Refactored chemsnap input options

examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1

@@ -74,7 +74,8 @@ SNAP keyword rmin0 0.0
 SNAP keyword bzeroflag 1 
 SNAP keyword quadraticflag 0 
 SNAP keyword wselfallflag 1 
-SNAP keyword alloyflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
 
 # Setup output
 
@@ -123,20 +124,20 @@ Step Temp E_pair E_mol TotEng Press
       80    151.50217   -3.4614195            0   -3.4418745    3840.7205 
       90    177.67607    -3.464797            0   -3.4418754    3527.9794 
      100    195.30359   -3.4670717            0   -3.4418761    3300.3795 
-Loop time of 18.1983 on 1 procs for 100 steps with 512 atoms
+Loop time of 18.0803 on 1 procs for 100 steps with 512 atoms
 
-Performance: 0.237 ns/day, 101.102 hours/ns, 5.495 timesteps/s
+Performance: 0.239 ns/day, 100.446 hours/ns, 5.531 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    | 18.196     | 18.196     | 18.196     |   0.0 | 99.99
+Pair    | 18.078     | 18.078     | 18.078     |   0.0 | 99.99
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00104    | 0.00104    | 0.00104    |   0.0 |  0.01
+Comm    | 0.000979   | 0.000979   | 0.000979   |   0.0 |  0.01
-Output  | 0.000262   | 0.000262   | 0.000262   |   0.0 |  0.00
+Output  | 0.000243   | 0.000243   | 0.000243   |   0.0 |  0.00
-Modify  | 0.000576   | 0.000576   | 0.000576   |   0.0 |  0.00
+Modify  | 0.000591   | 0.000591   | 0.000591   |   0.0 |  0.00
-Other   |            | 0.000486   |            |       |  0.00
+Other   |            | 0.000469   |            |       |  0.00
 
 Nlocal:    512 ave 512 max 512 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4

@@ -74,7 +74,8 @@ SNAP keyword rmin0 0.0
 SNAP keyword bzeroflag 1 
 SNAP keyword quadraticflag 0 
 SNAP keyword wselfallflag 1 
-SNAP keyword alloyflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
 
 # Setup output
 
@@ -123,20 +124,20 @@ Step Temp E_pair E_mol TotEng Press
       80    151.54241   -3.4614247            0   -3.4418746    3847.4617 
       90    176.92084   -3.4646996            0   -3.4418755    3548.7811 
      100     193.9555   -3.4668978            0   -3.4418761    3342.8083 
-Loop time of 5.73708 on 4 procs for 100 steps with 512 atoms
+Loop time of 4.99339 on 4 procs for 100 steps with 512 atoms
 
-Performance: 0.753 ns/day, 31.873 hours/ns, 17.430 timesteps/s
+Performance: 0.865 ns/day, 27.741 hours/ns, 20.026 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.5736     | 5.5812     | 5.591      |   0.3 | 97.28
+Pair    | 4.8898     | 4.907      | 4.9329     |   0.8 | 98.27
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.14432    | 0.15366    | 0.16168    |   1.6 |  2.68
+Comm    | 0.058815   | 0.084739   | 0.1019     |   6.1 |  1.70
-Output  | 0.000187   | 0.00024775 | 0.000419   |   0.0 |  0.00
+Output  | 0.000252   | 0.00038775 | 0.000777   |   0.0 |  0.01
-Modify  | 0.000293   | 0.00038075 | 0.000582   |   0.0 |  0.01
+Modify  | 0.000262   | 0.00026675 | 0.000272   |   0.0 |  0.01
-Other   |            | 0.00161    |            |       |  0.03
+Other   |            | 0.001039   |            |       |  0.02
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 4 0 0 0 0 0 0 0 0 0

potentials/InP_JCPA2020.snapparam

@@ -10,5 +10,6 @@
     bzeroflag 1
     quadraticflag 0
     wselfallflag 1
-    alloyflag 1
+    chemflag 1
+    bnormflag 1
     

src/KOKKOS/pair_snap_kokkos_impl.h

@@ -515,7 +515,7 @@ void PairSNAPKokkos<DeviceType>::coeff(int narg, char **arg)
   Kokkos::deep_copy(d_map,h_map);
 
