--- trunk/src/brains/Register.cpp	2005/11/16 21:20:11	744
+++ trunk/src/brains/Register.cpp	2014/08/06 19:27:37	2011
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,16 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "brains/Register.hpp"
@@ -49,51 +50,30 @@
 #include "integrators/NPTi.hpp"
 #include "integrators/NPTf.hpp"
 #include "integrators/NPTxyz.hpp"
+#include "integrators/NPTsz.hpp"
 #include "integrators/NPAT.hpp"
 #include "integrators/NPrT.hpp"
+#include "integrators/NPA.hpp"
+#include "integrators/NgammaT.hpp"
+#include "integrators/LangevinDynamics.hpp"
+#if defined(HAVE_QHULL)
+#include "integrators/LangevinHullDynamics.hpp"
+#endif
 
-#include "minimizers/MinimizerFactory.hpp"
-#include "minimizers/MinimizerCreator.hpp"
-#include "minimizers/PRCG.hpp"
-#include "minimizers/SDMinimizer.hpp"
-#include "UseTheForce/DUFF.hpp"
-#include "UseTheForce/EAM_FF.hpp"
-#include "UseTheForce/ForceFieldFactory.hpp"
-#include "UseTheForce/ForceFieldCreator.hpp"
-#include "UseTheForce/SHAPES_FF.hpp"
-#include "UseTheForce/SC_FF.hpp"
+#include "optimization/OptimizationFactory.hpp"
+#include "optimization/OptimizationCreator.hpp"
+#include "optimization/Method.hpp"
+#include "optimization/SteepestDescent.hpp"
+#include "optimization/ConjugateGradient.hpp"
+#include "optimization/BFGS.hpp"
+
 #include "lattice/LatticeFactory.hpp"
 #include "lattice/LatticeCreator.hpp"
 #include "lattice/FCCLattice.hpp"
 
-#include "openbabel/amberformat.hpp"
-#include "openbabel/fingerprintformat.hpp"
-#include "openbabel/gromos96format.hpp"
-#include "openbabel/oopseformat.hpp"
-#include "openbabel/pdbformat.hpp"
-#include "openbabel/povrayformat.hpp"
-#include "openbabel/smilesformat.hpp"
-#include "openbabel/tinkerformat.hpp"
-#include "openbabel/xyzformat.hpp"
+using namespace QuantLib;
+namespace OpenMD {
 
-
-namespace oopse {
-
-
-  void registerForceFields() {
-    /** @todo move to a seperate initialization module */
-    //DUFF, WATER and LJ are merged into one force field
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("DUFF"));
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("WATER"));
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("LJ"));
-    //in theory, EAM can also be merged
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EAM_FF>("EAM"));
-    //heck, that worked...  let's try merging SHAPES
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SHAPES_FF>("SHAPES"));
-    //Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not).
-    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SC_FF>("SC"));
-  }
-
   void registerIntegrators() {
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE"));
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT"));
@@ -101,34 +81,33 @@ namespace oopse {
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPTf>("NPTF"));
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPTxyz>("NPTXYZ"));
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPAT>("NPAT"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPA>("NPA"));
     IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPRT"));
-
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPGT"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGT"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGAMMAT"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LANGEVINDYNAMICS"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LD"));
+#if defined(HAVE_QHULL)
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LHULL"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LANGEVINHULL"));
+    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("SMIPD"));
+#endif
   }
 
-  void registerMinimizers() {
-    MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder<SDMinimizer>("SD"));
-    MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder<PRCGMinimizer>("CG"));
+  void registerOptimizers() {
+    OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::SteepestDescent>("SD"));
+    OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::ConjugateGradient>("CG"));
+    OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::BFGS>("BFGS"));
   }
 
   void registerLattice(){
     LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC"));
   }
 
-  void registerOBFormats(){
-    static OpenBabel::AmberPrepFormat amberFormatInstance;
-    static OpenBabel::FingerprintFormat fingerprintFormatInstance;
-    static OpenBabel::OOPSEFormat oopseFormatInstance;    
-    static OpenBabel::PDBFormat pdbFormatInstance;
-    static OpenBabel::PovrayFormat povaryFormatInstance;
-    static OpenBabel::SMIFormat smilesFormatInstance;
-    static OpenBabel::TinkerFormat tinkerFormatInstance;
-    static OpenBabel::XYZFormat xyzFormatInstance;    
-  }
-  
   void registerAll() {
-    registerForceFields();
     registerIntegrators();
-    registerMinimizers();
+    registerOptimizers();
   }
 
 }