src/io/Globals.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <string>

#include "io/Globals.hpp"
#include "utils/simError.h"
#ifdef IS_MPI
#include "io/mpiBASS.h"
#endif // is_mpi

#include "io/ParamConstraint.hpp"

#define DefineParameter(NAME,KEYWORD)                              \
  NAME.setKeyword(KEYWORD);                  \
  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));

#define DefineOptionalParameter(NAME,KEYWORD)                              \
  NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));

#define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
  NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));

#define CheckParameter(NAME, CONSTRAINT)                              \
  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();} }                 

Globals::Globals(){
 
  DefineParameter(ForceField, "forceField")
  DefineParameter(NComponents, "nComponents")
 
  DefineOptionalParameter(TargetTemp, "targetTemp");
  DefineOptionalParameter(Ensemble, "ensemble");
  DefineOptionalParameter(Dt, "dt");
  DefineOptionalParameter(RunTime, "runTime");
  DefineOptionalParameter(InitialConfig, "initialConfig");
  DefineOptionalParameter(FinalConfig, "finalConfig");
  DefineOptionalParameter(NMol, "nMol");
  DefineOptionalParameter(Density, "density");
  DefineOptionalParameter(Box, "box");
  DefineOptionalParameter(BoxX, "boxX");
  DefineOptionalParameter(BoxY, "boxY");
  DefineOptionalParameter(BoxZ, "boxZ");
  DefineOptionalParameter(SampleTime, "sampleTime");
  DefineOptionalParameter(ResetTime, "resetTime");
  DefineOptionalParameter(StatusTime, "statusTime");
  DefineOptionalParameter(CutoffRadius, "cutoffRadius");
  DefineOptionalParameter(SwitchingRadius, "switchingRadius");
  DefineOptionalParameter(Dielectric, "dielectric");
  DefineOptionalParameter(TempSet, "tempSet");
  DefineOptionalParameter(ThermalTime, "thermalTime");
  DefineOptionalParameter(TargetPressure, "targetPressure");
  DefineOptionalParameter(TauThermostat, "tauThermostat");
  DefineOptionalParameter(TauBarostat, "tauBarostat");
  DefineOptionalParameter(ZconsTime, "zconsTime");
  DefineOptionalParameter(NZconstraints, "nZconstraints");  
  DefineOptionalParameter(ZconsTol, "zconsTol");
  DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
  DefineOptionalParameter(Seed, "seed");
  DefineOptionalParameter(Minimizer, "minimizer");
  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
  DefineOptionalParameter(ZconsGap, "zconsGap");
  DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
  DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
  DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
  DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
  DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
  DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
  DefineOptionalParameter(SurfaceTension, "surfaceTension");
  DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
  
  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
  DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
  DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
  DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
  DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
  DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    

  
}

int Globals::globalAssign( event* the_event ){
  char errorMessage[65535]; 
  int key;
  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
  char* lhs = the_event->evt.asmt.lhs;
  std::string keyword(lhs);

  bool result = false;

  /**@todo fix memory leak */  
  ParamMap::iterator i =parameters_.find(keyword);
  if (i != parameters_.end()) {
    if( the_type == STRING ){
       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
       if (!result ) {
            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);
            the_event->err_msg = strdup(errorMessage);
       }
    } else if( the_type == DOUBLE ){
      result = i->second->setData(the_event->evt.asmt.rhs.dval);
       if (!result )
         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 );
       the_event->err_msg = strdup(errorMessage);
    }      
    else if (the_type == INT ){
      result = i->second->setData(the_event->evt.asmt.rhs.ival);
       if (!result )
         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 );
       the_event->err_msg = strdup(errorMessage);
      
