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Commit 7a05d87f authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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update USER-TALLY examples

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examples/USER/tally/log.21Aug15.force.1 → examples/USER/tally/log.12Jun17.force.1
+ 177
− 0
View file @ 7a05d87f
LAMMPS (21 Aug 2015-ICMS)
using 1 OpenMP thread(s) per MPI task
LAMMPS (19 May 2017)
units real
atom_style full
......@@ -50,10 +49,39 @@ 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 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 pe/tally compute and other computes and thermo keywords
# 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
......@@ -69,17 +97,19 @@ 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 c_c2
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
......@@ -87,38 +117,49 @@ PPPM initialization ...
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)
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 ...
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 = 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:
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 | 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
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
......@@ -127,10 +168,10 @@ 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: 0:00:15
examples/USER/tally/log.21Aug15.force.4 → examples/USER/tally/log.12Jun17.force.4
+ 177
− 0
View file @ 7a05d87f
LAMMPS (21 Aug 2015-ICMS)
using 1 OpenMP thread(s) per MPI task
LAMMPS (19 May 2017)
units real
atom_style full
......@@ -50,10 +49,39 @@ 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 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 pe/tally compute and other computes and thermo keywords
# 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
......@@ -69,17 +97,19 @@ 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 c_c2
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
......@@ -87,38 +117,49 @@ PPPM initialization ...
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)
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 ...
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 = 8.16441 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:
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 | 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
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
......@@ -127,10 +168,10 @@ 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: 0:00:04
examples/USER/tally/log.21Aug15.pe.1 → examples/USER/tally/log.12Jun17.pe.1
+ 71
− 31
View file @ 7a05d87f
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
examples/USER/tally/log.21Aug15.pe.4 → examples/USER/tally/log.12Jun17.pe.4
+ 71
− 31
View file @ 7a05d87f
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
examples/USER/tally/log.21Aug15.stress.1 → examples/USER/tally/log.12Jun17.stress.1
+ 56
− 33
View file @ 7a05d87f
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
examples/USER/tally/log.21Aug15.stress.4 → examples/USER/tally/log.12Jun17.stress.4
+ 57
− 34
View file @ 7a05d87f
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
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