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Backport MS-MEAM bugfix from upstream for L12 lattice

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This commit is contained in:
Aidan Thompson
2024-09-27 11:26:36 -06:00
committed by Axel Kohlmeyer
parent c4a822a4cf
commit 076c711dba
5 changed files with 99 additions and 97 deletions
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24
examples/meam/msmeam/log.1Mar2024.msmeam.g++.1 → examples/meam/msmeam/log.27Sep2024.msmeam.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-372-g51d104975a)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for HGa
@ -67,7 +67,7 @@ Created 1 atoms
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
@ -89,22 +89,22 @@ Neighbor list info ...
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.587 | 8.587 | 8.587 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
Loop time of 4.4446e-05 on 1 procs for 1 steps with 3 atoms
0 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
1 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
Loop time of 0.000144827 on 1 procs for 1 steps with 3 atoms
Performance: 1943.932 ns/day, 0.012 hours/ns, 22499.213 timesteps/s, 67.498 katom-step/s
31.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 596.574 ns/day, 0.040 hours/ns, 6904.790 timesteps/s, 20.714 katom-step/s
21.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9908e-05 | 2.9908e-05 | 2.9908e-05 | 0.0 | 67.29
Pair | 9.2136e-05 | 9.2136e-05 | 9.2136e-05 | 0.0 | 63.62
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.033e-06 | 1.033e-06 | 1.033e-06 | 0.0 | 2.32
Output | 9.347e-06 | 9.347e-06 | 9.347e-06 | 0.0 | 21.03
Modify | 2.02e-07 | 2.02e-07 | 2.02e-07 | 0.0 | 0.45
Other | | 3.956e-06 | | | 8.90
Comm | 4.389e-06 | 4.389e-06 | 4.389e-06 | 0.0 | 3.03
Output | 3.9556e-05 | 3.9556e-05 | 3.9556e-05 | 0.0 | 27.31
Modify | 9.92e-07 | 9.92e-07 | 9.92e-07 | 0.0 | 0.68
Other | | 7.754e-06 | | | 5.35
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0

24
examples/meam/msmeam/log.1Mar2024.msmeam.g++.4 → examples/meam/msmeam/log.27Sep2024.msmeam.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-372-g51d104975a)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for HGa
@ -67,7 +67,7 @@ Created 1 atoms
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
@ -89,22 +89,22 @@ Neighbor list info ...
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.965 | 8.123 | 8.594 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
Loop time of 8.70645e-05 on 4 procs for 1 steps with 3 atoms
0 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
1 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
Loop time of 0.000328503 on 4 procs for 1 steps with 3 atoms
Performance: 992.368 ns/day, 0.024 hours/ns, 11485.738 timesteps/s, 34.457 katom-step/s
29.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 263.011 ns/day, 0.091 hours/ns, 3044.110 timesteps/s, 9.132 katom-step/s
75.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3957e-05 | 4.67e-05 | 5.1056e-05 | 0.0 | 53.64
Pair | 0.0001419 | 0.0001471 | 0.00015891 | 0.0 | 44.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.105e-05 | 1.3822e-05 | 1.7033e-05 | 0.0 | 15.88
Output | 1.5765e-05 | 1.9045e-05 | 2.5216e-05 | 0.0 | 21.87
Modify | 2.58e-07 | 3.465e-07 | 3.81e-07 | 0.0 | 0.40
Other | | 7.151e-06 | | | 8.21
Comm | 2.2092e-05 | 2.8424e-05 | 3.667e-05 | 0.0 | 8.65
Output | 8.6275e-05 | 0.00010558 | 0.0001422 | 0.0 | 32.14
Modify | 1.093e-06 | 2.4148e-06 | 5.651e-06 | 0.0 | 0.74
Other | | 4.498e-05 | | | 13.69
Nlocal: 0.75 ave 3 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

1
src/MEAM/meam_setup_done.cpp
View File

@ -837,6 +837,7 @@ void MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, dou
} else
*rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
if (msmeamflag) {
*rho21 = 8. / 3. * (rhoa21 - rhoa22) * (rhoa21 - rhoa22);
*rho2m1 = 8. / 3. * (rhoa2m1 - rhoa2m2) * (rhoa2m1 - rhoa2m2);
}
break;