    } else {
        sprintf(errorMessage,  "Internal error of parser\n");
        the_event->err_msg = strdup(errorMessage);
    }
  } else {
    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
    the_event->err_msg = strdup(errorMessage);
  }

  if (keyword == "nComponents" && getNComponents() > 0) {
    components = new Component*[getNComponents()];
  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
    zConstraints = new ZconStamp*[getNZconstraints()];
  }
  
  return result;
}

int Globals::newComponent( event* the_event ){
  
  current_component = new Component;
  int index = the_event->evt.blk_index;
  char err[200];
  
  if( haveNComponents() && index < getNComponents() ) 
    components[index] = current_component;
  else{
    if( haveNComponents()  ){
      sprintf( err, "meta-data parsing error: %d out of nComponents range", 
               index );
      the_event->err_msg = strdup( err );
      return 0;
    }
    else{
      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
                                  " first component declaration." );
      return 0;
    }
  }  
 
  return 1;
}


int Globals::componentAssign( event* the_event ){

  switch( the_event->evt.asmt.asmt_type ){
    
  case STRING:
    return current_component->assignString( the_event->evt.asmt.lhs,
                                            the_event->evt.asmt.rhs.sval,
                                            &(the_event->err_msg));
    break;
    
  case DOUBLE:
    return current_component->assignDouble( the_event->evt.asmt.lhs,
                                            the_event->evt.asmt.rhs.dval,
                                            &(the_event->err_msg));
    break;
    
  case INT:
    return current_component->assignInt( the_event->evt.asmt.lhs,
                                         the_event->evt.asmt.rhs.ival,
                                         &(the_event->err_msg));
    break;
    
  default:
    the_event->err_msg = strdup( "Globals error. Invalid component"
                                 " assignment type" );
    return 0;
    break;
  }
  return 0;
}

int Globals::componentEnd( event* the_event ){

  the_event->err_msg = current_component->checkMe();
  if( the_event->err_msg != NULL ) return 0;

  return 1;
}

int Globals::newZconstraint( event* the_event ){
  

  int index = the_event->evt.blk_index;
  char err[200];
  current_zConstraint = new ZconStamp( index );
  
  if( haveNZconstraints() && index < getNZconstraints() ) 
    zConstraints[index] = current_zConstraint;
  else{
    if( haveNZconstraints() ){
      sprintf( err, "meta-data parsing error: %d out of nZconstraints range", 
               index );
      the_event->err_msg = strdup( err );
      return 0;
    }
    else{
      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
                                  " not given before"
                                  " first zConstraint declaration." );
      return 0;
    }
  }  

  return 1;
}


int Globals::zConstraintAssign( event* the_event ){

  switch( the_event->evt.asmt.asmt_type ){
    
  case STRING:
    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
                                              the_event->evt.asmt.rhs.sval,
                                              &(the_event->err_msg));
    break;
    
  case DOUBLE:
    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
                                              the_event->evt.asmt.rhs.dval,
                                              &(the_event->err_msg));
    break;
    
  case INT:
    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
                                           the_event->evt.asmt.rhs.ival,
                                           &(the_event->err_msg));
    break;
    
  default:
    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
                                 " assignment type" );
    return 0;
    break;
  }
  return 0;
}

int Globals::zConstraintEnd( event* the_event ){

  the_event->err_msg = current_zConstraint->checkMe();
  if( the_event->err_msg != NULL ) return 0;

  return 1;
}

char* Globals::checkMe( void ){


  std::string err("The following required keywords are missing:\n");
  short int have_err = 0;

  ParamMap::iterator i;
  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
    if (!i->second->isOptional() && i->second->empty()) {
        err +=  i->second->getKeyword() + "\n";
    }
  }

