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Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 2464 by gezelter, Mon Nov 21 22:59:36 2005 UTC vs.
Revision 2469 by tim, Fri Dec 2 15:38:03 2005 UTC

# Line 46 | Line 46
46  
47   #include "io/Globals.hpp"
48   #include "utils/simError.h"
49 – #ifdef IS_MPI
50 – #include "io/mpiBASS.h"
51 – #endif // is_mpi
49  
50   #include "io/ParamConstraint.hpp"
51  
52 < using namespace oopse;
53 <
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 127 | Line 114 | Globals::Globals(){
114    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
116  
130 –  
131 – }
117  
118 < Globals::~Globals(){
119 <  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 <  }  
284 <
285 <  return 1;
286 < }
287 <
288 <
289 <
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 ){
123 > Globals::~Globals() {
124  
323 –  the_event->err_msg = current_zConstraint->checkMe();
324 –  if( the_event->err_msg != NULL ) return 0;
125  
326 –  return 1;
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")) );
134    CheckParameter(Dt, isPositive());
135    CheckParameter(RunTime, isPositive());
136    CheckParameter(InitialConfig, isNotEmpty());
137    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());
138    CheckParameter(SampleTime, isNonNegative());
139    CheckParameter(ResetTime, isNonNegative());
140    CheckParameter(StatusTime, isNonNegative());
# Line 364 | Line 146 | char* Globals::checkMe( void ){
146    CheckParameter(TauThermostat, isPositive());
147    CheckParameter(TauBarostat, isPositive());
148    CheckParameter(ZconsTime, isPositive());
367 –  CheckParameter(NZconstraints, isPositive());  
149    CheckParameter(ZconsTol, isPositive());
369 –  //CheckParameter(ZconsForcePolicy,);
150    CheckParameter(Seed, isPositive());
151    CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
152    CheckParameter(MinimizerMaxIter, isPositive());
# Line 398 | Line 178 | char* Globals::checkMe( void ){
178    CheckParameter(ThermIntOmegaSpringConst, isPositive());
179    CheckParameter(DampingAlpha,isNonNegative());
180    CheckParameter(SkinThickness, isPositive());
401 –  
402 –  //@todo memory leak
403 –  if( have_err )
404 –    return strdup( err.c_str() );
405 –  
406 –  return NULL;
181  
182 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
183 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
184 +        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
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  
209 <  return 1;
209 >    }
210 >    return ret;
211   }
212 +
213 +
214 + }

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