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LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation.
Each of the 5 problems has 32,000 atoms and runs for 100 timesteps.
Each can be run as a serial benchmark (on one processor) or in
parallel. In parallel, each benchmark can be run as a fixed-size or
scaled-size problem. For fixed-size benchmarking, the same 32K atom
problem is run on various numbers of processors. For scaled-size
benchmarking, the model size is increased with the number of
processors. E.g. on 8 processors, a 256K-atom problem is run; on 1024
processors, a 32-million atom problem is run, etc.
A few sample log file outputs on different machines and different
numbers of processors are included in this directory to compare your
answers to. E.g. a log file like log.date.chain.lmp.scaled.foo.P is
for a scaled-size version of the Chain benchmark, run on P processors
of machine "foo" with the dated version of LAMMPS. Note that the Eam
and Lj benchmarks may not give identical answers on different machines
because of the "velocity loop geom" option that assigns velocities
based on atom coordinates - see the discussion in the documentation
for the velocity command for details.
The CPU time (in seconds) for the run is in the "Loop time" line
of the log files, e.g.
Loop time of 3.89418 on 8 procs for 100 steps with 32000 atoms
Timing results for these problems run on various machines are listed
on the Benchmarks page of the LAMMPS WWW Site.
----------------------------------------------------------------------
These are the 5 benchmark problems:
LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
neighbors per atom), NVE integration
Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
atom), NVE integration
EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
neighbors per atom), NVE integration
Chute = granular chute flow, frictional history potential with 1.1
sigma cutoff (7 neighbors per atom), NVE integration
Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
integration
----------------------------------------------------------------------
Here is how to run each problem, assuming the LAMMPS executable is
named lmp_foo, and you are using the mpirun command to launch parallel
runs:
Serial (one processor runs):
lmp_foo < in.lj
lmp_foo < in.chain
lmp_foo < in.eam
lmp_foo < in.chute
lmp_foo < in.rhodo
Parallel fixed-size runs (on 8 procs in this case):
mpirun -np 8 lmp_foo < in.lj
mpirun -np 8 lmp_foo < in.chain
mpirun -np 8 lmp_foo < in.eam
mpirun -np 8 lmp_foo < in.chute
mpirun -np 8 lmp_foo < in.rhodo
Parallel scaled-size runs (on 16 procs in this case):
mpirun -np 16 lmp_foo -var x 40 -var y 40 -var z 80 < in.lj
mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.chain.scaled
mpirun -np 16 lmp_foo -var x 40 -var y 40 -var z 80 < in.eam
mpirun -np 16 lmp_foo -var x 4 -var y 4 < in.chute.scaled
mpirun -np 16 lmp_foo -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
For each of the scaled-size runs you must set 3 variables as -var
command line switches. The variables are used in the input scripts to
scale up the problem size in each dimension. Imagine the P processors
arrayed as a 3d grid, so that P = Px * Py * Pz. For P = 16, you might
use Px = 2, Py = 2, Pz = 4. To scale up equally in all dimensions you
roughly want Px = Py = Pz.
For LJ and Eam runs, use Px,Py,Pz multiplied by 20 to set the variable
values of x,y,z, as in the example mpirun commands above.
For Chain and Rhodo runs, use Px,Py,Pz directly to set the variable
values of x,y,z, as in the example mpirun commands above.
For Chute runs, you must have Pz = 1. Therefore P = Px * Py and you
only need to set variables x and y. Use Px,Py directly to set the
values of x,y, as in the example mpirun command above.

