From 6fbcb848194f6607b44b0ffd24f02bc47e1ea434 Mon Sep 17 00:00:00 2001 From: Sievers Date: Mon, 22 Jun 2020 15:26:04 -0700 Subject: [PATCH] Update dynamical matrix examples --- .../Silicon/Si.opt.tersoff | 66 ---- .../Silicon/ff-silicon.lmp | 2 +- .../Silicon/results/dynmat.dat | 368 +++++++++--------- .../Silicon/results/out.silicon | 47 ++- .../dynamical_matrix_command/python/dynmat.py | 6 +- .../python/results/dynmat.dat | 192 +++++++++ .../python/results/out.dynamt | 71 ++++ 7 files changed, 478 insertions(+), 274 deletions(-) delete mode 100755 examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff mode change 100755 => 100644 examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat mode change 100755 => 100644 examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon create mode 100644 examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat create mode 100644 examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff b/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff deleted file mode 100755 index 3bc19f0581..0000000000 --- a/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff +++ /dev/null @@ -1,66 +0,0 @@ -# Tersoff parameters for various elements and mixtures -# multiple entries can be added to this file, LAMMPS reads the ones it needs -# these entries are in LAMMPS "metal" units: -# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms -# other quantities are unitless - -# Aidan Thompson (athomps at sandia.gov) takes full blame for this -# file. It specifies various potentials published by J. Tersoff for -# silicon, carbon and germanium. Since Tersoff published several -# different silicon potentials, I refer to them using atom types -# Si(B), Si(C) and Si(D). The last two are almost almost identical but -# refer to two different publications. These names should be used in -# the LAMMPS command when the file is invoked. For example: -# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials -# can be used pure silicon, pure carbon, pure germanium, binary SiC, -# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will -# generate an error if this file is used with any combination -# involving C and Ge, since there are no entries for the GeC -# interactions (Tersoff did not publish parameters for this -# cross-interaction.) - -# format of a single entry (one or more lines): -# element 1, element 2, element 3, -# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A - -# The original Tersoff potential for Silicon, Si(B) -# J. Tersoff, PRB, 37, 6991 (1988) - -Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956 - 0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7 - -# The later Tersoff potential for Silicon, Si(C) -# J. Tersoff, PRB, 38, 9902 (1988) - -Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734 - 1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 - -# The later Tersoff potential for Carbon, Silicon, and Germanium -# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248) -# The Si and C parameters are very close to those in SiC.tersoff - -C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6 -Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 -Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0 - -C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 -C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0 -C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 - -Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 -Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 -Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 - -Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 -Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 -Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 - -Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 -Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0 -Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 - -# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) -# element 