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update example logs and inputs

This commit is contained in:
Axel Kohlmeyer 2020-06-12 05:48:49 -04:00
parent 53e0cc1b88
commit 0bc1c3b2a2
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GPG Key ID: D9B44E93BF0C375A
7 changed files with 201 additions and 36 deletions
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1
examples/USER/mesont/MESONT-TABTP_10_10.xrs Symbolic link
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@ -0,0 +1 @@
../../../potentials/MESONT-TABTP_10_10.xrs

3
examples/USER/mesont/in.bundle
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@ -8,14 +8,13 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo_modify flush yes
thermo 10
reset_timestep 0

5
examples/USER/mesont/in.film
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@ -7,14 +7,13 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 ../../../potentials/MESONT-TABTP_10_10.xrs 1 0
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo_modify flush yes
thermo 10
reset_timestep 0
@ -26,4 +25,4 @@ compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 10
run 20

27
examples/USER/mesont/log.3Mar2020.bundle.g++.1 → examples/USER/mesont/log.2Jun2020.bundle.g++.1
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@ -1,5 +1,4 @@
LAMMPS (3 Mar 2020)
using 1 OpenMP thread(s) per MPI task
LAMMPS (5 May 2020)
processors 1 1 *
newton on
units metal
@ -11,19 +10,18 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
1 by 1 by 1 MPI processor grid
reading atoms ...
77 atoms
read_data CPU = 0.025475 secs
read_data CPU = 0.000613213 secs
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo_modify flush yes
thermo 10
reset_timestep 0
@ -33,7 +31,6 @@ compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708)
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 100
@ -62,20 +59,20 @@ Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
Loop time of 0.457417 on 1 procs for 100 steps with 77 atoms
Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms
Performance: 94.443 ns/day, 0.254 hours/ns, 218.619 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.45698 | 0.45698 | 0.45698 | 0.0 | 99.90
Neigh | 5.6982e-05 | 5.6982e-05 | 5.6982e-05 | 0.0 | 0.01
Comm | 4.4584e-05 | 4.4584e-05 | 4.4584e-05 | 0.0 | 0.01
Output | 0.00019693 | 0.00019693 | 0.00019693 | 0.0 | 0.04
Modify | 7.4863e-05 | 7.4863e-05 | 7.4863e-05 | 0.0 | 0.02
Other | | 6.318e-05 | | | 0.01
Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88
Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01
Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02
Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04
Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03
Other | | 8.702e-05 | | | 0.02
Nlocal: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0

90
examples/USER/mesont/log.2Jun2020.bundle.g++.4 Normal file
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@ -0,0 +1,90 @@
LAMMPS (5 May 2020)
processors 1 1 *
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary fs fs p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
1 by 1 by 4 MPI processor grid
reading atoms ...
77 atoms
read_data CPU = 0.000590563 secs
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 100
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 46
ghost atom cutoff = 46
binsize = 23, bins = 7 7 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.671 | 4.671 | 4.671 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms
Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s
95.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01
Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02
Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04
Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70
Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03
Other | | 0.001755 | | | 1.21
Nlocal: 19.25 ave 21 max 16 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 33.25 ave 40 max 28 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 555.5 ave 606 max 460 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 2222
Ave neighs/atom = 28.8571
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

30
examples/USER/mesont/log.3Mar2020.film.g++.1 → examples/USER/mesont/log.2Jun2020.film.g++.1
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@ -1,5 +1,4 @@
LAMMPS (3 Mar 2020)
using 1 OpenMP thread(s) per MPI task
LAMMPS (5 May 2020)
newton on
units metal
lattice sc 1.0
@ -10,19 +9,18 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 ../../../potentials/MESONT-TABTP_10_10.xrs 1 0
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
1 by 1 by 1 MPI processor grid
reading atoms ...
79596 atoms
read_data CPU = 0.110827 secs
read_data CPU = 0.0860629 secs
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo_modify flush yes
thermo 10
reset_timestep 0
@ -32,10 +30,9 @@ compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708)
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 10
run 20
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -52,20 +49,21 @@ Per MPI rank memory allocation (min/avg/max) = 37.43 | 37.43 | 37.43 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
Loop time of 5.41853 on 1 procs for 10 steps with 79596 atoms
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms
Performance: 1.595 ns/day, 15.051 hours/ns, 1.846 timesteps/s
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4022 | 5.4022 | 5.4022 | 0.0 | 99.70
Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052881 | 0.00052881 | 0.00052881 | 0.0 | 0.01
Output | 0.00029206 | 0.00029206 | 0.00029206 | 0.0 | 0.01
Modify | 0.012906 | 0.012906 | 0.012906 | 0.0 | 0.24
Other | | 0.002562 | | | 0.05
Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01
Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00
Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15
Other | | 0.001869 | | | 0.02
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -80,4 +78,4 @@ Total # of neighbors = 642270
Ave neighs/atom = 8.06912
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07
Total wall time: 0:00:11

81
examples/USER/mesont/log.2Jun2020.film.g++.4 Normal file
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@ -0,0 +1,81 @@
LAMMPS (5 May 2020)
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary p p fs
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
2 by 2 by 1 MPI processor grid
reading atoms ...
79596 atoms
read_data CPU = 0.0704217 secs
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 20
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 15.5, bins = 323 323 26
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.81 | 12.81 | 12.83 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms
Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s
95.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46
Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01
Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30
Other | | 0.001109 | | | 0.03
Nlocal: 19899 ave 21951 max 18667 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 970.75 ave 1031 max 920 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 160568 ave 181723 max 147382 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 642270
Ave neighs/atom = 8.06912
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:04