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Cu functions (universal 3)
29 63.550 3.6150 FCC
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2.0000139967999431e-02 1.9528853594166895e-02 1.9075514584991349e-02 1.8639062787818239e-02 1.8218510416650235e-02
1.7812937144080498e-02 1.7421485505751177e-02 1.7043356599549031e-02 1.6677806062561751e-02 1.6324140309613155e-02
1.5981713017976018e-02 1.5649921843605585e-02 1.5328205354974755e-02 1.5016040171312250e-02 1.4712938292708366e-02
1.4418444610242331e-02 1.4132134584901757e-02 1.3853612084676337e-02 1.3582507369821917e-02 1.3318475216818060e-02
1.3061193172097418e-02 1.2810359927147186e-02 1.2565693807050415e-02 1.2326931365025051e-02 1.2093826075940506e-02
1.1866147122233661e-02 1.1643678266026136e-02 1.1426216801644407e-02 1.1213572583084475e-02 1.1005567121320226e-02
1.0802032746662471e-02 1.0602811831688208e-02 1.0407756070544782e-02 1.0216725810699157e-02 1.0029589433467268e-02
9.8462227798860602e-03 9.6665086187306404e-03 9.4903361536790021e-03 9.3176005668363371e-03 9.1482025960089031e-03
8.9820481433065535e-03 8.8190479128032462e-03 8.6591170751522117e-03 8.5021749571883021e-03 8.3481447546937537e-03
8.1969532666261724e-03 8.0485306492223962e-03 7.9028101885199598e-03 7.7597280899136256e-03 7.6192232834934315e-03
7.4812372439735375e-03 7.3457138241272979e-03 7.2125991007052359e-03 7.0818412319012813e-03 6.9533903254870300e-03
6.8271983168139705e-03 6.7032188559211503e-03 6.5814072030662141e-03 6.4617201320263939e-03 6.3441158405819764e-03
6.2285538676237207e-03 6.1149950163802147e-03 6.0034012832899109e-03 5.8937357920846312e-03 5.7859627326801166e-03
5.6800473044990030e-03 5.5759556638887986e-03 5.4736548753111791e-03 5.3731128660109428e-03 5.2742983838981461e-03
5.1771809583849582e-03 5.0817308639591330e-03 4.9879190862693046e-03 4.8957172905357560e-03 4.8050977921015592e-03
4.7160335289582467e-03 4.6284980360953021e-03 4.5424654215287241e-03 4.4579103438822931e-03 4.3748079913988880e-03
4.2931340622749670e-03 4.2128647462132407e-03 4.1339767071033873e-03 4.0564470667446839e-03 3.9802533895282599e-03
3.9053736680121076e-03 3.8317863093158128e-03 3.7594701222811860e-03 3.6884043053326127e-03 3.6185684349951674e-03
3.5499424550168301e-03 3.4825066660512660e-03 3.4162417158645347e-03 3.3511285900229004e-03 3.2871486030347646e-03
3.2242833899080170e-03 3.1625148980992668e-03 3.1018253798278661e-03 3.0421973847258310e-03 2.9836137528083811e-03
2.9260576077371064e-03 2.8695123503632708e-03 2.8139616525287708e-03 2.7593894511106498e-03 2.7057799422959966e-03
2.6531175760685227e-03 2.6013870509009052e-03 2.5505733086344240e-03 2.5006615295404683e-03 2.4516371275501436e-03
2.4034857456453340e-03 2.3561932514012535e-03 2.3097457326723414e-03 2.2641294934160616e-03 2.2193310496436136e-03
2.1753371254977782e-03 2.1321346494441173e-03 2.0897107505768314e-03 2.0480527550303662e-03 2.0071481824917164e-03
1.9669847428123305e-03 1.9275503327108034e-03 1.8888330325659355e-03 1.8508211032951805e-03 1.8135029833145980e-03
1.7768672855772646e-03 1.7409027946878666e-03 1.7055984640891586e-03 1.6709434133182904e-03 1.6369269253308227e-03
1.6035384438881917e-03 1.5707675710093030e-03 1.5386040644797400e-03 1.5070378354209296e-03 1.4760589459142243e-03
1.4456576066784674e-03 1.4158241748004133e-03 1.3865491515145517e-03 1.3578231800324136e-03 1.3296370434173130e-03
1.3019816625059188e-03 1.2748480938728074e-03 1.2482275278369870e-03 1.2221112865106742e-03 1.1964908218862064e-03
1.1713577139624703e-03 1.1467036689077198e-03 1.1225205172586891e-03 1.0988002121543120e-03 1.0755348276031765e-03
1.0527165567835728e-03 1.0303377103750150e-03 1.0083907149206553e-03 9.8686811121878604e-04 9.6576255274356815e-04
9.4506680409354657e-04 9.2477373946662708e-04 9.0487634116191706e-04 8.8536769810608137e-04 8.6624100440530968e-04
8.4748955791986991e-04 8.2910675886310736e-04 8.1108610842155551e-04 7.9342120739794852e-04 7.7610575487466887e-04