  CheckParameter(ForceField, isNotEmpty());
  CheckParameter(NComponents,isPositive()); 
  CheckParameter(TargetTemp, isPositive());
  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
                                          isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))|| 
                                          isEqualIgnoreCase(std::string("NPTxyz")) );
  CheckParameter(Dt, isPositive());
  CheckParameter(RunTime, isPositive());
  CheckParameter(InitialConfig, isNotEmpty());
  CheckParameter(FinalConfig, isNotEmpty());
  CheckParameter(NMol, isPositive());
  CheckParameter(Density, isPositive());
  CheckParameter(Box, isPositive());
  CheckParameter(BoxX, isPositive());
  CheckParameter(BoxY, isPositive());
  CheckParameter(BoxZ, isPositive());
  CheckParameter(SampleTime, isNonNegative());
  CheckParameter(ResetTime, isNonNegative());
  CheckParameter(StatusTime, isNonNegative());
  CheckParameter(CutoffRadius, isPositive());
  CheckParameter(SwitchingRadius, isNonNegative());
  CheckParameter(Dielectric, isPositive());
  CheckParameter(ThermalTime,  isNonNegative());
  CheckParameter(TargetPressure,  isPositive());
  CheckParameter(TauThermostat, isPositive());
  CheckParameter(TauBarostat, isPositive());
  CheckParameter(ZconsTime, isPositive());
  CheckParameter(NZconstraints, isPositive());  
  CheckParameter(ZconsTol, isPositive());
  //CheckParameter(ZconsForcePolicy,);
  CheckParameter(Seed, isPositive());
  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
  CheckParameter(MinimizerMaxIter, isPositive());
  CheckParameter(MinimizerWriteFrq, isPositive());
  CheckParameter(MinimizerStepSize, isPositive());
  CheckParameter(MinimizerFTol, isPositive());
  CheckParameter(MinimizerGTol, isPositive());
  CheckParameter(MinimizerLSTol, isPositive());
  CheckParameter(MinimizerLSMaxIter, isPositive());
  CheckParameter(ZconsGap, isPositive());
  CheckParameter(ZconsFixtime, isPositive());
  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
  CheckParameter(ThermodynamicIntegrationK, isPositive());
  CheckParameter(ForceFieldVariant, isNotEmpty());
  CheckParameter(ForceFieldFileName, isNotEmpty());
  CheckParameter(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(SurfaceTension, isPositive());
  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE"))  || isEqualIgnoreCase(std::string("REACTION_FIELD")));
  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED"))); 
  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
  //CheckParameter(StatFileFormat,);     
  //CheckParameter(MixingRule,);
  CheckParameter(OrthoBoxTolerance, isPositive());  
  CheckParameter(ThermIntDistSpringConst, isPositive());
  CheckParameter(ThermIntThetaSpringConst, isPositive());
  CheckParameter(ThermIntOmegaSpringConst, isPositive());
  CheckParameter(DampingAlpha,isNonNegative());
  CheckParameter(SkinThickness, isPositive());
  
  //@todo memory leak
  if( have_err )
    return strdup( err.c_str() );
  
  return NULL;


}

int Globals::globalEnd( event* the_event ){
  
  the_event->err_msg = checkMe();
  if( the_event->err_msg != NULL ) return 0;

