| 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. |
| 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 |
|
|
| 42 |
|
#ifndef IO_FORCEFIELDOPTIONS_HPP |
| 43 |
|
#define IO_FORCEFIELDOPTIONS_HPP |
| 44 |
|
#include "utils/simError.h" |
| 45 |
+ |
#include "types/DataHolder.hpp" |
| 46 |
|
#include "utils/ParameterManager.hpp" |
| 47 |
|
#include "utils/StringUtils.hpp" |
| 48 |
|
#include "io/ParamConstraint.hpp" |
| 49 |
|
|
| 50 |
< |
namespace oopse { |
| 50 |
> |
namespace OpenMD { |
| 51 |
|
|
| 52 |
< |
class ForceFieldOptions { |
| 52 |
> |
class ForceFieldOptions : public DataHolder { |
| 53 |
|
DeclareParameter(Name, std::string); |
| 54 |
|
DeclareParameter(vdWtype, std::string); |
| 55 |
|
DeclareParameter(DistanceMixingRule, std::string); |
| 56 |
|
DeclareParameter(DistanceType, std::string); |
| 57 |
|
DeclareParameter(EnergyMixingRule, std::string); |
| 58 |
< |
DeclareParameter(EnergyUnitScaling, double); |
| 59 |
< |
DeclareParameter(DistanceUnitScaling, double); |
| 60 |
< |
DeclareParameter(AngleUnitScaling, double); |
| 58 |
> |
DeclareParameter(CutoffPolicy, std::string); |
| 59 |
> |
DeclareParameter(EnergyUnitScaling, RealType); |
| 60 |
> |
DeclareParameter(MetallicEnergyUnitScaling, RealType); |
| 61 |
> |
DeclareParameter(DistanceUnitScaling, RealType); |
| 62 |
> |
DeclareParameter(AngleUnitScaling, RealType); |
| 63 |
|
DeclareParameter(TorsionAngleConvention, std::string); |
| 64 |
< |
DeclareParameter(vdw14scale, double); |
| 65 |
< |
DeclareParameter(electrostatic14scale, double); |
| 66 |
< |
DeclareParameter(dielectric, double); |
| 64 |
> |
DeclareParameter(vdw12scale, RealType); |
| 65 |
> |
DeclareParameter(vdw13scale, RealType); |
| 66 |
> |
DeclareParameter(vdw14scale, RealType); |
| 67 |
> |
DeclareParameter(electrostatic12scale, RealType); |
| 68 |
> |
DeclareParameter(electrostatic13scale, RealType); |
| 69 |
> |
DeclareParameter(electrostatic14scale, RealType); |
| 70 |
> |
DeclareParameter(GayBerneMu, RealType); |
| 71 |
> |
DeclareParameter(GayBerneNu, RealType); |
| 72 |
> |
DeclareParameter(EAMMixingMethod, std::string); |
| 73 |
|
|
| 74 |
|
public: |
| 75 |
< |
ForceFieldOptions() { |
| 67 |
< |
DefineOptionalParameter(Name, "Name"); |
| 68 |
< |
DefineOptionalParameterWithDefaultValue(vdWtype, "vdWtype", "Lennard-Jones"); |
| 69 |
< |
DefineOptionalParameterWithDefaultValue(DistanceMixingRule, "DistanceMixingRule", "arithmetic"); |
| 70 |
< |
DefineOptionalParameterWithDefaultValue(DistanceType, "DistanceType", "sigma"); |
| 71 |
< |
DefineOptionalParameterWithDefaultValue(EnergyMixingRule, "EnergyMixingRule", "geometric"); |
| 72 |
< |
DefineOptionalParameterWithDefaultValue(EnergyUnitScaling, "EnergyUnitScaling", 1.0); |
| 73 |
< |
DefineOptionalParameterWithDefaultValue(DistanceUnitScaling, "DistanceUnitScaling", 1.0); |
| 74 |
< |
