--- trunk/src/io/ForceFieldOptions.cpp	2005/12/28 21:44:06	822
+++ trunk/src/io/ForceFieldOptions.cpp	2009/11/25 20:02:06	1390
@@ -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.
@@ -37,39 +28,64 @@
  * 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).                        
  */
-#define __C
+#define __OPENMD_C
 #include "io/ForceFieldOptions.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
     ForceFieldOptions::ForceFieldOptions() {
       DefineOptionalParameter(Name, "Name");
+      DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
       DefineOptionalParameterWithDefaultValue(vdWtype, "vdWtype", "Lennard-Jones");
       DefineOptionalParameterWithDefaultValue(DistanceMixingRule, "DistanceMixingRule", "arithmetic");
       DefineOptionalParameterWithDefaultValue(DistanceType, "DistanceType", "sigma");
       DefineOptionalParameterWithDefaultValue(EnergyMixingRule, "EnergyMixingRule", "geometric");
       DefineOptionalParameterWithDefaultValue(EnergyUnitScaling, "EnergyUnitScaling", 1.0);
+      DefineOptionalParameterWithDefaultValue(MetallicEnergyUnitScaling, "MetallicEnergyUnitScaling", 1.0);
       DefineOptionalParameterWithDefaultValue(DistanceUnitScaling, "DistanceUnitScaling", 1.0);
       DefineOptionalParameterWithDefaultValue(AngleUnitScaling, "AngleUnitScaling", 1.0);
-      DefineOptionalParameterWithDefaultValue(TorsionAngleConvention, "TorsionAngleConvention", "180 is trans");
+      DefineOptionalParameterWithDefaultValue(TorsionAngleConvention, "TorsionAngleConvention", "180_is_trans");
+      DefineOptionalParameterWithDefaultValue(vdw12scale, "vdW-12-scale", 0.0);
+      DefineOptionalParameterWithDefaultValue(vdw13scale, "vdW-13-scale", 0.0);
       DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0);
-      DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0);
-      DefineOptionalParameterWithDefaultValue(dielectric, "dielectric", 1.0);
+      DefineOptionalParameterWithDefaultValue(electrostatic12scale, "electrostatic-12-scale", 0.0)
+      DefineOptionalParameterWithDefaultValue(electrostatic13scale, "electrostatic-13-scale", 0.0)
+      DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0)
+      DefineOptionalParameterWithDefaultValue(GayBerneMu, "GayBerneMu", 2.0);
+      DefineOptionalParameterWithDefaultValue(GayBerneNu, "GayBerneNu", 1.0);
     }
 
 
   void ForceFieldOptions::makeFortranOptions(ForceOptions& fortranForceOptions){
     
+    fortranForceOptions.vdw12scale = this->getvdw12scale();
+    fortranForceOptions.vdw13scale = this->getvdw13scale();
     fortranForceOptions.vdw14scale = this->getvdw14scale();
+    fortranForceOptions.electrostatic12scale = this->getelectrostatic12scale();
+    fortranForceOptions.electrostatic13scale = this->getelectrostatic13scale();
     fortranForceOptions.electrostatic14scale = this->getelectrostatic14scale();
+    fortranForceOptions.GayBerneMu = this->getGayBerneMu();
+    fortranForceOptions.GayBerneNu = this->getGayBerneNu();
 
+
     std::string DistanceMix = this->getDistanceMixingRule();
     toUpper(DistanceMix);
     if(DistanceMix == "ARITHMETIC"){
       fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE;
     }else if(DistanceMix == "GEOMETRIC"){
       fortranForceOptions.DistanceMixingRule = GEOMETRIC_MIXING_RULE;
+    }else if(DistanceMix == "CUBIC"){
+      fortranForceOptions.DistanceMixingRule = CUBIC_MIXING_RULE;
     }else{
       fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE;
     }
@@ -79,6 +95,8 @@ namespace oopse {
       fortranForceOptions.EnergyMixingRule = ARITHMETIC_MIXING_RULE;
     }else if(EnergyMix == "GEOMETRIC"){
       fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE;
+    }else if(EnergyMix == "HHG"){
+      fortranForceOptions.EnergyMixingRule = HHG_MIXING_RULE;
     }else{
       fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE;
     }