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root/OpenMD/branches/development/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 721 by chrisfen, Tue Nov 8 13:32:27 2005 UTC vs.
Revision 1355 by gezelter, Mon Jul 20 17:50:40 2009 UTC

# 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 < #include "io/ParamConstraint.hpp"
53 <
55 < #define DefineParameter(NAME,KEYWORD)                              \
56 <  NAME.setKeyword(KEYWORD);                  \
57 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
58 <
59 < #define DefineOptionalParameter(NAME,KEYWORD)                              \
60 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
61 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
62 <
63 < #define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
64 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
65 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
66 <
67 < #define CheckParameter(NAME, CONSTRAINT)                              \
68 <  if (!NAME.empty()) { if (!(CONSTRAINT)(NAME.getData())) { sprintf(painCave.errMsg,"Error in checking %s : should be %s\n",NAME.getKeyword().c_str(),(CONSTRAINT).getConstraintDescription().c_str()); painCave.isFatal = 1; painCave.severity = OOPSE_ERROR; simError();} }                
69 <
70 < Globals::Globals(){
71 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
73 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
79 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
81 –  DefineOptionalParameter(NMol, "nMol");
82 –  DefineOptionalParameter(Density, "density");
83 –  DefineOptionalParameter(Box, "box");
84 –  DefineOptionalParameter(BoxX, "boxX");
85 –  DefineOptionalParameter(BoxY, "boxY");
86 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92 –  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");
99 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 115 | Line 87 | Globals::Globals(){
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 +  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92    DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93    DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
97 <  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99 +  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100 +  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101 +  DefineOptionalParameter(Viscosity, "viscosity");
102 +  DefineOptionalParameter(BeadSize, "beadSize");
103 +  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104 +  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 +  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
106 +  DefineOptionalParameter(ThermalLength, "thermalLength");
107 +  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108 +  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
109 +  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
110 +  DefineOptionalParameter(MTM_G, "MTM_G");
111 +  DefineOptionalParameter(MTM_Io, "MTM_Io");
112 +  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
113 +  DefineOptionalParameter(MTM_R, "MTM_R");
114    
115 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
115 >
116 >  
117    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
118 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
119    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
120    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
121    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 134 | Line 124 | Globals::Globals(){
124    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
125    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
126    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
127 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
127 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
128 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
129 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
130    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
131 <  DefineOptionalParameterWithDefaultValue(DumpForceVector, "dumpForceVector", 0);
131 >  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
132    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
133    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
134 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
135 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
136  
137 <  
138 < }
139 <
140 < int Globals::globalAssign( event* the_event ){
141 <  char errorMessage[65535];
142 <  int key;
143 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
144 <  char* lhs = the_event->evt.asmt.lhs;
145 <  std::string keyword(lhs);
