convert e3b and srp

doc/src/pair_e3b.rst

@@ -50,8 +50,9 @@ Examples
    pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
    pair_coeff * * e3b preset 2011
 
-   labelmap atom 1 C 2 H 3 O 4 N 5 OW 6 HW
    pair_style e3b OW
+   labelmap atom 1 C 2 H 3 O 4 N 5 OW 6 HW
+   pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572
 
 Used in example input script:
 
@@ -105,6 +106,11 @@ atom type is inferred from the ordering of the atoms.
    Each water molecule must have consecutive IDs with the oxygen first.
    This pair style does not test that this criteria is met.
 
+.. note::
+
+   If using type labels, the type labels must be defined before calling
+   the :doc:`pair_coeff <pair_coeff>` command.
+
 The *pair_coeff* command must have at least one keyword/value pair, as
 described above.  The *preset* keyword sets the potential parameters to
 the values used in :ref:`(Tainter 2011) <Tainter2011>` or

doc/src/pair_srp.rst

@@ -23,7 +23,7 @@ Syntax
 
   .. parsed-literal::
 
-       *bptype* value = atom type for bond particles
+       *bptype* value = atom type (numeric or type label) for bond particles
        *exclude* value = *yes* or *no*
 
 Examples
@@ -121,6 +121,11 @@ is used.
    between atom type *bptype* and all other types of atoms.  An error
    will be flagged if :doc:`pair_style hybrid <pair_hybrid>` is not used.
 
+.. note::
+
+   If using type labels, the type labels must be defined before calling
+   the :doc:`pair_coeff <pair_coeff>` command.
+
 The optional *exclude* keyword determines if forces are computed
 between first neighbor (directly connected) bonds.  For a setting of
 *no*, first neighbor forces are computed; for *yes* they are not

src/EXTRA-PAIR/pair_e3b.cpp

@@ -373,7 +373,7 @@ void PairE3B::allocateE3B()
 void PairE3B::settings(int narg, char **arg)
 {
   if (narg != 1) error->all(FLERR, "Illegal pair_style command");
-  typeO = utils::expand_type_int(FLERR, arg[0], Atom::ATOM, lmp);
+  typeO_str = arg[0];
 }
 
 /* ----------------------------------------------------------------------
@@ -387,6 +387,8 @@ void PairE3B::coeff(int narg, char **arg)
   //1=* 2=* 3/4=1st keyword/value
   if (narg < 4) error->all(FLERR, "There must be at least one keyword given to pair_coeff");
 
+  typeO = utils::expand_type_int(FLERR, typeO_str, Atom::ATOM, lmp);
+
   // clear setflag since coeff() called once with I,J = * *
   int n = atom->ntypes;
   for (int i = 1; i <= n; i++)

src/EXTRA-PAIR/pair_e3b.h

@@ -36,6 +36,7 @@ class PairE3B : public Pair {
 
  protected:
   //potential parameters
+  std::string typeO_str;
   int typeO;
   double ea, eb, ec;      //three body energies
   double k3;              //three body exponential decay (units inverse length)

src/MISC/pair_srp.cpp

@@ -353,9 +353,7 @@ void PairSRP::settings(int narg, char **arg)
   if (strcmp(arg[1],"*") == 0) {
     btype = 0;
   } else {
-    btype = utils::expand_type_int(FLERR, arg[1], Atom::BOND, lmp);
+    btype_str = arg[1];
-    if ((btype > atom->nbondtypes) || (btype <= 0))
-      error->all(FLERR,"Illegal pair_style command");
   }
 
   // settings
@@ -383,20 +381,10 @@ void PairSRP::settings(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"bptype") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
-      bptype = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
+      bptype_str = arg[iarg+1];
-      if ((bptype < 1) || (bptype > atom->ntypes))
-        error->all(FLERR,"Illegal bond particle type for srp");
       iarg += 2;
     } else error->all(FLERR,"Illegal pair srp command");
   }
-
-  // reset cutoffs if explicitly set
-  if (allocated) {
-    int i,j;
-    for (i = 1; i <= bptype; i++)
-      for (j = i; j <= bptype; j++)
-        if (setflag[i][j]) cut[i][j] = cut_global;
-  }
 }
 
 /* ----------------------------------------------------------------------
@@ -409,6 +397,22 @@ void PairSRP::coeff(int narg, char **arg)
     error->all(FLERR,"PairSRP: Incorrect args for pair coeff");
   if (!allocated) allocate();
 
+  btype = utils::expand_type_int(FLERR, btype_str, Atom::BOND, lmp);
+  if ((btype > atom->nbondtypes) || (btype <= 0))
+    error->all(FLERR,"Illegal pair_style command");
+
+  bptype = utils::expand_type_int(FLERR, bptype_str, Atom::ATOM, lmp);
+  if ((bptype < 1) || (bptype > atom->ntypes))
+    error->all(FLERR,"Illegal bond particle type for srp");
+
+  // reset cutoffs if explicitly set
+  if (allocated) {
+    int i,j;
+    for (i = 1; i <= bptype; i++)
+      for (j = i; j <= bptype; j++)
+        if (setflag[i][j]) cut[i][j] = cut_global;
+  }
+
   // set ij bond-bond cutoffs
   int ilo, ihi, jlo, jhi;
   utils::bounds(FLERR,arg[0], 1, bptype, ilo, ihi, error);

src/MISC/pair_srp.h

@@ -51,6 +51,7 @@ class PairSRP : public Pair {
   double **a0;
   double **srp;
   double cut_global;
+  std::string bptype_str, btype_str;
   int bptype;
   int btype;
   class Fix *f_srp;