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Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 2373 by tim, Mon Oct 17 03:06:29 2005 UTC vs.
Revision 2488 by tim, Mon Dec 5 23:37:56 2005 UTC

# Line 46 | Line 46
46  
47   #include "io/Globals.hpp"
48   #include "utils/simError.h"
49 – #ifdef IS_MPI
50 – #include "io/mpiBASS.h"
51 – #endif // is_mpi
49  
50   #include "io/ParamConstraint.hpp"
51  
52 < #define DefineParameter(NAME,KEYWORD)                              \
53 <  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())) { sprintf(painCave.errMsg,"Error in checking %s : should be %s\n",NAME.getKeyword().c_str(),(CONSTRAINT).getConstraintDescription().c_str()); painCave.isFatal = 1; painCave.severity = OOPSE_ERROR; simError();} }                
69 <
70 < Globals::Globals(){
71 <
52 > namespace oopse {
53 > Globals::Globals() {
54    DefineParameter(ForceField, "forceField")
73 –  DefineParameter(NComponents, "nComponents")
55  
56    DefineOptionalParameter(TargetTemp, "targetTemp");
57    DefineOptionalParameter(Ensemble, "ensemble");
# Line 78 | Line 59 | Globals::Globals(){
59    DefineOptionalParameter(RunTime, "runTime");
60    DefineOptionalParameter(InitialConfig, "initialConfig");
61    DefineOptionalParameter(FinalConfig, "finalConfig");
81 –  DefineOptionalParameter(NMol, "nMol");
82 –  DefineOptionalParameter(Density, "density");
83 –  DefineOptionalParameter(Box, "box");
84 –  DefineOptionalParameter(BoxX, "boxX");
85 –  DefineOptionalParameter(BoxY, "boxY");
86 –  DefineOptionalParameter(BoxZ, "boxZ");
62    DefineOptionalParameter(SampleTime, "sampleTime");
63    DefineOptionalParameter(ResetTime, "resetTime");
64    DefineOptionalParameter(StatusTime, "statusTime");
# Line 96 | Line 71 | Globals::Globals(){
71    DefineOptionalParameter(TauThermostat, "tauThermostat");
72    DefineOptionalParameter(TauBarostat, "tauBarostat");
73    DefineOptionalParameter(ZconsTime, "zconsTime");
99 –  DefineOptionalParameter(NZconstraints, "nZconstraints");  
74    DefineOptionalParameter(ZconsTol, "zconsTol");
75    DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76    DefineOptionalParameter(Seed, "seed");
# Line 121 | 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");    
126 <  
100 >  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101    DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102    DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
103    DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
# Line 134 | Line 108 | Globals::Globals(){
108    DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109    DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110    DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111 <  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
111 >  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
112    DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
113 +  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
114    DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115 <  
141 < }
142 <
143 < int Globals::globalAssign( event* the_event ){
144 <  char errorMessage[65535];
145 <  int key;
146 <  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
147 <  char* lhs = the_event->evt.asmt.lhs;
148 <  std::string keyword(lhs);
149 <
150 <  bool result = false;
151 <
152 <  /**@todo fix memory leak */  
153 <  ParamMap::iterator i =parameters_.find(keyword);
154 <  if (i != parameters_.end()) {
155 <    if( the_type == STRING ){
156 <       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
157 <       if (!result ) {
158 <            sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval);
159 <            the_event->err_msg = strdup(errorMessage);
160 <       }
161 <    } else if( the_type == DOUBLE ){
162 <      result = i->second->setData(the_event->evt.asmt.rhs.dval);
163 <       if (!result )
164 <         sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval );
165 <       the_event->err_msg = strdup(errorMessage);
166 <    }      
167 <    else if (the_type == INT ){
168 <      result = i->second->setData(the_event->evt.asmt.rhs.ival);
169 <       if (!result )
170 <         sprintf(errorMessage,  "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival );
171 <       the_event->err_msg = strdup(errorMessage);
172 <      
173 <    } else {
174 <        sprintf(errorMessage,  "Internal error of parser\n");
175 <        the_event->err_msg = strdup(errorMessage);
176 <    }
177 <  } else {
178 <    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
179 <    the_event->err_msg = strdup(errorMessage);
