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add log files for USER-AWPMD examples

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This commit is contained in:
Axel Kohlmeyer
2018-12-07 03:49:46 -05:00
parent 18f7e96e8a
commit cd0924ca4c
4 changed files with 400 additions and 0 deletions
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LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_atom
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
1 -266.3192 -266.3192 0 266.32746 0 -532.64666 0 0 159.30733 -0
2 -266.3192 -266.3192 1.7273458e-17 266.32797 0 -532.64718 0 5.7948873e-15 169.14686 6.6606909e-13
3 -266.3192 -266.3192 4.6899813e-15 266.32927 0 -532.64847 0 1.5733915e-12 194.06892 1.8084691e-10
4 -266.3192 -266.3192 1.4824973e-13 266.33199 0 -532.6512 0 4.9734712e-11 246.65762 5.7165485e-09
5 -266.3192 -266.3192 1.9298888e-12 266.33712 0 -532.65632 0 6.4743771e-10 345.53056 7.441702e-08
6 -266.3192 -266.3192 1.5343223e-11 266.34601 0 -532.66521 0 5.1473332e-09 516.91949 5.9163869e-07
7 -266.3192 -266.3192 8.8661674e-11 266.36051 0 -532.6797 0 2.9744154e-08 796.4357 3.4188175e-06
8 -266.31919 -266.31919 4.0865149e-10 266.38304 0 -532.70223 0 1.3709411e-07 1231.0302 1.5757709e-05
9 -266.31918 -266.31918 1.5889509e-09 266.41674 0 -532.73592 0 5.3306012e-07 1881.1652 6.1270366e-05
10 -266.31916 -266.31916 5.4070747e-09 266.46554 0 -532.7847 0 1.8139615e-06 2823.2238 0.00020849822
Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms
Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00030851 | 0.00030851 | 0.00030851 | 0.0 | 42.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001204 | 0.0001204 | 0.0001204 | 0.0 | 16.61
Output | 0.00028038 | 0.00028038 | 0.00028038 | 0.0 | 38.67
Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.85
Other | | 9.537e-06 | | | 1.32
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 248 ave 248 max 248 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 225 ave 225 max 225 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225
Ave neighs/atom = 112.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_atom
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
2 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
1 -266.3192 -266.3192 0 266.32789 0 -532.64709 0 0 167.49891 -0
2 -266.3192 -266.3192 1.219316e-15 266.3314 0 -532.6506 0 4.0905525e-13 235.2267 4.7017146e-11
3 -266.3192 -266.3192 8.3179871e-14 266.34548 0 -532.66468 0 2.7905123e-11 506.68594 3.2074377e-09
4 -266.3192 -266.3192 4.4091748e-12 266.39036 0 -532.70955 0 1.4791868e-09 1372.0565 1.7001894e-07
5 -266.31916 -266.31916 9.8904198e-11 266.51357 0 -532.83273 0 3.3180309e-08 3748.6725 3.8137718e-06
6 -266.31893 -266.31893 1.3132578e-09 266.81733 0 -533.13626 0 4.4057077e-07 9611.8807 5.0639565e-05
7 -266.31762 -266.31762 1.2317167e-08 267.50719 0 -533.82481 0 4.1321544e-06 22950.26 0.00047495321
8 -266.31123 -266.31123 9.0048883e-08 268.97689 0 -535.28812 0 3.0209534e-05 51470.197 0.0034723086
9 -266.28324 -266.28324 5.4612621e-07 271.95757 0 -538.24082 0 0.00018321403 109735.25 0.02105877
10 -266.17113 -266.17114 2.8729529e-06 277.79384 0 -543.96498 0 0.00096381615 225424.02 0.11078182
Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms
Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s
87.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3419e-05 | 0.00012642 | 0.00030923 | 0.0 | 7.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00073171 | 0.00086534 | 0.001025 | 0.0 | 49.01
Output | 0.00063562 | 0.00075388 | 0.00094962 | 0.0 | 42.70
Modify | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.25
Other | | 1.55e-05 | | | 0.88
Nlocal: 0.5 ave 2 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 249.5 ave 250 max 248 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 56.25 ave 225 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 225
