From 549c6343f3491edaaf24cbea7745808f8c5e3269 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Sun, 21 Jun 2020 18:05:34 -0600 Subject: [PATCH] Merged MLIAP package into latest LAMMPS created SNAP, quadratic SNAP, and ChemSNAP examples --- examples/mliap/InP_JCPA2020.mliap | 19 + examples/mliap/InP_JCPA2020.mliap.descriptor | 20 + examples/mliap/InP_JCPA2020.mliap.model | 485 ++++++++++++++++++ examples/mliap/Ta06A.mliap | 2 +- examples/mliap/Ta06A.mliap.descriptor | 2 +- examples/mliap/Ta06A.mliap.model | 2 +- examples/mliap/W.quadratic.mliap | 2 + examples/mliap/W.quadratic.mliap.descriptor | 2 + examples/mliap/W.quadratic.mliap.model | 2 + examples/mliap/WBe_Wood_PRB2019.mliap | 2 +- .../mliap/WBe_Wood_PRB2019.mliap.descriptor | 2 + examples/mliap/WBe_Wood_PRB2019.mliap.model | 1 + .../{in.mliap.Ta06A => in.mliap.snap.Ta06A} | 4 +- ....WBe.PRB2019 => in.mliap.snap.WBe.PRB2019} | 4 +- examples/mliap/in.mliap.snap.chem | 46 ++ ...liap.quadratic => in.mliap.snap.quadratic} | 7 +- .../mliap/log.21Jun20.mliap.snap.Ta06A.g++.1 | 156 ++++++ .../mliap/log.21Jun20.mliap.snap.Ta06A.g++.4 | 156 ++++++ ...> log.21Jun20.mliap.snap.WBe.PRB201.g++.1} | 94 ++-- .../log.21Jun20.mliap.snap.WBe.PRB201.g++.4 | 165 ++++++ .../mliap/log.21Jun20.mliap.snap.chem.g++.1 | 158 ++++++ .../mliap/log.21Jun20.mliap.snap.chem.g++.4 | 158 ++++++ .../log.21Jun20.mliap.snap.quadratic.g++.1 | 151 ++++++ .../log.21Jun20.mliap.snap.quadratic.g++.4 | 151 ++++++ examples/mliap/log.snap.quadratic.ref | 153 ------ potentials/InP_JCPA2020.snap | 2 +- potentials/InP_JCPA2020.snapparam | 22 +- potentials/WBe_Wood_PRB2019.snapcoeff | 1 + potentials/WBe_Wood_PRB2019.snapparam | 2 + src/MLIAP/mliap_descriptor_snap.cpp | 27 +- src/MLIAP/mliap_descriptor_snap.h | 4 +- src/MLIAP/mliap_model.cpp | 5 +- 32 files changed, 1768 insertions(+), 239 deletions(-) create mode 100644 examples/mliap/InP_JCPA2020.mliap create mode 100644 examples/mliap/InP_JCPA2020.mliap.descriptor create mode 100644 examples/mliap/InP_JCPA2020.mliap.model rename examples/mliap/{in.mliap.Ta06A => in.mliap.snap.Ta06A} (90%) rename examples/mliap/{in.mliap.WBe.PRB2019 => in.mliap.snap.WBe.PRB2019} (92%) create mode 100644 examples/mliap/in.mliap.snap.chem rename examples/mliap/{in.mliap.quadratic => in.mliap.snap.quadratic} (88%) create mode 100644 examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.1 create mode 100644 examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.4 rename examples/mliap/{log.snap.WBe.ref => log.21Jun20.mliap.snap.WBe.PRB201.g++.1} (52%) create mode 100644 examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4 create mode 100644 examples/mliap/log.21Jun20.mliap.snap.chem.g++.1 create mode 100644 examples/mliap/log.21Jun20.mliap.snap.chem.g++.4 create mode 100644 examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.1 create mode 100644 examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.4 delete mode 100644 examples/mliap/log.snap.quadratic.ref diff --git a/examples/mliap/InP_JCPA2020.mliap b/examples/mliap/InP_JCPA2020.mliap new file mode 100644 index 0000000000..19d044df97 --- /dev/null +++ b/examples/mliap/InP_JCPA2020.mliap @@ -0,0 +1,19 @@ +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# Definition of SNAP+ZBL potential. + +variable zblcutinner index 4 +variable zblcutouter index 4.2 +variable zblz1 index 49 +variable zblz2 index 15 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay & +zbl ${zblcutinner} ${zblcutouter} & +mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff * * mliap In P + diff --git a/examples/mliap/InP_JCPA2020.mliap.descriptor b/examples/mliap/InP_JCPA2020.mliap.descriptor new file mode 100644 index 0000000000..287eac59c4 --- /dev/null +++ b/examples/mliap/InP_JCPA2020.mliap.descriptor @@ -0,0 +1,20 @@ +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# required +rcutfac 1.0 +twojmax 6 + +# elements + +nelems 2 +elems In P +radelems 3.81205 3.82945 +welems 1 0.929316 + +# optional +rfac0 0.99363 +rmin0 0.0 +bzeroflag 1 +wselfallflag 1 +chemflag 1 +bnormflag 1 diff --git a/examples/mliap/InP_JCPA2020.mliap.model b/examples/mliap/InP_JCPA2020.mliap.model new file mode 100644 index 0000000000..7ef9039ba2 --- /dev/null +++ b/examples/mliap/InP_JCPA2020.mliap.model @@ -0,0 +1,485 @@ +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +2 241 + 0.000000000000 # B[0] Block = 1 Type = In + -0.000666721868 # B[1, 0, 0, 0] Block = 1 Type = In + 0.032408881964 # B[2, 1, 0, 1] Block = 1 Type = In + 0.182277739455 # B[3, 1, 1, 2] Block = 1 Type = In + 0.001455902168 # B[4, 2, 0, 2] Block = 1 Type = In + 0.086259367737 # B[5, 2, 1, 3] Block = 1 Type = In + -0.044840628371 # B[6, 2, 2, 2] Block = 1 Type = In + -0.175973261191 # B[7, 2, 2, 4] Block = 1 Type = In + -0.052429169415 # B[8, 3, 0, 3] Block = 1 Type = In + 0.195529228497 # B[9, 3, 1, 4] Block = 1 Type = In + 0.078718744520 # B[10, 3, 2, 3] Block = 1 Type = In + -0.688127658121 # B[11, 3, 2, 5] Block = 1 Type = In + 0.059084058400 # B[12, 3, 3, 4] Block = 1 Type = In + 0.006795099274 # B[13, 3, 3, 6] Block = 1 Type = In + -0.043061553886 # B[14, 4, 0, 4] Block = 1 Type = In + -0.046619800530 # B[15, 4, 1, 5] Block = 1 Type = In + -0.117451659827 # B[16, 4, 2, 4] Block = 1 Type = In + -0.233615100720 # B[17, 4, 2, 6] Block = 1 Type = In + 0.015358771114 # B[18, 4, 3, 5] Block = 1 Type = In + 0.022474133984 # B[19, 4, 4, 4] Block = 1 Type = In + 0.002165850235 # B[20, 4, 4, 6] Block = 1 Type = In + 0.003458938546 # B[21, 5, 0, 5] Block = 1 Type = In + -0.053507775670 # B[22, 5, 1, 6] Block = 1 Type = In + 0.120989101467 # B[23, 5, 2, 5] Block = 1 Type = In + 0.092637875162 # B[24, 5, 3, 6] Block = 1 Type = In + 0.071459233521 # B[25, 5, 4, 5] Block = 1 Type = In + 0.086291858607 # B[26, 5, 5, 6] Block = 1 Type = In + 0.006749966752 # B[27, 6, 0, 6] Block = 1 Type = In + 0.144917284093 # B[28, 6, 2, 6] Block = 1 Type = In + 0.055178211309 # B[29, 6, 4, 6] Block = 1 Type = In + -0.005619133266 # B[30, 6, 6, 6] Block = 1 Type = In + 0.005430513632 # B[1, 0, 0, 0] Block = 2 Type = In + 0.057269488101 # B[2, 1, 0, 1] Block = 2 Type = In + 0.320412300575 # B[3, 1, 1, 2] Block = 2 Type = In + 0.035481869944 # B[4, 2, 0, 2] Block = 2 Type = In + 0.111076763087 # B[5, 2, 1, 3] Block = 2 Type = In + 0.039770598731 # B[6, 2, 2, 2] Block = 2 Type = In + 0.141315510383 # B[7, 2, 2, 4] Block = 2 Type = In + 0.067792661762 # B[8, 3, 0, 3] Block = 2 Type = In + -0.080858457946 # B[9, 3, 1, 4] Block = 2 Type = In + 0.258942062632 # B[10, 3, 2, 3] Block = 2 Type = In + 0.061756985062 # B[11, 3, 2, 5] Block = 2 Type = In + -0.112424676196 # B[12, 3, 3, 4] Block = 2 Type = In + 0.168376857205 # B[13, 3, 3, 6] Block = 2 Type = In + -0.029743698629 # B[14, 4, 0, 4] Block = 2 Type = In + -0.093967263289 # B[15, 4, 1, 5] Block = 2 Type = In + 0.137229827290 # B[16, 4, 2, 4] Block = 2 Type = In + 0.056897919200 # B[17, 4, 2, 6] Block = 2 Type = In + 0.095137344320 # B[18, 4, 3, 5] Block = 2 Type = In + -0.008598816416 # B[19, 4, 4, 4] Block = 2 Type = In + 0.038890602482 # B[20, 4, 4, 6] Block = 2 Type = In + -0.034624751006 # B[21, 5, 0, 5] Block = 2 Type = In + -0.282625695473 # B[22, 5, 1, 6] Block = 2 Type = In + 0.103089891872 # B[23, 5, 2, 5] Block = 2 Type = In + -0.024380802146 # B[24, 5, 3, 6] Block = 2 Type = In + -0.063847809434 # B[25, 5, 4, 5] Block = 2 Type = In + -0.024896682749 # B[26, 5, 5, 6] Block = 2 Type = In + 0.000464369553 # B[27, 6, 0, 6] Block = 2 Type = In + 0.082229290277 # B[28, 6, 2, 6] Block = 2 Type = In + -0.008875503360 # B[29, 6, 4, 6] Block = 2 Type = In + -0.009039017094 # B[30, 6, 6, 6] Block = 2 Type = In + 0.005430513686 # B[1, 0, 0, 0] Block = 3 Type = In + -0.004352445887 # B[2, 1, 0, 1] Block = 3 Type = In + 0.149882860704 # B[3, 1, 1, 2] Block = 3 Type = In + -0.015528472583 # B[4, 2, 0, 2] Block = 3 Type = In + 0.558662861756 # B[5, 2, 1, 3] Block = 3 Type = In + 0.039770598731 # B[6, 2, 2, 2] Block = 3 Type = In + 0.179060667136 # B[7, 2, 2, 4] Block = 3 Type = In + 0.034759981675 # B[8, 3, 0, 3] Block = 3 Type = In + 0.603083480153 # B[9, 3, 1, 4] Block = 3 Type = In + 0.176946655350 # B[10, 3, 2, 3] Block = 3 Type = In + 0.165639632803 # B[11, 3, 2, 5] Block = 3 Type = In + 0.055627509305 # B[12, 3, 3, 4] Block = 3 Type = In + 0.049782791218 # B[13, 3, 3, 6] Block = 3 Type = In + 0.036078617029 # B[14, 4, 0, 4] Block = 3 Type = In + 0.064493563641 # B[15, 4, 1, 5] Block = 3 Type = In + 0.149250535822 # B[16, 4, 2, 4] Block = 3 Type = In + -0.060208330201 # B[17, 4, 2, 6] Block = 3 Type = In + 0.105119833648 # B[18, 4, 3, 5] Block = 3 Type = In + -0.008598816416 # B[19, 4, 4, 4] Block = 3 Type = In + 0.041210118888 # B[20, 4, 4, 6] Block = 3 Type = In + -0.002705345469 # B[21, 5, 0, 5] Block = 3 Type = In + 0.170191392493 # B[22, 5, 1, 6] Block = 3 Type = In + 0.226897293272 # B[23, 