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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 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");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
60 <  DefineOptionalParameter(InitialConfig, "initialConfig");
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");
65    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92 –  DefineOptionalParameter(Dielectric, "dielectric");
67    DefineOptionalParameter(TempSet, "tempSet");
68    DefineOptionalParameter(ThermalTime, "thermalTime");
69    DefineOptionalParameter(TargetPressure, "targetPressure");
70    DefineOptionalParameter(TauThermostat, "tauThermostat");
71    DefineOptionalParameter(TauBarostat, "tauBarostat");
72    DefineOptionalParameter(ZconsTime, "zconsTime");
99 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
73    DefineOptionalParameter(ZconsTol, "zconsTol");
74    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
75    DefineOptionalParameter(Seed, "seed");
# Line 121 | Line 94 | Globals::Globals(){
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96    DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
97 +  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99 +  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100 +  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101 +  DefineOptionalParameter(Viscosity, "viscosity");
102 +  DefineOptionalParameter(BeadSize, "beadSize");
103 +  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104 +  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105    
126 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
106    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
107    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
108    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
# Line 133 | Line 112 | Globals::Globals(){
112    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
113    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
114    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
115 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
115 >  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
116 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
117    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
118 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
120    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
121 <
122 <  
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 <  
260 <
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 <  }  
121 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
122 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
123  
282 –  return 1;
283 – }
124  
125 <
126 <
127 < int Globals::zConstraintAssign( event* the_event ){
288 <
289 <  switch( the_event->evt.asmt.asmt_type ){
125 >    deprecatedKeywords_.insert("nComponents");
126 >    deprecatedKeywords_.insert("nZconstraints");
127 >    deprecatedKeywords_.insert("initialConfig");
128      
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;
129   }
130  
131 < int Globals::zConstraintEnd( event* the_event ){
132 <
133 <  the_event->err_msg = current_zConstraint->checkMe();
321 <  if( the_event->err_msg != NULL ) return 0;
322 <
323 <  return 1;
131 > Globals::~Globals() {
132 >    MemoryUtils::deletePointers(components_);
133 >    MemoryUtils::deletePointers(zconstraints_);
134   }
135  
136 < char* Globals::checkMe( void ){
136 > void Globals::validate() {
137 >  DataHolder::validate();
138  
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 –
139    CheckParameter(ForceField, isNotEmpty());
340 –  CheckParameter(NComponents,isPositive());
140    CheckParameter(TargetTemp, isPositive());
141 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
343 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
344 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
141 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT"));
142    CheckParameter(Dt, isPositive());
143    CheckParameter(RunTime, isPositive());
144 <  CheckParameter(InitialConfig, isNotEmpty());
144 >  //CheckParameter(InitialConfig, isNotEmpty());
145    CheckParameter(FinalConfig, isNotEmpty());
349 –  CheckParameter(NMol, isPositive());
350 –  CheckParameter(Density, isPositive());
351 –  CheckParameter(Box, isPositive());
352 –  CheckParameter(BoxX, isPositive());
353 –  CheckParameter(BoxY, isPositive());
354 –  CheckParameter(BoxZ, isPositive());
146    CheckParameter(SampleTime, isNonNegative());
147    CheckParameter(ResetTime, isNonNegative());
148    CheckParameter(StatusTime, isNonNegative());
# Line 359 | Line 150 | char* Globals::checkMe( void ){
150    CheckParameter(SwitchingRadius, isNonNegative());
151    CheckParameter(Dielectric, isPositive());
152    CheckParameter(ThermalTime,  isNonNegative());
153 <  CheckParameter(TargetPressure,  isPositive());
153 >  //  CheckParameter(TargetPressure,  isPositive());
154    CheckParameter(TauThermostat, isPositive());
155    CheckParameter(TauBarostat, isPositive());
156    CheckParameter(ZconsTime, isPositive());
366 –  CheckParameter(NZconstraints, isPositive());  
157    CheckParameter(ZconsTol, isPositive());
368 –  //CheckParameter(ZconsForcePolicy,);
158    CheckParameter(Seed, isPositive());
159 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
159 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
160    CheckParameter(MinimizerMaxIter, isPositive());
161    CheckParameter(MinimizerWriteFrq, isPositive());
162    CheckParameter(MinimizerStepSize, isPositive());
# Line 377 | Line 166 | char* Globals::checkMe( void ){
166    CheckParameter(MinimizerLSMaxIter, isPositive());
167    CheckParameter(ZconsGap, isPositive());
168    CheckParameter(ZconsFixtime, isPositive());
169 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
169 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
170    CheckParameter(ThermodynamicIntegrationK, isPositive());
171    CheckParameter(ForceFieldVariant, isNotEmpty());
172    CheckParameter(ForceFieldFileName, isNotEmpty());
173    CheckParameter(ThermIntDistSpringConst, isPositive());
174    CheckParameter(ThermIntThetaSpringConst, isPositive());
175    CheckParameter(ThermIntOmegaSpringConst, isPositive());
176 <  CheckParameter(SurfaceTension, isPositive());
177 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
178 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
176 >  //  CheckParameter(SurfaceTension, isNonNegative());
177 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
178 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
179 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
180 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
181    //CheckParameter(StatFileFormat,);    
391 –  //CheckParameter(MixingRule,);
182    CheckParameter(OrthoBoxTolerance, isPositive());  
183    CheckParameter(ThermIntDistSpringConst, isPositive());
184    CheckParameter(ThermIntThetaSpringConst, isPositive());
185    CheckParameter(ThermIntOmegaSpringConst, isPositive());
186 <  CheckParameter(DampingAlpha,isPositive());
186 >  CheckParameter(DampingAlpha,isNonNegative());
187    CheckParameter(SkinThickness, isPositive());
188 <  
189 <  //@todo memory leak
190 <  if( have_err )
191 <    return strdup( err.c_str() );
192 <  
193 <  return NULL;
188 >  CheckParameter(Viscosity, isNonNegative());
189 >  CheckParameter(BeadSize, isPositive());
190 >  CheckParameter(FrozenBufferRadius, isPositive());
191 >  CheckParameter(LangevinBufferRadius, isPositive());
192 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
193 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
194 >        std::ostringstream oss;
195 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
196 >        throw OOPSEException(oss.str());          
197 >    }
198 >  }
199 > }
200 >    
201 > bool Globals::addComponent(Component* comp) {
202 >    components_.push_back(comp);
203 >    return true;
204 > }
205  
206 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
207 +    zconstraints_.push_back(zcons);
208 +    return true;
209 + }
210  
211 + bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
212 +    std::string molStampName = molStamp->getName();
213 +    std::map<std::string, MoleculeStamp*>::iterator i;
214 +    bool ret = false;
215 +    i = moleculeStamps_.find(molStampName);
216 +    if (i == moleculeStamps_.end()) {
217 +        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
218 +        ret = true;
219 +    } else {
220 +        std::ostringstream oss;
221 +        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
222 +        throw OOPSEException(oss.str());  
223 +    }
224 +    return ret;
225   }
226 +
227  
408 – int Globals::globalEnd( event* the_event ){
409 –  
410 –  the_event->err_msg = checkMe();
411 –  if( the_event->err_msg != NULL ) return 0;
412 –
413 –  return 1;
228   }

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