LAMMPS (30 Aug 2013) log log.polarize variable nstepsequil equal 1000000 variable nsteps equal 100 variable temp equal 300.0 variable tdamp equal 0.100 variable x_dim equal 50 variable y_dim equal 50 variable z_fluid equal 37.7919 variable efieldz equal -0.0723725329978652551934 variable x_max equal ${x_dim}/2 variable x_max equal 50/2 variable y_max equal ${y_dim}/2 variable y_max equal 50/2 variable fluid_half_thickness equal ${z_fluid}/2 variable fluid_half_thickness equal 37.791899999999998272/2 variable buffer equal 2.45 variable zhiwall equal ${fluid_half_thickness}+${buffer} variable zhiwall equal 18.895949999999999136+${buffer} variable zhiwall equal 18.895949999999999136+2.4500000000000001776 variable zlowall equal -${fluid_half_thickness}-${buffer} variable zlowall equal -18.895949999999999136-${buffer} variable zlowall equal -18.895949999999999136-2.4500000000000001776 variable zmaxatc equal ${fluid_half_thickness}+10 variable zmaxatc equal 18.895949999999999136+10 variable zmaxsub equal ${zmaxatc}-0.1 variable zmaxsub equal 28.895949999999999136-0.1 variable zmaxsup equal ${zmaxatc}+0.1 variable zmaxsup equal 28.895949999999999136+0.1 variable cellatc equal 5 units metal atom_style full dimension 3 newton off neighbor 2 bin neigh_modify every 1 delay 1 check no boundary p p f kspace_style pppm 1e-5 kspace_modify slab 3.0 pair_style lj/cut/coul/long 13.0 13.0 bond_style harmonic angle_style harmonic read_data waterequil.init Scanning data file ... 2 = max bonds/atom 1 = max angles/atom Reading data file ... orthogonal box = (-25 -25 -21.8959) to (25 25 21.8959) 2 by 2 by 1 MPI processor grid 9474 atoms 9474 velocities 6316 bonds 3158 angles Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors #velocity all create 0.0 482748 dist uniform lattice sc 0.05 Lattice spacing in x,y,z = 0.05 0.05 0.05 #region ATC block EDGE EDGE EDGE EDGE -${zmaxatc} ${zmaxatc} units box #variable nelemelec equal round(2*${zmaxatc}/0.05) region ATC block EDGE EDGE EDGE EDGE EDGE EDGE units box # region ATC block EDGE EDGE EDGE EDGE 0.0 0.05 units box #region ATC block -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} units box variable nelem equal 2 # variable nelem equal 1 group water type 1 2 9474 atoms in group water group hyd type 1 6316 atoms in group hyd group oxy type 2 3158 atoms in group oxy timestep 0.0005 dielectric 1.0 pair_coeff 1 * 0.0 0.0 pair_coeff 2 2 0.006596 3.1507 bond_coeff 1 19.513855 0.957200 angle_coeff 1 2.385027 104.519997 special_bonds amber Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors #fix 2 all nvt temp ${temp} ${temp} ${tdamp} fix lowall oxy wall/lj1043 zlo ${zlowall} 0.1351 3.1507 11.0275 units box fix lowall oxy wall/lj1043 zlo -21.345949999999998425 0.1351 3.1507 11.0275 units box fix hiwall oxy wall/lj1043 zhi ${zhiwall} 0.1351 3.1507 11.0275 units box fix hiwall oxy wall/lj1043 zhi 21.345949999999998425 0.1351 3.1507 11.0275 units box fix efield all efield 0. 