1) Dimension - 20, Temperature - 1000 Kelvin Test - Lammps File

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1)Dimension - 20,Temperature - 1000 kelvin

test.lammps file
######################################
# INITIALIZATION
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.05

######################################
# ATOM DEFINITION
lattice fcc ${latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region whole block 0 20 0 20 0 20
create_box 1 whole
create_atoms 1 region whole

######################################
# DEFINE INTERATOMIC POTENTIAL
pair_style eam/alloy
pair_coeff * * Al.eam.alloy Al

######################################
# DEFINE COMPUTES
compute csym all centro/atom fcc
compute peratom all pe/atom

######################################
# EQUILIBRATION
reset_timestep 0
timestep 0.001
velocity all create 1000 12345 mom yes rot no
fix 1 all npt temp 1000 1000 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 ${n_iter}
unfix 1

# Store final cell length for strain calculations


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

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

fix 1 all npt temp 1000 1000 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

# 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 Al_1000_20_tens_100.def1.txt screen no

# Use cfg for display


dump 1 all cfg 250 dump.tens_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz
dump_modify 1 element Al

# Display thermo
thermo 1000
thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press
run ${n_iter}

######################################
# SIMULATION DONE
print "All done"
Results After Simulation
user10@mt10:~/Navin$ lmp_mpi -in test.lammps
LAMMPS (23 Jun 2022 - Update 2)
Lattice spacing in x,y,z = 4.05 4.05 4.05
Created orthogonal box = (0 0 0) to (81 81 81)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
using lattice units in orthogonal box = (0 0 0) to (81 81 81)
create_atoms CPU = 0.012 seconds
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 20 20 20
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 22.37 | 22.37 | 22.37 Mbytes
Step Lx Ly Lz Press Pxx Pyy
Pzz PotEng Temp
0 81 81 81 8315.8668 8240.1271 8322.0919
8385.3813 -107520 1000
1000 81.58919 81.58919 81.58919 -295.22062 -270.326
-194.18377 -421.15209 -105371.33 508.33581
2000 81.616118 81.616118 81.616118 28.636313 46.863446
109.67725 -70.631756 -105254.18 531.78264
3000 81.649947 81.649947 81.649947 71.501449 -113.99631
84.022085 244.47858 -105150.07 559.25698
4000 81.693853 81.693853 81.693853 -55.113456 -59.744512
-116.72561 11.129751 -105021.57 581.30477
5000 81.73579 81.73579 81.73579 -167.72657 -142.61383
-108.48645 -252.07943 -104913.02 608.40715
6000 81.767275 81.767275 81.767275 159.85892 277.60509
212.58187 -10.610187 -104786.67 631.21542
7000 81.816201 81.816201 81.816201 -155.68001 -180.01797
-263.43477 -23.587289 -104682.48 659.1506
8000 81.85115 81.85115 81.85115 69.155544 302.4493
-50.985292 -43.99738 -104548.56 679.43056
9000 81.886261 81.886261 81.886261 1.9581619 -110.96108
74.71326 42.1223 -104459.71 709.88406
10000 81.930174 81.930174 81.930174 -116.62549 -92.349643
-44.351208 -213.17562 -104348.38 733.94903
11000 81.966994 81.966994 81.966994 -9.5295122 -212.24328
-138.93285 322.58759 -104225.99 754.15012
12000 82.008749 82.008749 82.008749 -58.845602 1.9153616
-233.39711 54.944937 -104112.43 775.08301
13000 82.044687 82.044687 82.044687 35.182156 25.475124
-32.340964 112.41231 -104000.66 794.78357
14000 82.087367 82.087367 82.087367 -83.889616 78.499262
-74.85019 -255.31792 -103893.23 813.71722
15000 82.111609 82.111609 82.111609 163.32843 158.6762
243.91258 87.396518 -103795.12 832.92862
16000 82.15398 82.15398 82.15398 -77.179498 -68.619222
17.141974 -180.06125 -103712.28 853.68876
17000 82.188167 82.188167 82.188167 -106.69283 -230.85143
70.924258 -160.15131 -103614.94 868.65478
18000 82.210315 82.210315 82.210315 169.22198 28.218797
302.31032 177.13683 -103545.77 888.04905
19000 82.239069 82.239069 82.239069 47.631683 183.28016
175.63555 -216.02066 -103466.68 902.58812
20000 82.284201 82.284201 82.284201 -485.59191 -426.95396
-646.17338 -383.6484 -103392.87 915.86136
Loop time of 1240.88 on 1 procs for 20000 steps with 32000 atoms

