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root/OpenMD/trunk/src/io/ForceFieldOptions.cpp
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Comparing trunk/src/io/ForceFieldOptions.cpp (file contents):
Revision 805 by gezelter, Thu Dec 8 22:05:16 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 <
41 > #define __OPENMD_C
42   #include "io/ForceFieldOptions.hpp"
43 – namespace oopse {
43  
44 + namespace OpenMD {
45 +
46      ForceFieldOptions::ForceFieldOptions() {
47        DefineOptionalParameter(Name, "Name");
48 +      DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
49        DefineOptionalParameterWithDefaultValue(vdWtype, "vdWtype", "Lennard-Jones");
50        DefineOptionalParameterWithDefaultValue(DistanceMixingRule, "DistanceMixingRule", "arithmetic");
51        DefineOptionalParameterWithDefaultValue(DistanceType, "DistanceType", "sigma");
52        DefineOptionalParameterWithDefaultValue(EnergyMixingRule, "EnergyMixingRule", "geometric");
53        DefineOptionalParameterWithDefaultValue(EnergyUnitScaling, "EnergyUnitScaling", 1.0);
54 +      DefineOptionalParameterWithDefaultValue(MetallicEnergyUnitScaling, "MetallicEnergyUnitScaling", 1.0);
55        DefineOptionalParameterWithDefaultValue(DistanceUnitScaling, "DistanceUnitScaling", 1.0);
56        DefineOptionalParameterWithDefaultValue(AngleUnitScaling, "AngleUnitScaling", 1.0);
57 <      DefineOptionalParameterWithDefaultValue(TorsionAngleConvention, "TorsionAngleConvention", "180 is trans");
57 >      DefineOptionalParameterWithDefaultValue(TorsionAngleConvention, "TorsionAngleConvention", "180_is_trans");
58 >      DefineOptionalParameterWithDefaultValue(vdw12scale, "vdW-12-scale", 0.0);
59 >      DefineOptionalParameterWithDefaultValue(vdw13scale, "vdW-13-scale", 0.0);
60        DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0);
61 <      DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0);
62 <      DefineOptionalParameterWithDefaultValue(dielectric, "dielectric", 1.0);
61 >      DefineOptionalParameterWithDefaultValue(electrostatic12scale, "electrostatic-12-scale", 0.0)
62 >      DefineOptionalParameterWithDefaultValue(electrostatic13scale, "electrostatic-13-scale", 0.0)
63 >      DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0)
64 >      DefineOptionalParameterWithDefaultValue(GayBerneMu, "GayBerneMu", 2.0);
65 >      DefineOptionalParameterWithDefaultValue(GayBerneNu, "GayBerneNu", 1.0);
66      }
67  
68 +
69 +  void ForceFieldOptions::makeFortranOptions(ForceOptions& fortranForceOptions){
70 +    
71 +    fortranForceOptions.vdw12scale = this->getvdw12scale();
72 +    fortranForceOptions.vdw13scale = this->getvdw13scale();
73 +    fortranForceOptions.vdw14scale = this->getvdw14scale();
74 +    fortranForceOptions.electrostatic12scale = this->getelectrostatic12scale();
75 +    fortranForceOptions.electrostatic13scale = this->getelectrostatic13scale();
76 +    fortranForceOptions.electrostatic14scale = this->getelectrostatic14scale();
77 +    fortranForceOptions.GayBerneMu = this->getGayBerneMu();
78 +    fortranForceOptions.GayBerneNu = this->getGayBerneNu();
79 +
80 +
81 +    std::string DistanceMix = this->getDistanceMixingRule();
82 +    toUpper(DistanceMix);
83 +    if(DistanceMix == "ARITHMETIC"){
84 +      fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE;
85 +    }else if(DistanceMix == "GEOMETRIC"){
86 +      fortranForceOptions.DistanceMixingRule = GEOMETRIC_MIXING_RULE;
87 +    }else if(DistanceMix == "CUBIC"){
88 +      fortranForceOptions.DistanceMixingRule = CUBIC_MIXING_RULE;
89 +    }else{
90 +      fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE;
91 +    }
92 +    std::string EnergyMix = this->getEnergyMixingRule();  
93 +    toUpper(EnergyMix);
94 +    if(EnergyMix == "ARITHMETIC"){
95 +      fortranForceOptions.EnergyMixingRule = ARITHMETIC_MIXING_RULE;
96 +    }else if(EnergyMix == "GEOMETRIC"){
97 +      fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE;
98 +    }else if(EnergyMix == "HHG"){
99 +      fortranForceOptions.EnergyMixingRule = HHG_MIXING_RULE;
100 +    }else{
101 +      fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE;
102 +    }
103 +
104 +
105 +  }
106 +
107   }

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