src/io/Globals.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <string>

#include "io/Globals.hpp"
#include "io/ParamConstraint.hpp"
#include "utils/MemoryUtils.hpp"
#include "utils/simError.h"

namespace oopse {
Globals::Globals() {
  DefineParameter(ForceField, "forceField")
 
  DefineOptionalParameter(TargetTemp, "targetTemp");
  DefineOptionalParameter(Ensemble, "ensemble");
  DefineOptionalParameter(Dt, "dt");
  DefineOptionalParameter(RunTime, "runTime");
  DefineOptionalParameter(InitialConfig, "initialConfig");
  DefineOptionalParameter(FinalConfig, "finalConfig");
  DefineOptionalParameter(SampleTime, "sampleTime");
  DefineOptionalParameter(ResetTime, "resetTime");
  DefineOptionalParameter(StatusTime, "statusTime");
  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
  DefineOptionalParameter(Dielectric, "dielectric");
  DefineOptionalParameter(TempSet, "tempSet");
  DefineOptionalParameter(ThermalTime, "thermalTime");
  DefineOptionalParameter(TargetPressure, "targetPressure");
  DefineOptionalParameter(TauThermostat, "tauThermostat");
  DefineOptionalParameter(TauBarostat, "tauBarostat");
  DefineOptionalParameter(ZconsTime, "zconsTime");
  DefineOptionalParameter(ZconsTol, "zconsTol");
  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
  DefineOptionalParameter(Seed, "seed");
  DefineOptionalParameter(Minimizer, "minimizer");
  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
  DefineOptionalParameter(ZconsGap, "zconsGap");
  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
  DefineOptionalParameter(SurfaceTension, "surfaceTension");
  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    


    deprecatedKeywords_.insert("nComponents");
    deprecatedKeywords_.insert("nZconstraints");
    
}

Globals::~Globals() {
    MemoryUtils::deletePointers(components_);
    MemoryUtils::deletePointers(zconstraints_);
}

void Globals::validate() {
  DataHolder::validate();

  CheckParameter(ForceField, isNotEmpty());
  CheckParameter(TargetTemp, isPositive());
  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  );
  CheckParameter(Dt, isPositive());
  CheckParameter(RunTime, isPositive());
  CheckParameter(InitialConfig, isNotEmpty());
  CheckParameter(FinalConfig, isNotEmpty());
  CheckParameter(SampleTime, isNonNegative());
  CheckParameter(ResetTime, isNonNegative());
  CheckParameter(StatusTime, isNonNegative());
  CheckParameter(CutoffRadius, isPositive());
  CheckParameter(SwitchingRadius, isNonNegative());
  CheckParameter(Dielectric, isPositive());
  CheckParameter(ThermalTime,  isNonNegative());
  CheckParameter(TargetPressure,  isPositive());
  CheckParameter(TauThermostat, isPositive());
  CheckParameter(TauBarostat, isPositive());
  CheckParameter(ZconsTime, isPositive());
  CheckParameter(ZconsTol, isPositive());
  CheckParameter(Seed, isPositive());
  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
  CheckParameter(MinimizerMaxIter, isPositive());
  CheckParameter(MinimizerWriteFrq, isPositive());
  CheckParameter(MinimizerStepSize, isPositive());
  CheckParameter(MinimizerFTol, isPositive());
  CheckParameter(MinimizerGTol, isPositive());
  CheckParameter(MinimizerLSTol, isPositive());
  CheckParameter(MinimizerLSMaxIter, isPositive());
  CheckParameter(ZconsGap, isPositive());
  CheckParameter(ZconsFixtime, isPositive());
  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
  CheckParameter(ThermodynamicIntegrationK, isPositive());
  CheckParameter(ForceFieldVariant, isNotEmpty());
  CheckParameter(ForceFieldFileName, isNotEmpty());
  CheckParameter(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(SurfaceTension, isPositive());
  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
  //CheckParameter(StatFileFormat,);     
  CheckParameter(OrthoBoxTolerance, isPositive());  
  CheckParameter(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(DampingAlpha,isNonNegative());
  CheckParameter(SkinThickness, isPositive());