Performance: 1.393 ns/day, 17.234 hours/ns, 16.118 timesteps/s


100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:


Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1197.4 | 1197.4 | 1197.4 | 0.0 | 96.49
Neigh | 17.387 | 17.387 | 17.387 | 0.0 | 1.40
Comm | 3.539 | 3.539 | 3.539 | 0.0 | 0.29
Output | 0.0059877 | 0.0059877 | 0.0059877 | 0.0 | 0.00
Modify | 20.163 | 20.163 | 20.163 | 0.0 | 1.62
Other | | 2.432 | | | 0.20

Nlocal: 32000 ave 32000 max 32000 min


Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 24253 ave 24253 max 24253 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.21454e+06 ave 2.21454e+06 max 2.21454e+06 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 = 2214542


Ave neighs/atom = 69.204437
Neighbor list builds = 387
Dangerous builds = 0
Initial Length, L0: 82.2842011900534
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 46.99 | 46.99 | 46.99 Mbytes
Step v_strain Temp v_p2 v_p3 v_p4 KinEng
PotEng Press
0 1.7270454e-16 915.86136 0.042695396 0.064617338 0.03836484
3788.1815 -103392.87 -485.59191
1000 0.01 921.49143 0.44967243 -0.0062552181 0.0042751694
3811.4686 -103282.54 -1492.3079
2000 0.02 934.54765 0.88896194 0.010213889 0.026969428
3865.4717 -103177.75 -3087.1509
3000 0.03 936.82754 1.3208335 0.025734863 -0.0041943119
3874.9017 -103019.6 -4474.5801
4000 0.04 947.26383 1.7212372 0.012569951 -0.01536767
3918.0683 -102888.34 -5728.1316
5000 0.05 951.43237 2.1218715 0.0066067689 0.0098762125
3935.3102 -102722.96 -7127.8484
6000 0.06 952.81072 2.5154189 -0.018434763 -0.053829647
3941.0113 -102537.06 -8143.8482
7000 0.07 950.90187 2.7994399 0.032794336 -0.0078492388
3933.1159 -102328.36 -9414.6167
8000 0.08 949.23646 3.0321235 0.010656393 0.044615766
3926.2275 -102110.9 -10291.319
9000 0.09 945.1969 3.2056145 0.026551298 0.025650152
3909.5191 -101874.96 -10859.386
10000 0.1 939.08864 3.0775496 -0.0048276123 -0.017094244
3884.2541 -101625.25 -10185.426
11000 0.11 949.67953 2.2747718 0.039103945 0.0073682083
3928.0601 -101457.83 -7737.4797
12000 0.12 972.78891 1.2979737 0.042017034 0.05486554
4023.645 -101390.33 -4649.521
13000 0.13 976.62672 0.73058903 0.025018926 0.0076833499
4039.5189 -101288.23 -2544.3043
14000 0.14 983.85088 0.58996804 0.020258981 0.064608347
4069.3995 -101222.34 -2249.4512
15000 0.15 987.38329 0.5363148 0.034974267 -0.014948698
4084.0102 -101152.48 -1854.4679
16000 0.16 992.84085 0.46219797 0.03774688 0.036891909
4106.5838 -101099.01 -1789.4559
17000 0.17 993.71775 0.37791508 -0.046935484 -0.0018019315
4110.2108 -101034.48 -1097.2589
18000 0.18 992.37831 0.34676668 -0.038462854 -0.079072665
4104.6706 -100961.77 -764.10386
19000 0.19 996.60504 0.26474135 -0.020456949 0.0012629482
4122.1532 -100922.95 -818.49115
20000 0.2 994.99111 0.30240842 -0.00035960048 -0.02644221
4115.4776 -100862.67 -918.68871
Loop time of 1201.1 on 1 procs for 20000 steps with 32000 atoms

