333 lines
12 KiB
Groff
333 lines
12 KiB
Groff
LAMMPS (29 Mar 2019)
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#LAMMPS input file
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#to simulate bulk E3B3 water model
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#####################################################################
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variable samp_rate equal 10
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variable thermo_rate equal 10
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variable Wlat equal 3.10744 #for water density 0.997g/mL
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variable L equal 3 #(L*2)^3 = Nmolec, L=3 -> N=216
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variable equil equal 100
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variable run equal 100
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variable ts equal 2.0
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variable Tdamp equal 100*${ts}
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variable Tdamp equal 100*2
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variable Pdamp equal 1000*${ts}
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variable Pdamp equal 1000*2
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variable myT equal 298.0
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variable myP equal 1.0
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units real
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atom_style full
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dimension 3
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boundary p p p
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#############################################################################
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#setup box
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read_data e3b_box.data
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orthogonal box = (-9.32232 -9.32232 -9.32232) to (9.32232 9.32232 9.32232)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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648 atoms
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reading velocities ...
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648 velocities
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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432 bonds
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reading angles ...
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216 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000257254 secs
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read_data CPU = 0.00286555 secs
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#############################################################################
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#set up potential
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pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.1546 8.5
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pair_modify table 0 table/disp 0 shift yes
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bond_style harmonic
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angle_style harmonic
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kspace_style pppm/tip4p 1.0e-6
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pair_coeff * * lj/cut/tip4p/long 0.0 0.0
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pair_coeff 1 1 lj/cut/tip4p/long 0.1852 3.1589
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pair_coeff * * e3b preset 2015
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#potential coeffs aren't too important since will be rigid anyways
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bond_coeff 1 554.13 0.9572
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angle_coeff 1 45.769 104.52
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#############################################################################
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#setup for run
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thermo ${thermo_rate}
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thermo 10
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thermo_style custom step vol temp epair pe etotal press density
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timestep ${ts}
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timestep 2
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run_style verlet
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neighbor 2.0 bin
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neigh_modify every 1 delay 3 check yes
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#############################################################################
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#dump positions only in first batch run
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#dump 7 all custom ${samp_rate} dump.lammpstrj id x y z
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#dump_modify 7 sort id
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#############################################################################
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#initialize velocity and rigid constraint
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fix rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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216 = # of frozen angles
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find clusters CPU = 0.000185728 secs
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velocity all create ${myT} 15856 dist gaussian rot yes mom yes
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velocity all create 298 15856 dist gaussian rot yes mom yes
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#scale velocity
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run 0
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PPPM initialization ...
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extracting TIP4P info from pair style
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using polynomial approximation for long-range coulomb (../kspace.cpp:319)
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G vector (1/distance) = 0.409658
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000341883
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estimated relative force accuracy = 1.02957e-06
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using double precision FFTs
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3d grid and FFT values/proc = 91125 46656
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Neighbor list info ...
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update every 1 steps, delay 3 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.8092
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ghost atom cutoff = 10.8092
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binsize = 5.4046, bins = 4 4 4
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair e3b, perpetual, skip from (2)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/cut/tip4p/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 16.4 | 16.4 | 16.4 Mbytes
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Step Volume Temp E_pair PotEng TotEng Press Density
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0 6481.2982 298 -512.62432 -512.62432 -129.77504 14088.322 0.99697602
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Loop time of 1.19209e-06 on 1 procs for 0 steps with 648 atoms
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251.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Kspace | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1.192e-06 | | |100.00
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Nlocal: 648 ave 648 max 648 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5943 ave 5943 max 5943 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 18984 ave 18984 max 18984 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 18984
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Ave neighs/atom = 29.2963
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Ave special neighs/atom = 2
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Neighbor list builds = 0
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Dangerous builds = 0
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velocity all scale ${myT}
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velocity all scale 298
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compute e3b all pe/e3b
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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"
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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"
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#############################################################################
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#equilibrate bulk water at NVT
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fix 1 all nvt temp ${myT} ${myT} ${Tdamp}
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fix 1 all nvt temp 298 ${myT} ${Tdamp}
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fix 1 all nvt temp 298 298 ${Tdamp}
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fix 1 all nvt temp 298 298 200
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run ${equil}
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run 100
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PPPM initialization ...
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extracting TIP4P info from pair style
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using polynomial approximation for long-range coulomb (../kspace.cpp:319)
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G vector (1/distance) = 0.409658
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000341883
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estimated relative force accuracy = 1.02957e-06
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using double precision FFTs
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3d grid and FFT values/proc = 91125 46656
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Neighbor list info ...
