--- trunk/src/io/ForceFieldOptions.cpp	2006/07/16 02:46:27	1004
+++ trunk/src/io/ForceFieldOptions.cpp	2012/08/22 02:28:28	1782
@@ -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.
@@ -37,62 +28,50 @@
  * 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
-#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(vdw14scale, "vdW-14-scale", 0.0);
-      DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0)
-      DefineOptionalParameterWithDefaultValue(dielectric, "dielectric", 1.0);
+      DefineOptionalParameter(vdw12scale, "vdW-12-scale");
+      DefineOptionalParameter(vdw13scale, "vdW-13-scale");
+      DefineOptionalParameter(vdw14scale, "vdW-14-scale");
+      DefineOptionalParameter(electrostatic12scale, "electrostatic-12-scale");
+      DefineOptionalParameter(electrostatic13scale, "electrostatic-13-scale");
+      DefineOptionalParameter(electrostatic14scale, "electrostatic-14-scale");
+
+      // DefineOptionalParameterWithDefaultValue(vdw12scale, "vdW-12-scale", 0.0);
+      // DefineOptionalParameterWithDefaultValue(vdw13scale, "vdW-13-scale", 0.0);
+      // DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0);
+      // 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);
-    }
+      DefineOptionalParameterWithDefaultValue(EAMMixingMethod, "EAMMixingMethod", "Johnson");
 
-
-  void ForceFieldOptions::makeFortranOptions(ForceOptions& fortranForceOptions){
-    
-    fortranForceOptions.vdw14scale = this->getvdw14scale();
-    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;
+      deprecatedKeywords_.insert("cutoffPolicy");
     }
-    std::string EnergyMix = this->getEnergyMixingRule();  
-    toUpper(EnergyMix);
-    if(EnergyMix == "ARITHMETIC"){
-      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;
-    }
-
-
-  }
-
 }