5
src/MEAM/pair_meam.cpp
View File

@ -547,9 +547,9 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
// open user param file on proc 0
std::shared_ptr<PotentialFileReader> reader;
PotentialFileReader *reader = nullptr;
if (comm->me == 0) reader = std::make_shared<PotentialFileReader>(lmp, userfile, "MEAM");
if (comm->me == 0) reader = new PotentialFileReader(lmp, userfile, "MEAM");
// read settings
// pass them one at a time to MEAM package
@ -623,6 +623,7 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
keyword, descr[errorflag]);
}
}
if (comm->me == 0) delete reader;
}
/* ---------------------------------------------------------------------- */

140
unittest/force-styles/tests/atomic-pair-meam_ms.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 7 Feb 2024
lammps_version: 29 Aug 2024
tags: slow
date_generated: Wed Feb 28 17:07:42 2024
date_generated: Fri Sep 27 14:17:24 2024
epsilon: 2.5e-11
skip_tests:
prerequisites: ! |
@ -17,78 +17,78 @@ pair_coeff: ! |
extract: ! |
scale 2
natoms: 32
init_vdwl: 785.6030480758675
init_vdwl: 785.8717242418628
init_coul: 0
init_stress: ! |2-
3.3484562777721521e+03 3.6420237714822438e+03 3.6353392995221716e+03 -3.1708756217128752e+02 -7.7972133915567312e+01 -1.9763732315997078e+02
3.3495532442374852e+03 3.6432232807542064e+03 3.6365677037507535e+03 -3.1719725584382360e+02 -7.8010203158766885e+01 -1.9773004470467086e+02
init_forces: ! |2
1 1.2671882952049245e+01 -1.3853231851077510e+00 4.5439363666101173e+01
2 -3.8831765890428208e+01 -1.5598031052421931e+02 -1.8130309648194238e+00
3 -6.1494363653409785e+01 2.6941705868913857e+02 -9.6911726427029521e+01
4 3.1464910628044116e+01 4.0207585968399570e+01 1.2103864047414767e+01
5 1.4903052489944621e+01 -3.4527783082194034e+01 6.6654211762662953e+01
6 5.5548661222686047e+00 -3.9623462470037410e+01 -2.8613497963820279e+01
7 8.0397023763303324e+00 -1.0757727989654303e+01 -4.3166301457121655e+01
8 -4.7852982145265067e+01 -4.5739689932561944e-02 1.1843318640063390e+02
9 9.3964008212392528e+01 -7.2172885595082938e+00 2.5433781685526100e+01
10 1.5271997609830436e+01 -5.8803169091726673e+01 -6.7108575386479288e+01
11 -2.5045971665663821e+01 1.1625946130045016e+02 -2.3085965300813825e+01
12 6.2629055188396414e+01 2.0611095490210126e+01 -2.8436306261149859e+01
13 -5.9236259945824884e+01 3.0240277910808498e+01 -1.9273929877935466e+01
14 6.8663923609350405e+01 -7.7397309055975725e+01 3.3069829655105920e+01
15 -4.9647288254699909e+01 -4.9489231564386692e+01 8.4478943742851953e+01
16 -1.2170657087644635e+01 -3.2040178726180827e+01 1.4894301261010035e+01
17 8.8923416811864868e+00 6.2137744083574610e+01 -4.0135012964265592e+01
18 -4.1397401572483183e+01 2.5783976616022077e+01 -4.0437450156810772e+00
19 -7.9531558557888033e+01 9.6620429213911947e+01 6.0896893032878161e+01
20 8.1086619135335383e+01 7.0912440236148569e+01 -7.1683775489576050e+01
21 1.0782008087175012e+02 -1.5990396045249986e+02 -2.5346325379258598e+01
22 -2.2473039860970294e+00 5.2408111378634587e+01 4.9048274485706003e+00
23 -2.7403676909994125e+01 8.1791101929225192e+01 4.6914817444621839e+01
24 -3.0326733771468501e+01 6.5019994519315844e+01 -2.8273999335586893e+01
25 -5.1399449796211421e+01 -3.1235356363355280e+01 -5.1117557575884405e+00
26 3.9830854256806596e+01 -5.5977510234235112e+01 -1.0703040355620866e+01
27 8.2947330460814442e+01 6.2103713508335836e+01 5.0160761445057645e+01
28 -7.8724584730369727e+01 -3.9670230601217270e+01 -2.7333809658021124e+00