   snaKK = SNAKokkos<DeviceType>(rfac0,twojmax,
-                  rmin0,switchflag,bzeroflag,alloyflag,wselfallflag,nelements);
+                  rmin0,switchflag,bzeroflag,chemflag,bnormflag,wselfallflag,nelements);
   snaKK.grow_rij(0,0);
   snaKK.init();
 }
@@ -584,7 +584,7 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeNeigh,const typen
         my_sna.inside(ii,offset) = j;
         my_sna.wj(ii,offset) = d_wjelem[elem_j];
         my_sna.rcutij(ii,offset) = (radi + d_radelem[elem_j])*rcutfac;
-        if (alloyflag)
+        if (chemflag)
           my_sna.element(ii,offset) = elem_j;
         else
           my_sna.element(ii,offset) = 0;

src/KOKKOS/sna_kokkos.h

@@ -210,7 +210,7 @@ inline
   int switch_flag;
 
   // Chem snap flags
-  int alloy_flag;
+  int chem_flag;
   int bnorm_flag;
   int nelements;
   int ndoubles;

src/KOKKOS/sna_kokkos_impl.h

@@ -29,7 +29,7 @@ template<class DeviceType>
 inline
 SNAKokkos<DeviceType>::SNAKokkos(double rfac0_in,
          int twojmax_in, double rmin0_in, int switch_flag_in, int bzero_flag_in,
-         int alloy_flag_in, int wselfall_flag_in, int nelements_in)
+         int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in)
 {
   wself = 1.0;
 
@@ -38,13 +38,13 @@ SNAKokkos<DeviceType>::SNAKokkos(double rfac0_in,
   switch_flag = switch_flag_in;
   bzero_flag = bzero_flag_in;
 
-  alloy_flag = alloy_flag_in;
+  chem_flag = chem_flag_in;
-  wselfall_flag = wselfall_flag_in;
+  if (chem_flag)
-  if (alloy_flag)
     nelements = nelements_in;
   else
     nelements = 1;
-  bnorm_flag = alloy_flag_in;
+  bnorm_flag = bnorm_flag_in;
+  wselfall_flag = wselfall_flag_in;
 
   twojmax = twojmax_in;
 
@@ -283,7 +283,7 @@ void SNAKokkos<DeviceType>::pre_ui(const typename Kokkos::TeamPolicy<DeviceType>
       // if m is on the "diagonal", initialize it with the self energy.
       // Otherwise zero it out
       SNAcomplex init = {0., 0.};
-      if (m % (j+2) == 0 && (!alloy_flag || ielem == jelem || wselfall_flag)) { init = {wself, 0.0}; } //need to map iatom to element
+      if (m % (j+2) == 0 && (!chem_flag || ielem == jelem || wselfall_flag)) { init = {wself, 0.0}; } //need to map iatom to element
 
       ulisttot(jelem*idxu_max+jjup, iatom) = init;
     });
@@ -1620,7 +1620,7 @@ int SNAKokkos<DeviceType>::compute_ncoeff()
 
   ndoubles = nelements*nelements;
   ntriples = nelements*nelements*nelements;
-  if (alloy_flag) ncount *= ntriples;
+  if (chem_flag) ncount *= ntriples;
 
   return ncount;
 }

src/SNAP/compute_sna_atom.cpp

@@ -34,7 +34,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
   radelem(NULL), wjelem(NULL)
 {
   double rmin0, rfac0;
-  int twojmax, switchflag, bzeroflag, bnormflag;
+  int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
   radelem = NULL;
   wjelem = NULL;
 
@@ -50,7 +50,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
   bzeroflag = 1;
   bnormflag = 0;
   quadraticflag = 0;
-  alloyflag = 0;
+  chemflag = 0;
+  bnormflag = 0;
   wselfallflag = 0;
   nelements = 1;
 
