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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 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 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 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
100 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101 >  DefineOptionalParameter(Viscosity, "viscosity");
102 >  DefineOptionalParameter(BeadSize, "beadSize");
103 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106 >  
107 >  
108    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
109 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
110    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
111    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
112    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 134 | Line 115 | Globals::Globals(){
115    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
118 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
118 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
119 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
125 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
127  
128 <  
129 < }
130 <
146 < int Globals::globalAssign( event* the_event ){
147 <  char errorMessage[65535];
148 <  int key;
149 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
150 <  char* lhs = the_event->evt.asmt.lhs;
151 <  std::string keyword(lhs);
152 <
153 <  bool result = false;
154 <
155 <  /**@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 ){
261 <  
262 <
263 <  int index = the_event->evt.blk_index;
264 <  char err[200];
265 <  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 ){
128 >  deprecatedKeywords_.insert("nComponents");
129 >  deprecatedKeywords_.insert("nZconstraints");
130 >  deprecatedKeywords_.insert("initialConfig");
131      
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;
132   }
133  
134 < int Globals::zConstraintEnd( event* the_event ){
135 <
136 <  the_event->err_msg = current_zConstraint->checkMe();
323 <  if( the_event->err_msg != NULL ) return 0;
324 <
325 <  return 1;
134 > Globals::~Globals() {
135 >    MemoryUtils::deletePointers(components_);
136 >    MemoryUtils::deletePointers(zconstraints_);
137   }
138  
139 < char* Globals::checkMe( void ){
139 > void Globals::validate() {
140 >  DataHolder::validate();
141  
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 –
142    CheckParameter(ForceField, isNotEmpty());
342 –  CheckParameter(NComponents,isPositive());
143    CheckParameter(TargetTemp, isPositive());
144 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
345 <                 isEqualIgnoreCase(std::string("NVT")) ||
346 <                 isEqualIgnoreCase(std::string("NPTi")) ||
347 <                 isEqualIgnoreCase(std::string("NPTf")) ||
348 <                 isEqualIgnoreCase(std::string("NPTxyz")) );
144 >  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"));
145    CheckParameter(Dt, isPositive());
146    CheckParameter(RunTime, isPositive());
351 –  CheckParameter(InitialConfig, isNotEmpty());
147    CheckParameter(FinalConfig, isNotEmpty());
353 –  CheckParameter(NMol, isPositive());
354 –  CheckParameter(Density, isPositive());
355 –  CheckParameter(Box, isPositive());
356 –  CheckParameter(BoxX, isPositive());
357 –  CheckParameter(BoxY, isPositive());
358 –  CheckParameter(BoxZ, isPositive());
148    CheckParameter(SampleTime, isNonNegative());
149    CheckParameter(ResetTime, isNonNegative());
150    CheckParameter(StatusTime, isNonNegative());
# Line 363 | Line 152 | char* Globals::checkMe( void ){
152    CheckParameter(SwitchingRadius, isNonNegative());
153    CheckParameter(Dielectric, isPositive());
154    CheckParameter(ThermalTime,  isNonNegative());
366 –  CheckParameter(TargetPressure,  isPositive());
155    CheckParameter(TauThermostat, isPositive());
156    CheckParameter(TauBarostat, isPositive());
157    CheckParameter(ZconsTime, isPositive());
370 –  CheckParameter(NZconstraints, isPositive());  
158    CheckParameter(ZconsTol, isPositive());
372 –  //CheckParameter(ZconsForcePolicy,);
159    CheckParameter(Seed, isPositive());
160 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
375 <                 isEqualIgnoreCase(std::string("CG")));
160 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
161    CheckParameter(MinimizerMaxIter, isPositive());
162    CheckParameter(MinimizerWriteFrq, isPositive());
163    CheckParameter(MinimizerStepSize, isPositive());
# Line 382 | Line 167 | char* Globals::checkMe( void ){
167    CheckParameter(MinimizerLSMaxIter, isPositive());
168    CheckParameter(ZconsGap, isPositive());
169    CheckParameter(ZconsFixtime, isPositive());
170 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
170 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
171    CheckParameter(ThermodynamicIntegrationK, isPositive());
172    CheckParameter(ForceFieldVariant, isNotEmpty());
173    CheckParameter(ForceFieldFileName, isNotEmpty());
174    CheckParameter(ThermIntDistSpringConst, isPositive());
175    CheckParameter(ThermIntThetaSpringConst, isPositive());
176    CheckParameter(ThermIntOmegaSpringConst, isPositive());
177 <  CheckParameter(SurfaceTension, isPositive());
178 <  CheckParameter(ElectrostaticSummationMethod,
179 <                 isEqualIgnoreCase(std::string("NONE")) ||
180 <                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
396 <                 isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
397 <                 isEqualIgnoreCase(std::string("REACTION_FIELD")));
398 <  CheckParameter(ElectrostaticScreeningMethod,
399 <                 isEqualIgnoreCase(std::string("UNDAMPED")) ||
400 <                 isEqualIgnoreCase(std::string("DAMPED")));
401 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
402 <                 isEqualIgnoreCase(std::string("MAX")) ||
403 <                 isEqualIgnoreCase(std::string("TRADITIONAL")));
404 <  CheckParameter(SwitchingFunctionType,
405 <                 isEqualIgnoreCase(std::string("CUBIC")) ||
406 <                 isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
177 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
179 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
180 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181    //CheckParameter(StatFileFormat,);    
408 –  //CheckParameter(MixingRule,);
182    CheckParameter(OrthoBoxTolerance, isPositive());  
183    CheckParameter(ThermIntDistSpringConst, isPositive());
184    CheckParameter(ThermIntThetaSpringConst, isPositive());
185    CheckParameter(ThermIntOmegaSpringConst, isPositive());
186    CheckParameter(DampingAlpha,isNonNegative());
187    CheckParameter(SkinThickness, isPositive());
188 <  
189 <  //@todo memory leak
190 <  if( have_err )
191 <    return strdup( err.c_str() );
192 <  
420 <  return NULL;
188 >  CheckParameter(Viscosity, isNonNegative());
189 >  CheckParameter(BeadSize, isPositive());
190 >  CheckParameter(FrozenBufferRadius, isPositive());
191 >  CheckParameter(LangevinBufferRadius, isPositive());
192 >  CheckParameter(NeighborListNeighbors, isPositive());
193  
194 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
195 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
196 +        std::ostringstream oss;
197 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
198 +        throw OOPSEException(oss.str());          
199 +    }
200 +  }
201 + }
202 +    
203 + bool Globals::addComponent(Component* comp) {
204 +    components_.push_back(comp);
205 +    return true;
206 + }
207  
208 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
209 +    zconstraints_.push_back(zcons);
210 +    return true;
211   }
212  
213 < int Globals::globalEnd( event* the_event ){
214 <  
215 <  the_event->err_msg = checkMe();
216 <  if( the_event->err_msg != NULL ) return 0;
213 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
214 >    std::string molStampName = molStamp->getName();
215 >    std::map<std::string, MoleculeStamp*>::iterator i;
216 >    bool ret = false;
217 >    i = moleculeStamps_.find(molStampName);
218 >    if (i == moleculeStamps_.end()) {
219 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
220 >        ret = true;
221 >    } else {
222 >        std::ostringstream oss;
223 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
224 >        throw OOPSEException(oss.str());  
225 >    }
226 >    return ret;
227 > }
228 >
229  
430 –  return 1;
230   }

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