7.5913354689786591e-04 7.4249847518158968e-04 7.2619452583109687e-04 7.1021577808524222e-04 6.9455640307671332e-04
6.7921066261025093e-04 6.6417290795844214e-04 6.4943757867335500e-04 6.3499920141575628e-04 6.2085238879914031e-04
6.0699183824991856e-04 5.9341233088238896e-04 5.8010873038847818e-04 5.6707598194186137e-04 5.5430911111587280e-04
5.4180322281523891e-04 5.2955350022104025e-04 5.1755520374872563e-04 5.0580367001857793e-04 4.9429431083891986e-04
4.8302261220136561e-04 4.7198413328763435e-04 4.6117450548847222e-04 4.5058943143359842e-04 4.4022468403297037e-04
4.3007610552883886e-04 4.2013960655883260e-04 4.1041116522908330e-04 4.0088682619821882e-04 3.9156269977118005e-04
3.8243496100300207e-04 3.7349984881274514e-04 3.6475366510662147e-04 3.5619277391102898e-04 3.4781360051482253e-04
3.3961263062063513e-04 3.3158640950565685e-04 3.2373154119109092e-04 3.1604468762060252e-04 3.0852256784754707e-04
3.0116195723081836e-04 2.9395968663908575e-04 2.8691264166377101e-04 2.8001776184017647e-04 2.7327203987681688e-04
2.6667252089326854e-04 2.6021630166557681e-04 2.5390052988028163e-04 2.4772240339593181e-04 2.4167916951265550e-04
2.3576812424967210e-04 2.2998661163024531e-04 2.2433202297460642e-04 2.1880179620031078e-04 2.1339341513026532e-04
2.0810440880823181e-04 2.0293235082175821e-04 1.9787485863260665e-04 1.9292959291436311e-04 1.8809425689761319e-04
1.8336659572205580e-04 1.7874439579616125e-04 1.7422548416372047e-04 1.6980772787763936e-04 1.6548903338088530e-04
1.6126734589430591e-04 1.5714064881157744e-04 1.5310696310104604e-04 1.4916434671449329e-04 1.4531089400280153e-04
1.4154473513841234e-04 1.3786403554466153e-04 1.3426699533172857e-04 1.3075184873951283e-04 1.2731686358694039e-04
1.2396034072819674e-04 1.2068061351527565e-04 1.1747604726729168e-04 1.1434503874632306e-04 1.1128601563955686e-04
1.0829743604811193e-04 1.0537778798212988e-04 1.0252558886227753e-04 9.9739385027582898e-05 9.7017751249615057e-05
9.4359290252773662e-05 9.1762632240957511e-05 8.9226434430383569e-05 8.6749380588361721e-05 8.4330180578390864e-05
8.1967569911181246e-05 7.9660309301724484e-05 7.7407184232279429e-05 7.5207004521348451e-05 7.3058603898526649e-05
7.0960839585107720e-05 6.8912591880629977e-05 6.6912763755002085e-05 6.4960280446513426e-05 6.3054089065330086e-05
6.1193158202771814e-05 5.9376477546041213e-05 5.7603057498502742e-05 5.5871928805544500e-05 5.4182142185708361e-05
5.2532767967318744e-05 5.0922895730446966e-05 4.9351633954125953e-05 4.7818109668823321e-05 4.6321468114150300e-05
4.4860872401664663e-05 4.3435503182825573e-05 4.2044558321957873e-05 4.0687252574273750e-05 3.9362817268785450e-05
3.8070499996214428e-05 3.6809564301621984e-05 3.5579289382025496e-05 3.4378969788611451e-05 3.3207915133769052e-05
3.2065449802711312e-05 3.0950912669766876e-05 2.9863656819185611e-05 2.8803049270468119e-05 2.7768470708167169e-05
2.6759315216115260e-05 2.5774990015931323e-05 2.4814915209964844e-05 2.3878523528387922e-05 2.2965260080560611e-05
2.2074582110528148e-05 2.1205958756658535e-05 2.0358870815317476e-05 1.9532810508535560e-05 1.8727281255713447e-05
1.7941797449145505e-05 1.7175884233475961e-05 1.6429077288930018e-05 1.5700922618341645e-05 1.4990976337865471e-05
1.4298804471386687e-05 1.3623982748522034e-05 1.2966096406226424e-05 1.2324739993882115e-05 1.1699517181902770e-05
1.1090040573734860e-05 1.0495931521266495e-05 9.9168199435395021e-06 9.3523441487842465e-06 8.8021506596591475e-06
8.2658940417265321e-06 7.7432367350197678e-06 7.2338488887770244e-06 6.7374081991923703e-06 6.2535997501888662e-06
5.7821158571569505e-06 5.3226559136389283e-06 4.8749262408651290e-06 4.4386399401326240e-06 4.0135167480073166e-06
3.5992828942305738e-06 3.1956709623667747e-06 2.8024197531120341e-06 2.4192741502208947e-06 2.0459849890155880e-06
1.6823089274468580e-06 1.3280083196495871e-06 9.8285109196557868e-07 6.4661062138351467e-07 3.1906561636122974e-07
0. 0. 0. 0. 0.

