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
