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root/OpenMD/branches/development/src/io/Globals.hpp

Comparing:
trunk/src/io/Globals.hpp (file contents), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/Globals.hpp (file contents), Revision 1729 by jmarr, Wed May 30 16:08:07 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. 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]  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
#	Line 49 | Line 50
50		#include <string>
51		#include <map>
52
52	–	#include "io/BASS_interface.h"
53		#include "types/Component.hpp"
54	<	#include "types/MakeStamps.hpp"
55	<	#include "types/ZconStamp.hpp"
56	<	#include "utils/CaseConversion.hpp"
54	>	#include "types/ZconsStamp.hpp"
55	>	#include "types/RestraintStamp.hpp"
56	>	#include "types/MoleculeStamp.hpp"
57	>	#include "utils/ParameterManager.hpp"
58
59	<	template<typename T>
60	<	struct ParameterTraits;
59	>	namespace OpenMD {
60	>	class Globals : public DataHolder {
61	>	public:
62	>	typedef std::pair<int, int> intPair;
63
64	<	//string
65	<	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	<	static std::string getParamType() { return "string";}
70	<	};
71	<	//bool
72	<	template<>
73	<	struct ParameterTraits<bool>{
74	<	typedef bool RepType;
75	<	template<typename T> static bool    convert(T, RepType&){return false;}
76	<	template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
77	<	static bool convert(std::string v, RepType& r) {
78	<	oopse::toLower(v);
79	<	bool result = false;
80	<	if (v == "true") {
81	<	r = true;
82	<	result = true;
83	<	} else if (v == "false") {
84	<	r = false;
85	<	result = true;
86	<	}
64	>	Globals();
65	>	virtual ~Globals();
66
67	<	return result;
68	<	}
69	<	static std::string getParamType() { return "bool";}
70	<	};
67	>	DeclareParameter(ForceField, std::string);
68	>	DeclareParameter(TargetTemp, RealType);
69	>	DeclareParameter(Ensemble, std::string);
70	>	DeclareParameter(Dt, RealType);
71	>	DeclareParameter(RunTime, RealType);
72	>	DeclareParameter(FinalConfig, std::string);
73	>	DeclareParameter(SampleTime, RealType);
74	>	DeclareParameter(ResetTime, RealType);
75	>	DeclareParameter(StatusTime, RealType);
76	>	DeclareParameter(CutoffRadius, RealType);
77	>	DeclareParameter(SwitchingRadius, RealType);
78	>	DeclareParameter(TempSet, bool);
79	>	DeclareParameter(ThermalTime, RealType);
80	>	DeclareParameter(UsePeriodicBoundaryConditions, bool);
81	>	DeclareParameter(TargetPressure, RealType);
82	>	DeclareParameter(UseAtomicVirial, bool);
83	>	DeclareParameter(TauThermostat, RealType);
84	>	DeclareParameter(TauBarostat, RealType);
85	>	DeclareParameter(ZconsTime, RealType);
86	>	DeclareParameter(ZconsTol, RealType);
87	>	DeclareParameter(ZconsForcePolicy, std::string);
88	>	DeclareParameter(Seed, unsigned long int);
89	>	DeclareParameter(UseInitalTime, bool);
90	>	DeclareParameter(UseIntialExtendedSystemState, bool);
91	>	DeclareParameter(OrthoBoxTolerance, RealType);
92	>	DeclareParameter(Minimizer, std::string);
93	>	DeclareParameter(MinimizerMaxIter, RealType);
94	>	DeclareParameter(MinimizerWriteFreq, int);
95	>	DeclareParameter(MinimizerStepSize, RealType);
96	>	DeclareParameter(MinimizerFTol, RealType);
97	>	DeclareParameter(MinimizerGTol, RealType);
98	>	DeclareParameter(MinimizerLSTol, RealType);
99	>	DeclareParameter(MinimizerLSMaxIter, int);
100	>	DeclareParameter(ZconsGap, RealType);
101	>	DeclareParameter(ZconsFixtime, RealType);
102	>	DeclareParameter(ZconsUsingSMD, bool);
103	>	DeclareParameter(UseThermodynamicIntegration, bool);
104	>	DeclareParameter(ThermodynamicIntegrationLambda, RealType);
105	>	DeclareParameter(ThermodynamicIntegrationK, RealType);
106	>	DeclareParameter(ForceFieldVariant, std::string);
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);
128	>	DeclareParameter(Viscosity, RealType);
129	>	DeclareParameter(BeadSize, RealType);
130	>	DeclareParameter(UseSphericalBoundaryConditions, bool);
131	>	DeclareParameter(FrozenBufferRadius, RealType);
132	>	DeclareParameter(LangevinBufferRadius, RealType);
133	>	DeclareParameter(AccumulateBoxDipole, bool);
134	>	DeclareParameter(NeighborListNeighbors, int);
135	>	DeclareParameter(UseMultipleTemperatureMethod, bool);
136	>	DeclareParameter(MTM_Ce, RealType);
137	>	DeclareParameter(MTM_G, RealType);
138	>	DeclareParameter(MTM_Io, RealType);
139	>	DeclareParameter(MTM_Sigma, RealType);
140	>	DeclareParameter(MTM_R, RealType);
