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Merge remote-tracking branch 'upstream/master' into 2020

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tomswinburne
2020-08-24 17:02:53 +02:00
parent e8fb7c7ece 7e1a3bd4d5
commit 2ee6e9077a
1456 changed files with 786486 additions and 2043386 deletions
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172
examples/USER/misc/cauchy/log.9Jan2020.cauchystat.g++.1
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LAMMPS (09 Jan 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
atom_modify map array
# Box and atom positions:
boundary p p p
# Defining lattice and creating simulation
# box with atoms inside
lattice fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region simbox prism 0 5 0 5 0 5 0 0 0 units lattice
create_box 2 simbox
Created triclinic box = (0 0 0) to (20.25 20.25 20.25) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 500 atoms
create_atoms CPU = 0.000987053 secs
# Atomic mass:
mass 1 58.69
mass 2 26.98154
# Potential, Al fcc crystal
pair_style eam/alloy
pair_coeff * * NiAlH_jea.eam.alloy Ni Al
Reading potential file NiAlH_jea.eam.alloy with DATE: 2007-11-30
neigh_modify delay 5
thermo 100
thermo_style custom step temp pxx pyy pzz pxy pxz pyz
compute cna all cna/atom 2.8
fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none alpha 0.001 continue no
Using fix npt/cauchy with alpha=0.001000
this is NOT a continuation run
# dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna
timestep 0.002
variable px equal pxx
variable py equal pyy
variable pz equal pzz
variable sxy equal pxy
variable sxz equal pxz
variable syz equal pyz
variable t equal temp
fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt
variable lx equal lx
variable ly equal ly
variable lz equal ly
variable xy equal xy
variable xz equal xz
variable yz equal yz
fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt
velocity all create 1200 4928459 rot yes dist gaussian
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
(2) compute cna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.04 | 4.04 | 4.04 Mbytes
Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
0 1200 9859.2374 9729.7389 10279.526 -110.10907 -391.60768 295.10918
100 461.95579 11262.405 9918.4702 7373.1896 1389.9833 -165.54737 -128.04989
200 452.7497 4758.0631 6285.2022 9593.9725 389.15901 835.71435 -1853.9679
300 451.50974 7980.6036 7524.3514 9584.5276 297.33672 -154.88768 -1927.573
400 461.52812 5074.9544 4877.0864 2689.9029 389.66084 224.44814 563.12739
500 458.17416 7672.6668 5358.5073 4670.0236 -1251.047 1175.8268 -373.96822
600 461.28593 3629.8562 7265.1611 6970.1746 523.3139 1295.8252 -121.17116
700 466.86592 5224.2421 4121.434 4368.4226 230.85768 -65.765274 -1271.8354
800 491.38828 -233.79818 2799.6028 5023.998 919.08469 -411.66796 422.33219
900 473.16465 6486.5426 4028.6955 2503.9771 451.96928 1309.8322 -557.83472
1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
Loop time of 1.24705 on 1 procs for 1000 steps with 500 atoms
Performance: 138.567 ns/day, 0.173 hours/ns, 801.892 timesteps/s
94.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.112 | 1.112 | 1.112 | 0.0 | 89.17
Neigh | 0.063329 | 0.063329 | 0.063329 | 0.0 | 5.08
Comm | 0.01994 | 0.01994 | 0.01994 | 0.0 | 1.60
Output | 0.0014246 | 0.0014246 | 0.0014246 | 0.0 | 0.11
Modify | 0.045429 | 0.045429 | 0.045429 | 0.0 | 3.64
Other | | 0.004881 | | | 0.39
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2017 ave 2017 max 2017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24689 ave 24689 max 24689 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24689
Ave neighs/atom = 49.378
Neighbor list builds = 34
Dangerous builds = 0
fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none alpha 0.001 continue yes
Using fix npt/cauchy with alpha=0.001000
this is a continuation run
run 1000
Per MPI rank memory allocation (min/avg/max) = 4.056 | 4.056 | 4.056 Mbytes
Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
1100 471.04772 5593.1614 5874.9867 3608.9922 -1861.938 459.86813 -813.36882
1200 473.34727 2337.4765 2050.4694 4330.2198 -3590.2198 -1285.2197 748.05137
1300 465.46145 4909.5722 2880.9183 4995.0091 -2860.6934 -895.40937 -382.07531
1400 508.53262 92.57534 3722.1136 557.50974 -3121.7615 349.6147 194.5089
1500 498.34579 -5755.2352 -3798.1466 -1445.2047 -3218.0887 1733.9103 -555.96371
1600 546.45882 -257.80132 407.73403 -39.803803 -3578.1137 1438.3526 -1710.3139
1700 570.72785 -2951.9658 -622.89945 1138.4113 -4573.7982 -984.65235 2906.3144
1800 650.75622 6086.1524 1111.2919 1726.5115 -3504.716 1140.9767 414.81284
1900 690.32264 2763.2044 -609.41535 289.85307 -3788.8761 -1306.8569 760.00116
2000 724.01451 -675.72484 522.04263 -468.58167 -6603.3906 -1712.7317 47.61212
Loop time of 1.27211 on 1 procs for 1000 steps with 500 atoms
Performance: 135.837 ns/day, 0.177 hours/ns, 786.093 timesteps/s
93.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0529 | 1.0529 | 1.0529 | 0.0 | 82.77
Neigh | 0.13671 | 0.13671 | 0.13671 | 0.0 | 10.75
Comm | 0.018747 | 0.018747 | 0.018747 | 0.0 | 1.47
Output | 0.00075722 | 0.00075722 | 0.00075722 | 0.0 | 0.06
Modify | 0.057984 | 0.057984 | 0.057984 | 0.0 | 4.56
Other | | 0.00499 | | | 0.39
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2040 ave 2040 max 2040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23757 ave 23757 max 23757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 23757
Ave neighs/atom = 47.514
Neighbor list builds = 78
Dangerous builds = 0
Total wall time: 0:00:02

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../../../../potentials/C_10_10.mesocnt

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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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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