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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 666 by chrisfen, Fri Oct 14 14:18:02 2005 UTC vs.
Revision 1423 by gezelter, Tue Mar 30 15:05:13 2010 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <stdlib.h>
# Line 45 | Line 45
45   #include <string>
46  
47   #include "io/Globals.hpp"
48 + #include "io/ParamConstraint.hpp"
49 + #include "utils/MemoryUtils.hpp"
50   #include "utils/simError.h"
49 – #ifdef IS_MPI
50 – #include "io/mpiBASS.h"
51 – #endif // is_mpi
51  
52 <
53 < #define DefineParameter(NAME,KEYWORD)                              \
55 <  NAME.setKeyword(KEYWORD);                  \
56 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
57 <
58 < #define DefineOptionalParameter(NAME,KEYWORD)                              \
59 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
60 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
61 <
62 < #define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
63 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
64 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
65 <
66 < Globals::Globals(){
67 <
52 > namespace OpenMD {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
69 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
75 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
77 –  DefineOptionalParameter(NMol, "nMol");
78 –  DefineOptionalParameter(Density, "density");
79 –  DefineOptionalParameter(Box, "box");
80 –  DefineOptionalParameter(BoxX, "boxX");
81 –  DefineOptionalParameter(BoxY, "boxY");
82 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
88 –  DefineOptionalParameter(Dielectric, "dielectric");
66    DefineOptionalParameter(TempSet, "tempSet");
67    DefineOptionalParameter(ThermalTime, "thermalTime");
68 <  DefineOptionalParameter(TargetPressure, "targetPressure");
68 >  DefineOptionalParameter(TargetPressure, "targetPressure");  
69    DefineOptionalParameter(TauThermostat, "tauThermostat");
70    DefineOptionalParameter(TauBarostat, "tauBarostat");
71    DefineOptionalParameter(ZconsTime, "zconsTime");
95 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
75    DefineOptionalParameter(Minimizer, "minimizer");
76    DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77 <  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
77 >  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
78    DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79    DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80    DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
# Line 111 | Line 87 | Globals::Globals(){
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
115 <  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
116 <  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
90 >  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
93 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96 <  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
96 >  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 >  DefineOptionalParameter(Viscosity, "viscosity");
99 >  DefineOptionalParameter(BeadSize, "beadSize");
100 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103 >  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104 >  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105 >  DefineOptionalParameter(MTM_G, "MTM_G");
106 >  DefineOptionalParameter(MTM_Io, "MTM_Io");
107 >  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108 >  DefineOptionalParameter(MTM_R, "MTM_R");
109 >  DefineOptionalParameter(Alpha, "alpha");
110 >
111    
123 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
112    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
113 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
114    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
117 <  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
118 <  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
119 <  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
131 <  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
132 <  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
133 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
117 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
120    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
123 <  
124 < }
123 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
124 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
125 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126  
127 < int Globals::globalAssign( event* the_event ){
128 <  
129 <  int key;
130 <  int token;
131 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
132 <  char* lhs = the_event->evt.asmt.lhs;
133 <  std::string keyword(lhs);
127 >  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130 >  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132 >  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135 >  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136 >  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137 >  DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138  
147 –  bool result;
139  
140 <
141 <  ParamMap::iterator i =parameters_.find(keyword);
142 <  if (i != parameters_.end()) {
