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5
examples/README
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@ -44,6 +44,11 @@ pour: pouring of granular particles into a 3d box, then chute flow
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the doc/Section_start.html for
more info about user packages.
Here is how you might run and visualize one of the sample problems:
cd indent

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LAMMPS cmm-cg example problems
Each of these sub-directories contains a sample problem for the CMM
coarse grained MD potentials that you can run with LAMMPS. The
represent some typical uses and are also used to verify the
implmentation in LAMMPS.
Each problem has an input script (in.*) and produces a log file
(log.*) and trajectory file in compressed .xtc format (*.xtc) when it
runs. Inputs are usually set up to read the start configuration and
topology from a data file (data.*) and the matching force field
parameter from an include file (parms.*).
A few sample log file outputs on different machines and different
numbers of processors are included in the directories to compare your
answers to. E.g. a log file like log.crack.date.foo.P means it ran on
P processors of machine "foo" with the dated version of LAMMPS. Note
that these problems should get statistically similar answers when run
on different machines or different numbers of processors, but not
identical answers to those in the log of dump files included here.
See the Errors section of the LAMMPS documentation for more
discussion.
The examples also provide matching topology files for visualization
(*.psf) so that the .xtc trajectories can be visualized with VMD.
These are the sample systems the various sub-directories:
peg-verlet: coarse grained PEG surfactant/water mixture lamella
verlet version
this example uses the plain LJ term only, no charges
(more to come)

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# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# read topology and force field
read_data data.pegc12e8
include parm.pegc12e8
neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
write_restart pegc12e8-1.restart

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# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# read topology and force field
read_data data.pegc12e8
include parm.pegc12e8-angle
neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
write_restart pegc12e8-angle-1.restart

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LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# read topology and force field
read_data data.pegc12e8
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
1 by 1 by 4 processor grid
40140 atoms
13284 bonds
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
include parm.pegc12e8
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style harmonic
special_bonds 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0
neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 4.43925 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 27.1134 (sec) ----------------
TotEng = -217991.2189 KinEng = 36188.3877 Temp = 302.4603
PotEng = -254179.6067 E_bond = 4590.3067 E_angle = 3421.2609
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262191.1742
E_coul = 0.0000 E_long = 0.0000 Press = 37.0652
---------------- Step 400 ----- CPU = 55.8229 (sec) ----------------
TotEng = -217934.5954 KinEng = 36330.2463 Temp = 303.6459
PotEng = -254264.8418 E_bond = 4626.8916 E_angle = 3512.1639
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262403.8973
E_coul = 0.0000 E_long = 0.0000 Press = 17.4311
---------------- Step 600 ----- CPU = 83.0111 (sec) ----------------
TotEng = -218281.8191 KinEng = 36141.0168 Temp = 302.0644
PotEng = -254422.8358 E_bond = 4628.2093 E_angle = 3492.7509
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262543.7960
E_coul = 0.0000 E_long = 0.0000 Press = 9.5773
---------------- Step 800 ----- CPU = 110.5361 (sec) ----------------
TotEng = -218232.9755 KinEng = 36343.0623 Temp = 303.7531
PotEng = -254576.0378 E_bond = 4659.4462 E_angle = 3567.9426
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262803.4265
E_coul = 0.0000 E_long = 0.0000 Press = -9.6008
---------------- Step 1000 ----- CPU = 137.3658 (sec) ----------------
TotEng = -218073.8055 KinEng = 36426.1635 Temp = 304.4476
PotEng = -254499.9689 E_bond = 4602.2406 E_angle = 3636.2557
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262738.4653
E_coul = 0.0000 E_long = 0.0000 Press = -11.9067
Loop time of 137.366 on 4 procs for 1000 steps with 40140 atoms
Performance: 3.145 ns/day 7.631 hours/ns
Pair time (%) = 59.0174 (42.9636)
Bond time (%) = 0.932444 (0.678802)
Neigh time (%) = 6.30874 (4.59265)
Comm time (%) = 69.5999 (50.6674)
Outpt time (%) = 0.0389841 (0.0283797)
Other time (%) = 1.46867 (1.06916)
Nlocal: 10035 ave 19552 max 532 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11779.5 ave 18122 max 5457 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19488e+06 ave 2.39205e+06 max 12991 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 4779515
Ave neighs/atom = 119.071
Ave special neighs/atom = 1.26861
Neighbor list builds = 61
Dangerous builds = 0
write_restart pegc12e8-1.restart