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update every 1 steps, delay 3 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.8092
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ghost atom cutoff = 10.8092
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binsize = 5.4046, bins = 4 4 4
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair e3b, perpetual, skip from (2)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/cut/tip4p/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes
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Step Volume Temp E_pair PotEng TotEng Press Density
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0 6481.2982 298 -512.33264 -512.33264 -129.48336 14091.383 0.99697602
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10 6481.2982 905.58028 -1442.0378 -1442.0378 -278.61245 -798.38952 0.99697602
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20 6481.2982 816.39844 -1363.5999 -1363.5999 -314.74903 3023.9064 0.99697602
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30 6481.2982 783.3897 -1370.6594 -1370.6594 -364.21587 7095.4765 0.99697602
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40 6481.2982 793.12519 -1425.8404 -1425.8404 -406.88933 7030.242 0.99697602
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50 6481.2982 810.90264 -1495.4822 -1495.4822 -453.69195 6944.2325 0.99697602
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60 6481.2982 766.64937 -1491.2317 -1491.2317 -506.29493 9062.0151 0.99697602
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70 6481.2982 761.77292 -1538.7368 -1538.7368 -560.06492 7693.2197 0.99697602
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80 6481.2982 730.44938 -1554.1818 -1554.1818 -615.75215 7345.9601 0.99697602
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90 6481.2982 695.46244 -1563.9869 -1563.9869 -670.50605 7809.0685 0.99697602
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100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7143.062 0.99697602
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Loop time of 1.94577 on 1 procs for 100 steps with 648 atoms
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Performance: 8.881 ns/day, 2.702 hours/ns, 51.393 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.91572 | 0.91572 | 0.91572 | 0.0 | 47.06
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Bond | 6.7234e-05 | 6.7234e-05 | 6.7234e-05 | 0.0 | 0.00
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Kspace | 0.92654 | 0.92654 | 0.92654 | 0.0 | 47.62
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Neigh | 0.087331 | 0.087331 | 0.087331 | 0.0 | 4.49
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Comm | 0.0054724 | 0.0054724 | 0.0054724 | 0.0 | 0.28
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Output | 0.0003047 | 0.0003047 | 0.0003047 | 0.0 | 0.02
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Modify | 0.0093319 | 0.0093319 | 0.0093319 | 0.0 | 0.48
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Other | | 0.001007 | | | 0.05
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Nlocal: 648 ave 648 max 648 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5911 ave 5911 max 5911 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 19136 ave 19136 max 19136 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 19136
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Ave neighs/atom = 29.5309
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Ave special neighs/atom = 2
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Neighbor list builds = 15
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Dangerous builds = 0
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#############################################################################
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#run at NVT
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#dump 1 all custom ${samp_rate} dump.lammpstrj id x y z type
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#dump_modify 1 sort id
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run ${run}
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run 100
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PPPM initialization ...
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extracting TIP4P info from pair style
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using polynomial approximation for long-range coulomb (../kspace.cpp:319)
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G vector (1/distance) = 0.409658
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000341883
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estimated relative force accuracy = 1.02957e-06
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using double precision FFTs
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3d grid and FFT values/proc = 91125 46656
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Neighbor list info ...
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update every 1 steps, delay 3 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.8092
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ghost atom cutoff = 10.8092
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binsize = 5.4046, bins = 4 4 4
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair e3b, perpetual, skip from (2)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/cut/tip4p/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 16.88 | 16.88 | 16.88 Mbytes
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Step Volume Temp E_pair PotEng TotEng Press Density
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100 6481.2982 691.5674 -1613.2754 -1613.2754 -724.79866 7131.3961 0.99697602
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110 6481.2982 668.27004 -1635.5867 -1635.5867 -777.04068 6965.8705 0.99697602
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120 6481.2982 646.18686 -1659.5025 -1659.5025 -829.32738 6196.7432 0.99697602
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130 6481.2982 650.7802 -1716.9557 -1716.9557 -880.87943 5626.5466 0.99697602
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140 6481.2982 586.262 -1681.8052 -1681.8052 -928.61728 6103.747 0.99697602
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150 6481.2982 615.88299 -1767.8614 -1767.8614 -976.61859 3897.648 0.99697602
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160 6481.2982 585.23516 -1773.2038 -1773.2038 -1021.3352 4821.7742 0.99697602
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170 6481.2982 558.77885 -1782.2817 -1782.2817 -1064.4022 5092.7248 0.99697602
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180 6481.2982 564.01576 -1830.0301 -1830.0301 -1105.4226 4316.1636 0.99697602
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190 6481.2982 526.53776 -1821.3122 -1821.3122 -1144.8538 4529.5062 0.99697602
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200 6481.2982 537.81273 -1873.6662 -1873.6662 -1182.7226 4244.313 0.99697602
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Loop time of 1.9157 on 1 procs for 100 steps with 648 atoms
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Performance: 9.020 ns/day, 2.661 hours/ns, 52.200 timesteps/s
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.90464 | 0.90464 | 0.90464 | 0.0 | 47.22
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Bond | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 | 0.0 | 0.00
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Kspace | 0.92769 | 0.92769 | 0.92769 | 0.0 | 48.43
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Neigh | 0.067551 | 0.067551 | 0.067551 | 0.0 | 3.53
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Comm | 0.0051386 | 0.0051386 | 0.0051386 | 0.0 | 0.27
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Output | 0.00029993 | 0.00029993 | 0.00029993 | 0.0 | 0.02
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Modify | 0.0092504 | 0.0092504 | 0.0092504 | 0.0 | 0.48
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Other | | 0.001062 | | | 0.06
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Nlocal: 648 ave 648 max 648 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5901 ave 5901 max 5901 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 18971 ave 18971 max 18971 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 18971
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Ave neighs/atom = 29.2762
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Ave special neighs/atom = 2
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Neighbor list builds = 12
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Dangerous builds = 0
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# write_restart lammps.restart
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:03
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