Loading examples/qeq/ffield.reax.cho 100755 → 100644 +0 −0 File mode changed from 100755 to 100644. View file examples/qeq/log.5Oct16.qeq.buck.g++.1→examples/qeq/log.27Nov18.qeq.buck.g++.1 +37 −25 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long Loading @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 1 by 1 MPI processor grid 9600 atoms Time spent = 0.00114894 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 Loading Loading @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 binsize = 6.5 -> bins = 8 8 9 Memory usage per processor = 110.875 Mbytes binsize = 6.5, bins = 8 8 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair buck/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) fix qeq/fire, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64960264 20 -27975.085 0.85968531 -0.42984266 -8.8220986e-11 0.55300005 30 -28552.628 0.86755661 -0.4337783 1.4142643e-10 0.52434987 40 -29133.643 0.87426387 -0.43713193 1.6871127e-10 0.52326849 50 -29697.011 0.8794039 -0.43970195 1.2460077e-10 0.52083626 60 -30342.001 0.88478594 -0.44239297 -4.3655746e-11 0.52824882 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.56010601 80 -31792.732 0.89506635 -0.44753317 -3.774403e-11 0.60040973 90 -32424.749 0.89714841 -0.44857421 -1.0004442e-10 0.57758717 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59560798 Loop time of 178.401 on 1 procs for 100 steps with 9600 atoms 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877 20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179 30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643 40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341 50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127 60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546 80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079 90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001 Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms Performance: 0.005 ns/day, 4955.597 hours/ns, 0.561 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.042 | 15.042 | 15.042 | 0.0 | 8.43 Kspace | 98.245 | 98.245 | 98.245 | 0.0 | 55.07 Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48 Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019511 | 0.019511 | 0.019511 | 0.0 | 0.01 Output | 0.0020375 | 0.0020375 | 0.0020375 | 0.0 | 0.00 Modify | 65.083 | 65.083 | 65.083 | 0.0 | 36.48 Other | | 0.009152 | | | 0.01 Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01 Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00 Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11 Other | | 0.007197 | | | 0.00 Nlocal: 9600 ave 9600 max 9600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:03:02 Total wall time: 0:03:01 examples/qeq/log.5Oct16.qeq.buck.g++.4→examples/qeq/log.27Nov18.qeq.buck.g++.4 +37 −25 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long Loading @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 2 by 2 MPI processor grid 9600 atoms Time spent = 0.000675201 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 Loading Loading @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 binsize = 6.5 -> bins = 8 8 9 Memory usage per processor = 46.867 Mbytes binsize = 6.5, bins = 8 8 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair buck/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) fix qeq/fire, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.561772 20 -27975.085 0.85968531 -0.42984266 9.777068e-11 2.1470405 30 -28552.627 0.86755661 -0.4337783 1.2823875e-10 2.0585052 40 -29133.643 0.87426387 -0.43713193 1.5506885e-10 2.0319632 50 -29697.01 0.8794039 -0.43970195 2.1873348e-10 2.0350244 60 -30342 0.88478594 -0.44239297 1.891749e-10 2.0793976 70 -31081.139 0.89069733 -0.44534866 1.4688339e-10 2.1759002 80 -31792.732 0.89506635 -0.44753317 1.4142643e-10 2.3320978 90 -32424.752 0.89714841 -0.44857421 9.9134922e-11 2.2673305 100 -32998.353 0.89755721 -0.44877861 1.5097612e-10 2.3389389 Loop time of 45.6331 on 4 procs for 100 steps with 9600 atoms 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312 20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316 30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335 40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139 50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263 60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722 70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406 80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813 90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145 100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486 Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms Performance: 0.019 ns/day, 1267.586 hours/ns, 2.191 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s 97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8297 | 3.8983 | 3.938 | 2.1 | 8.54 Kspace | 24.434 | 24.579 | 24.78 | 2.9 | 53.86 Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22 Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.078239 | 0.31795 | 0.53069 | 30.8 | 0.70 Output | 0.00097322 | 0.0010365 | 0.0011294 | 0.2 | 0.00 Modify | 16.831 | 16.832 | 16.832 | 0.0 | 36.88 Other | | 0.005259 | | | 0.01 Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75 Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00 Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03 Other | | 0.01409 | | | 0.03 Nlocal: 2400 ave 2400 max 2400 min Histogram: 4 0 0 0 0 0 0 0 0 0 Loading @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:46 Total wall time: 0:00:49 examples/qeq/log.5Oct16.qeq.reaxc.g++.1→examples/qeq/log.27Nov18.qeq.reaxc.g++.1 +23 −12 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # Loading Loading @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5 -> bins = 5 5 5 Memory usage per processor = 15.8004 Mbytes binsize = 5.5, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16 1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15 Loading @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15 9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16 10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15 Loop time of 0.0398569 on 1 procs for 10 steps with 105 atoms Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms Performance: 5.419 ns/day, 4.429 hours/ns, 250.898 timesteps/s 100.3% CPU use with 1 MPI tasks x no OpenMP threads Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034917 | 0.034917 | 0.034917 | 0.0 | 87.61 Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.2663e-05 | 3.2663e-05 | 3.2663e-05 | 0.0 | 0.08 Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.43 Modify | 0.0047123 | 0.0047123 | 0.0047123 | 0.0 | 11.82 Other | | 2.527e-05 | | | 0.06 Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16 Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85 Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57 Other | | 2.694e-05 | | | 0.08 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading examples/qeq/log.5Oct16.qeq.reaxc.g++.4→examples/qeq/log.27Nov18.qeq.reaxc.g++.4 +23 −12 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # Loading Loading @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5 -> bins = 5 5 5 Memory usage per processor = 11.6046 Mbytes binsize = 5.5, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15 1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15 Loading @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16 9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16 10 -10186.168 0.095747223 -0.15684634 -0.091183742 0 Loop time of 0.0217528 on 4 procs for 10 steps with 105 atoms Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms Performance: 9.930 ns/day, 2.417 hours/ns, 459.710 timesteps/s 93.1% CPU use with 4 MPI tasks x no OpenMP threads Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s 92.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012203 | 0.014022 | 0.015427 | 1.0 | 64.46 Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011754 | 0.0015323 | 0.0033445 | 3.0 | 7.04 Output | 0.00041366 | 0.00044626 | 0.00048447 | 0.1 | 2.05 Modify | 0.0056725 | 0.0056758 | 0.0056815 | 0.0 | 26.09 Other | | 7.629e-05 | | | 0.35 Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45 Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50 Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27 Other | | 0.0002902 | | | 1.57 Nlocal: 26.25 ave 35 max 15 min Histogram: 1 0 0 1 0 0 0 0 0 2 Loading Loading
examples/qeq/ffield.reax.cho 100755 → 100644 +0 −0 File mode changed from 100755 to 100644. View file
examples/qeq/log.5Oct16.qeq.buck.g++.1→examples/qeq/log.27Nov18.qeq.buck.g++.1 +37 −25 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long Loading @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 1 by 1 MPI processor grid 9600 atoms Time spent = 0.00114894 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 Loading Loading @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 binsize = 6.5 -> bins = 8 8 9 Memory usage per processor = 110.875 Mbytes binsize = 6.5, bins = 8 8 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair buck/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) fix qeq/fire, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64960264 20 -27975.085 0.85968531 -0.42984266 -8.8220986e-11 0.55300005 30 -28552.628 0.86755661 -0.4337783 1.4142643e-10 0.52434987 40 -29133.643 0.87426387 -0.43713193 1.6871127e-10 0.52326849 50 -29697.011 0.8794039 -0.43970195 1.2460077e-10 0.52083626 60 -30342.001 0.88478594 -0.44239297 -4.3655746e-11 0.52824882 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.56010601 80 -31792.732 0.89506635 -0.44753317 -3.774403e-11 0.60040973 90 -32424.749 0.89714841 -0.44857421 -1.0004442e-10 0.57758717 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59560798 Loop time of 178.401 on 1 procs for 100 steps with 9600 atoms 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877 20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179 30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643 40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341 50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127 60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546 80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079 90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001 Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms Performance: 0.005 ns/day, 4955.597 hours/ns, 0.561 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.042 | 15.042 | 15.042 | 0.0 | 8.43 Kspace | 98.245 | 98.245 | 98.245 | 0.0 | 55.07 Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48 Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019511 | 0.019511 | 0.019511 | 0.0 | 0.01 Output | 0.0020375 | 0.0020375 | 0.0020375 | 0.0 | 0.00 Modify | 65.083 | 65.083 | 65.083 | 0.0 | 36.48 Other | | 0.009152 | | | 0.01 Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01 Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00 Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11 Other | | 0.007197 | | | 0.00 Nlocal: 9600 ave 9600 max 9600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:03:02 Total wall time: 0:03:01
