LAMMPS (15 May 2015) Reading data file ... orthogonal box = (0 0 0) to (61.2 61.2 100) 2 by 2 by 2 MPI processor grid reading atoms ... 5000 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 15 = max dihedrals/atom reading bonds ... 4900 bonds reading angles ... 9600 angles reading dihedrals ... 13500 dihedrals Finding 1-2 1-3 1-4 neighbors ... Special bond factors lj: 0 0 0.5 Special bond factors coul: 0 0 0.5 4 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 12 = max # of 1-4 neighbors 16 = max # of special neighbors Setting atom values ... 200 settings made for charge Setting atom values ... 1400 settings made for charge Setting atom values ... 3400 settings made for charge Setting atom values ... 0 settings made for charge Lattice spacing in x,y,z = 4.08 4.08 4.08 Created 5850 atoms Created 5850 atoms 5850 atoms in group lower_g 5850 atoms in group upper_g 11700 atoms in group wall_g 5000 atoms in group flow_g WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) PPPM initialization ... G vector (1/distance) = 0.134852 grid = 8 8 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0236931 estimated relative force accuracy = 7.1351e-05 using double precision FFTs 3d grid and FFT values/proc = 3402 640 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes master list distance cutoff = 14 Setting up minimization ... Memory usage per processor = 15.2909 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 2524454.4 447.38169 2524901.7 2033351.6 118 0 -243035.78 203.36648 -242832.41 6536.7374 Loop time of 5.7782 on 8 procs for 118 steps with 16700 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 2524901.74856 -242832.239418 -242832.413451 Force two-norm initial, final = 6.37283e+07 32.3411 Force max component initial, final = 3.19506e+07 4.33021 Final line search alpha, max atom move = 0.00837535 0.036267 Iterations, force evaluations = 118 224 Pair time (%) = 4.2575 (73.6821) Bond time (%) = 0.271671 (4.70166) Kspce time (%) = 1.06643 (18.4561) Neigh time (%) = 0.0329494 (0.570236) Comm time (%) = 0.0930012 (1.60952) Outpt time (%) = 0 (0) Other time (%) = 0.0566486 (0.980385) Nlocal: 2087.5 ave 2176 max 2016 min Histogram: 2 1 1 0 0 1 1 0 1 1 Nghost: 7531.75 ave 7588 max 7476 min Histogram: 2 1 0 0 0 1 1 1 1 1 Neighs: 627460 ave 726014 max 541190 min Histogram: 3 1 0 0 0 0 0 1 1 2 Total # of neighbors = 5019679 Ave neighs/atom = 300.58 Ave special neighs/atom = 3.35329 Neighbor list builds = 1 Dangerous builds = 0 PPPM initialization ... G vector (1/distance) = 0.134852 grid = 8 8 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0236931 estimated relative force accuracy = 7.1351e-05 using double precision FFTs 3d grid and FFT values/proc = 3402 640 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 10 steps, check yes master list distance cutoff = 14 Setting up run ... Memory usage per processor = 15.2909 Mbytes Step thermo_f thermo_v thermo_v h_wall h_channe density_ mass_flo PotEng KinEng TotEng diss_ene diss_ene diss_ene 118 300 0 0 55.08 26.107187 0.23158241 22644.8 -242832.41 4470.3208 -238362.09 -0 -0 -0 218 226.66079 170.97213 166.07337 55.079915 26.284413 0.23002093 22644.8 -243457.8 5335.5913 -238122.2 -1969.7763 -1927.7489 -1962.0387 Loop time of 2.09156 on 8 procs for 100 steps with 16700 atoms Pair time (%) = 1.43245 (68.4872) Bond time (%) = 0.12146 (5.80712) Kspce time (%) = 0.440685 (21.0696) Neigh time (%) = 0 (0) Comm time (%) = 0.0417227 (1.99481) Outpt time (%) = 0.000359327 (0.0171798) Other time (%) = 0.0548837 (2.62405) Nlocal: 2087.5 ave 2177 max 2016 min Histogram: 2 1 1 0 0 1 1 0 1 1 Nghost: 7529.75 ave 7582 max 7474 min Histogram: 2 1 0 0 0 1 1 0 2 1 Neighs: 627681 ave 726661 max 541049 min Histogram: 3 1 0 0 0 0 0 1 1 2 Total # of neighbors = 5021447 Ave neighs/atom = 300.685 Ave special neighs/atom = 3.35329 Neighbor list builds = 0 Dangerous builds = 0 Steady state run starting... PPPM initialization ... G vector (1/distance) = 0.134852 grid = 8 8 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0236931 