forked from lijiext/lammps
Removed redundant element list from pair_coeff snap syntax
This commit is contained in:
Aidan Thompson
parent
67041a5446
commit
fa7e02ea71
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@ -16,7 +16,7 @@ pair_style snap :pre
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[Examples:]
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pair_style snap
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pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
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pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
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[Description:]
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@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
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the SNAP potential files themselves.
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Only a single pair_coeff command is used with the {snap} style which
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specifies two SNAP files and the list SNAP element(s) to be
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extracted.
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The SNAP elements are mapped to LAMMPS atom types by specifying
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N additional arguments after the 2nd filename in the pair_coeff
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command, where N is the number of LAMMPS atom types:
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specifies a SNAP coefficient file followed by a SNAP parameter file
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and then N additional arguments specifying the mapping of SNAP
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elements to LAMMPS atom types, where N is the number of
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LAMMPS atom types:
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SNAP element file
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Elem1, Elem2, ...
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SNAP coefficient file
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SNAP parameter file
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N element names = mapping of SNAP elements to atom types :ul
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@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
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types, with the first two being indium and the 3rd and 4th being
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phophorous, the pair_coeff command would look like this:
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pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
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pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The two filenames are for the element and parameter files, respectively.
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The 'In' and 'P' arguments (between the file names) are the two elements
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which will be extracted from the element file. The
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two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
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The two filenames are for the coefficient and parameter files, respectively.
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The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
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SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
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3 and 4 to the SNAP 'P' element.
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@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
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{hybrid} pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.
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The name of the SNAP element file usually ends in the
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The name of the SNAP coefficient file usually ends in the
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".snapcoeff" extension. It may contain coefficients
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for many SNAP elements.
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Only those elements listed in the pair_coeff command are extracted.
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for many SNAP elements. The only requirement is that it
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contain at least those element names appearing in the
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LAMMPS mapping list.
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The name of the SNAP parameter file usually ends in the ".snapparam"
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extension. It contains a small number
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of parameters that define the overall form of the SNAP potential.
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@ -110,8 +107,7 @@ It is convenient to keep these commands in a separate file that can
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be inserted in any LAMMPS input script using the "include"_include.html
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command.
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The top of the SNAP element file can contain any number of blank and comment
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lines (start with #), but follows a strict
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The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
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format after that. The first non-blank non-comment
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line must contain two integers:
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@ -1,7 +0,0 @@
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# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
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# Generated by Materials Virtual Lab
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# Definition of SNAP potential.
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pair_style snap
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pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
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@ -0,0 +1 @@
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../../potentials/Mo_Chen_PRM2017.snap
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@ -1,35 +0,0 @@
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# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
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# Generated by Materials Virtual Lab
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1 31
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Mo 0.5 1
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-17.2757958404
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0.00431015861472
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0.0657685117891
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0.477733335702
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0.0152688837211
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0.77559888196
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0.284846429566
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0.148804982644
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0.0573702179736
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0.19281989434
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0.323441703578
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0.101324335724
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0.0139639846514
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-0.0324444749083
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0.0349797952779
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0.0613023441282
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0.0881078513046
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0.118716074611
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0.0069662975532
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-0.0174658914685
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-0.0178902177779
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0.0195993756659
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0.0719238160707
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0.0344832661036
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-0.0358616891662
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-0.0292380783172
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-0.0334933909866
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0.00595462520243
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0.0754556638328
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-0.000972545258845
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-0.0100170422751
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@ -0,0 +1 @@
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../../potentials/Mo_Chen_PRM2017.snapcoeff
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@ -1,4 +0,0 @@
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# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
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# Generated by Materials Virtual Lab
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rcutfac 4.615858
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twojmax 6
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@ -0,0 +1 @@
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../../potentials/Mo_Chen_PRM2017.snapparam
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@ -1,17 +0,0 @@
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# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
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# Definition of SNAP potential Ta_Cand06A
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# Assumes 1 LAMMPS atom type
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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# Specify hybrid with SNAP, ZBL
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pair_style hybrid/overlay &
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zbl ${zblcutinner} ${zblcutouter} &
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snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
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@ -0,0 +1 @@
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../../potentials/Ta06A.snap
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@ -1,37 +0,0 @@
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# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
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# LAMMPS SNAP coefficients for Ta_Cand06A
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1 31
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Ta 0.5 1
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-2.92477
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-0.01137
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-0.00775
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-0.04907
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-0.15047
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0.09157
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0.05590
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0.05785
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-0.11615
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-0.17122
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-0.10583
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0.03941
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-0.11284
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0.03939
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-0.07331
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-0.06582
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-0.09341
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-0.10587
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-0.15497
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0.04820
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0.00205
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0.00060
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-0.04898
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-0.05084
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-0.03371
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-0.01441
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-0.01501
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-0.00599
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-0.06373
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0.03965
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0.01072
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@ -0,0 +1 @@
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../../potentials/Ta06A.snapcoeff
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@ -1,15 +0,0 @@
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# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
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# LAMMPS SNAP parameters for Ta_Cand06A
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# required
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rcutfac 4.67637
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twojmax 6
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# optional
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rfac0 0.99363
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rmin0 0
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diagonalstyle 3
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bzeroflag 0
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quadraticflag 0
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@ -0,0 +1 @@
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../../potentials/Ta06A.snapparam
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@ -1,16 +0,0 @@
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# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
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#
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# Definition of SNAP+ZBL potential.
