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root/OpenMD/branches/development/src/io/Globals.cpp
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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 765 by gezelter, Mon Nov 21 22:59:36 2005 UTC vs.
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 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 < using namespace oopse;
56 <
57 < Globals::Globals(){
58 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
60 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
66 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
68 –  DefineOptionalParameter(NMol, "nMol");
69 –  DefineOptionalParameter(Density, "density");
70 –  DefineOptionalParameter(Box, "box");
71 –  DefineOptionalParameter(BoxX, "boxX");
72 –  DefineOptionalParameter(BoxY, "boxY");
73 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
79 –  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");
86 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 102 | 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");
110 –  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
111 –  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
96    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
97    DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
98 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99 >  DefineOptionalParameter(Viscosity, "viscosity");
100 >  DefineOptionalParameter(BeadSize, "beadSize");
101 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
104 >  DefineOptionalParameter(TempDepViscosityA,"tempDepViscosityA");
105 >  DefineOptionalParameter(TempDepViscosityB,"tempDepViscosityB");
106 >  DefineOptionalParameter(TempDepViscosityC,"tempDepViscosityC");
107 >  DefineOptionalParameter(TempDepViscosityD,"tempDepViscosityD");
108 >
109 >  
110    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
111 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
112    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
113    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
114    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 121 | Line 117 | Globals::Globals(){
117    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
118    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
119    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
120 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
120 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
121 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
122 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
123    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
124    DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
125    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
126    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
127 <
128 <  
131 < }
132 <
133 < Globals::~Globals(){
134 <  int i;
135 <  if( components != NULL ){
136 <    for( i=0; i< getNComponents(); i++ ) delete components[i];
137 <    delete[] components;
138 <  }
139 <  
140 <  if( zConstraints != NULL ){
141 <    for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i];
142 <    delete[] zConstraints;
143 <  }
144 <  
145 < }
146 <
147 < int Globals::globalAssign( event* the_event ){
148 <  char errorMessage[65535];
149 <  int key;
150 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
151 <  char* lhs = the_event->evt.asmt.lhs;
152 <  std::string keyword(lhs);
153 <
154 <  bool result = false;
155 <
156 <  /**@todo fix memory leak */  
157 <  ParamMap::iterator i =parameters_.find(keyword);
158 <  if (i != parameters_.end()) {
159 <    if( the_type == STRING ){
160 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
161 <       if (!result ) {
162 <            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);
163 <            the_event->err_msg = strdup(errorMessage);
164 <       }
165 <    } else if( the_type == DOUBLE ){
166 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
167 <       if (!result )
168 <         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 );
169 <       the_event->err_msg = strdup(errorMessage);
170 <    }      
171 <    else if (the_type == INT ){
172 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
173 <       if (!result )
174 <         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 );
175 <       the_event->err_msg = strdup(errorMessage);
176 <      
177 <    } else {
178 <        sprintf(errorMessage,  "Internal error of parser\n");
179 <        the_event->err_msg = strdup(errorMessage);
180 <    }
181 <  } else {
182 <    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
183 <    the_event->err_msg = strdup(errorMessage);
184 <  }
185 <
186 <  if (keyword == "nComponents" && getNComponents() > 0) {
187 <    components = new Component*[getNComponents()];
188 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
189 <    zConstraints = new ZconStamp*[getNZconstraints()];
190 <  }
191 <  
192 <  return result;
193 < }
194 <