95710
bench/data.chain Normal file
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64015
bench/data.chute Normal file
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191072
bench/data.rhodo Normal file
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25
bench/in.chain Normal file
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# FENE beadspring benchmark
units lj
atom_style bond
special_bonds 0.0 1.0 1.0
read_data data.chain
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
run 100

32
bench/in.chain.scaled Normal file
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# FENE beadspring benchmark
variable x index 1
variable y index 1
variable z index 1
units lj
atom_style bond
atom_modify map hash
special_bonds 0.0 1.0 1.0
read_data data.chain
replicate $x $y $z
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
run 100

29
bench/in.chute Normal file
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# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style granular
boundary p p fs
newton off
read_data data.chute
pair_style gran/history 200000.0 50.0 0.5 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity chute 26.0
fix 2 bottom freeze
fix 3 active nve/gran
thermo_style granular
thermo 100
run 100

34
bench/in.chute.scaled Normal file
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# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
variable x index 1
variable y index 1
units lj
atom_style granular
boundary p p fs
newton off
read_data data.chute
replicate $x $y 1
pair_style gran/history 200000.0 50.0 0.5 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity chute 26.0
fix 2 bottom freeze
fix 3 active nve/gran
thermo_style granular
thermo 100
run 100

28
bench/in.eam Normal file
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# bulk Cu lattice
variable x index 20
variable y index 20
variable z index 20
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1
pair_style eam
pair_coeff 1 1 cuu3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100

27
bench/in.lj Normal file
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# 3d Lennard-Jones melt
variable x index 20
variable y index 20
variable z index 20
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100

27
bench/in.rhodo Normal file
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# Rhodopsin model
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt 300.0 300.0 100.0 &
aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100

34
bench/in.rhodo.scaled Normal file
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# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
replicate $x $y $z
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt 300.0 300.0 100.0 &
aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100

58
bench/log.1Oct06.chain.lmp.fixed.liberty.8 Normal file
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LAMMPS (1 Oct 2006)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds 0.0 1.0 1.0
read_data data.chain
1 = max bonds/atom
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
run 100
Memory usage per processor = 2.55132 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97000691 0.44751221 20.498199 22.400676 4.7159344
Loop time of 0.558263 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0848848 (15.2052)
Bond time (%) = 0.0478233 (8.56643)
Neigh time (%) = 0.136857 (24.5147)
Comm time (%) = 0.17255 (30.9083)
Outpt time (%) = 0.000431776 (0.0773427)
Other time (%) = 0.115718 (20.7281)
Nlocal: 4000 ave 4029 max 3985 min
Histogram: 2 0 2 1 2 0 0 0 0 1
Nghost: 2592.25 ave 2602 max 2566 min
Histogram: 1 0 0 0 0 1 1 1 0 4
Neighs: 19477.4 ave 19776 max 19279 min
Histogram: 1 2 2 0 0 0 1 1 0 1
Total # of neighbors = 155819
Ave neighs/atom = 4.86934
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

58
bench/log.1Oct06.chain.lmp.fixed.linux.1 Normal file
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LAMMPS (1 Oct 2006)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds 0.0 1.0 1.0
read_data data.chain
1 = max bonds/atom
1 by 1 by 1 processor grid
32000 atoms
32000 velocities
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
run 100
Memory usage per processor = 8.45251 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97434451 0.439712 20.499596 22.400779 4.6558589
Loop time of 7.46203 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 2.27111 (30.4355)
Bond time (%) = 0.614795 (8.23898)
Neigh time (%) = 2.60854 (34.9576)
Comm time (%) = 0.387562 (5.19379)
Outpt time (%) = 0.00133 (0.0178236)
Other time (%) = 1.57869 (21.1563)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9537 ave 9537 max 9537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155877 ave 155877 max 155877 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155877
Ave neighs/atom = 4.87116
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

