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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 748 by chuckv, Wed Nov 16 21:37:45 2005 UTC vs.
Revision 1331 by gezelter, Thu Apr 2 16:04:52 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 <
56 < Globals::Globals(){
57 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
59  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
65  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
67  DefineOptionalParameter(NMol, "nMol");
68  DefineOptionalParameter(Density, "density");
69  DefineOptionalParameter(Box, "box");
70  DefineOptionalParameter(BoxX, "boxX");
71  DefineOptionalParameter(BoxY, "boxY");
72  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
78  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");
85  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 101 | 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 >  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
107 >  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
108 >  DefineOptionalParameter(MTM_G, "MTM_G");
109 >  DefineOptionalParameter(MTM_Io, "MTM_Io");
110 >  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
111 >  DefineOptionalParameter(MTM_R, "MTM_R");
112 >  
113 >
114 >  
115    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
117    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
118    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
119    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 120 | Line 122 | Globals::Globals(){
122    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
125 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
126 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
127 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
128    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
130    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
131    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
132 +  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
133 +  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
134  
135 +  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137 +  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
138 +  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 +  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140    
130 }
141  
142 < int Globals::globalAssign( event* the_event ){
143 <  char errorMessage[65535];
144 <  int key;
135 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
136 <  char* lhs = the_event->evt.asmt.lhs;
137 <  std::string keyword(lhs);
138 <
139 <  bool result = false;
140 <
141 <  /**@todo fix memory leak */  
142 <  ParamMap::iterator i =parameters_.find(keyword);
143 <  if (i != parameters_.end()) {
144 <    if( the_type == STRING ){
145 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
146 <       if (!result ) {
147 <            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);
148 <            the_event->err_msg = strdup(errorMessage);
149 <       }
150 <    } else if( the_type == DOUBLE ){
151 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
152 <       if (!result )
153 <         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 );
154 <       the_event->err_msg = strdup(errorMessage);
155 <    }      
156 <    else if (the_type == INT ){
157 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
158 <       if (!result )
159 <         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 );
160 <       the_event->err_msg = strdup(errorMessage);
161 <      
162 <    } else {
163 <        sprintf(errorMessage,  "Internal error of parser\n");
164 <        the_event->err_msg = strdup(errorMessage);
165 <    }
166 <  } else {
167 <    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
168 <    the_event->err_msg = strdup(errorMessage);
169 <  }
170 <
171 <  if (keyword == "nComponents" && getNComponents() > 0) {
172 <    components = new Component*[getNComponents()];
173 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
174 <    zConstraints = new ZconStamp*[getNZconstraints()];
175 <  }
176 <  
177 <  return result;
178 < }
179 <
180 < int Globals::newComponent( event* the_event ){
181 <  
182 <  current_component = new Component;
183 <  int index = the_event->evt.blk_index;
184 <  char err[200];
185 <  
186 <  if( haveNComponents() && index < getNComponents() )
187 <    components[index] = current_component;
188 <  else{
189 <    if( haveNComponents()  ){
190 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
191 <               index );
192 <      the_event->err_msg = strdup( err );
193 <      return 0;
194 <    }
195 <    else{
196 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
197 <                                  " first component declaration." );
198 <      return 0;
199 <    }
200 <  }  
201 <
202 <  return 1;
203 < }
204 <
205 <
206 <
207 < int Globals::componentAssign( event* the_event ){
208 <
209 <  switch( the_event->evt.asmt.asmt_type ){
210 <    
211 <  case STRING:
212 <    return current_component->assignString( the_event->evt.asmt.lhs,
