (update->eflag_global != invoked_vector))
+ if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated energies across procs
diff --git a/src/USER-TALLY/compute_pe_mol_tally.h b/src/USER-TALLY/compute_pe_mol_tally.h
index b2c5ffab7fc3ee3d23b538c8d4e19cfbfacf8668..1b022a9ef578cfb4d2cdf817605ace0ca53bfc79 100644
--- a/src/USER-TALLY/compute_pe_mol_tally.h
+++ b/src/USER-TALLY/compute_pe_mol_tally.h
@@ -33,12 +33,13 @@ class ComputePEMolTally : public Compute {
void init();
void compute_vector();
+ void pair_setup_callback(int, int);
void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double);
private:
- bigint did_compute;
+ bigint did_setup;
int igroup2,groupbit2;
double etotal[4];
};
diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp
index 2117f2cb15952e09189d0600a4b96ad17ed39f74..e7c0bdd03cca25e152d24ef35df936edcede0fd9 100644
--- a/src/USER-TALLY/compute_pe_tally.cpp
+++ b/src/USER-TALLY/compute_pe_tally.cpp
@@ -44,7 +44,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
peflag = 1; // we need Pair::ev_tally() to be run
- did_compute = invoked_peratom = invoked_scalar = -1;
+ did_setup = invoked_peratom = invoked_scalar = -1;
nmax = -1;
eatom = NULL;
vector = new double[size_peratom_cols];
@@ -68,55 +68,51 @@ void ComputePETally::init()
else
force->pair->add_tally_callback(this);
- if (force->pair->single_enable == 0 || force->pair->manybody_flag)
- error->warning(FLERR,"Compute pe/tally used with incompatible pair style");
+ if (comm->me == 0) {
+ if (force->pair->single_enable == 0 || force->pair->manybody_flag)
+ error->warning(FLERR,"Compute pe/tally used with incompatible pair style");
- if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
- || force->improper || force->kspace))
- error->warning(FLERR,"Compute pe/tally only called from pair style");
-
- did_compute = -1;
+ if (force->bond || force->angle || force->dihedral
+ || force->improper || force->kspace)
+ error->warning(FLERR,"Compute pe/tally only called from pair style");
+ }
+ did_setup = -1;
}
-
/* ---------------------------------------------------------------------- */
-void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton,
- double evdwl, double ecoul, double,
- double, double, double)
+
+void ComputePETally::pair_setup_callback(int, int)
{
const int ntotal = atom->nlocal + atom->nghost;
- const int * const mask = atom->mask;
- // do setup work that needs to be done only once per timestep
+ // grow per-atom storage, if needed
- if (did_compute != update->ntimestep) {
- did_compute = update->ntimestep;
+ if (atom->nmax > nmax) {
+ memory->destroy(eatom);
+ nmax = atom->nmax;
+ memory->create(eatom,nmax,size_peratom_cols,"pe/tally:eatom");
+ array_atom = eatom;
+ }
- // grow local eatom array if necessary
- // needs to be atom->nmax in length
+ // clear storage
- if (atom->nmax > nmax) {
- memory->destroy(eatom);
- nmax = atom->nmax;
- memory->create(eatom,nmax,size_peratom_cols,"pe/tally:eatom");
- array_atom = eatom;
- }
+ for (int i=0; i < ntotal; ++i)
+ eatom[i][0] = eatom[i][1] = 0.0;
- // clear storage as needed
+ vector[0] = etotal[0] = vector[1] = etotal[1] = 0.0;
- if (newton) {
- for (int i=0; i < ntotal; ++i)
- eatom[i][0] = eatom[i][1] = 0.0;
- } else {
- for (int i=0; i < atom->nlocal; ++i)
- eatom[i][0] = eatom[i][1] = 0.0;
- }
+ did_setup = update->ntimestep;
+}
- vector[0] = etotal[0] = vector[1] = etotal[1] = 0.0;
- }
+/* ---------------------------------------------------------------------- */
+void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton,
+ double evdwl, double ecoul, double,
+ double, double, double)
+{
+ const int * const mask = atom->mask;
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
- || ((mask[i] & groupbit2) && (mask[j] & groupbit)) ){
+ || ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
evdwl *= 0.5; ecoul *= 0.5;
