rename example folders
This commit is contained in:
Axel Kohlmeyer
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# LAMMPS LATTICE DYNAMICS COMMANDS
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## DYNAMICAL MATRIX CALCULATOR
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This directory contains the ingredients to calculate a dynamical matrix with python.
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Example:
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```
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python dynmat.py
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```
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## Requires: MANYBODY and MOLECULE packages and the Python Library Interface
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../../../../../potentials/SiCGe.tersoff
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"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019"""
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# from mpi4py import MPI
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from lammps import lammps
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import numpy as np
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# comm = MPI.COMM_WORLD
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# rank = comm.Get_rank()
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""" LAMMPS VARIABLES """
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# data files
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infile = "silicon_input_file.lmp"
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ff_file = "ff-silicon.lmp"
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# full output useful for testing
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lmp = lammps()
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# reduced output useful reducing IO for production runs
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# lmp = lammps(cmdargs=["-screen", "none", "-log", "none"])
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# lammps commands
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lmp.command("atom_style full")
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lmp.command("units metal")
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lmp.command("processors * * *")
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lmp.command("neighbor 1 bin")
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lmp.command("boundary p p p")
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# read data and force field file
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lmp.command("read_data {}".format(infile))
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lmp.file("{}".format(ff_file))
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lmp.command("dynamical_matrix all eskm 0.000001 file dynmat.dat")
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dynmat = np.loadtxt("dynmat.dat")
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dynlen = int(3*np.sqrt(len(dynmat)/3))
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dynmat = dynmat.reshape((dynlen, dynlen))
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eigvals, eigvecs = np.linalg.eig(dynmat)
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# frequencies in THz
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omegas = np.sqrt(np.abs(eigvals))/2/np.pi
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print(omegas)
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../Silicon/ff-silicon.lmp
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5409.83472486 3.05075234 0.00000214
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-1277.48271855 -863.13225405 -862.89768612
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-193.14095469 0.12865732 0.00000061
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-1277.48271786 -863.13225450 862.89768520
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-193.17613450 -0.23660702 0.00000031
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-1276.01089136 861.66402482 -861.60900483
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83.46958227 -0.00634221 -0.00000026
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-1276.01088968 861.66402284 861.60900330
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3.05073556 5409.83419867 0.00000137
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-863.24919414 -1277.34161118 -862.97975804
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0.11071644 -193.14095221 0.00000015
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-863.24919482 -1277.34161057 862.97975774
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0.34066372 83.46934579 0.00000015
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861.54714972 -1276.15175730 861.52691337
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-0.09802844 -193.17585342 -0.00000005
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861.54715133 -1276.15175913 -861.52691490
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0.00000031 0.00000031 5410.11037330
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-862.95611222 -862.92132598 -1277.71824426
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-0.00000027 -0.00000023 83.84059068
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862.95611161 862.92132537 -1277.71824365
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-0.00000015 0.00000006 -193.17559671
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-861.62536929 861.66025668 -1276.08157121
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0.00000031 -0.00000000 -193.17573662
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861.62536952 -861.66025637 -1276.08157175
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-1277.48270695 -863.24917964 -862.95613831
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5409.83567791 3.04882503 2.82007909
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-1277.34160500 -863.13224794 862.92133361
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-193.14089232 0.11950085 -0.11994115
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-1277.52241409 863.24943335 -862.88111478
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-193.17596134 -0.16730494 0.02099535
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-1274.64156987 859.96383191 860.25587098
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83.46947136 0.16714109 -0.06108436
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-863.13224993 -1277.34160622 -862.92133430
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3.04882664 5409.83567981 -2.82007772
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-863.24917934 -1277.48270718 862.95613862
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0.11950077 -193.14089270 0.11994160
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863.24943366 -1277.52241409 862.88111478
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0.16714140 83.46947120 0.06108451
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859.96383191 -1274.64156979 -860.25587113
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-0.16730502 -193.17596118 -0.02099497
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-862.89766079 -862.97973912 -1277.71823542
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2.82004053 -2.82003977 5410.11000766
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862.97973867 862.89766003 -1277.71823633
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0.11994725 -0.11994740 83.84083859
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-863.11328229 863.11328297 -1277.34763999
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-0.02106026 0.06099877 -193.17561197
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860.17327676 -860.17327637 -1274.81551212
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-0.06099938 0.02106080 -193.17561235
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-193.14095266 0.11071661 0.00000023
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-1277.34161164 -863.24919490 862.97975758
