LAMMPS (3 Mar 2020)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)

using 1 OpenMP thread(s) per MPI task
#initialization
units metal
atom_style atomic
boundary p p p

#simulation_box
read_data InP.lmp
orthogonal box = (0 0 0) to (5.8688 5.8688 5.8688)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
read_data CPU = 0.00498605 secs

#simulation_settings
#force_field
pair_style vashishta
pair_coeff * * InP.vashishta.txt In P
Reading potential file InP.vashishta.txt with DATE: 2015-10-14
neighbor 0.3 bin
neigh_modify delay 5

# ------------------------- SETTINGS ---------------------------------

compute csym all centro/atom fcc
compute peratom all pe/atom

######################################
# EQUILIBRATION
reset_timestep 0
timestep 0.001
velocity all create 300 12345 mom yes rot no
fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1

# Set thermo output

thermo 1000
thermo_style custom step lx ly lz press pxx pyy pzz pe temp

# Run for at least 10 picosecond (assuming 1 fs timestep)

run 20000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.3
ghost atom cutoff = 6.3
binsize = 3.15, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) compute centro/atom, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes
Step Lx Ly Lz Press Pxx Pyy Pzz PotEng Temp
0 5.8688 5.8688 5.8688 1294.3858 926.33626
1064.2924 1892.5288 -27.862029 300
1000 5.8814206 5.8814206 5.8814206 -3391.2452 -2459.2694
-4067.7602 -3646.7059 -27.709433 171.66352
2000 5.8998248 5.8998248 5.8998248 -8614.2319 -7752.0567
-8252.1471 -9838.4919 -27.527437 43.648449
3000 5.8949419 5.8949419 5.8949419 -6233.6785 -6135.7289
-5352.179 -7213.1276 -27.551796 137.23366
4000 5.8842615 5.8842615 5.8842615 -3340.5417 -2427.1261
-4264.5105 -3329.9886 -27.62771 281.12256
5000 5.8776485 5.8776485 5.8776485 980.57539 2140.3577
165.95465 635.41378 -27.657348 355.65878
6000 5.8765183 5.8765183 5.8765183 2206.9218 2287.0516
3608.032 725.68187 -27.740456 472.89252
7000 5.8807971 5.8807971 5.8807971 -45.900694 -794.10297
1025.7849 -369.38403 -27.73566 472.94953
8000 5.8965651 5.8965651 5.8965651 -7692.167 -7762.1707
-9087.2689 -6227.0614 -27.614314 327.67725
9000 5.9054613 5.9054613 5.9054613 -12102.832 -11439.534
-15386.238 -9482.7245 -27.450064 139.76109
10000 5.9048023 5.9048023 5.9048023 -11602.209 -10665.465
-13498.902 -10642.26 -27.418279 90.362418
11000 5.8819511 5.8819511 5.8819511 -2122.2284 -1154.9956
-2223.574 -2988.1155 -27.559423 232.86488
12000 5.8700123 5.8700123 5.8700123 2567.4827 2850.3255
3162.4038 1689.7188 -27.670232 362.0812
13000 5.8698256 5.8698256 5.8698256 2258.7104 836.62694
1462.3311 4477.1733 -27.67632 387.60761
14000 5.8738766 5.8738766 5.8738766 17.663885 -1930.387
-2247.1083 4230.487 -27.64246 363.06488
15000 5.8767127 5.8767127 5.8767127 -579.79053 -2707.7524
-2034.5613 3002.9421 -27.654896 384.7997
16000 5.8757651 5.8757651 5.8757651 1802.7491 767.66774
1214.6057 3425.9739 -27.664743 392.20354
17000 5.8725544 5.8725544 5.8725544 3997.3854 4977.9037
4605.2388 2409.0137 -27.670911 373.40918
18000 5.8831581 5.8831581 5.8831581 -844.88077 -214.26443
-70.492568 -2249.8853 -27.58677 264.68065
19000 5.8950914 5.8950914 5.8950914 -8607.0995 -8385.03
-9015.7741 -8420.4945 -27.48199 160.60562
20000 5.8959764 5.8959764 5.8959764 -8410.8828 -8791.1257
-9885.8596 -6555.663 -27.403178 86.231317
Loop time of 1.48334 on 1 procs for 20000 steps with 8 atoms

Performance: 1164.939 ns/day, 0.021 hours/ns, 13483.085 timesteps/s

67.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:

Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60561 | 0.60561 | 0.60561 | 0.0 | 40.83
Neigh | 0.0070422 | 0.0070422 | 0.0070422 | 0.0 | 0.47
Comm | 0.029844 | 0.029844 | 0.029844 | 0.0 | 2.01
Output | 0.11201 | 0.11201 | 0.11201 | 0.0 | 7.55
Modify | 0.71092 | 0.71092 | 0.71092 | 0.0 | 47.93
Other | | 0.01792 | | | 1.21

Nlocal: 8 ave 8 max 8 min

Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 272 ave 272 max 272 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: 284 ave 284 max 284 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 284

