Loading examples/USER/awpmd/in.h_atom +1 −2 Original line number Diff line number Diff line variable sname index h_atom log ${sname}.spe.log units real newton on Loading Loading @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press run 0 run 10 examples/USER/awpmd/in.h_molecule +1 −2 Original line number Diff line number Diff line variable sname index h_molecule log ${sname}.spe.log units real newton on Loading Loading @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press run 0 run 10 examples/USER/bocs/log.20Apr18.methanol.g++.1→examples/USER/bocs/log.27Nov18.methanol.g++.1 +36 −37 Original line number Diff line number Diff line LAMMPS (20 Apr 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 Loading @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:481) Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin Loading Loading @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467 5500 292.23444 1029.5558 1871.905 20.764579 66683.876 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385 9500 297.46127 1034.5547 1891.97 54.23428 66892.627 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506 Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 2500 305.51905 1051.59 1932.2314 -34.076658 66487.327 3000 291.76224 1053.524 1894.5121 45.522865 65879.535 3500 297.65795 1017.1028 1875.085 -79.41965 67185.19 4000 285.98779 1042.3622 1866.7058 88.549172 66357.051 4500 295.35 1071.4505 1922.7801 -16.75965 65378.949 5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38 5500 292.40422 1085.3901 1928.2287 161.88502 65677.644 6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05 6500 308.03807 1046.1413 1934.0436 249.70237 66052.045 7000 289.33716 1037.9657 1871.9636 47.662734 66782.578 7500 297.3092 1032.356 1889.3329 -24.049617 66129.95 8000 298.27827 1044.118 1903.8882 -26.61809 66720.381 8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559 9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4 9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848 10000 309.9256 1043.5321 1936.875 -103.81403 66222.21 Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 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 | 33.324 | 33.324 | 33.324 | 0.0 | 96.80 Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35 Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25 Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00 Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24 Other | | 0.1252 | | | 0.36 Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39 Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44 Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68 Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00 Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25 Other | | 0.1042 | | | 0.25 Nlocal: 968 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9112 ave 9112 max 9112 min Nghost: 9215 ave 9215 max 9215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 404392 ave 404392 max 404392 min Neighs: 411837 ave 411837 max 411837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404392 Ave neighs/atom = 417.76 Total # of neighbors = 411837 Ave neighs/atom = 425.451 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:34 Total wall time: 0:00:42 examples/USER/bocs/log.20Apr18.methanol.g++.4→examples/USER/bocs/log.27Nov18.methanol.g++.4 +43 −44 Original line number Diff line number Diff line LAMMPS (20 Apr 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 Loading @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:481) Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin Loading Loading @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576 Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s 95.2% CPU use with 4 MPI tasks x 1 OpenMP threads 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 2500 305.51905 1051.59 1932.2314 -34.076657 66487.327 3000 291.76224 1053.524 1894.5121 45.522919 65879.535 3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183 4000 285.99141 1042.379 1866.733 88.735986 66356.756 4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597 5000 292.47 1012.3769 1855.405 -255.07433 67527.215 5500 294.04431 1080.4547 1928.0208 192.6588 65811.742 6000 300.45893 986.16669 1852.2225 -167.3405 67858.175 6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704 7000 312.11968 1032.7392 1932.4065 152.17956 66016.299 7500 306.80585 1032.1157 1916.4662 51.07705 66875.727 8000 292.30957 1048.9003 1891.4661 61.280503 65894.103 8500 297.79592 1013.4061 1871.786 -133.01136 66842.574 9000 290.36753 1043.7732 1880.7412 65.208248 66010.86 9500 288.92211 1077.8835 1910.6851 46.291982 65674.639 10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692 Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56 Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25 Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16 Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01 Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95 Other | | 0.3112 | | | 1.08 Nlocal: 242 ave 244 max 239 min Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35 Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33 Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42 Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02 Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28 Other | | 0.08323 | | | 0.60 Nlocal: 242 ave 248 max 232 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 5718.5 ave 5736 max 5702 min Histogram: 1 0 0 0 1 1 0 0 0 1 Neighs: 100703 ave 108064 max 93454 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 402813 Ave neighs/atom = 416.129 Neighbor list builds = 14 Nghost: 5845.75 ave 5877 max 5808 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 104313 ave 113860 max 95507 min Histogram: 1 1 0 0 0 0 0 1 0 1 Total # of neighbors = 417252 Ave neighs/atom = 431.045 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:28 Total wall time: 0:00:14 examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1→examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 +1 −1 Original line number Diff line number Diff line Loading @@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" run 1000000 run 10000 #write_restart config.${number}.* Loading