73
bench/log.1Oct06.chain.lmp.scaled.liberty.8 Normal file
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LAMMPS (1 Oct 2006)
# FENE beadspring benchmark
variable x index 1
variable y index 1
variable z index 1
units lj
atom_style bond
atom_modify map hash
special_bonds 0.0 1.0 1.0
read_data data.chain
1 = max bonds/atom
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
2 by 2 by 2 processor grid
256000 atoms
253440 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
run 100
Memory usage per processor = 10.1502 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97027119 0.44484087 20.494523 22.394765 4.6721833
100 0.97424237 0.44152909 20.501694 22.404581 4.6873411
Loop time of 5.67904 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 1.11213 (19.5831)
Bond time (%) = 0.547845 (9.64677)
Neigh time (%) = 1.54568 (27.2173)
Comm time (%) = 1.02577 (18.0624)
Outpt time (%) = 0.00302154 (0.0532051)
Other time (%) = 1.44459 (25.4372)
Nlocal: 32000 ave 32058 max 31953 min
Histogram: 1 1 0 1 2 1 1 0 0 1
Nghost: 9505.38 ave 9533 max 9479 min
Histogram: 2 0 0 1 0 2 1 1 0 1
Neighs: 155776 ave 156274 max 155380 min
Histogram: 1 0 1 1 3 1 0 0 0 1
Total # of neighbors = 1246208
Ave neighs/atom = 4.868
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

58
bench/log.1Oct06.chute.lmp.fixed.liberty.8 Normal file
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LAMMPS (1 Oct 2006)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style granular
boundary p p fs
newton off
read_data data.chute
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
pair_style gran/history 200000.0 50.0 0.5 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity chute 26.0
fix 2 bottom freeze
fix 3 active nve/gran
thermo_style granular
thermo 100
run 100
Memory usage per processor = 9.31091 Mbytes
Step Atoms Trans-KE Rot-KE Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 0.696548 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.306387 (43.9864)
Neigh time (%) = 0.0181609 (2.60727)
Comm time (%) = 0.160018 (22.9731)
Outpt time (%) = 0.000968486 (0.139041)
Other time (%) = 0.211014 (30.2942)
Nlocal: 4000 ave 4005 max 3995 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Nghost: 1736.5 ave 1739 max 1734 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Neighs: 15093 ave 15610 max 14576 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Total # of neighbors = 120744
Ave neighs/atom = 3.77325
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style granular
boundary p p fs
newton off
read_data data.chute
1 by 1 by 1 processor grid
32000 atoms
32000 velocities
pair_style gran/history 200000.0 50.0 0.5 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity chute 26.0
fix 2 bottom freeze
fix 3 active nve/gran
thermo_style granular
thermo 100
run 100
Memory usage per processor = 30.7824 Mbytes
Step Atoms Trans-KE Rot-KE Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 7.0548 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 4.59052 (65.0694)
Neigh time (%) = 0.444649 (6.30278)
Comm time (%) = 0.263586 (3.73626)
Outpt time (%) = 0.002312 (0.032772)
Other time (%) = 1.75374 (24.8588)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115133
Ave neighs/atom = 3.59791
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
variable x index 1
variable y index 1
units lj
atom_style granular
boundary p p fs
newton off
read_data data.chute
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
replicate $x $y 1
replicate 2 $y 1
replicate 2 4 1
2 by 4 by 1 processor grid
256000 atoms
pair_style gran/history 200000.0 50.0 0.5 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
7296 atoms in group bottom
group active subtract all bottom
248704 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity chute 26.0
fix 2 bottom freeze
fix 3 active nve/gran
thermo_style granular
thermo 100
run 100
ERROR: Pair style peri requires atoms have IDs

