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Commit 85a60a94 authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14607 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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bench/log.15May15.chain.fixed.icc.1 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.chain
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
master list distance cutoff = 1.52
Memory usage per processor = 11.5189 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 0.978717 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.195673 (19.9928)
Bond time (%) = 0.0878832 (8.97943)
Neigh time (%) = 0.448004 (45.7746)
Comm time (%) = 0.0329976 (3.37152)
Outpt time (%) = 0.000105143 (0.0107429)
Other time (%) = 0.214054 (21.8709)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9493 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155873 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0
bench/log.15May15.chain.fixed.icc.4 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.chain
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
master list distance cutoff = 1.52
Memory usage per processor = 3.91518 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97145835 0.43803883 20.502691 22.397872 4.626988
Loop time of 0.274371 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0504887 (18.4016)
Bond time (%) = 0.0229129 (8.35106)
Neigh time (%) = 0.119957 (43.7206)
Comm time (%) = 0.020835 (7.59373)
Outpt time (%) = 5.74589e-05 (0.0209421)
Other time (%) = 0.0601202 (21.912)
Nlocal: 8000 ave 8030 max 7974 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 4177 ave 4191 max 4160 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 38995.8 ave 39169 max 38852 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 155983
Ave neighs/atom = 4.87447
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0
bench/log.15May15.chain.scaled.icc.4 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# 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 fene
read_data data.chain
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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 1
orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
2 by 2 by 1 MPI processor grid
128000 atoms
126720 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
master list distance cutoff = 1.52
Memory usage per processor = 12.8735 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
Loop time of 1.19919 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 0.227794 (18.9957)
Bond time (%) = 0.0981662 (8.18606)
Neigh time (%) = 0.527868 (44.0188)
Comm time (%) = 0.0980042 (8.17255)
Outpt time (%) = 0.000200272 (0.0167006)
Other time (%) = 0.247155 (20.6102)
Nlocal: 32000 ave 32015 max 31983 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 9492 ave 9522 max 9432 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 155837 ave 156079 max 155506 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 623349
Ave neighs/atom = 4.86991
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0
bench/log.15May15.chute.fixed.icc.1 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
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 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 1.1
Memory usage per processor = 15.567 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.539647 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.328789 (60.9267)
Neigh time (%) = 0.0401711 (7.44397)
Comm time (%) = 0.0179052 (3.31795)
Outpt time (%) = 0.00019908 (0.0368907)
Other time (%) = 0.152582 (28.2745)
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 (30 Apr 2015)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
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 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 1.1
Memory usage per processor = 6.81783 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.146584 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0737562 (50.3167)
Neigh time (%) = 0.0105147 (7.17314)
Comm time (%) = 0.0147474 (10.0607)
Outpt time (%) = 0.000131965 (0.0900267)
Other time (%) = 0.0474337 (32.3594)
Nlocal: 8000 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2439 ave 2450 max 2428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 29500.5 ave 30488 max 28513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 118002
Ave neighs/atom = 3.68756
Neighbor list builds = 2
Dangerous builds = 0
bench/log.15May15.chute.scaled.icc.4 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# 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 sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
replicate $x $y 1
replicate 2 $y 1
replicate 2 2 1
orthogonal box = (0 0 0) to (80 40 37.2922)
2 by 2 by 1 MPI processor grid
128000 atoms
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
group bottom type 2
3648 atoms in group bottom
group active subtract all bottom
124352 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 1.1
Memory usage per processor = 15.7007 Mbytes
Step Atoms KinEng 1 Volume
0 128000 3136556.5 6404.5051 119335.13
100 128000 3137168.3 6284.3873 119338.83
Loop time of 0.899154 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 0.523338 (58.2033)
Neigh time (%) = 0.0433982 (4.82656)
Comm time (%) = 0.0642623 (7.14697)
Outpt time (%) = 0.000541449 (0.0602175)
Other time (%) = 0.267615 (29.7629)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 460532
Ave neighs/atom = 3.59791
Neighbor list builds = 2
Dangerous builds = 0
bench/log.15May15.eam.fixed.icc.1 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 5.95
Memory usage per processor = 10.2238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 5.89995 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 5.21525 (88.3948)
Neigh time (%) = 0.579447 (9.82122)
Comm time (%) = 0.0302751 (0.513142)
Outpt time (%) = 0.000234127 (0.00396829)
Other time (%) = 0.0747423 (1.26683)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0
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LAMMPS (30 Apr 2015)
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 5.95
Memory usage per processor = 5.09629 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 1.57597 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 1.36786 (86.7953)
Neigh time (%) = 0.152391 (9.6697)
Comm time (%) = 0.0353726 (2.2445)
Outpt time (%) = 0.000111699 (0.00708766)
Other time (%) = 0.0202255 (1.28337)
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9130.25 ave 9138 max 9122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 301946 ave 302392 max 301360 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0
bench/log.15May15.eam.scaled.icc.4 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 128000 atoms
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 5.95
Memory usage per processor = 10.1402 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -453120 0 -426647.73 18704.012
50 779.50001 -439457.02 0 -426560.06 52355.276
100 797.97828 -439764.76 0 -426562.07 51474.74
Loop time of 6.4972 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 5.61297 (86.3906)