143 <    if( the_type == STRING ){
144 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
145 <       if (!result ) {
146 <            sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
147 <       }
157 <    } else if( the_type == DOUBLE ){
158 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
159 <       if (!result )
160 <         sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() );
161 <    }      
162 <    else if (the_type == INT ){
163 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
164 <       if (!result )
165 <         sprintf(the_event->err_msg,  "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() );
166 <      
167 <    } else {
168 <    
169 <    }
170 <  }
171 <
172 <  if (keyword == "nComponents" && getNComponents() > 0) {
173 <    components = new Component*[getNComponents()];
174 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
175 <    zConstraints = new ZconStamp*[getNZconstraints()];
176 <  }
177 <  
178 <  return result;
179 < }
180 <
181 < int Globals::newComponent( event* the_event ){
182 <  
183 <  current_component = new Component;
184 <  int index = the_event->evt.blk_index;
185 <  char err[200];
186 <  
187 <  if( haveNComponents() && index < getNComponents() )
188 <    components[index] = current_component;
189 <  else{
190 <    if( haveNComponents()  ){
191 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
192 <               index );
193 <      the_event->err_msg = strdup( err );
194 <      return 0;
195 <    }
196 <    else{
197 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
198 <                                  " first component declaration." );
199 <      return 0;
200 <    }
201 <  }  
202 <
203 <  return 1;
204 < }
205 <
206 <
207 <
208 < int Globals::componentAssign( event* the_event ){
209 <
210 <  switch( the_event->evt.asmt.asmt_type ){
211 <    
212 <  case STRING:
213 <    return current_component->assignString( the_event->evt.asmt.lhs,
214 <                                            the_event->evt.asmt.rhs.sval,
215 <                                            &(the_event->err_msg));
216 <    break;
217 <    
218 <  case DOUBLE:
219 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
220 <                                            the_event->evt.asmt.rhs.dval,
221 <                                            &(the_event->err_msg));
222 <    break;
223 <    
224 <  case INT:
225 <    return current_component->assignInt( the_event->evt.asmt.lhs,
226 <                                         the_event->evt.asmt.rhs.ival,
227 <                                         &(the_event->err_msg));
228 <    break;
140 >  deprecatedKeywords_.insert("nComponents");
141 >  deprecatedKeywords_.insert("nZconstraints");
142 >  deprecatedKeywords_.insert("initialConfig");
143 >  deprecatedKeywords_.insert("thermIntDistSpringConst");
144 >  deprecatedKeywords_.insert("thermIntThetaSpringConst");
145 >  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
146 >  deprecatedKeywords_.insert("useSolidThermInt");  
147 >  deprecatedKeywords_.insert("useLiquidThermInt");
148      
230 –  default:
231 –    the_event->err_msg = strdup( "Globals error. Invalid component"
232 –                                 " assignment type" );
233 –    return 0;
234 –    break;
235 –  }
236 –  return 0;
149   }
150  
151 < int Globals::componentEnd( event* the_event ){
151 > Globals::~Globals() {
152 >    MemoryUtils::deletePointers(components_);
153 >    MemoryUtils::deletePointers(zconstraints_);
154 >    MemoryUtils::deletePointers(restraints_);
155 > }
156  
157 <  the_event->err_msg = current_component->checkMe();
158 <  if( the_event->err_msg != NULL ) return 0;
157 > void Globals::validate() {
158 >  DataHolder::validate();
159  
160 <  return 1;
161 < }
160 >  CheckParameter(ForceField, isNotEmpty());
161 >  CheckParameter(TargetTemp, isPositive());
162 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
163 >  CheckParameter(Dt, isPositive());
164 >  CheckParameter(RunTime, isPositive());
165 >  CheckParameter(FinalConfig, isNotEmpty());
166 >  CheckParameter(SampleTime, isNonNegative());
167 >  CheckParameter(ResetTime, isNonNegative());
168 >  CheckParameter(StatusTime, isNonNegative());
169 >  CheckParameter(CutoffRadius, isPositive());
170 >  CheckParameter(SwitchingRadius, isNonNegative());
171 >  CheckParameter(Dielectric, isPositive());
172 >  CheckParameter(ThermalTime,  isNonNegative());
173 >  CheckParameter(TauThermostat, isPositive());
174 >  CheckParameter(TauBarostat, isPositive());
175 >  CheckParameter(ZconsTime, isPositive());
176 >  CheckParameter(ZconsTol, isPositive());
177 >  CheckParameter(Seed, isPositive());
178 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
179 >  CheckParameter(MinimizerMaxIter, isPositive());
180 >  CheckParameter(MinimizerWriteFreq, isPositive());
181 >  CheckParameter(MinimizerStepSize, isPositive());
182 >  CheckParameter(MinimizerFTol, isPositive());
183 >  CheckParameter(MinimizerGTol, isPositive());
184 >  CheckParameter(MinimizerLSTol, isPositive());
185 >  CheckParameter(MinimizerLSMaxIter, isPositive());
186 >  CheckParameter(ZconsGap, isPositive());
187 >  CheckParameter(ZconsFixtime, isPositive());
188 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
189 >  CheckParameter(ThermodynamicIntegrationK, isPositive());
190 >  CheckParameter(ForceFieldVariant, isNotEmpty());
191 >  CheckParameter(ForceFieldFileName, isNotEmpty());
192 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
194 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196 >  //CheckParameter(StatFileFormat,);    
197 >  CheckParameter(OrthoBoxTolerance, isPositive());  
198 >  CheckParameter(DampingAlpha,isNonNegative());
199 >  CheckParameter(SkinThickness, isPositive());
200 >  CheckParameter(Viscosity, isNonNegative());
201 >  CheckParameter(BeadSize, isPositive());
202 >  CheckParameter(FrozenBufferRadius, isPositive());
203 >  CheckParameter(LangevinBufferRadius, isPositive());
204 >  CheckParameter(NeighborListNeighbors, isPositive());
205 >  CheckParameter(RNEMD_exchangeTime, isPositive());
206 >  CheckParameter(RNEMD_nBins, isPositive() && isEven());
207 >  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208 >  CheckParameter(RNEMD_targetFlux, isNonNegative());
209 >  CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210 >  CheckParameter(Alpha, isPositive());
211  
247 – int Globals::newZconstraint( event* the_event ){
212    
213 <
214 <  int index = the_event->evt.blk_index;
215 <  char err[200];
216 <  current_zConstraint = new ZconStamp( index );
217 <  
254 <  if( haveNZconstraints() && index < getNZconstraints() )
255 <    zConstraints[index] = current_zConstraint;
256 <  else{
257 <    if( haveNZconstraints() ){
258 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
259 <               index );
260 <      the_event->err_msg = strdup( err );
261 <      return 0;
213 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215 >        std::ostringstream oss;
216 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217 >        throw OpenMDException(oss.str());          
218      }
219 <    else{
264 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
265 <                                  " not given before"
266 <                                  " first zConstraint declaration." );
267 <      return 0;
268 <    }
269 <  }  
270 <
271 <  return 1;
219 >  }
220   }
221 +  
222 + bool Globals::addComponent(Component* comp) {
223 +    components_.push_back(comp);
224 +    return true;
225 + }
226  
227 <
228 <
229 < int Globals::zConstraintAssign( event* the_event ){
277 <
278 <  switch( the_event->evt.asmt.asmt_type ){
279 <    
280 <  case STRING:
281 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
282 <                                              the_event->evt.asmt.rhs.sval,
283 <                                              &(the_event->err_msg));
284 <    break;
285 <    
286 <  case DOUBLE:
287 <    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
288 <                                              the_event->evt.asmt.rhs.dval,
289 <                                              &(the_event->err_msg));
290 <    break;
291 <    
292 <  case INT:
293 <    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
294 <                                           the_event->evt.asmt.rhs.ival,
295 <                                           &(the_event->err_msg));
296 <    break;
297 <    
298 <  default:
299 <    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
300 <                                 " assignment type" );
301 <    return 0;
302 <    break;
303 <  }
304 <  return 0;
227 > bool Globals::addZConsStamp(ZConsStamp* zcons) {
228 >    zconstraints_.push_back(zcons);
229 >    return true;
230   }
231  
232 < int Globals::zConstraintEnd( event* the_event ){
233 <
234 <  the_event->err_msg = current_zConstraint->checkMe();
310 <  if( the_event->err_msg != NULL ) return 0;
311 <
312 <  return 1;
232 > bool Globals::addRestraintStamp(RestraintStamp* rest) {
233 >    restraints_.push_back(rest);
234 >    return true;
235   }
236  
237 < char* Globals::checkMe( void ){
238 <
239 <
240 <  std::string err("The following required keywords are missing:\n");
241 <  short int have_err = 0;
242 <
243 <  ParamMap::iterator i;
244 <  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
245 <    if (!i->second->isOptional() && i->second->empty()) {
246 <        err +=  i->second->getKeyword() + "\n";
237 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238 >    std::string molStampName = molStamp->getName();
239 >    std::map<std::string, MoleculeStamp*>::iterator i;
240 >    bool ret = false;
241 >    i = moleculeStamps_.find(molStampName);
242 >    if (i == moleculeStamps_.end()) {
243 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
244 >        ret = true;
245 >    } else {
246 >        std::ostringstream oss;
247 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248 >        throw OpenMDException(oss.str());  
249      }
250 <  }
327 <
328 <  //@todo memory leak
329 <  if( have_err )
330 <    return strdup( err.c_str() );
331 <  
332 <  return NULL;
333 <
334 <
250 >    return ret;
251   }
252 +
253  
337 – int Globals::globalEnd( event* the_event ){
338 –  
339 –  the_event->err_msg = checkMe();
340 –  if( the_event->err_msg != NULL ) return 0;
341 –
342 –  return 1;
254   }

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