195 < int Globals::newComponent( event* the_event ){
196 <  
197 <  current_component = new Component;
198 <  int index = the_event->evt.blk_index;
199 <  char err[200];
200 <  
201 <  if( haveNComponents() && index < getNComponents() )
202 <    components[index] = current_component;
203 <  else{
204 <    if( haveNComponents()  ){
205 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
206 <               index );
207 <      the_event->err_msg = strdup( err );
208 <      return 0;
209 <    }
210 <    else{
211 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
212 <                                  " first component declaration." );
213 <      return 0;
214 <    }
215 <  }  
216 <
217 <  return 1;
218 < }
219 <
220 <
221 <
222 < int Globals::componentAssign( event* the_event ){
223 <
224 <  switch( the_event->evt.asmt.asmt_type ){
225 <    
226 <  case STRING:
227 <    return current_component->assignString( the_event->evt.asmt.lhs,
228 <                                            the_event->evt.asmt.rhs.sval,
229 <                                            &(the_event->err_msg));
230 <    break;
231 <    
232 <  case DOUBLE:
233 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
234 <                                            the_event->evt.asmt.rhs.dval,
235 <                                            &(the_event->err_msg));
236 <    break;
237 <    
238 <  case INT:
239 <    return current_component->assignInt( the_event->evt.asmt.lhs,
240 <                                         the_event->evt.asmt.rhs.ival,
241 <                                         &(the_event->err_msg));
242 <    break;
243 <    
244 <  default:
245 <    the_event->err_msg = strdup( "Globals error. Invalid component"
246 <                                 " assignment type" );
247 <    return 0;
248 <    break;
249 <  }
250 <  return 0;
251 < }
252 <
253 < int Globals::componentEnd( event* the_event ){
254 <
255 <  the_event->err_msg = current_component->checkMe();
256 <  if( the_event->err_msg != NULL ) return 0;
127 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
128 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
129  
130 <  return 1;
131 < }
132 <
261 < int Globals::newZconstraint( event* the_event ){
262 <  
263 <
264 <  int index = the_event->evt.blk_index;
265 <  char err[200];
266 <  current_zConstraint = new ZconStamp( index );
267 <  
268 <  if( haveNZconstraints() && index < getNZconstraints() )
269 <    zConstraints[index] = current_zConstraint;
270 <  else{
271 <    if( haveNZconstraints() ){
272 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
273 <               index );
274 <      the_event->err_msg = strdup( err );
275 <      return 0;
276 <    }
277 <    else{
278 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
279 <                                  " not given before"
280 <                                  " first zConstraint declaration." );
281 <      return 0;
282 <    }
283 <  }  
284 <
285 <  return 1;
286 < }
287 <
288 <
289 <
290 < int Globals::zConstraintAssign( event* the_event ){
291 <
292 <  switch( the_event->evt.asmt.asmt_type ){
130 >  deprecatedKeywords_.insert("nComponents");
131 >  deprecatedKeywords_.insert("nZconstraints");
132 >  deprecatedKeywords_.insert("initialConfig");
133      
294 –  case STRING:
295 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
296 –                                              the_event->evt.asmt.rhs.sval,
297 –                                              &(the_event->err_msg));
298 –    break;
299 –    
300 –  case DOUBLE:
301 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
302 –                                              the_event->evt.asmt.rhs.dval,
303 –                                              &(the_event->err_msg));
304 –    break;
305 –    
306 –  case INT:
307 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
308 –                                           the_event->evt.asmt.rhs.ival,
309 –                                           &(the_event->err_msg));
310 –    break;
311 –    
312 –  default:
313 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
314 –                                 " assignment type" );
315 –    return 0;
316 –    break;
317 –  }
318 –  return 0;
134   }
135  
136 < int Globals::zConstraintEnd( event* the_event ){
137 <
138 <  the_event->err_msg = current_zConstraint->checkMe();
324 <  if( the_event->err_msg != NULL ) return 0;
325 <
326 <  return 1;
136 > Globals::~Globals() {
137 >    MemoryUtils::deletePointers(components_);
138 >    MemoryUtils::deletePointers(zconstraints_);
139   }
140  
141 < char* Globals::checkMe( void ){
141 > void Globals::validate() {
142 >  DataHolder::validate();
143  
331 –
332 –  std::string err("The following required keywords are missing:\n");
333 –  short int have_err = 0;
334 –
335 –  ParamMap::iterator i;
336 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
337 –    if (!i->second->isOptional() && i->second->empty()) {
338 –        err +=  i->second->getKeyword() + "\n";