@@ -108,11 +109,10 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Illegal compute sna/atom command");
       quadraticflag = atoi(arg[iarg+1]);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"alloy") == 0) {
+    } else if (strcmp(arg[iarg],"chem") == 0) {
       if (iarg+2+ntypes > narg)
         error->all(FLERR,"Illegal compute sna/atom command");
-      alloyflag = 1;
+      chemflag = 1;
-      bnormflag = alloyflag;
       memory->create(map,ntypes+1,"compute_sna_atom:map");
       nelements = force->inumeric(FLERR,arg[iarg+1]);
       for(int i = 0; i < ntypes; i++) {
@@ -123,6 +123,11 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
         map[i+1] = jelem;
       }
       iarg += 2+ntypes;
+    } else if (strcmp(arg[iarg],"bnormflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute sna/atom command");
+      bnormflag = atoi(arg[iarg+1]);
+      iarg += 2;
     } else if (strcmp(arg[iarg],"wselfall") == 0) {
       if (iarg+2 > narg)
         error->all(FLERR,"Illegal compute sna/atom command");
@@ -133,7 +138,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
 
   snaptr = new SNA(lmp, rfac0, twojmax,
                    rmin0, switchflag, bzeroflag,
-                   alloyflag, wselfallflag, nelements);
+                   chemflag, bnormflag, wselfallflag, nelements);
 
   ncoeff = snaptr->ncoeff;
   size_peratom_cols = ncoeff;
@@ -229,7 +234,7 @@ void ComputeSNAAtom::compute_peratom()
       const double ztmp = x[i][2];
       const int itype = type[i];
       int ielem = 0;
-      if (alloyflag)
+      if (chemflag)
         ielem = map[itype];
       const double radi = radelem[itype];
       const int* const jlist = firstneigh[i];
@@ -254,7 +259,7 @@ void ComputeSNAAtom::compute_peratom()
         const double rsq = delx*delx + dely*dely + delz*delz;
         int jtype = type[j];
         int jelem = 0;
-        if (alloyflag)
+        if (chemflag)
           int jelem = map[jtype];
         if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
           snaptr->rij[ninside][0] = delx;

src/SNAP/compute_sna_atom.h

@@ -43,7 +43,7 @@ class ComputeSNAAtom : public Compute {
   double *radelem;
   double *wjelem;
   int * map;  // map types to [0,nelements)
-  int nelements, alloyflag, wselfallflag;
+  int nelements, chemflag;
   class SNA* snaptr;
   double cutmax;
   int quadraticflag;

src/SNAP/compute_snad_atom.cpp

@@ -34,7 +34,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
   radelem(NULL), wjelem(NULL)
 {
   double rfac0, rmin0;
-  int twojmax, switchflag, bzeroflag, bnormflag;
+  int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
   radelem = NULL;
   wjelem = NULL;
 
@@ -50,7 +50,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
   bzeroflag = 1;
   bnormflag = 0;
   quadraticflag = 0;
-  alloyflag = 0;
+  chemflag = 0;
+  bnormflag = 0;
   wselfallflag = 0;
   nelements = 1;
 
@@ -106,11 +107,10 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Illegal compute snad/atom command");
       quadraticflag = atoi(arg[iarg+1]);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"alloy") == 0) {
+    } else if (strcmp(arg[iarg],"chem") == 0) {
       if (iarg+2+ntypes > narg)
         error->all(FLERR,"Illegal compute snad/atom command");
-      alloyflag = 1;
+      chemflag = 1;
-      bnormflag = alloyflag;
       memory->create(map,ntypes+1,"compute_snad_atom:map");
       nelements = force->inumeric(FLERR,arg[iarg+1]);
       for(int i = 0; i < ntypes; i++) {
@@ -131,7 +131,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
 
   snaptr = new SNA(lmp, rfac0, twojmax,
                    rmin0, switchflag, bzeroflag,
-                   alloyflag, wselfallflag, nelements);
+                   chemflag, bnormflag, wselfallflag, nelements);
 
   ncoeff = snaptr->ncoeff;
   nperdim = ncoeff;
@@ -241,7 +241,7 @@ void ComputeSNADAtom::compute_peratom()
       const double ztmp = x[i][2];
       const int itype = type[i];
       int ielem = 0;
-      if (alloyflag)
+      if (chemflag)
         ielem = map[itype];
       const double radi = radelem[itype];
       const int* const jlist = firstneigh[i];
@@ -272,7 +272,7 @@ void ComputeSNADAtom::compute_peratom()
         const double rsq = delx*delx + dely*dely + delz*delz;
         int jtype = type[j];
         int jelem = 0;
-        if (alloyflag)
+        if (chemflag)
             jelem = map[jtype];
         if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
           snaptr->rij[ninside][0] = delx;