Neigh time (%) = 0.655333 (10.0864)
Comm time (%) = 0.130434 (2.00755)
Outpt time (%) = 0.000279069 (0.00429522)
Other time (%) = 0.0981811 (1.51113)
Nlocal: 32000 ave 32092 max 31914 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 19910 ave 19997 max 19818 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 4829126
Ave neighs/atom = 37.7275
Neighbor list builds = 14
Dangerous builds = 0
bench/log.15May15.lj.fixed.icc.1 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
master list distance cutoff = 2.8
Memory usage per processor = 8.21387 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 2.25588 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 1.93512 (85.7815)
Neigh time (%) = 0.236483 (10.483)
Comm time (%) = 0.0239627 (1.06224)
Outpt time (%) = 0.000118017 (0.00523155)
Other time (%) = 0.0601869 (2.66801)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0
bench/log.15May15.lj.fixed.icc.4 deleted 100644 → 0
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LAMMPS (30 Apr 2015)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
master list distance cutoff = 2.8
Memory usage per processor = 4.09506 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.623887 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.50691 (81.2504)
Neigh time (%) = 0.0619052 (9.92251)
Comm time (%) = 0.0389298 (6.23989)
Outpt time (%) = 5.85914e-05 (0.00939135)
Other time (%) = 0.0160829 (2.57785)
Nlocal: 8000 ave 8037 max 7964 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9007.5 ave 9050 max 8968 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300708 ave 305113 max 297203 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0
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LAMMPS (30 Apr 2015)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*1
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 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 128000 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
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
master list distance cutoff = 2.8
Memory usage per processor = 8.13678 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
Loop time of 2.53011 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 2.09024 (82.6146)
Neigh time (%) = 0.24414 (9.64939)
Comm time (%) = 0.111739 (4.41638)
Outpt time (%) = 0.000135601 (0.00535947)
Other time (%) = 0.0838551 (3.31428)
Nlocal: 32000 ave 32060 max 31939 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 19630.8 ave 19681 max 19562 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Total # of neighbors = 4807797
Ave neighs/atom = 37.5609
Neighbor list builds = 5
Dangerous builds = 0
bench/log.15May15.rhodo.fixed.icc.1 deleted 100644 → 0
+ 0
− 110
View file @ de853a37
LAMMPS (30 Apr 2015)
# 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
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 41070 25600
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
Memory usage per processor = 91.7487 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
Volume = 307995.0335
---------------- Step 50 ----- CPU = 17.3751 (sec) ----------------
TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
Volume = 308031.5639
---------------- Step 100 ----- CPU = 35.3771 (sec) ----------------
TotEng = -25290.7593 KinEng = 21592.0117 Temp = 301.0920
PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408
E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
E_coul = 206659.2326 E_long = -270404.9733 Press = 6.9960
Volume = 308133.9888
Loop time of 35.3771 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 25.4765 (72.0139)
Bond time (%) = 1.27905 (3.61547)
Kspce time (%) = 3.22381 (9.11269)
Neigh time (%) = 4.26655 (12.0602)
Comm time (%) = 0.0692198 (0.195663)
Outpt time (%) = 0.000253916 (0.00071774)
Other time (%) = 1.06179 (3.00134)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
bench/log.15May15.rhodo.fixed.icc.4 deleted 100644 → 0
+ 0
− 110
View file @ de853a37
LAMMPS (30 Apr 2015)
# 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
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
Memory usage per processor = 36.629 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
Volume = 307995.0335
---------------- Step 50 ----- CPU = 4.6438 (sec) ----------------
TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
Volume = 308031.5639
---------------- Step 100 ----- CPU = 9.4301 (sec) ----------------
TotEng = -25290.7591 KinEng = 21592.0117 Temp = 301.0920
PotEng = -46882.7708 E_bond = 2567.9807 E_angle = 10781.9408
E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960
Volume = 308133.9888
Loop time of 9.43015 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 6.53815 (69.3324)
Bond time (%) = 0.323679 (3.43239)
Kspce time (%) = 1.02664 (10.8868)
Neigh time (%) = 1.11839 (11.8597)
Comm time (%) = 0.0812459 (0.861554)
Outpt time (%) = 0.000150442 (0.00159533)
Other time (%) = 0.341896 (3.62557)
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
bench/log.15May15.rhodo.scaled.icc.4 deleted 100644 → 0
+ 0
− 131
View file @ de853a37
LAMMPS (30 Apr 2015)
# 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
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
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 1
orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
2 by 2 by 1 MPI processor grid
128000 atoms
110892 bonds
161868 angles
227316 dihedrals
4136 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
6468 = # of size 2 clusters
14532 = # of size 3 clusters
2988 = # of size 4 clusters
16932 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248593
grid = 48 60 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0359793
estimated relative force accuracy = 0.00010835
using double precision FFTs
3d grid and FFT values/proc = 41615 25920
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
Memory usage per processor = 95.5339 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 18.5923 (sec) ----------------
TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118
PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922
E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457
E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161
Volume = 1232126.1855
---------------- Step 100 ----- CPU = 38.1551 (sec) ----------------
TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393
PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454
E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151
Volume = 1232535.8423
Loop time of 38.1551 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 26.4472 (69.3149)
Bond time (%) = 1.31402 (3.44388)
Kspce time (%) = 4.23553 (11.1008)
Neigh time (%) = 4.45503 (11.6761)
Comm time (%) = 0.208946 (0.547622)
Outpt time (%) = 0.000290096 (0.000760307)
Other time (%) = 1.49411 (3.91587)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 47957 ave 47957 max 47957 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 48112472
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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