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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 765 by gezelter, Mon Nov 21 22:59:36 2005 UTC vs.
Revision 849 by chrisfen, Thu Jan 12 04:13:46 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 < using namespace oopse;
56 <
57 < Globals::Globals(){
58 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
60 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
# Line 65 | Line 59 | Globals::Globals(){
59    DefineOptionalParameter(RunTime, "runTime");
60    DefineOptionalParameter(InitialConfig, "initialConfig");
61    DefineOptionalParameter(FinalConfig, "finalConfig");
68 –  DefineOptionalParameter(NMol, "nMol");
69 –  DefineOptionalParameter(Density, "density");
70 –  DefineOptionalParameter(Box, "box");
71 –  DefineOptionalParameter(BoxX, "boxX");
72 –  DefineOptionalParameter(BoxY, "boxY");
73 –  DefineOptionalParameter(BoxZ, "boxZ");
62    DefineOptionalParameter(SampleTime, "sampleTime");
63    DefineOptionalParameter(ResetTime, "resetTime");
64    DefineOptionalParameter(StatusTime, "statusTime");
# Line 83 | Line 71 | Globals::Globals(){
71    DefineOptionalParameter(TauThermostat, "tauThermostat");
72    DefineOptionalParameter(TauBarostat, "tauBarostat");
73    DefineOptionalParameter(ZconsTime, "zconsTime");
86 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
74    DefineOptionalParameter(ZconsTol, "zconsTol");
75    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76    DefineOptionalParameter(Seed, "seed");
# Line 126 | Line 113 | Globals::Globals(){
113    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
114    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
129 –
130 –  
131 – }
132 –
133 – Globals::~Globals(){
134 –  int i;
135 –  if( components != NULL ){
136 –    for( i=0; i< getNComponents(); i++ ) delete components[i];
137 –    delete[] components;
138 –  }
139 –  
140 –  if( zConstraints != NULL ){
141 –    for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i];
142 –    delete[] zConstraints;
143 –  }
144 –  
145 – }
146 –
147 – int Globals::globalAssign( event* the_event ){
148 –  char errorMessage[65535];
149 –  int key;
150 –  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
151 –  char* lhs = the_event->evt.asmt.lhs;
152 –  std::string keyword(lhs);
153 –
154 –  bool result = false;
155 –
156 –  /**@todo fix memory leak */  
157 –  ParamMap::iterator i =parameters_.find(keyword);
158 –  if (i != parameters_.end()) {
159 –    if( the_type == STRING ){
160 –       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
161 –       if (!result ) {
162 –            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);
163 –            the_event->err_msg = strdup(errorMessage);
164 –       }
165 –    } else if( the_type == DOUBLE ){
166 –      result = i->second->setData(the_event->evt.asmt.rhs.dval);
167 –       if (!result )
168 –         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 );
169 –       the_event->err_msg = strdup(errorMessage);
170 –    }      
171 –    else if (the_type == INT ){
172 –      result = i->second->setData(the_event->evt.asmt.rhs.ival);
173 –       if (!result )
174 –         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 );
175 –       the_event->err_msg = strdup(errorMessage);
176 –      
177 –    } else {
178 –        sprintf(errorMessage,  "Internal error of parser\n");
179 –        the_event->err_msg = strdup(errorMessage);
180 –    }
181 –  } else {
182 –    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
183 –    the_event->err_msg = strdup(errorMessage);
184 –  }
185 –
186 –  if (keyword == "nComponents" && getNComponents() > 0) {
187 –    components = new Component*[getNComponents()];
188 –  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
189 –    zConstraints = new ZconStamp*[getNZconstraints()];
190 –  }
191 –  
192 –  return result;
193 – }
194 –
195 – int Globals::newComponent( event* the_event ){
196 –  
197 –  current_component = new Component;
198 –  int index = the_event->evt.blk_index;
199 –  char err[200];
200 –  
201 –  if( haveNComponents() && index < getNComponents() )
202 –    components[index] = current_component;
203 –  else{
204 –    if( haveNComponents()  ){
205 –      sprintf( err, "meta-data parsing error: %d out of nComponents range",
206 –               index );
207 –      the_event->err_msg = strdup( err );
208 –      return 0;
209 –    }
210 –    else{
211 –      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
212 –                                  " first component declaration." );
213 –      return 0;
214 –    }
215 –  }  
216 –
217 –  return 1;
218 – }
219 –
220 –
