| 1 |
/* |
| 2 |
* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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_GLOBALS_HPP |
| 43 |
#define IO_GLOBALS_HPP |
| 44 |
|
| 45 |
#include <iostream> |
| 46 |
|
| 47 |
#include <stdlib.h> |
| 48 |
#include <vector> |
| 49 |
#include <string> |
| 50 |
#include <map> |
| 51 |
|
| 52 |
#include "types/Component.hpp" |
| 53 |
#include "types/ZconsStamp.hpp" |
| 54 |
#include "types/RestraintStamp.hpp" |
| 55 |
#include "types/MoleculeStamp.hpp" |
| 56 |
#include "utils/ParameterManager.hpp" |
| 57 |
|
| 58 |
namespace OpenMD { |
| 59 |
class Globals : public DataHolder { |
| 60 |
public: |
| 61 |
typedef std::pair<int, int> intPair; |
| 62 |
|
| 63 |
Globals(); |
| 64 |
virtual ~Globals(); |
| 65 |
|
| 66 |
DeclareParameter(ForceField, std::string); |
| 67 |
DeclareParameter(TargetTemp, RealType); |
| 68 |
DeclareParameter(Ensemble, std::string); |
| 69 |
DeclareParameter(Dt, RealType); |
| 70 |
DeclareParameter(RunTime, RealType); |
| 71 |
DeclareParameter(FinalConfig, std::string); |
| 72 |
DeclareParameter(SampleTime, RealType); |
| 73 |
DeclareParameter(ResetTime, RealType); |
| 74 |
DeclareParameter(StatusTime, RealType); |
| 75 |
DeclareParameter(CutoffRadius, RealType); |
| 76 |
DeclareParameter(SwitchingRadius, RealType); |
| 77 |
DeclareParameter(TempSet, bool); |
| 78 |
DeclareParameter(ThermalTime, RealType); |
| 79 |
DeclareParameter(UsePeriodicBoundaryConditions, bool); |
| 80 |
DeclareParameter(TargetPressure, RealType); |
| 81 |
DeclareParameter(UseAtomicVirial, bool); |
| 82 |
DeclareParameter(TauThermostat, RealType); |
| 83 |
DeclareParameter(TauBarostat, RealType); |
| 84 |
DeclareParameter(ZconsTime, RealType); |
| 85 |
DeclareParameter(ZconsTol, RealType); |
| 86 |
DeclareParameter(ZconsForcePolicy, std::string); |
| 87 |
DeclareParameter(Seed, unsigned long int); |
| 88 |
DeclareParameter(UseInitalTime, bool); |
| 89 |
DeclareParameter(UseIntialExtendedSystemState, bool); |
| 90 |
DeclareParameter(OrthoBoxTolerance, RealType); |
| 91 |
DeclareParameter(Minimizer, std::string); |
| 92 |
DeclareParameter(MinimizerMaxIter, RealType); |
| 93 |
DeclareParameter(MinimizerWriteFrq, int); |
| 94 |
DeclareParameter(MinimizerStepSize, RealType); |
| 95 |
DeclareParameter(MinimizerFTol, RealType); |
| 96 |
DeclareParameter(MinimizerGTol, RealType); |
| 97 |
DeclareParameter(MinimizerLSTol, RealType); |
| 98 |
DeclareParameter(MinimizerLSMaxIter, int); |
| 99 |
DeclareParameter(ZconsGap, RealType); |
| 100 |
DeclareParameter(ZconsFixtime, RealType); |
| 101 |
DeclareParameter(ZconsUsingSMD, bool); |
| 102 |
DeclareParameter(UseThermodynamicIntegration, bool); |
| 103 |
DeclareParameter(ThermodynamicIntegrationLambda, RealType); |
| 104 |
DeclareParameter(ThermodynamicIntegrationK, RealType); |
| 105 |
DeclareParameter(ForceFieldVariant, std::string); |
| 106 |
DeclareParameter(ForceFieldFileName, std::string); |
| 107 |
DeclareParameter(SurfaceTension, RealType); |
| 108 |
DeclareParameter(PrintPressureTensor, bool); |
| 109 |
DeclareParameter(TaggedAtomPair, intPair); |
| 110 |
DeclareParameter(PrintTaggedPairDistance, bool); |
| 111 |