estimated relative force accuracy = 7.1351e-05 using double precision FFTs 3d grid and FFT values/proc = 3402 640 Setting up run ... Memory usage per processor = 15.1969 Mbytes Step thermo_f thermo_v thermo_v h_wall h_channe density_ mass_flo PotEng KinEng TotEng diss_ene diss_ene friction 0 226.66079 170.97213 166.07337 55.079915 26.284413 0.23002093 22644.8 -237598.23 6024.0798 -231574.15 -0 -0 3.5046843e-06 100 211.65824 262.34572 256.48817 55.079657 26.585379 0.22741693 22644.8 -238408.91 6856.656 -231552.26 -955.49719 -984.63687 3.5886156e-06 Loop time of 2.15083 on 8 procs for 100 steps with 16700 atoms Pair time (%) = 1.46412 (68.0724) Bond time (%) = 0.123882 (5.75974) Kspce time (%) = 0.473767 (22.0271) Neigh time (%) = 0 (0) Comm time (%) = 0.0425639 (1.97895) Outpt time (%) = 0.000422955 (0.0196647) Other time (%) = 0.0460728 (2.14209) Nlocal: 2087.5 ave 2184 max 2011 min Histogram: 2 1 0 1 0 2 0 0 1 1 Nghost: 7534.75 ave 7579 max 7477 min Histogram: 3 0 0 0 0 0 0 1 1 3 Neighs: 627957 ave 728876 max 544015 min Histogram: 3 1 0 0 0 0 1 0 1 2 Total # of neighbors = 5023659 Ave neighs/atom = 300.818 Ave special neighs/atom = 3.35329 Neighbor list builds = 0 Dangerous builds = 0 Production run starting... ERROR: Invalid thermo keyword in variable formula (../variable.cpp:1716) [laptop:05735] *** Process received signal *** [laptop:05736] *** Process received signal *** [laptop:05738] *** Process received signal *** [laptop:05738] Signal: Segmentation fault (11) [laptop:05738] Signal code: (128) [laptop:05738] Failing at address: (nil) [laptop:05731] *** Process received signal *** [laptop:05731] Signal: Segmentation fault (11) [laptop:05731] Signal code: (128) [laptop:05731] Failing at address: (nil) [laptop:05732] *** Process received signal *** [laptop:05732] Signal: Segmentation fault (11) [laptop:05732] Signal code: (128) [laptop:05732] Failing at address: (nil) [laptop:05733] *** Process received signal *** [laptop:05733] Signal: Segmentation fault (11) [laptop:05733] Signal code: (128) [laptop:05733] Failing at address: (nil) [laptop:05734] *** Process received signal *** [laptop:05734] Signal: Segmentation fault (11) [laptop:05734] Signal code: (128) [laptop:05734] Failing at address: (nil) [laptop:05736] Signal: Segmentation fault (11) [laptop:05736] Signal code: (128) [laptop:05736] Failing at address: (nil) [laptop:05735] Signal: Segmentation fault (11) [laptop:05735] Signal code: (128) [laptop:05735] Failing at address: (nil) [laptop:05737] *** Process received signal *** [laptop:05737] Signal: Segmentation fault (11) [laptop:05737] Signal code: (128) [laptop:05737] Failing at address: (nil) [laptop:05738] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f0abfc59340] [laptop:05738] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7f0ac0709086] [laptop:05738] [ 2] lmp() [0x502316] [laptop:05738] [ 3] lmp() [0x64aabf] [laptop:05738] [ 4] lmp() [0x64ab79] [laptop:05738] [ 5] lmp() [0x502675] [laptop:05738] [ 6] lmp() [0x82aefe] [laptop:05731] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fa04815c340] [laptop:05731] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7fa048c0c086] [laptop:05731] [ 2] lmp() [0x502316] [laptop:05731] [ 3] lmp() [0x64aabf] [laptop:05731] [ 4] lmp() [0x64ab79] [laptop:05731] [ 5] lmp() [0x502675] [laptop:05731] [ 6] lmp() [0x82aefe] [laptop:05731] [ 7] lmp() [0x5d1e77] [laptop:05731] [ 8] lmp() [0x5d22ea] [laptop:05732] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f9958d26340] [laptop:05732] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7f99597d6086] [laptop:05732] [ 2] lmp() [0x502316] [laptop:05732] [ 3] lmp() [0x64aabf] [laptop:05732] [ 4] lmp() [0x64ab79] [laptop:05732] [ 5] lmp() [0x502675] [laptop:05732] [ 6] lmp() [0x82aefe] [laptop:05732] [ 7] lmp() [0x5d1e77] [laptop:05732] [ 8] lmp() [0x5d22ea] [laptop:05732] [ 9] lmp() [0x5d9848] [laptop:05733] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fb97b4de340] [laptop:05735] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fbaea47a340] [laptop:05735] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7fbaeaf2a086] [laptop:05735] [ 