examples/qeq/log.5Oct16.qeq.buck.g++.4→examples/qeq/log.27Nov18.qeq.buck.g++.4 +37 −25 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long Loading @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 2 by 2 MPI processor grid 9600 atoms Time spent = 0.000675201 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 Loading Loading @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 binsize = 6.5 -> bins = 8 8 9 Memory usage per processor = 46.867 Mbytes binsize = 6.5, bins = 8 8 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair buck/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) fix qeq/fire, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.561772 20 -27975.085 0.85968531 -0.42984266 9.777068e-11 2.1470405 30 -28552.627 0.86755661 -0.4337783 1.2823875e-10 2.0585052 40 -29133.643 0.87426387 -0.43713193 1.5506885e-10 2.0319632 50 -29697.01 0.8794039 -0.43970195 2.1873348e-10 2.0350244 60 -30342 0.88478594 -0.44239297 1.891749e-10 2.0793976 70 -31081.139 0.89069733 -0.44534866 1.4688339e-10 2.1759002 80 -31792.732 0.89506635 -0.44753317 1.4142643e-10 2.3320978 90 -32424.752 0.89714841 -0.44857421 9.9134922e-11 2.2673305 100 -32998.353 0.89755721 -0.44877861 1.5097612e-10 2.3389389 Loop time of 45.6331 on 4 procs for 100 steps with 9600 atoms 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312 20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316 30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335 40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139 50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263 60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722 70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406 80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813 90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145 100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486 Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms Performance: 0.019 ns/day, 1267.586 hours/ns, 2.191 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s 97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8297 | 3.8983 | 3.938 | 2.1 | 8.54 Kspace | 24.434 | 24.579 | 24.78 | 2.9 | 53.86 Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22 Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.078239 | 0.31795 | 0.53069 | 30.8 | 0.70 Output | 0.00097322 | 0.0010365 | 0.0011294 | 0.2 | 0.00 Modify | 16.831 | 16.832 | 16.832 | 0.0 | 36.88 Other | | 0.005259 | | | 0.01 Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75 Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00 Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03 Other | | 0.01409 | | | 0.03 Nlocal: 2400 ave 2400 max 2400 min Histogram: 4 0 0 0 0 0 0 0 0 0 Loading @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:46 Total wall time: 0:00:49
examples/qeq/log.5Oct16.qeq.reaxc.g++.1→examples/qeq/log.27Nov18.qeq.reaxc.g++.1 +23 −12 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # Loading Loading @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5 -> bins = 5 5 5 Memory usage per processor = 15.8004 Mbytes binsize = 5.5, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16 1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15 Loading @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15 9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16 10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15 Loop time of 0.0398569 on 1 procs for 10 steps with 105 atoms Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms Performance: 5.419 ns/day, 4.429 hours/ns, 250.898 timesteps/s 100.3% CPU use with 1 MPI tasks x no OpenMP threads Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034917 | 0.034917 | 0.034917 | 0.0 | 87.61 Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.2663e-05 | 3.2663e-05 | 3.2663e-05 | 0.0 | 0.08 Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.43 Modify | 0.0047123 | 0.0047123 | 0.0047123 | 0.0 | 11.82 Other | | 2.527e-05 | | | 0.06 Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16 Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85 Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57 Other | | 2.694e-05 | | | 0.08 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading
examples/qeq/log.5Oct16.qeq.reaxc.g++.4→examples/qeq/log.27Nov18.qeq.reaxc.g++.4 +23 −12 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # Loading Loading @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5 -> bins = 5 5 5 Memory usage per processor = 11.6046 Mbytes binsize = 5.5, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15 1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15 Loading @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16 9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16 10 -10186.168 0.095747223 -0.15684634 -0.091183742 0 Loop time of 0.0217528 on 4 procs for 10 steps with 105 atoms Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms Performance: 9.930 ns/day, 2.417 hours/ns, 459.710 timesteps/s 93.1% CPU use with 4 MPI tasks x no OpenMP threads Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s 92.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012203 | 0.014022 | 0.015427 | 1.0 | 64.46 Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011754 | 0.0015323 | 0.0033445 | 3.0 | 7.04 Output | 0.00041366 | 0.00044626 | 0.00048447 | 0.1 | 2.05 Modify | 0.0056725 | 0.0056758 | 0.0056815 | 0.0 | 26.09 Other | | 7.629e-05 | | | 0.35 Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45 Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50 Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27 Other | | 0.0002902 | | | 1.57 Nlocal: 26.25 ave 35 max 15 min Histogram: 1 0 0 1 0 0 0 0 0 2 Loading