339 –    }
340 –  }
341 –
144    CheckParameter(ForceField, isNotEmpty());
343 –  CheckParameter(NComponents,isPositive());
145    CheckParameter(TargetTemp, isPositive());
146 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
146 >  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"));
147    CheckParameter(Dt, isPositive());
148    CheckParameter(RunTime, isPositive());
348 –  CheckParameter(InitialConfig, isNotEmpty());
149    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());
150    CheckParameter(SampleTime, isNonNegative());
151    CheckParameter(ResetTime, isNonNegative());
152    CheckParameter(StatusTime, isNonNegative());
# Line 360 | Line 154 | char* Globals::checkMe( void ){
154    CheckParameter(SwitchingRadius, isNonNegative());
155    CheckParameter(Dielectric, isPositive());
156    CheckParameter(ThermalTime,  isNonNegative());
363 –  CheckParameter(TargetPressure,  isPositive());
157    CheckParameter(TauThermostat, isPositive());
158    CheckParameter(TauBarostat, isPositive());
159    CheckParameter(ZconsTime, isPositive());
367 –  CheckParameter(NZconstraints, isPositive());  
160    CheckParameter(ZconsTol, isPositive());
369 –  //CheckParameter(ZconsForcePolicy,);
161    CheckParameter(Seed, isPositive());
162 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
162 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
163    CheckParameter(MinimizerMaxIter, isPositive());
164    CheckParameter(MinimizerWriteFrq, isPositive());
165    CheckParameter(MinimizerStepSize, isPositive());
# Line 378 | Line 169 | char* Globals::checkMe( void ){
169    CheckParameter(MinimizerLSMaxIter, isPositive());
170    CheckParameter(ZconsGap, isPositive());
171    CheckParameter(ZconsFixtime, isPositive());
172 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
172 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
173    CheckParameter(ThermodynamicIntegrationK, isPositive());
174    CheckParameter(ForceFieldVariant, isNotEmpty());
175    CheckParameter(ForceFieldFileName, isNotEmpty());
176    CheckParameter(ThermIntDistSpringConst, isPositive());
177    CheckParameter(ThermIntThetaSpringConst, isPositive());
178    CheckParameter(ThermIntOmegaSpringConst, isPositive());
179 <  CheckParameter(SurfaceTension, isPositive());
180 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
181 <  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
182 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
392 <  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
179 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
180 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
181 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
182 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
183    //CheckParameter(StatFileFormat,);    
394 –  //CheckParameter(MixingRule,);
184    CheckParameter(OrthoBoxTolerance, isPositive());  
185    CheckParameter(ThermIntDistSpringConst, isPositive());
186    CheckParameter(ThermIntThetaSpringConst, isPositive());
187    CheckParameter(ThermIntOmegaSpringConst, isPositive());
188    CheckParameter(DampingAlpha,isNonNegative());
189    CheckParameter(SkinThickness, isPositive());
190 <  
191 <  //@todo memory leak
192 <  if( have_err )
193 <    return strdup( err.c_str() );
194 <  
406 <  return NULL;
190 >  CheckParameter(Viscosity, isNonNegative());
191 >  CheckParameter(BeadSize, isPositive());
192 >  CheckParameter(FrozenBufferRadius, isPositive());
193 >  CheckParameter(LangevinBufferRadius, isPositive());
194 >  CheckParameter(NeighborListNeighbors, isPositive());
195  
196 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
197 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
198 +        std::ostringstream oss;
199 +        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
200 +        throw OOPSEException(oss.str());          
201 +    }
202 +  }
203 + }
204 +    
205 + bool Globals::addComponent(Component* comp) {
206 +    components_.push_back(comp);
207 +    return true;
208 + }
209  
210 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
211 +    zconstraints_.push_back(zcons);
212 +    return true;
213   }
214  
215 < int Globals::globalEnd( event* the_event ){
216 <  
217 <  the_event->err_msg = checkMe();
218 <  if( the_event->err_msg != NULL ) return 0;
215 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
216 >    std::string molStampName = molStamp->getName();
217 >    std::map<std::string, MoleculeStamp*>::iterator i;
218 >    bool ret = false;
219 >    i = moleculeStamps_.find(molStampName);
220 >    if (i == moleculeStamps_.end()) {
221 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
222 >        ret = true;
223 >    } else {
224 >        std::ostringstream oss;
225 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
226 >        throw OOPSEException(oss.str());  
227 >    }
228 >    return ret;
229 > }
230 >
231  
416 –  return 1;
232   }

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