LAMMPS (29 Mar 2019) #LAMMPS input file #to simulate bulk E3B3 water model ##################################################################### variable samp_rate equal 10 variable thermo_rate equal 10 variable Wlat equal 3.10744 #for water density 0.997g/mL variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216 variable equil equal 100 variable run equal 100 variable ts equal 2.0 variable Tdamp equal 100*${ts} variable Tdamp equal 100*2 variable Pdamp equal 1000*${ts} variable Pdamp equal 1000*2 variable myT equal 298.0 variable myP equal 1.0 units real atom_style full dimension 3 boundary p p p ############################################################################# #setup box read_data e3b_box.data orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232) 1 by 2 by 2 MPI processor grid reading atoms ... 648 atoms reading velocities ... 648 velocities scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 432 bonds reading angles ... 216 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.00029397 secs read_data CPU = 0.00397325 secs ############################################################################# #set up potential pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5 pair_modify table 0 table/disp 0 shift yes bond_style harmonic angle_style harmonic kspace_style pppm/tip4p 1.0e-6 pair_coeff * * lj/cut/tip4p/long 0.0 0.0 pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589 pair_coeff * * e3b preset 2015 #potential coeffs aren't too important since will be rigid anyways bond_coeff 1 554.13 0.9572 angle_coeff 1 45.769 104.52 ############################################################################# #setup for run thermo ${thermo_rate} thermo 10 thermo_style custom step vol temp epair pe etotal press density timestep ${ts} timestep 2 run_style verlet neighbor 2.0 bin neigh_modify every 1 delay 3 check yes ############################################################################# #dump positions only in first batch run #dump 7 all custom ${samp_rate} dump.lammpstrj id x y z #dump_modify 7 sort id ############################################################################# #initialize velocity and rigid constraint fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 216 = # of frozen angles find clusters CPU = 0.000289917 secs velocity all create ${myT} 15856 dist gaussian rot yes mom yes velocity all create 298 15856 dist gaussian rot yes mom yes #scale velocity run 0 PPPM initialization ... extracting TIP4P info from pair style using polynomial approximation for long-range coulomb (../kspace.cpp:319) G vector (1/distance) = 0.409658 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.000341883 estimated relative force accuracy = 1.02957e-06 using double precision FFTs 3d grid and FFT values/proc = 32805 11664 Neighbor list info ... update every 1 steps, delay 3 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.8092 ghost atom cutoff = 10.8092 binsize = 5.4046, bins = 4 4 4 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair e3b, perpetual, skip from (2) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/tip4p/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.69 Mbytes Step Volume Temp E_pair PotEng TotEng Press Density 0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602 Loop time of 3.30806e-05 on 4 procs for 0 steps with 648 atoms 77.1% CPU use with 4 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 | | 3.308e-05 | | |100.00 Nlocal: 162 ave 168 max 157 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 3738 ave 3743 max 3732 min Histogram: 1 0 1 0 0 0 0 0 0 2 Neighs: 4746 ave 5380 max 4318 min Histogram: 1 1 0 0 1 0 0 0 0 1 Total # of neighbors = 18984 Ave neighs/atom = 29.2963 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 velocity all scale ${myT} velocity all scale 298 compute e3b all pe/e3b fix 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" fix 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" ############################################################################# #equilibrate bulk water at NVT fix 1 all nvt temp ${myT} ${myT} ${Tdamp} fix 1 all nvt temp 298 ${myT} ${Tdamp} fix 1 all nvt temp 298 298 ${Tdamp} fix 1 all nvt temp 298 298 200 run ${equil} run 100 PPPM initialization ... extracting TIP4P info from pair style using polynomial approximation for long-range coulomb (../kspace.cpp:319) G vector (1/distance) = 0.409658 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.000341883 estimated relative force accuracy = 1.02957e-06 using double precision FFTs 3d grid and FFT values/proc = 32805 11664 