Unverified Commit 795cdf45 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

simplify example and skip the system generation step, so it gives consistent... 

simplify example and skip the system generation step, so it gives consistent results in serial and parallel
parent e481c5f3

examples/USER/e3b/README

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The input script in.lammps simulates bulk water using the 2015 E3B potential.

It can be modified to use the 2011 E3B potential by

   1) using a tip4p molecule file instead of tip4p2005.mol

   2) changing the qdist parameter for lj/cut/tip4p/long in the pair_style

   hybrid/overlay command

   3) using the 2011 "preset" command in the e3b pair_coeff command



This script also demonstrates the use of compute pe/e3b to calculate the

potential energy contribution of the e3b pair style. These potential energy

contributions can be found in the output file e3b.txt. See the LAMMPS

examples/USER/e3b/e3b_box.data

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examples/USER/e3b/in.lammps→examples/USER/e3b/in.e3b-tip4p2005

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@@ -2,7 +2,6 @@ 
#to simulate bulk E3B3 water model



#####################################################################

clear



variable	samp_rate 	equal 10

variable	thermo_rate 	equal 10
@@ -27,20 +26,11 @@ boundary p p p 


#############################################################################

#setup box



lattice	  	sc ${Wlat}

region		simbox block -$L $L -$L $L -$L $L units lattice

read_data       e3b_box.data



#############################################################################

#set up potential



create_box	2 simbox bond/types 1 angle/types 1 extra/bond/per/atom 2 &

		extra/special/per/atom 2 extra/angle/per/atom 1



molecule 	h2o tip4p2005.mol

mass            1 15.9994 #oxygen

mass            2 1.008   #hydrogen



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
@@ -53,9 +43,9 @@ 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



#intramolecular bond/angle coeffs very stiff for minimization

bond_coeff	1 100000 0.9572

angle_coeff	1 100000 104.52

#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
@@ -69,25 +59,15 @@ neighbor 2.0 bin 
neigh_modify	every 1 delay 3 check yes



#############################################################################

#make atoms and rough minimze

create_atoms	0 box mol h2o 15856



#dump positions only in first batch run

dump 		7 all custom ${samp_rate} dump.lammpstrj id x y z

dump_modify	7 sort id



min_style 	cg

minimize	1.0e-4 1.0e-4 10000 100000



#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



#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 mol h2o

fix 		rigid all shake 1.0e-8 100 0 b 1 a 1 t 1 2

velocity 	all create ${myT} 15856 dist gaussian rot yes mom yes



#scale velocity
@@ -107,9 +87,9 @@ run ${equil} 
#############################################################################

#run at NVT



dump 		1 all custom ${samp_rate} dump.lammpstrj id x y z type

dump_modify	1 sort id

#dump 		1 all custom ${samp_rate} dump.lammpstrj id x y z type

#dump_modify	1 sort id



run 		${run}



write_restart 	lammps.restart
 
# write_restart 	lammps.restart

examples/USER/e3b/log.29Mar2019.e3b-tip4p2005.g++.1

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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 1 by 1 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 = 0.000257254 secs

  read_data CPU = 0.00286555 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 = 0.000185728 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 = 91125 46656

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) = 16.4 | 16.4 | 16.4 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 1.19209e-06 on 1 procs for 0 steps with 648 atoms



251.7% CPU use with 1 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   |            | 1.192e-06  |            |       |100.00



Nlocal:    648 ave 648 max 648 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    5943 ave 5943 max 5943 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    18984 ave 18984 max 18984 min

Histogram: 1 0 0 0 0 0 0 0 0 0



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 = 91125 46656

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) = 16.88 | 16.88 | 16.88 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 1.94577 on 1 procs for 100 steps with 648 atoms



Performance: 8.881 ns/day, 2.702 hours/ns, 51.393 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.91572    | 0.91572    | 0.91572    |   0.0 | 47.06

Bond    | 6.7234e-05 | 6.7234e-05 | 6.7234e-05 |   0.0 |  0.00

Kspace  | 0.92654    | 0.92654    | 0.92654    |   0.0 | 47.62

Neigh   | 0.087331   | 0.087331   | 0.087331   |   0.0 |  4.49

Comm    | 0.0054724  | 0.0054724  | 0.0054724  |   0.0 |  0.28

Output  | 0.0003047  | 0.0003047  | 0.0003047  |   0.0 |  0.02

Modify  | 0.0093319  | 0.0093319  | 0.0093319  |   0.0 |  0.48

Other   |            | 0.001007   |            |       |  0.05



Nlocal:    648 ave 648 max 648 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    5911 ave 5911 max 5911 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    19136 ave 19136 max 19136 min

Histogram: 1 0 0 0 0 0 0 0 0 0



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 = 91125 46656

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) = 16.88 | 16.88 | 16.88 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 1.9157 on 1 procs for 100 steps with 648 atoms



Performance: 9.020 ns/day, 2.661 hours/ns, 52.200 timesteps/s

99.6% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.90464    | 0.90464    | 0.90464    |   0.0 | 47.22

Bond    | 6.9141e-05 | 6.9141e-05 | 6.9141e-05 |   0.0 |  0.00

Kspace  | 0.92769    | 0.92769    | 0.92769    |   0.0 | 48.43

Neigh   | 0.067551   | 0.067551   | 0.067551   |   0.0 |  3.53

Comm    | 0.0051386  | 0.0051386  | 0.0051386  |   0.0 |  0.27

Output  | 0.00029993 | 0.00029993 | 0.00029993 |   0.0 |  0.02

Modify  | 0.0092504  | 0.0092504  | 0.0092504  |   0.0 |  0.48

Other   |            | 0.001062   |            |       |  0.06



Nlocal:    648 ave 648 max 648 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    5901 ave 5901 max 5901 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    18971 ave 18971 max 18971 min

Histogram: 1 0 0 0 0 0 0 0 0 0



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: 0:00:03

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