141	>	DeclareParameter(UseRNEMD, bool);
142	>	DeclareParameter(RNEMD_exchangeTime, RealType);
143	>	DeclareParameter(RNEMD_nBins, int);
144	>	DeclareParameter(RNEMD_logWidth, int);
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	>	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
93	–	//int
94	–	template<>
95	–	struct ParameterTraits<int>{
96	–	typedef int RepType;
97	–	template<typename T> static bool    convert(T, RepType&){return false;}
98	–	template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
99	–	static bool convert(RepType v, RepType& r)            { r=v; return true;}
100	–	static std::string getParamType() { return "int";}
101	–	};
102	–
103	–	//double
104	–	template<>
105	–	struct ParameterTraits<double>{
106	–	typedef double RepType;
107	–	template<typename T> static bool    convert(T, RepType&){return false;}
108	–	template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
109	–	static bool convert(RepType v, RepType& r)            {r=v; return true;}
110	–	static bool convert(int v, RepType& r)                {r = static_cast<double>(v); return true;}
111	–	static std::string getParamType() { return "double";}
112	–	};
113	–
114	–
115	–	class ParameterBase {
116	–	public:
117	–	ParameterBase() : keyword_(), optional_(false), defaultValue_(false), empty_(true) {}
118	–	virtual ~ParameterBase() {}
119	–	bool isOptional() {return optional_;}
120	–	void setOptional(bool optional) {optional_ = optional;}
121	–	bool hasDefaultValue() {return defaultValue_;}
122	–	virtual bool isValid() { return true;}
123	–	const std::string& getKeyword() {return keyword_;}
124	–	void setKeyword(const std::string& keyword) { keyword_ = keyword;}
125	–	bool empty() {return empty_;}
126	–	virtual bool setData(std::string) = 0;
127	–	virtual bool setData(int) = 0;
128	–	virtual bool setData(double) = 0;
129	–	virtual std::string getParamType() = 0;
130	–	protected:
131	–	std::string keyword_;
132	–	bool optional_;
133	–	bool defaultValue_;
134	–	bool empty_;
135	–	};
136	–
137	–	template<class ParamType>
138	–	class Parameter : public ParameterBase{
139	–	public:
140	–	typedef ParameterTraits<ParamType> ValueType;
141	–	void setDefaultValue(const ParamType& value) {data_ = value; defaultValue_ = true;}
142	–	ParamType getData() { return data_;}
143	–
144	–	virtual bool setData(std::string sval) {
145	–	return internalSetData<std::string>(sval);
146	–	}
147	–	virtual bool setData(int ival) {
148	–	return internalSetData<int>(ival);
149	–	}
150	–
151	–	virtual bool setData(double dval) {
152	–	return internalSetData<double>(dval);
153	–	}
154	–
155	–	virtual std::string getParamType() { return ParameterTraits<ParamType>::getParamType();}
156	–	private:
157	–	template<class T> bool internalSetData(T data) {
158	–	ParamType tmp;
159	–	bool result = ValueType::convert(data, tmp);
160	–	if (result) {
161	–	empty_ = false;
162	–	data_ = tmp;
163	–	}
164	–	return result;
165	–	}
166	–
167	–	private:
168	–	ParamType data_;
169	–
170	–	};
171	–
172	–	#define DeclareParameter(NAME, TYPE)         \
173	–	private:                                                   \
174	–	Parameter<TYPE> NAME;                                     \
175	–	public:                                                      \
176	–	bool have##NAME() { return !NAME.empty();}  \
177	–	TYPE get##NAME() { return NAME.getData();}
178	–
179	–
180	–	class Globals {
174		public:
175	<	Globals();
175	>	bool addComponent(Component* comp);
176	>	bool addZConsStamp(ZConsStamp* zcons);
177	>	bool addRestraintStamp(RestraintStamp* rest);
178	>	bool addMoleculeStamp(MoleculeStamp* molStamp);
179	>	int getNComponents() {return components_.size();}
180	>	std::vector<Component*> getComponents() {return components_;}
181	>	Component* getComponentAt(int index) {return components_.at(index);}
182
183	<	DeclareParameter(ForceField, std::string);
184	<	DeclareParameter(NComponents, int);
185	<	DeclareParameter(TargetTemp, double);
187	<	DeclareParameter(Ensemble, std::string);
188	<	DeclareParameter(Dt, double);
189	<	DeclareParameter(RunTime, double);
190	<	DeclareParameter(InitialConfig, std::string);
191	<	DeclareParameter(FinalConfig, std::string);
192	<	DeclareParameter(NMol, int);
193	<	DeclareParameter(Density, double);
194	<	DeclareParameter(Box, double);
195	<	DeclareParameter(BoxX, double);
196	<	DeclareParameter(BoxY, double);