213 <                                            the_event->evt.asmt.rhs.sval,
214 <                                            &(the_event->err_msg));
215 <    break;
216 <    
217 <  case DOUBLE:
218 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
219 <                                            the_event->evt.asmt.rhs.dval,
220 <                                            &(the_event->err_msg));
221 <    break;
222 <    
223 <  case INT:
224 <    return current_component->assignInt( the_event->evt.asmt.lhs,
225 <                                         the_event->evt.asmt.rhs.ival,
226 <                                         &(the_event->err_msg));
227 <    break;
228 <    
229 <  default:
230 <    the_event->err_msg = strdup( "Globals error. Invalid component"
231 <                                 " assignment type" );
232 <    return 0;
233 <    break;
234 <  }
235 <  return 0;
236 < }
237 <
238 < int Globals::componentEnd( event* the_event ){
239 <
240 <  the_event->err_msg = current_component->checkMe();
241 <  if( the_event->err_msg != NULL ) return 0;
242 <
243 <  return 1;
244 < }
245 <
246 < int Globals::newZconstraint( event* the_event ){
247 <  
248 <
249 <  int index = the_event->evt.blk_index;
250 <  char err[200];
251 <  current_zConstraint = new ZconStamp( index );
252 <  
253 <  if( haveNZconstraints() && index < getNZconstraints() )
254 <    zConstraints[index] = current_zConstraint;
255 <  else{
256 <    if( haveNZconstraints() ){
257 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
258 <               index );
259 <      the_event->err_msg = strdup( err );
260 <      return 0;
261 <    }
262 <    else{
263 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
264 <                                  " not given before"
265 <                                  " first zConstraint declaration." );
266 <      return 0;
267 <    }
268 <  }  
269 <
270 <  return 1;
271 < }
272 <
273 <
274 <
275 < int Globals::zConstraintAssign( event* the_event ){
276 <
277 <  switch( the_event->evt.asmt.asmt_type ){
142 >  deprecatedKeywords_.insert("nComponents");
143 >  deprecatedKeywords_.insert("nZconstraints");
144 >  deprecatedKeywords_.insert("initialConfig");
145      
279  case STRING:
280    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
281                                              the_event->evt.asmt.rhs.sval,
282                                              &(the_event->err_msg));
283    break;
284    
285  case DOUBLE:
286    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
287                                              the_event->evt.asmt.rhs.dval,
288                                              &(the_event->err_msg));
289    break;
290    
291  case INT:
292    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
293                                           the_event->evt.asmt.rhs.ival,
294                                           &(the_event->err_msg));
295    break;
296    
297  default:
298    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
299                                 " assignment type" );
300    return 0;
301    break;
302  }
303  return 0;
146   }
147  
148 < int Globals::zConstraintEnd( event* the_event ){
149 <
150 <  the_event->err_msg = current_zConstraint->checkMe();
309 <  if( the_event->err_msg != NULL ) return 0;
310 <
311 <  return 1;
148 > Globals::~Globals() {
149 >    MemoryUtils::deletePointers(components_);
150 >    MemoryUtils::deletePointers(zconstraints_);
151   }
152  
153 < char* Globals::checkMe( void ){
153 > void Globals::validate() {
154 >  DataHolder::validate();
155  
316
317  std::string err("The following required keywords are missing:\n");
318  short int have_err = 0;
319
320  ParamMap::iterator i;
321  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
322    if (!i->second->isOptional() && i->second->empty()) {
323        err +=  i->second->getKeyword() + "\n";
324    }
325  }
326
156    CheckParameter(ForceField, isNotEmpty());
328  CheckParameter(NComponents,isPositive());
157    CheckParameter(TargetTemp, isPositive());
158 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
331 <                 isEqualIgnoreCase(std::string("NVT")) ||
332 <                 isEqualIgnoreCase(std::string("NPTi")) ||
333 <                 isEqualIgnoreCase(std::string("NPTf")) ||
334 <                 isEqualIgnoreCase(std::string("NPTxyz")) );
158 >  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"));
159    CheckParameter(Dt, isPositive());
160    CheckParameter(RunTime, isPositive());
337  CheckParameter(InitialConfig, isNotEmpty());
161    CheckParameter(FinalConfig, isNotEmpty());
339  CheckParameter(NMol, isPositive());
340  CheckParameter(Density, isPositive());
341  CheckParameter(Box, isPositive());
342  CheckParameter(BoxX, isPositive());
343  CheckParameter(BoxY, isPositive());
344  CheckParameter(BoxZ, isPositive());
162    CheckParameter(SampleTime, isNonNegative());
163    CheckParameter(ResetTime, isNonNegative());
164    CheckParameter(StatusTime, isNonNegative());
