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Comparing trunk/OOPSE-4/src/io/Globals.cpp (file contents):
Revision 2372 by tim, Mon Oct 17 00:51:16 2005 UTC vs.
Revision 3463 by chuckv, Thu Oct 16 18:25:36 2008 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())) std::cout <<"Error in parsing " << NAME.getKeyword() << " : "<< (CONSTRAINT).getConstraintDescription() << std::endl; }                
69 <
70 <
71 < Globals::Globals(){
72 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
74 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
80 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
82 –  DefineOptionalParameter(NMol, "nMol");
83 –  DefineOptionalParameter(Density, "density");
84 –  DefineOptionalParameter(Box, "box");
85 –  DefineOptionalParameter(BoxX, "boxX");
86 –  DefineOptionalParameter(BoxY, "boxY");
87 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
93 –  DefineOptionalParameter(Dielectric, "dielectric");
66    DefineOptionalParameter(TempSet, "tempSet");
67    DefineOptionalParameter(ThermalTime, "thermalTime");
68 <  DefineOptionalParameter(TargetPressure, "targetPressure");
68 >  DefineOptionalParameter(TargetPressure, "targetPressure");  
69    DefineOptionalParameter(TauThermostat, "tauThermostat");
70    DefineOptionalParameter(TauBarostat, "tauBarostat");
71    DefineOptionalParameter(ZconsTime, "zconsTime");
100 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 116 | Line 87 | Globals::Globals(){
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 +  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92    DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93    DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94    DefineOptionalParameter(SurfaceTension, "surfaceTension");
95    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
96 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99 <  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
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 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106 >  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
107 >  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
108 >  DefineOptionalParameter(MTM_G, "MTM_G");
109 >  DefineOptionalParameter(MTM_Io, "MTM_Io");
110 >  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
111 >  DefineOptionalParameter(MTM_R, "MTM_R");
112    
113 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
113 >  
114    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
115 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
116    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 135 | Line 121 | Globals::Globals(){
121    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
122    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
123    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
124 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
124 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
125 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
126 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
127    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
128 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
129    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
130 <  
131 < }
132 <
144 < int Globals::globalAssign( event* the_event ){
145 <  
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 <  ParamMap::iterator i =parameters_.find(keyword);
154 <  if (i != parameters_.end()) {
155 <    if( the_type == STRING ){
156 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
157 <       if (!result ) {
158 <            sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %s.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.sval);
159 <       }
160 <    } else if( the_type == DOUBLE ){
161 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
162 <       if (!result )
163 <         sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %f.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.dval );
164 <    }      
165 <    else if (the_type == INT ){
166 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
167 <       if (!result )
168 <         sprintf(the_event->err_msg,  "Error in parsing %s: expect %s, but get %d.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.ival );
169 <      
170 <    } else {
171 <        sprintf(the_event->err_msg,  "%s is an unrecognized keyword\n", keyword.c_str() );
172 <    }
173 <  }
174 <
175 <  if (keyword == "nComponents" && getNComponents() > 0) {
176 <    components = new Component*[getNComponents()];
177 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
178 <    zConstraints = new ZconStamp*[getNZconstraints()];
179 <  }
180 <  
181 <  return result;
182 < }
183 <
184 < int Globals::newComponent( event* the_event ){
185 <  
186 <  current_component = new Component;
187 <  int index = the_event->evt.blk_index;
188 <  char err[200];
189 <  
190 <  if( haveNComponents() && index < getNComponents() )
191 <    components[index] = current_component;
192 <  else{