DefineOptionalParameterWithDefaultValue(AngleUnitScaling, "AngleUnitScaling", 1.0); |
| 75 |
< |
DefineOptionalParameterWithDefaultValue(TorsionAngleConvention, "TorsionAngleConvention", "180 is trans"); |
| 76 |
< |
DefineOptionalParameterWithDefaultValue(vdw14scale, "vdW-14-scale", 0.0); |
| 77 |
< |
DefineOptionalParameterWithDefaultValue(electrostatic14scale, "electrostatic-14-scale", 0.0); |
| 78 |
< |
DefineOptionalParameterWithDefaultValue(dielectric, "dielectric", 1.0); |
| 79 |
< |
} |
| 80 |
< |
|
| 75 |
> |
ForceFieldOptions(); |
| 76 |
|
ForceFieldOptions(const ForceFieldOptions&); |
| 77 |
|
ForceFieldOptions& operator = (const ForceFieldOptions&); |
| 78 |
|
|
| 79 |
|
void validateOptions() { |
| 80 |
|
CheckParameter(vdWtype, isEqualIgnoreCase(std::string("Lennard-Jones"))); |
| 81 |
< |
CheckParameter(DistanceMixingRule, isEqualIgnoreCase(std::string("arithmetic")) || isEqualIgnoreCase(std::string("geometric"))); |
| 81 |
> |
CheckParameter(DistanceMixingRule, isEqualIgnoreCase(std::string("arithmetic")) || isEqualIgnoreCase(std::string("geometric")) || isEqualIgnoreCase(std::string("cubic"))); |
| 82 |
|
CheckParameter(DistanceType, isEqualIgnoreCase(std::string("sigma")) || isEqualIgnoreCase(std::string("Rmin"))); |
| 83 |
< |
CheckParameter(EnergyMixingRule, isEqualIgnoreCase(std::string("arithmetic")) || isEqualIgnoreCase(std::string("geometric"))); |
| 83 |
> |
CheckParameter(EnergyMixingRule, isEqualIgnoreCase(std::string("arithmetic")) || isEqualIgnoreCase(std::string("geometric")) || isEqualIgnoreCase(std::string("hhg"))); |
| 84 |
|
CheckParameter(TorsionAngleConvention, isEqualIgnoreCase(std::string("180 is trans")) || isEqualIgnoreCase(std::string("0 is trans"))); |
| 85 |
< |
} |
| 85 |
> |
CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL"))); |
| 86 |
> |
CheckParameter(EAMMixingMethod, isEqualIgnoreCase(std::string("JOHNSON")) || isEqualIgnoreCase(std::string("DAW"))); |
| 87 |
> |
} |
| 88 |
|
|
| 89 |
|
bool setData(const std::string& keyword, const std::string& value) { |
| 90 |
|
bool result; |
| 91 |
|
ParamMap::iterator i =parameters_.find(keyword); |
| 92 |
|
if (i != parameters_.end()) { |
| 93 |
< |
if(isType<int>(value)){ |
| 93 |
> |
if(isInteger(value)){ |
| 94 |
|
int ival = lexi_cast<int>(value); |
| 95 |
|
result = i->second->setData(ival); |
| 96 |
|
} |
| 97 |
< |
else if (isType<double>(value)){ |
| 98 |
< |
double dval = lexi_cast<double>(value); |
| 97 |
> |
else if (isType<RealType>(value)){ |
| 98 |
> |
RealType dval = lexi_cast<RealType>(value); |
| 99 |
|
result = i->second->setData(dval); |
| 100 |
|
} else{ |
| 101 |
|
result = i->second->setData(value); |
| 108 |
|
|
| 109 |
|
return result; |
| 110 |
|
} |
| 111 |
< |
|
| 111 |
> |
|
| 112 |
|
private: |
| 113 |
|
typedef std::map<std::string, ParameterBase*> ParamMap; |
| 114 |
|
ParamMap parameters_; |
