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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 681 by tim, Mon Oct 17 23:13:44 2005 UTC vs.
Revision 906 by tim, Fri Mar 17 23:20:35 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 121 | Line 95 | Globals::Globals(){
95    DefineOptionalParameter(SurfaceTension, "surfaceTension");
96    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97    DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 +  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100 +  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101 +  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
102 +  DefineOptionalParameter(Viscosity, "viscosity");
103 +  DefineOptionalParameter(BeadSize, "beadSize");
104    
126 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
105    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
106    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
107    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
# Line 133 | Line 111 | Globals::Globals(){
111    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
112    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
113    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
114 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
114 >  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
115    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
116 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
117    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
118    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
140 –
141 –  
142 – }
143 –
144 – int Globals::globalAssign( event* the_event ){
145 –  char errorMessage[65535];
146 –  int key;
147 –  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
148 –  char* lhs = the_event->evt.asmt.lhs;
149 –  std::string keyword(lhs);
150 –
151 –  bool result = false;
152 –
153 –  /**@todo fix memory leak */  
154 –  ParamMap::iterator i =parameters_.find(keyword);
155 –  if (i != parameters_.end()) {
156 –    if( the_type == STRING ){
157 –       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
158 –       if (!result ) {
159 –            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);
160 –            the_event->err_msg = strdup(errorMessage);
161 –       }
162 –    } else if( the_type == DOUBLE ){
163 –      result = i->second->setData(the_event->evt.asmt.rhs.dval);
164 –       if (!result )
165 –         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 );
166 –       the_event->err_msg = strdup(errorMessage);
167 –    }      
168 –    else if (the_type == INT ){
169 –      result = i->second->setData(the_event->evt.asmt.rhs.ival);
170 –       if (!result )
171 –         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 );
172 –       the_event->err_msg = strdup(errorMessage);
173 –      
174 –    } else {
175 –        sprintf(errorMessage,  "Internal error of parser\n");
176 –        the_event->err_msg = strdup(errorMessage);
177 –    }
178 –  } else {
179 –    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
180 –    the_event->err_msg = strdup(errorMessage);
181 –  }
182 –
183 –  if (keyword == "nComponents" && getNComponents() > 0) {
184 –    components = new Component*[getNComponents()];
185 –  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
186 –    zConstraints = new ZconStamp*[getNZconstraints()];
187 –  }
188 –  
189 –  return result;
190 – }
191 –
192 – int Globals::newComponent( event* the_event ){
193 –  
194 –  current_component = new Component;
195 –  int index = the_event->evt.blk_index;
196 –  char err[200];
197 –  
198 –  if( haveNComponents() && index < getNComponents() )
199 –    components[index] = current_component;
200 –  else{
201 –    if( haveNComponents()  ){
202 –      sprintf( err, "meta-data parsing error: %d out of nComponents range",
203 –               index );
204 –      the_event->err_msg = strdup( err );
205 –      return 0;
206 –    }
207 –    else{
208 –      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
209 –                                  " first component declaration." );
210 –      return 0;
211 –    }
212 –  }  
213 –
214 –  return 1;
215 – }
216 –
217 –
218 –
219 – int Globals::componentAssign( event* the_event ){
220 –
221 –  switch( the_event->evt.asmt.asmt_type ){
222 –    
223 –  case STRING:
224 –    return current_component->assignString( the_event->evt.asmt.lhs,
225 –                                            the_event->evt.asmt.rhs.sval,
226 –                                            &(the_event->err_msg));
227 –    break;
228 –    
229 –  case DOUBLE:
230 –    return current_component->assignDouble( the_event->evt.asmt.lhs,
231 –                                            the_event->evt.asmt.rhs.dval,
232 –                                            &(the_event->err_msg));
233 –    break;
234 –    
235 –  case INT:
236 –    return current_component->assignInt( the_event->evt.asmt.lhs,
237 –                                         the_event->evt.asmt.rhs.ival,
238 –                                         &(the_event->err_msg));
239 –    break;
240 –    
241 –  default:
242 –    the_event->err_msg = strdup( "Globals error. Invalid component"
243 –                                 " assignment type" );
244 –    return 0;
245 –    break;
246 –  }
247 –  return 0;
248 – }
249 –
250 – int Globals::componentEnd( event* the_event ){
251 –
252 –  the_event->err_msg = current_component->checkMe();
253 –  if( the_event->err_msg != NULL ) return 0;
254 –
255 –  return 1;
256 – }
257 –
258 – int Globals::newZconstraint( event* the_event ){
259 –  
119  
261 –  int index = the_event->evt.blk_index;
262 –  char err[200];
263 –  current_zConstraint = new ZconStamp( index );
264 –  
265 –  if( haveNZconstraints() && index < getNZconstraints() )
266 –    zConstraints[index] = current_zConstraint;
267 –  else{
268 –    if( haveNZconstraints() ){
269 –      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
270 –               index );
271 –      the_event->err_msg = strdup( err );
272 –      return 0;
273 –    }
274 –    else{
275 –      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
276 –                                  " not given before"
