Removed redundant element list from pair_coeff snap syntax

doc/src/pair_snap.txt

@@ -16,7 +16,7 @@ pair_style snap :pre
 [Examples:]
 
 pair_style snap
-pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
+pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
 
 [Description:]
 
@@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
 the SNAP potential files themselves.
 
 Only a single pair_coeff command is used with the {snap} style which
-specifies two SNAP files and the list SNAP element(s) to be
+specifies a SNAP coefficient file followed by a SNAP parameter file
-extracted.
+and then N additional arguments specifying the mapping of SNAP
-The SNAP elements are mapped to LAMMPS atom types by specifying
+elements to LAMMPS atom types, where N is the number of 
-N additional arguments after the 2nd filename in the pair_coeff
+LAMMPS atom types:
-command, where N is the number of LAMMPS atom types:
 
-SNAP element file
+SNAP coefficient file
-Elem1, Elem2, ...
 SNAP parameter file
 N element names = mapping of SNAP elements to atom types :ul
 
@@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
 types, with the first two being indium and the 3rd and 4th being
 phophorous, the pair_coeff command would look like this:
 
-pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
+pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
 
 The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The two filenames are for the element and parameter files, respectively.
+The two filenames are for the coefficient and parameter files, respectively.
-The 'In' and 'P' arguments (between the file names) are the two elements
+The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
-which will be extracted from the element file. The
-two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
 SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
 3 and 4 to the SNAP 'P' element.
 
@@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
 {hybrid} pair style.  The NULL values are placeholders for atom types
 that will be used with other potentials.
 
-The name of the SNAP element file usually ends in the
+The name of the SNAP coefficient file usually ends in the
 ".snapcoeff" extension. It may contain coefficients
-for many SNAP elements.
+for many SNAP elements. The only requirement is that it
-Only those elements listed in the pair_coeff command are extracted.
+contain at least those element names appearing in the
+LAMMPS mapping list. 
 The name of the SNAP parameter file usually ends in the ".snapparam"
 extension. It contains a small number
 of parameters that define the overall form of the SNAP potential.
@@ -110,8 +107,7 @@ It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the "include"_include.html
 command.
 
-The top of the SNAP element file can contain any number of blank and comment
+The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
-lines (start with #), but follows a strict
 format after that. The first non-blank non-comment
 line must contain two integers:
 

examples/snap/Mo_Chen_PRM2017.snap

@@ -1,7 +0,0 @@
-
-# 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)
-# Generated by Materials Virtual Lab
-# Definition of SNAP potential.
-pair_style snap
-pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
-

examples/snap/Mo_Chen_PRM2017.snap

@@ -0,0 +1 @@
+../../potentials/Mo_Chen_PRM2017.snap

examples/snap/Mo_Chen_PRM2017.snapcoeff

@@ -1,35 +0,0 @@
-# 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)
-# Generated by Materials Virtual Lab
-1 31
-Mo 0.5 1
--17.2757958404
-0.00431015861472
-0.0657685117891
-0.477733335702
-0.0152688837211
-0.77559888196
-0.284846429566
-0.148804982644
-0.0573702179736
-0.19281989434
-0.323441703578
-0.101324335724
-0.0139639846514
--0.0324444749083
-0.0349797952779
-0.0613023441282
-0.0881078513046
-0.118716074611
-0.0069662975532
--0.0174658914685
--0.0178902177779
-0.0195993756659
-0.0719238160707
-0.0344832661036
--0.0358616891662
--0.0292380783172
--0.0334933909866
-0.00595462520243
-0.0754556638328
--0.000972545258845
--0.0100170422751

examples/snap/Mo_Chen_PRM2017.snapcoeff

@@ -0,0 +1 @@
+../../potentials/Mo_Chen_PRM2017.snapcoeff

examples/snap/Mo_Chen_PRM2017.snapparam

@@ -1,4 +0,0 @@
-# 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)
-# Generated by Materials Virtual Lab
-rcutfac 4.615858
-twojmax 6

