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 "utils/simError.h"

#include "io/ParamConstraint.hpp"

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(MixingRule, "mixingRule", "standard");
  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() {


}

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

  CheckParameter(ForceField, isNotEmpty());
  CheckParameter(TargetTemp, isPositive());
  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
  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(std::string("SD")) || isEqualIgnoreCase(std::string("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(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED"))); 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
  //CheckParameter(StatFileFormat,);     
  //CheckParameter(MixingRule,);
  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::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
    }
  }
}
    
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 {

    }
    return ret;
}
 

}
Revision:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (19 years, 10 months ago) by tim
File size:	10822 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	Content
1	/*
2	* 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	#include <stdlib.h>
43	#include <stdio.h>
44	#include <string.h>
45	#include <string>
46
47	#include "io/Globals.hpp"
48	#include "utils/simError.h"
49
50	#include "io/ParamConstraint.hpp"
51
52	namespace oopse {
53	Globals::Globals() {
54	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	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
103	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
104	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
105	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
106	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
107	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
108	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
112	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
113	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
114	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
116
117
118	deprecatedKeywords_.insert("nComponents");
119	deprecatedKeywords_.insert("nZconstraints");
120
121	}
122
123	Globals::~Globals() {
124
125
126	}
127
128	void Globals::validate() {
129	DataHolder::validate();
130
131	CheckParameter(ForceField, isNotEmpty());
132	CheckParameter(TargetTemp, isPositive());
133	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) \|\| isEqualIgnoreCase(std::string("NVT")) \|\| isEqualIgnoreCase(std::string("NPTi")) \|\| isEqualIgnoreCase(std::string("NPTf")) \|\| isEqualIgnoreCase(std::string("NPTxyz")) );
134	CheckParameter(Dt, isPositive());
135	CheckParameter(RunTime, isPositive());
136	CheckParameter(InitialConfig, isNotEmpty());
137	CheckParameter(FinalConfig, isNotEmpty());
138	CheckParameter(SampleTime, isNonNegative());
139	CheckParameter(ResetTime, isNonNegative());
140	CheckParameter(StatusTime, isNonNegative());
141	CheckParameter(CutoffRadius, isPositive());
142	CheckParameter(SwitchingRadius, isNonNegative());
143	CheckParameter(Dielectric, isPositive());
144	CheckParameter(ThermalTime, isNonNegative());
145	CheckParameter(TargetPressure, isPositive());
146	CheckParameter(TauThermostat, isPositive());
147	CheckParameter(TauBarostat, isPositive());
148	CheckParameter(ZconsTime, isPositive());
149	CheckParameter(ZconsTol, isPositive());
150	CheckParameter(Seed, isPositive());
151	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) \|\| isEqualIgnoreCase(std::string("CG")));
152	CheckParameter(MinimizerMaxIter, isPositive());
153	CheckParameter(MinimizerWriteFrq, isPositive());
154	CheckParameter(MinimizerStepSize, isPositive());
155	CheckParameter(MinimizerFTol, isPositive());
156	CheckParameter(MinimizerGTol, isPositive());
157	CheckParameter(MinimizerLSTol, isPositive());
158	CheckParameter(MinimizerLSMaxIter, isPositive());
159	CheckParameter(ZconsGap, isPositive());
160	CheckParameter(ZconsFixtime, isPositive());
161	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
162	CheckParameter(ThermodynamicIntegrationK, isPositive());
163	CheckParameter(ForceFieldVariant, isNotEmpty());
164	CheckParameter(ForceFieldFileName, isNotEmpty());
165	CheckParameter(ThermIntDistSpringConst, isPositive());
166	CheckParameter(ThermIntThetaSpringConst, isPositive());
167	CheckParameter(ThermIntOmegaSpringConst, isPositive());
168	CheckParameter(SurfaceTension, isPositive());
169	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) \|\| isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) \|\| isEqualIgnoreCase(std::string("SHIFTED_FORCE")) \|\| isEqualIgnoreCase(std::string("REACTION_FIELD")));
170	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) \|\| isEqualIgnoreCase(std::string("DAMPED")));
171	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) \|\| isEqualIgnoreCase(std::string("MAX")) \|\| isEqualIgnoreCase(std::string("TRADITIONAL")));
172	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) \|\| isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
173	//CheckParameter(StatFileFormat,);
174	//CheckParameter(MixingRule,);
175	CheckParameter(OrthoBoxTolerance, isPositive());
176	CheckParameter(ThermIntDistSpringConst, isPositive());
177	CheckParameter(ThermIntThetaSpringConst, isPositive());
178	CheckParameter(ThermIntOmegaSpringConst, isPositive());
179	CheckParameter(DampingAlpha,isNonNegative());
180	CheckParameter(SkinThickness, isPositive());
181
182	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
183	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
184	std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
185	}
186	}
187	}
188
189	bool Globals::addComponent(Component* comp) {
190	components_.push_back(comp);
191	return true;
192	}
193
194	bool Globals::addZConsStamp(ZConsStamp* zcons) {
195	zconstraints_.push_back(zcons);
196	return true;
197	}
198
199	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
209	}
210	return ret;
211	}
212
213
214	}