1, element 2, element 3, -# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A -C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6 - diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp b/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp index f3b895f168..5768408b61 100755 --- a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp @@ -16,4 +16,4 @@ mass ${Si} 28.08550 ########################### pair_style tersoff -pair_coeff * * Si.opt.tersoff Si(D) +pair_coeff * * ../../../../../potentials/SiCGe.tersoff Si(D) diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat old mode 100755 new mode 100644 index 676f897416..b6712ea4f9 --- a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat @@ -1,192 +1,192 @@ 5409.83472486 3.05075234 0.00000214 --1277.48270695 -863.24917964 -862.95613831 --193.14095266 0.11071645 0.00000015 --1277.48270619 -863.24917934 862.95613793 --193.17613831 0.34066975 -0.00000031 --1276.01088244 861.54715125 -861.62537402 -83.46959051 -0.09801326 0.00000000 --1276.01088167 861.54715064 861.62537387 -3.05073556 5409.83419867 0.00000137 --863.13224993 -1277.34160622 -862.92133430 -0.12865796 -193.14095472 -0.00000023 --863.13224825 -1277.34160485 862.92133392 --0.23661028 83.46934214 -0.00000046 -861.66402909 -1276.15172701 861.66024333 --0.00634065 -193.17585981 -0.00000015 -861.66402909 -1276.15172686 -861.66024394 -0.00000031 0.00000031 5410.11037330 --862.89766079 -862.97973912 -1277.71823542 -0.00000000 -0.00000008 83.84059083 -862.89766018 862.97973851 -1277.71823557 -0.00000015 0.00000015 -193.17558390 --861.60900269 861.52691291 -1276.08157137 --0.00000015 -0.00000031 -193.17573821 -861.60900330 -861.52691284 -1276.08157236 --1277.48271824 -863.13225435 -862.89768596 -5409.83567916 3.04882502 2.82007861 --1277.34161080 -863.24919475 862.97975804 --193.14089260 0.11950100 0.11994134 --1277.52243157 863.24943259 -863.11331046 --193.17597070 0.16713301 -0.02106496 --1274.64156872 859.96385388 860.17328202 -83.46945758 -0.16730525 -0.06100253 --863.24919444 -1277.34161103 -862.97975804 -3.04882666 5409.83567944 -2.82007731 --863.13225496 -1277.48271916 862.89768688 -0.11950094 -193.14089255 -0.11994043 -863.24943320 -1277.52243118 863.11331076 --0.16730522 83.46945778 0.06100314 -859.96385365 -1274.64156819 -860.17328225 -0.16713979 -193.17596607 0.02106008 --862.95611199 -862.92132598 -1277.71824411 -2.82004085 -2.82004013 5410.11000835 -862.92132743 862.95611344 -1277.71824587 --0.11994722 0.11994786 83.84083834 --862.88110757 862.88110699 -1277.34764097 -0.02099713 0.06108924 -193.17561785 -860.25587487 -860.25587502 -1274.81548840 --0.06108897 -0.02099687 -193.17561808 --193.14095465 0.12865765 0.00000015 --1277.34160508 -863.13224794 862.92133361 -5409.83419867 3.05073968 0.00000092 --1277.34160584 -863.13224924 -862.92133483 -83.46934214 -0.23660998 -0.00000076 --1276.15172724 861.66402917 861.66024325 --193.17585988 -0.00634042 -0.00000031 --1276.15172694 861.66402940 -861.66024325 -0.11071645 -193.14095243 0.00000046 --863.24917949 -1277.48270718 862.95613831 -3.05075524 5409.83472478 -0.00000046 --863.24918117 -1277.48270825 -862.95613923 -0.34066922 -193.17613823 0.00000046 -861.54715094 -1276.01088228 -861.62537295 --0.09801303 83.46959035 0.00000015 -861.54713538 -1276.01088145 861.62537387 --0.00000046 -0.00000023 83.84059068 -862.97973867 862.89766010 -1277.71823633 --0.00000214 -0.00000053 5410.11037574 --862.97973943 -862.89766079 -1277.71823633 -0.00000015 0.00000008 -193.17558374 -861.52691291 -861.60900269 -1276.08157198 --0.00000015 -0.00000015 -193.17573814 --861.52691368 861.60900261 -1276.08157243 +-1277.48271855 -863.13225405 -862.89768612 +-193.14095469 0.12865732 0.00000061 -1277.48271786 -863.13225450 862.89768520 --193.14089232 0.11950085 -0.11994115 --1277.34161255 -863.24919673 -862.97975957 -5409.83568051 3.04882517 -2.82007644 --1277.52243110 863.24943259 863.11330990 -83.46945732 -0.16730494 