Commit aaadfa57 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@653 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 33372132

bench/log.22Jun07.chain.fixed.linux.1

0 → 100644
+59 −0
Original line number Diff line number Diff line 
LAMMPS (22 June 2007)

# FENE beadspring benchmark



units		lj

atom_style	bond

special_bonds   0.0 1.0 1.0



read_data	data.chain

  1 = max bonds/atom

  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)

  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 = 8.52881 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 7.13438 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 2.21672 (31.0709)

Bond  time (%) = 0.614869 (8.61839)

Neigh time (%) = 2.68187 (37.5908)

Comm  time (%) = 0.329216 (4.6145)

Outpt time (%) = 0.001037 (0.0145353)

Other time (%) = 1.29067 (18.0908)



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

bench/log.22Jun07.chute.fixed.linux.1

0 → 100644
+59 −0
Original line number Diff line number Diff line 
LAMMPS (22 June 2007)

# 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

  orthogonal box = (0 0 0) to (40 20 37.2886)

  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 = 30.935 Mbytes

Step Atoms KinEng RotKEgrn Volume 

       0    32000    784139.13    1601.1263     29830.88 

     100    32000    784289.99    1571.0137    29831.804 

Loop time of 6.87253 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 4.6578 (67.7741)

Neigh time (%) = 0.45709 (6.65097)

Comm  time (%) = 0.247749 (3.60492)

Outpt time (%) = 0.001582 (0.0230192)

Other time (%) = 1.50831 (21.9469)



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

bench/log.22Jun07.eam.fixed.linux.1

0 → 100644
+60 −0
Original line number Diff line number Diff line 
LAMMPS (22 June 2007)

# bulk Cu lattice



variable	x index 20

variable	y index 20

variable	z index 20



units		metal

atom_style	atomic



lattice		fcc 3.615

Lattice spacing in x,y,z = 3.615 3.615 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 orthogonal box = (0 0 0) to (72.3 72.3 72.3)

  1 by 1 by 1 processor grid

create_atoms	1 box

Created 32000 atoms



pair_style	eam

pair_coeff	1 1 Cu_u3.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 = 15.2616 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         1600      -113280            0   -106662.09    18703.573 

      50    781.37184   -109870.67            0   -106638.76     52616.84 

     100    792.19277   -109916.21            0   -106639.54     51739.67 

Loop time of 31.0146 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 27.1822 (87.6433)

Neigh time (%) = 2.71986 (8.76962)

Comm  time (%) = 0.338775 (1.09231)

Outpt time (%) = 0.002124 (0.00684839)

Other time (%) = 0.771616 (2.48791)



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:    1.20989e+06 ave 1.20989e+06 max 1.20989e+06 min

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



Total # of neighbors = 1209894

Ave neighs/atom = 37.8092

Neighbor list builds = 13

Dangerous builds = 0

bench/log.22Jun07.lj.fixed.linux.1

0 → 100644
+57 −0
Original line number Diff line number Diff line 
LAMMPS (22 June 2007)

# 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

Lattice spacing in x,y,z = 1.6796 1.6796 1.6796

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 orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)

  1 by 1 by 1 processor grid

create_atoms	1 box

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 = 13.4306 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 13.8981 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 12.0067 (86.3907)

Neigh time (%) = 1.07342 (7.72346)

Comm  time (%) = 0.271477 (1.95334)

Outpt time (%) = 0.000835 (0.00600801)

Other time (%) = 0.545714 (3.92653)



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

bench/log.22Jun07.rhodo.fixed.linux.1

0 → 100644
+96 −0
Original line number Diff line number Diff line 
LAMMPS (22 June 2007)

# 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

  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)

  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 = 134.779 Mbytes

---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------

TotEng   =    -25355.8254 KinEng   =     21444.8313 Temp     =       299.0397 

PotEng   =    -46800.6567 E_bond   =      2537.9940 E_angle  =     10921.3742 

E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 

E_coul   =    203820.0671 E_long   =   -267197.5267 Press    =      -142.0456 

Volume   =    307995.0335 

---------------- Step       50 ----- CPU =    152.6104 (sec) ----------------

TotEng   =    -25329.9175 KinEng   =     21500.9583 Temp     =       299.8223 

PotEng   =    -46830.8758 E_bond   =      2471.7583 E_angle  =     10836.5458 

E_dihed  =      5239.7029 E_impro  =       227.1302 E_vdwl   =     -1992.9669 

E_coul   =    203591.3230 E_long   =   -267204.3691 Press    =       238.4815 

Volume   =    308031.8243 

---------------- Step      100 ----- CPU =    309.5271 (sec) ----------------

TotEng   =    -25291.5484 KinEng   =     21589.5399 Temp     =       301.0576 

PotEng   =    -46881.0883 E_bond   =      2568.0537 E_angle  =     10781.7480 

E_dihed  =      5198.3744 E_impro  =       216.6829 E_vdwl   =     -1898.4511 

E_coul   =    203451.2661 E_long   =   -267198.7623 Press    =        10.7451 

Volume   =    308134.7692 

Loop time of 309.527 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 231.215 (74.6994)

Bond  time (%) = 6.3242 (2.04318)

Kspce time (%) = 19.1711 (6.19366)

Neigh time (%) = 46.0779 (14.8865)

Comm  time (%) = 0.796922 (0.257464)

Outpt time (%) = 0.002562 (0.000827714)

Other time (%) = 5.93944 (1.91888)



FFT time (% of Kspce) = 3.96566 (20.6857)

FFT Gflps 3d 1d-only = 0.11672 0.259612



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 = 12027978

Ave neighs/atom = 375.874

Ave special neighs/atom = 7.43187

Neighbor list builds = 11

Dangerous builds = 0

CRA Git | Maintained and supported by SUSTech CRA and CCSE