  return 1;
}
Revision:	2415
Committed:	Thu Nov 3 23:12:27 2005 UTC (20 years ago) by chrisfen
File size:	17021 byte(s)
Log Message:	improvements in shifted-force
#	User	Rev	Content
1	gezelter	2088	/*
2	gezelter	1930	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	1490	#include <stdlib.h>
43			#include <stdio.h>
44			#include <string.h>
45	tim	2364	#include <string>
46	gezelter	1490
47	tim	1492	#include "io/Globals.hpp"
48			#include "utils/simError.h"
49	gezelter	1490	#ifdef IS_MPI
50	tim	1492	#include "io/mpiBASS.h"
51	gezelter	1490	#endif // is_mpi
52
53	tim	2371	#include "io/ParamConstraint.hpp"
54	gezelter	1490
55	tim	2364	#define DefineParameter(NAME,KEYWORD) \
56			NAME.setKeyword(KEYWORD); \
57			parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
58	gezelter	1490
59	tim	2364	#define DefineOptionalParameter(NAME,KEYWORD) \
60			NAME.setKeyword(KEYWORD); NAME.setOptional(true); \
61			parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
62	chrisfen	2101
63	tim	2364	#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	tim	2371	#define CheckParameter(NAME, CONSTRAINT) \
68	tim	2373	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	tim	2371
70	gezelter	1490	Globals::Globals(){
71	tim	2364
72			DefineParameter(ForceField, "forceField")
73			DefineParameter(NComponents, "nComponents")
74
75			DefineOptionalParameter(TargetTemp, "targetTemp");
76			DefineOptionalParameter(Ensemble, "ensemble");
77			DefineOptionalParameter(Dt, "dt");
78			DefineOptionalParameter(RunTime, "runTime");
79			DefineOptionalParameter(InitialConfig, "initialConfig");
80			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");
87			DefineOptionalParameter(SampleTime, "sampleTime");
88			DefineOptionalParameter(ResetTime, "resetTime");
89			DefineOptionalParameter(StatusTime, "statusTime");
90			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
91			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92			DefineOptionalParameter(Dielectric, "dielectric");
93			DefineOptionalParameter(TempSet, "tempSet");
94			DefineOptionalParameter(ThermalTime, "thermalTime");
95			DefineOptionalParameter(TargetPressure, "targetPressure");
96			DefineOptionalParameter(TauThermostat, "tauThermostat");
97			DefineOptionalParameter(TauBarostat, "tauBarostat");
98			DefineOptionalParameter(ZconsTime, "zconsTime");
99			DefineOptionalParameter(NZconstraints, "nZconstraints");
100			DefineOptionalParameter(ZconsTol, "zconsTol");
101			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
102			DefineOptionalParameter(Seed, "seed");
103			DefineOptionalParameter(Minimizer, "minimizer");
104			DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
105			DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
106			DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
107			DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
108			DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
109			DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
110			DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
111			DefineOptionalParameter(ZconsGap, "zconsGap");
112			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
113			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
114			DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
115			DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
116			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
117			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
118			DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
119			DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
120			DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
121			DefineOptionalParameter(SurfaceTension, "surfaceTension");
122			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
123			DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
124	chrisfen	2415	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
125	tim	2364	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
126
127			DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
128			DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
129			DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
130			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
131			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
132			DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
133			DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
134	chrisfen	2365	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
135			DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
136			DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
137	chrisfen	2415	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
138	tim	2364	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
139			DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