if (newton || i < nlocal) {
@@ -164,7 +160,8 @@ void ComputePETally::unpack_reverse_comm(int n, int *list, double *buf)
double ComputePETally::compute_scalar()
{
invoked_scalar = update->ntimestep;
- if ((did_compute != invoked_scalar) || (update->eflag_global != invoked_scalar))
+ if ((did_setup != invoked_scalar)
+ || (update->eflag_global != invoked_scalar))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated energies across procs
@@ -180,13 +177,16 @@ double ComputePETally::compute_scalar()
void ComputePETally::compute_peratom()
{
invoked_peratom = update->ntimestep;
- if ((did_compute != invoked_peratom) || (update->eflag_global != invoked_peratom))
+ if ((did_setup != invoked_peratom)
+ || (update->eflag_global != invoked_peratom))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
if (force->newton_pair) {
comm->reverse_comm_compute(this);
+
+ // clear out ghost atom data after it has been collected to local atoms
const int nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; ++i)
eatom[i][0] = eatom[i][1] = 0.0;
diff --git a/src/USER-TALLY/compute_pe_tally.h b/src/USER-TALLY/compute_pe_tally.h
index 2335bbeceeac278d45e9f62bfe8868a868a8071d..cd972e49dba3d0afce0e9387c7e0a461a9b1e881 100644
--- a/src/USER-TALLY/compute_pe_tally.h
+++ b/src/USER-TALLY/compute_pe_tally.h
@@ -39,12 +39,13 @@ class ComputePETally : public Compute {
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
+ void pair_setup_callback(int, int);
void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double);
private:
- bigint did_compute;
+ bigint did_setup;
int nmax,igroup2,groupbit2;
double **eatom;
double etotal[2];
diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp
index 66df9f6e4ffc28d9dc68587e1393c03a7caf3f34..28baafb9f8f451f37771ea84d3e4a1b432fcb62f 100644
--- a/src/USER-TALLY/compute_stress_tally.cpp
+++ b/src/USER-TALLY/compute_stress_tally.cpp
@@ -44,11 +44,11 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) :
extscalar = 0;
peflag = 1; // we need Pair::ev_tally() to be run
- did_compute = 0;
- invoked_peratom = invoked_scalar = -1;
+ did_setup = invoked_peratom = invoked_scalar = -1;
nmax = -1;
stress = NULL;
vector = new double[size_peratom_cols];
+ virial = new double[size_peratom_cols];
}
/* ---------------------------------------------------------------------- */
@@ -57,6 +57,7 @@ ComputeStressTally::~ComputeStressTally()
{
if (force && force->pair) force->pair->del_tally_callback(this);
memory->destroy(stress);
+ delete[] virial;
delete[] vector;
}
@@ -69,55 +70,50 @@ void ComputeStressTally::init()
else
force->pair->add_tally_callback(this);
- if (force->pair->single_enable == 0 || force->pair->manybody_flag)
- error->warning(FLERR,"Compute stress/tally used with incompatible pair style");
+ if (comm->me == 0) {
+ if (force->pair->single_enable == 0 || force->pair->manybody_flag)
+ error->warning(FLERR,"Compute stress/tally used with incompatible pair style");
- if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
- || force->improper || force->kspace))
- error->warning(FLERR,"Compute stress/tally only called from pair style");
-
- did_compute = -1;
+ if (force->bond || force->angle || force->dihedral
+ || force->improper || force->kspace)
+ error->warning(FLERR,"Compute stress/tally only called from pair style");
+ }
+ did_setup = -1;
}
-
/* ---------------------------------------------------------------------- */
-void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newton,
- double, double, double fpair,
- double dx, double dy, double dz)
+
+void ComputeStressTally::pair_setup_callback(int, int)
{
const int ntotal = atom->nlocal + atom->nghost;
- const int * const mask = atom->mask;
- // do setup work that needs to be done only once per timestep
+ // grow per-atom storage, if needed
- if (did_compute != update->ntimestep) {