277 –                                  " first zConstraint declaration." );
278 –      return 0;
279 –    }
280 –  }  
120  
121 <  return 1;
122 < }
284 <
285 <
286 <
287 < int Globals::zConstraintAssign( event* the_event ){
288 <
289 <  switch( the_event->evt.asmt.asmt_type ){
121 >    deprecatedKeywords_.insert("nComponents");
122 >    deprecatedKeywords_.insert("nZconstraints");
123      
291 –  case STRING:
292 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
293 –                                              the_event->evt.asmt.rhs.sval,
294 –                                              &(the_event->err_msg));
295 –    break;
296 –    
297 –  case DOUBLE:
298 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
299 –                                              the_event->evt.asmt.rhs.dval,
300 –                                              &(the_event->err_msg));
301 –    break;
302 –    
303 –  case INT:
304 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
305 –                                           the_event->evt.asmt.rhs.ival,
306 –                                           &(the_event->err_msg));
307 –    break;
308 –    
309 –  default:
310 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
311 –                                 " assignment type" );
312 –    return 0;
313 –    break;
314 –  }
315 –  return 0;
124   }
125  
126 < int Globals::zConstraintEnd( event* the_event ){
127 <
128 <  the_event->err_msg = current_zConstraint->checkMe();
321 <  if( the_event->err_msg != NULL ) return 0;
322 <
323 <  return 1;
126 > Globals::~Globals() {
127 >    MemoryUtils::deletePointers(components_);
128 >    MemoryUtils::deletePointers(zconstraints_);
129   }
130  
131 < char* Globals::checkMe( void ){
131 > void Globals::validate() {
132 >  DataHolder::validate();
133  
328 –
329 –  std::string err("The following required keywords are missing:\n");
330 –  short int have_err = 0;
331 –
332 –  ParamMap::iterator i;
333 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
334 –    if (!i->second->isOptional() && i->second->empty()) {
335 –        err +=  i->second->getKeyword() + "\n";
336 –    }
337 –  }
338 –
134    CheckParameter(ForceField, isNotEmpty());
340 –  CheckParameter(NComponents,isPositive());
135    CheckParameter(TargetTemp, isPositive());
136 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
343 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
344 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
345 <
136 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") );
137    CheckParameter(Dt, isPositive());
138    CheckParameter(RunTime, isPositive());
139    CheckParameter(InitialConfig, isNotEmpty());
140    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());
141    CheckParameter(SampleTime, isNonNegative());
142    CheckParameter(ResetTime, isNonNegative());
143    CheckParameter(StatusTime, isNonNegative());
# Line 364 | Line 149 | char* Globals::checkMe( void ){
149    CheckParameter(TauThermostat, isPositive());
150    CheckParameter(TauBarostat, isPositive());
151    CheckParameter(ZconsTime, isPositive());
367 –  CheckParameter(NZconstraints, isPositive());  
152    CheckParameter(ZconsTol, isPositive());
369 –  //CheckParameter(ZconsForcePolicy,);
153    CheckParameter(Seed, isPositive());
154 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
154 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
155    CheckParameter(MinimizerMaxIter, isPositive());
156    CheckParameter(MinimizerWriteFrq, isPositive());
157    CheckParameter(MinimizerStepSize, isPositive());
# Line 386 | Line 169 | char* Globals::checkMe( void ){
169    CheckParameter(ThermIntThetaSpringConst, isPositive());
170    CheckParameter(ThermIntOmegaSpringConst, isPositive());
171    CheckParameter(SurfaceTension, isPositive());
172 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
173 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
173 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
174 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
175 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
176    //CheckParameter(StatFileFormat,);    
392 –  //CheckParameter(MixingRule,);
177    CheckParameter(OrthoBoxTolerance, isPositive());  
178    CheckParameter(ThermIntDistSpringConst, isPositive());
179    CheckParameter(ThermIntThetaSpringConst, isPositive());
180    CheckParameter(ThermIntOmegaSpringConst, isPositive());
181 <  CheckParameter(DampingAlpha,isPositive());
181 >  CheckParameter(DampingAlpha,isNonNegative());
182    CheckParameter(SkinThickness, isPositive());
183 <  
184 <  //@todo memory leak
185 <  if( have_err )
186 <    return strdup( err.c_str() );
187 <  
188 <  return NULL;
183 >  CheckParameter(Viscosity,isNonNegative());
184 >  CheckParameter(BeadSize,isPositive());
185 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
186 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
187 >        std::ostringstream oss;
188 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
189 >        throw OOPSEException(oss.str());          
190 >    }
191 >  }
192 > }
193 >    
194 > bool Globals::addComponent(Component* comp) {
195 >    components_.push_back(comp);
196 >    return true;
197 > }
198  
199 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
200 +    zconstraints_.push_back(zcons);
201 +    return true;
202 + }
203  
204 + bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
205 +    std::string molStampName = molStamp->getName();
206 +    std::map<std::string, MoleculeStamp*>::iterator i;
207 +    bool ret = false;
208 +    i = moleculeStamps_.find(molStampName);
209 +    if (i == moleculeStamps_.end()) {
210 +        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
211 +        ret = true;
212 +    } else {
213 +        std::ostringstream oss;
214 +        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
215 +        throw OOPSEException(oss.str());  
216 +    }
217 +    return ret;
218   }
219 +
220  
409 – int Globals::globalEnd( event* the_event ){
410 –  
411 –  the_event->err_msg = checkMe();
412 –  if( the_event->err_msg != NULL ) return 0;
413 –
414 –  return 1;
221   }

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