140	tim	2380	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME\|TOTAL_ENERGY\|POTENTIAL_ENERGY\|KINETIC_ENERGY\|TEMPERATURE\|PRESSURE\|VOLUME\|CONSERVED_QUANTITY");
141
142	tim	2364
143	gezelter	1490	}
144
145	tim	2364	int Globals::globalAssign( event* the_event ){
146	tim	2373	char errorMessage[65535];
147	tim	2364	int key;
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	chrisfen	2101
152	tim	2372	bool result = false;
153	gezelter	1490
154	tim	2373	/*@todo fix memory leak /
155	tim	2364	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	tim	2373	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);
161			the_event->err_msg = strdup(errorMessage);
162	tim	2364	}
163			} else if( the_type == DOUBLE ){
164			result = i->second->setData(the_event->evt.asmt.rhs.dval);
165			if (!result )
166	tim	2373	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 );
167			the_event->err_msg = strdup(errorMessage);
168	tim	2364	}
169			else if (the_type == INT ){
170			result = i->second->setData(the_event->evt.asmt.rhs.ival);
171			if (!result )
172	tim	2373	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 );
173			the_event->err_msg = strdup(errorMessage);
174	tim	2364
175			} else {
176	tim	2373	sprintf(errorMessage, "Internal error of parser\n");
177			the_event->err_msg = strdup(errorMessage);
178	tim	2364	}
179	tim	2373	} else {
180			sprintf(errorMessage, "%s is an unrecognized keyword\n", keyword.c_str() );
181			the_event->err_msg = strdup(errorMessage);
182	tim	2364	}
183
184			if (keyword == "nComponents" && getNComponents() > 0) {
185			components = new Component*[getNComponents()];
186			}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
187			zConstraints = new ZconStamp*[getNZconstraints()];
188			}
189	gezelter	1490
190	tim	2364	return result;
191	gezelter	1490	}
192
193			int Globals::newComponent( event* the_event ){
194
195			current_component = new Component;
196			int index = the_event->evt.blk_index;
197			char err[200];
198
199	tim	2364	if( haveNComponents() && index < getNComponents() )
200	gezelter	1490	components[index] = current_component;
201			else{
202	tim	2364	if( haveNComponents() ){
203	gezelter	1490	sprintf( err, "meta-data parsing error: %d out of nComponents range",
204			index );
205			the_event->err_msg = strdup( err );
206			return 0;
207			}
208			else{
209			the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
210			" first component declaration." );
211			return 0;
212			}
213			}
214
215			return 1;
216			}
217
218
219
220			int Globals::componentAssign( event* the_event ){
221
222			switch( the_event->evt.asmt.asmt_type ){
223
224			case STRING:
225			return current_component->assignString( the_event->evt.asmt.lhs,
226			the_event->evt.asmt.rhs.sval,
227			&(the_event->err_msg));
228			break;
229
230			case DOUBLE:
231			return current_component->assignDouble( the_event->evt.asmt.lhs,
232			the_event->evt.asmt.rhs.dval,
233			&(the_event->err_msg));
234			break;
235
236			case INT:
237			return current_component->assignInt( the_event->evt.asmt.lhs,
238			the_event->evt.asmt.rhs.ival,
239			&(the_event->err_msg));
240			break;
241
242			default:
243			the_event->err_msg = strdup( "Globals error. Invalid component"
244			" assignment type" );
245			return 0;
246			break;
247			}
248			return 0;
249			}
250
251			int Globals::componentEnd( event* the_event ){
252
253			the_event->err_msg = current_component->checkMe();
254			if( the_event->err_msg != NULL ) return 0;
255
256			return 1;
257			}
258
259			int Globals::newZconstraint( event* the_event ){
260
261
262			int index = the_event->evt.blk_index;
263			char err[200];
264			current_zConstraint = new ZconStamp( index );
265
266	tim	2364	if( haveNZconstraints() && index < getNZconstraints() )
267	gezelter	1490	zConstraints[index] = current_zConstraint;
268			else{
269	tim	2364	if( haveNZconstraints() ){
270	gezelter	1490	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
271			index );
272			the_event->err_msg = strdup( err );
273			return 0;
274			}
275			else{
276			the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
277			" not given before"
278			" first zConstraint declaration." );
279			return 0;
280			}
281			}
282	tim	2364
283	gezelter	1490	return 1;
284			}
285
286
287
288			int Globals::zConstraintAssign( event* the_event ){
289
290			switch( the_event->evt.asmt.asmt_type ){
291
292			case STRING:
293			return current_zConstraint->assignString( the_event->evt.asmt.lhs,
294			the_event->evt.asmt.rhs.sval,
295			&(the_event->err_msg));
296			break;
297
298			case DOUBLE:
299			return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
300			the_event->evt.asmt.rhs.dval,
301			&(the_event->err_msg));
302			break;
303
304			case INT:
305			return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
306			the_event->evt.asmt.rhs.ival,