src/SNAP/compute_snad_atom.h

@@ -45,7 +45,7 @@ class ComputeSNADAtom : public Compute {
   double *radelem;
   double *wjelem;
   int *map;  // map types to [0,nelements)
-  int nelements, alloyflag, wselfallflag;
+  int nelements, chemflag;
   class SNA* snaptr;
   double cutmax;
   int quadraticflag;

src/SNAP/compute_snap.cpp

@@ -41,7 +41,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   extarray = 0;
 
   double rfac0, rmin0;
-  int twojmax, switchflag, bzeroflag;
+  int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
   radelem = NULL;
   wjelem = NULL;
 
@@ -56,7 +56,8 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
   switchflag = 1;
   bzeroflag = 1;
   quadraticflag = 0;
-  alloyflag = 0;
+  chemflag = 0;
+  bnormflag = 0;
   wselfallflag = 0;
   nelements = 1;
 
@@ -112,10 +113,10 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Illegal compute snap command");
       quadraticflag = atoi(arg[iarg+1]);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"alloyflag") == 0) {
+    } else if (strcmp(arg[iarg],"chem") == 0) {
       if (iarg+2 > narg)
         error->all(FLERR,"Illegal compute snap command");
-      alloyflag = 1;
+      chemflag = 1;
       memory->create(map,ntypes+1,"compute_snap:map");
       nelements = force->inumeric(FLERR,arg[iarg+1]);
       for(int i = 0; i < ntypes; i++) {
@@ -126,6 +127,11 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
         map[i+1] = jelem;
       }
       iarg += 2+ntypes;
+    } else if (strcmp(arg[iarg],"bnormflag") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute snap command");
+      bnormflag = atoi(arg[iarg+1]);
+      iarg += 2;
     } else if (strcmp(arg[iarg],"wselfallflag") == 0) {
       if (iarg+2 > narg)
         error->all(FLERR,"Illegal compute snap command");
@@ -136,7 +142,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
 
   snaptr = new SNA(lmp, rfac0, twojmax,
                    rmin0, switchflag, bzeroflag,
-                   alloyflag, wselfallflag, nelements);
+                   chemflag, bnormflag, wselfallflag, nelements);
 
   ncoeff = snaptr->ncoeff;
   nperdim = ncoeff;
@@ -168,7 +174,7 @@ ComputeSnap::~ComputeSnap()
   memory->destroy(cutsq);
   delete snaptr;
 
-  if (alloyflag) memory->destroy(map);
+  if (chemflag) memory->destroy(map);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -300,7 +306,7 @@ void ComputeSnap::compute_array()
       const double ztmp = x[i][2];
       const int itype = type[i];
       int ielem = 0;
-      if (alloyflag)
+      if (chemflag)
         ielem = map[itype];
       const double radi = radelem[itype];
       const int* const jlist = firstneigh[i];
@@ -328,7 +334,7 @@ void ComputeSnap::compute_array()
         const double rsq = delx*delx + dely*dely + delz*delz;
         int jtype = type[j];
         int jelem = 0;
-        if (alloyflag)
+        if (chemflag)
           jelem = map[jtype];
         if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
           snaptr->rij[ninside][0] = delx;

src/SNAP/compute_snap.h

@@ -45,7 +45,7 @@ class ComputeSnap : public Compute {
   double *radelem;
   double *wjelem;
   int *map;  // map types to [0,nelements)
-  int nelements, alloyflag, wselfallflag;
+  int nelements, chemflag;
   class SNA* snaptr;
   double cutmax;
   int quadraticflag;

src/SNAP/compute_snav_atom.cpp

@@ -33,7 +33,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
   radelem(NULL), wjelem(NULL)
 {
   double rfac0, rmin0;
-  int twojmax, switchflag, bzeroflag, bnormflag;
+  int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
   radelem = NULL;
   wjelem = NULL;
 