# Line 349 | Line 166 | char* Globals::checkMe( void ){
166    CheckParameter(SwitchingRadius, isNonNegative());
167    CheckParameter(Dielectric, isPositive());
168    CheckParameter(ThermalTime,  isNonNegative());
352  CheckParameter(TargetPressure,  isPositive());
169    CheckParameter(TauThermostat, isPositive());
170    CheckParameter(TauBarostat, isPositive());
171    CheckParameter(ZconsTime, isPositive());
356  CheckParameter(NZconstraints, isPositive());  
172    CheckParameter(ZconsTol, isPositive());
358  //CheckParameter(ZconsForcePolicy,);
173    CheckParameter(Seed, isPositive());
174 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
361 <                 isEqualIgnoreCase(std::string("CG")));
174 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175    CheckParameter(MinimizerMaxIter, isPositive());
176    CheckParameter(MinimizerWriteFrq, isPositive());
177    CheckParameter(MinimizerStepSize, isPositive());
# Line 368 | Line 181 | char* Globals::checkMe( void ){
181    CheckParameter(MinimizerLSMaxIter, isPositive());
182    CheckParameter(ZconsGap, isPositive());
183    CheckParameter(ZconsFixtime, isPositive());
184 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
184 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185    CheckParameter(ThermodynamicIntegrationK, isPositive());
186    CheckParameter(ForceFieldVariant, isNotEmpty());
187    CheckParameter(ForceFieldFileName, isNotEmpty());
188    CheckParameter(ThermIntDistSpringConst, isPositive());
189    CheckParameter(ThermIntThetaSpringConst, isPositive());
190    CheckParameter(ThermIntOmegaSpringConst, isPositive());
191 <  CheckParameter(SurfaceTension, isPositive());
192 <  CheckParameter(ElectrostaticSummationMethod,
193 <                 isEqualIgnoreCase(std::string("NONE")) ||
194 <                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
382 <                 isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
383 <                 isEqualIgnoreCase(std::string("REACTION_FIELD")));
384 <  CheckParameter(ElectrostaticScreeningMethod,
385 <                 isEqualIgnoreCase(std::string("UNDAMPED")) ||
386 <                 isEqualIgnoreCase(std::string("DAMPED")));
387 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
388 <                 isEqualIgnoreCase(std::string("MAX")) ||
389 <                 isEqualIgnoreCase(std::string("TRADITIONAL")));
390 <  CheckParameter(SwitchingFunctionType,
391 <                 isEqualIgnoreCase(std::string("CUBIC")) ||
392 <                 isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
191 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
194 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195    //CheckParameter(StatFileFormat,);    
394  //CheckParameter(MixingRule,);
196    CheckParameter(OrthoBoxTolerance, isPositive());  
197    CheckParameter(ThermIntDistSpringConst, isPositive());
198    CheckParameter(ThermIntThetaSpringConst, isPositive());
199    CheckParameter(ThermIntOmegaSpringConst, isPositive());
200    CheckParameter(DampingAlpha,isNonNegative());
201    CheckParameter(SkinThickness, isPositive());
202 <  
203 <  //@todo memory leak
204 <  if( have_err )
205 <    return strdup( err.c_str() );
206 <  
207 <  return NULL;
202 >  CheckParameter(Viscosity, isNonNegative());
203 >  CheckParameter(BeadSize, isPositive());
204 >  CheckParameter(FrozenBufferRadius, isPositive());
205 >  CheckParameter(LangevinBufferRadius, isPositive());
206 >  CheckParameter(NeighborListNeighbors, isPositive());
207 >  CheckParameter(RNEMD_swapTime, isPositive());
208 >  CheckParameter(RNEMD_nBins, isPositive());
209 >  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210  
211 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
212 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
213 +        std::ostringstream oss;
214 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
215 +        throw OOPSEException(oss.str());          
216 +    }
217 +  }
218 + }
219 +    
220 + bool Globals::addComponent(Component* comp) {
221 +    components_.push_back(comp);
222 +    return true;
223 + }
224  
225 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
226 +    zconstraints_.push_back(zcons);
227 +    return true;
228   }
229  
230 < int Globals::globalEnd( event* the_event ){
231 <  
232 <  the_event->err_msg = checkMe();
233 <  if( the_event->err_msg != NULL ) return 0;
230 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
231 >    std::string molStampName = molStamp->getName();
232 >    std::map<std::string, MoleculeStamp*>::iterator i;
233 >    bool ret = false;
234 >    i = moleculeStamps_.find(molStampName);
235 >    if (i == moleculeStamps_.end()) {
236 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
237 >        ret = true;
238 >    } else {
239 >        std::ostringstream oss;
240 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
241 >        throw OOPSEException(oss.str());  
242 >    }
243 >    return ret;
244 > }
245 >
246  
416  return 1;
247   }

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