0.06100319 --1274.64156796 859.96385342 -860.17328103 --193.17597041 0.16713331 0.02106477 --863.24919482 -1277.34161057 862.97975774 -0.11950077 -193.14089270 0.11994160 --863.13225473 -1277.48271839 -862.89768673 -3.04882502 5409.83568081 2.82007903 -863.24943084 -1277.52242966 -863.11330868 -0.16713324 -193.17597064 -0.02106522 -859.96385510 -1274.64156926 860.17328255 --0.16730411 83.46945641 -0.06100350 -862.95611161 862.92132537 -1277.71824365 -0.11994725 -0.11994740 83.84083859 --862.92132606 -862.95611207 -1277.71824548 --2.82003936 2.82004013 5410.11000806 -862.88110509 -862.88110547 -1277.34764015 -0.06108893 0.02099703 -193.17561792 --860.25587388 860.25587441 -1274.81548916 --0.02099726 -0.06108878 -193.17561777 --193.17613465 -0.23660693 0.00000015 --1277.52241409 863.24943328 -862.88111478 -83.46934549 0.34066334 -0.00000015 --1277.52241425 863.24943335 862.88111508 -5404.58897235 -9.71806749 0.00000015 --1273.31333522 -858.38273960 -858.96245956 --193.21062369 -0.11938368 0.00000000 --1273.31333598 -858.38273967 858.96245926 -0.34066342 83.46934572 0.00000015 -863.24943335 -1277.52241402 862.88111478 --0.23660723 -193.17613480 -0.00000046 -863.24943320 -1277.52241425 -862.88111432 --9.71806582 5404.58897135 -0.00000183 --858.38273891 -1273.31333552 -858.96245926 --0.11938338 -193.21062369 0.00000000 --858.38273937 -1273.31333598 858.96245987 --0.00000031 -0.00000008 -193.17559595 --863.11328229 863.11328297 -1277.34763999 -0.00000000 -0.00000015 -193.17559595 -863.11328305 -863.11328282 -1277.34763984 -0.00000122 -0.00000259 5404.30470550 --858.80486827 -858.80486866 -1273.17865241 --0.00000031 0.00000000 83.09905870 -858.80486827 858.80486812 -1273.17865272 +-193.17613450 -0.23660702 0.00000031 -1276.01089136 861.66402482 -861.60900483 --193.17596134 -0.16730494 0.02099535 --1276.15175745 861.54714988 861.52691337 -83.46947097 0.16714109 0.06108436 --1273.31334651 -858.38273311 -858.80488185 -5404.58493608 -3.04507687 -2.81778617 --1276.19187193 -861.66399965 861.74280750 --193.21058304 -0.11920641 -0.12012575 -861.54714972 -1276.15175730 861.52691337 -0.16714140 83.46947120 0.06108451 -861.66402345 -1276.01089022 -861.60900330 --0.16730487 -193.17596164 0.02099489 --858.38273281 -1273.31334681 -858.80488063 --3.04507603 5404.58493554 -2.81778617 --861.66400079 -1276.19187270 861.74280887 --0.11920511 -193.21058281 -0.12012498 --861.62536929 861.66025668 -1276.08157121 --0.02106026 0.06099877 -193.17561197 -861.66025752 -861.62537051 -1276.08157274 -0.06099923 -0.02106049 -193.17561227 --858.96244980 -858.96244965 -1273.17866523 --2.81780608 -2.81780615 5404.30474272 -861.58531232 861.58531248 -1275.71087663 -0.12013467 0.12013460 83.09915619 -83.46958166 -0.00634218 -0.00000023 --1274.64157002 859.96383191 860.25587098 --193.17585332 -0.09802844 0.00000023 --1274.64157155 859.96383290 -860.25587243 --193.21062064 -0.11939070 -0.00000008 --1276.19189573 -861.66398638 861.58531118 -5404.58377546 3.62403097 0.00000015 --1276.19189558 -861.66398615 -861.58531103 --0.09802859 -193.17585355 -0.00000015 -859.96383206 -1274.64156979 -860.25587113 --0.00634187 83.46958204 -0.00000008 -859.96383282 -1274.64157132 860.25587212 --0.11939055 -193.21062041 0.00000000 --861.66398576 -1276.19189528 861.58531087 -3.62402982 5404.58377698 -0.00000076 --861.66398927 -1276.19189772 -861.58531331 -0.00000000 0.00000000 -193.17573654 -860.17327676 -860.17327637 -1274.81551212 -0.00000031 0.00000023 -193.17573676 --860.17327615 860.17327645 -1274.81551258 -0.00000000 0.00000015 83.09907327 -861.74281299 861.74281299 -1275.71086763 --0.00000046 -0.00000015 5404.30514861 --861.74281406 -861.74281421 -1275.71086938 +83.46958227 -0.00634221 -0.00000026 -1276.01088968 861.66402284 861.60900330 -83.46947136 0.16714109 -0.06108436 --1276.15175722 861.54714957 -861.52691391 --193.17596141 -0.16730510 -0.02099527 --1273.31334666 -858.38273281 858.80488124 --193.21058304 -0.11920641 0.12012636 --1276.19187285 -861.66400087 -861.74280773 -5404.58493638 -3.04507565 2.81778602 +3.05073556 5409.83419867 0.00000137 +-863.24919414 -1277.34161118 -862.97975804 +0.11071644 -193.14095221 0.00000015 +-863.24919482 -1277.34161057 862.97975774 +0.34066372 83.46934579 0.00000015 +861.54714972 -1276.15175730 861.52691337 +-0.09802844 -193.17585342 -0.00000005 861.54715133 -1276.15175913 -861.52691490 --0.16730502 -193.17596118 -0.02099497 -861.66402314 -1276.01088976 861.60900383 -0.16714125 83.46947151 -0.06108497 --858.38273296 -1273.31334681 858.80488139 --0.11920686 -193.21058311 0.12012605 --861.66400079 -1276.19187255 -861.74280811 --3.04506703 5404.58493432 2.81779319 +0.00000031 0.00000031 5410.11037330 +-862.95611222 -862.92132598 -1277.71824426 +-0.00000027 -0.00000023 83.84059068 +862.95611161 862.92132537 -1277.71824365 +-0.00000015 0.00000006 -193.17559671 +-861.62536929 861.66025668 -1276.08157121 +0.00000031 -0.00000000 -193.17573662 861.62536952 -861.66025637 -1276.08157175 +-1277.48270695 -863.24917964 -862.95613831 +5409.83567791 3.04882503 2.82007909 +-1277.34160500 -863.13224794 862.92133361 +-193.14089232 0.11950085 -0.11994115 +-1277.52241409 863.24943335 -862.88111478 +-193.17596134 -0.16730494 0.02099535 +-1274.64156987 859.96383191 860.25587098 +83.46947136 0.16714109 -0.06108436 +-863.13224993 -1277.34160622 -862.92133430 +3.04882664 5409.83567981 -2.82007772 +-863.24917934 -1277.48270718 862.95613862 +0.11950077 -193.14089270 0.11994160 +863.24943366 -1277.52241409 862.88111478 +0.16714140 83.46947120 0.06108451 +859.96383191 -1274.64156979 -860.25587113 +-0.16730502 -193.17596118 -0.02099497 +-862.89766079 -862.97973912 -1277.71823542 +2.82004053 -2.82003977 5410.11000766 +862.97973867 862.89766003 -1277.71823633 +0.11994725 -0.11994740 83.84083859 +-863.11328229 863.11328297 -1277.34763999 +-0.02106026 0.06099877 -193.17561197 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0.12013460 83.09915604 +-861.74281406 -861.74281426 -1275.71086942 +2.81780737 2.81780737 5404.30474524 diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon old mode 100755 new mode 100644 index 9920ddac51..1f39f3b830 --- a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon @@ -1,7 +1,7 @@ -LAMMPS (16 Jul 2018) +LAMMPS (15 Jun 2020) Reading data file ... - orthogonal box = (0 0 0) to (5.431 5.431 5.431) - 1 by 2 by 2 MPI processor grid + orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431) + 1 by 1 by 1 MPI processor grid reading atoms ... 8 atoms Finding 1-2 1-3 1-4 neighbors ... @@ -11,6 +11,9 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors + special bonds CPU = 4.2e-05 secs + read_data CPU = 0.002 secs +Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -23,36 +26,40 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Calculating Dynamical Matrix... -Dynamical Matrix calculation took 0.001183 seconds +Calculating Dynamical Matrix ... + Total # of atoms = 8 + Atoms in group = 8 + Total dynamical matrix elements = 576 + 10% 20% 30% 50% 60% 70% 80% Finished Calculating Dynamical Matrix -Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms +Loop time of 0.000775099 on 1 procs for 48 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5350.544 ns/day, 0.004 hours/ns, 61927.589 timesteps/s +91.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00016781 | 0.00041345 | 0.00051464 | 0.0 | 0.00 -Bond | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 | 0.0 | 0.00 +Pair | 0.00074148 | 0.00074148 | 0.00074148 | 0.0 | 95.66 +Bond | 3.8147e-06 | 3.8147e-06 | 3.8147e-06 | 0.0 | 0.