@@ -49,7 +49,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
   bzeroflag = 1;
   bnormflag = 0;
   quadraticflag = 0;
-  alloyflag = 0;
+  chemflag = 0;
+  bnormflag = 0;
   wselfallflag = 0;
   nelements = 1;
 
@@ -101,11 +102,10 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Illegal compute snav/atom command");
       quadraticflag = atoi(arg[iarg+1]);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"alloy") == 0) {
+    } else if (strcmp(arg[iarg],"chem") == 0) {
       if (iarg+2+ntypes > narg)
         error->all(FLERR,"Illegal compute sna/atom command");
-      alloyflag = 1;
+      chemflag = 1;
-      bnormflag = alloyflag;
       memory->create(map,ntypes+1,"compute_sna_atom:map");
       nelements = force->inumeric(FLERR,arg[iarg+1]);
       for(int i = 0; i < ntypes; i++) {
@@ -126,7 +126,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
 
   snaptr = new SNA(lmp, rfac0, twojmax,
                    rmin0, switchflag, bzeroflag,
-                   alloyflag, wselfallflag, nelements);
+                   chemflag, bnormflag, wselfallflag, nelements);
 
   ncoeff = snaptr->ncoeff;
   nperdim = ncoeff;
@@ -236,7 +236,7 @@ void ComputeSNAVAtom::compute_peratom()
       const double ztmp = x[i][2];
       const int itype = type[i];
       int ielem = 0;
-      if (alloyflag)
+      if (chemflag)
         ielem = map[itype];
       const double radi = radelem[itype];
 
@@ -265,7 +265,7 @@ void ComputeSNAVAtom::compute_peratom()
         const double rsq = delx*delx + dely*dely + delz*delz;
         int jtype = type[j];
         int jelem = 0;
-        if (alloyflag)
+        if (chemflag)
           jelem = map[jtype];
         if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
           snaptr->rij[ninside][0] = delx;

src/SNAP/compute_snav_atom.h

@@ -45,7 +45,7 @@ class ComputeSNAVAtom : public Compute {
   double *radelem;
   double *wjelem;
   int *map;  // map types to [0,nelements)
-  int nelements, alloyflag, wselfallflag;
+  int nelements, chemflag;
   class SNA* snaptr;
   int quadraticflag;
 };

src/SNAP/pair_snap.cpp

@@ -156,14 +156,14 @@ void PairSNAP::compute(int eflag, int vflag)
         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;
         ninside++;
       }
     }
 
     // compute Ui, Yi for atom I
 
-    if (alloyflag)
+    if (chemflag)
       snaptr->compute_ui(ninside, ielem);
     else
       snaptr->compute_ui(ninside, 0);
@@ -176,7 +176,7 @@ void PairSNAP::compute(int eflag, int vflag)
 
     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
@@ -328,17 +328,17 @@ void PairSNAP::compute_bispectrum()
         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;
         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);
@@ -418,7 +418,6 @@ void PairSNAP::coeff(int narg, char **arg)
     ncoeffq = (ncoeff*(ncoeff+1))/2;
     int ntmp = 1+ncoeff+ncoeffq;
     if (ntmp != ncoeffall) {
-      printf("ncoeffall = %d ntmp = %d ncoeff = %d \n",ncoeffall,ntmp,ncoeff);
       error->all(FLERR,"Incorrect SNAP coeff file");
     }
   }
@@ -461,7 +460,7 @@ void PairSNAP::coeff(int narg, char **arg)
 
   snaptr = new SNA(lmp, rfac0, twojmax,
                    rmin0, switchflag, bzeroflag,
-                   alloyflag, wselfallflag, nelements);
+                   chemflag, bnormflag, wselfallflag, nelements);
 
   if (ncoeff != snaptr->ncoeff) {
     if (comm->me == 0)
@@ -655,7 +654,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
   bzeroflag = 1;
   bnormflag = 0;
   quadraticflag = 0;
-  alloyflag = 0;
+  chemflag = 0;
+  bnormflag = 0;
   wselfallflag = 0;
   chunksize = 2000;
 
