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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
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* |
| 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 |
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* distribution. |
| 28 |
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* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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|
*/ |
| 42 |
< |
#define __C |
| 42 |
> |
#define __OPENMD_C |
| 43 |
|
#include "io/ForceFieldOptions.hpp" |
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|
|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
| 47 |
|
ForceFieldOptions::ForceFieldOptions() { |
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|
DefineOptionalParameter(Name, "Name"); |
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– |
DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); |
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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"); |
| 58 |
< |
DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0); |
| 59 |
< |
DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0); |
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< |
DefineOptionalParameterWithDefaultValue(dielectric, "dielectric", 1.0); |
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< |
} |
| 58 |
> |
DefineOptionalParameter(vdw12scale, "vdW-12-scale"); |
| 59 |
> |
DefineOptionalParameter(vdw13scale, "vdW-13-scale"); |
| 60 |
> |
DefineOptionalParameter(vdw14scale, "vdW-14-scale"); |
| 61 |
> |
DefineOptionalParameter(electrostatic12scale, "electrostatic-12-scale"); |
| 62 |
> |
DefineOptionalParameter(electrostatic13scale, "electrostatic-13-scale"); |
| 63 |
> |
DefineOptionalParameter(electrostatic14scale, "electrostatic-14-scale"); |
| 64 |
|
|
| 65 |
+ |
// DefineOptionalParameterWithDefaultValue(vdw12scale, "vdW-12-scale", 0.0); |
| 66 |
+ |
// DefineOptionalParameterWithDefaultValue(vdw13scale, "vdW-13-scale", 0.0); |
| 67 |
+ |
// DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0); |
| 68 |
+ |
// DefineOptionalParameterWithDefaultValue(electrostatic12scale, "electrostatic-12-scale", 0.0); |
| 69 |
+ |
// DefineOptionalParameterWithDefaultValue(electrostatic13scale, "electrostatic-13-scale", 0.0); |
| 70 |
+ |
// DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0); |
| 71 |
+ |
DefineOptionalParameterWithDefaultValue(GayBerneMu, "GayBerneMu", 2.0); |
| 72 |
+ |
DefineOptionalParameterWithDefaultValue(GayBerneNu, "GayBerneNu", 1.0); |
| 73 |
+ |
DefineOptionalParameterWithDefaultValue(EAMMixingMethod, "EAMMixingMethod", "Johnson"); |
| 74 |
|
|
| 75 |
< |
void ForceFieldOptions::makeFortranOptions(ForceOptions& fortranForceOptions){ |
| 64 |
< |
|
| 65 |
< |
fortranForceOptions.vdw14scale = this->getvdw14scale(); |
| 66 |
< |
fortranForceOptions.electrostatic14scale = this->getelectrostatic14scale(); |
| 67 |
< |
|
| 68 |
< |
std::string DistanceMix = this->getDistanceMixingRule(); |
| 69 |
< |
toUpper(DistanceMix); |
| 70 |
< |
if(DistanceMix == "ARITHMETIC"){ |
| 71 |
< |
fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE; |
| 72 |
< |
}else if(DistanceMix == "GEOMETRIC"){ |
| 73 |
< |
fortranForceOptions.DistanceMixingRule = GEOMETRIC_MIXING_RULE; |
| 74 |
< |
}else{ |
| 75 |
< |
fortranForceOptions.DistanceMixingRule = ARITHMETIC_MIXING_RULE; |
| 75 |
> |
deprecatedKeywords_.insert("cutoffPolicy"); |
| 76 |
|
} |
| 77 |
– |
std::string EnergyMix = this->getEnergyMixingRule(); |
| 78 |
– |
toUpper(EnergyMix); |
| 79 |
– |
if(EnergyMix == "ARITHMETIC"){ |
| 80 |
– |
fortranForceOptions.EnergyMixingRule = ARITHMETIC_MIXING_RULE; |
| 81 |
– |
}else if(EnergyMix == "GEOMETRIC"){ |
| 82 |
– |
fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE; |
| 83 |
– |
}else{ |
| 84 |
– |
fortranForceOptions.EnergyMixingRule = GEOMETRIC_MIXING_RULE; |
| 85 |
– |
} |
| 86 |
– |
|
| 87 |
– |
|
| 88 |
– |
} |
| 89 |
– |
|
| 77 |
|
} |
