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repeatable example

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phankl
2022-08-31 12:42:47 +01:00
parent 4e1a346f5a
commit 2bded3da5e
5 changed files with 253 additions and 237 deletions
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2
examples/PACKAGES/mesont/in.film_mesocnt
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@ -18,7 +18,7 @@ bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 30 chain
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
# output

118
examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.1
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@ -1,118 +0,0 @@
LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
1 by 1 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.012 seconds
read_data CPU = 0.158 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 30 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
thermo 100
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair
dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
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 = 32
ghost atom cutoff = 32
binsize = 16, bins = 313 313 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 58.03 | 58.03 | 58.03 Mbytes
Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901
100 1 3.0380832 322.67058 1292.7084 3319.7837 -2027.0754 1107.8055 2092.5049 -5227.3858
Loop time of 3.03811 on 1 procs for 100 steps with 79596 atoms
Performance: 28.439 ns/day, 0.844 hours/ns, 32.915 timesteps/s
99.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5683 | 2.5683 | 2.5683 | 0.0 | 84.53
Bond | 0.2957 | 0.2957 | 0.2957 | 0.0 | 9.73
Neigh | 0.057597 | 0.057597 | 0.057597 | 0.0 | 1.90
Comm | 0.0020917 | 0.0020917 | 0.0020917 | 0.0 | 0.07
Output | 0.00011104 | 0.00011104 | 0.00011104 | 0.0 | 0.00
Modify | 0.10993 | 0.10993 | 0.10993 | 0.0 | 3.62
Other | | 0.004415 | | | 0.15
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1935 ave 1935 max 1935 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: 659576 ave 659576 max 659576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 659576
Ave neighs/atom = 8.2865471
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:04

118
examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.4
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@ -1,118 +0,0 @@
LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
2 by 2 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.154 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 30 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
thermo 100
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair
dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
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 = 32
ghost atom cutoff = 32
binsize = 16, bins = 313 313 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 21.56 | 21.57 | 21.6 Mbytes
Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901
100 1 0.92993546 322.71889 1293.8436 3320.2808 -2026.4371 1107.7962 2093.0006 -5227.234
Loop time of 0.929957 on 4 procs for 100 steps with 79596 atoms
Performance: 92.908 ns/day, 0.258 hours/ns, 107.532 timesteps/s
98.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.58144 | 0.67551 | 0.78613 | 9.0 | 72.64
Bond | 0.072245 | 0.077166 | 0.085344 | 1.8 | 8.30
Neigh | 0.016299 | 0.016303 | 0.016308 | 0.0 | 1.75
Comm | 0.011498 | 0.13156 | 0.23472 | 22.2 | 14.15
Output | 6.3584e-05 | 6.9594e-05 | 8.0167e-05 | 0.0 | 0.01
Modify | 0.020663 | 0.026031 | 0.028517 | 1.9 | 2.80
Other | | 0.003318 | | | 0.36
Nlocal: 19899 ave 21952 max 18667 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1000.75 ave 1070 max 947 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: 164894 ave 187180 max 151353 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 659576
Ave neighs/atom = 8.2865471
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02

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examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1 Normal file
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@ -0,0 +1,126 @@
LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
1 by 1 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.012 seconds
read_data CPU = 0.160 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
thermo 10
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022 loop geom
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
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 = 42
ghost atom cutoff = 42
binsize = 21, bins = 239 239 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.89 | 49.89 | 49.89 Mbytes
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
Loop time of 4.1637 on 1 procs for 100 steps with 79596 atoms
Performance: 20.751 ns/day, 1.157 hours/ns, 24.017 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.705 | 3.705 | 3.705 | 0.0 | 88.98
Bond | 0.29317 | 0.29317 | 0.29317 | 0.0 | 7.04
Neigh | 0.078491 | 0.078491 | 0.078491 | 0.0 | 1.89
Comm | 0.0019462 | 0.0019462 | 0.0019462 | 0.0 | 0.05
Output | 0.00099817 | 0.00099817 | 0.00099817 | 0.0 | 0.02
Modify | 0.079874 | 0.079874 | 0.079874 | 0.0 | 1.92
Other | | 0.004224 | | | 0.10
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2567 ave 2567 max 2567 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: 1.1337e+06 ave 1.1337e+06 max 1.1337e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1133696
Ave neighs/atom = 14.243128
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05

126
examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4 Normal file
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LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
2 by 2 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.156 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
thermo 10
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022 loop geom
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
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 = 42
ghost atom cutoff = 42
binsize = 21, bins = 239 239 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.47 | 16.58 | 16.89 Mbytes
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
Loop time of 1.25052 on 4 procs for 100 steps with 79596 atoms
Performance: 69.091 ns/day, 0.347 hours/ns, 79.967 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87036 | 0.97558 | 1.1135 | 9.0 | 78.01
Bond | 0.071751 | 0.076357 | 0.084244 | 1.7 | 6.11
Neigh | 0.023232 | 0.023239 | 0.023244 | 0.0 | 1.86
Comm | 0.0046002 | 0.15227 | 0.26319 | 24.1 | 12.18
Output | 0.00032696 | 0.00037811 | 0.00045537 | 0.0 | 0.03
Modify | 0.019263 | 0.020646 | 0.023155 | 1.1 | 1.65
Other | | 0.00204 | | | 0.16
Nlocal: 19899 ave 21951 max 18670 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1323.5 ave 1412 max 1255 min
Histogram: 1 0 1 0 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: 283424 ave 325466 max 258171 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1133696
Ave neighs/atom = 14.243128
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02