examples/snap/Mo_Chen_PRM2017.snapparam

@@ -0,0 +1 @@
+../../potentials/Mo_Chen_PRM2017.snapparam

examples/snap/Ta06A.snap

@@ -1,17 +0,0 @@
-# DATE: 2014-09-05 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} &
-snap
-pair_coeff 1 1 zbl ${zblz} ${zblz}
-pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
-

examples/snap/Ta06A.snap

@@ -0,0 +1 @@
+../../potentials/Ta06A.snap

examples/snap/Ta06A.snapcoeff

@@ -1,37 +0,0 @@
-# DATE: 2014-09-05 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 31
-Ta 0.5 1
--2.92477
--0.01137
--0.00775
--0.04907
--0.15047
-0.09157
-0.05590
-0.05785
--0.11615
--0.17122
--0.10583
-0.03941
--0.11284
-0.03939
--0.07331
--0.06582
--0.09341
--0.10587
--0.15497
-0.04820
-0.00205
-0.00060
--0.04898
--0.05084
--0.03371
--0.01441
--0.01501
--0.00599
--0.06373
-0.03965
-0.01072

examples/snap/Ta06A.snapcoeff

@@ -0,0 +1 @@
+../../potentials/Ta06A.snapcoeff

examples/snap/Ta06A.snapparam

@@ -1,15 +0,0 @@
-# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) 
-
-# LAMMPS SNAP parameters for Ta_Cand06A
-
-# required
-rcutfac 4.67637
-twojmax 6
-
-# optional
-
-rfac0 0.99363
-rmin0 0
-diagonalstyle 3
-bzeroflag 0
-quadraticflag 0

examples/snap/Ta06A.snapparam

@@ -0,0 +1 @@
+../../potentials/Ta06A.snapparam

examples/snap/W_2940_2017_2.snap

@@ -1,16 +0,0 @@
-# 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]
-#
-# 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_coeff 1 1 zbl ${zblz} ${zblz}
-pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
-
-#Nomenclature on the snap files are Element_DakotaID_Year_Month

examples/snap/W_2940_2017_2.snap

@@ -0,0 +1 @@
+../../potentials/W_2940_2017_2.snap

examples/snap/W_2940_2017_2.snapcoeff

@@ -1,62 +0,0 @@
-# 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]
-# 
-# LAMMPS SNAP coefficients for W
-
-1 56
-W 0.5 1
-  0.781170857801
- -0.001794941735
- -0.016628679036
- -0.066625537037
- -0.073716343967
- -0.062913923923
-  0.032552694672
- -0.134901744419
- -0.075076334103
- -0.148558616547
- -0.140808831101
- -0.166749145704
- -0.047487675984
- -0.049892090603
- -0.032483739965
- -0.114766534860
- -0.106759718242
- -0.125894850485
- -0.103409735225
- -0.095247335447
- -0.061998736346
- -0.053895610976
- -0.010799734206
- -0.011644828900
- -0.028316826924
-  0.011176085541
-  0.064619474684
- -0.023886279996
- -0.004099224312
- -0.056084222496
- -0.035551497650
- -0.056678501024
- -0.004905851656
- -0.015701146162
- -0.008462280779
-  0.016429018676
-  0.032432633993
- -0.010805361272
- -0.014841893457
-  0.019414134562
- -0.008112452759
- -0.002700775447
-  0.007032887063
- -0.009706065042
-  0.008385967833
-  0.028606085876
- -0.007003591067
-  0.006467260152
- -0.006666986361
-  0.029243285316
-  0.002477673872
- -0.000199497504
-  0.004068954075
-  0.006036129972
- -0.013010633924
- -0.008314173699

examples/snap/W_2940_2017_2.snapcoeff

@@ -0,0 +1 @@
+../../potentials/W_2940_2017_2.snapcoeff

examples/snap/W_2940_2017_2.snapparam

@@ -1,13 +0,0 @@
-# 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]
-# 
-# required
-rcutfac 4.73442
-twojmax 8
-
-# optional
-
-rfac0 0.99363
-rmin0 0
-diagonalstyle 3
-bzeroflag 0
-quadraticflag 0

examples/snap/W_2940_2017_2.snapparam

@@ -0,0 +1 @@
+../../potentials/W_2940_2017_2.snapparam

examples/snap/W_2940_2017_2_He_JW2013.snap

@@ -1,17 +0,0 @@
-# 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]
-#
-# Definition of SNAP+ZBL+Tabulated 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 table spline 10000 table spline 10000
-pair_coeff 	1 1 zbl ${zblz} ${zblz}
-pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
-pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
-pair_coeff      1 2 table 2 W_He_JW2013.table WHe
-#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
-#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
-

examples/snap/W_2940_2017_2_He_JW2013.snap

@@ -0,0 +1 @@
+../../potentials/W_2940_2017_2_He_JW2013.snap

potentials/Mo_Chen_PRM2017.snap

@@ -1,6 +1,7 @@
+
 # 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)
 # Generated by Materials Virtual Lab
 # Definition of SNAP potential.
 pair_style snap
-pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
 

potentials/Ta06A.snap

@@ -13,5 +13,5 @@ pair_style hybrid/overlay &
 zbl ${zblcutinner} ${zblcutouter} &
 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
-pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
+pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 

potentials/Ta06A.snapparam

@@ -8,7 +8,8 @@ twojmax 6
 
 # optional
 
-gamma 1
 rfac0 0.99363
 rmin0 0
 diagonalstyle 3
+bzeroflag 0
+quadraticflag 0

potentials/W_2940_2017_2.snap

@@ -5,12 +5,12 @@ variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay &
 zbl ${zblcutinner} ${zblcutouter} &
 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
-pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
 
 #Nomenclature on the snap files are Element_DakotaID_Year_Month

potentials/W_2940_2017_2.snapparam

@@ -6,7 +6,8 @@ twojmax 8
 
 # optional
 
-gamma 1
 rfac0 0.99363
 rmin0 0
 diagonalstyle 3
+bzeroflag 0
+quadraticflag 0

potentials/W_2940_2017_2_He_JW2013.snap

@@ -5,11 +5,11 @@ variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 74
 
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
 
 pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
 pair_coeff 	1 1 zbl ${zblz} ${zblz}
-pair_coeff      * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
+pair_coeff 	* * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
 pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
 pair_coeff      1 2 table 2 W_He_JW2013.table WHe
 #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here

src/SNAP/pair_snap.cpp

@@ -1416,11 +1416,7 @@ void PairSNAP::settings(int narg, char **arg)
 
 void PairSNAP::coeff(int narg, char **arg)
 {
-  // read SNAP element names between 2 filenames
+  if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients");
-  // nelements = # of SNAP elements
-  // elements = list of unique element names
-
-  if (narg < 6) 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];
-  char* paramfilename = arg[3+nelements];
+  char** elemtypes = &arg[4];
-  char** elemtypes = &arg[4+nelements];
 
   // 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];
+  // Loop over nelements blocks in the SNAP coefficient file
-  for (int ielem = 0; ielem < nelements; ielem++)
-    found[ielem] = 0;
 
-  // Loop over elements in the SNAP coefficient file
+  for (int ielem = 0; ielem < nelements; ielem++) {
-
-  for (int ielemfile = 0; ielemfile < nelemfile; ielemfile++) {
 
     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]);
+    int n = strlen(elemtmp) + 1;
-    double wjtmp = atof(words[2]);
+    elements[ielem] = new char[n];
+    strcpy(elements[ielem],elemtmp);
 
-    // skip if element name isn't in element list
+    radelem[ielem] = atof(words[1]);
-
+    wjelem[ielem] = atof(words[2]);
-    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;
 
 
     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;
 }
 
 /* ----------------------------------------------------------------------

src/SNAP/pair_snap.h

@@ -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.
+
 */