Move find_identical_nuclei() function from guess to a proper function…

… in BasisSet

src/basis.cpp

@@ -1770,9 +1770,17 @@ arma::ivec BasisSet::get_m_values() const {
 arma::ivec BasisSet::unique_m_values() const {
   // Find unique m values
   arma::ivec mval(get_m_values());
-  arma::uvec muni_idx(arma::find_unique(mval));
-  arma::ivec muni(mval(muni_idx));
-  return arma::sort(muni);
+  arma::sword mmin=0;
+  arma::sword mmax=arma::max(arma::abs(mval));
+
+  std::vector<arma::sword> mvals;
+  mvals.push_back(0);
+  for(int am=1;am<=mmax;am++) {
+    mvals.push_back(-am);
+    mvals.push_back(am);
+  }
+
+  return arma::conv_to<arma::ivec>::from(mvals);
 }
 
 std::map<int, arma::uword> BasisSet::unique_m_map() const {
@@ -4214,3 +4222,83 @@ arma::ivec m_classify(const arma::mat & C, const arma::ivec & mv) {
 
   return oclass;
 }
+
+ std::vector< std::vector<size_t> > BasisSet::find_identical_nuclei() const {
+  // Index list
+  std::vector< std::vector<size_t> > ret;
+
+  // Loop over nuclei
+  for(size_t i=0;i<get_Nnuc();i++) {
+    // Check that nucleus isn't BSSE
+    nucleus_t nuc=get_nucleus(i);
+    if(nuc.bsse)
+      continue;
+
+    // Get the shells on the nucleus
+    std::vector<GaussianShell> shi=get_funcs(i);
+
+    // Check if there something already on the list
+    bool found=false;
+    for(size_t j=0;j<ret.size();j++) {
+      std::vector<GaussianShell> shj=get_funcs(ret[j][0]);
+
+      // Check nuclear type
+      if(get_symbol(i).compare(get_symbol(ret[j][0]))!=0)
+	continue;
+      // Check charge status
+      if(get_nucleus(i).Q != get_nucleus(ret[j][0]).Q)
+	continue;
+
+      // Do comparison
+      if(shi.size()!=shj.size())
+	continue;
+      else {
+
+	bool same=true;
+	for(size_t ii=0;ii<shi.size();ii++) {
+	  // Check angular momentum
+	  if(shi[ii].get_am()!=shj[ii].get_am()) {
+	    same=false;
+	    break;
+	  }
+
+	  // and exponents
+	  std::vector<contr_t> lhc=shi[ii].get_contr();
+	  std::vector<contr_t> rhc=shj[ii].get_contr();
+
+	  if(lhc.size() != rhc.size()) {
+	    same=false;
+	    break;
+	  }
+	  for(size_t ic=0;ic<lhc.size();ic++) {
+	    if(!(lhc[ic]==rhc[ic])) {
+	      same=false;
+	      break;
+	    }
+	  }
+
+	  if(!same)
+	    break;
+	}
+
+	if(same) {
+	  // Found identical atom.
+	  found=true;
+
+	  // Add it to the list.
+	  ret[j].push_back(i);
+	}
+      }
+    }
+
+    if(!found) {
+      // Didn't find the atom, add it to the list.
+      std::vector<size_t> tmp;
+      tmp.push_back(i);
+
+      ret.push_back(tmp);
+    }
+  }
+
+  return ret;
+}

src/basis.h

@@ -496,6 +496,8 @@ class BasisSet {
 
   /// Find "identical" shells in basis set.
   std::vector< std::vector<size_t> > find_identical_shells() const;
+  /// Find "identical" nuclei
+  std::vector< std::vector<size_t> > find_identical_nuclei() const;
 };
 
 /// Compute three-center overlap integral

src/guess.cpp

@@ -180,7 +180,7 @@ arma::mat atomic_guess_wrk(const BasisSet & basis, atomic_guess_t type, double K
   // the way that the basis sets coincide.
 