DeclareParameter(ElectrostaticSummationMethod, std::string); |
| 112 |
DeclareParameter(ElectrostaticScreeningMethod, std::string); |
| 113 |
DeclareParameter(DampingAlpha, RealType); |
| 114 |
DeclareParameter(Dielectric, RealType); |
| 115 |
DeclareParameter(CutoffPolicy, std::string); |
| 116 |
DeclareParameter(SwitchingFunctionType, std::string); |
| 117 |
DeclareParameter(CompressDumpFile, bool); |
| 118 |
DeclareParameter(OutputForceVector, bool); |
| 119 |
DeclareParameter(SkinThickness, RealType); |
| 120 |
DeclareParameter(StatFileFormat, std::string); |
| 121 |
DeclareParameter(HydroPropFile, std::string); |
| 122 |
DeclareParameter(Viscosity, RealType); |
| 123 |
DeclareParameter(BeadSize, RealType); |
| 124 |
DeclareParameter(UseSphericalBoundaryConditions, bool); |
| 125 |
DeclareParameter(FrozenBufferRadius, RealType); |
| 126 |
DeclareParameter(LangevinBufferRadius, RealType); |
| 127 |
DeclareParameter(AccumulateBoxDipole, bool); |
| 128 |
DeclareParameter(NeighborListNeighbors, int); |
| 129 |
DeclareParameter(UseMultipleTemperatureMethod, bool); |
| 130 |
DeclareParameter(MTM_Ce, RealType); |
| 131 |
DeclareParameter(MTM_G, RealType); |
| 132 |
DeclareParameter(MTM_Io, RealType); |
| 133 |
DeclareParameter(MTM_Sigma, RealType); |
| 134 |
DeclareParameter(MTM_R, RealType); |
| 135 |
DeclareParameter(UseRNEMD, bool); |
| 136 |
DeclareParameter(RNEMD_exchangeTime, RealType); |
| 137 |
DeclareParameter(RNEMD_nBins, int); |
| 138 |
DeclareParameter(RNEMD_logWidth, int); |
| 139 |
DeclareParameter(RNEMD_exchangeType, std::string); |
| 140 |
DeclareParameter(RNEMD_objectSelection, std::string); |
| 141 |
DeclareParameter(RNEMD_targetFlux, RealType); |
| 142 |
DeclareParameter(UseRestraints, bool); |
| 143 |
DeclareParameter(Restraint_file, std::string); |
| 144 |
DeclareParameter(HULL_Method, std::string); |
| 145 |
DeclareParameter(Alpha, RealType); |
| 146 |
|
| 147 |
public: |
| 148 |
bool addComponent(Component* comp); |
| 149 |
bool addZConsStamp(ZConsStamp* zcons); |
| 150 |
bool addRestraintStamp(RestraintStamp* rest); |
| 151 |
bool addMoleculeStamp(MoleculeStamp* molStamp); |
| 152 |
int getNComponents() {return components_.size();} |
| 153 |
std::vector<Component*> getComponents() {return components_;} |
| 154 |
Component* getComponentAt(int index) {return components_.at(index);} |
| 155 |
|
| 156 |
int getNZconsStamps() {return zconstraints_.size();} |
| 157 |
std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;} |
| 158 |
ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);} |
| 159 |
|
| 160 |
int getNRestraintStamps() {return restraints_.size();} |
| 161 |
std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;} |
| 162 |
RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);} |
| 163 |
|
| 164 |
//std::string getRestraint_file(){ |
| 165 |
|
| 166 |
virtual void validate(); |
| 167 |
private: |
| 168 |
|
| 169 |
std::vector<Component*> components_; |
| 170 |
std::vector<ZConsStamp*> zconstraints_; |
| 171 |
std::vector<RestraintStamp*> restraints_; |
| 172 |
std::map<std::string, MoleculeStamp*> moleculeStamps_; |
| 173 |
std::pair<int, int> taggedAtomPair_; |
| 174 |
}; |
| 175 |
} |
| 176 |
#endif |