examples/USER/awpmd/in.h_atom +1 −2 Original line number Diff line number Diff line variable sname index h_atom log ${sname}.spe.log units real newton on Loading Loading @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press run 0 run 10
examples/USER/awpmd/in.h_molecule +1 −2 Original line number Diff line number Diff line variable sname index h_molecule log ${sname}.spe.log units real newton on Loading Loading @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press run 0 run 10
examples/USER/bocs/log.20Apr18.methanol.g++.1→examples/USER/bocs/log.27Nov18.methanol.g++.1 +36 −37 Original line number Diff line number Diff line LAMMPS (20 Apr 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 Loading @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:481) Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin Loading Loading @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467 5500 292.23444 1029.5558 1871.905 20.764579 66683.876 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385 9500 297.46127 1034.5547 1891.97 54.23428 66892.627 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506 Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 2500 305.51905 1051.59 1932.2314 -34.076658 66487.327 3000 291.76224 1053.524 1894.5121 45.522865 65879.535 3500 297.65795 1017.1028 1875.085 -79.41965 67185.19 4000 285.98779 1042.3622 1866.7058 88.549172 66357.051 4500 295.35 1071.4505 1922.7801 -16.75965 65378.949 5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38 5500 292.40422 1085.3901 1928.2287 161.88502 65677.644 6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05 6500 308.03807 1046.1413 1934.0436 249.70237 66052.045 7000 289.33716 1037.9657 1871.9636 47.662734 66782.578 7500 297.3092 1032.356 1889.3329 -24.049617 66129.95 8000 298.27827 1044.118 1903.8882 -26.61809 66720.381 8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559 9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4 9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848 10000 309.9256 1043.5321 1936.875 -103.81403 66222.21 Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 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 | 33.324 | 33.324 | 33.324 | 0.0 | 96.80 Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35 Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25 Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00 Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24 Other | | 0.1252 | | | 0.36 Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39 Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44 Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68 Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00 Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25 Other | | 0.1042 | | | 0.25 Nlocal: 968 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9112 ave 9112 max 9112 min Nghost: 9215 ave 9215 max 9215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 404392 ave 404392 max 404392 min Neighs: 411837 ave 411837 max 411837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404392 Ave neighs/atom = 417.76 Total # of neighbors = 411837 Ave neighs/atom = 425.451 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:34 Total wall time: 0:00:42
examples/USER/bocs/log.20Apr18.methanol.g++.4→examples/USER/bocs/log.27Nov18.methanol.g++.4 +43 −44 Original line number Diff line number Diff line LAMMPS (20 Apr 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 Loading @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:481) Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin Loading Loading @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576 Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s 95.2% CPU use with 4 MPI tasks x 1 OpenMP threads 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 2500 305.51905 1051.59 1932.2314 -34.076657 66487.327 3000 291.76224 1053.524 1894.5121 45.522919 65879.535 3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183 4000 285.99141 1042.379 1866.733 88.735986 66356.756 4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597 5000 292.47 1012.3769 1855.405 -255.07433 67527.215 5500 294.04431 1080.4547 1928.0208 192.6588 65811.742 6000 300.45893 986.16669 1852.2225 -167.3405 67858.175 6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704 7000 312.11968 1032.7392 1932.4065 152.17956 66016.299 7500 306.80585 1032.1157 1916.4662 51.07705 66875.727 8000 292.30957 1048.9003 1891.4661 61.280503 65894.103 8500 297.79592 1013.4061 1871.786 -133.01136 66842.574 9000 290.36753 1043.7732 1880.7412 65.208248 66010.86 9500 288.92211 1077.8835 1910.6851 46.291982 65674.639 10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692 Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56 Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25 Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16 Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01 Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95 Other | | 0.3112 | | | 1.08 Nlocal: 242 ave 244 max 239 min Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35 Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33 Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42 Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02 Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28 Other | | 0.08323 | | | 0.60 Nlocal: 242 ave 248 max 232 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 5718.5 ave 5736 max 5702 min Histogram: 1 0 0 0 1 1 0 0 0 1 Neighs: 100703 ave 108064 max 93454 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 402813 Ave neighs/atom = 416.129 Neighbor list builds = 14 Nghost: 5845.75 ave 5877 max 5808 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 104313 ave 113860 max 95507 min Histogram: 1 1 0 0 0 0 0 1 0 1 Total # of neighbors = 417252 Ave neighs/atom = 431.045 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:28 Total wall time: 0:00:14
examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1→examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 +1 −1 Original line number Diff line number Diff line Loading @@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" run 1000000 run 10000 #write_restart config.${number}.*
