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iafoss
2020-05-18 17:28:48 -04:00
parent be93ef7b20
commit e26be18b1e
66 changed files with 3277 additions and 3532 deletions
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1
examples/USER/mesont/README
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@ -11,4 +11,3 @@ Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
"film" is an example with a film composed of 396 200-nm-long
nanotubes (79596 nodes).

10
examples/USER/mesont/in.bundle
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@ -1,3 +1,4 @@
processors 1 1 *
newton on
units metal
lattice sc 1.0
@ -7,7 +8,7 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 ../../../potentials/CNT_10_10 0 0
pair_style mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
pair_coeff * *
@ -22,11 +23,8 @@ compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
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
run 100

9
examples/USER/mesont/in.film
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@ -7,7 +7,7 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 25.0 ../../../potentials/CNT_10_10 1 0
pair_style mesont/tpm 30.0 ../../../potentials/MESONT-TABTP_10_10.xrs 1 0
read_data data.film
pair_coeff * *
@ -22,11 +22,8 @@ compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
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 10

31
examples/USER/mesont/log.3Mar2020.bundle.g++.1
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@ -1,4 +1,6 @@
LAMMPS (3 Mar 2020)
using 1 OpenMP thread(s) per MPI task
processors 1 1 *
newton on
units metal
lattice sc 1.0
@ -9,13 +11,13 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 ../../../potentials/CNT_10_10 0 0
pair_style mesont/tpm 45.0 ../../../potentials/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 = 0.442627 secs
read_data CPU = 0.025475 secs
pair_coeff * *
velocity all create 6000.0 2019
@ -29,11 +31,8 @@ compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
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
@ -51,7 +50,7 @@ Neighbor list info ...
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es_tot c_Eb_tot c_Et_tot
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
@ -63,20 +62,20 @@ Step Time Temp TotEng KinEng PotEng c_Es_tot c_Eb_tot c_Et_tot
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 0.455531 on 1 procs for 100 steps with 77 atoms
Loop time of 0.457417 on 1 procs for 100 steps with 77 atoms
Performance: 94.834 ns/day, 0.253 hours/ns, 219.524 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4551 | 0.4551 | 0.4551 | 0.0 | 99.91
Neigh | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.01
Comm | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.01
Output | 0.00020385 | 0.00020385 | 0.00020385 | 0.0 | 0.04
Modify | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.02
Other | | 4.697e-05 | | | 0.01
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
Nlocal: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0

50
examples/USER/mesont/log.3Mar2020.film.g++.1
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@ -1,4 +1,5 @@
LAMMPS (3 Mar 2020)
using 1 OpenMP thread(s) per MPI task
newton on
units metal
lattice sc 1.0
@ -9,13 +10,13 @@ neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 25.0 ../../../potentials/CNT_10_10 1 0
pair_style mesont/tpm 30.0 ../../../potentials/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 = 0.0903821 secs
read_data CPU = 0.110827 secs
pair_coeff * *
velocity all create 600.0 2019
@ -29,11 +30,8 @@ compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
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
@ -41,45 +39,45 @@ run 10
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 26
ghost atom cutoff = 26
binsize = 13, bins = 385 385 31
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) = 44.83 | 44.83 | 44.83 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es_tot c_Eb_tot c_Et_tot
0 0 600 1347.2177 6173.0767 -4825.859 28.669574 21.29406 -4875.8226
10 0.1 389.40755 1373.7883 4006.4045 -2632.6161 848.00269 1404.4323 -4885.0511
Loop time of 4.21003 on 1 procs for 10 steps with 79596 atoms
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
Performance: 2.052 ns/day, 11.695 hours/ns, 2.375 timesteps/s
97.8% CPU use with 1 MPI tasks x no OpenMP threads
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1942 | 4.1942 | 4.1942 | 0.0 | 99.62
Pair | 5.4022 | 5.4022 | 5.4022 | 0.0 | 99.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00046039 | 0.00046039 | 0.00046039 | 0.0 | 0.01
Output | 0.00029182 | 0.00029182 | 0.00029182 | 0.0 | 0.01
Modify | 0.012385 | 0.012385 | 0.012385 | 0.0 | 0.29
Other | | 0.002726 | | | 0.06
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
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1567 ave 1567 max 1567 min
Nghost: 1879 ave 1879 max 1879 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
FullNghs: 412798 ave 412798 max 412798 min
FullNghs: 642270 ave 642270 max 642270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 412798
Ave neighs/atom = 5.18617
Total # of neighbors = 642270
Ave neighs/atom = 8.06912
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:07