--- trunk/src/io/Globals.cpp	2009/09/07 16:31:51	1360
+++ trunk/src/io/Globals.cpp	2010/03/30 15:05:13	1423
@@ -1,24 +1,15 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
  * 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 +28,15 @@
  * 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, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 #include <stdlib.h>
@@ -49,7 +49,7 @@
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 Globals::Globals() {
   DefineParameter(ForceField, "forceField")
  
@@ -74,7 +74,7 @@ Globals::Globals() {
   DefineOptionalParameter(Seed, "seed");
   DefineOptionalParameter(Minimizer, "minimizer");
   DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
-  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
+  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
   DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
   DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
   DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
@@ -99,8 +99,6 @@ Globals::Globals() {
   DefineOptionalParameter(BeadSize, "beadSize");
   DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
   DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
-  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
-  DefineOptionalParameter(ThermalLength, "thermalLength");
   DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
   DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
   DefineOptionalParameter(MTM_Ce, "MTM_Ce");
@@ -108,7 +106,7 @@ Globals::Globals() {
   DefineOptionalParameter(MTM_Io, "MTM_Io");
   DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
   DefineOptionalParameter(MTM_R, "MTM_R");
-  
+  DefineOptionalParameter(Alpha, "alpha");
 
   
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
@@ -127,13 +125,16 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
 
   DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
-  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
   DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
-  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
+  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
+  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
+  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
   DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
   DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
   DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
   DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
+  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
 
 
   deprecatedKeywords_.insert("nComponents");
@@ -176,7 +177,7 @@ void Globals::validate() {
   CheckParameter(Seed, isPositive());
   CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
   CheckParameter(MinimizerMaxIter, isPositive());
-  CheckParameter(MinimizerWriteFrq, isPositive());
+  CheckParameter(MinimizerWriteFreq, isPositive());
   CheckParameter(MinimizerStepSize, isPositive());
   CheckParameter(MinimizerFTol, isPositive());
   CheckParameter(MinimizerGTol, isPositive());
@@ -197,25 +198,27 @@ void Globals::validate() {
   CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
   CheckParameter(Viscosity, isNonNegative());
-  CheckParameter(ThermalConductivity, isNonNegative());
-  CheckParameter(ThermalLength, isNonNegative());
   CheckParameter(BeadSize, isPositive());
   CheckParameter(FrozenBufferRadius, isPositive());
   CheckParameter(LangevinBufferRadius, isPositive());
   CheckParameter(NeighborListNeighbors, isPositive());
-  CheckParameter(RNEMD_swapTime, isPositive());
+  CheckParameter(RNEMD_exchangeTime, isPositive());
   CheckParameter(RNEMD_nBins, isPositive() && isEven());
-  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
+  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
+  CheckParameter(RNEMD_targetFlux, isNonNegative());
+  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); 
+  CheckParameter(Alpha, isPositive()); 
 
+  
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
         std::ostringstream oss;
         oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
-        throw OOPSEException(oss.str());           
+        throw OpenMDException(oss.str());           
     }
   }
 }
-    
+  
 bool Globals::addComponent(Component* comp) {
     components_.push_back(comp);
     return true;
@@ -242,7 +245,7 @@ bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
     } else {
         std::ostringstream oss;
         oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
-        throw OOPSEException(oss.str());  
+        throw OpenMDException(oss.str());  
     }
     return ret;
 }