221 –
222 – int Globals::componentAssign( event* the_event ){
223 –
224 –  switch( the_event->evt.asmt.asmt_type ){
225 –    
226 –  case STRING:
227 –    return current_component->assignString( the_event->evt.asmt.lhs,
228 –                                            the_event->evt.asmt.rhs.sval,
229 –                                            &(the_event->err_msg));
230 –    break;
231 –    
232 –  case DOUBLE:
233 –    return current_component->assignDouble( the_event->evt.asmt.lhs,
234 –                                            the_event->evt.asmt.rhs.dval,
235 –                                            &(the_event->err_msg));
236 –    break;
237 –    
238 –  case INT:
239 –    return current_component->assignInt( the_event->evt.asmt.lhs,
240 –                                         the_event->evt.asmt.rhs.ival,
241 –                                         &(the_event->err_msg));
242 –    break;
243 –    
244 –  default:
245 –    the_event->err_msg = strdup( "Globals error. Invalid component"
246 –                                 " assignment type" );
247 –    return 0;
248 –    break;
249 –  }
250 –  return 0;
251 – }
252 –
253 – int Globals::componentEnd( event* the_event ){
254 –
255 –  the_event->err_msg = current_component->checkMe();
256 –  if( the_event->err_msg != NULL ) return 0;
257 –
258 –  return 1;
259 – }
260 –
261 – int Globals::newZconstraint( event* the_event ){
262 –  
263 –
264 –  int index = the_event->evt.blk_index;
265 –  char err[200];
266 –  current_zConstraint = new ZconStamp( index );
267 –  
268 –  if( haveNZconstraints() && index < getNZconstraints() )
269 –    zConstraints[index] = current_zConstraint;
270 –  else{
271 –    if( haveNZconstraints() ){
272 –      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
273 –               index );
274 –      the_event->err_msg = strdup( err );
275 –      return 0;
276 –    }
277 –    else{
278 –      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
279 –                                  " not given before"
280 –                                  " first zConstraint declaration." );
281 –      return 0;
282 –    }
283 –  }  
116  
285 –  return 1;
286 – }
117  
118 <
119 <
290 < int Globals::zConstraintAssign( event* the_event ){
291 <
292 <  switch( the_event->evt.asmt.asmt_type ){
118 >    deprecatedKeywords_.insert("nComponents");
119 >    deprecatedKeywords_.insert("nZconstraints");
120      
294 –  case STRING:
295 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
296 –                                              the_event->evt.asmt.rhs.sval,
297 –                                              &(the_event->err_msg));
298 –    break;
299 –    
300 –  case DOUBLE:
301 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
302 –                                              the_event->evt.asmt.rhs.dval,
303 –                                              &(the_event->err_msg));
304 –    break;
305 –    
306 –  case INT:
307 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
308 –                                           the_event->evt.asmt.rhs.ival,
309 –                                           &(the_event->err_msg));
310 –    break;
311 –    
312 –  default:
313 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
314 –                                 " assignment type" );
315 –    return 0;
316 –    break;
317 –  }
318 –  return 0;
121   }
122  
123 < int Globals::zConstraintEnd( event* the_event ){
124 <
125 <  the_event->err_msg = current_zConstraint->checkMe();
324 <  if( the_event->err_msg != NULL ) return 0;
325 <
326 <  return 1;
123 > Globals::~Globals() {
124 >    MemoryUtils::deletePointers(components_);
125 >    MemoryUtils::deletePointers(zconstraints_);
126   }
127  
128 < char* Globals::checkMe( void ){
128 > void Globals::validate() {
129 >  DataHolder::validate();
130  
331 –
332 –  std::string err("The following required keywords are missing:\n");
333 –  short int have_err = 0;
334 –
335 –  ParamMap::iterator i;
336 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
337 –    if (!i->second->isOptional() && i->second->empty()) {
338 –        err +=  i->second->getKeyword() + "\n";
339 –    }
340 –  }
341 –
131    CheckParameter(ForceField, isNotEmpty());
343 –  CheckParameter(NComponents,isPositive());
132    CheckParameter(TargetTemp, isPositive());
133 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
133 >  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
134 >                 isEqualIgnoreCase(std::string("NVT")) ||
135 >                 isEqualIgnoreCase(std::string("NPTi")) ||
136 >                 isEqualIgnoreCase(std::string("NPTf")) ||