0. v_efieldz # assign SHAKE fixes fix 1 all shake 0.00001 500 5000 b 1 a 1 Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3158 = # of frozen angles thermo 100 thermo_style custom step temp ke pe etotal f_efield f_lowall f_hiwall variable dumpfreq equal 1 #dump 1 all atom 500 waterequil.dump #dump_modify 1 image yes scale no flush yes #run ${nstepsequil} #write_restart waterequil.restart #unfix 2 fix 3 all nve fix AtC all atc hardy ATC: constructing kernel field estimate ATC: version 2.0 ATC: peratom PE compute created with ID: 3 fix_modify AtC mesh create 1 1 ${nelem} ATC p p f fix_modify AtC mesh create 1 1 2 ATC p p f ATC: created uniform mesh with 12 nodes, 3 unique nodes, and 2 elements #fix_modify AtC_half mesh create 1 1 ${nelem} ATC p p f fix_modify AtC kernel cell 25 25 ${cellatc} fix_modify AtC kernel cell 25 25 5 fix_modify AtC atom_element_map eulerian ${dumpfreq} fix_modify AtC atom_element_map eulerian 1 fix_modify AtC fields none fix_modify AtC fields add dipole_moment mass_density fix_modify AtC add_molecule small Water water fix_modify AtC output polarizeFE ${dumpfreq} text vector_components fix_modify AtC output polarizeFE 1 text vector_components ATC: Warning : text output can create _LARGE_ files ATC: output custom names: run ${nsteps} run 100 PPPM initialization ... G vector (1/distance) = 0.229056 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.000159261 estimated relative force accuracy = 1.10601e-05 using double precision FFTs 3d grid and FFT values/proc = 31944 14400 Setting up run ... SHAKE stats (type/ave/delta) on step 0 1 0.9572 3.63187e-08 1 104.52 3.67915e-06 ATC: computing kernel matrix molecule ...done Memory usage per processor = 50.0731 Mbytes Step Temp KinEng PotEng TotEng efield lowall hiwall 0 295.19689 240.96267 -1265.6426 -1024.6799 0 -25.236036 -26.079483 ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done ATC: computing kernel matrix molecule ...done 100 296.18885 241.77239 -1266.3101 -1024.5377 0 -25.105524 -26.164269 Loop time of 39.4264 on 4 procs for 100 steps with 9474 atoms Pair time (%) = 15.485 (39.2757) Bond time (%) = 0.00152647 (0.00387171) Kspce time (%) = 2.45746 (6.23305) Neigh time (%) = 19.0463 (48.3087) Comm time (%) = 0.193679 (0.491242) Outpt time (%) = 0.000291049 (0.00073821) Other time (%) = 2.24208 (5.68676) FFT time (% of Kspce) = 0.656798 (26.7267) FFT Gflps 3d (1d only) = 1.92257 5.45241 Nlocal: 2368.5 ave 2387 max 2357 min Histogram: 1 1 0 0 1 0 0 0 0 1 Nghost: 9049.75 ave 9086 max 9029 min Histogram: 2 0 0 0 1 0 0 0 0 1 Neighs: 1.94028e+06 ave 1.95668e+06 max 1.92845e+06 min Histogram: 1 0 1 1 0 0 0 0 0 1 FullNghs: 2.74796e+06 ave 2.77359e+06 max 2.72966e+06 min Histogram: 1 0 1 0 1 0 0 0 0 1 Total # of neighbors = 10991852 Ave neighs/atom = 1160.21 Ave special neighs/atom = 2 Neighbor list builds = 100 Dangerous builds = 0 #fix AtCH hyd atc field #fix_modify AtCH mesh create 1 1 ${nelemelec} ATC p p f #fix_modify AtCH atom_element_map eulerian ${dumpfreq} #fix_modify AtCH fields add number_density #fix_modify AtCH output FEH ${dumpfreq} text binary #fix AtCO oxy atc field #fix_modify AtCO mesh create 1 1 ${nelemelec} ATC p p f #fix_modify AtCO atom_element_map eulerian ${dumpfreq} #fix_modify AtCO fields add number_density #fix_modify AtCO output FEO ${dumpfreq} text binary #run ${nsteps} #write_restart waterendpolarize.restart