197	<	DeclareParameter(BoxZ, double);
198	<	DeclareParameter(SampleTime, double);
199	<	DeclareParameter(ResetTime, double);
200	<	DeclareParameter(StatusTime, double);
201	<	DeclareParameter(CutoffRadius, double);
202	<	DeclareParameter(SwitchingRadius, double);
203	<	DeclareParameter(Dielectric, double);
204	<	DeclareParameter(TempSet, bool);
205	<	DeclareParameter(ThermalTime, double);
206	<	DeclareParameter(MixingRule, std::string);
207	<	DeclareParameter(UsePeriodicBoundaryConditions, bool);
208	<	DeclareParameter(TargetPressure, double);
209	<	DeclareParameter(TauThermostat, double);
210	<	DeclareParameter(TauBarostat, double);
211	<	DeclareParameter(ZconsTime, double);
212	<	DeclareParameter(NZconstraints, int);
213	<	DeclareParameter(ZconsTol, double);
214	<	DeclareParameter(ZconsForcePolicy, std::string);
215	<	DeclareParameter(Seed, int);
216	<	DeclareParameter(UseInitalTime, bool);
217	<	DeclareParameter(UseIntialExtendedSystemState, bool);
218	<	DeclareParameter(OrthoBoxTolerance, double);
219	<	DeclareParameter(Minimizer, std::string);
220	<	DeclareParameter(MinimizerMaxIter, double);
221	<	DeclareParameter(MinimizerWriteFrq, int);
222	<	DeclareParameter(MinimizerStepSize, double);
223	<	DeclareParameter(MinimizerFTol, double);
224	<	DeclareParameter(MinimizerGTol, double);
225	<	DeclareParameter(MinimizerLSTol, double);
226	<	DeclareParameter(MinimizerLSMaxIter, int);
227	<	DeclareParameter(ZconsGap, double);
228	<	DeclareParameter(ZconsFixtime, double);
229	<	DeclareParameter(ZconsUsingSMD, bool);
230	<	DeclareParameter(UseSolidThermInt, bool);
231	<	DeclareParameter(UseLiquidThermInt, bool);
232	<	DeclareParameter(ThermodynamicIntegrationLambda, double);
233	<	DeclareParameter(ThermodynamicIntegrationK, double);
234	<	DeclareParameter(ForceFieldVariant, std::string);
235	<	DeclareParameter(ForceFieldFileName, std::string);
236	<	DeclareParameter(ThermIntDistSpringConst, double);
237	<	DeclareParameter(ThermIntThetaSpringConst, double);
238	<	DeclareParameter(ThermIntOmegaSpringConst, double);
239	<	DeclareParameter(SurfaceTension, double);
240	<	DeclareParameter(PrintPressureTensor, bool);
241	<	DeclareParameter(ElectrostaticSummationMethod, std::string);
242	<	DeclareParameter(ElectrostaticScreeningMethod, std::string);
243	<	DeclareParameter(DampingAlpha, double);
244	<	DeclareParameter(CutoffPolicy, std::string);
245	<	DeclareParameter(SwitchingFunctionType, std::string);
246	<	DeclareParameter(CompressDumpFile, bool);
247	<	DeclareParameter(OutputForceVector, bool);
248	<	DeclareParameter(SkinThickness, double);
249	<	DeclareParameter(StatFileFormat, std::string);
183	>	int getNZconsStamps() {return zconstraints_.size();}
184	>	std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
185	>	ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}
186
187	+	int getNRestraintStamps() {return restraints_.size();}
188	+	std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
189	+	RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}
190	+
191	+	virtual void validate();
192		private:
252	–	typedef std::map<std::string, ParameterBase*> ParamMap;
253	–	ParamMap parameters_;
193
194	<	Component* current_component;
195	<	Component** components; // the array of components
196	<
197	<	ZconStamp* current_zConstraint;
198	<	ZconStamp** zConstraints; // the array of zConstraints
260	<
261	<	char* checkMe();
262	<
263	<	public:
264	<	int newComponent( event* the_event );
265	<	int componentAssign( event* the_event );
266	<	int componentEnd( event* the_event );
267	<
268	<	int newZconstraint( event* the_event );
269	<	int zConstraintAssign( event* the_event );
270	<	int zConstraintEnd( event* the_event );
271	<
272	<	int globalAssign( event* the_event );
273	<	int globalEnd( event* the_event );
274	<
275	<	ZconStamp** getZconStamp() {return zConstraints;}
276	<	Component** getComponents() {return components;}
194	>	std::vector<Component*> components_;
195	>	std::vector<ZConsStamp*> zconstraints_;
196	>	std::vector<RestraintStamp*> restraints_;
197	>	std::map<std::string, MoleculeStamp*> moleculeStamps_;
198	>	std::pair<int, int> taggedAtomPair_;
199		};
200	+	}
201		#endif
279	–

Comparing:
trunk/src/io/Globals.hpp (property svn:keywords), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/Globals.hpp (property svn:keywords), Revision 1729 by jmarr, Wed May 30 16:08:07 2012 UTC

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