180 <  }
181 <
182 <  if (keyword == "nComponents" && getNComponents() > 0) {
183 <    components = new Component*[getNComponents()];
184 <  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
185 <    zConstraints = new ZconStamp*[getNZconstraints()];
186 <  }
187 <  
188 <  return result;
189 < }
190 <
191 < int Globals::newComponent( event* the_event ){
192 <  
193 <  current_component = new Component;
194 <  int index = the_event->evt.blk_index;
195 <  char err[200];
196 <  
197 <  if( haveNComponents() && index < getNComponents() )
198 <    components[index] = current_component;
199 <  else{
200 <    if( haveNComponents()  ){
201 <      sprintf( err, "meta-data parsing error: %d out of nComponents range",
202 <               index );
203 <      the_event->err_msg = strdup( err );
204 <      return 0;
205 <    }
206 <    else{
207 <      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
208 <                                  " first component declaration." );
209 <      return 0;
210 <    }
211 <  }  
212 <
213 <  return 1;
214 < }
215 <
216 <
217 <
218 < int Globals::componentAssign( event* the_event ){
219 <
220 <  switch( the_event->evt.asmt.asmt_type ){
221 <    
222 <  case STRING:
223 <    return current_component->assignString( the_event->evt.asmt.lhs,
224 <                                            the_event->evt.asmt.rhs.sval,
225 <                                            &(the_event->err_msg));
226 <    break;
227 <    
228 <  case DOUBLE:
229 <    return current_component->assignDouble( the_event->evt.asmt.lhs,
230 <                                            the_event->evt.asmt.rhs.dval,
231 <                                            &(the_event->err_msg));
232 <    break;
233 <    
234 <  case INT:
235 <    return current_component->assignInt( the_event->evt.asmt.lhs,
236 <                                         the_event->evt.asmt.rhs.ival,
237 <                                         &(the_event->err_msg));
238 <    break;
239 <    
240 <  default:
241 <    the_event->err_msg = strdup( "Globals error. Invalid component"
242 <                                 " assignment type" );
243 <    return 0;
244 <    break;
245 <  }
246 <  return 0;
247 < }
248 <
249 < int Globals::componentEnd( event* the_event ){
250 <
251 <  the_event->err_msg = current_component->checkMe();
252 <  if( the_event->err_msg != NULL ) return 0;
115 >  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
116  
254 –  return 1;
255 – }
117  
118 < int Globals::newZconstraint( event* the_event ){
119 <  
259 <
260 <  int index = the_event->evt.blk_index;
261 <  char err[200];
262 <  current_zConstraint = new ZconStamp( index );
263 <  
264 <  if( haveNZconstraints() && index < getNZconstraints() )
265 <    zConstraints[index] = current_zConstraint;
266 <  else{
267 <    if( haveNZconstraints() ){
268 <      sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
269 <               index );
270 <      the_event->err_msg = strdup( err );
271 <      return 0;
272 <    }
273 <    else{
274 <      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
275 <                                  " not given before"
276 <                                  " first zConstraint declaration." );
277 <      return 0;
278 <    }
279 <  }  
280 <
281 <  return 1;
282 < }
283 <
284 <
285 <
286 < int Globals::zConstraintAssign( event* the_event ){
287 <
288 <  switch( the_event->evt.asmt.asmt_type ){
118 >    deprecatedKeywords_.insert("nComponents");
119 >    deprecatedKeywords_.insert("nZconstraints");
120      
290 –  case STRING:
291 –    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
292 –                                              the_event->evt.asmt.rhs.sval,
293 –                                              &(the_event->err_msg));
294 –    break;
295 –    
296 –  case DOUBLE:
297 –    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
298 –                                              the_event->evt.asmt.rhs.dval,
299 –                                              &(the_event->err_msg));
300 –    break;
301 –    
302 –  case INT:
303 –    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
304 –                                           the_event->evt.asmt.rhs.ival,
305 –                                           &(the_event->err_msg));
306 –    break;
307 –    
308 –  default:
309 –    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
310 –                                 " assignment type" );
311 –    return 0;
312 –    break;
313 –  }
314 –  return 0;
121   }
122  
123 < int Globals::zConstraintEnd( event* the_event ){