5, 2, 5] Block = 3 Type = In + 0.013009034793 # B[24, 5, 3, 6] Block = 3 Type = In + -0.020734586320 # B[25, 5, 4, 5] Block = 3 Type = In + -0.018139074523 # B[26, 5, 5, 6] Block = 3 Type = In + -0.016001848874 # B[27, 6, 0, 6] Block = 3 Type = In + 0.016663324316 # B[28, 6, 2, 6] Block = 3 Type = In + -0.024245533697 # B[29, 6, 4, 6] Block = 3 Type = In + -0.009039017094 # B[30, 6, 6, 6] Block = 3 Type = In + -0.005654800687 # B[1, 0, 0, 0] Block = 4 Type = In + -0.071064263981 # B[2, 1, 0, 1] Block = 4 Type = In + -0.009868049046 # B[3, 1, 1, 2] Block = 4 Type = In + -0.061297753855 # B[4, 2, 0, 2] Block = 4 Type = In + -0.239682636759 # B[5, 2, 1, 3] Block = 4 Type = In + 0.015954956116 # B[6, 2, 2, 2] Block = 4 Type = In + 0.176005610703 # B[7, 2, 2, 4] Block = 4 Type = In + -0.081125948095 # B[8, 3, 0, 3] Block = 4 Type = In + -0.170847987084 # B[9, 3, 1, 4] Block = 4 Type = In + 0.242239715395 # B[10, 3, 2, 3] Block = 4 Type = In + 0.082507688294 # B[11, 3, 2, 5] Block = 4 Type = In + 0.247785108978 # B[12, 3, 3, 4] Block = 4 Type = In + -0.008194303016 # B[13, 3, 3, 6] Block = 4 Type = In + 0.014786217107 # B[14, 4, 0, 4] Block = 4 Type = In + -0.096877379511 # B[15, 4, 1, 5] Block = 4 Type = In + 0.164908528605 # B[16, 4, 2, 4] Block = 4 Type = In + 0.151575252604 # B[17, 4, 2, 6] Block = 4 Type = In + 0.099757230122 # B[18, 4, 3, 5] Block = 4 Type = In + 0.035047662350 # B[19, 4, 4, 4] Block = 4 Type = In + 0.007150552805 # B[20, 4, 4, 6] Block = 4 Type = In + 0.019198319779 # B[21, 5, 0, 5] Block = 4 Type = In + -0.127113932870 # B[22, 5, 1, 6] Block = 4 Type = In + 0.114478010571 # B[23, 5, 2, 5] Block = 4 Type = In + 0.050915227324 # B[24, 5, 3, 6] Block = 4 Type = In + 0.096853268510 # B[25, 5, 4, 5] Block = 4 Type = In + 0.067894750884 # B[26, 5, 5, 6] Block = 4 Type = In + -0.002405537661 # B[27, 6, 0, 6] Block = 4 Type = In + 0.058549926350 # B[28, 6, 2, 6] Block = 4 Type = In + 0.009481237049 # B[29, 6, 4, 6] Block = 4 Type = In + -0.008649958571 # B[30, 6, 6, 6] Block = 4 Type = In + 0.005430513686 # B[1, 0, 0, 0] Block = 5 Type = In + 0.057269488102 # B[2, 1, 0, 1] Block = 5 Type = In + 0.149882860704 # B[3, 1, 1, 2] Block = 5 Type = In + 0.035481869944 # B[4, 2, 0, 2] Block = 5 Type = In + 0.378916788823 # B[5, 2, 1, 3] Block = 5 Type = In + 0.039770598731 # B[6, 2, 2, 2] Block = 5 Type = In + 0.179060667136 # B[7, 2, 2, 4] Block = 5 Type = In + 0.067792661762 # B[8, 3, 0, 3] Block = 5 Type = In + 0.272613304171 # B[9, 3, 1, 4] Block = 5 Type = In + 0.258942062632 # B[10, 3, 2, 3] Block = 5 Type = In + 0.100130474069 # B[11, 3, 2, 5] Block = 5 Type = In + 0.055627509305 # B[12, 3, 3, 4] Block = 5 Type = In + 0.049782791218 # B[13, 3, 3, 6] Block = 5 Type = In + -0.029743698629 # B[14, 4, 0, 4] Block = 5 Type = In + -0.013420300314 # B[15, 4, 1, 5] Block = 5 Type = In + 0.137229827290 # B[16, 4, 2, 4] Block = 5 Type = In + -0.034447269506 # B[17, 4, 2, 6] Block = 5 Type = In + -0.033847124314 # B[18, 4, 3, 5] Block = 5 Type = In + -0.008598816416 # B[19, 4, 4, 4] Block = 5 Type = In + 0.041210118888 # B[20, 4, 4, 6] Block = 5 Type = In + -0.034624751006 # B[21, 5, 0, 5] Block = 5 Type = In + 0.041662678638 # B[22, 5, 1, 6] Block = 5 Type = In + 0.103089891872 # B[23, 5, 2, 5] Block = 5 Type = In + -0.044572198386 # B[24, 5, 3, 6] Block = 5 Type = In + -0.063847809434 # B[25, 5, 4, 5] Block = 5 Type = In + -0.018139074523 # B[26, 5, 5, 6] Block = 5 Type = In + 0.000464369553 # B[27, 6, 0, 6] Block = 5 Type = In + 0.082229290277 # B[28, 6, 2, 6] Block = 5 Type = In + -0.008875503360 # B[29, 6, 4, 6] Block = 5 Type = In + -0.009039017094 # B[30, 6, 6, 6] Block = 5 Type = In + -0.005654800687 # B[1, 0, 0, 0] Block = 6 Type = In + -0.001217874195 # B[2, 1, 0, 1] Block = 6 Type = In + -0.009868049046 # B[3, 1, 1, 2] Block = 6 Type = In + -0.092827766060 # B[4, 2, 0, 2] Block = 6 Type = In + 0.439274283244 # B[5, 2, 1, 3] Block = 6 Type = In + 0.015954956116 # B[6, 2, 2, 2] Block = 6 Type = In + 0.176005610703 # B[7, 2, 2, 4] Block = 6 Type = In + 0.102468480364 # B[8, 3, 0, 3] Block = 6 Type = In + 0.674122225402 # B[9, 3, 1, 4] Block = 6 Type = In + 0.072529538087 # B[10, 3, 2, 3] Block = 6 Type = In + 0.330711171466 # B[11, 3, 2, 5] Block = 6 Type = In + 0.247785108978 # B[12, 3, 3, 4] Block = 6 Type = In + -0.008194303016 # B[13, 3, 3, 6] Block = 6 Type = In + 0.052250780232 # B[14, 4, 0, 4] Block = 6 Type = In + 0.374231060518 # B[15, 4, 1, 5] Block = 6 Type = In + 0.326667869620 # B[16, 4, 2, 4] Block = 6 Type = In + 0.079031873518 # B[17, 4, 2, 6] Block = 6 Type = In + 0.224004472527 # B[18, 4, 3, 5] Block = 6 Type = In + 0.035047662350 # B[19, 4, 4, 4] Block = 6 Type = In + 0.007150552805 # B[20, 4, 4, 6] Block = 6 Type = In + 0.040682917098 # B[21, 5, 0, 5] Block = 6 Type = In + 0.046855927526 # B[22, 5, 1, 6] Block = 6 Type = In + 0.219695071346 # B[23, 5, 2, 5] Block = 6 Type = In + -0.001426581661 # B[24, 5, 3, 6] Block = 6 Type = In + 0.028514699601 # B[25, 5, 4, 5] Block = 6 Type = In + 0.067894750884 # B[26, 5, 5, 6] Block = 6 Type = In + -0.049888149225 # B[27, 6, 0, 6] Block = 6 Type = In + 0.009259151039 # B[28, 6, 2, 6] Block = 6 Type = In + 0.003868002128 # B[29, 6, 4, 6] Block = 6 Type = In + -0.008649958571 # B[30, 6, 6, 6] Block = 6 Type = In + -0.005654800692 # B[1, 0, 0, 0] Block = 7 Type = In + -0.071064263981 # B[2, 1, 0, 1] Block = 7 Type = In + -0.085085203640 # B[3, 1, 1, 2] Block = 7 Type = In + -0.061297753855 # B[4, 2, 0, 2] Block = 7 Type = In + 0.223668616358 # B[5, 2, 1, 3] Block = 7 Type = In + 0.015954956116 # B[6, 2, 2, 2] Block = 7 Type = In + 0.033706085249 # B[7, 2, 2, 4] Block = 7 Type = In + -0.081125948095 # B[8, 3, 0, 3] Block = 7 Type = In + -0.005054494008 # B[9, 3, 1, 4] Block = 7 Type = In + 0.242239715395 # B[10, 3, 2, 3] Block = 7 Type = In + -0.000886414104 # B[11, 3, 2, 5] Block = 7 Type = In + 0.059178212190 # B[12, 3, 3, 4] Block = 7 Type = In + 0.008498646326 # B[13, 3, 3, 6] Block = 7 Type = In + 0.014786217107 # B[14, 4, 0, 4] Block = 7 Type = In + -0.178665293356 # B[15, 4, 1, 5] Block = 7 Type = In + 0.164908528605 # B[16, 4, 2, 4] Block = 7 Type = In + -0.117717485069 # B[17, 4, 2, 6] Block = 7 Type = In + 0.146739677531 # B[18, 4, 3, 5] Block = 7 Type = In + 0.035047662350 # B[19, 4, 4, 4] Block = 7 Type = In + 0.088770688382 # B[20, 4, 4, 6] Block = 7 Type = In + 0.019198319779 # B[21, 5, 0, 5] Block = 7 Type = In + -0.148162265312 # B[22, 5, 1, 6] Block = 7 Type = In + 0.114478010571 # B[23, 5, 2, 5] Block = 7 Type = In + 0.114731400461 # B[24, 5, 3, 6] Block = 7 Type = In + 0.096853268510 # B[25, 5, 4, 5] Block = 7 Type = In + 0.031183854107 # B[26, 5, 5, 6] Block = 7 Type = In + -0.002405537661 # B[27, 6, 0, 6] Block = 7 Type = In + 0.058549926350 # B[28, 6, 2, 6] Block = 7 Type = In + 0.009481237049 # B[29, 6, 4, 6] Block = 7 Type = In + -0.008649958571 # B[30, 6, 6, 6] Block = 7 Type = In + 0.017733403092 # B[1, 0, 0, 0] Block = 8 Type = In + 0.015168905151 # B[2, 1, 0, 1] Block = 8 Type = In + -0.212358294308 # B[3, 1, 1, 2] Block = 8 Type = In + 0.115608035432 # B[4, 2, 0, 2] Block = 8 Type = In + 0.128621845177 # B[5, 2, 1, 3] Block = 8 Type = In + -0.055682216710 # B[6, 2, 2, 2] Block = 8 Type = In + 0.168986321733 # B[7, 2, 2, 4] Block = 8 Type = In + -0.087186888529 # B[8, 3, 0, 3] Block = 8 Type = In + 0.378810692322 # B[9, 3, 1, 4] Block = 8 Type = In + 0.036128510376 # B[10, 3, 2, 3] Block = 8 Type = In + 0.179888488204 # B[11, 3, 2, 5] Block = 8 Type = In + -0.001405954437 # B[12, 3, 3, 4] Block = 8 Type = In + 0.010551104009 # B[13, 3, 3, 6] Block = 8 Type = In + -0.059381370200 # B[14, 4, 0, 4] Block = 8 Type = In + 0.475432753620 # B[15, 4, 1, 5] Block = 8 Type = In + 0.095868282640 # B[16, 4, 2, 4] Block = 8 Type = In + 0.106524975238 # B[17, 4, 2, 6] Block = 8 Type = In + 0.058941182257 # B[18, 4, 3, 5] Block = 8 Type = In + 0.012512778321 # B[19, 4, 4, 4] Block = 8 Type = In + 0.080549204239 # B[20, 4, 4, 6] Block = 8 Type = In + -0.068536821891 # B[21, 5, 0, 5] Block = 8 Type = In + 0.089459777664 # B[22, 5, 1, 6] Block = 8 Type = In + 0.163187761880 # B[23, 5, 2, 5] Block = 8 Type = In + 0.139719330200 # B[24, 5, 3, 6] Block = 8 Type = In + 0.145095171389 # B[25, 5, 4, 5] Block = 8 Type = In + 0.074157391376 # B[26, 5, 5, 6] Block = 8 Type = In + 0.018646775951 # B[27, 6, 0, 6] Block = 8 Type = In + 0.035882498943 # B[28, 6, 2, 6] Block = 8 Type = In + 0.050420424420 # B[29, 6, 4, 6] Block = 8 Type = In + 0.009994821144 # B[30, 6, 6, 6] Block = 8 Type = In + 0.000000000000 # B[0] Block = 1 Type = P + -0.002987589706 # B[1, 0, 0, 0] Block = 1 Type = P + -0.072158389412 # B[2, 1, 0, 1] Block = 1 Type = P + -0.025322250603 # B[3, 1, 1, 2] Block = 1 Type = P + -0.030241379192 # B[4, 2, 0, 2] Block = 1 Type = P + -0.676287334962 # B[5, 2, 1, 3] Block = 1 Type = P + -0.172216278028 # B[6, 2, 2, 2] Block = 1 Type = P + -0.246535097343 # B[7, 2, 2, 4] Block = 1 Type = P + -0.035782528462 # B[8, 3, 0, 3] Block = 1 Type = P + -0.560641780823 # B[9, 3, 1, 4] Block = 1 Type = P + -0.549579515296 # B[10, 3, 2, 3] Block = 1 Type = P + -0.016920837991 # B[11, 3, 2, 5] Block = 1 Type = P + -0.288447245376 # B[12, 3, 3, 4] Block = 1 Type = P + 0.069076859372 # B[13, 3, 3, 6] Block = 1 Type = P + -0.052298717507 # B[14, 4, 0, 4] Block = 1 Type = P + -0.434250953671 # B[15, 4, 1, 5] Block = 1 Type = P + -0.322043860507 # B[16, 4, 2, 4] Block = 1 Type = P + -0.096837010372 # B[17, 4, 2, 6] Block = 1 Type = P + -0.213169352789 # B[18, 4, 3, 5] Block = 1 Type = P + -0.019566740546 # B[19, 4, 4, 4] Block = 1 Type = P + -0.029415128740 # B[20, 4, 4, 6] Block = 1 Type = P + -0.036591077655 # B[21, 5, 0, 5] Block = 1 Type = P + -0.300384511072 # B[22, 5, 1, 6] Block = 1 Type = P + -0.111126537447 # B[23, 5, 2, 5] Block = 1 Type = P + -0.000209831053 # B[24, 5, 3, 6] Block = 1 Type = P + -0.000023632674 # B[25, 5, 4, 5] Block = 1 Type = P + 0.009497323905 # B[26, 5, 5, 6] Block = 1 Type = P + -0.042287705828 # B[27, 6, 0, 6] Block = 1 Type = P + -0.113311457350 # B[28, 6, 2, 6] Block = 1 Type = P + 0.029574563913 # B[29, 6, 4, 6] Block = 1 Type = P + -0.027748295426 # B[30, 6, 6, 6] Block = 1 Type = P + -0.001747658243 # B[1, 0, 0, 0] Block = 2 Type = P + -0.026182047943 # B[2, 1, 0, 1] Block = 2 Type = P + 0.089481157533 # B[3, 1, 1, 2] Block = 2 Type = P + -0.076525139004 # B[4, 2, 0, 2] Block = 2 Type = P + -0.107925591359 # B[5, 2, 1, 3] Block = 2 Type = P + -0.059117110271 # B[6, 2, 2, 2] Block = 2 Type = P + -0.256324252168 # B[7, 2, 2, 4] Block = 2 Type = P + -0.020755324452 # B[8, 3, 0, 3] Block = 2 Type = P + -0.337284108142 # B[9, 3, 1, 4] Block = 2 Type = P + -0.073956723908 # B[10, 3, 2, 3] Block = 2 Type = P + -0.149119927857 # B[11, 3, 2, 5] Block = 2 Type = P + 0.047627781519 # B[12, 3, 3, 4] Block = 2 Type = P + 0.061394929126 # B[13, 3, 3, 6] Block = 2 Type = P + -0.082660360252 # B[14, 4, 0, 4] Block = 2 Type = P + -0.183225932285 # B[15, 4, 1, 5] Block = 2 Type = P + -0.046981555049 # B[16, 4, 2, 4] Block = 2 Type = P + -0.046846685850 # B[17, 4, 2, 6] Block = 2 Type = P + -0.014388943769 # B[18, 4, 3, 5] Block = 2 Type = P + 0.012133725790 # B[19, 4, 4, 4] Block = 2 Type = P + 0.085321452425 # B[20, 4, 4, 6] Block = 2 Type = P + -0.034945525448 # B[21, 5, 0, 5] Block = 2 Type = P + -0.028326642109 # B[22, 5, 1, 6] Block = 2 Type = P + -0.085701075837 # B[23, 5, 2, 5] Block = 2 Type = P + 0.108257997015 # B[24, 5, 3, 6] Block = 2 Type = P + 0.045837409910 # B[25, 5, 4, 5] Block = 2 Type = P + -0.014180512722 # B[26, 5, 5, 6] Block = 2 Type = P + 0.010756044042 # B[27, 6, 0, 6] Block = 2 Type = P + 0.023429477590 # B[28, 6, 2, 6] Block = 2 Type = P + -0.007794133717 # B[29, 6, 4, 6] Block = 2 Type = P + 0.002019828318 # B[30, 6, 6, 6] Block = 2 Type = P + -0.001747658242 # B[1, 0, 0, 0] Block = 3 Type = P + 0.047070626642 # B[2, 1, 0, 1] Block = 3 Type = P + -0.126595340298 # B[3, 1, 1, 2] Block = 3 Type = P + 0.022286899829 # B[4, 2, 0, 2] Block = 3 Type = P + -0.483695340547 # B[5, 2, 1, 3] Block = 3 Type = P + -0.059117110271 # B[6, 2, 2, 2] Block = 3 Type = P + -0.067694089340 # B[7, 2, 2, 4] Block = 3 Type = P + 0.034974727122 # B[8, 3, 0, 3] Block = 3 Type = P + -0.226290583408 # B[9, 3, 1, 4] Block = 3 Type = P + -0.184699579267 # B[10, 3, 2, 3] Block = 3 Type = P + 0.063122270285 # B[11, 3, 2, 5] Block = 3 Type = P + 0.041271206739 # B[12, 3, 3, 4] Block = 3 Type = P + -0.004229157928 # B[13, 3, 3, 6] Block = 3 Type = P + 0.050689134214 # B[14, 4, 0, 4] Block = 3 Type = P + -0.138276744014 # B[15, 4, 1, 5] Block = 3 Type = P + 0.097985494164 # B[16, 4, 2, 4] Block = 3 Type = P + -0.083537235645 # B[17, 4, 2, 6] Block = 3 Type = P + 0.098390585361 # B[18, 4, 3, 5] Block = 3 Type = P + 0.012133725790 # B[19, 4, 4, 4] Block = 3 Type = P + -0.038067814334 # B[20, 4, 4, 6] Block = 3 Type = P + 0.029636266108 # B[21, 5, 0, 5] Block = 3 Type = P + -0.157117938354 # B[22, 5, 1, 6] Block = 3 Type = P + -0.027712542047 # B[23, 5, 2, 5] Block = 3 Type = P + 0.084730212710 # B[24, 5, 3, 6] Block = 3 Type = P + 0.023437407693 # B[25, 5, 4, 5] Block = 3 Type = P + 0.017747856995 # B[26, 5, 5, 6] Block = 3 Type = P + 0.050161344183 # B[27, 6, 0, 6] Block = 3 Type = P + -0.098577816149 # B[28, 6, 2, 6] Block = 3 Type = P + -0.046997533090 # B[29, 6, 4, 6] Block = 3 Type = P + 0.002019828318 # B[30, 6, 6, 6] Block = 3 Type = P + -0.003152987881 # B[1, 0, 0, 0] Block = 4 Type = P + 0.014621850469 # B[2, 1, 0, 1] Block = 4 Type = P + 0.098860641022 # B[3, 1, 1, 2] Block = 4 Type = P + 0.069546644549 # B[4, 2, 0, 2] Block = 4 Type = P + 0.180804700658 # B[5, 2, 1, 3] Block = 4 Type = P + 0.034244852922 # B[6, 2, 2, 2] Block = 4 Type = P + 0.044579888557 # B[7, 2, 2, 4] Block = 4 Type = P + 0.001526239292 # B[8, 3, 0, 3] Block = 4 Type = P + 0.203861850923 # B[9, 3, 1, 4] Block = 4 Type = P + 0.021679218740 # B[10, 3, 2, 3] Block = 4 Type = P + 0.185899872703 # B[11, 3, 2, 5] Block = 4 Type = P + -0.063472862380 # B[12, 3, 3, 4] Block = 4 Type = P + -0.015662648111 # B[13, 3, 3, 6] Block = 4 Type = P + 0.076209869795 # B[14, 4, 0, 4] Block = 4 Type = P + -0.050213789331 # B[15, 4, 1, 5] Block = 4 Type = P + 0.038175316256 # B[16, 4, 2, 4] Block = 4 Type = P + 0.041946424186 # B[17, 4, 2, 6] Block = 4 Type = P + -0.023902281235 # B[18, 4, 3, 5] Block = 4 Type = P + 0.008537822812 # B[19, 4, 4, 4] Block = 4 Type = P + 0.039989757491 # B[20, 4, 4, 6] Block = 4 Type = P + 0.022210126714 # B[21, 5, 0, 5] Block = 4 Type = P + 0.010855258243 # B[22, 5, 1, 6] Block = 4 Type = P + 0.021570527219 # B[23, 5, 2, 5] Block = 4 Type = P + -0.119983534986 # B[24, 5, 3, 6] Block = 4 Type = P + -0.019726935513 # B[25, 5, 4, 5] Block = 4 Type = P + -0.015720476443 # B[26, 5, 5, 6] Block = 4 Type = P + -0.024522109113 # B[27, 6, 0, 6] Block = 4 Type = P + -0.051478859538 # B[28, 6, 2, 6] Block = 4 Type = P + 0.017216285614 # B[29, 6, 4, 6] Block = 4 Type = P + -0.003565797401 # B[30, 6, 6, 6] Block = 4 Type = P + -0.001747658242 # B[1, 0, 0, 0] Block = 5 Type = P + -0.026182047943 # B[2, 1, 0, 1] Block = 5 Type = P + -0.126595340298 # B[3, 1, 1, 2] Block = 5 Type = P + -0.076525139004 # B[4, 2, 0, 2] Block = 5 Type = P + -0.157814129312 # B[5, 2, 1, 3] Block = 5 Type = P + -0.059117110271 # B[6, 2, 2, 2] Block = 5 Type = P + -0.067694089340 # B[7, 2, 2, 4] Block = 5 Type = P + -0.020755324452 # B[8, 3, 0, 3] Block = 5 Type = P + -0.216746420586 # B[9, 3, 1, 4] Block = 5 Type = P + -0.073956723908 # B[10, 3, 2, 3] Block = 5 Type = P + -0.263593571569 # B[11, 3, 2, 5] Block = 5 Type = P + 0.041271206739 # B[12, 3, 3, 4] Block = 5 Type = P + -0.004229157928 # B[13, 3, 3, 6] Block = 5 Type = P + -0.082660360252 # B[14, 4, 0, 4] Block = 5 Type = P + -0.305032662779 # B[15, 4, 1, 5] Block = 5 Type = P + -0.046981555049 # B[16, 4, 2, 4] Block = 5 Type = P + -0.187955078269 # B[17, 4, 2, 6] Block = 5 Type = P + -0.121808447372 # B[18, 4, 3, 5] Block = 5 Type = P + 0.012133725790 # B[19, 4, 4, 4] Block = 5 Type = P + -0.038067814334 # B[20, 4, 4, 6] Block = 5 Type = P + -0.034945525448 # B[21, 5, 0, 5] Block = 5 Type = P + -0.226555787648 # B[22, 5, 1, 6] Block = 5 Type = P + -0.085701075837 # B[23, 5, 2, 5] Block = 5 Type = P + -0.121081797087 # B[24, 5, 3, 6] Block = 5 Type = P + 0.045837409910 # B[25, 5, 4, 5] Block = 5 Type = P + 0.017747856995 # B[26, 5, 5, 6] Block = 5 Type = P + 0.010756044042 # B[27, 6, 0, 6] Block = 5 Type = P + 0.023429477590 # B[28, 6, 2, 6] Block = 5 Type = P + -0.007794133717 # B[29, 6, 4, 6] Block = 5 Type = P + 0.002019828318 # B[30, 6, 6, 6] Block = 5 Type = P + -0.003152987881 # B[1, 0, 0, 0] Block = 6 Type = P + -0.003431824919 # B[2, 1, 0, 1] Block = 6 Type = P + 0.098860641022 # B[3, 1, 1, 2] Block = 6 Type = P + -0.049867192647 # B[4, 2, 0, 2] Block = 6 Type = P + 0.130247785083 # B[5, 2, 1, 3] Block = 6 Type = P + 0.034244852922 # B[6, 2, 2, 2] Block = 6 Type = P + 0.044579888557 # B[7, 2, 2, 4] Block = 6 Type = P + 0.051064338359 # B[8, 3, 0, 3] Block = 6 Type = P + -0.034769100897 # B[9, 3, 1, 4] Block = 6 Type = P + -0.055923569507 # B[10, 3, 2, 3] Block = 6 Type = P + 0.101065442824 # B[11, 3, 2, 5] Block = 6 Type = P + -0.063472862380 # B[12, 3, 3, 4] Block = 6 Type = P + -0.015662648111 # B[13, 3, 3, 6] Block = 6 Type = P + -0.020942037301 # B[14, 4, 0, 4] Block = 6 Type = P + 0.057686438719 # B[15, 4, 1, 5] Block = 6 Type = P + 0.061281723131 # B[16, 4, 2, 4] Block = 6 Type = P + 0.041003214284 # B[17, 4, 2, 6] Block = 6 Type = P + 0.104968889582 # B[18, 4, 3, 5] Block = 6 Type = P + 0.008537822812 # B[19, 4, 4, 4] Block = 6 Type = P + 0.039989757491 # B[20, 4, 4, 6] Block = 6 Type = P + 0.058310887739 # B[21, 5, 0, 5] Block = 6 Type = P + 0.043642228702 # B[22, 5, 1, 6] Block = 6 Type = P + 0.119827018636 # B[23, 5, 2, 5] Block = 6 Type = P + -0.017878741482 # B[24, 5, 3, 6] Block = 6 Type = P + 0.013615249763 # B[25, 5, 4, 5] Block = 6 Type = P + -0.015720476443 # B[26, 5, 5, 6] Block = 6 Type = P + 0.028210503571 # B[27, 6, 0, 6] Block = 6 Type = P + 0.138982983531 # B[28, 6, 2, 6] Block = 6 Type = P + 0.020848948259 # B[29, 6, 4, 6] Block = 6 Type = P + -0.003565797401 # B[30, 6, 6, 6] Block = 6 Type = P + -0.003152987876 # B[1, 0, 0, 0] Block = 7 Type = P + 0.014621850469 # B[2, 1, 0, 1] Block = 7 Type = P + 0.136917412546 # B[3, 1, 1, 2] Block = 7 Type = P + 0.069546644549 # B[4, 2, 0, 2] Block = 7 Type = P + 0.134471034367 # B[5, 2, 1, 3] Block = 7 Type = P + 0.034244852922 # B[6, 2, 2, 2] Block = 7 Type = P + 0.073714102880 # B[7, 2, 2, 4] Block = 7 Type = P + 0.001526239292 # B[8, 3, 0, 3] Block = 7 Type = P + 0.029314077312 # B[9, 3, 1, 4] Block = 7 Type = P + 0.021679218740 # B[10, 3, 2, 3] Block = 7 Type = P + 0.005384023182 # B[11, 3, 2, 5] Block = 7 Type = P + 0.029912954139 # B[12, 3, 3, 4] Block = 7 Type = P + 0.036308629380 # B[13, 3, 3, 6] Block = 7 Type = P + 0.076209869795 # B[14, 4, 0, 4] Block = 7 Type = P + -0.095659211777 # B[15, 4, 1, 5] Block = 7 Type = P + 0.038175316256 # B[16, 4, 2, 4] Block = 7 Type = P + -0.054559433157 # B[17, 4, 2, 6] Block = 7 Type = P + -0.079205893849 # B[18, 4, 3, 5] Block = 7 Type = P + 0.008537822812 # B[19, 4, 4, 4] Block = 7 Type = P + 0.072688459278 # B[20, 4, 4, 6] Block = 7 Type = P + 0.022210126714 # B[21, 5, 0, 5] Block = 7 Type = P + 0.032318678024 # B[22, 5, 1, 6] Block = 7 Type = P + 0.021570527219 # B[23, 5, 2, 5] Block = 7 Type = P + 0.038881258714 # B[24, 5, 3, 6] Block = 7 Type = P + -0.019726935513 # B[25, 5, 4, 5] Block = 7 Type = P + 0.030961312127 # B[26, 5, 5, 6] Block = 7 Type = P + -0.024522109113 # B[27, 6, 0, 6] Block = 7 Type = P + -0.051478859538 # B[28, 6, 2, 6] Block = 7 Type = P + 0.017216285614 # B[29, 6, 4, 6] Block = 7 Type = P + -0.003565797401 # B[30, 6, 6, 6] Block = 7 Type = P + 0.000279543258 # B[1, 0, 0, 0] Block = 8 Type = P + 0.031561006068 # B[2, 1, 0, 1] Block = 8 Type = P + 0.164297477481 # B[3, 1, 1, 2] Block = 8 Type = P + 0.020394103829 # B[4, 2, 0, 2] Block = 8 Type = P + -0.136924810031 # B[5, 2, 1, 3] Block = 8 Type = P + 0.011488762740 # B[6, 2, 2, 2] Block = 8 Type = P + -0.174577132596 # B[7, 2, 2, 4] Block = 8 Type = P + -0.104272988787 # B[8, 3, 0, 3] Block = 8 Type = P + -0.126737159959 # B[9, 3, 1, 4] Block = 8 Type = P + 0.006355291540 # B[10, 3, 2, 3] Block = 8 Type = P + -0.116847920709 # B[11, 3, 2, 5] Block = 8 Type = P + 0.093716628094 # B[12, 3, 3, 4] Block = 8 Type = P + -0.015327516258 # B[13, 3, 3, 6] Block = 8 Type = P + -0.015071645969 # B[14, 4, 0, 4] Block = 8 Type = P + 0.054380965184 # B[15, 4, 1, 5] Block = 8 Type = P + 0.113826098444 # B[16, 4, 2, 4] Block = 8 Type = P + 0.012970945123 # B[17, 4, 2, 6] Block = 8 Type = P + -0.047881183904 # B[18, 4, 3, 5] Block = 8 Type = P + -0.010520024430 # B[19, 4, 4, 4] Block = 8 Type = P + -0.077321883428 # B[20, 4, 4, 6] Block = 8 Type = P + -0.087378280220 # B[21, 5, 0, 5] Block = 8 Type = P + -0.221370705680 # B[22, 5, 1, 6] Block = 8 Type = P + 0.004554405520 # B[23, 5, 2, 5] Block = 8 Type = P + -0.164836672985 # B[24, 5, 3, 6] Block = 8 Type = P + -0.015080843808 # B[25, 5, 4, 5] Block = 8 Type = P + -0.010907038616 # B[26, 5, 5, 6] Block = 8 Type = P + -0.022228801431 # B[27, 6, 0, 6] Block = 8 Type = P + -0.055154587470 # B[28, 6, 2, 6] Block = 8 Type = P + 0.007347917376 # B[29, 6, 4, 6] Block = 8 Type = P + -0.009369956559 # B[30, 6, 6, 6] Block = 8 Type = P diff --git a/examples/mliap/Ta06A.mliap b/examples/mliap/Ta06A.mliap index 5c1776d01e..21d3bab6e3 100644 --- a/examples/mliap/Ta06A.mliap +++ b/examples/mliap/Ta06A.mliap @@ -1,4 +1,4 @@ -# DATE: 2020-04-04 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A # Assumes 1 LAMMPS atom type diff --git a/examples/mliap/Ta06A.mliap.descriptor b/examples/mliap/Ta06A.mliap.descriptor index 6e7a10f9d1..481ebf7e44 100644 --- a/examples/mliap/Ta06A.mliap.descriptor +++ b/examples/mliap/Ta06A.mliap.descriptor @@ -1,4 +1,4 @@ -# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # LAMMPS SNAP parameters for Ta_Cand06A diff --git a/examples/mliap/Ta06A.mliap.model b/examples/mliap/Ta06A.mliap.model index 12761d94c8..a7e36f1648 100644 --- a/examples/mliap/Ta06A.mliap.model +++ b/examples/mliap/Ta06A.mliap.model @@ -1,4 +1,4 @@ -# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # LAMMPS SNAP coefficients for Ta_Cand06A diff --git a/examples/mliap/W.quadratic.mliap b/examples/mliap/W.quadratic.mliap index a2fc84c50f..36cb352f84 100644 --- a/examples/mliap/W.quadratic.mliap +++ b/examples/mliap/W.quadratic.mliap @@ -1,3 +1,5 @@ +# DATE: 2020-06-21 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: none + # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 diff --git a/examples/mliap/W.quadratic.mliap.descriptor b/examples/mliap/W.quadratic.mliap.descriptor index cc47dafd39..7db38ba7f5 100644 --- a/examples/mliap/W.quadratic.mliap.descriptor +++ b/examples/mliap/W.quadratic.mliap.descriptor @@ -1,3 +1,5 @@ +# DATE: 2020-06-21 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: none + # required rcutfac 4.73442 diff --git a/examples/mliap/W.quadratic.mliap.model b/examples/mliap/W.quadratic.mliap.model index 713e07eb61..d16b535fb9 100644 --- a/examples/mliap/W.quadratic.mliap.model +++ b/examples/mliap/W.quadratic.mliap.model @@ -1,3 +1,5 @@ +# DATE: 2020-06-21 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: none + # LAMMPS SNAP coefficients for Quadratic W # nelements ncoeff diff --git a/examples/mliap/WBe_Wood_PRB2019.mliap b/examples/mliap/WBe_Wood_PRB2019.mliap index 0ad35747dc..9298bf8fdf 100644 --- a/examples/mliap/WBe_Wood_PRB2019.mliap +++ b/examples/mliap/WBe_Wood_PRB2019.mliap @@ -1,4 +1,4 @@ -# DATE: 2020-04-04 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 diff --git a/examples/mliap/WBe_Wood_PRB2019.mliap.descriptor b/examples/mliap/WBe_Wood_PRB2019.mliap.descriptor index 855e5ec97a..0ba762fcfa 100644 --- a/examples/mliap/WBe_Wood_PRB2019.mliap.descriptor +++ b/examples/mliap/WBe_Wood_PRB2019.mliap.descriptor @@ -1,3 +1,5 @@ +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) + # required rcutfac 4.8123 diff --git a/examples/mliap/WBe_Wood_PRB2019.mliap.model b/examples/mliap/WBe_Wood_PRB2019.mliap.model index 6b96561ed0..b25398e91a 100644 --- a/examples/mliap/WBe_Wood_PRB2019.mliap.model +++ b/examples/mliap/WBe_Wood_PRB2019.mliap.model @@ -1,3 +1,4 @@ +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) # LAMMPS SNAP coefficients for WBe # nelements ncoeff diff --git a/examples/mliap/in.mliap.Ta06A b/examples/mliap/in.mliap.snap.Ta06A similarity index 90% rename from examples/mliap/in.mliap.Ta06A rename to examples/mliap/in.mliap.snap.Ta06A index 2c8c7932df..3d94d5c9fc 100644 --- a/examples/mliap/in.mliap.Ta06A +++ b/examples/mliap/in.mliap.snap.Ta06A @@ -1,4 +1,4 @@ -# Demonstrate SNAP Ta potential +# Demonstrate MLIAP interface to kinear SNAP potential # Initialize simulation @@ -47,7 +47,7 @@ neigh_modify once no every 1 delay 0 check yes # Run MD -velocity all create 300.0 4928459 +velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} diff --git a/examples/mliap/in.mliap.WBe.PRB2019 b/examples/mliap/in.mliap.snap.WBe.PRB2019 similarity index 92% rename from examples/mliap/in.mliap.WBe.PRB2019 rename to examples/mliap/in.mliap.snap.WBe.PRB2019 index 24a212b2c6..84d40d321f 100644 --- a/examples/mliap/in.mliap.WBe.PRB2019 +++ b/examples/mliap/in.mliap.snap.WBe.PRB2019 @@ -1,4 +1,4 @@ -# Demonstrate SNAP W-Be potential +# Demonstrate MLIAP interface to SNAP W-Be potential # Initialize simulation @@ -50,7 +50,7 @@ neigh_modify once no every 1 delay 0 check yes # Run MD -velocity all create 300.0 4928459 +velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} diff --git a/examples/mliap/in.mliap.snap.chem b/examples/mliap/in.mliap.snap.chem new file mode 100644 index 0000000000..499601059e --- /dev/null +++ b/examples/mliap/in.mliap.snap.chem @@ -0,0 +1,46 @@ +# Demonstrate MLIAP interface to ChemSNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice diamond $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 2 box +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 + +mass 1 114.76 +mass 2 30.98 + +# choose potential + +include InP_JCPA2020.mliap + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + diff --git a/examples/mliap/in.mliap.quadratic b/examples/mliap/in.mliap.snap.quadratic similarity index 88% rename from examples/mliap/in.mliap.quadratic rename to examples/mliap/in.mliap.snap.quadratic index 636d0de3e6..9f7d4d702d 100644 --- a/examples/mliap/in.mliap.quadratic +++ b/examples/mliap/in.mliap.snap.quadratic @@ -1,9 +1,10 @@ -# Demonstrate SNAP Ta potential + +# Demonstrate MLIAP interface to quadratic SNAP potential # Initialize simulation variable nsteps index 100 -variable nrep equal 1 +variable nrep equal 4 variable a equal 3.1803 units metal @@ -48,7 +49,7 @@ neigh_modify once no every 1 delay 0 check no # Run MD -velocity all create 300.0 4928459 +velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} diff --git a/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.1 b/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.1 new file mode 100644 index 0000000000..2a6d16a187 --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.1 @@ -0,0 +1,156 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to kinear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +include Ta06A.mliap +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) + +# Definition of SNAP potential Ta_Cand06A +# Assumes 1 LAMMPS atom type + +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 73 + +# Specify hybrid with SNAP, ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +Reading potential file Ta06A.mliap.model with DATE: 2014-09-05 +Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 +SNAP keyword rcutfac 4.67637 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Ta +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 73 ${zblz} +pair_coeff 1 1 zbl 73 73 +pair_coeff * * mliap Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8 + ghost atom cutoff = 5.8 + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.592 | 6.592 | 6.592 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 + 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 + 20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527 + 30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131 + 40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684 + 50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899 + 60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757 + 70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351 + 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 + 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 + 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 +Loop time of 0.931876 on 1 procs for 100 steps with 128 atoms + +Performance: 4.636 ns/day, 5.177 hours/ns, 107.310 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.93067 | 0.93067 | 0.93067 | 0.0 | 99.87 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.000377 | 0.000377 | 0.000377 | 0.0 | 0.04 +Output | 0.000467 | 0.000467 | 0.000467 | 0.0 | 0.05 +Modify | 0.000162 | 0.000162 | 0.000162 | 0.0 | 0.02 +Other | | 0.000196 | | | 0.02 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3712 ave 3712 max 3712 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.4 b/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.4 new file mode 100644 index 0000000000..e2778b21ec --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.4 @@ -0,0 +1,156 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to kinear SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + +# choose potential + +include Ta06A.mliap +# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) + +# Definition of SNAP potential Ta_Cand06A +# Assumes 1 LAMMPS atom type + +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 73 + +# Specify hybrid with SNAP, ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor +Reading potential file Ta06A.mliap.model with DATE: 2014-09-05 +Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 +SNAP keyword rcutfac 4.67637 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems Ta +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 0 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 73 ${zblz} +pair_coeff 1 1 zbl 73 73 +pair_coeff * * mliap Ta + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8 + ghost atom cutoff = 5.8 + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.528 | 6.528 | 6.528 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 + 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 + 20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527 + 30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131 + 40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684 + 50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899 + 60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757 + 70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351 + 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 + 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 + 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 +Loop time of 0.256886 on 4 procs for 100 steps with 128 atoms + +Performance: 16.817 ns/day, 1.427 hours/ns, 389.278 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24436 | 0.24636 | 0.25027 | 0.5 | 95.90 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.005652 | 0.0095395 | 0.01154 | 2.4 | 3.71 +Output | 0.000472 | 0.0005085 | 0.000617 | 0.0 | 0.20 +Modify | 6.2e-05 | 6.75e-05 | 7.3e-05 | 0.0 | 0.03 +Other | | 0.0004105 | | | 0.16 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 928 ave 928 max 928 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/mliap/log.snap.WBe.ref b/examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.1 similarity index 52% rename from examples/mliap/log.snap.WBe.ref rename to examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.1 index f689c7e6b1..b83422657c 100644 --- a/examples/mliap/log.snap.WBe.ref +++ b/examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.1 @@ -1,5 +1,5 @@ -LAMMPS (19 Mar 2020) -# Demonstrate SNAP W-Be potential +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to SNAP W-Be potential # Initialize simulation @@ -27,24 +27,23 @@ region box block 0 4 0 ${ny} 0 ${nz} region box block 0 4 0 4 0 ${nz} region box block 0 4 0 4 0 4 create_box 2 box -Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) +Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms - create_atoms CPU = 0.000231 secs + create_atoms CPU = 0.000 seconds mass 1 183.84 mass 2 9.012182 set group all type/fraction 2 0.05 3590153 # Change 5% of W to He - 5 settings made for type/fraction -group tungsten type 1 + 5 settings made for type/fractiongroup tungsten type 1 123 atoms in group tungsten group beryllium type 2 5 atoms in group beryllium # choose potential -include WBe_Wood_PRB2019.snap -# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) +include WBe_Wood_PRB2019.mliap +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 @@ -53,9 +52,20 @@ variable zblz2 equal 4 # Specify hybrid with SNAP and ZBL -pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 4.8 snap +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +Reading potential file WBe_Wood_PRB2019.mliap.model with DATE: 2019-09-18 +Reading potential file WBe_Wood_PRB2019.mliap.descriptor with DATE: 2019-09-18 +SNAP keyword rcutfac 4.8123 +SNAP keyword twojmax 8 +SNAP keyword nelems 2 +SNAP keyword elems W +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 pair_coeff 1 1 zbl ${zblz1} ${zblz1} pair_coeff 1 1 zbl 74 ${zblz1} pair_coeff 1 1 zbl 74 74 @@ -65,15 +75,7 @@ pair_coeff 1 2 zbl 74 4 pair_coeff 2 2 zbl ${zblz2} ${zblz2} pair_coeff 2 2 zbl 4 ${zblz2} pair_coeff 2 2 zbl 4 4 -pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be -SNAP Element = W, Radius 0.5, Weight 1 -SNAP Element = Be, Radius 0.417932, Weight 0.959049 -SNAP keyword rcutfac 4.8123 -SNAP keyword twojmax 8 -SNAP keyword rfac0 0.99363 -SNAP keyword rmin0 0 -SNAP keyword bzeroflag 1 -SNAP keyword quadraticflag 0 +pair_coeff * * mliap W Be # Setup output @@ -97,7 +99,7 @@ neigh_modify once no every 1 delay 0 check yes # Run MD -velocity all create 300.0 4928459 +velocity all create 300.0 4928459 loop geom fix 1 all nve run ${nsteps} run 100 @@ -113,7 +115,7 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none - (2) pair snap, perpetual + (2) pair mliap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d @@ -121,43 +123,43 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 300 -8.5980876 -8.5980876 -8.5596125 -35284.855 35284.855 - 10 299.29029 -8.5979965 -8.5979965 -8.5596125 -35299.259 35299.259 - 20 288.99334 -8.5966759 -8.5966759 -8.5596124 -35004.093 35004.093 - 30 269.91027 -8.5942284 -8.5942284 -8.5596123 -34447.077 34447.077 - 40 243.57361 -8.5908505 -8.5908505 -8.5596121 -33687.105 33687.105 - 50 212.21385 -8.5868284 -8.5868284 -8.5596119 -32821.864 32821.864 - 60 178.77144 -8.5825391 -8.5825391 -8.5596116 -31971.17 31971.17 - 70 146.71854 -8.578428 -8.578428 -8.5596113 -31245.51 31245.51 - 80 119.50956 -8.5749383 -8.5749383 -8.5596111 -30724.137 30724.137 - 90 99.872785 -8.5724197 -8.5724197 -8.559611 -30440.244 30440.244 - 100 89.604584 -8.5711027 -8.5711027 -8.5596109 -30392.805 30392.805 -Loop time of 3.17984 on 1 procs for 100 steps with 128 atoms + 10 296.32664 -8.5976164 -8.5976164 -8.5596124 -35188.339 35188.339 + 20 282.41417 -8.595832 -8.595832 -8.5596123 -34782.293 34782.293 + 30 259.69014 -8.5929175 -8.5929175 -8.5596121 -34113.316 34113.316 + 40 230.50415 -8.5891741 -8.5891741 -8.5596119 -33260.777 33260.777 + 50 197.88816 -8.5849908 -8.5849908 -8.5596116 -32309.975 32309.975 + 60 165.27259 -8.5808076 -8.5808076 -8.5596113 -31365.766 31365.766 + 70 136.15697 -8.5770733 -8.5770733 -8.5596111 -30542.657 30542.657 + 80 113.58947 -8.5741788 -8.5741788 -8.5596109 -29939.23 29939.23 + 90 99.477916 -8.572369 -8.572369 -8.5596109 -29619.939 29619.939 + 100 94.121939 -8.5716822 -8.5716822 -8.559611 -29598.002 29598.002 +Loop time of 2.95019 on 1 procs for 100 steps with 128 atoms -Performance: 1.359 ns/day, 17.666 hours/ns, 31.448 timesteps/s -99.