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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 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 < #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");
# Line 78 | Line 59 | Globals::Globals(){
59    DefineOptionalParameter(RunTime, "runTime");
60    DefineOptionalParameter(InitialConfig, "initialConfig");
61    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");
62    DefineOptionalParameter(SampleTime, "sampleTime");
63    DefineOptionalParameter(ResetTime, "resetTime");
64    DefineOptionalParameter(StatusTime, "statusTime");
# Line 96 | Line 71 | Globals::Globals(){
71    DefineOptionalParameter(TauThermostat, "tauThermostat");
72    DefineOptionalParameter(TauBarostat, "tauBarostat");
73    DefineOptionalParameter(ZconsTime, "zconsTime");
99 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
74    DefineOptionalParameter(ZconsTol, "zconsTol");
75    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76    DefineOptionalParameter(Seed, "seed");
# Line 139 | 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");    
142 –
143 –  
144 – }
145 –
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;
116  
257 –  return 1;
258 – }
117  
118 < int Globals::newZconstraint( event* the_event ){
119 <  
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 ){
118 >    deprecatedKeywords_.insert("nComponents");
119 >    deprecatedKeywords_.insert("nZconstraints");
120      
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;
121   }
122  
123 < int Globals::zConstraintEnd( event* the_event ){
124 <
125 <  the_event->err_msg = current_zConstraint->checkMe();
323 <  if( the_event->err_msg != NULL ) return 0;
324 <
325 <  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  
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 –
131    CheckParameter(ForceField, isNotEmpty());
342 –  CheckParameter(NComponents,isPositive());
132    CheckParameter(TargetTemp, isPositive());
133    CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
134 <                 isEqualIgnoreCase(std::string("NVT")) ||
134 >                 isEqualIgnoreCase(std::string("NVT")) ||
135                   isEqualIgnoreCase(std::string("NPTi")) ||
136                   isEqualIgnoreCase(std::string("NPTf")) ||
137                   isEqualIgnoreCase(std::string("NPTxyz")) );
# Line 350 | Line 139 | char* Globals::checkMe( void ){
139    CheckParameter(RunTime, isPositive());
140    CheckParameter(InitialConfig, isNotEmpty());
141    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());
142    CheckParameter(SampleTime, isNonNegative());
143    CheckParameter(ResetTime, isNonNegative());
144    CheckParameter(StatusTime, isNonNegative());
# Line 367 | Line 150 | char* Globals::checkMe( void ){
150    CheckParameter(TauThermostat, isPositive());
151    CheckParameter(TauBarostat, isPositive());
152    CheckParameter(ZconsTime, isPositive());
370 –  CheckParameter(NZconstraints, isPositive());  
153    CheckParameter(ZconsTol, isPositive());
372 –  //CheckParameter(ZconsForcePolicy,);
154    CheckParameter(Seed, isPositive());
155    CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
156                   isEqualIgnoreCase(std::string("CG")));
# Line 412 | Line 193 | char* Globals::checkMe( void ){
193    CheckParameter(ThermIntOmegaSpringConst, isPositive());
194    CheckParameter(DampingAlpha,isNonNegative());
195    CheckParameter(SkinThickness, isPositive());
415 –  
416 –  //@todo memory leak
417 –  if( have_err )
418 –    return strdup( err.c_str() );
419 –  
420 –  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  
430 –  return 1;
233   }

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