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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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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snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
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#Nomenclature on the snap files are Element_DakotaID_Year_Month
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@ -0,0 +1 @@
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../../potentials/W_2940_2017_2.snap
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@ -1,62 +0,0 @@
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# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
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#
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# LAMMPS SNAP coefficients for W
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1 56
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W 0.5 1
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0.781170857801
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-0.001794941735
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-0.016628679036
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-0.066625537037
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-0.073716343967
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-0.062913923923
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0.032552694672
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-0.134901744419
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-0.075076334103
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-0.148558616547
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-0.140808831101
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-0.166749145704
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-0.047487675984
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-0.049892090603
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-0.032483739965
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-0.114766534860
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-0.106759718242
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-0.125894850485
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-0.103409735225
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-0.095247335447
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-0.061998736346
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-0.053895610976
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-0.010799734206
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-0.011644828900
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-0.028316826924
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0.011176085541
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0.064619474684
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-0.023886279996
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-0.004099224312
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-0.056084222496
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-0.035551497650
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-0.056678501024
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-0.004905851656
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-0.015701146162
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-0.008462280779
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0.016429018676
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0.032432633993
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-0.010805361272
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-0.014841893457
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0.019414134562
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-0.008112452759
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-0.002700775447
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0.007032887063
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-0.009706065042
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0.008385967833
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0.028606085876
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-0.007003591067
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0.006467260152
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-0.006666986361
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0.029243285316
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0.002477673872
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-0.000199497504
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0.004068954075
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0.006036129972
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-0.013010633924
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-0.008314173699
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@ -0,0 +1 @@
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../../potentials/W_2940_2017_2.snapcoeff
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@ -1,13 +0,0 @@
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# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
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#
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# required
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rcutfac 4.73442
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twojmax 8
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# optional
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rfac0 0.99363
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rmin0 0
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diagonalstyle 3
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bzeroflag 0
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quadraticflag 0
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@ -0,0 +1 @@
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../../potentials/W_2940_2017_2.snapparam
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@ -1,17 +0,0 @@
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# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
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#
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# Definition of SNAP+ZBL+Tabulated potential.
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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# Specify hybrid with SNAP and ZBL
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pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
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pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
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pair_coeff 1 2 table 2 W_He_JW2013.table WHe
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#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
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#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
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@ -0,0 +1 @@
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../../potentials/W_2940_2017_2_He_JW2013.snap
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@ -1,6 +1,7 @@
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# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
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# Generated by Materials Virtual Lab
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# Definition of SNAP potential.
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pair_style snap
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pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
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pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
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@ -2,7 +2,7 @@
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# Definition of SNAP potential Ta_Cand06A
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# Assumes 1 LAMMPS atom type
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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@ -13,5 +13,5 @@ pair_style hybrid/overlay &
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zbl ${zblcutinner} ${zblcutouter} &
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snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
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pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
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@ -8,7 +8,8 @@ twojmax 6
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# optional
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gamma 1
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rfac0 0.99363
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rmin0 0
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diagonalstyle 3
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bzeroflag 0
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quadraticflag 0
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@ -5,12 +5,12 @@ variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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# Specify hybrid with SNAP, ZBL, and long-range Coulomb
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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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snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
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pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
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#Nomenclature on the snap files are Element_DakotaID_Year_Month
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@ -6,7 +6,8 @@ twojmax 8
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# optional
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gamma 1
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rfac0 0.99363
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rmin0 0
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diagonalstyle 3
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bzeroflag 0
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quadraticflag 0
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@ -5,11 +5,11 @@ variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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# Specify hybrid with SNAP, ZBL, and long-range Coulomb
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# Specify hybrid with SNAP and ZBL
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pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
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pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
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pair_coeff 1 2 table 2 W_He_JW2013.table WHe
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#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
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@ -1416,11 +1416,7 @@ void PairSNAP::settings(int narg, char **arg)
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void PairSNAP::coeff(int narg, char **arg)
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{
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// read SNAP element names between 2 filenames
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// nelements = # of SNAP elements
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// elements = list of unique element names
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if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients");
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if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
if (nelements) {
|
||||
|
|
@ -1432,30 +1428,17 @@ void PairSNAP::coeff(int narg, char **arg)
|
|||
memory->destroy(coeffelem);
|
||||
}
|
||||
|
||||
nelements = narg - 4 - atom->ntypes;
|
||||
if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
char* type1 = arg[0];
|
||||
char* type2 = arg[1];
|
||||
char* coefffilename = arg[2];
|
||||
char** elemlist = &arg[3];
|
||||
char* paramfilename = arg[3+nelements];
|
||||
char** elemtypes = &arg[4+nelements];
|
||||
char* paramfilename = arg[3];
|
||||
char** elemtypes = &arg[4];
|
||||
|
||||
// insure I,J args are * *
|
||||
|
||||
if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
elements = new char*[nelements];
|
||||
|
||||
for (int i = 0; i < nelements; i++) {
|
||||
char* elemname = elemlist[i];
|
||||
int n = strlen(elemname) + 1;
|
||||
elements[i] = new char[n];
|
||||
strcpy(elements[i],elemname);
|
||||
}
|
||||
|
||||
// read snapcoeff and snapparam files
|
||||
|
||||
read_files(coefffilename,paramfilename);
|
||||
|
|
@ -1631,22 +1614,19 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
|||
iword = 1;
|
||||
words[iword] = strtok(NULL,"' \t\n\r\f");
|
||||
|
||||
int nelemfile = atoi(words[0]);
|
||||
nelements = atoi(words[0]);
|
||||
ncoeffall = atoi(words[1]);
|
||||
|
||||
// Set up element lists
|
||||
// set up element lists
|
||||
|
||||
elements = new char*[nelements];
|
||||
memory->create(radelem,nelements,"pair:radelem");
|
||||
memory->create(wjelem,nelements,"pair:wjelem");
|
||||
memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem");
|
||||
|
||||
int *found = new int[nelements];
|
||||
for (int ielem = 0; ielem < nelements; ielem++)
|
||||
found[ielem] = 0;
|
||||
// Loop over nelements blocks in the SNAP coefficient file
|
||||
|
||||
// Loop over elements in the SNAP coefficient file
|
||||
|
||||
for (int ielemfile = 0; ielemfile < nelemfile; ielemfile++) {
|
||||
for (int ielem = 0; ielem < nelements; ielem++) {
|
||||
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fpcoeff);
|
||||
|
|
@ -1673,33 +1653,12 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
|||
words[iword] = strtok(NULL,"' \t\n\r\f");
|
||||
|
||||
char* elemtmp = words[0];
|
||||
double radtmp = atof(words[1]);
|
||||
double wjtmp = atof(words[2]);
|
||||
int n = strlen(elemtmp) + 1;
|
||||
elements[ielem] = new char[n];
|
||||
strcpy(elements[ielem],elemtmp);
|
||||
|
||||
// skip if element name isn't in element list
|
||||
|
||||
int ielem;
|
||||
for (ielem = 0; ielem < nelements; ielem++)
|
||||
if (strcmp(elemtmp,elements[ielem]) == 0) break;
|
||||
if (ielem == nelements) {
|
||||
if (comm->me == 0)
|
||||
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
|
||||
ptr = fgets(line,MAXLINE,fpcoeff);
|
||||
continue;
|
||||
}
|
||||
|
||||
// skip if element already appeared
|
||||
|
||||
if (found[ielem]) {
|
||||
if (comm->me == 0)
|
||||
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
|
||||
ptr = fgets(line,MAXLINE,fpcoeff);
|
||||
continue;
|
||||
}
|
||||
|
||||
found[ielem] = 1;
|
||||
radelem[ielem] = radtmp;
|
||||
wjelem[ielem] = wjtmp;
|
||||
radelem[ielem] = atof(words[1]);
|
||||
wjelem[ielem] = atof(words[2]);
|
||||
|
||||
|
||||
if (comm->me == 0) {
|
||||
|
|
@ -1821,7 +1780,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
|
|||
if (rcutfacflag == 0 || twojmaxflag == 0)
|
||||
error->all(FLERR,"Incorrect SNAP parameter file");
|
||||
|
||||
delete[] found;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -173,4 +173,8 @@ E: Incorrect format in SNAP parameter file
|
|||
|
||||
Incorrect number of words per line in the parameter file.
|
||||
|
||||
E: Did not find all elements in SNAP coefficient file.
|
||||
|
||||
One or more elements listed in the pair_coeff command were not found in the coefficient file.
|
||||
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in New Issue