Ave neighs/atom = 35.5
Neighbor list builds = 579
Dangerous builds = 0
unfix 1

# Store final cell length for strain calculations

variable tmp equal "lx"
variable L0 equal ${tmp}
variable L0 equal 5.895976366103
print "Initial Length, L0: ${L0}"
Initial Length, L0: 5.895976366103

######################################
# DEFORMATION
reset_timestep 0

fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1

variable srate equal 1.0e10
variable srate1 equal "v_srate / 1.0e12"
fix 2 all deform 1 x erate ${srate1} units box remap x
fix 2 all deform 1 x erate 0.01 units box remap x

# Output strain and stress info to file

# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
# p2, p3, p4 are in GPa
variable strain equal "(lx - v_L0)/v_L0"
variable p1 equal "v_strain"
variable p2 equal "-pxx/10000"
variable p3 equal "-pyy/10000"
variable p4 equal "-pzz/10000"
fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file In_P_100.def1.txt screen no

# Use cfg for AtomEye

dump 1 all cfg 250 dump.tensile_*.cfg mass type xs ys zs c_csym c_peratom fx
fy fz

# Display thermo
thermo 1000
thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press

run 20000
Per MPI rank memory allocation (min/avg/max) = 4.965 | 4.965 | 4.965 Mbytes
Step v_strain Temp v_p2 v_p3 v_p4 KinEng PotEng Press
0 6.0256579e-16 86.231317 0.87911257 0.98858596 0.6555663
0.078023908 -27.403178 -8410.8828
1000 0.01 172.38849 1.0482055 0.59998076 0.10960386
0.15598073 -27.470984 -5859.3003
2000 0.02 303.04591 1.3543233 0.40171053 -0.084052291
0.27420231 -27.565195 -5573.2718
3000 0.03 370.474 1.4701511 -0.18369646 -0.12318381
0.33521266 -27.604822 -3877.5694
4000 0.04 380.4792 1.7328476 -0.59815911 -0.30565525
0.34426558 -27.589302 -2763.4442
5000 0.05 376.50136 2.1100552 -0.37331473 0.17158655
0.34066635 -27.55975 -6361.0901
6000 0.06 367.6147 2.0086111 -0.58934348 -0.24679578
0.3326255 -27.522289 -3908.2396
7000 0.07 312.20535 2.6669181 -0.15075629 0.27078451
0.28248996 -27.440517 -9289.8211
8000 0.08 230.50116 2.8124019 -0.046195127 -0.30377988
0.20856229 -27.326522 -8208.0898
9000 0.09 83.233623 3.696036 1.1886739 0.60849798
0.075311531 -27.151755 -18310.693
10000 0.1 224.49545 3.7188832 0.654095 0.24280095
0.20312821 -27.233607 -15385.931
11000 0.11 456.79238 3.7417776 -1.0694755 -0.31085295
0.41331534 -27.392451 -7871.4972
12000 0.12 243.33409 4.4621182 0.53979561 0.36327043
0.22017379 -27.152164 -17883.948
13000 0.13 259.17092 4.788064 0.56368507 0.30483432
0.2345033 -27.102059 -18855.278
14000 0.14 330.84101 4.7249713 -0.46017217 -0.2692653
0.2993519 -27.107652 -13318.446
15000 0.15 301.13643 5.3075425 0.27510951 0.39681679
0.27247457 -27.014597 -19931.563
16000 0.16 193.2597 5.9170592 0.97900842 0.48338659
0.17486544 -26.845761 -24598.181
17000 0.17 403.28025 6.0017221 -0.76379208 -0.51840021
0.36489645 -26.958218 -15731.766
18000 0.18 264.95148 5.8927219 -0.60013839 -0.43561761
0.23973367 -26.75465 -16189.886
19000 0.19 260.13533 7.0420342 0.2223344 0.07747408
0.23537592 -26.67292 -24472.809
20000 0.2 242.62353 7.3800127 0.47421927 0.54939816
0.21953087 -26.567316 -28012.101
Loop time of 1.57953 on 1 procs for 20000 steps with 8 atoms

Performance: 1093.994 ns/day, 0.022 hours/ns, 12661.962 timesteps/s

72.2% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:

Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.5911 | 0.5911 | 0.5911 | 0.0 | 37.42
Neigh | 0.0049701 | 0.0049701 | 0.0049701 | 0.0 | 0.31
Comm | 0.034893 | 0.034893 | 0.034893 | 0.0 | 2.21
Output | 0.17007 | 0.17007 | 0.17007 | 0.0 | 10.77
Modify | 0.76443 | 0.76443 | 0.76443 | 0.0 | 48.40
Other | | 0.01407 | | | 0.89

Nlocal: 8 ave 8 max 8 min

Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 222 ave 222 max 222 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: 282 ave 282 max 282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 282
Ave neighs/atom = 35.25
Neighbor list builds = 596
Dangerous builds = 0

######################################
# SIMULATION DONE
print "All done"
All done
Total wall time: 0:00:03