| 52 | 
  | 
 | 
| 53 | 
  | 
#include "io/ParamConstraint.hpp" | 
| 54 | 
  | 
 | 
| 55 | 
– | 
#define DefineParameter(NAME,KEYWORD)                              \ | 
| 56 | 
– | 
  NAME.setKeyword(KEYWORD);                  \ | 
| 57 | 
– | 
  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME)); | 
| 55 | 
  | 
 | 
| 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 | 
– | 
 | 
| 56 | 
  | 
Globals::Globals(){ | 
| 57 | 
  | 
  | 
| 58 | 
  | 
  DefineParameter(ForceField, "forceField") | 
| 107 | 
  | 
  DefineOptionalParameter(SurfaceTension, "surfaceTension"); | 
| 108 | 
  | 
  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); | 
| 109 | 
  | 
  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); | 
| 110 | 
+ | 
  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); | 
| 111 | 
  | 
  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); | 
| 112 | 
< | 
  DefineOptionalParameter(StatFileFormat, "statFileFormat");     | 
| 127 | 
< | 
   | 
| 112 | 
> | 
  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); | 
| 113 | 
  | 
  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard"); | 
| 114 | 
  | 
  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); | 
| 115 | 
  | 
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); | 
| 120 | 
  | 
  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); | 
| 121 | 
  | 
  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); | 
| 122 | 
  | 
  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); | 
| 123 | 
< | 
  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5); | 
| 123 | 
> | 
  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2); | 
| 124 | 
  | 
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); | 
| 125 | 
+ | 
  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); | 
| 126 | 
  | 
  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); | 
| 127 | 
+ | 
  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");     | 
| 128 | 
+ | 
 | 
| 129 | 
  | 
   | 
| 130 | 
  | 
} | 
| 131 | 
  | 
 | 
| 132 | 
  | 
int Globals::globalAssign( event* the_event ){ | 
| 133 | 
< | 
   | 
| 133 | 
> | 
  char errorMessage[65535];  | 
| 134 | 
  | 
  int key; | 
| 147 | 
– | 
  int token; | 
| 135 | 
  | 
  interface_assign_type the_type =  the_event->evt.asmt.asmt_type; | 
| 136 | 
  | 
  char* lhs = the_event->evt.asmt.lhs; | 
| 137 | 
  | 
  std::string keyword(lhs); | 
| 138 | 
  | 
 | 
| 139 | 
< | 
  bool result; | 
| 139 | 
> | 
  bool result = false; | 
| 140 | 
  | 
 | 
| 141 | 
< | 
 | 
| 141 | 
> | 
  /**@todo fix memory leak */   | 
| 142 | 
  | 
  ParamMap::iterator i =parameters_.find(keyword); | 
| 143 | 
  | 
  if (i != parameters_.end()) { | 
| 144 | 
  | 
    if( the_type == STRING ){ | 
| 145 | 
  | 
       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval)); | 
| 146 | 
  | 
       if (!result ) { | 
| 147 | 
< | 
            sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() ); | 
| 147 | 
> | 
            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); | 
| 148 | 
> | 
            the_event->err_msg = strdup(errorMessage); | 
| 149 | 
  | 
       } | 
| 150 | 
  | 
    } else if( the_type == DOUBLE ){ | 
| 151 | 
  | 
      result = i->second->setData(the_event->evt.asmt.rhs.dval); | 
| 152 | 
  | 
       if (!result ) | 
| 153 | 
< | 
         sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() ); | 
| 153 | 
> | 
         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 ); | 
| 154 | 
> | 
       the_event->err_msg = strdup(errorMessage); | 
| 155 | 
  | 
    }       | 
| 156 | 
  | 
    else if (the_type == INT ){ | 
| 157 | 
  | 
      result = i->second->setData(the_event->evt.asmt.rhs.ival); | 
| 158 | 
  | 
       if (!result ) | 
| 159 | 
< | 
         sprintf(the_event->err_msg,  "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() ); | 
| 159 | 
> | 
         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 ); | 
| 160 | 
> | 
       the_event->err_msg = strdup(errorMessage); | 
| 161 | 
  | 
       | 
| 162 | 
  | 
    } else { | 
| 163 | 
< | 
     | 
| 163 | 
> | 
        sprintf(errorMessage,  "Internal error of parser\n"); | 
