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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 998 by chrisfen, Mon Jul 3 13:18:43 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");
# Line 74 | Line 59 | Globals::Globals(){
59    DefineOptionalParameter(RunTime, "runTime");
60    DefineOptionalParameter(InitialConfig, "initialConfig");
61    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");
62    DefineOptionalParameter(SampleTime, "sampleTime");
63    DefineOptionalParameter(ResetTime, "resetTime");
64    DefineOptionalParameter(StatusTime, "statusTime");
# Line 92 | Line 71 | Globals::Globals(){
71    DefineOptionalParameter(TauThermostat, "tauThermostat");
72    DefineOptionalParameter(TauBarostat, "tauBarostat");
73    DefineOptionalParameter(ZconsTime, "zconsTime");
95 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
74    DefineOptionalParameter(ZconsTol, "zconsTol");
75    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76    DefineOptionalParameter(Seed, "seed");
# Line 117 | Line 95 | Globals::Globals(){
95    DefineOptionalParameter(SurfaceTension, "surfaceTension");
96    DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97    DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98 +  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99    DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100 <  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
100 >  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101 >  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
102 >  DefineOptionalParameter(Viscosity, "viscosity");
103 >  DefineOptionalParameter(BeadSize, "beadSize");
104 >  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
105 >  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
106    
123 –  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
107    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
108    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
109    DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
110    DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
111    DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
112    DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
113 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
113 >  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
114 >  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
115 >  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
116 >  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
117    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
118 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
119    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
120 <  
121 < }
120 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
121 >  DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
122 >  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
123  
136 – int Globals::globalAssign( event* the_event ){
137 –  
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);
124  
125 <  bool result;
126 <
146 <
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 {
125 >    deprecatedKeywords_.insert("nComponents");
126 >    deprecatedKeywords_.insert("nZconstraints");
127      
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;
128   }
129  
130 < int Globals::newComponent( event* the_event ){
131 <  
132 <  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;
242 < }
243 <
244 < int Globals::newZconstraint( event* the_event ){
245 <  
246 <
247 <  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;
130 > Globals::~Globals() {
131 >    MemoryUtils::deletePointers(components_);
132 >    MemoryUtils::deletePointers(zconstraints_);
133   }
134  
135 + void Globals::validate() {
136 +  DataHolder::validate();
137  
138 <
139 < int Globals::zConstraintAssign( event* the_event ){
140 <
141 <  switch( the_event->evt.asmt.asmt_type ){
142 <    
143 <  case STRING:
144 <    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
145 <                                              the_event->evt.asmt.rhs.sval,
146 <                                              &(the_event->err_msg));
147 <    break;
148 <    
149 <  case DOUBLE:
150 <    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
151 <                                              the_event->evt.asmt.rhs.dval,
152 <                                              &(the_event->err_msg));
153 <    break;
154 <    
155 <  case INT:
156 <    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
157 <                                           the_event->evt.asmt.rhs.ival,
158 <                                           &(the_event->err_msg));
159 <    break;
160 <    
161 <  default:
162 <    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
163 <                                 " assignment type" );
164 <    return 0;
165 <    break;