Performance: 1.439 ns/day, 16.682 hours/ns, 16.651 timesteps/s


100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:


Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1133.3 | 1133.3 | 1133.3 | 0.0 | 94.35
Neigh | 21.721 | 21.721 | 21.721 | 0.0 | 1.81
Comm | 2.6054 | 2.6054 | 2.6054 | 0.0 | 0.22
Output | 17.367 | 17.367 | 17.367 | 0.0 | 1.45
Modify | 24.149 | 24.149 | 24.149 | 0.0 | 2.01
Other | | 1.986 | | | 0.17

Nlocal: 32000 ave 32000 max 32000 min


Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 23230 ave 23230 max 23230 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.11378e+06 ave 2.11378e+06 max 2.11378e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.22654e+06 ave 4.22654e+06 max 4.22654e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4226543


Ave neighs/atom = 132.07947
Neighbor list builds = 492
Dangerous builds = 0
All done
Total wall time: 0:40:42

new_python_file_with_output

import matplotlib.pyplot as plt


import numpy as np
import csv

results = []
with open("Al_1000_20_tens_100.def1.txt",newline='') as file:
reader = csv.reader(file, delimiter=' ')
next(reader) # Skip header row.
for row in reader:
row2 = [float(i) for i in row]
results.append(row2)
print(row2)
results2 = np.transpose(results)
plt.plot(results2[0],results2[1], '-or', label='Stress in X', lw=2, markersize = 5, mec = 'r', mfc = 'r')
plt.plot(results2[0],results2[2], '-ob', label='Stress in Y', lw=2, markersize = 5, mec = 'b', mfc = 'b')
plt.plot(results2[0],results2[3], '-og', label='Stress in Z', lw=2, markersize = 5, mec = 'g', mfc = 'g')
plt.xlabel('Strain',fontsize=16)
plt.ylabel('Stress (GPa)',fontsize=16)
plt.title('Stress versus Strain',fontsize=16)
plt.legend(fontsize=12)
plt.axis()
plt.ylim(0,10)
plt.show()

[1.72704535131585e-16, 0.0426953955874614, 0.0646173380130449, 0.0383648397365286]