   // Get list of identical nuclei
-  std::vector< std::vector<size_t> > idnuc=identical_nuclei(basis);
+  std::vector< std::vector<size_t> > idnuc=basis.find_identical_nuclei();
 
   // Amount of basis functions is
   size_t Nbf=basis.get_Nbf();
@@ -422,85 +422,6 @@ arma::mat minimal_basis_projection(const BasisSet & basis) {
   return atomic_guess_wrk(basis,FORM_MINBAS,0.0);
 }
 
-std::vector< std::vector<size_t> > identical_nuclei(const BasisSet & basis) {
-  // Returned list
-  std::vector< std::vector<size_t> > ret;
-
-  // Loop over nuclei
-  for(size_t i=0;i<basis.get_Nnuc();i++) {
-    // Check that nucleus isn't BSSE
-    nucleus_t nuc=basis.get_nucleus(i);
-    if(nuc.bsse)
-      continue;
-
-    // Get the shells on the nucleus
-    std::vector<GaussianShell> shi=basis.get_funcs(i);
-
-    // Check if there something already on the list
-    bool found=false;
-    for(size_t j=0;j<ret.size();j++) {
-      std::vector<GaussianShell> shj=basis.get_funcs(ret[j][0]);
-
-      // Check nuclear type
-      if(basis.get_symbol(i).compare(basis.get_symbol(ret[j][0]))!=0)
-	continue;
-      // Check charge status
-      if(basis.get_nucleus(i).Q != basis.get_nucleus(ret[j][0]).Q)
-	continue;
-
-      // Do comparison
-      if(shi.size()!=shj.size())
-	continue;
-      else {
-
-	bool same=true;
-	for(size_t ii=0;ii<shi.size();ii++) {
-	  // Check angular momentum
-	  if(shi[ii].get_am()!=shj[ii].get_am()) {
-	    same=false;
-	    break;
-	  }
-
-	  // and exponents
-	  std::vector<contr_t> lhc=shi[ii].get_contr();
-	  std::vector<contr_t> rhc=shj[ii].get_contr();
-
-	  if(lhc.size() != rhc.size()) {
-	    same=false;
-	    break;
-	  }
-	  for(size_t ic=0;ic<lhc.size();ic++) {
-	    if(!(lhc[ic]==rhc[ic])) {
-	      same=false;
-	      break;
-	    }
-	  }
-
-	  if(!same)
-	    break;
-	}
-
-	if(same) {
-	  // Found identical atom.
-	  found=true;
-
-	  // Add it to the list.
-	  ret[j].push_back(i);
-	}
-      }
-    }
-
-    if(!found) {
-      // Didn't find the atom, add it to the list.
-      std::vector<size_t> tmp;
-      tmp.push_back(i);
-
-      ret.push_back(tmp);
-    }
-  }
-
-  return ret;
-}
 
 
 bool operator<(const el_conf_t & lhs, const el_conf_t & rhs) {

src/guess.h

@@ -72,9 +72,6 @@ arma::mat minimal_basis_projection(const BasisSet & basis);
  */
 void atomic_guess(const BasisSet & basis, size_t inuc, const std::string & method, std::vector<size_t> & shellidx, BasisSet & atbas, arma::vec & atE, arma::mat & atC, arma::mat & atP, arma::mat & atF, int Q);
 
-/// Determine list of identical nuclei, determined by nucleus and basis set
-std::vector< std::vector<size_t> > identical_nuclei(const BasisSet & basis);
-
 /// Electronic configuration
 typedef struct {
   /// Primary quantum number

src/hirshfeld.cpp

@@ -132,7 +132,7 @@ void Hirshfeld::compute(const BasisSet & basis, std::string method) {
   atoms.resize(basis.get_Nnuc());
 
   // Get list of identical nuclei
-  std::vector< std::vector<size_t> > idnuc=identical_nuclei(basis);
+  std::vector< std::vector<size_t> > idnuc=basis.find_identical_nuclei();
 
   // Loop over list of identical nuclei
   for(size_t i=0;i<idnuc.size();i++) {

src/hirshfeldi.cpp

@@ -45,7 +45,7 @@ void HirshfeldI::compute(const BasisSet & basis, const arma::mat & P, std::strin
   atQ.resize(basis.get_Nnuc());
 
   // Get list of identical nuclei
-  std::vector< std::vector<size_t> > idnuc=identical_nuclei(basis);
+  std::vector< std::vector<size_t> > idnuc=basis.find_identical_nuclei();
 
   Timer t;
   if(verbose)