146 <
147 <  bool result = false;
148 <
149 <  /**@todo fix memory leak */  
156 <  ParamMap::iterator i =parameters_.find(keyword);
157 <  if (i != parameters_.end()) {
158 <    if( the_type == STRING ){
159 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
160 <       if (!result ) {
161 <            sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval);
162 <            the_event->err_msg = strdup(errorMessage);
163 <       }
164 <    } else if( the_type == DOUBLE ){
165 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
166 <       if (!result )
167 <         sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval );
168 <       the_event->err_msg = strdup(errorMessage);
169 <    }      
170 <    else if (the_type == INT ){
171 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
172 <       if (!result )
173 <         sprintf(errorMessage,  "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival );
174 <       the_event->err_msg = strdup(errorMessage);
175 <      
176 <    } else {
177 <        sprintf(errorMessage,  "Internal error of parser\n");
178 <        the_event->err_msg = strdup(errorMessage);
179 <    }
180 <  } else {
181 <    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
182 <    the_event->err_msg = strdup(errorMessage);
183 <  }
184 <
185 <  if (keyword == "nComponents" && getNComponents() > 0) {
186 <    components = new Component*[getNComponents()];
187 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
188 <    zConstraints = new ZconStamp*[getNZconstraints()];
189 <  }
190 <  
191 <  return result;
192 < }
193 <
194 < int Globals::newComponent( event* the_event ){
195 <  
196 <  current_component = new Component;
197 <  int index = the_event->evt.blk_index;
198 <  char err[200];
199 <  
200 <  if( haveNComponents() && index < getNComponents() )
201 <    components[index] = current_component;
202 <  else{
203 <    if( haveNComponents()  ){
204 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
205 <               index );
206 <      the_event->err_msg = strdup( err );
207 <      return 0;
208 <    }
209 <    else{
210 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
211 <                                  " first component declaration." );
212 <      return 0;
213 <    }
214 <  }  
215 <
216 <  return 1;
217 < }
218 <
219 <
220 <
221 < int Globals::componentAssign( event* the_event ){
222 <
223 <  switch( the_event->evt.asmt.asmt_type ){
224 <    
225 <  case STRING:
226 <    return current_component->assignString( the_event->evt.asmt.lhs,
227 <                                            the_event->evt.asmt.rhs.sval,
228 <                                            &(the_event->err_msg));
229 <    break;
230 <    
231 <  case DOUBLE:
232 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
233 <                                            the_event->evt.asmt.rhs.dval,
234 <                                            &(the_event->err_msg));
235 <    break;
236 <    
237 <  case INT:
238 <    return current_component->assignInt( the_event->evt.asmt.lhs,
239 <                                         the_event->evt.asmt.rhs.ival,
240 <                                         &(the_event->err_msg));
241 <    break;
242 <    
243 <  default:
244 <    the_event->err_msg = strdup( "Globals error. Invalid component"
245 <                                 " assignment type" );
246 <    return 0;
247 <    break;
248 <  }
249 <  return 0;
250 < }
251 <
252 < int Globals::componentEnd( event* the_event ){
253 <
254 <  the_event->err_msg = current_component->checkMe();
255 <  if( the_event->err_msg != NULL ) return 0;
256 <
257 <  return 1;
258 < }
259 <
260 < int Globals::newZconstraint( event* the_event ){
137 >  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
138 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
139 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
140 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
141 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
142 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "UseRestraints", false);
143 >  DefineOptionalParameterWithDefaultValue(Restraint_objectSelection, "Restraint_objectSelection", "select all");
144 >  DefineOptionalParameterWithDefaultValue(Restraint_type, "Restraint_type", "positional");
145 >  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
146 >  DefineOptionalParameterWithDefaultValue(Restraint_DisplacementSpringConstant, "Restraint_DisplacementSpringConstant", 0.0);
147 >  DefineOptionalParameterWithDefaultValue(Restraint_RollSpringConstant, "Restraint_RollSpringConstant", 0.0);   // phi
148 >  DefineOptionalParameterWithDefaultValue(Restraint_PitchSpringConstant, "Restraint_PitchSpringConstant", 0.0); // theta
149 >  DefineOptionalParameterWithDefaultValue(Restraint_YawSpringConstant, "Restraint_YawSpringConstant", 0.0);     // psi
150    
151  
152 <  int index = the_event->evt.blk_index;
153 <  char err[200];
154 <  current_zConstraint = new ZconStamp( index );
266 <  
267 <  if( haveNZconstraints() && index < getNZconstraints() )
268 <    zConstraints[index] = current_zConstraint;
269 <  else{
270 <    if( haveNZconstraints() ){
271 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
272 <               index );
273 <      the_event->err_msg = strdup( err );
274 <      return 0;
275 <    }
276 <    else{
277 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
278 <                                  " not given before"
279 <                                  " first zConstraint declaration." );
280 <      return 0;
281 <    }
282 <  }  
283 <
284 <  return 1;
285 < }
286 <
287 <
288 <
289 < int Globals::zConstraintAssign( event* the_event ){
290 <
291 <  switch( the_event->evt.asmt.asmt_type ){
152 >  deprecatedKeywords_.insert("nComponents");
153 >  deprecatedKeywords_.insert("nZconstraints");
154 >  deprecatedKeywords_.insert("initialConfig");
155      
293 –  case STRING:
294 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
295 –                                              the_event->evt.asmt.rhs.sval,
296 –                                              &(the_event->err_msg));
297 –    break;
298 –    
299 –  case DOUBLE:
300 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
301 –                                              the_event->evt.asmt.rhs.dval,
302 –                                              &(the_event->err_msg));
303 –    break;
304 –    
305 –  case INT:
306 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
307 –                                           the_event->evt.asmt.rhs.ival,
308 –                                           &(the_event->err_msg));
309 –    break;
310 –    
311 –  default:
312 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
313 –                                 " assignment type" );
314 –    return 0;
315 –    break;
316 –  }
317 –  return 0;
156   }
157  
158 < int Globals::zConstraintEnd( event* the_event ){
159 <
160 <  the_event->err_msg = current_zConstraint->checkMe();
323 <  if( the_event->err_msg != NULL ) return 0;
324 <
325 <  return 1;
158 > Globals::~Globals() {
159 >    MemoryUtils::deletePointers(components_);
160 >    MemoryUtils::deletePointers(zconstraints_);
161   }
162  
163 < char* Globals::checkMe( void ){
163 > void Globals::validate() {
164 >  DataHolder::validate();
165  
330 –
331 –  std::string err("The following required keywords are missing:\n");
332 –  short int have_err = 0;
333 –
334 –  ParamMap::iterator i;
335 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
336 –    if (!i->second->isOptional() && i->second->empty()) {
337 –        err +=  i->second->getKeyword() + "\n";
338 –    }
339 –  }
340 –
166    CheckParameter(ForceField, isNotEmpty());
342 –  CheckParameter(NComponents,isPositive());
167    CheckParameter(TargetTemp, isPositive());
168 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
345 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
346 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
168 >  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"));
169    CheckParameter(Dt, isPositive());
170    CheckParameter(RunTime, isPositive());
349 –  CheckParameter(InitialConfig, isNotEmpty());
171    CheckParameter(FinalConfig, isNotEmpty());
351 –  CheckParameter(NMol, isPositive());
352 –  CheckParameter(Density, isPositive());
353 –  CheckParameter(Box, isPositive());
354 –  CheckParameter(BoxX, isPositive());
355 –  CheckParameter(BoxY, isPositive());
356 –  CheckParameter(BoxZ, isPositive());
172    CheckParameter(SampleTime, isNonNegative());
173    CheckParameter(ResetTime, isNonNegative());
174    CheckParameter(StatusTime, isNonNegative());
# Line 361 | Line 176 | char* Globals::checkMe( void ){
176    CheckParameter(SwitchingRadius, isNonNegative());
177    CheckParameter(Dielectric, isPositive());
178    CheckParameter(ThermalTime,  isNonNegative());
364 –  CheckParameter(TargetPressure,  isPositive());
179    CheckParameter(TauThermostat, isPositive());
180    CheckParameter(TauBarostat, isPositive());
181    CheckParameter(ZconsTime, isPositive());
368 –  CheckParameter(NZconstraints, isPositive());  
182    CheckParameter(ZconsTol, isPositive());
370 –  //CheckParameter(ZconsForcePolicy,);
183    CheckParameter(Seed, isPositive());
184 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
184 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
185    CheckParameter(MinimizerMaxIter, isPositive());
186    CheckParameter(MinimizerWriteFrq, isPositive());
187    CheckParameter(MinimizerStepSize, isPositive());
# Line 379 | Line 191 | char* Globals::checkMe( void ){
191    CheckParameter(MinimizerLSMaxIter, isPositive());
192    CheckParameter(ZconsGap, isPositive());
193    CheckParameter(ZconsFixtime, isPositive());
194 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
194 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
195    CheckParameter(ThermodynamicIntegrationK, isPositive());
196    CheckParameter(ForceFieldVariant, isNotEmpty());
197    CheckParameter(ForceFieldFileName, isNotEmpty());
198    CheckParameter(ThermIntDistSpringConst, isPositive());
199    CheckParameter(ThermIntThetaSpringConst, isPositive());
200    CheckParameter(ThermIntOmegaSpringConst, isPositive());
201 <  CheckParameter(SurfaceTension, isPositive());
202 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE"))  || isEqualIgnoreCase(std::string("REACTION_FIELD")));
203 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
204 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
201 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
202 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
203 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
204 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
205    //CheckParameter(StatFileFormat,);    
394 –  //CheckParameter(MixingRule,);
206    CheckParameter(OrthoBoxTolerance, isPositive());  
207    CheckParameter(ThermIntDistSpringConst, isPositive());
208    CheckParameter(ThermIntThetaSpringConst, isPositive());
209    CheckParameter(ThermIntOmegaSpringConst, isPositive());
210    CheckParameter(DampingAlpha,isNonNegative());
211    CheckParameter(SkinThickness, isPositive());
212 <  
213 <  //@todo memory leak
214 <  if( have_err )
215 <    return strdup( err.c_str() );
216 <  
217 <  return NULL;
212 >  CheckParameter(Viscosity, isNonNegative());
213 >  CheckParameter(ThermalConductivity, isNonNegative());
214 >  CheckParameter(ThermalLength, isNonNegative());
215 >  CheckParameter(BeadSize, isPositive());
216 >  CheckParameter(FrozenBufferRadius, isPositive());
217 >  CheckParameter(LangevinBufferRadius, isPositive());
218 >  CheckParameter(NeighborListNeighbors, isPositive());
219 >  CheckParameter(RNEMD_swapTime, isPositive());
220 >  CheckParameter(RNEMD_nBins, isPositive() && isEven());
221 >  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
222 >  CheckParameter(Restraint_DisplacementSpringConstant, isNonNegative());
223 >  CheckParameter(Restraint_RollSpringConstant, isNonNegative());
224 >  CheckParameter(Restraint_PitchSpringConstant, isNonNegative());
225 >  CheckParameter(Restraint_YawSpringConstant, isNonNegative());
226 >  CheckParameter(Restraint_type, isEqualIgnoreCase("P") || isEqualIgnoreCase("O") || isEqualIgnoreCase("P+O") || isEqualIgnoreCase("RMSD_P") || isEqualIgnoreCase("RMSD_O") || isEqualIgnoreCase("RMSD_P+RMSD_O"));
227  
228 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
229 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
230 +        std::ostringstream oss;
231 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
232 +        throw OOPSEException(oss.str());          
233 +    }
234 +  }
235 + }
236 +    
237 + bool Globals::addComponent(Component* comp) {
238 +    components_.push_back(comp);
239 +    return true;
240 + }
241  
242 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
243 +    zconstraints_.push_back(zcons);
244 +    return true;
245   }
246  
247 < int Globals::globalEnd( event* the_event ){
248 <  
249 <  the_event->err_msg = checkMe();
250 <  if( the_event->err_msg != NULL ) return 0;
247 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
248 >    std::string molStampName = molStamp->getName();
249 >    std::map<std::string, MoleculeStamp*>::iterator i;
250 >    bool ret = false;
251 >    i = moleculeStamps_.find(molStampName);
252 >    if (i == moleculeStamps_.end()) {
253 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
254 >        ret = true;
255 >    } else {
256 >        std::ostringstream oss;
257 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
258 >        throw OOPSEException(oss.str());  
259 >    }
260 >    return ret;
261 > }
262 >
263  
416 –  return 1;
264   }

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