# Force field definition. boundary p p p units real atom_style full pair_style lj/cut/coul/long 10.0 10.0 bond_style harmonic kspace_style pppm 0.0001 special_bonds lj/coul 0 0 0 # ----------------- Atom Definition Section ----------------- read_data "toy01.data" Reading data file ... orthogonal box = (0.0000000 0.0000000 0.0000000) to (15.000000 15.000000 14.000000) 1 by 1 by 1 MPI processor grid reading atoms ... 288 atoms scanning bonds ... 1 = max bonds/atom reading bonds ... 216 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.0 special bond factors coul: 0.0 0.0 0.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 3 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.004 seconds # Neighbour list. neighbor 1.0 bin # ----------------- Settings Section ----------------- mass 1 20 mass 2 20 pair_coeff * * 0.15 2.5 bond_coeff 1 0.000 0.900 # Compute the intermolecular energy in various ways. compute inter1 all group/group all pair yes kspace yes molecule inter compute inter2 all pair lj/cut/coul/long epair # Physical observables. thermo 1 thermo_style custom step evdwl ecoul elong ebond pe c_inter1 c_inter2 thermo_modify flush yes # Single point. rerun toy01.dump dump x y z box yes WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:328) G vector (1/distance) = 0.25293351 grid = 8 8 6 stencil order = 5 estimated absolute RMS force accuracy = 0.013459416 estimated relative force accuracy = 4.0532631e-05 using double precision KISS FFT 3d grid and FFT values/proc = 1859 384 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5, bins = 3 3 3 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) = 6.905 | 6.905 | 6.905 Mbytes Step E_vdwl E_coul E_long E_bond PotEng c_inter1 c_inter2 0 -305.81328 2197.266 -1129.391 0 762.06174 -443.27641 1891.4527 Loop time of 0.0125753 on 1 procs for 1 steps with 288 atoms Performance: 6.871 ns/day, 3.493 hours/ns, 79.521 timesteps/s 99.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01258 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4212.00 ave 4212 max 4212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74304.0 ave 74304 max 74304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74304 Ave neighs/atom = 258.00000 Ave special neighs/atom = 3.0000000 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00