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LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# read topology and force field
read_data data.pegc12e8
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
1 by 1 by 4 processor grid
40140 atoms
13284 bonds
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
include parm.pegc12e8-angle
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style cg/cmm
special_bonds 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0 lj9_6 0.4400 3.8900
angle_coeff 2 3.400 132.0 lj9_6 0.4050 4.2500
angle_coeff 3 3.200 146.0 lj9_6 0.3770 4.2740
angle_coeff 4 1.500 172.0 lj9_6 0.3770 4.2740
angle_coeff 5 1.190 173.0 lj9_6 0.4200 4.5060
angle_coeff 6 1.600 172.0 lj9_6 0.3620 4.3635
neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 4.43925 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 29.9183 (sec) ----------------
TotEng = -218051.4566 KinEng = 36272.3725 Temp = 303.1622
PotEng = -254323.8292 E_bond = 4530.3699 E_angle = 3351.7084
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.9074
E_coul = 0.0000 E_long = 0.0000 Press = 36.2458
---------------- Step 400 ----- CPU = 60.9372 (sec) ----------------
TotEng = -218054.5847 KinEng = 36253.0519 Temp = 303.0008
PotEng = -254307.6366 E_bond = 4620.3304 E_angle = 3417.4287
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262345.3957
E_coul = 0.0000 E_long = 0.0000 Press = 12.6545
---------------- Step 600 ----- CPU = 89.8983 (sec) ----------------
TotEng = -218042.2111 KinEng = 36394.6544 Temp = 304.1843
PotEng = -254436.8655 E_bond = 4623.6900 E_angle = 3419.7393
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262480.2949
E_coul = 0.0000 E_long = 0.0000 Press = 20.4952
---------------- Step 800 ----- CPU = 119.1245 (sec) ----------------
TotEng = -217865.4500 KinEng = 36565.4671 Temp = 305.6119
PotEng = -254430.9171 E_bond = 4590.5794 E_angle = 3466.0941
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262487.5906
E_coul = 0.0000 E_long = 0.0000 Press = 2.9466
---------------- Step 1000 ----- CPU = 147.8398 (sec) ----------------
TotEng = -218219.2310 KinEng = 36266.8018 Temp = 303.1157
PotEng = -254486.0328 E_bond = 4542.7739 E_angle = 3415.8267
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262444.6334
E_coul = 0.0000 E_long = 0.0000 Press = -8.6110
Loop time of 147.84 on 4 procs for 1000 steps with 40140 atoms
Performance: 2.922 ns/day 8.213 hours/ns
Pair time (%) = 61.7803 (41.7886)
Bond time (%) = 1.17913 (0.797574)
Neigh time (%) = 6.23896 (4.22007)
Comm time (%) = 76.805 (51.9514)
Outpt time (%) = 0.0374529 (0.0253334)
Other time (%) = 1.79919 (1.21699)
Nlocal: 10035 ave 19571 max 538 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11797.5 ave 18129 max 5484 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19407e+06 ave 2.388e+06 max 12690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 4776294
Ave neighs/atom = 118.991
Ave special neighs/atom = 1.26861
Neighbor list builds = 59
Dangerous builds = 0
write_restart pegc12e8-angle-1.restart

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# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style harmonic
special_bonds 0.0 0.0 1.0
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0

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# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
bond_style harmonic
angle_style cg/cmm
special_bonds 0.0 0.0 1.0
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0 lj9_6 0.4400 3.8900
angle_coeff 2 3.400 132.0 lj9_6 0.4050 4.2500
angle_coeff 3 3.200 146.0 lj9_6 0.3770 4.2740
angle_coeff 4 1.500 172.0 lj9_6 0.3770 4.2740
angle_coeff 5 1.190 173.0 lj9_6 0.4200 4.5060
angle_coeff 6 1.600 172.0 lj9_6 0.3620 4.3635

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