Neighbor list info ... update every 1 steps, delay 3 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.8092 ghost atom cutoff = 10.8092 binsize = 5.4046, bins = 4 4 4 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair e3b, perpetual, skip from (2) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/tip4p/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 11.18 | 11.18 | 11.18 Mbytes Step Volume Temp E_pair PotEng TotEng Press Density 0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602 10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602 20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602 30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602 40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602 50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602 60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602 70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602 80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602 90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602 Loop time of 1.20724 on 4 procs for 100 steps with 648 atoms Performance: 14.314 ns/day, 1.677 hours/ns, 82.834 timesteps/s 97.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37421 | 0.39416 | 0.42739 | 3.2 | 32.65 Bond | 5.8651e-05 | 7.1406e-05 | 8.2016e-05 | 0.0 | 0.01 Kspace | 0.67929 | 0.71762 | 0.74038 | 2.8 | 59.44 Neigh | 0.042206 | 0.042236 | 0.042263 | 0.0 | 3.50 Comm | 0.0248 | 0.031467 | 0.035969 | 2.7 | 2.61 Output | 0.00064564 | 0.0008018 | 0.0012648 | 0.0 | 0.07 Modify | 0.018263 | 0.01869 | 0.019076 | 0.2 | 1.55 Other | | 0.002194 | | | 0.18 Nlocal: 162 ave 170 max 151 min Histogram: 1 0 0 0 0 1 0 1 0 1 Nghost: 3726.75 ave 3737 max 3720 min Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 4784 ave 5474 max 4389 min Histogram: 1 1 1 0 0 0 0 0 0 1 Total # of neighbors = 19136 Ave neighs/atom = 29.5309 Ave special neighs/atom = 2 Neighbor list builds = 15 Dangerous builds = 0 ############################################################################# #run at NVT #dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type #dump_modify 1 sort id run ${run} run 100 PPPM initialization ... extracting TIP4P info from pair style using polynomial approximation for long-range coulomb (../kspace.cpp:319) G vector (1/distance) = 0.409658 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.000341883 estimated relative force accuracy = 1.02957e-06 using double precision FFTs 3d grid and FFT values/proc = 32805 11664 Neighbor list info ... update every 1 steps, delay 3 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.8092 ghost atom cutoff = 10.8092 binsize = 5.4046, bins = 4 4 4 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair e3b, perpetual, skip from (2) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/tip4p/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 11.18 | 11.18 | 11.18 Mbytes Step Volume Temp E_pair PotEng TotEng Press Density 100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602 110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602 120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602 130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602 140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602 150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602 160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602 170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602 180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602 190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602 200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602 Loop time of 1.21286 on 4 procs for 100 steps with 648 atoms Performance: 14.247 ns/day, 1.685 hours/ns, 82.450 timesteps/s 97.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37664 | 0.39663 | 0.4367 | 3.8 | 32.70 Bond | 6.175e-05 | 6.7353e-05 | 7.4148e-05 | 0.0 | 0.01 Kspace | 0.6969 | 0.73237 | 0.75103 | 2.5 | 60.38 Neigh | 0.033138 | 0.03317 | 0.033202 | 0.0 | 2.73 Comm | 0.022651 | 0.02763 | 0.034947 | 3.0 | 2.28 Output | 0.00065303 | 0.00096697 | 0.0018971 | 0.0 | 0.08 Modify | 0.017379 | 0.018252 | 0.018955 | 0.4 | 1.50 Other | | 0.003775 | | | 0.31 Nlocal: 162 ave 175 max 156 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 3689.5 ave 3721 max 3651 min Histogram: 1 0 0 0 0 1 1 0 0 1 Neighs: 4742.75 ave 5159 max 4485 min Histogram: 2 0 0 0 1 0 0 0 0 1 Total # of neighbors = 18971 Ave neighs/atom = 29.2762 Ave special neighs/atom = 2 Neighbor list builds = 12 Dangerous builds = 0 # write_restart lammps.restart Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:02