@@ -721,8 +721,10 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
       bzeroflag = atoi(keyval);
     else if (strcmp(keywd,"quadraticflag") == 0)
       quadraticflag = atoi(keyval);
-    else if (strcmp(keywd,"alloyflag") == 0)
+    else if (strcmp(keywd,"chemflag") == 0)
-      alloyflag = atoi(keyval);
+      chemflag = atoi(keyval);
+    else if (strcmp(keywd,"bnormflag") == 0)
+      bnormflag = atoi(keyval);
     else if (strcmp(keywd,"wselfallflag") == 0)
       wselfallflag = atoi(keyval);
     else if (strcmp(keywd,"chunksize") == 0)
@@ -731,8 +733,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
       error->all(FLERR,"Incorrect SNAP parameter file");
   }
 
-  bnormflag = alloyflag;
-
   if (rcutfacflag == 0 || twojmaxflag == 0)
     error->all(FLERR,"Incorrect SNAP parameter file");
 

src/SNAP/pair_snap.h

@@ -59,7 +59,7 @@ protected:
   double** bispectrum;          // bispectrum components for all atoms in list
   int *map;                     // mapping from atom types to elements
   int twojmax, switchflag, bzeroflag, bnormflag;
-  int alloyflag, wselfallflag;
+  int chemflag, wselfallflag;
   int chunksize;
   double rfac0, rmin0, wj1, wj2;
   int rcutfacflag, twojmaxflag; // flags for required parameters

src/SNAP/sna.cpp

@@ -109,7 +109,7 @@ using namespace MathConst;
 
 SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
          double rmin0_in, int switch_flag_in, int bzero_flag_in,
-         int alloy_flag_in, int wselfall_flag_in, int nelements_in) : Pointers(lmp)
+         int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in) : Pointers(lmp)
 {
   wself = 1.0;
 
@@ -117,11 +117,15 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
   rmin0 = rmin0_in;
   switch_flag = switch_flag_in;
   bzero_flag = bzero_flag_in;
-  bnorm_flag = alloy_flag_in;
+  chem_flag = chem_flag_in;
-  alloy_flag = alloy_flag_in;
+  bnorm_flag = bnorm_flag_in;
   wselfall_flag = wselfall_flag_in;
 
-  if (alloy_flag)
+  if (bnorm_flag != chem_flag)
+    lmp->error->warning(FLERR, "bnormflag and chemflag are not equal."
+                        "This is probably not what you intended");
+
+  if (chem_flag)
     nelements = nelements_in;
   else
     nelements = 1;
@@ -351,7 +355,7 @@ void SNA::compute_ui(int jnum, int ielem)
     z0 = r / tan(theta0);
 
     compute_uarray(x, y, z, z0, r, j);
-    if (alloy_flag)
+    if (chem_flag)
       add_uarraytot(r, wj[j], rcutij[j], j, element[j]);
     else
       add_uarraytot(r, wj[j], rcutij[j], j, 0);
@@ -1688,7 +1692,7 @@ void SNA::compute_ncoeff()
 
   ndoubles = nelements*nelements;
   ntriples = nelements*nelements*nelements;
-  if (alloy_flag)
+  if (chem_flag)
     ncoeff = ncount*ntriples;
   else
     ncoeff = ncount;

src/SNAP/sna.h

@@ -33,7 +33,7 @@ struct SNA_BINDICES {
 class SNA : protected Pointers {
 
 public:
-  SNA(LAMMPS*, double, int, double, int, int, int, int, int);
+  SNA(LAMMPS*, double, int, double, int, int, int, int, int, int);
 
   SNA(LAMMPS* lmp) : Pointers(lmp) {};
   ~SNA();
@@ -129,7 +129,7 @@ private:
   int bzero_flag; // 1 if bzero subtracted from barray
   double* bzero;  // array of B values for isolated atoms
   int bnorm_flag; // 1 if barray divided by j+1
-  int alloy_flag; // 1 for multi-element bispectrum components
+  int chem_flag; // 1 for multi-element bispectrum components
   int wselfall_flag; // 1 for adding wself to all element labelings
   int nelements;  // number of elements
   int ndoubles;   // number of multi-element pairs