ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-2.0/src/io/Globals.cpp
(Generate patch)

Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 2409 by chrisfen, Wed Nov 2 20:36:25 2005 UTC vs.
Revision 2515 by tim, Fri Dec 16 18:26:41 2005 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 121 | Line 95 | Globals::Globals(){
95    DefineOptionalParameter(SurfaceTension, "surfaceTension");
96    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97    DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 <  DefineOptionalParameter(ScreeningMethod, "screeningMethod");
98 >  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100 <  
100 >  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101    DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
103    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
# Line 134 | Line 108 | Globals::Globals(){
108    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
111 >  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
112    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
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");    
141 –
142 –  
143 – }
144 –
145 – int Globals::globalAssign( event* the_event ){
146 –  char errorMessage[65535];
147 –  int key;
148 –  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
149 –  char* lhs = the_event->evt.asmt.lhs;
150 –  std::string keyword(lhs);
151 –
152 –  bool result = false;
153 –
154 –  /**@todo fix memory leak */  
155 –  ParamMap::iterator i =parameters_.find(keyword);
156 –  if (i != parameters_.end()) {
157 –    if( the_type == STRING ){
158 –       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
159 –       if (!result ) {
160 –            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);
161 –            the_event->err_msg = strdup(errorMessage);
162 –       }
163 –    } else if( the_type == DOUBLE ){
164 –      result = i->second->setData(the_event->evt.asmt.rhs.dval);
165 –       if (!result )
166 –         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 );
167 –       the_event->err_msg = strdup(errorMessage);
168 –    }      
169 –    else if (the_type == INT ){
170 –      result = i->second->setData(the_event->evt.asmt.rhs.ival);
171 –       if (!result )
172 –         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 );
173 –       the_event->err_msg = strdup(errorMessage);
174 –      
175 –    } else {
176 –        sprintf(errorMessage,  "Internal error of parser\n");
177 –        the_event->err_msg = strdup(errorMessage);
178 –    }
179 –  } else {
180 –    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
181 –    the_event->err_msg = strdup(errorMessage);
182 –  }
183 –
184 –  if (keyword == "nComponents" && getNComponents() > 0) {
185 –    components = new Component*[getNComponents()];
186 –  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
187 –    zConstraints = new ZconStamp*[getNZconstraints()];
188 –  }
189 –  
190 –  return result;
191 – }
192 –
193 – int Globals::newComponent( event* the_event ){
194 –  
195 –  current_component = new Component;
196 –  int index = the_event->evt.blk_index;
197 –  char err[200];
198 –  
199 –  if( haveNComponents() && index < getNComponents() )
200 –    components[index] = current_component;
201 –  else{
202 –    if( haveNComponents()  ){
203 –      sprintf( err, "meta-data parsing error: %d out of nComponents range",
204 –               index );
205 –      the_event->err_msg = strdup( err );
206 –      return 0;
207 –    }
208 –    else{
209 –      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
210 –                                  " first component declaration." );
211 –      return 0;
212 –    }
213 –  }  
214 –
215 –  return 1;
216 – }
217 –
218 –
219 –
220 – int Globals::componentAssign( event* the_event ){
221 –
222 –  switch( the_event->evt.asmt.asmt_type ){
223 –    
224 –  case STRING:
225 –    return current_component->assignString( the_event->evt.asmt.lhs,
226 –                                            the_event->evt.asmt.rhs.sval,
227 –                                            &(the_event->err_msg));
228 –    break;
229 –    
230 –  case DOUBLE:
231 –    return current_component->assignDouble( the_event->evt.asmt.lhs,
232 –                                            the_event->evt.asmt.rhs.dval,
233 –                                            &(the_event->err_msg));
234 –    break;
235 –    
236 –  case INT:
237 –    return current_component->assignInt( the_event->evt.asmt.lhs,
238 –                                         the_event->evt.asmt.rhs.ival,
239 –                                         &(the_event->err_msg));
240 –    break;
241 –    
242 –  default:
243 –    the_event->err_msg = strdup( "Globals error. Invalid component"
244 –                                 " assignment type" );