123 > Globals::~Globals() {
124  
319 –  the_event->err_msg = current_zConstraint->checkMe();
320 –  if( the_event->err_msg != NULL ) return 0;
125  
322 –  return 1;
126   }
127  
128 < char* Globals::checkMe( void ){
128 > void Globals::validate() {
129 >  DataHolder::validate();
130  
327 –
328 –  std::string err("The following required keywords are missing:\n");
329 –  short int have_err = 0;
330 –
331 –  ParamMap::iterator i;
332 –  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
333 –    if (!i->second->isOptional() && i->second->empty()) {
334 –        err +=  i->second->getKeyword() + "\n";
335 –    }
336 –  }
337 –
131    CheckParameter(ForceField, isNotEmpty());
339 –  CheckParameter(NComponents,isPositive());
132    CheckParameter(TargetTemp, isPositive());
133 <  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
342 <                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
343 <                                          isEqualIgnoreCase(std::string("NPTxyz")) );
344 <
133 >  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
134    CheckParameter(Dt, isPositive());
135    CheckParameter(RunTime, isPositive());
136    CheckParameter(InitialConfig, isNotEmpty());
137    CheckParameter(FinalConfig, isNotEmpty());
349 –  CheckParameter(NMol, isPositive());
350 –  CheckParameter(Density, isPositive());
351 –  CheckParameter(Box, isPositive());
352 –  CheckParameter(BoxX, isPositive());
353 –  CheckParameter(BoxY, isPositive());
354 –  CheckParameter(BoxZ, isPositive());
138    CheckParameter(SampleTime, isNonNegative());
139    CheckParameter(ResetTime, isNonNegative());
140    CheckParameter(StatusTime, isNonNegative());
# Line 363 | Line 146 | char* Globals::checkMe( void ){
146    CheckParameter(TauThermostat, isPositive());
147    CheckParameter(TauBarostat, isPositive());
148    CheckParameter(ZconsTime, isPositive());
366 –  CheckParameter(NZconstraints, isPositive());  
149    CheckParameter(ZconsTol, isPositive());
368 –  //CheckParameter(ZconsForcePolicy,);
150    CheckParameter(Seed, isPositive());
151    CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
152    CheckParameter(MinimizerMaxIter, isPositive());
# Line 385 | Line 166 | char* Globals::checkMe( void ){
166    CheckParameter(ThermIntThetaSpringConst, isPositive());
167    CheckParameter(ThermIntOmegaSpringConst, isPositive());
168    CheckParameter(SurfaceTension, isPositive());
169 <  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
169 >  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
170 >  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
171    CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172 +  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
173    //CheckParameter(StatFileFormat,);    
174    //CheckParameter(MixingRule,);
175    CheckParameter(OrthoBoxTolerance, isPositive());  
176    CheckParameter(ThermIntDistSpringConst, isPositive());
177    CheckParameter(ThermIntThetaSpringConst, isPositive());
178    CheckParameter(ThermIntOmegaSpringConst, isPositive());
179 <  CheckParameter(DampingAlpha,isPositive());
179 >  CheckParameter(DampingAlpha,isNonNegative());
180    CheckParameter(SkinThickness, isPositive());
398 –  
399 –  //@todo memory leak
400 –  if( have_err )
401 –    return strdup( err.c_str() );
402 –  
403 –  return NULL;
181  
182 +  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
183 +    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
184 +        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
185 +    }
186 +  }
187 + }
188 +    
189 + bool Globals::addComponent(Component* comp) {
190 +    components_.push_back(comp);
191 +    return true;
192 + }
193  
194 + bool Globals::addZConsStamp(ZConsStamp* zcons) {
195 +    zconstraints_.push_back(zcons);
196 +    return true;
197   }
198  
199 < int Globals::globalEnd( event* the_event ){
200 <  
201 <  the_event->err_msg = checkMe();
202 <  if( the_event->err_msg != NULL ) return 0;
199 > bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
200 >    std::string molStampName = molStamp->getName();
201 >    std::map<std::string, MoleculeStamp*>::iterator i;
202 >    bool ret = false;
203 >    i = moleculeStamps_.find(molStampName);
204 >    if (i == moleculeStamps_.end()) {
205 >        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
206 >        ret = true;
207 >    } else {
208 >        std::cout << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
209 >    }
210 >    return ret;
211 > }
212 >
213  
413 –  return 1;
214   }

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