  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
        std::ostringstream oss;
        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
        throw OOPSEException(oss.str());           
    }
  }
}
    
bool Globals::addComponent(Component* comp) {
    components_.push_back(comp);
    return true;
}

bool Globals::addZConsStamp(ZConsStamp* zcons) {
    zconstraints_.push_back(zcons);
    return true;
}

bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
    std::string molStampName = molStamp->getName();
    std::map<std::string, MoleculeStamp*>::iterator i;
    bool ret = false;
    i = moleculeStamps_.find(molStampName);
    if (i == moleculeStamps_.end()) {
        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
        ret = true;
    } else {
        std::ostringstream oss;
        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
        throw OOPSEException(oss.str());  
    }
    return ret;
}
 

}
Revision:	867
Committed:	Fri Jan 13 21:57:48 2006 UTC (19 years, 3 months ago) by chuckv
File size:	10902 byte(s)
Log Message:	Removed MixingRule from Globals. Handled by forceField now.
#	User	Rev	Content
1	gezelter	404	/*
2	gezelter	246	* Copyright (c) 2005 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	2	#include <stdlib.h>
43			#include <stdio.h>
44			#include <string.h>
45	tim	665	#include <string>
46	gezelter	2
47	tim	3	#include "io/Globals.hpp"
48	tim	816	#include "io/ParamConstraint.hpp"
49			#include "utils/MemoryUtils.hpp"
50	tim	3	#include "utils/simError.h"
51	gezelter	2
52	tim	770	namespace oopse {
53			Globals::Globals() {
54	tim	665	DefineParameter(ForceField, "forceField")
55
56			DefineOptionalParameter(TargetTemp, "targetTemp");
57			DefineOptionalParameter(Ensemble, "ensemble");
58			DefineOptionalParameter(Dt, "dt");
59			DefineOptionalParameter(RunTime, "runTime");
60			DefineOptionalParameter(InitialConfig, "initialConfig");
61			DefineOptionalParameter(FinalConfig, "finalConfig");
62			DefineOptionalParameter(SampleTime, "sampleTime");
63			DefineOptionalParameter(ResetTime, "resetTime");
64			DefineOptionalParameter(StatusTime, "statusTime");
65			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67			DefineOptionalParameter(Dielectric, "dielectric");
68			DefineOptionalParameter(TempSet, "tempSet");
69			DefineOptionalParameter(ThermalTime, "thermalTime");
70			DefineOptionalParameter(TargetPressure, "targetPressure");
71			DefineOptionalParameter(TauThermostat, "tauThermostat");
72			DefineOptionalParameter(TauBarostat, "tauBarostat");
73			DefineOptionalParameter(ZconsTime, "zconsTime");
74			DefineOptionalParameter(ZconsTol, "zconsTol");
75			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76			DefineOptionalParameter(Seed, "seed");
77			DefineOptionalParameter(Minimizer, "minimizer");
78			DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
79			DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
80			DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
81			DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
82			DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
83			DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
84			DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
85			DefineOptionalParameter(ZconsGap, "zconsGap");
86			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
87			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
88			DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
89			DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
90			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
91			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
92			DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93			DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94			DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
95			DefineOptionalParameter(SurfaceTension, "surfaceTension");
96			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97			DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98	chrisfen	716	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99	tim	665	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100	chrisfen	726	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101	tim	665	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
102			DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
103			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
104			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
105			DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
106			DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
107	chrisfen	666	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
108			DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
109			DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
110	chrisfen	716	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
111	tim	665	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
112	chrisfen	726	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
113	tim	665	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
114	tim	681	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
115
116	gezelter	2
117	tim	770	deprecatedKeywords_.insert("nComponents");
118			deprecatedKeywords_.insert("nZconstraints");
119	gezelter	2
120			}
121
122	tim	770	Globals::~Globals() {
123	tim	816	MemoryUtils::deletePointers(components_);
124			MemoryUtils::deletePointers(zconstraints_);
125	gezelter	2	}
126
127	tim	770	void Globals::validate() {
128			DataHolder::validate();
129	gezelter	2
130	tim	672	CheckParameter(ForceField, isNotEmpty());
131			CheckParameter(TargetTemp, isPositive());
132	chuckv	866	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") \|\| isEqualIgnoreCase("NVT") \|\| isEqualIgnoreCase("NPTi") \|\| isEqualIgnoreCase("NPTf") \|\| isEqualIgnoreCase("NPTxyz") \|\| isEqualIgnoreCase("NPAT") );
133	tim	672	CheckParameter(Dt, isPositive());
134			CheckParameter(RunTime, isPositive());
135			CheckParameter(InitialConfig, isNotEmpty());
136			CheckParameter(FinalConfig, isNotEmpty());
137			CheckParameter(SampleTime, isNonNegative());
138			CheckParameter(ResetTime, isNonNegative());
139			CheckParameter(StatusTime, isNonNegative());
140			CheckParameter(CutoffRadius, isPositive());
141			CheckParameter(SwitchingRadius, isNonNegative());
142			CheckParameter(Dielectric, isPositive());
143			CheckParameter(ThermalTime, isNonNegative());
144			CheckParameter(TargetPressure, isPositive());
145			CheckParameter(TauThermostat, isPositive());
146			CheckParameter(TauBarostat, isPositive());
147			CheckParameter(ZconsTime, isPositive());
148			CheckParameter(ZconsTol, isPositive());
149			CheckParameter(Seed, isPositive());
150	tim	850	CheckParameter(Minimizer, isEqualIgnoreCase("SD") \|\| isEqualIgnoreCase("CG"));
151	tim	672	CheckParameter(MinimizerMaxIter, isPositive());
152			CheckParameter(MinimizerWriteFrq, isPositive());
153			CheckParameter(MinimizerStepSize, isPositive());
154			CheckParameter(MinimizerFTol, isPositive());
155			CheckParameter(MinimizerGTol, isPositive());
156			CheckParameter(MinimizerLSTol, isPositive());
157			CheckParameter(MinimizerLSMaxIter, isPositive());
158			CheckParameter(ZconsGap, isPositive());
159			CheckParameter(ZconsFixtime, isPositive());
160			CheckParameter(ThermodynamicIntegrationLambda, isPositive());
161			CheckParameter(ThermodynamicIntegrationK, isPositive());
162			CheckParameter(ForceFieldVariant, isNotEmpty());
163			CheckParameter(ForceFieldFileName, isNotEmpty());
164			CheckParameter(ThermIntDistSpringConst, isPositive());
165			CheckParameter(ThermIntThetaSpringConst, isPositive());
166			CheckParameter(ThermIntOmegaSpringConst, isPositive());
167			CheckParameter(SurfaceTension, isPositive());
168	tim	850	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") \|\| isEqualIgnoreCase("SHIFTED_POTENTIAL") \|\| isEqualIgnoreCase("SHIFTED_FORCE") \|\| isEqualIgnoreCase("REACTION_FIELD"));
169			CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") \|\| isEqualIgnoreCase("DAMPED"));
170			CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") \|\| isEqualIgnoreCase("MAX") \|\| isEqualIgnoreCase("TRADITIONAL"));
171			CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") \|\| isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
172	tim	672	//CheckParameter(StatFileFormat,);
173			CheckParameter(OrthoBoxTolerance, isPositive());
174			CheckParameter(ThermIntDistSpringConst, isPositive());
175			CheckParameter(ThermIntThetaSpringConst, isPositive());
176			CheckParameter(ThermIntOmegaSpringConst, isPositive());
177	chrisfen	716	CheckParameter(DampingAlpha,isNonNegative());
178	tim	672	CheckParameter(SkinThickness, isPositive());
179	gezelter	2
180	tim	770	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
181			if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
182	tim	845	std::ostringstream oss;
183			oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
184			throw OOPSEException(oss.str());
185	tim	770	}
186			}
187			}
188
189			bool Globals::addComponent(Component* comp) {
190			components_.push_back(comp);
191			return true;
192			}
193	gezelter	2
194	tim	770	bool Globals::addZConsStamp(ZConsStamp* zcons) {
195			zconstraints_.push_back(zcons);
196			return true;
197	gezelter	2	}
198
199	tim	770	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
200			std::string molStampName = molStamp->getName();
201			std::map<std::string, MoleculeStamp*>::iterator i;
202			bool ret = false;
203			i = moleculeStamps_.find(molStampName);
204			if (i == moleculeStamps_.end()) {
205			moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
206			ret = true;
207			} else {
208	tim	845	std::ostringstream oss;
209			oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
210			throw OOPSEException(oss.str());
211	tim	770	}
212			return ret;
213	gezelter	2	}
214	tim	770
215
216			}