| 164 | 
> | 
        the_event->err_msg = strdup(errorMessage); | 
| 165 | 
  | 
    } | 
| 166 | 
+ | 
  } else { | 
| 167 | 
+ | 
    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() ); | 
| 168 | 
+ | 
    the_event->err_msg = strdup(errorMessage); | 
| 169 | 
  | 
  } | 
| 170 | 
  | 
 | 
| 171 | 
  | 
  if (keyword == "nComponents" && getNComponents() > 0) { | 
| 327 | 
  | 
  CheckParameter(ForceField, isNotEmpty()); | 
| 328 | 
  | 
  CheckParameter(NComponents,isPositive());  | 
| 329 | 
  | 
  CheckParameter(TargetTemp, isPositive()); | 
| 330 | 
< | 
  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || | 
| 331 | 
< | 
                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||  | 
| 332 | 
< | 
                                          isEqualIgnoreCase(std::string("NPTxyz")) ); | 
| 333 | 
< | 
 | 
| 330 | 
> | 
  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||  | 
| 331 | 
> | 
                 isEqualIgnoreCase(std::string("NVT")) || | 
| 332 | 
> | 
                 isEqualIgnoreCase(std::string("NPTi")) ||  | 
| 333 | 
> | 
                 isEqualIgnoreCase(std::string("NPTf")) ||  | 
| 334 | 
> | 
                 isEqualIgnoreCase(std::string("NPTxyz")) ); | 
| 335 | 
  | 
  CheckParameter(Dt, isPositive()); | 
| 336 | 
  | 
  CheckParameter(RunTime, isPositive()); | 
| 337 | 
  | 
  CheckParameter(InitialConfig, isNotEmpty()); | 
| 357 | 
  | 
  CheckParameter(ZconsTol, isPositive()); | 
| 358 | 
  | 
  //CheckParameter(ZconsForcePolicy,); | 
| 359 | 
  | 
  CheckParameter(Seed, isPositive()); | 
| 360 | 
< | 
  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG"))); | 
| 360 | 
> | 
  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||  | 
| 361 | 
> | 
                 isEqualIgnoreCase(std::string("CG"))); | 
| 362 | 
  | 
  CheckParameter(MinimizerMaxIter, isPositive()); | 
| 363 | 
  | 
  CheckParameter(MinimizerWriteFrq, isPositive()); | 
| 364 | 
  | 
  CheckParameter(MinimizerStepSize, isPositive()); | 
| 376 | 
  | 
  CheckParameter(ThermIntThetaSpringConst, isPositive()); | 
| 377 | 
  | 
  CheckParameter(ThermIntOmegaSpringConst, isPositive()); | 
| 378 | 
  | 
  CheckParameter(SurfaceTension, isPositive()); | 
| 379 | 
< | 
  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) ); | 
| 380 | 
< | 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL"))); | 
| 379 | 
> | 
  CheckParameter(ElectrostaticSummationMethod,  | 
| 380 | 
> | 
                 isEqualIgnoreCase(std::string("NONE")) ||  | 
| 381 | 
> | 
                 isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||  | 
| 382 | 
> | 
                 isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||  | 
| 383 | 
> | 
                 isEqualIgnoreCase(std::string("REACTION_FIELD"))); | 
| 384 | 
> | 
  CheckParameter(ElectrostaticScreeningMethod,  | 
| 385 | 
> | 
                 isEqualIgnoreCase(std::string("UNDAMPED")) ||  | 
| 386 | 
> | 
                 isEqualIgnoreCase(std::string("DAMPED")));  | 
| 387 | 
> | 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||  | 
| 388 | 
> | 
                 isEqualIgnoreCase(std::string("MAX")) ||  | 
| 389 | 
> | 
                 isEqualIgnoreCase(std::string("TRADITIONAL"))); | 
| 390 | 
> | 
  CheckParameter(SwitchingFunctionType,  | 
| 391 | 
> | 
                 isEqualIgnoreCase(std::string("CUBIC")) ||  | 
| 392 | 
> | 
                 isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL"))); | 
| 393 | 
  | 
  //CheckParameter(StatFileFormat,);      | 
| 394 | 
  | 
  //CheckParameter(MixingRule,); | 
| 395 | 
  | 
  CheckParameter(OrthoBoxTolerance, isPositive());   | 
| 396 | 
  | 
  CheckParameter(ThermIntDistSpringConst, isPositive()); | 
| 397 | 
  | 
  CheckParameter(ThermIntThetaSpringConst, isPositive()); | 
| 398 | 
  | 
  CheckParameter(ThermIntOmegaSpringConst, isPositive()); | 
| 399 | 
< | 
  CheckParameter(DampingAlpha,isPositive()); | 
| 399 | 
> | 
  CheckParameter(DampingAlpha,isNonNegative()); | 
| 400 | 
  | 
  CheckParameter(SkinThickness, isPositive()); | 
| 401 | 
  | 
   | 
| 402 | 
  | 
  //@todo memory leak |