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Comparing trunk/src/io/Globals.cpp (file contents):
Revision 666 by chrisfen, Fri Oct 14 14:18:02 2005 UTC vs.
Revision 1331 by gezelter, Thu Apr 2 16:04:52 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(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 >  
115    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116 +  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
117    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
118    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
119    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
# Line 130 | Line 122 | Globals::Globals(){
122    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
125 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
126 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
127 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
128    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
130    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
131 <  
132 < }
131 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
132 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
133 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
134  
135 < int Globals::globalAssign( event* the_event ){
135 >  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
138 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140    
141 –  int key;
142 –  int token;
143 –  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
144 –  char* lhs = the_event->evt.asmt.lhs;
145 –  std::string keyword(lhs);
141  
142 <  bool result;
143 <
144 <
150 <  ParamMap::iterator i =parameters_.find(keyword);
151 <  if (i != parameters_.end()) {
152 <    if( the_type == STRING ){
153 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
154 <       if (!result ) {
155 <            sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
156 <       }
157 <    } else if( the_type == DOUBLE ){
158 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
159 <       if (!result )
160 <         sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() );
161 <    }      
162 <    else if (the_type == INT ){
163 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
164 <       if (!result )
165 <         sprintf(the_event->err_msg,  "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() );
166 <      
167 <    } else {
142 >  deprecatedKeywords_.insert("nComponents");
143 >  deprecatedKeywords_.insert("nZconstraints");
144 >  deprecatedKeywords_.insert("initialConfig");
145      
169 –    }
170 –  }
171 –
172 –  if (keyword == "nComponents" && getNComponents() > 0) {
173 –    components = new Component*[getNComponents()];
174 –  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
175 –    zConstraints = new ZconStamp*[getNZconstraints()];
176 –  }
177 –  
178 –  return result;
179 – }
180 –
181 – int Globals::newComponent( event* the_event ){
182 –  
183 –  current_component = new Component;
184 –  int index = the_event->evt.blk_index;
185 –  char err[200];
186 –  
187 –  if( haveNComponents() && index < getNComponents() )
188 –    components[index] = current_component;
189 –  else{
190 –    if( haveNComponents()  ){
191 –      sprintf( err, "meta-data parsing error: %d out of nComponents range",
192 –               index );
193 –      the_event->err_msg = strdup( err );
194 –      return 0;
195 –    }
196 –    else{
197 –      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
198 –                                  " first component declaration." );
199 –      return 0;
200 –    }
201 –  }  
202 –
203 –  return 1;
204 – }
205 –
206 –
207 –
208 – int Globals::componentAssign( event* the_event ){
209 –
210 –  switch( the_event->evt.asmt.asmt_type ){
211 –    
212 –  case STRING:
213 –    return current_component->assignString( the_event->evt.asmt.lhs,
214 –                                            the_event->evt.asmt.rhs.sval,
215 –                                            &(the_event->err_msg));
216 –    break;
217 –    
218 –  case DOUBLE:
219 –    return current_component->assignDouble( the_event->evt.asmt.lhs,
220 –                                            the_event->evt.asmt.rhs.dval,
221 –                                            &(the_event->err_msg));
222 –    break;
223 –    
224 –  case INT:
225 –    return current_component->assignInt( the_event->evt.asmt.lhs,
226 –                                         the_event->evt.asmt.rhs.ival,
227 –                                         &(the_event->err_msg));
228 –    break;
229 –    
230 –  default:
231 –    the_event->err_msg = strdup( "Globals error. Invalid component"
232 –                                 " assignment type" );
233 –    return 0;
234 –    break;
235 –  }
236 –  return 0;
237 – }
238 –
239 – int Globals::componentEnd( event* the_event ){
240 –
241 –  the_event->err_msg = current_component->checkMe();
242 –  if( the_event->err_msg != NULL ) return 0;
243 –
244 –  return 1;
146   }
147  
148 < int Globals::newZconstraint( event* the_event ){
149 <  
150 <
250 <  int index = the_event->evt.blk_index;
251 <  char err[200];
252 <  current_zConstraint = new ZconStamp( index );
253 <  
254 <  if( haveNZconstraints() && index < getNZconstraints() )
255 <    zConstraints[index] = current_zConstraint;
256 <  else{
257 <    if( haveNZconstraints() ){
258 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
259 <               index );
260 <      the_event->err_msg = strdup( err );
261 <      return 0;
262 <    }
263 <    else{
264 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
265 <                                  " not given before"
266 <                                  " first zConstraint declaration." );
267 <      return 0;
268 <    }
269 <  }  
270 <
271 <  return 1;
148 > Globals::~Globals() {
149 >    MemoryUtils::deletePointers(components_);
150 >    MemoryUtils::deletePointers(zconstraints_);
151   }
152  
153 + void Globals::validate() {
154 +  DataHolder::validate();
155  
156 +  CheckParameter(ForceField, isNotEmpty());
157 +  CheckParameter(TargetTemp, isPositive());
158 +  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"));
159 +  CheckParameter(Dt, isPositive());
160 +  CheckParameter(RunTime, isPositive());
161 +  CheckParameter(FinalConfig, isNotEmpty());
162 +  CheckParameter(SampleTime, isNonNegative());
163 +  CheckParameter(ResetTime, isNonNegative());
164 +  CheckParameter(StatusTime, isNonNegative());
165 +  CheckParameter(CutoffRadius, isPositive());
166 +  CheckParameter(SwitchingRadius, isNonNegative());
167 +  CheckParameter(Dielectric, isPositive());
168 +  CheckParameter(ThermalTime,  isNonNegative());
169 +  CheckParameter(TauThermostat, isPositive());
170 +  CheckParameter(TauBarostat, isPositive());
171 +  CheckParameter(ZconsTime, isPositive());
172 +  CheckParameter(ZconsTol, isPositive());
173 +  CheckParameter(Seed, isPositive());
174 +  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175 +  CheckParameter(MinimizerMaxIter, isPositive());
176 +  CheckParameter(MinimizerWriteFrq, isPositive());
177 +  CheckParameter(MinimizerStepSize, isPositive());
178 +  CheckParameter(MinimizerFTol, isPositive());
179 +  CheckParameter(MinimizerGTol, isPositive());
180 +  CheckParameter(MinimizerLSTol, isPositive());
181 +  CheckParameter(MinimizerLSMaxIter, isPositive());
182 +  CheckParameter(ZconsGap, isPositive());
183 +  CheckParameter(ZconsFixtime, isPositive());
184 +  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185 +  CheckParameter(ThermodynamicIntegrationK, isPositive());
186 +  CheckParameter(ForceFieldVariant, isNotEmpty());
187 +  CheckParameter(ForceFieldFileName, isNotEmpty());
188 +  CheckParameter(ThermIntDistSpringConst, isPositive());
189 +  CheckParameter(ThermIntThetaSpringConst, isPositive());
190 +  CheckParameter(ThermIntOmegaSpringConst, isPositive());
191 +  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192 +  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193 +  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
194 +  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195 +  //CheckParameter(StatFileFormat,);    
196 +  CheckParameter(OrthoBoxTolerance, isPositive());  
197 +  CheckParameter(ThermIntDistSpringConst, isPositive());
198 +  CheckParameter(ThermIntThetaSpringConst, isPositive());
199 +  CheckParameter(ThermIntOmegaSpringConst, isPositive());
200 +  CheckParameter(DampingAlpha,isNonNegative());
201 +  CheckParameter(SkinThickness, isPositive());
202 +  CheckParameter(Viscosity, isNonNegative());
203 +  CheckParameter(BeadSize, isPositive());
204 +  CheckParameter(FrozenBufferRadius, isPositive());
205 +  CheckParameter(LangevinBufferRadius, isPositive());
206 +  CheckParameter(NeighborListNeighbors, isPositive());
207 +  CheckParameter(RNEMD_swapTime, isPositive());
208 +  CheckParameter(RNEMD_nBins, isPositive());
209 +  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210  
211 < int Globals::zConstraintAssign( event* the_event ){
212 <
213 <  switch( the_event->evt.asmt.asmt_type ){
214 <    
215 <  case STRING:
216 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
282 <                                              the_event->evt.asmt.rhs.sval,
283 <                                              &(the_event->err_msg));
284 <    break;
285 <    
286 <  case DOUBLE:
287 <    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
288 <                                              the_event->evt.asmt.rhs.dval,
289 <                                              &(the_event->err_msg));
290 <    break;
291 <    
292 <  case INT:
293 <    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
294 <                                           the_event->evt.asmt.rhs.ival,
295 <                                           &(the_event->err_msg));
296 <    break;
297 <    
298 <  default:
299 <    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
300 <                                 " assignment type" );
301 <    return 0;
302 <    break;
211 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
212 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
213 >        std::ostringstream oss;
214 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
215 >        throw OOPSEException(oss.str());          
216 >    }
217    }
304 –  return 0;
218   }
219 +    
220 + bool Globals::addComponent(Component* comp) {
221 +    components_.push_back(comp);
222 +    return true;
223 + }
224  
225 < int Globals::zConstraintEnd( event* the_event ){
226 <
227 <  the_event->err_msg = current_zConstraint->checkMe();
310 <  if( the_event->err_msg != NULL ) return 0;
311 <
312 <  return 1;
225 > bool Globals::addZConsStamp(ZConsStamp* zcons) {
226 >    zconstraints_.push_back(zcons);
227 >    return true;
228   }
229  
230 < char* Globals::checkMe( void ){
231 <
232 <
233 <  std::string err("The following required keywords are missing:\n");
234 <  short int have_err = 0;
235 <
236 <  ParamMap::iterator i;
237 <  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
238 <    if (!i->second->isOptional() && i->second->empty()) {
239 <        err +=  i->second->getKeyword() + "\n";
230 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
231 >    std::string molStampName = molStamp->getName();
232 >    std::map<std::string, MoleculeStamp*>::iterator i;
233 >    bool ret = false;
234 >    i = moleculeStamps_.find(molStampName);
235 >    if (i == moleculeStamps_.end()) {
236 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
237 >        ret = true;
238 >    } else {
239 >        std::ostringstream oss;
240 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
241 >        throw OOPSEException(oss.str());  
242      }
243 <  }
327 <
328 <  //@todo memory leak
329 <  if( have_err )
330 <    return strdup( err.c_str() );
331 <  
332 <  return NULL;
333 <
334 <
243 >    return ret;
244   }
245 +
246  
337 – int Globals::globalEnd( event* the_event ){
338 –  
339 –  the_event->err_msg = checkMe();
340 –  if( the_event->err_msg != NULL ) return 0;
341 –
342 –  return 1;
247   }

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