Support predefined valences in BVParametersTable.

Add methods getAtomValence, setAtomValence, resetAtomValences to
extract valence from atom or ion symbol.  Adjust serialization
to store these custom valences.

Author: pavoljuhas

src/diffpy/srreal/BVParametersTable.cpp

@@ -41,6 +41,26 @@ const BVParam& BVParametersTable::none()
 
 // Public Methods ------------------------------------------------------------
 
+int BVParametersTable::getAtomValence(const string& smbl) const
+{
+    AtomTypeValence::const_iterator ii = matomvalence.find(smbl);
+    int rv = (ii != matomvalence.end()) ? ii->second : atomValence(smbl);
+    return rv;
+}
+
+
+void BVParametersTable::setAtomValence(const string& smbl, int value)
+{
+    matomvalence[smbl] = value;
+}
+
+
+void BVParametersTable::resetAtomValences()
+{
+    matomvalence.clear();
+}
+
+
 const BVParam& BVParametersTable::lookup(const BVParam& bpk) const
 {
     SetOfBVParam::const_iterator bpit;
@@ -66,9 +86,11 @@ const BVParam& BVParametersTable::lookup(const BVParam& bpk) const
 const BVParam&
 BVParametersTable::lookup(const string& smbl0, const string& smbl1) const
 {
+    const int v0 = this->getAtomValence(smbl0);
+    const int v1 = this->getAtomValence(smbl1);
     const BVParam& rv = this->lookup(
-            atomBareSymbol(smbl0), atomValence(smbl0),
-            atomBareSymbol(smbl1), atomValence(smbl1));
+            atomBareSymbol(smbl0), v0,
+            atomBareSymbol(smbl1), v1);
     return rv;
 }
 

src/diffpy/srreal/BVParametersTable.hpp

@@ -82,11 +82,18 @@ class BVParametersTable
             void serialize(Archive& ar, const unsigned int version)
         {
             ar & mcustomtable;
+            if (version >= 1) {
+                ar & matomvalence;
+            }
         }
 
 };  // class BVParametersTable
 
 }   // namespace srreal
 }   // namespace diffpy
 
+// Serialization -------------------------------------------------------------
+
+BOOST_CLASS_VERSION(diffpy::srreal::BVParametersTable, 1)
+
 #endif  // BVPARAMETERSTABLE_HPP_INCLUDED

src/tests/TestBVParametersTable.hpp

@@ -70,6 +70,16 @@ class TestBVParametersTable : public CxxTest::TestSuite
         }
 
 
+        void test_atomvalence()
+        {
+            TS_ASSERT_EQUALS(0, mbvtb->getAtomValence("O"));
+            mbvtb->setAtomValence("O", -2);
+            TS_ASSERT_EQUALS(-2, mbvtb->getAtomValence("O"));
+            mbvtb->resetAtomValences();
+            TS_ASSERT_EQUALS(0, mbvtb->getAtomValence("O"));
+        }
+
+
         void test_lookup()
         {
             BVParam bp = mbvtb->lookup("Xx", 0, "Yy", 3);
@@ -90,6 +100,11 @@ class TestBVParametersTable : public CxxTest::TestSuite
             const BVParam& bnacl0 = mbvtb->lookup("Na", 1, "Cl", -1);
             TS_ASSERT_EQUALS(&bnacl0, &mbvtb->lookup("Na+", "Cl-"));
             TS_ASSERT_EQUALS(&bnacl0, &mbvtb->lookup("Cl1-", "Na1+"));
+            const BVParam& bpnone = BVParametersTable::none();
+            TS_ASSERT_EQUALS(&bpnone, &mbvtb->lookup("Na", "Cl"));
+            mbvtb->setAtomValence("Na", +1);
+            mbvtb->setAtomValence("Cl", -1);
+            TS_ASSERT_EQUALS(&bnacl0, &mbvtb->lookup("Na", "Cl"));
         }
 
 
@@ -201,6 +216,13 @@ class TestBVParametersTable : public CxxTest::TestSuite
             BVParametersTable tb2 = dumpandload(*mbvtb);
             TS_ASSERT_EQUALS(2u, tb2.getAllCustom().size());
             TS_ASSERT_EQUALS(mynacl, tb2.lookup("Cl-", "Na+"));
+            // check serialization of customized valences
+            tb2.setAtomValence("Na", 1);
+            tb2.setAtomValence("Cl", -1);
+            BVParametersTable tb3 = dumpandload(tb2);
+            TS_ASSERT_EQUALS(mynacl, tb3.lookup("Cl", "Na"));
+            const BVParam& bpnone = BVParametersTable::none();
+            TS_ASSERT_EQUALS(bpnone, mbvtb->lookup("Cl", "Na"));
         }
 
 };  // class TestBVParametersTable