193 <    if( haveNComponents()  ){
194 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
195 <               index );
196 <      the_event->err_msg = strdup( err );
197 <      return 0;
198 <    }
199 <    else{
200 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
201 <                                  " first component declaration." );
202 <      return 0;
203 <    }
204 <  }  
205 <
206 <  return 1;
207 < }
208 <
209 <
210 <
211 < int Globals::componentAssign( event* the_event ){
212 <
213 <  switch( the_event->evt.asmt.asmt_type ){
214 <    
215 <  case STRING:
216 <    return current_component->assignString( the_event->evt.asmt.lhs,
217 <                                            the_event->evt.asmt.rhs.sval,
218 <                                            &(the_event->err_msg));
219 <    break;
220 <    
221 <  case DOUBLE:
222 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
223 <                                            the_event->evt.asmt.rhs.dval,
224 <                                            &(the_event->err_msg));
225 <    break;
226 <    
227 <  case INT:
228 <    return current_component->assignInt( the_event->evt.asmt.lhs,
229 <                                         the_event->evt.asmt.rhs.ival,
230 <                                         &(the_event->err_msg));
231 <    break;
232 <    
233 <  default:
234 <    the_event->err_msg = strdup( "Globals error. Invalid component"
235 <                                 " assignment type" );
236 <    return 0;
237 <    break;
238 <  }
239 <  return 0;
240 < }
241 <
242 < int Globals::componentEnd( event* the_event ){
243 <
244 <  the_event->err_msg = current_component->checkMe();
245 <  if( the_event->err_msg != NULL ) return 0;
246 <
247 <  return 1;
248 < }
130 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
131 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
132 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
133  
134 < int Globals::newZconstraint( event* the_event ){
135 <  
136 <
253 <  int index = the_event->evt.blk_index;
254 <  char err[200];
255 <  current_zConstraint = new ZconStamp( index );
256 <  
257 <  if( haveNZconstraints() && index < getNZconstraints() )
258 <    zConstraints[index] = current_zConstraint;
259 <  else{
260 <    if( haveNZconstraints() ){
261 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
262 <               index );
263 <      the_event->err_msg = strdup( err );
264 <      return 0;
265 <    }
266 <    else{
267 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
268 <                                  " not given before"
269 <                                  " first zConstraint declaration." );
270 <      return 0;
271 <    }
272 <  }  
273 <
274 <  return 1;
275 < }
276 <
277 <
278 <
279 < int Globals::zConstraintAssign( event* the_event ){
280 <
281 <  switch( the_event->evt.asmt.asmt_type ){
134 >  deprecatedKeywords_.insert("nComponents");
135 >  deprecatedKeywords_.insert("nZconstraints");
136 >  deprecatedKeywords_.insert("initialConfig");
137      
283 –  case STRING:
284 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
285 –                                              the_event->evt.asmt.rhs.sval,
286 –                                              &(the_event->err_msg));
287 –    break;
288 –    
289 –  case DOUBLE:
290 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
291 –                                              the_event->evt.asmt.rhs.dval,
292 –                                              &(the_event->err_msg));
293 –    break;
294 –    
295 –  case INT:
296 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
297 –                                           the_event->evt.asmt.rhs.ival,
298 –                                           &(the_event->err_msg));
299 –    break;
300 –    
301 –  default:
302 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
303 –                                 " assignment type" );
304 –    return 0;
305 –    break;
306 –  }
307 –  return 0;
138   }
139  
140 < int Globals::zConstraintEnd( event* the_event ){
141 <
142 <  the_event->err_msg = current_zConstraint->checkMe();
313 <  if( the_event->err_msg != NULL ) return 0;
314 <
315 <  return 1;
140 > Globals::~Globals() {
141 >    MemoryUtils::deletePointers(components_);
142 >    MemoryUtils::deletePointers(zconstraints_);
143   }
144  
145 < char* Globals::checkMe( void ){
145 > void Globals::validate() {
146 >  DataHolder::validate();
147  
320 –
321 –  std::string err("The following required keywords are missing:\n");
322 –  short int have_err = 0;
323 –
324 –  ParamMap::iterator i;
325 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
326 –    if (!i->second->isOptional() && i->second->empty()) {
327 –        err +=  i->second->getKeyword() + "\n";
328 –    }
329 –  }
330 –
148    CheckParameter(ForceField, isNotEmpty());
332 –  CheckParameter(NComponents,isPositive());
149    CheckParameter(TargetTemp, isPositive());
150 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
