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Merge branch 'develop' into dielectric-force-tests

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This commit is contained in:
Axel Kohlmeyer
2022-09-08 16:21:27 -04:00
parent 0e5c758fb8 94a72352f2
commit d434031200
295 changed files with 246966 additions and 6549 deletions
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#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
replicate 1 2 2
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * C_10_10.mesocnt
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000

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# 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
# 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
# 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

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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)
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

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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

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LAMMPS (09 Jan 2020)
#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
orthogonal box = (0 0 0) to (600 600 60)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
498 bonds
reading angles ...
496 angles
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 = 0.000180006 secs
read_data CPU = 0.00125766 secs
replicate 1 2 2
orthogonal box = (0 0 0) to (600 1200 120)
1 by 1 by 1 MPI processor grid
2000 atoms
1992 bonds
1984 angles
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 = 0.00054121 secs
replicate CPU = 0.000902414 secs
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * 10_10.cnt
Reading potential file 10_10.cnt with DATE: 2020-01-13
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.177
ghost atom cutoff = 11
binsize = 5.0885, bins = 118 236 24
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) = 11.21 | 11.21 | 11.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757
3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539
4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866
5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738
6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986
7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796
8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885
9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197
10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903
Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38
Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57
Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03
Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05
Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52
Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37
Other | | 0.04409 | | | 1.09
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13320
Ave neighs/atom = 6.66
Ave special neighs/atom = 5.952
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (09 Jan 2020)
#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
orthogonal box = (0 0 0) to (600 600 60)
2 by 2 by 1 MPI processor grid
reading atoms ...
500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
498 bonds
reading angles ...
496 angles
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 = 0.000354767 secs
read_data CPU = 0.00286365 secs
replicate 1 2 2
orthogonal box = (0 0 0) to (600 1200 120)
1 by 4 by 1 MPI processor grid
2000 atoms
1992 bonds
1984 angles
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 = 0.00019598 secs
replicate CPU = 0.00055337 secs
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * 10_10.cnt
Reading potential file 10_10.cnt with DATE: 2020-01-13
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.177
ghost atom cutoff = 11
binsize = 5.0885, bins = 118 236 24
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) = 2.725 | 2.725 | 2.725 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738
3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513
4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101
5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633
6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686
7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831
8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264
9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773
10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282
Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms
Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s
96.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34
Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80
Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04
Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32
Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59
Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45
Other | | 0.04279 | | | 3.46
Nlocal: 500 ave 504 max 496 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 22 ave 24 max 20 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
FullNghs: 3330 ave 3368 max 3292 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13320
Ave neighs/atom = 6.66
Ave special neighs/atom = 5.952
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02