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.464 ns/day, 16.390 hours/ns, 33.896 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.1748 | 3.1748 | 3.1748 | 0.0 | 99.84 -Neigh | 0.000314 | 0.000314 | 0.000314 | 0.0 | 0.01 -Comm | 0.000371 | 0.000371 | 0.000371 | 0.0 | 0.01 -Output | 0.00386 | 0.00386 | 0.00386 | 0.0 | 0.12 -Modify | 0.000236 | 0.000236 | 0.000236 | 0.0 | 0.01 -Other | | 0.000289 | | | 0.01 +Pair | 2.9486 | 2.9486 | 2.9486 | 0.0 | 99.95 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.000379 | 0.000379 | 0.000379 | 0.0 | 0.01 +Output | 0.000633 | 0.000633 | 0.000633 | 0.0 | 0.02 +Modify | 0.000207 | 0.000207 | 0.000207 | 0.0 | 0.01 +Other | | 0.000341 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 727 ave 727 max 727 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3710 ave 3710 max 3710 min +Neighs: 3712 ave 3712 max 3712 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 7420 ave 7420 max 7420 min +FullNghs: 7424 ave 7424 max 7424 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 7420 -Ave neighs/atom = 57.9688 -Neighbor list builds = 1 +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:03 diff --git a/examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4 b/examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4 new file mode 100644 index 0000000000..53f9fc2a15 --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4 @@ -0,0 +1,165 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to SNAP W-Be potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.1803 +Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds +mass 1 183.84 +mass 2 9.012182 + +set group all type/fraction 2 0.05 3590153 # Change 5% of W to He + 5 settings made for type/fractiongroup tungsten type 1 +123 atoms in group tungsten +group beryllium type 2 +5 atoms in group beryllium +# choose potential + +include WBe_Wood_PRB2019.mliap +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz1 equal 74 +variable zblz2 equal 4 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor +Reading potential file WBe_Wood_PRB2019.mliap.model with DATE: 2019-09-18 +Reading potential file WBe_Wood_PRB2019.mliap.descriptor with DATE: 2019-09-18 +SNAP keyword rcutfac 4.8123 +SNAP keyword twojmax 8 +SNAP keyword nelems 2 +SNAP keyword elems W +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 74 ${zblz1} +pair_coeff 1 1 zbl 74 74 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 74 ${zblz2} +pair_coeff 1 2 zbl 74 4 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 4 ${zblz2} +pair_coeff 2 2 zbl 4 4 +pair_coeff * * mliap W Be + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8123 + ghost atom cutoff = 5.8123 + binsize = 2.90615, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.793 | 6.793 | 6.793 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -8.5980876 -8.5980876 -8.5596125 -35284.855 35284.855 + 10 296.32664 -8.5976164 -8.5976164 -8.5596124 -35188.339 35188.339 + 20 282.41417 -8.595832 -8.595832 -8.5596123 -34782.293 34782.293 + 30 259.69014 -8.5929175 -8.5929175 -8.5596121 -34113.316 34113.316 + 40 230.50415 -8.5891741 -8.5891741 -8.5596119 -33260.777 33260.777 + 50 197.88816 -8.5849908 -8.5849908 -8.5596116 -32309.975 32309.975 + 60 165.27259 -8.5808076 -8.5808076 -8.5596113 -31365.766 31365.766 + 70 136.15697 -8.5770733 -8.5770733 -8.5596111 -30542.657 30542.657 + 80 113.58947 -8.5741788 -8.5741788 -8.5596109 -29939.23 29939.23 + 90 99.477916 -8.572369 -8.572369 -8.5596109 -29619.939 29619.939 + 100 94.121939 -8.5716822 -8.5716822 -8.559611 -29598.002 29598.002 +Loop time of 0.897476 on 4 procs for 100 steps with 128 atoms + +Performance: 4.813 ns/day, 4.986 hours/ns, 111.424 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.84854 | 0.85737 | 0.87512 | 1.1 | 95.53 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.021045 | 0.038782 | 0.047601 | 5.3 | 4.32 +Output | 0.00061 | 0.0006525 | 0.000774 | 0.0 | 0.07 +Modify | 0.00011 | 0.00011375 | 0.000117 | 0.0 | 0.01 +Other | | 0.0005625 | | | 0.06 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 928 ave 928 max 928 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/mliap/log.21Jun20.mliap.snap.chem.g++.1 b/examples/mliap/log.21Jun20.mliap.snap.chem.g++.1 new file mode 100644 index 0000000000..ab9af08d8a --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.chem.g++.1 @@ -0,0 +1,158 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to ChemSNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + create_atoms CPU = 0.000 seconds + +mass 1 114.76 +mass 2 30.98 + +# choose potential + +include InP_JCPA2020.mliap +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# Definition of SNAP+ZBL potential. + +variable zblcutinner index 4 +variable zblcutouter index 4.2 +variable zblz1 index 49 +variable zblz2 index 15 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01 +Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01 +SNAP keyword rcutfac 1.0 +SNAP keyword twojmax 6 +SNAP keyword nelems 2 +SNAP keyword elems In +SNAP keyword radelems 3.81205 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0.0 +SNAP keyword bzeroflag 1 +SNAP keyword wselfallflag 1 +SNAP keyword chemflag 1 +SNAP keyword bnormflag 1 +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 49 ${zblz1} +pair_coeff 1 1 zbl 49 49 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 49 ${zblz2} +pair_coeff 1 2 zbl 49 15 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 15 ${zblz2} +pair_coeff 2 2 zbl 15 15 +pair_coeff * * mliap In P + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.6589 + ghost atom cutoff = 8.6589 + binsize = 4.32945, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.03 | 6.03 | 6.03 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -3.4805794 0 -3.4418771 1353.5968 + 10 285.84677 -3.4787531 0 -3.4418766 1611.7131 + 20 248.14649 -3.4738884 0 -3.4418756 2312.0308 + 30 198.94136 -3.4675394 0 -3.4418744 3168.1543 + 40 152.74831 -3.4615791 0 -3.4418734 3903.5749 + 50 121.9796 -3.4576091 0 -3.4418728 4387.1254 + 60 113.27555 -3.4564863 0 -3.4418729 4556.3003 + 70 125.68089 -3.4580873 0 -3.4418735 4431.2083 + 80 151.47475 -3.4614159 0 -3.4418745 4107.2369 + 90 179.18708 -3.4649919 0 -3.4418754 3739.5881 + 100 197.50662 -3.4673559 0 -3.441876 3492.7778 +Loop time of 16.748 on 1 procs for 100 steps with 512 atoms + +Performance: 0.258 ns/day, 93.045 hours/ns, 5.971 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.746 | 16.746 | 16.746 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.001033 | 0.001033 | 0.001033 | 0.0 | 0.01 +Output | 0.000235 | 0.000235 | 0.000235 | 0.0 | 0.00 +Modify | 0.000688 | 0.000688 | 0.000688 | 0.0 | 0.00 +Other | | 0.000497 | | | 0.00 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1959 ave 1959 max 1959 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31232 ave 31232 max 31232 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 62464 ave 62464 max 62464 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 62464 +Ave neighs/atom = 122 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:17 diff --git a/examples/mliap/log.21Jun20.mliap.snap.chem.g++.4 b/examples/mliap/log.21Jun20.mliap.snap.chem.g++.4 new file mode 100644 index 0000000000..34f7dadb6a --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.chem.g++.4 @@ -0,0 +1,158 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to ChemSNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 5.83 +units metal + +# generate the box and atom positions using a FCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice diamond $a +lattice diamond 5.83 +Lattice spacing in x,y,z = 5.83 5.83 5.83 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 +Created 512 atoms + create_atoms CPU = 0.000 seconds + +mass 1 114.76 +mass 2 30.98 + +# choose potential + +include InP_JCPA2020.mliap +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) + +# Definition of SNAP+ZBL potential. + +variable zblcutinner index 4 +variable zblcutouter index 4.2 +variable zblz1 index 49 +variable zblz2 index 15 