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5409.83419895 3.05073908 0.00000031
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-1277.34161248 -863.24919704 -862.97976018
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83.46934641 0.34066377 0.00000031
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-1276.15175798 861.54714988 861.52691307
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-193.17585317 -0.09802854 0.00000018
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-1276.15175745 861.54714957 -861.52691314
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0.12865765 -193.14095472 0.00000000
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-863.13225527 -1277.48271931 862.89768673
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3.05075511 5409.83472469 -0.00000046
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-863.13225489 -1277.48271839 -862.89768612
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-0.23660723 -193.17613471 0.00000061
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861.66402345 -1276.01089068 -861.60900391
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-0.00634202 83.46958197 0.00000012
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861.66402314 -1276.01088961 861.60900353
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-0.00000015 -0.00000015 83.84059098
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862.92132797 862.95611360 -1277.71824533
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-0.00000145 -0.00000137 5410.11037498
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-862.92132598 -862.95611222 -1277.71824426
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-0.00000031 -0.00000009 -193.17559671
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861.66025660 -861.62536929 -1276.08157182
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0.00000015 0.00000014 -193.17573668
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-861.66025615 861.62536929 -1276.08157190
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-1277.48270619 -863.24917934 862.95613793
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-193.14089264 0.11950070 0.11994149
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-1277.34160589 -863.13224892 -862.92133438
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5409.83568112 3.04882502 -2.82007598
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-1277.52241409 863.24943313 862.88111386
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83.46947128 0.16714155 0.06108420
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-1274.64157216 859.96383297 -860.25587243
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-193.17596164 -0.16730510 -0.02099535
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-863.13224825 -1277.34160470 862.92133392
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0.11950069 -193.14089248 -0.11994088
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-863.24918118 -1277.48270824 -862.95613907
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3.04882479 5409.83568081 2.82007857
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863.24943366 -1277.52241409 -862.88111386
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-0.16730494 -193.17596164 0.02099504
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859.96383191 -1274.64157155 860.25587228
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0.16714109 83.46947120 -0.06108481
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862.89766018 862.97973836 -1277.71823542
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-0.11994717 0.11994762 83.84083846
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-862.97973940 -862.89766100 -1277.71823603
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-2.82004089 2.82004165 5410.11001111
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863.11328534 -863.11328473 -1277.34764213
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0.06099900 -0.02106019 -193.17561197
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-860.17327706 860.17327752 -1274.81551319
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0.02106049 -0.06099877 -193.17561212
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-193.17613831 0.34066975 0.00000000
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-1277.52243217 863.24943252 -863.11331043
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83.46934255 -0.23660983 0.00000046
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-1277.52243126 863.24943229 863.11330975
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5404.58897296 -9.71806756 0.00000046
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-1273.31334689 -858.38273326 -858.80488185
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-193.21062125 -0.11939087 -0.00000018
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-1273.31334666 -858.38273265 858.80488124
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-0.23661028 83.46934221 -0.00000038
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863.24943259 -1277.52243133 863.11331043
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0.34066924 -193.17613846 -0.00000015
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863.24943168 -1277.52243072 -863.11330883
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-9.71806704 5404.58897205 -0.00000107
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-858.38273265 -1273.31334697 -858.80488063
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-0.11939101 -193.21062043 0.00000006
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-858.38273296 -1273.31334681 858.80488139
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0.00000015 0.00000000 -193.17558413
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-862.88110730 862.88110699 -1277.34764060
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-0.00000001 -0.00000001 -193.17558374
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862.88110539 -862.88110516 -1277.34764030
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0.00000122 -0.00000264 5404.30470473
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-858.96244965 -858.96244934 -1273.17866523
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-0.00000046 0.00000006 83.09907322
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858.96245026 858.96245041 -1273.17866553
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-1276.01088335 861.54715186 -861.62537494
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-193.17596632 0.16713991 -0.02106865
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-1276.15172701 861.66401376 861.66024356
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83.46945641 -0.16730418 0.06100182
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-1273.31333507 -858.38273911 -858.96245926
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5404.58493280 -3.04507046 -2.81778113
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-1276.19189558 -861.66398654 861.58531085
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-193.21058250 -0.11920503 0.12012704
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861.66401292 -1276.15172617 861.66024257
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-0.16730418 83.46945627 0.06100192
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861.54715110 -1276.01088167 -861.62537387
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0.16713972 -193.17596591 -0.02106965
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-858.38273891 -1273.31333542 -858.96245910
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-3.04506741 5404.58493142 -2.81778205
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-861.66398683 -1276.19189578 861.58531200
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-0.11920541 -193.21058250 0.12012674
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-861.60900269 861.52691291 -1276.08157152
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0.02099737 0.06108917 -193.17561785