[0.00100000000000012, 0.101224244077074, 0.0113100288868497, 0.03102901839188]
[0.00200000000000007, 0.13212917551276, -0.0151408361195248, 0.00809356941157473]
[0.00300000000000002, 0.163008258823886, -0.0301701349072989, -0.00496445729136916]
[0.00400000000000014, 0.221261470160836, 0.0135157553296967, -0.0134051353487728]
[0.00500000000000008, 0.238379990235581, 0.0340608505025484, 0.00853597395025766]
[0.00600000000000003, 0.297091069972794, 0.0143106962945687, 0.00431398599968199]
[0.00700000000000015, 0.306804386211684, 0.0232809518606071, -0.0301310105995339]
[0.0080000000000001, 0.393559646053928, -0.0171641497504879, 0.00217415894536212]
[0.00900000000000005, 0.422779441001525, 0.0433878487445048, 0.0193908634571641]
[0.0100000000000002, 0.44967243207152, -0.00625521805667297, 0.0042751694372367]
[0.0110000000000001, 0.528295309912105, 0.00642330523052109, -0.00224769995298907]
[0.0120000000000001, 0.482748188515817, -0.00523789613429813, 0.00175816031232284]
[0.013, 0.594293502755175, -0.0175541672939255, -0.016236096995295]
[0.0140000000000001, 0.633824723917384, 0.0325159994148387, 0.0511454236284907]
[0.0150000000000001, 0.676783143694667, 0.0230942521975044, -0.00180912680827957]
[0.016, 0.705219601062887, -0.0167964754387784, 0.0146119654684816]
[0.0170000000000001, 0.759064869949791, 0.0237998623744511, 0.030513830462043]
[0.0180000000000001, 0.795638177896393, -0.00504006506952844, 0.0100347390793408]
[0.019, 0.831966251864467, 0.0148465299517512, 0.037607334173483]
[0.0200000000000002, 0.888961941410611, 0.0102138887375102, 0.0269694277093224]
[0.0210000000000001, 0.923593567649723, -0.0297160478088924, -0.00718820662659116]
[0.0220000000000001, 0.981494155685483, -0.00506559443911789, -0.0211638018728447]
[0.023, 1.07147690379052, 0.0174671298832142, 0.0109400659117886]
[0.0240000000000001, 1.06490770868229, -0.0435556824791841, 0.00288007558801237]
[0.0250000000000001, 1.12976403011927, 0.0232291536928408, -0.00499334319165139]
[0.026, 1.16059416792755, 0.0293761115616044, -0.00120163510828903]
[0.0270000000000001, 1.20514948501412, 0.00116709402459282, -0.0269503760846251]
[0.0280000000000001, 1.25655961730072, -0.0131174821461695, -0.0100486159839779]
[0.029, 1.29176217241386, 0.0304848767734675, -0.00137522991616782]
[0.03, 1.32083348465345, 0.0257348627370781, -0.00419431185763594]
[0.0310000000000001, 1.40687331256522, -0.00612345155631453, -0.0104746535219247]
[0.032, 1.39555919321809, -0.025639506205598, 0.00526539770083996]
[0.0330000000000002, 1.48461421674412, 0.0327562408436015, -0.00494347861654963]
[0.0340000000000001, 1.48778173284238, -0.0351393947732444, -0.0125679653030455]
[0.0350000000000001, 1.54632465916262, 0.0182042483488365, 0.0205157739547941]
[0.036, 1.61472701339198, 0.0194717194677008, 0.00977191156578541]
[0.0370000000000001, 1.64481348754529, -0.0212461819915644, -0.0156049240252826]
[0.0380000000000001, 1.62147976083083, -0.00100944382551618, -0.031392220378696]
[0.039, 1.71610764024288, 0.0109791094115602, 0.0164713877081712]
[0.0400000000000002, 1.72123719262779, 0.0125699509931002, -0.0153676699152061]
[0.0410000000000001, 1.76110756561722, 0.0221417162084708, -0.00167847411148515]
[0.042, 1.80639029929427, 0.0136692851498758, 0.0139854081148411]
[0.043, 1.81500663043759, -0.0188177191000363, 0.0146574057129007]
[0.0440000000000001, 1.87718013730277, 0.0108876294491538, -0.0511662155654136]
[0.0450000000000001, 1.94585986414023, -0.0286126902436368, -0.0110711264213724]
[0.0460000000000002, 1.99082619918758, -0.0142307519144501, 0.0320380622506726]
[0.0470000000000001, 2.00151292941331, 0.0162525933468542, 0.00662571768509143]