Ave neighs/atom = 112.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable sname index h_molecule
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_molecule
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
1 30360.49 30360.489 0.0009272222 39540.081 2.0463631e-12 -9179.5926 0 0.10368794 1.3476061e+09 35.753932
2 67447.779 67447.776 0.00370884 80547.07 -1.1368684e-12 -13099.294 0 0.41474633 2.8529839e+09 143.01385
3 3713046.5 3713046.5 0.0041850026 3803060.3 -1.29603e-10 -90013.788 0 0.46799388 1.4486958e+11 161.3748
4 2445632.1 2445620 12.171486 2452194.4 -9.777068e-11 -6574.4062 0 1361.0937 -6.5572589e+08 469335.68
5 2434860.1 2434845.9 14.215419 2433638.8 -1.0663825e-10 1207.1541 0 1589.6595 -359380.29 548150.31
6 2444984.1 2444969.8 14.215428 2451100 5.1841198e-11 -6130.1373 0 1589.6605 -5.6327282e+08 548150.63
7 2436128.7 2436110.9 17.793789 2434903.7 2.0190782e-10 1207.154 0 1989.8158 -221406.77 686133.18
8 2444786.5 2444768.7 17.793798 2450583.8 -1.1027623e-10 -5815.0651 0 1989.8169 -5.0227031e+08 686133.54
9 2437198.9 2437175.9 22.942086 2435968.8 2.2600943e-10 1207.1538 0 2565.5315 -22903.736 884652.88
10 2444787.1 2444764.2 22.942097 2450333.1 -3.1832315e-11 -5568.9214 0 2565.5327 -4.5741803e+08 884653.3
Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms
Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s
85.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00088882 | 0.00088882 | 0.00088882 | 0.0 | 56.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00031352 | 0.00031352 | 0.00031352 | 0.0 | 19.79
Output | 0.00036216 | 0.00036216 | 0.00036216 | 0.0 | 22.86
Modify | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.38
Other | | 1.407e-05 | | | 0.89
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 596 ave 596 max 596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 966 ave 966 max 966 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 966
Ave neighs/atom = 241.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable sname index h_molecule
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_molecule
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
4 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
1 30360.982 30360.981 0.0009272222 39540.638 -1.1368684e-12 -9179.6571 0 0.10368794 1.3476263e+09 35.753932
2 67459.392 67459.388 0.0037086548 80559.71 6.5938366e-12 -13100.322 0 0.41472561 2.8534514e+09 143.0067
3 3732209.2 3732209.2 0.0041861902 3822452.2 -3.1604941e-11 -90242.984 0 0.46812669 1.4561246e+11 161.42059
4 2482974.7 2482961.9 12.860712 2489531.2 -2.2896529e-10 -6569.2968 0 1438.1675 -6.5458119e+08 495912.44
5 2472238.2 2472223.2 14.933049 2471015.7 -1.6120794e-10 1207.5188 0 1669.9095 -324992.65 575822.3
6 2482233.1 2482218.1 14.933057 2488321.7 -2.0691004e-11 -6103.5677 0 1669.9104 -5.5786438e+08 575822.62
7 2473498.5 2473479.8 18.61401 2472272.3 1.459739e-10 1207.5167 0 2081.5382 -183348.11 717761.12
8 2481621.3 2481602.6 18.614019 2487299.1 7.0258466e-11 -5696.4589 0 2081.5393 -4.7962801e+08 717761.48
9 2474506.2 2474482.2 24.021181 2473274.7 2.1395863e-10 1207.508 0 2686.2029 24318.554 926263.07
10 2480376.3 2480352.2 24.021192 2485505 -8.5719876e-11 -5152.7478 0 2686.2041 -3.8355089e+08 926263.48
Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms
Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00011826 | 0.00027376 | 0.00073862 | 0.0 | 10.23
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00080514 | 0.0011864 | 0.001574 | 0.9 | 44.31
Output | 0.00094914 | 0.0011944 | 0.0017326 | 0.9 | 44.61
Modify | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.17
Other | | 1.824e-05 | | | 0.68
Nlocal: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 599 ave 600 max 596 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 241.5 ave 966 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 966
Ave neighs/atom = 241.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00