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861.52691246 -861.60900299 -1276.08157243
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0.06108909 0.02099718 -193.17561746
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-858.80486827 -858.80486867 -1273.17865256
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-2.81780745 -2.81780722 5404.30474364
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861.74281375 861.74281365 -1275.71086885
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-0.12013460 -0.12013475 83.09915550
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83.46959035 -0.09801326 0.00000000
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-1274.64156874 859.96385402 860.17328225
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-193.17585994 -0.00634034 0.00000031
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-1274.64156789 859.96385357 -860.17328072
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-193.21062369 -0.11938345 0.00000015
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-1276.19187300 -861.66400056 861.74280857
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5404.58377637 3.62403189 -0.00000071
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-1276.19187285 -861.66400087 -861.74280780
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-0.00634065 -193.17585981 -0.00000015
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859.96385345 -1274.64156845 -860.17328227
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-0.09801307 83.46959066 0.00000092
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859.96385342 -1274.64156728 860.17328103
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-0.11938399 -193.21062370 0.00000031
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-861.66399988 -1276.19187163 861.74280780
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3.62403013 5404.58377402 0.00000142
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-861.66400079 -1276.19187255 -861.74280803
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-0.00000031 -0.00000038 -193.17573821
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860.25587448 -860.25587441 -1274.81548871
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0.00000000 -0.00000026 -193.17573875
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-860.25587388 860.25587456 -1274.81548916
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0.00000015 -0.00000009 83.09905855
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861.58531164 861.58531156 -1275.71087571
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0.00000046 0.00000089 5404.30514766
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-861.58531232 -861.58531217 -1275.71087655
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-1276.01088198 861.54713523 861.62537356
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83.46945674 -0.16730402 -0.06100344
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-1276.15172688 861.66402939 -861.66024402
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-193.17596584 0.16713972 0.02106034
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-1273.31333552 -858.38273940 858.96245956
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-193.21058227 -0.11920503 -0.12012498
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-1276.19189573 -861.66398605 -861.58531085
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5404.58493188 -3.04506924 2.81779059
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861.66402925 -1276.15172686 -861.66024394
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0.16713982 -193.17596610 0.02106041
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861.54713537 -1276.01088130 861.62537448
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-0.16730426 83.46945625 -0.06100350
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-858.38273967 -1273.31333570 858.96245987
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-0.11920511 -193.21058281 -0.12012514
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-861.66398958 -1276.19189780 -861.58531314
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-3.04506687 5404.58493417 2.81779303
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861.60900299 -861.52691253 -1276.08157236
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-0.06108885 -0.02099714 -193.17561830
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-861.52691343 861.60900260 -1276.08157198
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-0.02099726 -0.06108848 -193.17561792
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858.80486782 858.80486829 -1273.17865256
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0.12013467 0.12013460 83.09915604
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-861.74281406 -861.74281426 -1275.71086942
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2.81780737 2.81780737 5404.30474524
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@ -0,0 +1,71 @@
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LAMMPS (15 Jun 2020)
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Reading data file ...
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orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 4.2e-05 secs
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read_data CPU = 0.001 secs
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Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4
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ghost atom cutoff = 4
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binsize = 2, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Calculating Dynamical Matrix ...
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Total # of atoms = 8
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Atoms in group = 8
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Total dynamical matrix elements = 576
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10% 20% 30% 50% 60% 70% 80%[3.34264870e-05 6.09176101e-05 1.72068597e-04 1.60807822e+01
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1.60807027e+01 1.60806903e+01 1.48964054e+01 1.49012648e+01
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1.49129598e+01 1.49081641e+01 1.48999471e+01 1.49095175e+01
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1.21983946e+01 1.21957091e+01 1.22010862e+01 1.22037817e+01
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1.22037910e+01 1.22037868e+01 6.89648276e+00 6.89524412e+00
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6.89619622e+00 6.89553366e+00 6.89615471e+00 6.89557491e+00]
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Finished Calculating Dynamical Matrix
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Loop time of 0.000677109 on 1 procs for 48 steps with 8 atoms
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Performance: 6124.865 ns/day, 0.004 hours/ns, 70889.645 timesteps/s
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91.3% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00064349 | 0.00064349 | 0.00064349 | 0.0 | 95.04
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Bond | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.1683e-05 | 1.1683e-05 | 1.1683e-05 | 0.0 | 1.73
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14
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Other | | 2.003e-05 | | | 2.96
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Nlocal: 8 ave 8 max 8 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 86 ave 86 max 86 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 128
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Ave neighs/atom = 16
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Ave special neighs/atom = 0
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:00
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@ -0,0 +1 @@
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../Silicon/silicon_input_file.lmp
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Reference in New Issue
Block a user