[0.0480000000000001, 2.06841166073041, 0.0355270458962328, 0.0359743143006468]
[0.049, 2.08647741578179, 0.00471471216652824, -0.0347863572728965]
[0.0500000000000001, 2.12187154420996, 0.00660676894186906, 0.00987621250560643]
[0.0510000000000001, 2.13609412994105, 0.0129851990406461, 0.0107776736984075]
[0.052, 2.16161269490806, 0.00554874809548665, -0.0220660413065599]
[0.0530000000000002, 2.22457390877139, -0.0177027209296214, 0.0365501071661052]
[0.0540000000000001, 2.25527440910272, -0.00567886735421584, 0.0100180701763804]
[0.0550000000000001, 2.30556639872288, -0.028267639509582, 0.00637085841460865]
[0.056, 2.36222726737208, 0.0360525835664081, -0.0257463204372329]
[0.0570000000000001, 2.34607267430824, 0.0411749327366988, 0.0091286733366974]
[0.0580000000000001, 2.42470056971507, 0.0521659193874798, 0.0180810103620053]
[0.059, 2.40636230392365, -0.0216505274285926, 0.0386893650894137]
[0.0600000000000001, 2.51541888120604, -0.0184347630502236, -0.0538296465149732]
[0.0610000000000001, 2.50531551900747, 0.00298102397600214, -0.0321152668218055]
[0.062, 2.58236625758243, 0.0145295851201305, 0.0411126821636606]
[0.063, 2.59817006936361, 0.0236852106952345, 0.0197678037841143]
[0.0640000000000001, 2.56159544623278, -0.0279368336968506, -0.0631496680464376]
[0.0650000000000001, 2.60459845330659, -0.0124081522469857, -0.00569334056408403]
[0.0660000000000002, 2.68531896294085, 0.0337851409199487, 0.0591077473550898]
[0.0670000000000001, 2.7273353229177, 0.000326997234726072, 0.0180009485011378]
[0.0680000000000001, 2.70940462562228, -0.0395394072620104, -0.024280959095672]
[0.069, 2.71670164166549, 0.0196232026269883, 0.0528100803224838]
[0.07, 2.79943990225581, 0.0327943361566453, -0.0078492388472582]
[0.0710000000000001, 2.81546813765944, -0.0252905223833188, 0.011502814246625]
[0.072, 2.84556060974721, -0.0279410770000587, -0.0129262083026421]
[0.0730000000000001, 2.87363082768106, 0.0432252971592663, 0.000777644210515635]
[0.0740000000000001, 2.91336895861719, 0.0415433393750432, 0.00679876387873902]
[0.0750000000000001, 2.88372007177446, -0.0143459933828577, -0.0587193816475998]
[0.076, 2.96797725575418, 0.0133917872979422, -0.0194640001573522]
[0.0770000000000001, 2.96245704068035, 0.00656795019770426, -0.0238249477437864]
[0.0780000000000001, 3.00756854737323, -0.0406855663366747, -0.0198837738917239]
[0.0790000000000002, 3.04913554623981, 0.0336757635048264, -0.0130246556747117]
[0.0800000000000001, 3.03212353113915, 0.0106563934483636, 0.0446157655418596]
[0.0810000000000001, 3.05507216260354, -0.0484817320301495, 0.00555274418870188]
[0.082, 3.08968266644649, 0.0142496111619807, 0.00854349708303606]
[0.083, 3.15372833760319, -0.0392928026871464, 0.00891802392857325]
[0.0840000000000001, 3.12176908357807, 0.0119329602040971, 0.0181385412642531]
[0.085, 3.13481875403292, -0.0197614073587103, -0.00163721603393965]
[0.0860000000000002, 3.15693430638895, 0.0459933833219075, 0.0151197747618299]
[0.0870000000000001, 3.16278671983422, 0.00105401333490764, 0.00370589102451266]
[0.0880000000000001, 3.1933222677758, 0.00491729434788808, -0.00407139074244926]
[0.089, 3.15812793139923, -0.02322137390913, -0.0365277138413404]
[0.0900000000000001, 3.20561448244546, 0.0265512975972933, 0.025650152024296]
[0.0910000000000001, 3.15811307832032, 0.0149877331855132, 0.0168330674749403]
[0.0920000000000002, 3.17441651958093, -0.0345570867742934, -0.00274083390040619]
[0.0930000000000001, 3.16467686501918, 0.00991090255458642, -0.0254004530691078]
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[0.095, 3.24069428938173, -0.0289589275436247, -0.00166204449557083]
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