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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 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  
42   #ifndef IO_GLOBALS_HPP
# Line 49 | Line 49
49   #include <string>
50   #include <map>
51  
52 – #include "io/BASS_interface.h"
52   #include "types/Component.hpp"
53 < #include "types/MakeStamps.hpp"
54 < #include "types/ZconStamp.hpp"
55 < #include "utils/CaseConversion.hpp"
53 > #include "types/ZconsStamp.hpp"
54 > #include "types/RestraintStamp.hpp"
55 > #include "types/MoleculeStamp.hpp"
56 > #include "utils/ParameterManager.hpp"
57  
58 < template<typename T>
59 < struct ParameterTraits;
58 > namespace OpenMD {
59 >  class Globals : public DataHolder {
60 >  public:
61 >    typedef std::pair<int, int> intPair;
62  
63 < //string
64 < template<>                    
63 < struct ParameterTraits<std::string>{
64 <  typedef std::string RepType;       // Representation type of the value
65 <
66 < template<typename T> static bool    convert(T v, RepType& r){return false;} // !NB everything is ok
67 < template<typename T> static RepType convert(T v)            {RepType tmp; convert(v,tmp);return tmp;}
68 <  static bool convert(RepType v, RepType& r) { r = v; return true;}
69 < };
70 < //bool
71 < template<>                    
72 < struct ParameterTraits<bool>{
73 <  typedef bool RepType;
74 <  template<typename T> static bool    convert(T, RepType&){return false;}
75 <  template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
76 <  static bool convert(std::string v, RepType& r) {
77 <    oopse::toLower(v);
78 <    bool result = false;
79 <    if (v == "true") {
80 <        r = true;
81 <        result = true;
82 <    } else if (v == "false") {
83 <        r = false;
84 <        result = true;
85 <    }
63 >    Globals();
64 >    virtual ~Globals();
65      
66 <     return result;
67 <  }
68 < };
69 <
70 < //int  
71 < template<>
72 < struct ParameterTraits<int>{
73 <    typedef int RepType;
74 <    template<typename T> static bool    convert(T, RepType&){return false;}
75 <    template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
76 <    static bool convert(RepType v, RepType& r)            { r=v; return true;}
77 < };
78 <
79 < //double
80 < template<>                    
81 < struct ParameterTraits<double>{
82 <    typedef double RepType;
83 <    template<typename T> static bool    convert(T, RepType&){return false;}
84 <    template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
85 <    static bool convert(RepType v, RepType& r)            {r=v; return true;}
86 <    static bool convert(int v, RepType& r)                {r = static_cast<double>(v); return true;}
87 < };
88 <
89 <
90 < class ParameterBase {
91 <  public:    
92 <    ParameterBase() : keyword_(), optional_(false), defaultValue_(false), empty_(true) {}
93 <    bool isOptional() {return optional_;}
94 <    void setOptional(bool optional) {optional_ = optional;}
95 <    bool hasDefaultValue() {return defaultValue_;}
96 <    virtual bool isValid() { return true;}
97 <    const std::string& getKeyword() {return keyword_;}
98 <    void setKeyword(const std::string& keyword) { keyword_ = keyword;}
99 <    bool empty() {return empty_;}
100 <    virtual bool setData(std::string) = 0;
101 <    virtual bool setData(int) = 0;
102 <    virtual bool setData(double) = 0;
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(ThermalConductivity, RealType);
125 >    DeclareParameter(ThermalLength, RealType);
126 >    DeclareParameter(UseSphericalBoundaryConditions, bool);
127 >    DeclareParameter(FrozenBufferRadius, RealType);
128 >    DeclareParameter(LangevinBufferRadius, RealType);
129 >    DeclareParameter(AccumulateBoxDipole, bool);
130 >    DeclareParameter(NeighborListNeighbors, int);
131 >    DeclareParameter(UseMultipleTemperatureMethod, bool);
132 >    DeclareParameter(MTM_Ce, RealType);
133 >    DeclareParameter(MTM_G, RealType);
134 >    DeclareParameter(MTM_Io, RealType);
135 >    DeclareParameter(MTM_Sigma, RealType);    
136 >    DeclareParameter(MTM_R, RealType);    
137 >    DeclareParameter(UseRNEMD, bool);
138 >    DeclareParameter(RNEMD_exchangeTime, RealType);
139 >    DeclareParameter(RNEMD_nBins, int);
140 >    DeclareParameter(RNEMD_logWidth, int);
141 >    DeclareParameter(RNEMD_exchangeType, std::string);
142 >    DeclareParameter(RNEMD_objectSelection, std::string);
143 >    DeclareParameter(RNEMD_targetFlux, RealType);
144 >    DeclareParameter(UseRestraints, bool);
145 >    DeclareParameter(Restraint_file, std::string);
146      
147 <  protected:
148 <    std::string keyword_;
149 <    bool optional_;
150 <    bool defaultValue_;
151 <    bool empty_;
152 < };
153 <
154 < template<class ParamType>
133 < class Parameter : public ParameterBase{
134 <   public:    
135 <    typedef ParameterTraits<ParamType> ValueType;
136 <     void setDefaultValue(const ParamType& value) {data_ = value; defaultValue_ = true;}
137 <     ParamType getData() { return data_;}
138 <
139 <    virtual bool setData(std::string sval) {
140 <        return internalSetData<std::string>(sval);
141 <    }
142 <    virtual bool setData(int ial) {
143 <        return internalSetData<int>(ial);
144 <    }
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 <    virtual bool setData(double dval) {
157 <        return internalSetData<double>(dval);
158 <    }