245 –    return 0;
246 –    break;
247 –  }
248 –  return 0;
249 – }
250 –
251 – int Globals::componentEnd( event* the_event ){
252 –
253 –  the_event->err_msg = current_component->checkMe();
254 –  if( the_event->err_msg != NULL ) return 0;
116  
256 –  return 1;
257 – }
117  
118 < int Globals::newZconstraint( event* the_event ){
119 <  
261 <
262 <  int index = the_event->evt.blk_index;
263 <  char err[200];
264 <  current_zConstraint = new ZconStamp( index );
265 <  
266 <  if( haveNZconstraints() && index < getNZconstraints() )
267 <    zConstraints[index] = current_zConstraint;
268 <  else{
269 <    if( haveNZconstraints() ){
270 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
271 <               index );
272 <      the_event->err_msg = strdup( err );
273 <      return 0;
274 <    }
275 <    else{
276 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
277 <                                  " not given before"
278 <                                  " first zConstraint declaration." );
279 <      return 0;
280 <    }
281 <  }  
282 <
283 <  return 1;
284 < }
285 <
286 <
287 <
288 < int Globals::zConstraintAssign( event* the_event ){
289 <
290 <  switch( the_event->evt.asmt.asmt_type ){
118 >    deprecatedKeywords_.insert("nComponents");
119 >    deprecatedKeywords_.insert("nZconstraints");
120      
292 –  case STRING:
293 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
294 –                                              the_event->evt.asmt.rhs.sval,
295 –                                              &(the_event->err_msg));
296 –    break;
297 –    
298 –  case DOUBLE:
299 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
300 –                                              the_event->evt.asmt.rhs.dval,
301 –                                              &(the_event->err_msg));
302 –    break;
303 –    
304 –  case INT:
305 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
306 –                                           the_event->evt.asmt.rhs.ival,
307 –                                           &(the_event->err_msg));
308 –    break;
309 –    
310 –  default:
311 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
312 –                                 " assignment type" );
313 –    return 0;
314 –    break;
315 –  }
316 –  return 0;
121   }
122  
123 < int Globals::zConstraintEnd( event* the_event ){
124 <
125 <  the_event->err_msg = current_zConstraint->checkMe();
322 <  if( the_event->err_msg != NULL ) return 0;
323 <
324 <  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  
329 –
330 –  std::string err("The following required keywords are missing:\n");
331 –  short int have_err = 0;
332 –
333 –  ParamMap::iterator i;
334 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
335 –    if (!i->second->isOptional() && i->second->empty()) {
336 –        err +=  i->second->getKeyword() + "\n";
337 –    }
338 –  }
339 –
131    CheckParameter(ForceField, isNotEmpty());
341 –  CheckParameter(NComponents,isPositive());
132    CheckParameter(TargetTemp, isPositive());
133 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
344 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
345 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
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 386 | Line 166 | char* Globals::checkMe( void ){
166    CheckParameter(ThermIntThetaSpringConst, isPositive());
167    CheckParameter(ThermIntOmegaSpringConst, isPositive());
168    CheckParameter(SurfaceTension, isPositive());
169 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE"))  || isEqualIgnoreCase(std::string("REACTION_FIELD")));
170 <  CheckParameter(ScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
169 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
170 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
171    CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172 +  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
173    //CheckParameter(StatFileFormat,);    
174    //CheckParameter(MixingRule,);
175    CheckParameter(OrthoBoxTolerance, isPositive());  
176    CheckParameter(ThermIntDistSpringConst, isPositive());
177    CheckParameter(ThermIntThetaSpringConst, isPositive());
178    CheckParameter(ThermIntOmegaSpringConst, isPositive());
179 <  CheckParameter(DampingAlpha,isPositive());
179 >  CheckParameter(DampingAlpha,isNonNegative());
180    CheckParameter(SkinThickness, isPositive());
400 –  
401 –  //@todo memory leak
402 –  if( have_err )
403 –    return strdup( err.c_str() );
404 –  
405 –  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 >        std::cout << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
209 >    }
210 >    return ret;
211 > }
212 >
213  
415 –  return 1;
214   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines