| 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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#ifndef IO_GLOBALS_HPP |
| 107 |
|
DeclareParameter(ForceFieldFileName, std::string); |
| 108 |
|
DeclareParameter(SurfaceTension, RealType); |
| 109 |
|
DeclareParameter(PrintPressureTensor, bool); |
| 110 |
+ |
DeclareParameter(PrintHeatFlux, bool); |
| 111 |
|
DeclareParameter(TaggedAtomPair, intPair); |
| 112 |
|
DeclareParameter(PrintTaggedPairDistance, bool); |
| 113 |
|
DeclareParameter(ElectrostaticSummationMethod, std::string); |
| 114 |
|
DeclareParameter(ElectrostaticScreeningMethod, std::string); |
| 115 |
|
DeclareParameter(DampingAlpha, RealType); |
| 116 |
|
DeclareParameter(Dielectric, RealType); |
| 117 |
+ |
DeclareParameter(CutoffMethod, std::string); |
| 118 |
|
DeclareParameter(CutoffPolicy, std::string); |
| 119 |
|
DeclareParameter(SwitchingFunctionType, std::string); |
| 120 |
|
DeclareParameter(CompressDumpFile, bool); |
| 121 |
|
DeclareParameter(OutputForceVector, bool); |
| 122 |
+ |
DeclareParameter(OutputParticlePotential, bool); |
| 123 |
+ |
DeclareParameter(OutputElectricField, bool); |
| 124 |
+ |
DeclareParameter(OutputFluctuatingCharges, bool); |
| 125 |
|
DeclareParameter(SkinThickness, RealType); |
| 126 |
|
DeclareParameter(StatFileFormat, std::string); |
| 127 |
|
DeclareParameter(HydroPropFile, std::string); |
| 145 |
|
DeclareParameter(RNEMD_exchangeType, std::string); |
| 146 |
|
DeclareParameter(RNEMD_objectSelection, std::string); |
| 147 |
|
DeclareParameter(RNEMD_targetFlux, RealType); |
| 148 |
+ |
DeclareParameter(RNEMD_targetJzKE, RealType); |
| 149 |
+ |
DeclareParameter(RNEMD_targetJzpx, RealType); |
| 150 |
+ |
DeclareParameter(RNEMD_targetJzpy, RealType); |
| 151 |
+ |
DeclareParameter(RNEMD_targetJzpz, RealType); |
| 152 |
+ |
DeclareParameter(RNEMD_binShift, bool); |
| 153 |
+ |
DeclareParameter(RNEMD_outputTemperature, bool); |
| 154 |
+ |
DeclareParameter(RNEMD_outputVx, bool); |
| 155 |
+ |
DeclareParameter(RNEMD_outputVy, bool); |
| 156 |
+ |
// James put this in. |
| 157 |
+ |
DeclareParameter(RNEMD_outputDen, bool); |
| 158 |
+ |
DeclareParameter(RNEMD_outputVz, bool); |
| 159 |
+ |
DeclareParameter(RNEMD_outputAh, bool); |
| 160 |
+ |
DeclareParameter(RNEMD_outputXyzTemperature, bool); |
| 161 |
+ |
DeclareParameter(RNEMD_outputRotTemperature, bool); |
| 162 |
|
DeclareParameter(UseRestraints, bool); |
| 163 |
|
DeclareParameter(Restraint_file, std::string); |
| 164 |
|
DeclareParameter(HULL_Method, std::string); |
| 165 |
|
DeclareParameter(Alpha, RealType); |
| 166 |
< |
|
| 166 |
> |
DeclareParameter(FlucQPropagator, std::string); |
| 167 |
> |
DeclareParameter(FlucQFriction, RealType); |
| 168 |
> |
DeclareParameter(FlucQTolerance, RealType); |
| 169 |
> |
DeclareParameter(FlucQMaxIterations, int); |
| 170 |
> |
DeclareParameter(FlucQTargetTemp, RealType); |
| 171 |
> |
DeclareParameter(FlucQtauThermostat, RealType); |
| 172 |
> |
DeclareAlterableParameter(MDfileVersion, int); |
| 173 |
> |
|
| 174 |
|
public: |
| 175 |
|
bool addComponent(Component* comp); |
| 176 |
|
bool addZConsStamp(ZConsStamp* zcons); |
| 187 |
|
int getNRestraintStamps() {return restraints_.size();} |
| 188 |
|
std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;} |
| 189 |
|
RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);} |
| 163 |
– |
|
| 164 |
– |
//std::string getRestraint_file(){ |
| 190 |
|
|
| 191 |
|
virtual void validate(); |
| 192 |
|
private: |