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00056143 | 0.00066602 | 0.00090865 | 0.0 | 0.00 +Comm | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.224e+06 | | |100.00 +Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.12 +Other | | 2.098e-05 | | | 2.71 -Nlocal: 2 ave 3 max 1 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 56 ave 57 max 55 min -Histogram: 1 0 0 0 0 2 0 0 0 1 +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 86 ave 86 max 86 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 32 ave 48 max 16 min -Histogram: 1 0 0 0 0 2 0 0 0 1 +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128 Ave neighs/atom = 16 Ave special neighs/atom = 0 -Neighbor list builds = 0 +Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:00 diff --git a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py index 2a3a0b5a2f..33cc3419b3 100644 --- a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py +++ b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py @@ -9,8 +9,8 @@ import numpy as np """ LAMMPS VARIABLES """ # data files -infile = "silicon_input_file.lmp" -ff_file = "ff-silicon.lmp" +infile = "../Silicon/silicon_input_file.lmp" +ff_file = "../Silicon/ff-silicon.lmp" # full output useful for testing lmp = lammps() @@ -38,5 +38,5 @@ dynmat = dynmat.reshape((dynlen, dynlen)) eigvals, eigvecs = np.linalg.eig(dynmat) # frequencies in THz -omegas = np.sqrt(np.abs(eigvals)) +omegas = np.sqrt(np.abs(eigvals))/2/np.pi print(omegas) diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat b/examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat new file mode 100644 index 0000000000..b6712ea4f9 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat @@ -0,0 +1,192 @@ +5409.83472486 3.05075234 0.00000214 +-1277.48271855 -863.13225405 -862.89768612 +-193.14095469 0.12865732 0.00000061 +-1277.48271786 -863.13225450 862.89768520 +-193.17613450 -0.23660702 0.00000031 +-1276.01089136 861.66402482 -861.60900483 +83.46958227 -0.00634221 -0.00000026 +-1276.01088968 861.66402284 861.60900330 +3.05073556 5409.83419867 0.00000137 +-863.24919414 -1277.34161118 -862.97975804 +0.11071644 -193.14095221 0.00000015 +-863.24919482 -1277.34161057 862.97975774 +0.34066372 83.46934579 0.00000015 +861.54714972 -1276.15175730 861.52691337 +-0.09802844 -193.17585342 -0.00000005 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+858.80486782 858.80486829 -1273.17865256 +0.12013467 0.12013460 83.09915604 +-861.74281406 -861.74281426 -1275.71086942 +2.81780737 2.81780737 5404.30474524 diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt b/examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt new file mode 100644 index 0000000000..812af4b2a5 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt @@ -0,0 +1,71 @@ +LAMMPS (15 Jun 2020) +Reading data file ... + orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 4.2e-05 secs + read_data CPU = 0.001 secs +Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4 + ghost atom cutoff = 4 + binsize = 2, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Calculating Dynamical Matrix ... + Total # of atoms = 8 + Atoms in group = 8 + Total dynamical matrix elements = 576 + 10% 20% 30% 50% 60% 70% 80%[3.34264870e-05 6.09176101e-05 1.72068597e-04 1.60807822e+01 + 1.60807027e+01 1.60806903e+01 1.48964054e+01 1.49012648e+01 + 1.49129598e+01 1.49081641e+01 1.48999471e+01 1.49095175e+01 + 1.21983946e+01 1.21957091e+01 1.22010862e+01 1.22037817e+01 + 1.22037910e+01 1.22037868e+01 6.89648276e+00 6.89524412e+00 + 6.89619622e+00 6.89553366e+00 6.89615471e+00 6.89557491e+00] + +Finished Calculating Dynamical Matrix +Loop time of 0.000677109 on 1 procs for 48 steps with 8 atoms + +Performance: 6124.865 ns/day, 0.004 hours/ns, 70889.645 timesteps/s +91.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00064349 | 0.00064349 | 0.00064349 | 0.0 | 95.04 +Bond | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.1683e-05 | 1.1683e-05 | 1.1683e-05 | 0.0 | 1.73 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.14 +Other | | 2.003e-05 | | | 2.96 + +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 86 ave 86 max 86 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: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 128 +Ave neighs/atom = 16 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:00