29 6.8825650256056235e+01 -6.1113096673842620e+01 -1.5031235234703393e+01
30 -2.4157792055811530e+01 -1.9333002107500442e+02 -2.6525581060126832e+01
31 7.7150429127214139e+01 -6.9426709034866391e+01 -5.5252913067136127e+01
32 -1.5024891495451018e+02 8.4411417529769210e+01 2.9865316672080176e+01
run_vdwl: 682.3135170292994
1 1.2678031763768246e+01 -1.3854742508554718e+00 4.5454792887005731e+01
2 -3.8844981281875995e+01 -1.5603552819975877e+02 -1.8118923154738256e+00
3 -6.1521100806352393e+01 2.6952064016220777e+02 -9.6945673391405251e+01
4 3.1474918811637131e+01 4.0221864481237098e+01 1.2106991684033252e+01
5 1.4909314739281982e+01 -3.4536196834067184e+01 6.6680113316670372e+01
6 5.5607589249640776e+00 -3.9634976929591176e+01 -2.8624069008648654e+01
7 8.0414671017475250e+00 -1.0757410086264327e+01 -4.3180176341738033e+01
8 -4.7873817108912888e+01 -4.7420260529060343e-02 1.1847882375259158e+02
9 9.3996311097334058e+01 -7.2230333911033835e+00 2.5439738584791549e+01
10 1.5276599260379086e+01 -5.8829432213236764e+01 -6.7137053986625617e+01
11 -2.5054152079132052e+01 1.1629384609515466e+02 -2.3089487061908105e+01
12 6.2647097499564396e+01 2.0615344433669222e+01 -2.8446593251382438e+01
13 -5.9256263857726850e+01 3.0249354974368117e+01 -1.9285948232134174e+01
14 6.8692971659580280e+01 -7.7423992900729019e+01 3.3088032924225352e+01
15 -4.9664996131324450e+01 -4.9505326080123282e+01 8.4506814079408798e+01
16 -1.2171749225905778e+01 -3.2053078930294205e+01 1.4901314161249992e+01
17 8.9019136643456704e+00 6.2170468054303171e+01 -4.0153594811039476e+01
18 -4.1412343566976787e+01 2.5794429840154532e+01 -4.0452395104665770e+00
19 -7.9564629952098812e+01 9.6651354759152042e+01 6.0917538476309034e+01
20 8.1113225492719948e+01 7.0936914728750452e+01 -7.1709964771002802e+01
21 1.0786611258149451e+02 -1.5995593790998802e+02 -2.5357133081597116e+01
22 -2.2483895934790117e+00 5.2422862488362668e+01 4.9054605585862063e+00
23 -2.7411037080061696e+01 8.1824682560423952e+01 4.6924090717621404e+01
24 -3.0337790467628789e+01 6.5042256803587094e+01 -2.8281618777457169e+01
25 -5.1415393535843094e+01 -3.1244066397305112e+01 -5.1143010322252600e+00
26 3.9844215835017884e+01 -5.6005352146508933e+01 -1.0697304736074248e+01
27 8.2979029329921474e+01 6.2118434060881889e+01 5.0173878089540807e+01
28 -7.8756083263727049e+01 -3.9682964173922336e+01 -2.7297307297757669e+00
29 6.8847386805449901e+01 -6.1132449248608829e+01 -1.5035416587044770e+01
30 -2.4167347842918304e+01 -1.9339953044247520e+02 -2.6538712090889941e+01
31 7.7180780195802967e+01 -6.9452945194801330e+01 -5.5269947455868873e+01
32 -1.5031005896904509e+02 8.4442662147909857e+01 2.9876267940724031e+01
run_vdwl: 682.5163056385919
run_coul: 0
run_stress: ! |2-
3.2220423802202231e+03 3.3749844973876429e+03 3.3217643573058244e+03 -2.8493376779188281e+02 -5.1850956493150733e+00 -3.1548413267512802e+02
3.2230508407097536e+03 3.3760038825364995e+03 3.3227514025504679e+03 -2.8503754654683991e+02 -5.2173119201137954e+00 -3.1564189857665059e+02
run_forces: ! |2
1 -1.2080548564836072e+01 -2.5477429439416710e+01 1.3806658731417755e+01
2 -3.7225520761818601e+01 -1.5818788485602025e+02 3.6451090218322113e+00
3 -3.2025464407673795e+01 2.5325620480420051e+02 -6.1031861941385266e+01
4 2.8988993769053742e+01 4.8033753615324457e+01 4.5694168356438283e+00
5 -1.2111374313827447e+01 -2.6961881177725004e+01 4.9632634513889542e+01
6 1.1311954816991424e+01 -5.0058087854226159e+01 -2.3204914001781273e+01