2] lmp() [0x502316] [laptop:05735] [ 3] lmp() [0x64aabf] [laptop:05735] [ 4] lmp() [0x64ab79] [laptop:05735] [ 5] lmp() [0x502675] [laptop:05735] [ 6] lmp() [0x82aefe] [laptop:05735] [ 7] lmp() [0x5d1e77] [laptop:05735] [ 8] lmp() [0x5d22ea] [laptop:05735] [ 9] lmp() [0x5d9848] [laptop:05735] [10] lmp() [0x405af6] [laptop:05735] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fbaea0c6ec5] [laptop:05734] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fcc5f443340] [laptop:05734] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7fcc5fef3086] [laptop:05734] [ 2] lmp() [0x502316] [laptop:05734] [ 3] lmp() [0x64aabf] [laptop:05734] [ 4] lmp() [0x64ab79] [laptop:05734] [ 5] lmp() [0x502675] [laptop:05734] [ 6] lmp() [0x82aefe] [laptop:05734] [ 7] lmp() [0x5d1e77] [laptop:05734] [ 8] lmp() [0x5d22ea] [laptop:05734] [ 9] lmp() [0x5d9848] [laptop:05734] [10] lmp() [0x405af6] [laptop:05734] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fcc5f08fec5] [laptop:05734] [12] lmp() [0x405b5a] [laptop:05734] *** End of error message *** [laptop:05738] [ 7] lmp() [0x5d1e77] [laptop:05738] [ 8] lmp() [0x5d22ea] [laptop:05738] [ 9] lmp() [0x5d9848] [laptop:05738] [10] lmp() [0x405af6] [laptop:05738] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f0abf8a5ec5] [laptop:05738] [12] lmp() [0x405b5a] [laptop:05738] *** End of error message *** [laptop:05731] [ 9] lmp() [0x5d9848] [laptop:05731] [10] lmp() [0x405af6] [laptop:05731] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fa047da8ec5] [laptop:05731] [12] lmp() [0x405b5a] [laptop:05731] *** End of error message *** [laptop:05732] [10] lmp() [0x405af6] [laptop:05732] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f9958972ec5] [laptop:05732] [12] lmp() [0x405b5a] [laptop:05732] *** End of error message *** [laptop:05736] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f38f3a09340] [laptop:05736] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7f38f44b9086] [laptop:05736] [ 2] lmp() [0x502316] [laptop:05736] [ 3] lmp() [0x64aabf] [laptop:05736] [ 4] lmp() [0x64ab79] [laptop:05736] [ 5] lmp() [0x502675] [laptop:05736] [ 6] lmp() [0x82aefe] [laptop:05736] [ 7] lmp() [0x5d1e77] [laptop:05736] [ 8] lmp() [0x5d22ea] [laptop:05736] [ 9] lmp() [0x5d9848] [laptop:05736] [10] lmp() [0x405af6] [laptop:05736] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f38f3655ec5] [laptop:05736] [12] lmp() [0x405b5a] [laptop:05736] *** End of error message *** [laptop:05735] [12] lmp() [0x405b5a] [laptop:05735] *** End of error message *** [laptop:05733] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7fb97bf8e086] [laptop:05737] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f4d7e5fe340] [laptop:05737] [ 1] /usr/lib/libmpi.so.1(PMPI_File_close+0x56) [0x7f4d7f0ae086] [laptop:05737] [ 2] lmp() [0x502316] [laptop:05737] [ 3] lmp() [0x64aabf] [laptop:05737] [ 4] lmp() [0x64ab79] [laptop:05737] [ 5] lmp() [0x502675] [laptop:05737] [ 6] lmp() [0x82aefe] [laptop:05737] [ 7] lmp() [0x5d1e77] [laptop:05737] [ 8] lmp() [0x5d22ea] [laptop:05737] [ 9] lmp() [0x5d9848] [laptop:05737] [10] lmp() [0x405af6] [laptop:05737] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f4d7e24aec5] [laptop:05737] [12] lmp() [0x405b5a] [laptop:05737] *** End of error message *** [laptop:05733] [ 2] lmp() [0x502316] [laptop:05733] [ 3] lmp() [0x64aabf] [laptop:05733] [ 4] lmp() [0x64ab79] [laptop:05733] [ 5] lmp() [0x502675] [laptop:05733] [ 6] lmp() [0x82aefe] [laptop:05733] [ 7] lmp() [0x5d1e77] [laptop:05733] [ 8] lmp() [0x5d22ea] [laptop:05733] [ 9] lmp() [0x5d9848] [laptop:05733] [10] lmp() [0x405af6] [laptop:05733] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fb97b12aec5] [laptop:05733] [12] lmp() [0x405b5a] [laptop:05733] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 6 with PID 5737 on node laptop exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- 7 total processes killed (some possibly by mpirun during cleanup)