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