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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 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1367 by skuang, Mon Oct 19 13:35:42 2009 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 <
53 < #define DefineParameter(NAME,KEYWORD)                              \
55 <  NAME.setKeyword(KEYWORD);                  \
56 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
57 <
58 < #define DefineOptionalParameter(NAME,KEYWORD)                              \
59 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
60 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
61 <
62 < #define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
63 <  NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
64 <  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
65 <
66 < Globals::Globals(){
67 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
69 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
75 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
77 –  DefineOptionalParameter(NMol, "nMol");
78 –  DefineOptionalParameter(Density, "density");
79 –  DefineOptionalParameter(Box, "box");
80 –  DefineOptionalParameter(BoxX, "boxX");
81 –  DefineOptionalParameter(BoxY, "boxY");
82 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
88 –  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");
95 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 111 | Line 87 | Globals::Globals(){
87    DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88    DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89    DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90 <  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
115 <  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
116 <  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
90 >  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91    DefineOptionalParameter(SurfaceTension, "surfaceTension");
92    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93 <  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
93 >  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94 >  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96 <  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
96 >  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98 >  DefineOptionalParameter(Viscosity, "viscosity");
99 >  DefineOptionalParameter(BeadSize, "beadSize");
100 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102 >  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
103 >  DefineOptionalParameter(ThermalLength, "thermalLength");
104 >  DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
105 >  DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
106 >  DefineOptionalParameter(MTM_Ce, "MTM_Ce");
107 >  DefineOptionalParameter(MTM_G, "MTM_G");
108 >  DefineOptionalParameter(MTM_Io, "MTM_Io");
109 >  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
110 >  DefineOptionalParameter(MTM_R, "MTM_R");
111    
112 <  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
112 >
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);  
119 <  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
120 <  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
121 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
119 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
120 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
121 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
122    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
123 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
124    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125 <  
126 < }
125 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
126 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128  
129 < int Globals::globalAssign( event* the_event ){
130 <  
131 <  int key;
132 <  int token;
133 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
134 <  char* lhs = the_event->evt.asmt.lhs;
135 <  std::string keyword(lhs);
129 >  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
130 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
131 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
132 >  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
133 >  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
134 >  DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
135 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
136 >  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
137 >  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
138 >  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
139  
144 –  bool result;
140  
141 <
142 <  ParamMap::iterator i =parameters_.find(keyword);
143 <  if (i != parameters_.end()) {
144 <    if( the_type == STRING ){
145 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
146 <       if (!result ) {
147 <            sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
148 <       }
154 <    } else if( the_type == DOUBLE ){
155 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
156 <       if (!result )
157 <         sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() );
158 <    }      
159 <    else if (the_type == INT ){
160 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
161 <       if (!result )
162 <         sprintf(the_event->err_msg,  "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() );
163 <      
164 <    } else {
141 >  deprecatedKeywords_.insert("nComponents");
142 >  deprecatedKeywords_.insert("nZconstraints");
143 >  deprecatedKeywords_.insert("initialConfig");
144 >  deprecatedKeywords_.insert("thermIntDistSpringConst");
145 >  deprecatedKeywords_.insert("thermIntThetaSpringConst");
146 >  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
147 >  deprecatedKeywords_.insert("useSolidThermInt");  
148 >  deprecatedKeywords_.insert("useLiquidThermInt");
149      
166 –    }
167 –  }
168 –
169 –  if (keyword == "nComponents" && getNComponents() > 0) {
170 –    components = new Component*[getNComponents()];
171 –  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
172 –    zConstraints = new ZconStamp*[getNZconstraints()];
173 –  }
174 –  
175 –  return result;
176 – }
177 –
178 – int Globals::newComponent( event* the_event ){
179 –  
180 –  current_component = new Component;
181 –  int index = the_event->evt.blk_index;
182 –  char err[200];
183 –  
184 –  if( haveNComponents() && index < getNComponents() )
185 –    components[index] = current_component;
186 –  else{
187 –    if( haveNComponents()  ){
188 –      sprintf( err, "meta-data parsing error: %d out of nComponents range",
189 –               index );
190 –      the_event->err_msg = strdup( err );
191 –      return 0;
192 –    }
193 –    else{
194 –      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
195 –                                  " first component declaration." );
196 –      return 0;
197 –    }
198 –  }  
199 –
200 –  return 1;
201 – }
202 –
203 –
204 –
205 – int Globals::componentAssign( event* the_event ){
206 –
207 –  switch( the_event->evt.asmt.asmt_type ){
208 –    
209 –  case STRING:
210 –    return current_component->assignString( the_event->evt.asmt.lhs,
211 –                                            the_event->evt.asmt.rhs.sval,
212 –                                            &(the_event->err_msg));
213 –    break;
214 –    
215 –  case DOUBLE:
216 –    return current_component->assignDouble( the_event->evt.asmt.lhs,
217 –                                            the_event->evt.asmt.rhs.dval,
218 –                                            &(the_event->err_msg));
219 –    break;
220 –    
221 –  case INT:
222 –    return current_component->assignInt( the_event->evt.asmt.lhs,
223 –                                         the_event->evt.asmt.rhs.ival,
224 –                                         &(the_event->err_msg));
225 –    break;
226 –    
227 –  default:
228 –    the_event->err_msg = strdup( "Globals error. Invalid component"
229 –                                 " assignment type" );
230 –    return 0;
231 –    break;
232 –  }
233 –  return 0;
234 – }
235 –
236 – int Globals::componentEnd( event* the_event ){
237 –
238 –  the_event->err_msg = current_component->checkMe();
239 –  if( the_event->err_msg != NULL ) return 0;
240 –
241 –  return 1;
150   }
151  
152 < int Globals::newZconstraint( event* the_event ){
153 <  
154 <
155 <  int index = the_event->evt.blk_index;
248 <  char err[200];
249 <  current_zConstraint = new ZconStamp( index );
250 <  
251 <  if( haveNZconstraints() && index < getNZconstraints() )
252 <    zConstraints[index] = current_zConstraint;
253 <  else{
254 <    if( haveNZconstraints() ){
255 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
256 <               index );
257 <      the_event->err_msg = strdup( err );
258 <      return 0;
259 <    }
260 <    else{
261 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
262 <                                  " not given before"
263 <                                  " first zConstraint declaration." );
264 <      return 0;
265 <    }
266 <  }  
267 <
268 <  return 1;
152 > Globals::~Globals() {
153 >    MemoryUtils::deletePointers(components_);
154 >    MemoryUtils::deletePointers(zconstraints_);
155 >    MemoryUtils::deletePointers(restraints_);
156   }
157  
158 + void Globals::validate() {
159 +  DataHolder::validate();
160  
161 +  CheckParameter(ForceField, isNotEmpty());
162 +  CheckParameter(TargetTemp, isPositive());
163 +  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"));
164 +  CheckParameter(Dt, isPositive());
165 +  CheckParameter(RunTime, isPositive());
166 +  CheckParameter(FinalConfig, isNotEmpty());
167 +  CheckParameter(SampleTime, isNonNegative());
168 +  CheckParameter(ResetTime, isNonNegative());
169 +  CheckParameter(StatusTime, isNonNegative());
170 +  CheckParameter(CutoffRadius, isPositive());
171 +  CheckParameter(SwitchingRadius, isNonNegative());
172 +  CheckParameter(Dielectric, isPositive());
173 +  CheckParameter(ThermalTime,  isNonNegative());
174 +  CheckParameter(TauThermostat, isPositive());
175 +  CheckParameter(TauBarostat, isPositive());
176 +  CheckParameter(ZconsTime, isPositive());
177 +  CheckParameter(ZconsTol, isPositive());
