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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 674 by tim, Mon Oct 17 03:06:29 2005 UTC vs.
Revision 1306 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())) { 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");
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 134 | 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 <
143 < int Globals::globalAssign( event* the_event ){
144 <  char errorMessage[65535];
145 <  int key;
146 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
147 <  char* lhs = the_event->evt.asmt.lhs;
148 <  std::string keyword(lhs);
149 <
150 <  bool result = false;
151 <
152 <  /**@todo fix memory leak */  
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(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);
159 <            the_event->err_msg = strdup(errorMessage);
160 <       }
161 <    } else if( the_type == DOUBLE ){
162 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
163 <       if (!result )
164 <         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 );
165 <       the_event->err_msg = strdup(errorMessage);
166 <    }      
167 <    else if (the_type == INT ){
168 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
169 <       if (!result )
170 <         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 );
171 <       the_event->err_msg = strdup(errorMessage);
172 <      
173 <    } else {
174 <        sprintf(errorMessage,  "Internal error of parser\n");
175 <        the_event->err_msg = strdup(errorMessage);
176 <    }
177 <  } else {
178 <    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
179 <    the_event->err_msg = strdup(errorMessage);
180 <  }
181 <
182 <  if (keyword == "nComponents" && getNComponents() > 0) {
183 <    components = new Component*[getNComponents()];
184 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
185 <    zConstraints = new ZconStamp*[getNZconstraints()];
186 <  }
187 <  
188 <  return result;
189 < }
190 <
191 < int Globals::newComponent( event* the_event ){
192 <  
193 <  current_component = new Component;
194 <  int index = the_event->evt.blk_index;
195 <  char err[200];
196 <  
197 <  if( haveNComponents() && index < getNComponents() )
198 <    components[index] = current_component;
199 <  else{
200 <    if( haveNComponents()  ){
201 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
202 <               index );
203 <      the_event->err_msg = strdup( err );
204 <      return 0;
205 <    }
206 <    else{
207 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
208 <                                  " first component declaration." );
209 <      return 0;
210 <    }
211 <  }  
212 <
213 <  return 1;
214 < }
215 <
216 <
217 <
218 < int Globals::componentAssign( event* the_event ){
219 <
220 <  switch( the_event->evt.asmt.asmt_type ){
221 <    
222 <  case STRING:
223 <    return current_component->assignString( the_event->evt.asmt.lhs,
224 <                                            the_event->evt.asmt.rhs.sval,
225 <                                            &(the_event->err_msg));
226 <    break;
227 <    
228 <  case DOUBLE:
229 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
230 <                                            the_event->evt.asmt.rhs.dval,
231 <                                            &(the_event->err_msg));
232 <    break;
233 <    
234 <  case INT:
235 <    return current_component->assignInt( the_event->evt.asmt.lhs,
236 <                                         the_event->evt.asmt.rhs.ival,
237 <                                         &(the_event->err_msg));
238 <    break;
239 <    
240 <  default:
241 <    the_event->err_msg = strdup( "Globals error. Invalid component"
242 <                                 " assignment type" );
243 <    return 0;
244 <    break;
245 <  }
246 <  return 0;
247 < }
248 <
249 < int Globals::componentEnd( event* the_event ){
250 <
251 <  the_event->err_msg = current_component->checkMe();
252 <  if( the_event->err_msg != NULL ) return 0;
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 <  return 1;
135 < }
136 <
257 < int Globals::newZconstraint( event* the_event ){
258 <  
259 <
260 <  int index = the_event->evt.blk_index;
261 <  char err[200];
262 <  current_zConstraint = new ZconStamp( index );
263 <  
264 <  if( haveNZconstraints() && index < getNZconstraints() )
265 <    zConstraints[index] = current_zConstraint;
266 <  else{
267 <    if( haveNZconstraints() ){
268 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
269 <               index );
270 <      the_event->err_msg = strdup( err );
271 <      return 0;
272 <    }
273 <    else{
274 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
275 <                                  " not given before"
276 <                                  " first zConstraint declaration." );
277 <      return 0;
278 <    }
279 <  }  
280 <
281 <  return 1;
282 < }
283 <
284 <
285 <
286 < int Globals::zConstraintAssign( event* the_event ){
287 <
288 <  switch( the_event->evt.asmt.asmt_type ){
134 >  deprecatedKeywords_.insert("nComponents");
135 >  deprecatedKeywords_.insert("nZconstraints");
136 >  deprecatedKeywords_.insert("initialConfig");
137      
290 –  case STRING:
291 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
292 –                                              the_event->evt.asmt.rhs.sval,
293 –                                              &(the_event->err_msg));
294 –    break;
295 –    
296 –  case DOUBLE:
297 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
298 –                                              the_event->evt.asmt.rhs.dval,
299 –                                              &(the_event->err_msg));
300 –    break;
301 –    
302 –  case INT:
303 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
304 –                                           the_event->evt.asmt.rhs.ival,
305 –                                           &(the_event->err_msg));
306 –    break;
307 –    
308 –  default:
309 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
310 –                                 " assignment type" );
311 –    return 0;
312 –    break;
313 –  }
314 –  return 0;
138   }
139  
140 < int Globals::zConstraintEnd( event* the_event ){
141 <
142 <  the_event->err_msg = current_zConstraint->checkMe();
320 <  if( the_event->err_msg != NULL ) return 0;
321 <
322 <  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  
327 –
328 –  std::string err("The following required keywords are missing:\n");
329 –  short int have_err = 0;
330 –
331 –  ParamMap::iterator i;
332 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
333 –    if (!i->second->isOptional() && i->second->empty()) {
334 –        err +=  i->second->getKeyword() + "\n";
335 –    }
336 –  }
337 –
148    CheckParameter(ForceField, isNotEmpty());
339 –  CheckParameter(NComponents,isPositive());
149    CheckParameter(TargetTemp, isPositive());
150 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
342 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
343 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
344 <
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());
347 –  CheckParameter(InitialConfig, isNotEmpty());
153    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());
154    CheckParameter(SampleTime, isNonNegative());
155    CheckParameter(ResetTime, isNonNegative());
156    CheckParameter(StatusTime, isNonNegative());
# Line 359 | Line 158 | char* Globals::checkMe( void ){
158    CheckParameter(SwitchingRadius, isNonNegative());
159    CheckParameter(Dielectric, isPositive());
160    CheckParameter(ThermalTime,  isNonNegative());
362 –  CheckParameter(TargetPressure,  isPositive());
161    CheckParameter(TauThermostat, isPositive());
162    CheckParameter(TauBarostat, isPositive());
163    CheckParameter(ZconsTime, isPositive());
366 –  CheckParameter(NZconstraints, isPositive());  
164    CheckParameter(ZconsTol, isPositive());
368 –  //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 377 | 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,);    
391 –  //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 <  
403 <  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  
413 –  return 1;
236   }

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