--- trunk/src/io/ForceFieldOptions.cpp	2005/12/05 23:37:56	789
+++ trunk/src/io/ForceFieldOptions.cpp	2009/11/25 20:02:06	1390
@@ -1,18 +1,107 @@
-#include "io/ForceFieldOptions.hpp"
-namespace oopse {
-    ForceFieldOptions::ForceFieldOptions() {
-      std::cout << "\n";
+/*
+ * Copyright (c) 2005 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. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 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.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * 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 __OPENMD_C
+#include "io/ForceFieldOptions.hpp"
+
+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;
+    }
+    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;
+    }
+
+
+  }
+
+}