ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/Globals.cpp
(Generate patch)

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 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 <
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);  
120    DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121    DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
122 >  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123 >  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124 >  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
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", 16);
138 >  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139 >  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140    
138 –  int key;
139 –  int token;
140 –  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
141 –  char* lhs = the_event->evt.asmt.lhs;
142 –  std::string keyword(lhs);
141  
142 <  bool result;
143 <
144 <
147 <  ParamMap::iterator i =parameters_.find(keyword);
148 <  if (i != parameters_.end()) {
149 <    if( the_type == STRING ){
150 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
151 <       if (!result ) {
152 <            sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
153 <       }
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 {
142 >  deprecatedKeywords_.insert("nComponents");
143 >  deprecatedKeywords_.insert("nZconstraints");
144 >  deprecatedKeywords_.insert("initialConfig");
145      
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;
146   }
147  
148 < int Globals::newComponent( event* the_event ){
149 <  
150 <  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;
148 > Globals::~Globals() {
149 >    MemoryUtils::deletePointers(components_);
150 >    MemoryUtils::deletePointers(zconstraints_);
151   }
152  
153 < int Globals::newZconstraint( event* the_event ){
154 <  
153 > void Globals::validate() {
154 >  DataHolder::validate();
155  
156 <  int index = the_event->evt.blk_index;
157 <  char err[200];
158 <  current_zConstraint = new ZconStamp( index );
159 <  
160 <  if( haveNZconstraints() && index < getNZconstraints() )
161 <    zConstraints[index] = current_zConstraint;
162 <  else{
163 <    if( haveNZconstraints() ){
164 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
165 <               index );
166 <      the_event->err_msg = strdup( err );
167 <      return 0;
168 <    }
169 <    else{
170 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
171 <                                  " not given before"
172 <                                  " first zConstraint declaration." );
173 <      return 0;
174 <    }
175 <  }  
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() && isEven());
209 >  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210  
211 <  return 1;
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   }
270 –
271 –
272 –
273 – int Globals::zConstraintAssign( event* the_event ){
274 –
275 –  switch( the_event->evt.asmt.asmt_type ){
219      
220 <  case STRING:
221 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
222 <                                              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;
300 <  }
301 <  return 0;
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();
307 <  if( the_event->err_msg != NULL ) return 0;
308 <
309 <  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 <  }
324 <
325 <  //@todo memory leak
326 <  if( have_err )
327 <    return strdup( err.c_str() );
328 <  
329 <  return NULL;
330 <
331 <
243 >    return ret;
244   }
245 +
246  
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;
247   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines