forked from lijiext/lammps
Merged MLIAP package into latest LAMMPS created SNAP, quadratic SNAP, and ChemSNAP examples
This commit is contained in:
Aidan Thompson
parent
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# 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)
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# Definition of SNAP+ZBL potential.
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variable zblcutinner index 4
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variable zblcutouter index 4.2
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variable zblz1 index 49
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variable zblz2 index 15
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# Specify hybrid with SNAP and ZBL
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pair_style hybrid/overlay &
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zbl ${zblcutinner} ${zblcutouter} &
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mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
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pair_coeff 1 1 zbl ${zblz1} ${zblz1}
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pair_coeff 1 2 zbl ${zblz1} ${zblz2}
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pair_coeff 2 2 zbl ${zblz2} ${zblz2}
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pair_coeff * * mliap In P
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@ -0,0 +1,20 @@
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# 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)
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# required
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rcutfac 1.0
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twojmax 6
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# elements
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nelems 2
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elems In P
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radelems 3.81205 3.82945
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welems 1 0.929316
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# optional
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rfac0 0.99363
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rmin0 0.0
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bzeroflag 1
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wselfallflag 1
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chemflag 1
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bnormflag 1
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@ -0,0 +1,485 @@
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# 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)
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2 241
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0.000000000000 # B[0] Block = 1 Type = In
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-0.000666721868 # B[1, 0, 0, 0] Block = 1 Type = In
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0.032408881964 # B[2, 1, 0, 1] Block = 1 Type = In
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0.182277739455 # B[3, 1, 1, 2] Block = 1 Type = In
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0.001455902168 # B[4, 2, 0, 2] Block = 1 Type = In
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0.086259367737 # B[5, 2, 1, 3] Block = 1 Type = In
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-0.044840628371 # B[6, 2, 2, 2] Block = 1 Type = In
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-0.175973261191 # B[7, 2, 2, 4] Block = 1 Type = In
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-0.052429169415 # B[8, 3, 0, 3] Block = 1 Type = In
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0.195529228497 # B[9, 3, 1, 4] Block = 1 Type = In
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0.078718744520 # B[10, 3, 2, 3] Block = 1 Type = In
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-0.688127658121 # B[11, 3, 2, 5] Block = 1 Type = In
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0.059084058400 # B[12, 3, 3, 4] Block = 1 Type = In
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0.006795099274 # B[13, 3, 3, 6] Block = 1 Type = In
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-0.043061553886 # B[14, 4, 0, 4] Block = 1 Type = In
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-0.046619800530 # B[15, 4, 1, 5] Block = 1 Type = In
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-0.117451659827 # B[16, 4, 2, 4] Block = 1 Type = In
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-0.233615100720 # B[17, 4, 2, 6] Block = 1 Type = In
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0.015358771114 # B[18, 4, 3, 5] Block = 1 Type = In
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0.022474133984 # B[19, 4, 4, 4] Block = 1 Type = In
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0.002165850235 # B[20, 4, 4, 6] Block = 1 Type = In
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0.003458938546 # B[21, 5, 0, 5] Block = 1 Type = In
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-0.053507775670 # B[22, 5, 1, 6] Block = 1 Type = In
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0.120989101467 # B[23, 5, 2, 5] Block = 1 Type = In
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0.092637875162 # B[24, 5, 3, 6] Block = 1 Type = In
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0.071459233521 # B[25, 5, 4, 5] Block = 1 Type = In
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0.086291858607 # B[26, 5, 5, 6] Block = 1 Type = In
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0.006749966752 # B[27, 6, 0, 6] Block = 1 Type = In
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0.144917284093 # B[28, 6, 2, 6] Block = 1 Type = In
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0.055178211309 # B[29, 6, 4, 6] Block = 1 Type = In
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-0.005619133266 # B[30, 6, 6, 6] Block = 1 Type = In
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0.005430513632 # B[1, 0, 0, 0] Block = 2 Type = In
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0.057269488101 # B[2, 1, 0, 1] Block = 2 Type = In
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0.320412300575 # B[3, 1, 1, 2] Block = 2 Type = In
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0.035481869944 # B[4, 2, 0, 2] Block = 2 Type = In
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0.111076763087 # B[5, 2, 1, 3] Block = 2 Type = In
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0.039770598731 # B[6, 2, 2, 2] Block = 2 Type = In
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0.141315510383 # B[7, 2, 2, 4] Block = 2 Type = In
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0.067792661762 # B[8, 3, 0, 3] Block = 2 Type = In
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-0.080858457946 # B[9, 3, 1, 4] Block = 2 Type = In
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0.258942062632 # B[10, 3, 2, 3] Block = 2 Type = In
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0.061756985062 # B[11, 3, 2, 5] Block = 2 Type = In
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-0.112424676196 # B[12, 3, 3, 4] Block = 2 Type = In
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0.168376857205 # B[13, 3, 3, 6] Block = 2 Type = In
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-0.029743698629 # B[14, 4, 0, 4] Block = 2 Type = In
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-0.093967263289 # B[15, 4, 1, 5] Block = 2 Type = In
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0.137229827290 # B[16, 4, 2, 4] Block = 2 Type = In
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0.056897919200 # B[17, 4, 2, 6] Block = 2 Type = In
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0.095137344320 # B[18, 4, 3, 5] Block = 2 Type = In
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-0.008598816416 # B[19, 4, 4, 4] Block = 2 Type = In
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0.038890602482 # B[20, 4, 4, 6] Block = 2 Type = In
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-0.034624751006 # B[21, 5, 0, 5] Block = 2 Type = In
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-0.282625695473 # B[22, 5, 1, 6] Block = 2 Type = In
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0.103089891872 # B[23, 5, 2, 5] Block = 2 Type = In
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-0.024380802146 # B[24, 5, 3, 6] Block = 2 Type = In
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-0.063847809434 # B[25, 5, 4, 5] Block = 2 Type = In
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-0.024896682749 # B[26, 5, 5, 6] Block = 2 Type = In
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0.000464369553 # B[27, 6, 0, 6] Block = 2 Type = In
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0.082229290277 # B[28, 6, 2, 6] Block = 2 Type = In
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-0.008875503360 # B[29, 6, 4, 6] Block = 2 Type = In
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-0.009039017094 # B[30, 6, 6, 6] Block = 2 Type = In
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0.005430513686 # B[1, 0, 0, 0] Block = 3 Type = In
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-0.004352445887 # B[2, 1, 0, 1] Block = 3 Type = In
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0.149882860704 # B[3, 1, 1, 2] Block = 3 Type = In
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-0.015528472583 # B[4, 2, 0, 2] Block = 3 Type = In
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0.558662861756 # B[5, 2, 1, 3] Block = 3 Type = In
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0.039770598731 # B[6, 2, 2, 2] Block = 3 Type = In
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0.179060667136 # B[7, 2, 2, 4] Block = 3 Type = In
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0.034759981675 # B[8, 3, 0, 3] Block = 3 Type = In
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||||
0.603083480153 # B[9, 3, 1, 4] Block = 3 Type = In
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0.176946655350 # B[10, 3, 2, 3] Block = 3 Type = In
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0.165639632803 # B[11, 3, 2, 5] Block = 3 Type = In
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||||
0.055627509305 # B[12, 3, 3, 4] Block = 3 Type = In
|
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0.049782791218 # B[13, 3, 3, 6] Block = 3 Type = In
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0.036078617029 # B[14, 4, 0, 4] Block = 3 Type = In
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0.064493563641 # B[15, 4, 1, 5] Block = 3 Type = In
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||||
0.149250535822 # B[16, 4, 2, 4] Block = 3 Type = In
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-0.060208330201 # B[17, 4, 2, 6] Block = 3 Type = In
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0.105119833648 # B[18, 4, 3, 5] Block = 3 Type = In
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-0.008598816416 # B[19, 4, 4, 4] Block = 3 Type = In
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0.041210118888 # B[20, 4, 4, 6] Block = 3 Type = In
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-0.002705345469 # B[21, 5, 0, 5] Block = 3 Type = In
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0.170191392493 # B[22, 5, 1, 6] Block = 3 Type = In
|
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0.226897293272 # B[23, 5, 2, 5] Block = 3 Type = In
|
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0.013009034793 # B[24, 5, 3, 6] Block = 3 Type = In
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||||
-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
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-0.024245533697 # B[29, 6, 4, 6] Block = 3 Type = In
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-0.009039017094 # B[30, 6, 6, 6] Block = 3 Type = In
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-0.005654800687 # B[1, 0, 0, 0] Block = 4 Type = In
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-0.071064263981 # B[2, 1, 0, 1] Block = 4 Type = In
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-0.009868049046 # B[3, 1, 1, 2] Block = 4 Type = In
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-0.061297753855 # B[4, 2, 0, 2] Block = 4 Type = In
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-0.239682636759 # B[5, 2, 1, 3] Block = 4 Type = In
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0.015954956116 # B[6, 2, 2, 2] Block = 4 Type = In
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0.176005610703 # B[7, 2, 2, 4] Block = 4 Type = In
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-0.081125948095 # B[8, 3, 0, 3] Block = 4 Type = In
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-0.170847987084 # B[9, 3, 1, 4] Block = 4 Type = In
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0.242239715395 # B[10, 3, 2, 3] Block = 4 Type = In
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0.082507688294 # B[11, 3, 2, 5] Block = 4 Type = In
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0.247785108978 # B[12, 3, 3, 4] Block = 4 Type = In
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-0.008194303016 # B[13, 3, 3, 6] Block = 4 Type = In
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0.014786217107 # B[14, 4, 0, 4] Block = 4 Type = In
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||||
-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
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||||
0.099757230122 # B[18, 4, 3, 5] Block = 4 Type = In
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||||
0.035047662350 # B[19, 4, 4, 4] Block = 4 Type = In
|
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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
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||||
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
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||||
0.009481237049 # B[29, 6, 4, 6] Block = 4 Type = In
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||||
-0.008649958571 # B[30, 6, 6, 6] Block = 4 Type = In
|
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0.005430513686 # B[1, 0, 0, 0] Block = 5 Type = In
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||||
0.057269488102 # B[2, 1, 0, 1] Block = 5 Type = In
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0.149882860704 # B[3, 1, 1, 2] Block = 5 Type = In
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0.035481869944 # B[4, 2, 0, 2] Block = 5 Type = In
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0.378916788823 # B[5, 2, 1, 3] Block = 5 Type = In
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0.039770598731 # B[6, 2, 2, 2] Block = 5 Type = In
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0.179060667136 # B[7, 2, 2, 4] Block = 5 Type = In
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0.067792661762 # B[8, 3, 0, 3] Block = 5 Type = In
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0.272613304171 # B[9, 3, 1, 4] Block = 5 Type = In
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0.258942062632 # B[10, 3, 2, 3] Block = 5 Type = In
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0.100130474069 # B[11, 3, 2, 5] Block = 5 Type = In
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0.055627509305 # B[12, 3, 3, 4] Block = 5 Type = In
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0.049782791218 # B[13, 3, 3, 6] Block = 5 Type = In
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-0.029743698629 # B[14, 4, 0, 4] Block = 5 Type = In
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-0.013420300314 # B[15, 4, 1, 5] Block = 5 Type = In
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0.137229827290 # B[16, 4, 2, 4] Block = 5 Type = In
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-0.034447269506 # B[17, 4, 2, 6] Block = 5 Type = In
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-0.033847124314 # B[18, 4, 3, 5] Block = 5 Type = In
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-0.008598816416 # B[19, 4, 4, 4] Block = 5 Type = In
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0.041210118888 # B[20, 4, 4, 6] Block = 5 Type = In
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-0.034624751006 # B[21, 5, 0, 5] Block = 5 Type = In
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0.041662678638 # B[22, 5, 1, 6] Block = 5 Type = In
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0.103089891872 # B[23, 5, 2, 5] Block = 5 Type = In
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-0.044572198386 # B[24, 5, 3, 6] Block = 5 Type = In
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-0.063847809434 # B[25, 5, 4, 5] Block = 5 Type = In
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-0.018139074523 # B[26, 5, 5, 6] Block = 5 Type = In
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0.000464369553 # B[27, 6, 0, 6] Block = 5 Type = In
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0.082229290277 # B[28, 6, 2, 6] Block = 5 Type = In
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-0.008875503360 # B[29, 6, 4, 6] Block = 5 Type = In
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-0.009039017094 # B[30, 6, 6, 6] Block = 5 Type = In
