1LAMMPS (29 Mar 2019) 2#LAMMPS input file 3#to simulate bulk E3B3 water model 4 5##################################################################### 6 7variable samp_rate equal 10 8variable thermo_rate equal 10 9variable Wlat equal 3.10744 #for water density 0.997g/mL 10variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216 11 12variable equil equal 100 13variable run equal 100 14 15variable ts equal 2.0 16variable Tdamp equal 100*${ts} 17variable Tdamp equal 100*2 18variable Pdamp equal 1000*${ts} 19variable Pdamp equal 1000*2 20variable myT equal 298.0 21variable myP equal 1.0 22 23units real 24atom_style full 25 26dimension 3 27 28boundary p p p 29 30############################################################################# 31#setup box 32read_data e3b_box.data 33 orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232) 34 1 by 1 by 1 MPI processor grid 35 reading atoms ... 36 648 atoms 37 reading velocities ... 38 648 velocities 39 scanning bonds ... 40 2 = max bonds/atom 41 scanning angles ... 42 1 = max angles/atom 43 reading bonds ... 44 432 bonds 45 reading angles ... 46 216 angles 47 2 = max # of 1-2 neighbors 48 1 = max # of 1-3 neighbors 49 1 = max # of 1-4 neighbors 50 2 = max # of special neighbors 51 special bonds CPU = 0.000257254 secs 52 read_data CPU = 0.00286555 secs 53 54############################################################################# 55#set up potential 56 57pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5 58pair_modify table 0 table/disp 0 shift yes 59 60bond_style harmonic 61angle_style harmonic 62 63kspace_style pppm/tip4p 1.0e-6 64 65pair_coeff * * lj/cut/tip4p/long 0.0 0.0 66pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589 67pair_coeff * * e3b preset 2015 68 69#potential coeffs aren't too important since will be rigid anyways 70bond_coeff 1 554.13 0.9572 71angle_coeff 1 45.769 104.52 72 73############################################################################# 74#setup for run 75thermo ${thermo_rate} 76thermo 10 77thermo_style custom step vol temp epair pe etotal press density 78 79timestep ${ts} 80timestep 2 81run_style verlet 82 83neighbor 2.0 bin 84neigh_modify every 1 delay 3 check yes 85 86############################################################################# 87 88#dump positions only in first batch run 89#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z 90#dump_modify 7 sort id 91 92############################################################################# 93#initialize velocity and rigid constraint 94 95fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2 96 0 = # of size 2 clusters 97 0 = # of size 3 clusters 98 0 = # of size 4 clusters 99 216 = # of frozen angles 100 find clusters CPU = 0.000185728 secs 101velocity all create ${myT} 15856 dist gaussian rot yes mom yes 102velocity all create 298 15856 dist gaussian rot yes mom yes 103 104#scale velocity 105run 0 106PPPM initialization ... 107 extracting TIP4P info from pair style 108 using polynomial approximation for long-range coulomb (../kspace.cpp:319) 109 G vector (1/distance) = 0.409658 110 grid = 36 36 36 111 stencil order = 5 112 estimated absolute RMS force accuracy = 0.000341883 113 estimated relative force accuracy = 1.02957e-06 114 using double precision FFTs 115 3d grid and FFT values/proc = 91125 46656 116Neighbor list info ... 117 update every 1 steps, delay 3 steps, check yes 118 max neighbors/atom: 2000, page size: 100000 119 master list distance cutoff = 10.8092 120 ghost atom cutoff = 10.8092 121 binsize = 5.4046, bins = 4 4 4 122 2 neighbor lists, perpetual/occasional/extra = 2 0 0 123 (1) pair e3b, perpetual, skip from (2) 124 attributes: half, newton on 125 pair build: skip 126 stencil: none 127 bin: none 128 (2) pair lj/cut/tip4p/long, perpetual 129 attributes: half, newton on 130 pair build: half/bin/newton 131 stencil: half/bin/3d/newton 132 bin: standard 133Per MPI rank memory allocation (min/avg/max) = 16.4 | 16.4 | 16.4 Mbytes 134Step Volume Temp E_pair PotEng TotEng Press Density 135 0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602 136Loop time of 1.19209e-06 on 1 procs for 0 steps with 648 atoms 137 138251.7% CPU use with 1 MPI tasks x no OpenMP threads 139 140MPI task timing breakdown: 141Section | min time | avg time | max time |%varavg| %total 142--------------------------------------------------------------- 143Pair | 0 | 0 | 0 | 0.0 | 0.00 144Bond | 0 | 0 | 0 | 0.0 | 0.00 145Kspace | 0 | 0 | 0 | 0.0 | 0.00 146Neigh | 0 | 0 | 0 | 0.0 | 0.00 147Comm | 0 | 0 | 0 | 0.0 | 0.00 148Output | 0 | 0 | 0 | 0.0 | 0.00 149Modify | 0 | 0 | 0 | 0.0 | 0.00 150Other | | 1.192e-06 | | |100.00 151 152Nlocal: 648 ave 648 max 648 min 153Histogram: 1 0 0 0 0 0 0 0 0 0 154Nghost: 5943 ave 5943 max 5943 min 155Histogram: 1 0 0 0 0 0 0 0 0 0 156Neighs: 18984 ave 18984 max 18984 min 157Histogram: 1 0 0 0 0 0 0 0 0 0 158 159Total # of neighbors = 18984 160Ave neighs/atom = 29.2963 161Ave special neighs/atom = 2 162Neighbor list builds = 0 163Dangerous builds = 0 164velocity all scale ${myT} 165velocity all scale 298 166 167compute e3b all pe/e3b 168fix e3b all ave/time 1 1 ${thermo_rate} c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" 169fix e3b all ave/time 1 1 10 c_e3b c_e3b[*] file e3b.txt title2 "step pe_e3b pe_ea pe_eb pe_ec pe_e2" 170 171############################################################################# 172#equilibrate bulk water at NVT 173 174fix 1 all nvt temp ${myT} ${myT} ${Tdamp} 175fix 1 all nvt temp 298 ${myT} ${Tdamp} 176fix 1 all nvt temp 298 298 ${Tdamp} 177fix 1 all nvt temp 298 298 200 178run ${equil} 179run 100 180PPPM initialization ... 181 extracting TIP4P info from pair style 182 using polynomial approximation for long-range coulomb (../kspace.cpp:319) 183 G vector (1/distance) = 0.409658 184 grid = 36 36 36 185 stencil order = 5 186 estimated absolute RMS force accuracy = 0.000341883 187 estimated relative force accuracy = 1.02957e-06 188 using double precision FFTs 189 3d grid and FFT values/proc = 91125 46656 190Neighbor list info ... 191 update every 1 steps, delay 3 steps, check yes 192 max neighbors/atom: 2000, page size: 100000 193 master list distance cutoff = 10.8092 194 ghost atom cutoff = 10.8092 195 binsize = 5.4046, bins = 4 4 4 196 2 neighbor lists, perpetual/occasional/extra = 2 0 0 197 (1) pair e3b, perpetual, skip from (2) 198 attributes: half, newton on 199 pair build: skip 200 stencil: none 201 bin: none 202 (2) pair lj/cut/tip4p/long, perpetual 203 attributes: half, newton on 204 pair build: half/bin/newton 205 stencil: half/bin/3d/newton 206 bin: standard 207Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes 208Step Volume Temp E_pair PotEng TotEng Press Density 209 0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602 210 10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602 211 20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602 212 30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602 213 40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602 214 50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602 215 60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602 216 70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602 217 80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602 218 90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602 219 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602 220Loop time of 1.94577 on 1 procs for 100 steps with 648 atoms 221 222Performance: 8.881 ns/day, 2.702 hours/ns, 51.393 timesteps/s 22399.7% CPU use with 1 MPI tasks x no OpenMP threads 224 225MPI task timing breakdown: 226Section | min time | avg time | max time |%varavg| %total 227--------------------------------------------------------------- 228Pair | 0.91572 | 0.91572 | 0.91572 | 0.0 | 47.06 229Bond | 6.7234e-05 | 6.7234e-05 | 6.7234e-05 | 0.0 | 0.00 230Kspace | 0.92654 | 0.92654 | 0.92654 | 0.0 | 47.62 231Neigh | 0.087331 | 0.087331 | 0.087331 | 0.0 | 4.49 232Comm | 0.0054724 | 0.0054724 | 0.0054724 | 0.0 | 0.28 233Output | 0.0003047 | 0.0003047 | 0.0003047 | 0.0 | 0.02 234Modify | 0.0093319 | 0.0093319 | 0.0093319 | 0.0 | 0.48 235Other | | 0.001007 | | | 0.05 236 237Nlocal: 648 ave 648 max 648 min 238Histogram: 1 0 0 0 0 0 0 0 0 0 239Nghost: 5911 ave 5911 max 5911 min 240Histogram: 1 0 0 0 0 0 0 0 0 0 241Neighs: 19136 ave 19136 max 19136 min 242Histogram: 1 0 0 0 0 0 0 0 0 0 243 244Total # of neighbors = 19136 245Ave neighs/atom = 29.5309 246Ave special neighs/atom = 2 247Neighbor list builds = 15 248Dangerous builds = 0 249 250############################################################################# 251#run at NVT 252 253#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type 254#dump_modify 1 sort id 255 256run ${run} 257run 100 258PPPM initialization ... 259 extracting TIP4P info from pair style 260 using polynomial approximation for long-range coulomb (../kspace.cpp:319) 261 G vector (1/distance) = 0.409658 262 grid = 36 36 36 263 stencil order = 5 264 estimated absolute RMS force accuracy = 0.000341883 265 estimated relative force accuracy = 1.02957e-06 266 using double precision FFTs 267 3d grid and FFT values/proc = 91125 46656 268Neighbor list info ... 269 update every 1 steps, delay 3 steps, check yes 270 max neighbors/atom: 2000, page size: 100000 271 master list distance cutoff = 10.8092 272 ghost atom cutoff = 10.8092 273 binsize = 5.4046, bins = 4 4 4 274 2 neighbor lists, perpetual/occasional/extra = 2 0 0 275 (1) pair e3b, perpetual, skip from (2) 276 attributes: half, newton on 277 pair build: skip 278 stencil: none 279 bin: none 280 (2) pair lj/cut/tip4p/long, perpetual 281 attributes: half, newton on 282 pair build: half/bin/newton 283 stencil: half/bin/3d/newton 284 bin: standard 285Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes 286Step Volume Temp E_pair PotEng TotEng Press Density 287 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602 288 110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602 289 120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602 290 130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602 291 140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602 292 150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602 293 160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602 294 170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602 295 180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602 296 190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602 297 200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602 298Loop time of 1.9157 on 1 procs for 100 steps with 648 atoms 299 300Performance: 9.020 ns/day, 2.661 hours/ns, 52.200 timesteps/s 30199.6% CPU use with 1 MPI tasks x no OpenMP threads 302 303MPI task timing breakdown: 304Section | min time | avg time | max time |%varavg| %total 305--------------------------------------------------------------- 306Pair | 0.90464 | 0.90464 | 0.90464 | 0.0 | 47.22 307Bond | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 | 0.0 | 0.00 308Kspace | 0.92769 | 0.92769 | 0.92769 | 0.0 | 48.43 309Neigh | 0.067551 | 0.067551 | 0.067551 | 0.0 | 3.53 310Comm | 0.0051386 | 0.0051386 | 0.0051386 | 0.0 | 0.27 311Output | 0.00029993 | 0.00029993 | 0.00029993 | 0.0 | 0.02 312Modify | 0.0092504 | 0.0092504 | 0.0092504 | 0.0 | 0.48 313Other | | 0.001062 | | | 0.06 314 315Nlocal: 648 ave 648 max 648 min 316Histogram: 1 0 0 0 0 0 0 0 0 0 317Nghost: 5901 ave 5901 max 5901 min 318Histogram: 1 0 0 0 0 0 0 0 0 0 319Neighs: 18971 ave 18971 max 18971 min 320Histogram: 1 0 0 0 0 0 0 0 0 0 321 322Total # of neighbors = 18971 323Ave neighs/atom = 29.2762 324Ave special neighs/atom = 2 325Neighbor list builds = 12 326Dangerous builds = 0 327 328# write_restart lammps.restart 329 330Please see the log.cite file for references relevant to this simulation 331 332Total wall time: 0:00:03 333