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor +Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01 +Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01 +SNAP keyword rcutfac 1.0 +SNAP keyword twojmax 6 +SNAP keyword nelems 2 +SNAP keyword elems In +SNAP keyword radelems 3.81205 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0.0 +SNAP keyword bzeroflag 1 +SNAP keyword wselfallflag 1 +SNAP keyword chemflag 1 +SNAP keyword bnormflag 1 +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 49 ${zblz1} +pair_coeff 1 1 zbl 49 49 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 49 ${zblz2} +pair_coeff 1 2 zbl 49 15 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 15 ${zblz2} +pair_coeff 2 2 zbl 15 15 +pair_coeff * * mliap In P + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.6589 + ghost atom cutoff = 8.6589 + binsize = 4.32945, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -3.4805794 0 -3.4418771 1353.5968 + 10 285.84677 -3.4787531 0 -3.4418766 1611.7131 + 20 248.14649 -3.4738884 0 -3.4418756 2312.0308 + 30 198.94136 -3.4675394 0 -3.4418744 3168.1543 + 40 152.74831 -3.4615791 0 -3.4418734 3903.5749 + 50 121.9796 -3.4576091 0 -3.4418728 4387.1254 + 60 113.27555 -3.4564863 0 -3.4418729 4556.3003 + 70 125.68089 -3.4580873 0 -3.4418735 4431.2083 + 80 151.47475 -3.4614159 0 -3.4418745 4107.2369 + 90 179.18708 -3.4649919 0 -3.4418754 3739.5881 + 100 197.50662 -3.4673559 0 -3.441876 3492.7778 +Loop time of 5.01913 on 4 procs for 100 steps with 512 atoms + +Performance: 0.861 ns/day, 27.884 hours/ns, 19.924 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.9328 | 4.9409 | 4.952 | 0.3 | 98.44 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.065669 | 0.076754 | 0.084728 | 2.5 | 1.53 +Output | 0.000173 | 0.00028775 | 0.000617 | 0.0 | 0.01 +Modify | 0.000256 | 0.00026675 | 0.000281 | 0.0 | 0.01 +Other | | 0.0009633 | | | 0.02 + +Nlocal: 128 ave 128 max 128 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 7808 ave 7808 max 7808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 15616 ave 15616 max 15616 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 62464 +Ave neighs/atom = 122 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.1 b/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.1 new file mode 100644 index 0000000000..e412df5404 --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.1 @@ -0,0 +1,151 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to quadratic SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.1803 +Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds +displace_atoms all random 0.01 0.01 0.01 12345 + +mass 1 183.84 + +# choose potential + +include W.quadratic.mliap +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 74 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +SNAP keyword rcutfac 4.73442 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems W +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 74 ${zblz} +pair_coeff 1 1 zbl 74 74 +pair_coeff * * mliap W + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check no + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8 + ghost atom cutoff = 5.8 + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.093 | 6.093 | 6.093 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -1.1602728 -1.1602728 -1.1217977 600047.3 -600047.3 + 10 288.46387 -1.1587932 -1.1587932 -1.1217976 600359.75 -600359.75 + 20 268.69718 -1.1562579 -1.1562579 -1.1217974 600870.22 -600870.22 + 30 243.19855 -1.1529874 -1.1529874 -1.1217971 601511.5 -601511.5 + 40 215.13122 -1.1493875 -1.1493875 -1.1217969 602202.36 -602202.36 + 50 187.82673 -1.1458855 -1.1458855 -1.1217966 602860.26 -602860.26 + 60 164.26822 -1.1428639 -1.1428639 -1.1217965 603413.25 -603413.25 + 70 146.65179 -1.1406045 -1.1406045 -1.1217964 603809.35 -603809.35 + 80 136.10769 -1.1392522 -1.1392522 -1.1217964 604022.32 -604022.32 + 90 132.62756 -1.138806 -1.138806 -1.1217964 604053.33 -604053.33 + 100 135.19841 -1.1391358 -1.1391358 -1.1217966 603928.48 -603928.48 +Loop time of 1.69996 on 1 procs for 100 steps with 128 atoms + +Performance: 2.541 ns/day, 9.444 hours/ns, 58.825 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6676 | 1.6676 | 1.6676 | 0.0 | 98.09 +Neigh | 0.03029 | 0.03029 | 0.03029 | 0.0 | 1.78 +Comm | 0.001238 | 0.001238 | 0.001238 | 0.0 | 0.07 +Output | 0.000452 | 0.000452 | 0.000452 | 0.0 | 0.03 +Modify | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.01 +Other | | 0.000241 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3712 ave 3712 max 3712 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 100 +Dangerous builds not checked + +Total wall time: 0:00:01 diff --git a/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.4 b/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.4 new file mode 100644 index 0000000000..f8ebb89fc6 --- /dev/null +++ b/examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.4 @@ -0,0 +1,151 @@ +LAMMPS (15 Jun 2020) +# Demonstrate MLIAP interface to quadratic SNAP potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.1803 +Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000 seconds +displace_atoms all random 0.01 0.01 0.01 12345 + +mass 1 183.84 + +# choose potential + +include W.quadratic.mliap +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz equal 74 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor +SNAP keyword rcutfac 4.73442 +SNAP keyword twojmax 6 +SNAP keyword nelems 1 +SNAP keyword elems W +SNAP keyword radelems 0.5 +SNAP keyword welems 1 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff 1 1 zbl 74 ${zblz} +pair_coeff 1 1 zbl 74 74 +pair_coeff * * mliap W + + +# Setup output + +compute eatom all pe/atom +compute energy all reduce sum c_eatom + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) + +thermo_style custom step temp epair c_energy etotal press v_press +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check no + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8 + ghost atom cutoff = 5.8 + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair mliap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.031 | 6.032 | 6.033 Mbytes +Step Temp E_pair c_energy TotEng Press v_press + 0 300 -1.1602728 -1.1602728 -1.1217977 600047.3 -600047.3 + 10 288.46387 -1.1587932 -1.1587932 -1.1217976 600359.75 -600359.75 + 20 268.69718 -1.1562579 -1.1562579 -1.1217974 600870.22 -600870.22 + 30 243.19855 -1.1529874 -1.1529874 -1.1217971 601511.5 -601511.5 + 40 215.13122 -1.1493875 -1.1493875 -1.1217969 602202.36 -602202.36 + 50 187.82673 -1.1458855 -1.1458855 -1.1217966 602860.26 -602860.26 + 60 164.26822 -1.1428639 -1.1428639 -1.1217965 603413.25 -603413.25 + 70 146.65179 -1.1406045 -1.1406045 -1.1217964 603809.35 -603809.35 + 80 136.10769 -1.1392522 -1.1392522 -1.1217964 604022.32 -604022.32 + 90 132.62756 -1.138806 -1.138806 -1.1217964 604053.33 -604053.33 + 100 135.19841 -1.1391358 -1.1391358 -1.1217966 603928.48 -603928.48 +Loop time of 0.520935 on 4 procs for 100 steps with 128 atoms + +Performance: 8.293 ns/day, 2.894 hours/ns, 191.963 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.4001 | 0.44784 | 0.49877 | 6.8 | 85.97 +Neigh | 0.00728 | 0.0080255 | 0.008793 | 0.8 | 1.54 +Comm | 0.012664 | 0.064342 | 0.11287 | 18.2 | 12.35 +Output | 0.000511 | 0.00053725 | 0.000613 | 0.0 | 0.10 +Modify | 7.3e-05 | 7.925e-05 | 8.3e-05 | 0.0 | 0.02 +Other | | 0.0001087 | | | 0.02 + +Nlocal: 32 ave 35 max 29 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 431 ave 434 max 428 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 928 ave 1019 max 837 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 1856 ave 2030 max 1682 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 100 +Dangerous builds not checked + +Total wall time: 0:00:00 diff --git a/examples/mliap/log.snap.quadratic.ref b/examples/mliap/log.snap.quadratic.ref deleted file mode 100644 index 472080f7a4..0000000000 --- a/examples/mliap/log.snap.quadratic.ref +++ /dev/null @@ -1,153 +0,0 @@ -LAMMPS (19 Mar 2020) -# Demonstrate SNAP Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 1 -variable a equal 3.1803 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 1 -variable ny equal ${nrep} -variable ny equal 1 -variable nz equal ${nrep} -variable nz equal 1 - -boundary p p p - -lattice bcc $a -lattice bcc 3.1803 -Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 1 0 ${ny} 0 ${nz} -region box block 0 1 0 1 0 ${nz} -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (3.1803 3.1803 3.1803) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 2 atoms - create_atoms CPU = 0.000215 secs -displace_atoms all random 0.01 0.01 0.01 12345 - -mass 1 183.84 - -# choose potential - -include W.snap.quadratic -# -# -# Definition of SNAP+ZBL potential. -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 74 - -# Specify hybrid with SNAP and ZBL - -pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 4.8 snap -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff 1 1 zbl 74 ${zblz} -pair_coeff 1 1 zbl 74 74 -pair_coeff * * snap W.quadratic.snapcoeff W.quadratic.snapparam W -SNAP Element = W, Radius 0.5, Weight 1 -SNAP keyword rcutfac 4.73442 -SNAP keyword twojmax 6 -SNAP keyword rfac0 0.99363 -SNAP keyword rmin0 0 -SNAP keyword bzeroflag 1 -SNAP keyword quadraticflag 1 - - -# Setup output - -compute eatom all pe/atom -compute energy all reduce sum c_eatom - -compute satom all stress/atom NULL -compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] -variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) - -thermo_style custom step temp epair c_energy etotal press v_press -thermo 10 -thermo_modify norm yes - -dump 1 all custom 100 dump.quadratic.