using 8 OpenMP thread(s) per MPI task using multi-threaded neighbor list subroutines Reading restart file ... restart file = 29 Aug 2024, LAMMPS = 29 Aug 2024 restoring atom style full from restart orthogonal box = (-22.256144 -11.128072 -11.128072) to (22.256144 11.128072 11.128072) 1 by 1 by 1 MPI processor grid restoring pair style lj/cut/coul/long/omp from restart restoring bond style harmonic/omp from restart restoring angle style harmonic/omp from restart restoring dihedral style harmonic/omp from restart 2100 atoms 1400 bonds 700 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0.5 special bond factors coul: 0 0 1 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 15 = max # of special neighbors special bonds CPU = 0.001 seconds read_restart CPU = 0.005 seconds Read molecule template pegmol: PEG molecule 1 molecules 0 fragments 59 atoms with max type 6 58 bonds with max type 6 104 angles with max type 7 116 dihedrals with max type 4 0 impropers with max type 0 Created 59 atoms using lattice units in orthogonal box = (-22.256144 -11.128072 -11.128072) to (22.256144 11.128072 11.128072) create_atoms CPU = 0.000 seconds 59 atoms in group PEG System init for delete_atoms ... PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.30147332 grid = 32 20 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0034375004 estimated relative force accuracy = 1.035193e-05 using double precision KISS FFT 3d grid and FFT values/proc = 28431 12800 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Unused restart file global fix info: fix style: npt, fix ID: mynpt Last active /omp style is kspace_style pppm/omp Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 4 4 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on, omp pair build: full/bin/omp stencil: full/bin/3d bin: standard (2) pair lj/cut/coul/long/omp, perpetual attributes: half, newton on, omp pair build: half/bin/newton/omp stencil: half/bin/3d bin: standard WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141) Deleted 96 atoms, new total = 2063 Deleted 64 bonds, new total = 1394 Deleted 32 angles, new total = 772 Deleted 0 dihedrals, new total = 116 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.30147173 grid = 32 20 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0033561701 estimated relative force accuracy = 1.0107007e-05 using double precision KISS FFT 3d grid and FFT values/proc = 28431 12800 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Last active /omp style is kspace_style pppm/omp Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long/omp, perpetual attributes: half, newton on, omp pair build: half/bin/newton/omp stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : real Current step : 15000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 21.57 | 21.57 | 21.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15000 293.96336 -6937.5692 809.92925 -4320.8147 -324.16098 22048.535 15500 303.55223 -7052.6966 800.95294 -4385.981 159.56378 22126.265 16000 299.6112 -7008.7809 788.22037 -4379.0211 -521.48094 22225.118 16500 297.84365 -7024.1933 799.14999 -4394.368 -549.95427 22078.839 17000 304.4771 -7151.7783 828.86978 -4451.4613 -1196.0884 21797.644 17500 297.2736 -7140.0735 799.15477 -4513.7472 -64.748238 21483.268 18000 290.38437 -7125.4702 772.583 -4568.0599 -147.3855 21603.548 18500 300.21995 -7069.3954 797.33657 -4426.7778 -858.54751 21744.808 19000 304.5521 -7222.3234 892.996 -4457.4191 -299.2864 21693.475 19500 300.26279 -7212.0992 892.97173 -4473.5832 317.78627 21838.822 20000 296.16369 -7088.4563 790.03404 -4478.0727 -324.19543 21847.186 20500 294.2846 -7173.3437 862.60611 -4501.9378 -10.865505 21688.816 21000 307.82989 -7129.0355 839.23064 -4397.7499 483.90536 21507.857 21500 298.67151 -7128.1414 811.38427 -4480.9935 508.12832 21488.203 22000 293.33114 -7103.4785 840.9377 -4459.6014 1534.3863 21399.357 22500 300.04254 -7088.2347 811.98583 -4432.0583 13.37241 21477.914 23000 297.09602 -7052.5148 855.06239 -4371.3725 -99.140411 21868.119 23500 304.62568 -7119.4796 835.07566 -4412.0435 -66.958474 21978.769 24000 301.80283 -7134.5524 806.69856 -4472.8438 399.88923 21660.515 24500 296.45896 -7156.1096 838.01791 -4495.9273 456.62139 21628.227 25000 297.98494 -7041.5008 828.93835 -4381.0188 146.83299 21852.916 Loop time of 68.6241 on 8 procs for 10000 steps with 2063 atoms Performance: 12.590 ns/day, 1.906 hours/ns, 145.721 timesteps/s, 300.623 katom-step/s 713.6% CPU use with 1 MPI tasks x 8 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.648 | 21.648 | 21.648 | 0.0 | 31.55 Bond | 0.39399 | 0.39399 | 0.39399 | 0.0 | 0.57 Kspace | 25.793 | 25.793 | 25.793 | 0.0 | 37.59 Neigh | 2.7759 | 2.7759 | 2.7759 | 0.0 | 4.05 Comm | 0.82742 | 0.82742 | 0.82742 | 0.0 | 1.21 Output | 10.283 | 10.283 | 10.283 | 0.0 | 14.98 Modify | 6.8375 | 6.8375 | 6.8375 | 0.0 | 9.96 Other | | 0.06478 | | | 0.09 Nlocal: 2063 ave 2063 max 2063 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11827 ave 11827 max 11827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 703928 ave 703928 max 703928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 703928 Ave neighs/atom = 341.21571 Ave special neighs/atom = 2.2171595 Neighbor list builds = 542 Dangerous builds = 0 System init for write_restart ... PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.30178312 grid = 32 20 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0033082643 estimated relative force accuracy = 9.9627396e-06 using double precision KISS FFT 3d grid and FFT values/proc = 28431 12800 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Last active /omp style is kspace_style pppm/omp