335 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
336 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
337 <
150 >  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") || isEqualIgnoreCase("SMIPD"));
151    CheckParameter(Dt, isPositive());
152    CheckParameter(RunTime, isPositive());
340 –  CheckParameter(InitialConfig, isNotEmpty());
153    CheckParameter(FinalConfig, isNotEmpty());
342 –  CheckParameter(NMol, isPositive());
343 –  CheckParameter(Density, isPositive());
344 –  CheckParameter(Box, isPositive());
345 –  CheckParameter(BoxX, isPositive());
346 –  CheckParameter(BoxY, isPositive());
347 –  CheckParameter(BoxZ, isPositive());
154    CheckParameter(SampleTime, isNonNegative());
155    CheckParameter(ResetTime, isNonNegative());
156    CheckParameter(StatusTime, isNonNegative());
# Line 352 | Line 158 | char* Globals::checkMe( void ){
158    CheckParameter(SwitchingRadius, isNonNegative());
159    CheckParameter(Dielectric, isPositive());
160    CheckParameter(ThermalTime,  isNonNegative());
355 –  CheckParameter(TargetPressure,  isPositive());
161    CheckParameter(TauThermostat, isPositive());
162    CheckParameter(TauBarostat, isPositive());
163    CheckParameter(ZconsTime, isPositive());
359 –  CheckParameter(NZconstraints, isPositive());  
164    CheckParameter(ZconsTol, isPositive());
361 –  //CheckParameter(ZconsForcePolicy,);
165    CheckParameter(Seed, isPositive());
166 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
166 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
167    CheckParameter(MinimizerMaxIter, isPositive());
168    CheckParameter(MinimizerWriteFrq, isPositive());
169    CheckParameter(MinimizerStepSize, isPositive());
# Line 370 | Line 173 | char* Globals::checkMe( void ){
173    CheckParameter(MinimizerLSMaxIter, isPositive());
174    CheckParameter(ZconsGap, isPositive());
175    CheckParameter(ZconsFixtime, isPositive());
176 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
176 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
177    CheckParameter(ThermodynamicIntegrationK, isPositive());
178    CheckParameter(ForceFieldVariant, isNotEmpty());
179    CheckParameter(ForceFieldFileName, isNotEmpty());
180    CheckParameter(ThermIntDistSpringConst, isPositive());
181    CheckParameter(ThermIntThetaSpringConst, isPositive());
182    CheckParameter(ThermIntOmegaSpringConst, isPositive());
183 <  CheckParameter(SurfaceTension, isPositive());
184 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
185 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
183 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
184 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
185 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
186 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
187    //CheckParameter(StatFileFormat,);    
384 –  //CheckParameter(MixingRule,);
188    CheckParameter(OrthoBoxTolerance, isPositive());  
189    CheckParameter(ThermIntDistSpringConst, isPositive());
190    CheckParameter(ThermIntThetaSpringConst, isPositive());
191    CheckParameter(ThermIntOmegaSpringConst, isPositive());
192 <  CheckParameter(DampingAlpha,isPositive());
192 >  CheckParameter(DampingAlpha,isNonNegative());
193    CheckParameter(SkinThickness, isPositive());
194 <  
195 <  //@todo memory leak
196 <  if( have_err )
197 <    return strdup( err.c_str() );
198 <  
396 <  return NULL;
194 >  CheckParameter(Viscosity, isNonNegative());
195 >  CheckParameter(BeadSize, isPositive());
196 >  CheckParameter(FrozenBufferRadius, isPositive());
197 >  CheckParameter(LangevinBufferRadius, isPositive());
198 >  CheckParameter(NeighborListNeighbors, isPositive());
199  
200 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
201 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
202 +        std::ostringstream oss;
203 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
204 +        throw OOPSEException(oss.str());          
205 +    }
206 +  }
207 + }
208 +    
209 + bool Globals::addComponent(Component* comp) {
210 +    components_.push_back(comp);
211 +    return true;
212 + }
213  
214 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
215 +    zconstraints_.push_back(zcons);
216 +    return true;
217   }
218  
219 < int Globals::globalEnd( event* the_event ){
220 <  
221 <  the_event->err_msg = checkMe();
222 <  if( the_event->err_msg != NULL ) return 0;
219 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
220 >    std::string molStampName = molStamp->getName();
221 >    std::map<std::string, MoleculeStamp*>::iterator i;
222 >    bool ret = false;
223 >    i = moleculeStamps_.find(molStampName);
224 >    if (i == moleculeStamps_.end()) {
225 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
226 >        ret = true;
227 >    } else {
228 >        std::ostringstream oss;
229 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
230 >        throw OOPSEException(oss.str());  
231 >    }
232 >    return ret;
233 > }
234 >
235  
406 –  return 1;
236   }

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