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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 1078 by gezelter, Wed Oct 18 21:58:48 2006 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");
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");
119 –  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
96    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
97 <  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
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    
123 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
104    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
105    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
106    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
# Line 130 | Line 110 | Globals::Globals(){
110    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
111    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
112    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
113 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
113 >  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
114 >  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
115 >  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
116    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
117 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
118    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
119 <  
120 < }
119 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
120 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
121 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
122  
123 < int Globals::globalAssign( event* the_event ){
124 <  
125 <  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);
146 <
147 <  bool result;
148 <
149 <
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 {
123 >  deprecatedKeywords_.insert("nComponents");
124 >  deprecatedKeywords_.insert("nZconstraints");
125 >  deprecatedKeywords_.insert("initialConfig");
126      
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;
127   }
128  
129 < int Globals::newComponent( event* the_event ){
130 <  
131 <  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;
245 < }
246 <
247 < int Globals::newZconstraint( event* the_event ){
248 <  
249 <
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;
129 > Globals::~Globals() {
130 >    MemoryUtils::deletePointers(components_);
131 >    MemoryUtils::deletePointers(zconstraints_);
132   }
133  
134 + void Globals::validate() {
135 +  DataHolder::validate();
136  
137 <
138 < int Globals::zConstraintAssign( event* the_event ){
139 <
140 <  switch( the_event->evt.asmt.asmt_type ){
141 <    
142 <  case STRING:
143 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
144 <                                              the_event->evt.asmt.rhs.sval,
145 <                                              &(the_event->err_msg));
146 <    break;
147 <    
148 <  case DOUBLE:
149 <    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
150 <                                              the_event->evt.asmt.rhs.dval,
151 <                                              &(the_event->err_msg));
152 <    break;
153 <    
154 <  case INT:
155 <    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
156 <                                           the_event->evt.asmt.rhs.ival,
157 <                                           &(the_event->err_msg));
158 <    break;
159 <    
160 <  default:
161 <    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
162 <                                 " assignment type" );
163 <    return 0;
164 <    break;
137 >  CheckParameter(ForceField, isNotEmpty());
138 >  CheckParameter(TargetTemp, isPositive());
139 >  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"));
140 >  CheckParameter(Dt, isPositive());
141 >  CheckParameter(RunTime, isPositive());
142 >  CheckParameter(FinalConfig, isNotEmpty());
143 >  CheckParameter(SampleTime, isNonNegative());
144 >  CheckParameter(ResetTime, isNonNegative());
145 >  CheckParameter(StatusTime, isNonNegative());
146 >  CheckParameter(CutoffRadius, isPositive());
147 >  CheckParameter(SwitchingRadius, isNonNegative());
148 >  CheckParameter(Dielectric, isPositive());
149 >  CheckParameter(ThermalTime,  isNonNegative());
150 >  CheckParameter(TauThermostat, isPositive());
151 >  CheckParameter(TauBarostat, isPositive());
152 >  CheckParameter(ZconsTime, isPositive());
153 >  CheckParameter(ZconsTol, isPositive());
154 >  CheckParameter(Seed, isPositive());
155 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
156 >  CheckParameter(MinimizerMaxIter, isPositive());
157 >  CheckParameter(MinimizerWriteFrq, isPositive());
158 >  CheckParameter(MinimizerStepSize, isPositive());
159 >  CheckParameter(MinimizerFTol, isPositive());
160 >  CheckParameter(MinimizerGTol, isPositive());
161 >  CheckParameter(MinimizerLSTol, isPositive());
162 >  CheckParameter(MinimizerLSMaxIter, isPositive());
163 >  CheckParameter(ZconsGap, isPositive());
164 >  CheckParameter(ZconsFixtime, isPositive());
165 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
166 >  CheckParameter(ThermodynamicIntegrationK, isPositive());
167 >  CheckParameter(ForceFieldVariant, isNotEmpty());
168 >  CheckParameter(ForceFieldFileName, isNotEmpty());
169 >  CheckParameter(ThermIntDistSpringConst, isPositive());
170 >  CheckParameter(ThermIntThetaSpringConst, isPositive());
171 >  CheckParameter(ThermIntOmegaSpringConst, isPositive());
172 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
173 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
174 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
175 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
176 >  //CheckParameter(StatFileFormat,);    
177 >  CheckParameter(OrthoBoxTolerance, isPositive());  
178 >  CheckParameter(ThermIntDistSpringConst, isPositive());
179 >  CheckParameter(ThermIntThetaSpringConst, isPositive());
180 >  CheckParameter(ThermIntOmegaSpringConst, isPositive());
181 >  CheckParameter(DampingAlpha,isNonNegative());
182 >  CheckParameter(SkinThickness, isPositive());
183 >  CheckParameter(Viscosity, isNonNegative());
184 >  CheckParameter(BeadSize, isPositive());
185 >  CheckParameter(FrozenBufferRadius, isPositive());
186 >  CheckParameter(LangevinBufferRadius, isPositive());
187 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
188 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
189 >        std::ostringstream oss;
190 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
191 >        throw OOPSEException(oss.str());          
192 >    }
193    }
304 –  return 0;
194   }
195 +    
196 + bool Globals::addComponent(Component* comp) {
197 +    components_.push_back(comp);
198 +    return true;
199 + }
200  
201 < int Globals::zConstraintEnd( event* the_event ){
202 <
203 <  the_event->err_msg = current_zConstraint->checkMe();
310 <  if( the_event->err_msg != NULL ) return 0;
311 <
312 <  return 1;
201 > bool Globals::addZConsStamp(ZConsStamp* zcons) {
202 >    zconstraints_.push_back(zcons);
203 >    return true;
204   }
205  
206 < char* Globals::checkMe( void ){
207 <
208 <
209 <  std::string err("The following required keywords are missing:\n");
210 <  short int have_err = 0;
211 <
212 <  ParamMap::iterator i;
213 <  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
214 <    if (!i->second->isOptional() && i->second->empty()) {
215 <        err +=  i->second->getKeyword() + "\n";
206 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
207 >    std::string molStampName = molStamp->getName();
208 >    std::map<std::string, MoleculeStamp*>::iterator i;
209 >    bool ret = false;
210 >    i = moleculeStamps_.find(molStampName);
211 >    if (i == moleculeStamps_.end()) {
212 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
213 >        ret = true;
214 >    } else {
215 >        std::ostringstream oss;
216 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
217 >        throw OOPSEException(oss.str());  
218      }
219 <  }
327 <
328 <  //@todo memory leak
329 <  if( have_err )
330 <    return strdup( err.c_str() );
331 <  
332 <  return NULL;
333 <
334 <
219 >    return ret;
220   }
221 +
222  
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;
223   }

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