59
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LAMMPS (1 Oct 2006)
# bulk Cu lattice
variable x index 20
variable y index 20
variable z index 20
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 $x 0 $y 0 $z
region box block 0 20 0 $y 0 $z
region box block 0 20 0 20 0 $z
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (72.3 72.3 72.3)
2 by 2 by 2 processor grid
create_atoms 1
Created 32000 atoms
pair_style eam
pair_coeff 1 1 cuu3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Memory usage per processor = 2.51765 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.35 18700.769
50 781.34228 -109870.68 0 -106639.02 52610.512
100 792.17919 -109916.28 0 -106639.81 51732.452
Loop time of 2.76732 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 2.17097 (78.4503)
Neigh time (%) = 0.18389 (6.64505)
Comm time (%) = 0.337954 (12.2123)
Outpt time (%) = 0.000817209 (0.0295307)
Other time (%) = 0.0736872 (2.66277)
Nlocal: 4000 ave 4026 max 3981 min
Histogram: 1 1 0 2 1 2 0 0 0 1
Nghost: 5840.62 ave 5860 max 5815 min
Histogram: 1 0 0 0 3 0 2 0 1 1
Neighs: 151237 ave 152083 max 150650 min
Histogram: 2 1 0 0 3 0 1 0 0 1
Total # of neighbors = 1209898
Ave neighs/atom = 37.8093
Neighbor list builds = 13
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# bulk Cu lattice
variable x index 20
variable y index 20
variable z index 20
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 $x 0 $y 0 $z
region box block 0 20 0 $y 0 $z
region box block 0 20 0 20 0 $z
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (72.3 72.3 72.3)
1 by 1 by 1 processor grid
create_atoms 1
Created 32000 atoms
pair_style eam
pair_coeff 1 1 cuu3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Memory usage per processor = 15.1091 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.35 18700.769
50 781.34228 -109870.68 0 -106639.02 52610.512
100 792.17919 -109916.28 0 -106639.81 51732.452
Loop time of 31.1581 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 27.3229 (87.6912)
Neigh time (%) = 2.60888 (8.37301)
Comm time (%) = 0.368158 (1.18158)
Outpt time (%) = 0.001816 (0.00582833)
Other time (%) = 0.85635 (2.7484)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.2099e+06 ave 1.2099e+06 max 1.2099e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209898
Ave neighs/atom = 37.8093
Neighbor list builds = 13
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# bulk Cu lattice
variable x index 20
variable y index 20
variable z index 20
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 $x 0 $y 0 $z
region box block 0 40 0 $y 0 $z
region box block 0 40 0 40 0 $z
region box block 0 40 0 40 0 40
create_box 1 box
Created box = (0 0 0) to (144.6 144.6 144.6)
2 by 2 by 2 processor grid
create_atoms 1
Created 256000 atoms
pair_style eam
pair_coeff 1 1 cuu3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Memory usage per processor = 14.9873 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -906240 0 -853297.36 18701.28
50 799.87665 -879587.33 0 -853120.09 51528.346
100 784.7092 -879087.36 0 -853121.99 51929.574
Loop time of 23.074 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 18.7307 (81.1765)
Neigh time (%) = 1.95514 (8.47332)
Comm time (%) = 1.47881 (6.40896)
Outpt time (%) = 0.00384498 (0.0166636)
Other time (%) = 0.905552 (3.92455)
Nlocal: 32000 ave 32128 max 31853 min
Histogram: 1 0 1 1 0 1 1 2 0 1
Nghost: 19909.9 ave 20057 max 19782 min
Histogram: 1 0 2 1 1 0 1 1 0 1
Neighs: 1.20868e+06 ave 1.21395e+06 max 1.20305e+06 min
Histogram: 1 2 0 0 0 0 2 2 0 1
Total # of neighbors = 9669468
Ave neighs/atom = 37.7714
Neighbor list builds = 14
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# 3d Lennard-Jones melt
variable x index 20
variable y index 20
variable z index 20
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
region box block 0 20 0 $y 0 $z
region box block 0 20 0 20 0 $z
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
2 by 2 by 2 processor grid
create_atoms 1
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 2.13618 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.77196819 -5.7795465 0 -4.6216304 0.079908069
Loop time of 1.2329 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.803863 (65.2008)
Neigh time (%) = 0.0741274 (6.01243)
Comm time (%) = 0.294729 (23.9053)
Outpt time (%) = 0.000427932 (0.0347093)
Other time (%) = 0.059756 (4.84677)
Nlocal: 4000 ave 4038 max 3962 min
Histogram: 2 1 0 1 0 0 2 0 0 2
Nghost: 5778.12 ave 5820 max 5742 min
Histogram: 2 0 2 0 0 1 0 2 0 1
Neighs: 150441 ave 152219 max 147904 min
Histogram: 1 0 0 2 0 1 0 2 0 2
Total # of neighbors = 1203529
Ave neighs/atom = 37.6103
Neighbor list builds = 5
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# 3d Lennard-Jones melt
variable x index 20
variable y index 20
variable z index 20
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
region box block 0 20 0 $y 0 $z
region box block 0 20 0 20 0 $z
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 processor grid
create_atoms 1
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 13.278 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.77196819 -5.7795465 0 -4.6216304 0.079908069
Loop time of 15.8447 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 13.7396 (86.7142)