307			&(the_event->err_msg));
308			break;
309
310			default:
311			the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
312			" assignment type" );
313			return 0;
314			break;
315			}
316			return 0;
317			}
318
319			int Globals::zConstraintEnd( event* the_event ){
320
321			the_event->err_msg = current_zConstraint->checkMe();
322			if( the_event->err_msg != NULL ) return 0;
323
324			return 1;
325			}
326
327	tim	2364	char* Globals::checkMe( void ){
328	tim	2109
329	gezelter	1490
330	tim	2364	std::string err("The following required keywords are missing:\n");
331			short int have_err = 0;
332	gezelter	1490
333	tim	2364	ParamMap::iterator i;
334			for (i = parameters_.begin(); i != parameters_.end(); ++i) {
335			if (!i->second->isOptional() && i->second->empty()) {
336			err += i->second->getKeyword() + "\n";
337	gezelter	1490	}
338			}
339
340	tim	2371	CheckParameter(ForceField, isNotEmpty());
341			CheckParameter(NComponents,isPositive());
342			CheckParameter(TargetTemp, isPositive());
343			CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) \|\| isEqualIgnoreCase(std::string("NVT")) \|\|
344			isEqualIgnoreCase(std::string("NPTi")) \|\| isEqualIgnoreCase(std::string("NPTf"))\|\|
345			isEqualIgnoreCase(std::string("NPTxyz")) );
346			CheckParameter(Dt, isPositive());
347			CheckParameter(RunTime, isPositive());
348			CheckParameter(InitialConfig, isNotEmpty());
349			CheckParameter(FinalConfig, isNotEmpty());
350			CheckParameter(NMol, isPositive());
351			CheckParameter(Density, isPositive());
352			CheckParameter(Box, isPositive());
353			CheckParameter(BoxX, isPositive());
354			CheckParameter(BoxY, isPositive());
355			CheckParameter(BoxZ, isPositive());
356			CheckParameter(SampleTime, isNonNegative());
357			CheckParameter(ResetTime, isNonNegative());
358			CheckParameter(StatusTime, isNonNegative());
359			CheckParameter(CutoffRadius, isPositive());
360			CheckParameter(SwitchingRadius, isNonNegative());
361			CheckParameter(Dielectric, isPositive());
362			CheckParameter(ThermalTime, isNonNegative());
363			CheckParameter(TargetPressure, isPositive());
364			CheckParameter(TauThermostat, isPositive());
365			CheckParameter(TauBarostat, isPositive());
366			CheckParameter(ZconsTime, isPositive());
367			CheckParameter(NZconstraints, isPositive());
368			CheckParameter(ZconsTol, isPositive());
369			//CheckParameter(ZconsForcePolicy,);
370			CheckParameter(Seed, isPositive());
371			CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) \|\| isEqualIgnoreCase(std::string("CG")));
372			CheckParameter(MinimizerMaxIter, isPositive());
373			CheckParameter(MinimizerWriteFrq, isPositive());
374			CheckParameter(MinimizerStepSize, isPositive());
375			CheckParameter(MinimizerFTol, isPositive());
376			CheckParameter(MinimizerGTol, isPositive());
377			CheckParameter(MinimizerLSTol, isPositive());
378			CheckParameter(MinimizerLSMaxIter, isPositive());
379			CheckParameter(ZconsGap, isPositive());
380			CheckParameter(ZconsFixtime, isPositive());
381			CheckParameter(ThermodynamicIntegrationLambda, isPositive());
382			CheckParameter(ThermodynamicIntegrationK, isPositive());
383			CheckParameter(ForceFieldVariant, isNotEmpty());
384			CheckParameter(ForceFieldFileName, isNotEmpty());
385			CheckParameter(ThermIntDistSpringConst, isPositive());
386			CheckParameter(ThermIntThetaSpringConst, isPositive());
387			CheckParameter(ThermIntOmegaSpringConst, isPositive());
388			CheckParameter(SurfaceTension, isPositive());
389	chrisfen	2409	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) \|\| isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) \|\| isEqualIgnoreCase(std::string("SHIFTED_FORCE")) \|\| isEqualIgnoreCase(std::string("REACTION_FIELD")));
390	chrisfen	2415	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) \|\| isEqualIgnoreCase(std::string("DAMPED")));
391	tim	2371	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) \|\| isEqualIgnoreCase(std::string("MAX")) \|\| isEqualIgnoreCase(std::string("TRADITIONAL")));
392			//CheckParameter(StatFileFormat,);
393			//CheckParameter(MixingRule,);
394			CheckParameter(OrthoBoxTolerance, isPositive());
395			CheckParameter(ThermIntDistSpringConst, isPositive());
396			CheckParameter(ThermIntThetaSpringConst, isPositive());
397			CheckParameter(ThermIntOmegaSpringConst, isPositive());
398	chrisfen	2415	CheckParameter(DampingAlpha,isNonNegative());
399	tim	2371	CheckParameter(SkinThickness, isPositive());
400
401	tim	2364	//@todo memory leak
402			if( have_err )
403			return strdup( err.c_str() );
404	gezelter	1490
405	tim	2364	return NULL;
406	gezelter	1490
407
408			}
409
410			int Globals::globalEnd( event* the_event ){
411
412			the_event->err_msg = checkMe();
413			if( the_event->err_msg != NULL ) return 0;
414
415			return 1;
416			}