138 >  CheckParameter(ForceField, isNotEmpty());
139 >  CheckParameter(TargetTemp, isPositive());
140 >  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT"));
141 >  CheckParameter(Dt, isPositive());
142 >  CheckParameter(RunTime, isPositive());
143 >  CheckParameter(InitialConfig, isNotEmpty());
144 >  CheckParameter(FinalConfig, isNotEmpty());
145 >  CheckParameter(SampleTime, isNonNegative());
146 >  CheckParameter(ResetTime, isNonNegative());
147 >  CheckParameter(StatusTime, isNonNegative());
148 >  CheckParameter(CutoffRadius, isPositive());
149 >  CheckParameter(SwitchingRadius, isNonNegative());
150 >  CheckParameter(Dielectric, isPositive());
151 >  CheckParameter(ThermalTime,  isNonNegative());
152 >  CheckParameter(TargetPressure,  isPositive());
153 >  CheckParameter(TauThermostat, isPositive());
154 >  CheckParameter(TauBarostat, isPositive());
155 >  CheckParameter(ZconsTime, isPositive());
156 >  CheckParameter(ZconsTol, isPositive());
157 >  CheckParameter(Seed, isPositive());
158 >  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
159 >  CheckParameter(MinimizerMaxIter, isPositive());
160 >  CheckParameter(MinimizerWriteFrq, isPositive());
161 >  CheckParameter(MinimizerStepSize, isPositive());
162 >  CheckParameter(MinimizerFTol, isPositive());
163 >  CheckParameter(MinimizerGTol, isPositive());
164 >  CheckParameter(MinimizerLSTol, isPositive());
165 >  CheckParameter(MinimizerLSMaxIter, isPositive());
166 >  CheckParameter(ZconsGap, isPositive());
167 >  CheckParameter(ZconsFixtime, isPositive());
168 >  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
169 >  CheckParameter(ThermodynamicIntegrationK, isPositive());
170 >  CheckParameter(ForceFieldVariant, isNotEmpty());
171 >  CheckParameter(ForceFieldFileName, isNotEmpty());
172 >  CheckParameter(ThermIntDistSpringConst, isPositive());
173 >  CheckParameter(ThermIntThetaSpringConst, isPositive());
174 >  CheckParameter(ThermIntOmegaSpringConst, isPositive());
175 >  CheckParameter(SurfaceTension, isNonNegative());
176 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
177 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
178 >  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
179 >  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
180 >  //CheckParameter(StatFileFormat,);    
181 >  CheckParameter(OrthoBoxTolerance, isPositive());  
182 >  CheckParameter(ThermIntDistSpringConst, isPositive());
183 >  CheckParameter(ThermIntThetaSpringConst, isPositive());
184 >  CheckParameter(ThermIntOmegaSpringConst, isPositive());
185 >  CheckParameter(DampingAlpha,isNonNegative());
186 >  CheckParameter(SkinThickness, isPositive());
187 >  CheckParameter(Viscosity, isNonNegative());
188 >  CheckParameter(BeadSize, isPositive());
189 >  CheckParameter(FrozenBufferRadius, isPositive());
190 >  CheckParameter(LangevinBufferRadius, isPositive());
191 >  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
192 >    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
193 >        std::ostringstream oss;
194 >        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
195 >        throw OOPSEException(oss.str());          
196 >    }
197    }
301 –  return 0;
198   }
199 +    
200 + bool Globals::addComponent(Component* comp) {
201 +    components_.push_back(comp);
202 +    return true;
203 + }
204  
205 < int Globals::zConstraintEnd( event* the_event ){
206 <
207 <  the_event->err_msg = current_zConstraint->checkMe();
307 <  if( the_event->err_msg != NULL ) return 0;
308 <
309 <  return 1;
205 > bool Globals::addZConsStamp(ZConsStamp* zcons) {
206 >    zconstraints_.push_back(zcons);
207 >    return true;
208   }
209  
210 < char* Globals::checkMe( void ){
211 <
212 <
213 <  std::string err("The following required keywords are missing:\n");
214 <  short int have_err = 0;
215 <
216 <  ParamMap::iterator i;
217 <  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
218 <    if (!i->second->isOptional() && i->second->empty()) {
219 <        err +=  i->second->getKeyword() + "\n";
210 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
211 >    std::string molStampName = molStamp->getName();
212 >    std::map<std::string, MoleculeStamp*>::iterator i;
213 >    bool ret = false;
214 >    i = moleculeStamps_.find(molStampName);
215 >    if (i == moleculeStamps_.end()) {
216 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
217 >        ret = true;
218 >    } else {
219 >        std::ostringstream oss;
220 >        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
221 >        throw OOPSEException(oss.str());  
222      }
223 <  }
324 <
325 <  //@todo memory leak
326 <  if( have_err )
327 <    return strdup( err.c_str() );
328 <  
329 <  return NULL;
330 <
331 <
223 >    return ret;
224   }
225 +
226  
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;
227   }

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