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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 867 by chuckv, Fri Jan 13 21:57:48 2006 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");
# Line 64 | Line 59 | Globals::Globals(){
59    DefineOptionalParameter(RunTime, "runTime");
60    DefineOptionalParameter(InitialConfig, "initialConfig");
61    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");
62    DefineOptionalParameter(SampleTime, "sampleTime");
63    DefineOptionalParameter(ResetTime, "resetTime");
64    DefineOptionalParameter(StatusTime, "statusTime");
# Line 82 | Line 71 | Globals::Globals(){
71    DefineOptionalParameter(TauThermostat, "tauThermostat");
72    DefineOptionalParameter(TauBarostat, "tauBarostat");
73    DefineOptionalParameter(ZconsTime, "zconsTime");
85 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
74    DefineOptionalParameter(ZconsTol, "zconsTol");
75    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76    DefineOptionalParameter(Seed, "seed");
# Line 110 | Line 98 | Globals::Globals(){
98    DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
113 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
101    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
102    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
103    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
# Line 126 | Line 113 | Globals::Globals(){
113    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
114    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
115  
129 –  
130 – }
116  
117 < int Globals::globalAssign( event* the_event ){
118 <  char errorMessage[65535];
134 <  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 ){
117 >    deprecatedKeywords_.insert("nComponents");
118 >    deprecatedKeywords_.insert("nZconstraints");
119      
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;
120   }
121  
122 < int Globals::zConstraintEnd( event* the_event ){
123 <
124 <  the_event->err_msg = current_zConstraint->checkMe();
309 <  if( the_event->err_msg != NULL ) return 0;
310 <
311 <  return 1;
122 > Globals::~Globals() {
123 >    MemoryUtils::deletePointers(components_);
124 >    MemoryUtils::deletePointers(zconstraints_);
125   }
126  
127 < char* Globals::checkMe( void ){
127 > void Globals::validate() {
128 >  DataHolder::validate();
129  
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 –
130    CheckParameter(ForceField, isNotEmpty());
328 –  CheckParameter(NComponents,isPositive());
131    CheckParameter(TargetTemp, isPositive());
132 <  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")) );
132 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  );
133    CheckParameter(Dt, isPositive());
134    CheckParameter(RunTime, isPositive());
135    CheckParameter(InitialConfig, isNotEmpty());
136    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());
137    CheckParameter(SampleTime, isNonNegative());
138    CheckParameter(ResetTime, isNonNegative());
139    CheckParameter(StatusTime, isNonNegative());
# Line 353 | Line 145 | char* Globals::checkMe( void ){
145    CheckParameter(TauThermostat, isPositive());
146    CheckParameter(TauBarostat, isPositive());
147    CheckParameter(ZconsTime, isPositive());
356 –  CheckParameter(NZconstraints, isPositive());  
148    CheckParameter(ZconsTol, isPositive());
358 –  //CheckParameter(ZconsForcePolicy,);
149    CheckParameter(Seed, isPositive());
150 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
361 <                 isEqualIgnoreCase(std::string("CG")));
150 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
151    CheckParameter(MinimizerMaxIter, isPositive());
152    CheckParameter(MinimizerWriteFrq, isPositive());
153    CheckParameter(MinimizerStepSize, isPositive());
# Line 376 | Line 165 | char* Globals::checkMe( void ){
165    CheckParameter(ThermIntThetaSpringConst, isPositive());
166    CheckParameter(ThermIntOmegaSpringConst, isPositive());
167    CheckParameter(SurfaceTension, isPositive());
168 <  CheckParameter(ElectrostaticSummationMethod,
169 <                 isEqualIgnoreCase(std::string("NONE")) ||
170 <                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
171 <                 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")));
168 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
169 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
170 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
171 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
172    //CheckParameter(StatFileFormat,);    
394 –  //CheckParameter(MixingRule,);
173    CheckParameter(OrthoBoxTolerance, isPositive());  
174    CheckParameter(ThermIntDistSpringConst, isPositive());
175    CheckParameter(ThermIntThetaSpringConst, isPositive());
176    CheckParameter(ThermIntOmegaSpringConst, isPositive());
177    CheckParameter(DampingAlpha,isNonNegative());
178    CheckParameter(SkinThickness, isPositive());
401 –  
402 –  //@todo memory leak
403 –  if( have_err )
404 –    return strdup( err.c_str() );
405 –  
406 –  return NULL;
179  
180 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
181 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
182 +        std::ostringstream oss;
183 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
184 +        throw OOPSEException(oss.str());          
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 < int Globals::globalEnd( event* the_event ){
200 <  
201 <  the_event->err_msg = checkMe();
202 <  if( the_event->err_msg != NULL ) return 0;
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 >        std::ostringstream oss;
209 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
210 >        throw OOPSEException(oss.str());  
211 >    }
212 >    return ret;
213 > }
214 >
215  
416 –  return 1;
216   }

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