Neigh time (%) = 1.07461 (6.78214)
Comm time (%) = 0.327973 (2.06993)
Outpt time (%) = 0.001538 (0.00970674)
Other time (%) = 0.700972 (4.42403)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19715 ave 19715 max 19715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20353e+06 ave 1.20353e+06 max 1.20353e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1203529
Ave neighs/atom = 37.6103
Neighbor list builds = 5
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# 3d Lennard-Jones melt
variable x index 20
variable y index 20
variable z index 20
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
region box block 0 40 0 $y 0 $z
region box block 0 40 0 40 0 $z
region box block 0 40 0 40 0 40
create_box 1 box
Created box = (0 0 0) to (67.1838 67.1838 67.1838)
2 by 2 by 2 processor grid
create_atoms 1
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 13.1944 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6133765 -5.019674
100 0.7616931 -5.7642895 0 -4.6217544 0.20907141
Loop time of 9.80536 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 7.10165 (72.4262)
Neigh time (%) = 0.641534 (6.54269)
Comm time (%) = 1.25001 (12.7483)
Outpt time (%) = 0.00192311 (0.0196129)
Other time (%) = 0.810236 (8.2632)
Nlocal: 32000 ave 32077 max 31945 min
Histogram: 2 2 0 1 0 0 0 1 1 1
Nghost: 19666.1 ave 19728 max 19582 min
Histogram: 1 0 1 1 0 1 0 2 0 2
Neighs: 1.20362e+06 ave 1.20977e+06 max 1.19745e+06 min
Histogram: 1 2 0 0 1 0 2 0 0 2
Total # of neighbors = 9628940
Ave neighs/atom = 37.613
Neighbor list builds = 5
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# Rhodopsin model
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector = 0.245875
grid = 24 32 30
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 7140 3072 3780
Memory usage per processor = 29.8784 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8070 KinEng = 21444.8287 Temp = 299.0420
PotEng = -46800.6357 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 203819.9996 E_long = -267197.4382 Press = -142.0854
Volume = 307995.0335
---------------- Step 50 ----- CPU = 10.3500 (sec) ----------------
TotEng = -25330.0515 KinEng = 21500.8719 Temp = 299.8235
PotEng = -46830.9234 E_bond = 2471.7510 E_angle = 10836.5171
E_dihed = 5239.6981 E_impro = 227.1295 E_vdwl = -1992.9813
E_coul = 203591.2432 E_long = -267204.2808 Press = 238.5401
Volume = 308031.8248
---------------- Step 100 ----- CPU = 21.1191 (sec) ----------------
TotEng = -25291.9828 KinEng = 21589.3087 Temp = 301.0567
PotEng = -46881.2915 E_bond = 2568.0314 E_angle = 10781.6607
E_dihed = 5198.3574 E_impro = 216.6809 E_vdwl = -1898.4756
E_coul = 203451.1288 E_long = -267198.6749 Press = 10.7061
Volume = 308134.7569
Loop time of 21.1201 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 13.2797 (62.8773)
Bond time (%) = 0.57078 (2.70255)
Kspce time (%) = 3.77787 (17.8876)
Neigh time (%) = 1.58397 (7.49984)
Comm time (%) = 0.793642 (3.75777)
Outpt time (%) = 0.00181401 (0.00858903)
Other time (%) = 1.11227 (5.2664)
FFT time (% of Kspce) = 0.459179 (12.1545)
FFT Gflps 3d 1d-only = 1.00804 7.35704
Nlocal: 4000 ave 4083 max 3940 min
Histogram: 2 1 0 1 2 0 0 0 1 1
Nghost: 16028.4 ave 16084 max 15941 min
Histogram: 1 0 0 2 0 1 0 0 2 2
Neighs: 1.5035e+06 ave 1.55024e+06 max 1.46322e+06 min
Histogram: 2 0 1 0 2 1 0 0 0 2
Total # of neighbors = 12027974
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# Rhodopsin model
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
1 by 1 by 1 processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector = 0.245875
grid = 24 32 30
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 37555 23040 11655
Memory usage per processor = 134.397 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8070 KinEng = 21444.8287 Temp = 299.0420
PotEng = -46800.6357 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 203819.9996 E_long = -267197.4382 Press = -142.0854
Volume = 307995.0335
---------------- Step 50 ----- CPU = 158.6744 (sec) ----------------
TotEng = -25330.0515 KinEng = 21500.8719 Temp = 299.8235
PotEng = -46830.9234 E_bond = 2471.7510 E_angle = 10836.5171
E_dihed = 5239.6981 E_impro = 227.1295 E_vdwl = -1992.9813
E_coul = 203591.2432 E_long = -267204.2808 Press = 238.5401
Volume = 308031.8248
---------------- Step 100 ----- CPU = 322.3292 (sec) ----------------
TotEng = -25291.9828 KinEng = 21589.3087 Temp = 301.0567
PotEng = -46881.2915 E_bond = 2568.0314 E_angle = 10781.6607
E_dihed = 5198.3574 E_impro = 216.6809 E_vdwl = -1898.4756
E_coul = 203451.1288 E_long = -267198.6749 Press = 10.7061
Volume = 308134.7569
Loop time of 322.329 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 239.178 (74.203)
Bond time (%) = 7.33387 (2.27527)
Kspce time (%) = 19.0626 (5.914)
Neigh time (%) = 49.7111 (15.4224)
Comm time (%) = 0.930179 (0.28858)
Outpt time (%) = 0.003927 (0.00121832)
Other time (%) = 6.10957 (1.89544)
FFT time (% of Kspce) = 4.06694 (21.3347)
FFT Gflps 3d 1d-only = 0.113814 0.261395
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47962 ave 47962 max 47962 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12027974
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