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-0.005654800687 # B[1, 0, 0, 0] Block = 6 Type = In
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-0.001217874195 # B[2, 1, 0, 1] Block = 6 Type = In
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-0.009868049046 # B[3, 1, 1, 2] Block = 6 Type = In
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-0.092827766060 # B[4, 2, 0, 2] Block = 6 Type = In
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0.439274283244 # B[5, 2, 1, 3] Block = 6 Type = In
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0.015954956116 # B[6, 2, 2, 2] Block = 6 Type = In
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0.176005610703 # B[7, 2, 2, 4] Block = 6 Type = In
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0.102468480364 # B[8, 3, 0, 3] Block = 6 Type = In
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0.674122225402 # B[9, 3, 1, 4] Block = 6 Type = In
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0.072529538087 # B[10, 3, 2, 3] Block = 6 Type = In
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0.330711171466 # B[11, 3, 2, 5] Block = 6 Type = In
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0.247785108978 # B[12, 3, 3, 4] Block = 6 Type = In
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-0.008194303016 # B[13, 3, 3, 6] Block = 6 Type = In
|
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0.052250780232 # B[14, 4, 0, 4] Block = 6 Type = In
|
||||
0.374231060518 # B[15, 4, 1, 5] Block = 6 Type = In
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||||
0.326667869620 # B[16, 4, 2, 4] Block = 6 Type = In
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0.079031873518 # B[17, 4, 2, 6] Block = 6 Type = In
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0.224004472527 # B[18, 4, 3, 5] Block = 6 Type = In
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0.035047662350 # B[19, 4, 4, 4] Block = 6 Type = In
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0.007150552805 # B[20, 4, 4, 6] Block = 6 Type = In
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0.040682917098 # B[21, 5, 0, 5] Block = 6 Type = In
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0.046855927526 # B[22, 5, 1, 6] Block = 6 Type = In
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0.219695071346 # B[23, 5, 2, 5] Block = 6 Type = In
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-0.001426581661 # B[24, 5, 3, 6] Block = 6 Type = In
|
||||
0.028514699601 # B[25, 5, 4, 5] Block = 6 Type = In
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||||
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
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||||
-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
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||||
-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
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||||
0.008498646326 # B[13, 3, 3, 6] Block = 7 Type = In
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0.014786217107 # B[14, 4, 0, 4] Block = 7 Type = In
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-0.178665293356 # B[15, 4, 1, 5] Block = 7 Type = In
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0.164908528605 # B[16, 4, 2, 4] Block = 7 Type = In
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||||
-0.117717485069 # B[17, 4, 2, 6] Block = 7 Type = In
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0.146739677531 # B[18, 4, 3, 5] Block = 7 Type = In
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0.035047662350 # B[19, 4, 4, 4] Block = 7 Type = In
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0.088770688382 # B[20, 4, 4, 6] Block = 7 Type = In
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0.019198319779 # B[21, 5, 0, 5] Block = 7 Type = In
|
||||
-0.148162265312 # B[22, 5, 1, 6] Block = 7 Type = In
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||||
0.114478010571 # B[23, 5, 2, 5] Block = 7 Type = In
|
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0.114731400461 # B[24, 5, 3, 6] Block = 7 Type = In
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0.096853268510 # B[25, 5, 4, 5] Block = 7 Type = In
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0.031183854107 # B[26, 5, 5, 6] Block = 7 Type = In
|
||||
-0.002405537661 # B[27, 6, 0, 6] Block = 7 Type = In
|
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0.058549926350 # B[28, 6, 2, 6] Block = 7 Type = In
|
||||
0.009481237049 # B[29, 6, 4, 6] Block = 7 Type = In
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||||
-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
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||||
-0.212358294308 # B[3, 1, 1, 2] Block = 8 Type = In
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
-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
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
# DATE: 2020-06-21 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: none
|
||||
|
||||
# required
|
||||
|
||||
rcutfac 4.73442
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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}
|
||||
|
||||
|
|
@ -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}
|
||||
|
||||
|
|
@ -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}
|
||||
|
||||
|
|
@ -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}
|
||||
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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.
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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");
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -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");
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue