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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 672 by tim, Fri Oct 14 21:43:13 2005 UTC vs.
Revision 1341 by skuang, Fri May 8 19:47:05 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 < #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())) std::cout <<"Error in parsing " << NAME.getKeyword() << " : "<< (CONSTRAINT).getConstraintDescription() << std::endl; }                
69 <
70 <
71 < Globals::Globals(){
72 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
74 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
58    DefineOptionalParameter(Dt, "dt");
59    DefineOptionalParameter(RunTime, "runTime");
80 –  DefineOptionalParameter(InitialConfig, "initialConfig");
60    DefineOptionalParameter(FinalConfig, "finalConfig");
82 –  DefineOptionalParameter(NMol, "nMol");
83 –  DefineOptionalParameter(Density, "density");
84 –  DefineOptionalParameter(Box, "box");
85 –  DefineOptionalParameter(BoxX, "boxX");
86 –  DefineOptionalParameter(BoxY, "boxY");
87 –  DefineOptionalParameter(BoxZ, "boxZ");
61    DefineOptionalParameter(SampleTime, "sampleTime");
62    DefineOptionalParameter(ResetTime, "resetTime");
63    DefineOptionalParameter(StatusTime, "statusTime");
64    DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65    DefineOptionalParameter(SwitchingRadius, "switchingRadius");
93 –  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");
100 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
72    DefineOptionalParameter(ZconsTol, "zconsTol");
73    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74    DefineOptionalParameter(Seed, "seed");
# Line 116 | 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 135 | 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 < }
133 <
144 < int Globals::globalAssign( event* the_event ){
145 <  
146 <  int key;
147 <  int token;
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;
153 <
154 <
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(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
161 <       }
162 <    } else if( the_type == DOUBLE ){
163 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
164 <       if (!result )
165 <         sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() );
166 <    }      
167 <    else if (the_type == INT ){
168 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
169 <       if (!result )
170 <         sprintf(the_event->err_msg,  "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() );
171 <      
172 <    } else {
173 <    
174 <    }
175 <  }
176 <
177 <  if (keyword == "nComponents" && getNComponents() > 0) {
178 <    components = new Component*[getNComponents()];
179 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
180 <    zConstraints = new ZconStamp*[getNZconstraints()];
181 <  }
182 <  
183 <  return result;
184 < }
185 <
186 < int Globals::newComponent( event* the_event ){
187 <  
188 <  current_component = new Component;
189 <  int index = the_event->evt.blk_index;
190 <  char err[200];
191 <  
192 <  if( haveNComponents() && index < getNComponents() )
193 <    components[index] = current_component;
194 <  else{
195 <    if( haveNComponents()  ){
196 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
197 <               index );
198 <      the_event->err_msg = strdup( err );
199 <      return 0;
200 <    }
201 <    else{
202 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
203 <                                  " first component declaration." );
204 <      return 0;
205 <    }
206 <  }  
207 <
208 <  return 1;
209 < }
210 <
211 <
212 <
213 < int Globals::componentAssign( event* the_event ){
214 <
215 <  switch( the_event->evt.asmt.asmt_type ){
216 <    
217 <  case STRING:
218 <    return current_component->assignString( the_event->evt.asmt.lhs,
219 <                                            the_event->evt.asmt.rhs.sval,
220 <                                            &(the_event->err_msg));
221 <    break;
222 <    
223 <  case DOUBLE:
224 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
225 <                                            the_event->evt.asmt.rhs.dval,
226 <                                            &(the_event->err_msg));
227 <    break;
228 <    
229 <  case INT:
230 <    return current_component->assignInt( the_event->evt.asmt.lhs,
231 <                                         the_event->evt.asmt.rhs.ival,
232 <                                         &(the_event->err_msg));
233 <    break;
234 <    
235 <  default:
236 <    the_event->err_msg = strdup( "Globals error. Invalid component"
237 <                                 " assignment type" );
238 <    return 0;
239 <    break;
240 <  }
241 <  return 0;
242 < }
243 <
244 < int Globals::componentEnd( event* the_event ){
245 <
246 <  the_event->err_msg = current_component->checkMe();
247 <  if( the_event->err_msg != NULL ) return 0;
248 <
249 <  return 1;
250 < }
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::newZconstraint( event* the_event ){
135 >  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137 >  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
138 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140    
141  
142 <  int index = the_event->evt.blk_index;
143 <  char err[200];
144 <  current_zConstraint = new ZconStamp( index );
258 <  
259 <  if( haveNZconstraints() && index < getNZconstraints() )
260 <    zConstraints[index] = current_zConstraint;
261 <  else{
262 <    if( haveNZconstraints() ){
263 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
264 <               index );
265 <      the_event->err_msg = strdup( err );
266 <      return 0;
267 <    }
268 <    else{
269 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
270 <                                  " not given before"
271 <                                  " first zConstraint declaration." );