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LAMMPS (1 Oct 2006)
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
2 by 2 by 2 processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector = 0.245875
grid = 48 64 60
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 37555 24576 11655
Memory usage per processor = 140.353 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -202846.4560 KinEng = 171558.6298 Temp = 299.0311
PotEng = -374405.0858 E_bond = 20303.9521 E_angle = 87370.9937
E_dihed = 41694.2920 E_impro = 1708.0927 E_vdwl = -18462.9073
E_coul = 1630559.9965 E_long = -2137579.5054 Press = -142.0854
Volume = 2463960.2680
---------------- Step 50 ----- CPU = 80.3339 (sec) ----------------
TotEng = -202634.6400 KinEng = 172010.0889 Temp = 299.8180
PotEng = -374644.7289 E_bond = 19774.2719 E_angle = 86693.1834
E_dihed = 41917.7603 E_impro = 1817.0606 E_vdwl = -15943.4739
E_coul = 1628730.7042 E_long = -2137634.2354 Press = 238.6347
Volume = 2464254.6396
---------------- Step 100 ----- CPU = 165.2014 (sec) ----------------
TotEng = -202318.7870 KinEng = 172723.1177 Temp = 301.0609
PotEng = -375041.9047 E_bond = 20545.0687 E_angle = 86256.5048
E_dihed = 41587.4799 E_impro = 1733.5220 E_vdwl = -15187.0971
E_coul = 1627611.9671 E_long = -2137589.3501 Press = 10.9015
Volume = 2465078.6410
Loop time of 165.202 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 109.485 (66.2732)
Bond time (%) = 4.55416 (2.75672)
Kspce time (%) = 26.1207 (15.8114)
Neigh time (%) = 14.7538 (8.93074)
Comm time (%) = 2.72842 (1.65156)
Outpt time (%) = 0.00508916 (0.00308057)
Other time (%) = 7.55527 (4.57335)
FFT time (% of Kspce) = 6.32901 (24.2299)
FFT Gflps 3d 1d-only = 0.7062 7.01015
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 47962 ave 47962 max 47962 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 1.2028e+07 ave 1.2057e+07 max 1.19989e+07 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Total # of neighbors = 96223728
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0