- did_compute = update->ntimestep;
+ if (atom->nmax > nmax) {
+ memory->destroy(stress);
+ nmax = atom->nmax;
+ memory->create(stress,nmax,size_peratom_cols,"stress/tally:stress");
+ array_atom = stress;
+ }
- // grow local stress array if necessary
- // needs to be atom->nmax in length
+ // clear storage
- if (atom->nmax > nmax) {
- memory->destroy(stress);
- nmax = atom->nmax;
- memory->create(stress,nmax,size_peratom_cols,"stress/tally:stress");
- array_atom = stress;
- }
+ for (int i=0; i < ntotal; ++i)
+ for (int j=0; j < size_peratom_cols; ++j)
+ stress[i][j] = 0.0;
- // clear storage as needed
+ for (int i=0; i < size_peratom_cols; ++i)
+ vector[i] = virial[i] = 0.0;
- if (newton) {
- for (int i=0; i < ntotal; ++i)
- for (int j=0; j < size_peratom_cols; ++j)
- stress[i][j] = 0.0;
- } else {
- for (int i=0; i < atom->nlocal; ++i)
- for (int j=0; j < size_peratom_cols; ++j)
- stress[i][j] = 0.0;
- }
+ did_setup = update->ntimestep;
+}
- for (int i=0; i < size_peratom_cols; ++i)
- vector[i] = virial[i] = 0.0;
- }
+/* ---------------------------------------------------------------------- */
+void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newton,
+ double, double, double fpair,
+ double dx, double dy, double dz)
+{
+ const int * const mask = atom->mask;
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
@@ -191,7 +187,8 @@ void ComputeStressTally::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeStressTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
- if ((did_compute != invoked_scalar) || (update->eflag_global != invoked_scalar))
+ if ((did_setup != invoked_scalar)
+ || (update->eflag_global != invoked_scalar))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated forces across procs
@@ -211,7 +208,8 @@ double ComputeStressTally::compute_scalar()
void ComputeStressTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
- if ((did_compute != invoked_peratom) || (update->eflag_global != invoked_peratom))
+ if ((did_setup != invoked_peratom)
+ || (update->eflag_global != invoked_peratom))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
diff --git a/src/USER-TALLY/compute_stress_tally.h b/src/USER-TALLY/compute_stress_tally.h
index a677d2eef6b58909a104e272af70e9493df8e79c..22f27a4a41b4e04953b20a61b6f311e1e9b9d9b7 100644
--- a/src/USER-TALLY/compute_stress_tally.h
+++ b/src/USER-TALLY/compute_stress_tally.h
@@ -39,15 +39,16 @@ class ComputeStressTally : public Compute {
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
+ void pair_setup_callback(int, int);
void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double);
private:
- bigint did_compute;
+ bigint did_setup;
int nmax,igroup2,groupbit2;
double **stress;
- double virial[6];
+ double *virial;
};
}
diff --git a/src/compute.h b/src/compute.h
index 7f12cd97e20d1c25b5d6b4e9eddffd81cd2657a5..8fd3880aa71f112ae9b69f012b3ea64f1bacd8dc 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -135,6 +135,7 @@ class Compute : protected Pointers {
virtual double memory_usage() {return 0.0;}
+ virtual void pair_setup_callback(int, int) {}
virtual void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double) {}
diff --git a/src/pair.cpp b/src/pair.cpp
index d90ed8bb43a90e422dccf6b39a296b092d2e938f..06792060ce507ad32ee9c97fd2481c47ca8a2a7d 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -814,6 +814,16 @@ void Pair::ev_setup(int eflag, int vflag, int alloc)
if (vflag_atom == 0) vflag_either = 0;
if (vflag_either == 0 && eflag_either == 0) evflag = 0;
} else vflag_fdotr = 0;
+
+
+ // run ev_setup option for USER-TALLY computes
+
+ if (num_tally_compute > 0) {
+ for (int k=0; k < num_tally_compute; ++k) {
+ Compute *c = list_tally_compute[k];
+ c->pair_setup_callback(eflag,vflag);
+ }
+ }
}
/* ----------------------------------------------------------------------