7 2.1516323786702536e+01 -5.0655040143290933e+00 -3.8825663342733620e+01
8 -5.6894831060887554e+01 1.3949056084318798e+01 1.1660108213204735e+02
9 7.2998009821741320e+01 4.8416842517465923e+00 2.3999831954683799e+01
10 1.7317912093622368e+01 -3.0947927635823405e+01 -1.2110169744224052e+01
11 -1.1067246227356863e+01 9.1960655066099605e+01 -2.2189177432965508e+01
12 4.1022329509360503e+01 1.2454231845197597e+01 -2.6395875385015671e+01
13 -5.2111607038923381e+01 3.3882585667855231e+01 -1.8629522935187623e+01
14 8.4036225281616041e+01 -9.3803437140562750e+01 1.6331247969198998e+01
15 -4.2720657484421395e+01 -4.3226247350447558e+01 7.1228336312410107e+01
16 -1.5337511847731712e+01 -3.3391288191194008e+01 2.4548585347623519e+01
17 -1.1747625966656585e+00 4.5776133215622977e+01 -3.9163692487889747e+01
18 -1.9491081233389249e+01 8.1566249764824512e+00 -7.8409414667475472e+00
19 -6.3157066638040050e+01 1.1562375461943864e+02 2.4100335394819872e+01
20 8.5633177613771736e+01 8.3249649056120163e+01 -6.5949837133210536e+01
21 7.2627995354135379e+01 -1.0905523323056843e+02 -9.7050849900191878e+00
22 -6.9254927960387569e+00 5.3565487765173124e+01 3.5264724633499451e+00
23 -2.6913648610060896e+01 5.7376365847813567e+01 2.7795031305112104e+01
24 -4.2988718884544781e+01 5.0965555337988739e+01 -4.0879720794423847e+01
25 -4.1545681275179334e+01 -2.6070548274497312e+01 4.6030493990981363e+00
26 4.7343706717511481e+01 -5.2491830895913587e+01 -7.5334343348923181e+00
27 7.1967929368447670e+01 6.4565679128450881e+01 4.3787238332434981e+01
28 -8.4353146891369605e+01 -3.5766877650630498e+01 -1.8194167121606220e+01
29 6.8890904369057438e+01 -6.3904080920499425e+01 -1.5203579536664831e+01
30 -1.0556200802502623e+01 -1.7613156919674918e+02 7.5443620074181723e+00
31 5.4944350533734486e+01 -4.1411243100978645e+01 -4.7232700660537759e+01
32 -1.0991925160047839e+02 3.4293649647748623e+01 1.8370951588304823e+01
1 -1.2090173295580399e+01 -2.5487883945517630e+01 1.3808838454744908e+01
2 -3.7237910628063261e+01 -1.5824464170923355e+02 3.6503404792558127e+00
3 -3.2043035190157688e+01 2.5334019834530716e+02 -6.1034051445150155e+01
4 2.8998234751624985e+01 4.8055299345669440e+01 4.5656027808244133e+00
5 -1.2112869933423042e+01 -2.6974221683197079e+01 4.9628143533381760e+01
6 1.1320499764680376e+01 -5.0075627603859388e+01 -2.3210788856798693e+01
7 2.1525286596972293e+01 -5.0612198361667318e+00 -3.8835531029268516e+01
8 -5.6920318481334483e+01 1.3956984193319112e+01 1.1664367763180698e+02
9 7.3014299955127811e+01 4.8453448145331830e+00 2.4005633336000450e+01
10 1.7334247568589937e+01 -3.0951264895930947e+01 -1.2098494158427552e+01
11 -1.1068236390689501e+01 9.1978964379138006e+01 -2.2192310200658977e+01
12 4.1024777584281992e+01 1.2450909775738268e+01 -2.6406356553381471e+01
13 -5.2125188945456109e+01 3.3894870845912308e+01 -1.8641032580242040e+01
14 8.4073387111870915e+01 -9.3839905507037258e+01 1.6333318901064604e+01
15 -4.2733775860448283e+01 -4.3238316015855247e+01 7.1246856036892538e+01
16 -1.5340501821929074e+01 -3.3400662017224057e+01 2.4562380519255392e+01
17 -1.1715139816660738e+00 4.5788292882495313e+01 -3.9174666280409781e+01
18 -1.9491459474534334e+01 8.1545423197633173e+00 -7.8445502241667988e+00
19 -6.3181153697293830e+01 1.1567329898860092e+02 2.4099836723818225e+01
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21 7.2638295944390450e+01 -1.0906810299911923e+02 -9.7045146810280265e+00
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...