Added code to use new mathkernel generated kernels.

Author: Christian Schafmeisterr

include/cando/chem/energyAngle.h

@@ -23,8 +23,6 @@ THE SOFTWARE.
 This is an open source license for the CANDO software from Temple University, but it is not the only one. Contact Temple University at mailto:[email protected] if you would like a different license.
 */
 /* -^- */
-       
-       
 
 //
 // (C) 2004 Christian E. Schafmeister
@@ -232,6 +230,9 @@ class EnergyAngle_O : public EnergyComponent_O
 
   EnergyAngle_sp copyFilter(core::T_sp keepInteractionFactory);
 
+  virtual void emitTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
+  virtual void runTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
+
   EnergyAngle_O( const EnergyAngle_O& ss ); //!< Copy constructor
 
   EnergyAngle_O() : EnergyComponent_O() {};

include/cando/chem/energyComponent.h

@@ -208,6 +208,36 @@ inline string	atomLabel(Atom_sp a)
   }
 
 
+// ----------------------------------------------------------------------
+// New kernel function accumulators
+// ----------------------------------------------------------------------
+
+
+#define KernelGradientAcc(ii1,oo1,vv1) force[ii1+oo1] += (-vv1)
+
+//
+// Accumulate an off diagonal Hessian element
+//
+#define	KernelOffDiagHessAcc(i1,o1,i2,o2,v) {\
+    auto v22 = v*dvec[i2+o2];\
+    auto v11 = v*dvec[i1+o1];\
+    hdvec[i1+o1] += v22; \
+    hdvec[i2+o2] += v11; \
+  }
+
+//
+// Accumulate a diagonal Hessian element
+//
+#define	KernelDiagHessAcc(i1,o1,i2,o2,v) {\
+      auto vd = v*dvec[i1+o1];\
+      hdvec[i1+o1] += vd; \
+  }
+
+
+// ----------------------------------------------------------------------
+// Old accumulators
+// ----------------------------------------------------------------------
+
 #define	ForceAcc(i,o,v) {\
       if ( hasForce ) {\
         force->setElement((i)+(o),(v)+force->getElement((i)+(o)));\
@@ -325,6 +355,9 @@ class EnergyComponent_O : public core::CxxObject_O
   CL_LISPIFY_NAME("energy-component-evaluations");
   CL_DEFMETHOD 	size_t	evaluations() const { return this->_Evaluations; };
 
+  CL_DEFMETHOD virtual void emitTestCalls(core::T_sp stream, chem::NVector_sp pos) const {SUBCLASS_MUST_IMPLEMENT(); };
+  CL_DEFMETHOD virtual void runTestCalls(core::T_sp stream, chem::NVector_sp pos) const {SUBCLASS_MUST_IMPLEMENT(); };
+  
   CL_DEFMETHOD virtual core::List_sp extract_vectors_as_alist() const { SUBCLASS_MUST_IMPLEMENT(); };
 
   string enabledAsString();
@@ -373,5 +406,22 @@ void copyEnergyComponent(EnergyComponent_sp newComponent, EnergyComponent_sp ori
 ;
 };
 
+namespace chem {
+
+void test_zero( size_t num,
+                double* force_new, double* force_ground,
+                double* hessian_new, double* hessian_ground,
+                double* dvec_new, double* dvec_ground,
+                double* hdvec_new, double* hdvec_ground );
+
+bool test_match( core::T_sp stream, const char* label, size_t num,
+                double* force_new, double* force_ground,
+                double* hessian_new, double* hessian_ground,
+                double* hdvec_new, double* hdvec_ground );
+
+void test_position(core::T_sp stream, size_t pos_size, double* position );
+
+
+};
 
 #endif

include/cando/chem/energyDihedral.h

@@ -317,6 +317,8 @@ class EnergyDihedral_O : public EnergyComponent_O
 
   core::List_sp lookupDihedralTerms(AtomTable_sp at, Atom_sp a1, Atom_sp a2, Atom_sp a3, Atom_sp a4, core::HashTable_sp atomTypes );
 