* id type fx fy fz c_eatom - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check no - -# Run MD - -velocity all create 300.0 4928459 -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5.8 - ghost atom cutoff = 5.8 - binsize = 2.9, bins = 2 2 2 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair zbl, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none - (2) pair snap, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.284 | 7.284 | 7.284 Mbytes -Step Temp E_pair c_energy TotEng Press v_press - 0 300 -1.1575362 -1.1575362 -1.1381472 600966 -600966 - 10 349.32287 -1.1607243 -1.1607243 -1.1381475 599985.48 -599985.48 - 20 384.27065 -1.1629832 -1.1629832 -1.1381478 599287.89 -599287.89 - 30 399.34846 -1.1639578 -1.1639578 -1.1381478 598986.42 -598986.42 - 40 392.19413 -1.1634953 -1.1634953 -1.1381478 599130.05 -599130.05 - 50 363.93932 -1.161669 -1.161669 -1.1381476 599694.93 -599694.93 - 60 319.03014 -1.1587663 -1.1587663 -1.1381473 600588.89 -600588.89 - 70 264.53512 -1.1552439 -1.1552439 -1.138147 601667.76 -601667.76 - 80 209.04294 -1.1516571 -1.1516571 -1.1381466 602760.01 -602760.01 - 90 161.3157 -1.1485722 -1.1485722 -1.1381463 603694.49 -603694.49 - 100 128.9054 -1.1464773 -1.1464773 -1.1381461 604326.7 -604326.7 -Loop time of 0.030198 on 1 procs for 100 steps with 2 atoms - -Performance: 143.056 ns/day, 0.168 hours/ns, 3311.478 timesteps/s -98.4% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.028723 | 0.028723 | 0.028723 | 0.0 | 95.12 -Neigh | 0.000515 | 0.000515 | 0.000515 | 0.0 | 1.71 -Comm | 0.000263 | 0.000263 | 0.000263 | 0.0 | 0.87 -Output | 0.000618 | 0.000618 | 0.000618 | 0.0 | 2.05 -Modify | 2.7e-05 | 2.7e-05 | 2.7e-05 | 0.0 | 0.09 -Other | | 5.2e-05 | | | 0.17 - -Nlocal: 2 ave 2 max 2 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 187 ave 187 max 187 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 58 ave 58 max 58 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 116 ave 116 max 116 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 116 -Ave neighs/atom = 58 -Neighbor list builds = 100 -Dangerous builds not checked - -Total wall time: 0:00:00 diff --git a/potentials/InP_JCPA2020.snap b/potentials/InP_JCPA2020.snap index a1ba9e7a94..1af0008b6f 100644 --- a/potentials/InP_JCPA2020.snap +++ b/potentials/InP_JCPA2020.snap @@ -1,4 +1,4 @@ -# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) +# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) # Definition of SNAP+ZBL potential. diff --git a/potentials/InP_JCPA2020.snapparam b/potentials/InP_JCPA2020.snapparam index 880ba6671c..0e764ac7ca 100644 --- a/potentials/InP_JCPA2020.snapparam +++ b/potentials/InP_JCPA2020.snapparam @@ -1,14 +1,14 @@ # DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020) - # required - rcutfac 1.0 - twojmax 6 +# required +rcutfac 1.0 +twojmax 6 - # optional - rfac0 0.99363 - rmin0 0.0 - bzeroflag 1 - quadraticflag 0 - wselfallflag 1 - chemflag 1 - bnormflag 1 +# optional +rfac0 0.99363 +rmin0 0.0 +bzeroflag 1 +quadraticflag 0 +wselfallflag 1 +chemflag 1 +bnormflag 1 diff --git a/potentials/WBe_Wood_PRB2019.snapcoeff b/potentials/WBe_Wood_PRB2019.snapcoeff index c72baabd74..965059f8b5 100644 --- a/potentials/WBe_Wood_PRB2019.snapcoeff +++ b/potentials/WBe_Wood_PRB2019.snapcoeff @@ -1,3 +1,4 @@ +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) # LAMMPS SNAP coefficients for WBe 2 56 diff --git a/potentials/WBe_Wood_PRB2019.snapparam b/potentials/WBe_Wood_PRB2019.snapparam index e4fc4b4459..e96458651c 100644 --- a/potentials/WBe_Wood_PRB2019.snapparam +++ b/potentials/WBe_Wood_PRB2019.snapparam @@ -1,3 +1,5 @@ +# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) + # required rcutfac 4.8123 twojmax 8 diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index 832efec48a..db677881d5 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -20,6 +20,7 @@ #include "atom.h" #include "force.h" #include "comm.h" +#include "utils.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -119,17 +120,17 @@ void MLIAPDescriptorSNAP::forward(int* map, NeighList* list, double **descriptor snaptr->inside[ninside] = j; snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac; - snaptr->element[ninside] = jelem; // element index for alloy snap + snaptr->element[ninside] = jelem; // element index for chem snap ninside++; } } - if (alloyflag) + if (chemflag) snaptr->compute_ui(ninside, ielem); else snaptr->compute_ui(ninside, 0); snaptr->compute_zi(); - if (alloyflag) + if (chemflag) snaptr->compute_bi(ielem); else snaptr->compute_bi(0); @@ -201,14 +202,14 @@ void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double snaptr->inside[ninside] = j; snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac; - snaptr->element[ninside] = jelem; // element index for alloy snap + snaptr->element[ninside] = jelem; // element index for chem snap ninside++; } } // compute Ui, Yi for atom I - if (alloyflag) + if (chemflag) snaptr->compute_ui(ninside, ielem); else snaptr->compute_ui(ninside, 0); @@ -224,7 +225,7 @@ void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double for (int jj = 0; jj < ninside; jj++) { int j = snaptr->inside[jj]; - if(alloyflag) + if(chemflag) snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj], snaptr->rcutij[jj],jj, snaptr->element[jj]); else @@ -263,7 +264,7 @@ void MLIAPDescriptorSNAP::init() snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, - alloyflag, wselfallflag, nelements); + chemflag, bnormflag, wselfallflag, nelements); snaptr->init(); @@ -291,8 +292,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) rmin0 = 0.0; switchflag = 1; bzeroflag = 1; + chemflag = 0; bnormflag = 0; - alloyflag = 0; wselfallflag = 0; // open SNAP parameter file on proc 0 @@ -327,7 +328,7 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) // strip comment, skip line if blank if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); + nwords = utils::count_words(line); if (nwords == 0) continue; // words = ptrs to all words in line @@ -400,8 +401,10 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) switchflag = atoi(keyval); else if (strcmp(keywd,"bzeroflag") == 0) bzeroflag = atoi(keyval); - else if (strcmp(keywd,"alloyflag") == 0) - alloyflag = atoi(keyval); + else if (strcmp(keywd,"chemflag") == 0) + chemflag = atoi(keyval); + else if (strcmp(keywd,"bnormflag") == 0) + bnormflag = atoi(keyval); else if (strcmp(keywd,"wselfallflag") == 0) wselfallflag = atoi(keyval); else @@ -410,8 +413,6 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) } } - bnormflag = alloyflag; - if (!rcutfacflag || !twojmaxflag || !nelementsflag || !elementsflag || !radelemflag || !wjelemflag) error->all(FLERR,"Incorrect SNAP parameter file"); diff --git a/src/MLIAP/mliap_descriptor_snap.h b/src/MLIAP/mliap_descriptor_snap.h index da2018b94f..15691fabfe 100644 --- a/src/MLIAP/mliap_descriptor_snap.h +++ b/src/MLIAP/mliap_descriptor_snap.h @@ -39,8 +39,8 @@ protected: double *radelem; // element radii double *wjelem; // elements weights - int twojmax, switchflag, bzeroflag, bnormflag; - int alloyflag, wselfallflag; + int twojmax, switchflag, bzeroflag; + int chemflag, bnormflag, wselfallflag; double rfac0, rmin0; }; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index db5d2b7c04..5c689c8369 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "force.h" #include "comm.h" +#include "utils.h" #include "neigh_list.h" #include "memory.h" #include "error.h" @@ -89,7 +90,7 @@ void MLIAPModel::read_coeffs(char *coefffilename) // strip comment, skip line if blank if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); + nwords = utils::count_words(line); } if (nwords != 2) error->all(FLERR,"Incorrect format in MLIAPModel coefficient file"); @@ -128,7 +129,7 @@ void MLIAPModel::read_coeffs(char *coefffilename) MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); - nwords = atom->count_words(line); + nwords = utils::trim_and_count_words(line); if (nwords != 1) error->all(FLERR,"Incorrect format in coefficient file");