178 +  CheckParameter(Seed, isPositive());
179 +  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
180 +  CheckParameter(MinimizerMaxIter, isPositive());
181 +  CheckParameter(MinimizerWriteFrq, isPositive());
182 +  CheckParameter(MinimizerStepSize, isPositive());
183 +  CheckParameter(MinimizerFTol, isPositive());
184 +  CheckParameter(MinimizerGTol, isPositive());
185 +  CheckParameter(MinimizerLSTol, isPositive());
186 +  CheckParameter(MinimizerLSMaxIter, isPositive());
187 +  CheckParameter(ZconsGap, isPositive());
188 +  CheckParameter(ZconsFixtime, isPositive());
189 +  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
190 +  CheckParameter(ThermodynamicIntegrationK, isPositive());
191 +  CheckParameter(ForceFieldVariant, isNotEmpty());
192 +  CheckParameter(ForceFieldFileName, isNotEmpty());
193 +  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
194 +  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
195 +  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
196 +  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
197 +  //CheckParameter(StatFileFormat,);    
198 +  CheckParameter(OrthoBoxTolerance, isPositive());  
199 +  CheckParameter(DampingAlpha,isNonNegative());
200 +  CheckParameter(SkinThickness, isPositive());
201 +  CheckParameter(Viscosity, isNonNegative());
202 +  CheckParameter(ThermalConductivity, isNonNegative());
203 +  CheckParameter(ThermalLength, isNonNegative());
204 +  CheckParameter(BeadSize, isPositive());
205 +  CheckParameter(FrozenBufferRadius, isPositive());
206 +  CheckParameter(LangevinBufferRadius, isPositive());
207 +  CheckParameter(NeighborListNeighbors, isPositive());
208 +  CheckParameter(RNEMD_exchangeTime, isPositive());
209 +  CheckParameter(RNEMD_nBins, isPositive() && isEven());
210 +  CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
211 +  CheckParameter(RNEMD_targetFlux, isNonNegative());
212  
213 < int Globals::zConstraintAssign( event* the_event ){
214 <
215 <  switch( the_event->evt.asmt.asmt_type ){
216 <    
217 <  case STRING:
218 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
279 <                                              the_event->evt.asmt.rhs.sval,
280 <                                              &(the_event->err_msg));
281 <    break;
282 <    
283 <  case DOUBLE:
284 <    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
285 <                                              the_event->evt.asmt.rhs.dval,
286 <                                              &(the_event->err_msg));
287 <    break;
288 <    
289 <  case INT:
290 <    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
291 <                                           the_event->evt.asmt.rhs.ival,
292 <                                           &(the_event->err_msg));
293 <    break;
294 <    
295 <  default:
296 <    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
297 <                                 " assignment type" );
298 <    return 0;
299 <    break;
213 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215 >        std::ostringstream oss;
216 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217 >        throw OOPSEException(oss.str());          
218 >    }
219    }
301 –  return 0;
220   }
221 +  
222 + bool Globals::addComponent(Component* comp) {
223 +    components_.push_back(comp);
224 +    return true;
225 + }
226  
227 < int Globals::zConstraintEnd( event* the_event ){
227 > bool Globals::addZConsStamp(ZConsStamp* zcons) {
228 >    zconstraints_.push_back(zcons);
229 >    return true;
230 > }
231  
232 <  the_event->err_msg = current_zConstraint->checkMe();
233 <  if( the_event->err_msg != NULL ) return 0;
234 <
309 <  return 1;
232 > bool Globals::addRestraintStamp(RestraintStamp* rest) {
233 >    restraints_.push_back(rest);
234 >    return true;
235   }
236  
237 < char* Globals::checkMe( void ){
238 <
239 <
240 <  std::string err("The following required keywords are missing:\n");
241 <  short int have_err = 0;
242 <
243 <  ParamMap::iterator i;
244 <  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
245 <    if (!i->second->isOptional() && i->second->empty()) {
246 <        err +=  i->second->getKeyword() + "\n";
237 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238 >    std::string molStampName = molStamp->getName();
239 >    std::map<std::string, MoleculeStamp*>::iterator i;
240 >    bool ret = false;
241 >    i = moleculeStamps_.find(molStampName);
242 >    if (i == moleculeStamps_.end()) {
243 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
244 >        ret = true;
245 >    } else {
246 >        std::ostringstream oss;
247 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248 >        throw OOPSEException(oss.str());  
249      }
250 <  }
324 <
325 <  //@todo memory leak
326 <  if( have_err )
327 <    return strdup( err.c_str() );
328 <  
329 <  return NULL;
330 <
331 <
250 >    return ret;
251   }
252 +
253  
334 – int Globals::globalEnd( event* the_event ){
335 –  
336 –  the_event->err_msg = checkMe();
337 –  if( the_event->err_msg != NULL ) return 0;
338 –
339 –  return 1;
254   }

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