# Neighbour list. neighbor 2.0 bin neigh_modify check yes # 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 1 1 # ----------------- 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 1.0 1.0 special bond factors coul: 0.0 1.0 1.0 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.005 seconds # ----------------- Settings Section ----------------- include "toy01.in.settings" mass 1 20 mass 2 20 pair_coeff * * 0.15 2.5 bond_coeff 1 0.000 0.900 # ----------------- Run Section ----------------- include "toy01.in.run" # 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 # Save UNWRAPPED coordinates. dump 1 all custom 1 ${run}.dump id type xu yu zu mol dump 1 all custom 1 toy01.dump id type xu yu zu mol # Single point. run 0 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 = 2475 384 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, 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) = 8.310 | 8.310 | 8.310 Mbytes Step E_vdwl E_coul E_long E_bond PotEng c_inter1 c_inter2 0 -316.99691 1445.8533 -1129.391 0 -0.53462769 -443.27641 1128.8564 Loop time of 9.57e-07 on 1 procs for 0 steps with 288 atoms 209.0% 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 | | 9.57e-07 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4662.00 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95184.0 ave 95184 max 95184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95184 Ave neighs/atom = 330.50000 Ave special neighs/atom = 1.5000000 Neighbor list builds = 0 Dangerous builds = 0 # ----------------- Run Section ----------------- # The lines above define the system you want to simulate. # What you do next is up to you. # Typically a user would minimize and equilibrate # the system using commands similar to the following: # ---- examples ---- # # -- minimize -- # minimize 1.0e-5 1.0e-7 1000 10000 # (Note: Some fixes, for example "shake", interfere with the minimize command, # You can use the "unfix" command to disable them before minimization.) # -- declare time step for normal MD -- # timestep 1.0 # -- run at constant pressure (Nose-Hoover)-- # fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 # -- ALTERNATELY, run at constant volume (Nose-Hoover) -- # fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 # -- ALTERNATELY, run at constant volume using Langevin dynamics. -- # -- (This is good for sparse CG polymers in implicit solvent.) -- # fix fxLAN all langevin 300.0 300.0 5000 48279 # fix fxNVE all nve #(<--needed by fix langevin) # -- Now, finally run the simulation -- # run 50000 # ---- (end of examples) ---- Total wall time: 0:00:00