git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11410 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,77 +0,0 @@
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LAMMPS (18 Feb 2013)
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# 3d Lennard-Jones melt
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||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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*2
|
||||
|
||||
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 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 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
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 46.8462 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
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||||
100 0.75865618 -5.760326 0 -4.6223462 0.19586078
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||||
200 0.75643081 -5.7572862 0 -4.6226445 0.22641252
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||||
300 0.74927357 -5.7463992 0 -4.6224932 0.2973801
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||||
400 0.7404924 -5.7329247 0 -4.6221905 0.37767073
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||||
500 0.73092032 -5.7182616 0 -4.6218854 0.46900679
|
||||
600 0.72315678 -5.706314 0 -4.621583 0.5348031
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||||
700 0.71597165 -5.6952207 0 -4.6212675 0.59549602
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||||
800 0.71194748 -5.6889042 0 -4.6209871 0.63784817
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||||
900 0.70596464 -5.6796285 0 -4.6206857 0.68573109
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||||
1000 0.70323336 -5.67534 0 -4.6204941 0.7069076
|
||||
Loop time of 19.9863 on 1 procs for 1000 steps with 256000 atoms
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||||
|
||||
Pair time (%) = 12.3568 (61.8261)
|
||||
Neigh time (%) = 7.41482e-05 (0.000370995)
|
||||
Comm time (%) = 1.09925 (5.50003)
|
||||
Outpt time (%) = 0.0106428 (0.0532503)
|
||||
Other time (%) = 6.51958 (32.6202)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 69905 ave 69905 max 69905 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
@ -1,77 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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*2
|
||||
|
||||
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 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 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
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 14.5208 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
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||||
100 0.75865619 -5.7603258 0 -4.622346 0.19586113
|
||||
200 0.75643076 -5.7572857 0 -4.6226439 0.22641355
|
||||
300 0.74927365 -5.7463989 0 -4.6224928 0.29738053
|
||||
400 0.74049513 -5.7329265 0 -4.6221881 0.37765479
|
||||
500 0.73092165 -5.7182628 0 -4.6218846 0.46899675
|
||||
600 0.72307341 -5.7061845 0 -4.6215786 0.53536825
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||||
700 0.71593631 -5.6951696 0 -4.6212694 0.59644919
|
||||
800 0.71106107 -5.6875486 0 -4.6209611 0.6450072
|
||||
900 0.70789378 -5.6825117 0 -4.6206752 0.67079907
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||||
1000 0.70324302 -5.6753075 0 -4.6204471 0.71004301
|
||||
Loop time of 7.94848 on 4 procs for 1000 steps with 256000 atoms
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||||
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||||
Pair time (%) = 4.79772 (60.3603)
|
||||
Neigh time (%) = 5.11408e-05 (0.000643403)
|
||||
Comm time (%) = 1.32216 (16.6341)
|
||||
Outpt time (%) = 0.0349077 (0.439174)
|
||||
Other time (%) = 1.79364 (22.5658)
|
||||
|
||||
Nlocal: 64000 ave 64090 max 63900 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 30521 ave 30604 max 30461 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
@ -1,77 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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*2
|
||||
|
||||
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 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 58.5717 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
|
||||
100 0.7599844 -6.1430228 0 -5.0030506 -0.43702259
|
||||
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563906
|
||||
300 0.75029981 -6.1286575 0 -5.0032122 -0.33104595
|
||||
400 0.73999172 -6.1132482 0 -5.003265 -0.24002804
|
||||
500 0.73224839 -6.101694 0 -5.0033257 -0.16523398
|
||||
600 0.72448053 -6.0900827 0 -5.0033661 -0.099467461
|
||||
700 0.71878931 -6.0815935 0 -5.0034138 -0.044377743
|
||||
800 0.71440115 -6.0750377 0 -5.0034401 -0.008074032
|
||||
900 0.70942787 -6.0675896 0 -5.0034519 0.032869143
|
||||
1000 0.70453362 -6.0602662 0 -5.0034699 0.069294492
|
||||
Loop time of 43.6376 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 35.9388 (82.3573)
|
||||
Neigh time (%) = 7.1764e-05 (0.000164454)
|
||||
Comm time (%) = 1.41024 (3.23171)
|
||||
Outpt time (%) = 0.0104296 (0.0239005)
|
||||
Other time (%) = 6.27813 (14.387)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 141796 ave 141796 max 141796 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
@ -1,77 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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*2
|
||||
|
||||
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 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 20.382 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
|
||||
100 0.75998442 -6.1430228 0 -5.0030506 -0.43702261
|
||||
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563886
|
||||
300 0.75029993 -6.1286577 0 -5.0032122 -0.33104749
|
||||
400 0.73999255 -6.1132496 0 -5.0032651 -0.24002869
|
||||
500 0.73223505 -6.1016739 0 -5.0033256 -0.16512851
|
||||
600 0.72450374 -6.090118 0 -5.0033666 -0.099412819
|
||||
700 0.71914115 -6.082123 0 -5.0034155 -0.04585998
|
||||
800 0.71391558 -6.0743087 0 -5.0034395 -0.0061018629
|
||||
900 0.70919683 -6.0672408 0 -5.0034497 0.033186808
|
||||
1000 0.7053422 -6.0614666 0 -5.0034575 0.062941897
|
||||
Loop time of 21.0469 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 17.4649 (82.9807)
|
||||
Neigh time (%) = 5.51939e-05 (0.000262242)
|
||||
Comm time (%) = 1.69517 (8.05425)
|
||||
Outpt time (%) = 0.0226806 (0.107762)
|
||||
Other time (%) = 1.86413 (8.85702)
|
||||
|
||||
Nlocal: 64000 ave 64103 max 63848 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 64417.2 ave 64486 max 64349 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
@ -1,75 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
10950 atoms
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1520875 1259712
|
||||
Memory usage per processor = 266.927 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.97088 4242016.4
|
||||
100 411.69681 -2392428.5 0 -2376695.3 7046.6795 4308883.5
|
||||
200 401.284 -2394152.5 0 -2378817.2 3243.274 4334284.4
|
||||
Loop time of 156.48 on 1 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 12.2461 (7.82602)
|
||||
Kspce time (%) = 81.8041 (52.2777)
|
||||
Neigh time (%) = 0.0129185 (0.00825567)
|
||||
Comm time (%) = 0.346706 (0.221566)
|
||||
Outpt time (%) = 0.00171018 (0.0010929)
|
||||
Other time (%) = 62.0683 (39.6654)
|
||||
|
||||
FFT time (% of Kspce) = 57.1943 (69.9162)
|
||||
FFT Gflps 3d (1d only) = 1.23749 2.95335
|
||||
|
||||
Nlocal: 295650 ave 295650 max 295650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 226982 ave 226982 max 226982 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
@ -1,75 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
10950 atoms
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 427915 314928
|
||||
Memory usage per processor = 80.0769 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.971 4242016.4
|
||||
100 411.6968 -2392428.5 0 -2376695.3 7046.6956 4308883.5
|
||||
200 401.28397 -2394152.5 0 -2378817.2 3243.2753 4334284.4
|
||||
Loop time of 64.6184 on 4 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 5.24801 (8.12154)
|
||||
Kspce time (%) = 42.7106 (66.0967)
|
||||
Neigh time (%) = 0.00641513 (0.00992772)
|
||||
Comm time (%) = 0.553393 (0.856402)
|
||||
Outpt time (%) = 0.000457346 (0.000707766)
|
||||
Other time (%) = 16.0995 (24.9147)
|
||||
|
||||
FFT time (% of Kspce) = 22.695 (53.1367)
|
||||
FFT Gflps 3d (1d only) = 3.11864 11.5832
|
||||
|
||||