+  virtual void emitTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
+
   EnergyDihedral_sp copyFilter(core::T_sp keepInteractionFactory);
 
 public:

include/cando/chem/energyNonbond.h

@@ -166,6 +166,9 @@ class EnergyNonbond_O : public EnergyComponent_O
  public: // instance variables
   double		_EnergyElectrostatic;
   bool                _UsesExcludedAtoms;
+  double              _Nonbond_r_switch;
+  double              _Nonbond_r_cut;
+  double              _Nonbond_invdd; // Distance dependent dielectric reciprocal
     size_t                              _NonbondsKept;
     size_t                              _NonbondsDiscarded;
     // Original way of defining nonbonds with list of nonbond terms
@@ -194,6 +197,7 @@ class EnergyNonbond_O : public EnergyComponent_O
   core::SimpleVector_int32_t_sp   _ExcludedAtomIndexes;
   size_t _InteractionsKept;
   size_t _InteractionsDiscarded;
+
  public:
   typedef gctools::Vec0<TermType>::iterator iterator;
   iterator begin() { return this->_Terms.begin(); };
@@ -205,6 +209,9 @@ class EnergyNonbond_O : public EnergyComponent_O
   void callForEachTerm(core::Function_sp callback);
  public:
 
+  void runTestCalls(core::T_sp stream, chem::NVector_sp coords) const;
+  void set_nonbond_pairlist_parameters(double r_switch, double r_cut, double distance_dielectric);
+
   CL_DEFMETHOD core::SimpleVector_int32_t_sp number_excluded_atoms() const { return this->_NumberOfExcludedAtomIndexes;}
   CL_DEFMETHOD core::SimpleVector_int32_t_sp excluded_atom_list() const { return this->_ExcludedAtomIndexes;}
  public:
@@ -275,11 +282,17 @@ class EnergyNonbond_O : public EnergyComponent_O
   void setNonbondExcludedAtomInfo(AtomTable_sp atom_table, core::SimpleVector_int32_t_sp excluded_atoms_list, core::SimpleVector_int32_t_sp number_excluded_atoms);
   void checkEnergyNonbond();
   EnergyNonbond_sp copyFilter(core::T_sp keepInteractionFactory);
+
+  virtual void emitTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
+
  public:
   EnergyNonbond_O( const EnergyNonbond_O& ss ); //!< Copy constructor
 
   EnergyNonbond_O() :
       _UsesExcludedAtoms(true),
+      _Nonbond_r_switch(10.0),
+      _Nonbond_r_cut(12.0),
+      _Nonbond_invdd(1.0),
       _FFNonbondDb(nil<core::T_O>()),
       _InteractionsKept(0),
       _InteractionsDiscarded(0)

include/cando/chem/energyStretch.h

@@ -192,6 +192,8 @@ class EnergyStretch_O : public EnergyComponent_O
     virtual void setupHessianPreconditioner(NVector_sp nvPosition,
 					    AbstractLargeSquareMatrix_sp m,
                                             core::T_sp activeAtomMask);
+  virtual void emitTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
+  virtual void runTestCalls(core::T_sp stream, chem::NVector_sp pos) const;
   virtual double evaluateAllComponent( ScoringFunction_sp scorer,
                                          NVector_sp 	pos,
                                        core::T_sp energyScale,

include/cando/chem/energy_functions/_Angle_termCode.cc

@@ -283,7 +283,7 @@
 	 tx149 = tx143 + tx145 + tx146; 		/* rule 282 */
 	 tx150 = power2(tx67); 		/* rule 283 */
 	 tx151 = tx102 + tx142 + tx144 + tx147 + tx148 + tzz548; 		/* rule 284 */
-	 tx152 = tx151*tzz471; 		/* rule 285 */
+	 tx152 = 3.0*tx151*tzz471; 		/* rule 285 */
 	 tzz518 = tx67*tzz470; 		/* rule 286 */
 	 tx153 = tx149*tzz518; 		/* rule 287 */
 	 tx154 = tx150*tzz473; 		/* rule 288 */