272 <      return 0;
273 <    }
274 <  }  
275 <
276 <  return 1;
277 < }
278 <
279 <
280 <
281 < int Globals::zConstraintAssign( event* the_event ){
282 <
283 <  switch( the_event->evt.asmt.asmt_type ){
142 >  deprecatedKeywords_.insert("nComponents");
143 >  deprecatedKeywords_.insert("nZconstraints");
144 >  deprecatedKeywords_.insert("initialConfig");
145      
285 –  case STRING:
286 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
287 –                                              the_event->evt.asmt.rhs.sval,
288 –                                              &(the_event->err_msg));
289 –    break;
290 –    
291 –  case DOUBLE:
292 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
293 –                                              the_event->evt.asmt.rhs.dval,
294 –                                              &(the_event->err_msg));
295 –    break;
296 –    
297 –  case INT:
298 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
299 –                                           the_event->evt.asmt.rhs.ival,
300 –                                           &(the_event->err_msg));
301 –    break;
302 –    
303 –  default:
304 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
305 –                                 " assignment type" );
306 –    return 0;
307 –    break;
308 –  }
309 –  return 0;
146   }
147  
148 < int Globals::zConstraintEnd( event* the_event ){
149 <
150 <  the_event->err_msg = current_zConstraint->checkMe();
315 <  if( the_event->err_msg != NULL ) return 0;
316 <
317 <  return 1;
148 > Globals::~Globals() {
149 >    MemoryUtils::deletePointers(components_);
150 >    MemoryUtils::deletePointers(zconstraints_);
151   }
152  
153 < char* Globals::checkMe( void ){
153 > void Globals::validate() {
154 >  DataHolder::validate();
155  
322 –
323 –  std::string err("The following required keywords are missing:\n");
324 –  short int have_err = 0;
325 –
326 –  ParamMap::iterator i;
327 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
328 –    if (!i->second->isOptional() && i->second->empty()) {
329 –        err +=  i->second->getKeyword() + "\n";
330 –    }
331 –  }
332 –
156    CheckParameter(ForceField, isNotEmpty());
334 –  CheckParameter(NComponents,isPositive());
157    CheckParameter(TargetTemp, isPositive());
158 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
337 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
338 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
339 <
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());
342 –  CheckParameter(InitialConfig, isNotEmpty());
161    CheckParameter(FinalConfig, isNotEmpty());
344 –  CheckParameter(NMol, isPositive());
345 –  CheckParameter(Density, isPositive());
346 –  CheckParameter(Box, isPositive());
347 –  CheckParameter(BoxX, isPositive());
348 –  CheckParameter(BoxY, isPositive());
349 –  CheckParameter(BoxZ, isPositive());
162    CheckParameter(SampleTime, isNonNegative());
163    CheckParameter(ResetTime, isNonNegative());
164    CheckParameter(StatusTime, isNonNegative());
# Line 354 | Line 166 | char* Globals::checkMe( void ){
166    CheckParameter(SwitchingRadius, isNonNegative());
167    CheckParameter(Dielectric, isPositive());
168    CheckParameter(ThermalTime,  isNonNegative());
357 –  CheckParameter(TargetPressure,  isPositive());
169    CheckParameter(TauThermostat, isPositive());
170    CheckParameter(TauBarostat, isPositive());
171    CheckParameter(ZconsTime, isPositive());
361 –  CheckParameter(NZconstraints, isPositive());  
172    CheckParameter(ZconsTol, isPositive());
363 –  //CheckParameter(ZconsForcePolicy,);
173    CheckParameter(Seed, isPositive());
174 <  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
174 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175    CheckParameter(MinimizerMaxIter, isPositive());
176    CheckParameter(MinimizerWriteFrq, isPositive());
177    CheckParameter(MinimizerStepSize, isPositive());
# Line 372 | Line 181 | char* Globals::checkMe( void ){
181    CheckParameter(MinimizerLSMaxIter, isPositive());
182    CheckParameter(ZconsGap, isPositive());
183    CheckParameter(ZconsFixtime, isPositive());
184 <  CheckParameter(ThermodynamicIntegrationLambda, 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(SurfaceTension, isPositive());
192 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
193 <  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
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,);    
386 –  //CheckParameter(MixingRule,);
196    CheckParameter(OrthoBoxTolerance, isPositive());  
197    CheckParameter(ThermIntDistSpringConst, isPositive());
198    CheckParameter(ThermIntThetaSpringConst, isPositive());
199    CheckParameter(ThermIntOmegaSpringConst, isPositive());
200 <  CheckParameter(DampingAlpha,isPositive());
200 >  CheckParameter(DampingAlpha,isNonNegative());
201    CheckParameter(SkinThickness, isPositive());
202 <  
203 <  //@todo memory leak
204 <  if( have_err )
205 <    return strdup( err.c_str() );
206 <  
207 <  return NULL;
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() && isEven());
209 >  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210  
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 +  }
218 + }
219 +    
220 + bool Globals::addComponent(Component* comp) {
221 +    components_.push_back(comp);
222 +    return true;
223 + }
224  
225 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
226 +    zconstraints_.push_back(zcons);
227 +    return true;
228   }
229  
230 < int Globals::globalEnd( event* the_event ){
231 <  
232 <  the_event->err_msg = checkMe();
233 <  if( the_event->err_msg != NULL ) return 0;
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 >    return ret;
244 > }
245 >
246  
408 –  return 1;
247   }

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