137 >                 isEqualIgnoreCase(std::string("NPTxyz")) );
138    CheckParameter(Dt, isPositive());
139    CheckParameter(RunTime, isPositive());
140    CheckParameter(InitialConfig, isNotEmpty());
141    CheckParameter(FinalConfig, isNotEmpty());
350 –  CheckParameter(NMol, isPositive());
351 –  CheckParameter(Density, isPositive());
352 –  CheckParameter(Box, isPositive());
353 –  CheckParameter(BoxX, isPositive());
354 –  CheckParameter(BoxY, isPositive());
355 –  CheckParameter(BoxZ, isPositive());
142    CheckParameter(SampleTime, isNonNegative());
143    CheckParameter(ResetTime, isNonNegative());
144    CheckParameter(StatusTime, isNonNegative());
# Line 364 | Line 150 | char* Globals::checkMe( void ){
150    CheckParameter(TauThermostat, isPositive());
151    CheckParameter(TauBarostat, isPositive());
152    CheckParameter(ZconsTime, isPositive());
367 –  CheckParameter(NZconstraints, isPositive());  
153    CheckParameter(ZconsTol, isPositive());
369 –  //CheckParameter(ZconsForcePolicy,);
154    CheckParameter(Seed, isPositive());
155 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
155 >  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
156 >                 isEqualIgnoreCase(std::string("CG")));
157    CheckParameter(MinimizerMaxIter, isPositive());
158    CheckParameter(MinimizerWriteFrq, isPositive());
159    CheckParameter(MinimizerStepSize, isPositive());
# Line 386 | Line 171 | char* Globals::checkMe( void ){
171    CheckParameter(ThermIntThetaSpringConst, isPositive());
172    CheckParameter(ThermIntOmegaSpringConst, isPositive());
173    CheckParameter(SurfaceTension, isPositive());
174 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
175 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
176 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
177 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
174 >  CheckParameter(ElectrostaticSummationMethod,
175 >                 isEqualIgnoreCase(std::string("NONE")) ||
176 >                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
177 >                 isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
178 >                 isEqualIgnoreCase(std::string("REACTION_FIELD")));
179 >  CheckParameter(ElectrostaticScreeningMethod,
180 >                 isEqualIgnoreCase(std::string("UNDAMPED")) ||
181 >                 isEqualIgnoreCase(std::string("DAMPED")));
182 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
183 >                 isEqualIgnoreCase(std::string("MAX")) ||
184 >                 isEqualIgnoreCase(std::string("TRADITIONAL")));
185 >  CheckParameter(SwitchingFunctionType,
186 >                 isEqualIgnoreCase(std::string("CUBIC")) ||
187 >                 isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
188    //CheckParameter(StatFileFormat,);    
189    //CheckParameter(MixingRule,);
190    CheckParameter(OrthoBoxTolerance, isPositive());  
# Line 398 | Line 193 | char* Globals::checkMe( void ){
193    CheckParameter(ThermIntOmegaSpringConst, isPositive());
194    CheckParameter(DampingAlpha,isNonNegative());
195    CheckParameter(SkinThickness, isPositive());
401 –  
402 –  //@todo memory leak
403 –  if( have_err )
404 –    return strdup( err.c_str() );
405 –  
406 –  return NULL;
196  
197 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
198 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
199 +        std::ostringstream oss;
200 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
201 +        throw OOPSEException(oss.str());          
202 +    }
203 +  }
204 + }
205 +    
206 + bool Globals::addComponent(Component* comp) {
207 +    components_.push_back(comp);
208 +    return true;
209 + }
210  
211 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
212 +    zconstraints_.push_back(zcons);
213 +    return true;
214   }
215  
216 < int Globals::globalEnd( event* the_event ){
217 <  
218 <  the_event->err_msg = checkMe();
219 <  if( the_event->err_msg != NULL ) return 0;
216 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
217 >    std::string molStampName = molStamp->getName();
218 >    std::map<std::string, MoleculeStamp*>::iterator i;
219 >    bool ret = false;
220 >    i = moleculeStamps_.find(molStampName);
221 >    if (i == moleculeStamps_.end()) {
222 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
223 >        ret = true;
224 >    } else {
225 >        std::ostringstream oss;
226 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
227 >        throw OOPSEException(oss.str());  
228 >    }
229 >    return ret;
230 > }
231 >
232  
416 –  return 1;
233   }

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