156 >    int getNZconsStamps() {return zconstraints_.size();}
157 >    std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
158 >    ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    
159  
160 <   private:
161 <     template<class T> bool internalSetData(T data) {
162 <        ParamType tmp;
153 <        bool result = ValueType::convert(data, tmp);
154 <        if (result) {
155 <            empty_ = false;
156 <            data_ = tmp;
157 <        }
158 <        return result;
159 <     }
160 <    
161 <   private:
162 <     ParamType data_;
163 <      
164 < };
160 >    int getNRestraintStamps() {return restraints_.size();}
161 >    std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
162 >    RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
163  
164 < #define DeclareParameter(NAME, TYPE)         \
167 <    private:                                                   \
168 <      Parameter<TYPE> NAME;                                     \
169 <    public:                                                      \
170 <      bool have##NAME() { return !NAME.empty();}  \
171 <      TYPE get##NAME() { return NAME.getData();}
172 <
173 <
174 < class Globals {
175 <  public:
176 <    Globals();
164 >    //std::string getRestraint_file(){
165      
166 <  DeclareParameter(ForceField, std::string);
179 <  DeclareParameter(NComponents, int);  
180 <  DeclareParameter(TargetTemp, double);
181 <  DeclareParameter(Ensemble, std::string);
182 <  DeclareParameter(Dt, double);
183 <  DeclareParameter(RunTime, double);
184 <  DeclareParameter(InitialConfig, std::string);
185 <  DeclareParameter(FinalConfig, std::string);
186 <  DeclareParameter(NMol, int);
187 <  DeclareParameter(Density, double);
188 <  DeclareParameter(Box, double);
189 <  DeclareParameter(BoxX, double);
190 <  DeclareParameter(BoxY, double);
191 <  DeclareParameter(BoxZ, double);
192 <  DeclareParameter(SampleTime, double);
193 <  DeclareParameter(ResetTime, double);
194 <  DeclareParameter(StatusTime, double);
195 <  DeclareParameter(CutoffRadius, double);
196 <  DeclareParameter(SwitchingRadius, double);
197 <  DeclareParameter(Dielectric, double);
198 <  DeclareParameter(TempSet, bool);
199 <  DeclareParameter(ThermalTime, double);
200 <  DeclareParameter(MixingRule, std::string);
201 <  DeclareParameter(UsePeriodicBoundaryConditions, bool);
202 <  DeclareParameter(TargetPressure, double);
203 <  DeclareParameter(TauThermostat, double);
204 <  DeclareParameter(TauBarostat, double);
205 <  DeclareParameter(ZconsTime, double);
206 <  DeclareParameter(NZconstraints, int);
207 <  DeclareParameter(ZconsTol, double);
208 <  DeclareParameter(ZconsForcePolicy, std::string);
209 <  DeclareParameter(Seed, int);
210 <  DeclareParameter(UseInitalTime, bool);
211 <  DeclareParameter(UseIntialExtendedSystemState, bool);
212 <  DeclareParameter(OrthoBoxTolerance, double);
213 <  DeclareParameter(Minimizer, std::string);
214 <  DeclareParameter(MinimizerMaxIter, double);
215 <  DeclareParameter(MinimizerWriteFrq, int);
216 <  DeclareParameter(MinimizerStepSize, double);
217 <  DeclareParameter(MinimizerFTol, double);
218 <  DeclareParameter(MinimizerGTol, double);
219 <  DeclareParameter(MinimizerLSTol, double);
220 <  DeclareParameter(MinimizerLSMaxIter, int);
221 <  DeclareParameter(ZconsGap, double);
222 <  DeclareParameter(ZconsFixtime, double);
223 <  DeclareParameter(ZconsUsingSMD, bool);
224 <  DeclareParameter(UseSolidThermInt, bool);
225 <  DeclareParameter(UseLiquidThermInt, bool);
226 <  DeclareParameter(ThermodynamicIntegrationLambda, double);
227 <  DeclareParameter(ThermodynamicIntegrationK, double);
228 <  DeclareParameter(ForceFieldVariant, std::string);
229 <  DeclareParameter(ForceFieldFileName, std::string);
230 <  DeclareParameter(ThermIntDistSpringConst, double);
231 <  DeclareParameter(ThermIntThetaSpringConst, double);
232 <  DeclareParameter(ThermIntOmegaSpringConst, double);
233 <  DeclareParameter(SurfaceTension, double);
234 <  DeclareParameter(PrintPressureTensor, bool);
235 <  DeclareParameter(ElectrostaticSummationMethod, std::string);
236 <  DeclareParameter(DampingAlpha, double);
237 <  DeclareParameter(CutoffPolicy, std::string);
238 <  DeclareParameter(CompressDumpFile, bool);
239 <  DeclareParameter(SkinThickness, double);
240 <  DeclareParameter(StatFileFormat, std::string);    
241 <
166 >    virtual void validate();
167    private:
243 –    typedef std::map<std::string, ParameterBase*> ParamMap;
244 –    ParamMap parameters_;
168      
169 <    Component* current_component;
170 <    Component** components; // the array of components
171 <
172 <    ZconStamp* current_zConstraint;
173 <    ZconStamp** zConstraints; // the array of zConstraints
251 <
252 <    char* checkMe();
253 <
254 <  public:
255 <    int newComponent( event* the_event );
256 <    int componentAssign( event* the_event );
257 <    int componentEnd( event* the_event );
258 <
259 <    int newZconstraint( event* the_event );
260 <    int zConstraintAssign( event* the_event );
261 <    int zConstraintEnd( event* the_event );
262 <  
263 <    int globalAssign( event* the_event );
264 <    int globalEnd( event* the_event );    
265 <
266 <    ZconStamp** getZconStamp() {return zConstraints;}
267 <    Component** getComponents() {return components;}
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
270 –

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