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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 710 by chrisfen, Wed Nov 2 20:36:25 2005 UTC vs.
Revision 1147 by chuckv, Wed Jul 4 04:47:53 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 < #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");
79 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    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");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92 –  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");
99 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 115 | 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");
123 –  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
124 –  DefineOptionalParameter(ScreeningMethod, "screeningMethod");
96    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
97 +  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
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    
105 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
105 >  
106    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
107 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
108    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
109    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
110    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 134 | Line 113 | Globals::Globals(){
113    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
116 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
116 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
117 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
118 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
119    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
120 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
121    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
122    DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
123 <
124 <  
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;
255 <
256 <  return 1;
257 < }
123 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
124 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
125  
126 < int Globals::newZconstraint( event* the_event ){
127 <  
128 <
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 ){
126 >  deprecatedKeywords_.insert("nComponents");
127 >  deprecatedKeywords_.insert("nZconstraints");
128 >  deprecatedKeywords_.insert("initialConfig");
129      
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;
130   }
131  
132 < int Globals::zConstraintEnd( event* the_event ){
133 <
134 <  the_event->err_msg = current_zConstraint->checkMe();
322 <  if( the_event->err_msg != NULL ) return 0;
323 <
324 <  return 1;
132 > Globals::~Globals() {
133 >    MemoryUtils::deletePointers(components_);
134 >    MemoryUtils::deletePointers(zconstraints_);
135   }
136  
137 < char* Globals::checkMe( void ){
137 > void Globals::validate() {
138 >  DataHolder::validate();
139  
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 –
140    CheckParameter(ForceField, isNotEmpty());
341 –  CheckParameter(NComponents,isPositive());
141    CheckParameter(TargetTemp, isPositive());
142 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
344 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
345 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
142 >  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"));
143    CheckParameter(Dt, isPositive());
144    CheckParameter(RunTime, isPositive());
348 –  CheckParameter(InitialConfig, isNotEmpty());
145    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());
146    CheckParameter(SampleTime, isNonNegative());
147    CheckParameter(ResetTime, isNonNegative());
148    CheckParameter(StatusTime, isNonNegative());
# Line 360 | Line 150 | char* Globals::checkMe( void ){
150    CheckParameter(SwitchingRadius, isNonNegative());
151    CheckParameter(Dielectric, isPositive());
152    CheckParameter(ThermalTime,  isNonNegative());
363 –  CheckParameter(TargetPressure,  isPositive());
153    CheckParameter(TauThermostat, isPositive());
154    CheckParameter(TauBarostat, isPositive());
155    CheckParameter(ZconsTime, isPositive());
367 –  CheckParameter(NZconstraints, isPositive());  
156    CheckParameter(ZconsTol, isPositive());
369 –  //CheckParameter(ZconsForcePolicy,);
157    CheckParameter(Seed, isPositive());
158 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
158 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
159    CheckParameter(MinimizerMaxIter, isPositive());
160    CheckParameter(MinimizerWriteFrq, isPositive());
161    CheckParameter(MinimizerStepSize, isPositive());
# Line 378 | Line 165 | char* Globals::checkMe( void ){
165    CheckParameter(MinimizerLSMaxIter, isPositive());
166    CheckParameter(ZconsGap, isPositive());
167    CheckParameter(ZconsFixtime, isPositive());
168 <  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
168 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
169    CheckParameter(ThermodynamicIntegrationK, isPositive());
170    CheckParameter(ForceFieldVariant, isNotEmpty());
171    CheckParameter(ForceFieldFileName, isNotEmpty());
172    CheckParameter(ThermIntDistSpringConst, isPositive());
173    CheckParameter(ThermIntThetaSpringConst, isPositive());
174    CheckParameter(ThermIntOmegaSpringConst, isPositive());
175 <  CheckParameter(SurfaceTension, isPositive());
176 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE"))  || isEqualIgnoreCase(std::string("REACTION_FIELD")));
177 <  CheckParameter(ScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
178 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
175 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
176 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
177 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
178 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
179    //CheckParameter(StatFileFormat,);    
393 –  //CheckParameter(MixingRule,);
180    CheckParameter(OrthoBoxTolerance, isPositive());  
181    CheckParameter(ThermIntDistSpringConst, isPositive());
182    CheckParameter(ThermIntThetaSpringConst, isPositive());
183    CheckParameter(ThermIntOmegaSpringConst, isPositive());
184 <  CheckParameter(DampingAlpha,isPositive());
184 >  CheckParameter(DampingAlpha,isNonNegative());
185    CheckParameter(SkinThickness, isPositive());
186 <  
187 <  //@todo memory leak
188 <  if( have_err )
189 <    return strdup( err.c_str() );
190 <  
405 <  return NULL;
186 >  CheckParameter(Viscosity, isNonNegative());
187 >  CheckParameter(BeadSize, isPositive());
188 >  CheckParameter(FrozenBufferRadius, isPositive());
189 >  CheckParameter(LangevinBufferRadius, isPositive());
190 >  CheckParameter(NeighborListNeighbors, isPositive());
191  
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 < int Globals::globalEnd( event* the_event ){
212 <  
213 <  the_event->err_msg = checkMe();
214 <  if( the_event->err_msg != NULL ) return 0;
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  
415 –  return 1;
228   }

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