Nlocal: 73912.5 ave 74223 max 73638 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 105257 ave 105797 max 104698 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
@ -1,122 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
18 = max angles/atom
|
||||
40 = max dihedrals/atom
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 1 by 1 MPI 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
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 1 by 1 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 237705 184320
|
||||
Memory usage per processor = 760.048 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0524 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5631 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
|
||||
E_coul = 1894295.6653 E_long = -2130488.8032 Press = 9562.1554
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 36.9731 (sec) ----------------
|
||||
TotEng = -233301.5647 KinEng = 123222.8702 Temp = 214.7790
|
||||
PotEng = -356524.4350 E_bond = 13098.4680 E_angle = 56766.9162
|
||||
E_dihed = 45556.8237 E_impro = 1313.9365 E_vdwl = -40863.9296
|
||||
E_coul = 1705084.9441 E_long = -2137481.5939 Press = -1634.3724
|
||||
Volume = 2522232.6324
|
||||
---------------- Step 200 ----- CPU = 71.7796 (sec) ----------------
|
||||
TotEng = -308341.5902 KinEng = 108937.0512 Temp = 189.8786
|
||||
PotEng = -417278.6414 E_bond = 9579.0189 E_angle = 47373.5018
|
||||
E_dihed = 39847.3805 E_impro = 967.6494 E_vdwl = -23632.3384
|
||||
E_coul = 1646631.2737 E_long = -2138045.1272 Press = -1185.5582
|
||||
Volume = 2554682.9557
|
||||
Loop time of 71.7796 on 1 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 10.4771 (14.5962)
|
||||
Bond time (%) = 27.3962 (38.1671)
|
||||
Kspce time (%) = 7.23529 (10.0799)
|
||||
Neigh time (%) = 5.6228 (7.83343)
|
||||
Comm time (%) = 0.678451 (0.945186)
|
||||
Outpt time (%) = 0.001441 (0.00200754)
|
||||
Other time (%) = 20.3683 (28.3762)
|
||||
|
||||
FFT time (% of Kspce) = 5.21147 (72.0284)
|
||||
FFT Gflps 3d (1d only) = 1.71528 2.99119
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 161665 ave 161665 max 161665 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
@ -1,122 +0,0 @@
|
||||
LAMMPS (18 Feb 2013)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
18 = max angles/atom
|
||||
40 = max dihedrals/atom
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 2 by 2 MPI 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
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 2 by 2 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 68635 46080
|
||||
Memory usage per processor = 250.358 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0492 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5663 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
|
||||
E_coul = 1894295.6622 E_long = -2130488.8032 Press = 9562.1554
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 12.1280 (sec) ----------------
|
||||
TotEng = -233301.6590 KinEng = 123222.8183 Temp = 214.7789
|
||||
PotEng = -356524.4772 E_bond = 13098.4683 E_angle = 56766.9228
|
||||
E_dihed = 45556.8211 E_impro = 1313.9369 E_vdwl = -40863.9000
|
||||
E_coul = 1705084.8591 E_long = -2137481.5855 Press = -1634.3808
|
||||
Volume = 2522232.6313
|
||||
---------------- Step 200 ----- CPU = 23.3169 (sec) ----------------
|
||||
TotEng = -308342.2597 KinEng = 108936.8553 Temp = 189.8783
|
||||
PotEng = -417279.1150 E_bond = 9579.0042 E_angle = 47373.6037
|
||||
E_dihed = 39847.3737 E_impro = 967.6451 E_vdwl = -23631.6382
|
||||
E_coul = 1646630.1738 E_long = -2138045.2773 Press = -1185.5491
|
||||
Volume = 2554682.9808
|
||||
Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 4.29395 (18.4156)
|
||||
Bond time (%) = 6.57406 (28.1944)
|
||||
Kspce time (%) = 4.75311 (20.3848)
|
||||
Neigh time (%) = 1.32057 (5.66359)
|
||||
Comm time (%) = 0.555436 (2.38212)
|
||||
Outpt time (%) = 0.000431776 (0.00185177)
|
||||
Other time (%) = 5.81936 (24.9577)
|
||||
|
||||
FFT time (% of Kspce) = 1.78333 (37.5192)
|
||||
FFT Gflps 3d (1d only) = 5.0126 11.639
|
||||
|
||||
Nlocal: 64000 ave 64003 max 63997 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 70636.8 ave 70640 max 70632 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
Reference in New Issue
Block a user