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())) std::cout <<"Error in parsing " << NAME.getKeyword() << " : "<< (CONSTRAINT).getConstraintDescription() << std::endl; }                 


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(CutoffPolicy, "cutoffPolicy");
  DefineOptionalParameter(StatFileFormat, "statFileFormat");    
  
  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", 1.5);
  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
  DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
  
}

int Globals::globalAssign( event* the_event ){
  
  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;

  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(the_event->err_msg, "Error in parsing %s: expect %s, but get %s.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.sval);
       }
    } else if( the_type == DOUBLE ){
      result = i->second->setData(the_event->evt.asmt.rhs.dval);
       if (!result )
         sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %f.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.dval );
    }      
    else if (the_type == INT ){
      result = i->second->setData(the_event->evt.asmt.rhs.ival);
       if (!result )
         sprintf(the_event->err_msg,  "Error in parsing %s: expect %s, but get %d.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.ival );
      
    } else {
        sprintf(the_event->err_msg,  "%s is an unrecognized keyword\n", keyword.c_str() );
    }
  }

  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("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
  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,isPositive());
  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:	2372
Committed:	Mon Oct 17 00:51:16 2005 UTC (18 years, 9 months ago) by tim
File size:	16177 byte(s)
Log Message:	Change error message in Globals
#	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			if (!NAME.empty()) { if (!(CONSTRAINT)(NAME.getData())) std::cout <<"Error in parsing " << NAME.getKeyword() << " : "<< (CONSTRAINT).getConstraintDescription() << std::endl; }
69
70
71	gezelter	1490	Globals::Globals(){
72	tim	2364
73			DefineParameter(ForceField, "forceField")
74			DefineParameter(NComponents, "nComponents")
75
76			DefineOptionalParameter(TargetTemp, "targetTemp");
77			DefineOptionalParameter(Ensemble, "ensemble");
78			DefineOptionalParameter(Dt, "dt");
79			DefineOptionalParameter(RunTime, "runTime");
80			DefineOptionalParameter(InitialConfig, "initialConfig");
81			DefineOptionalParameter(FinalConfig, "finalConfig");
82			DefineOptionalParameter(NMol, "nMol");
83			DefineOptionalParameter(Density, "density");
84			DefineOptionalParameter(Box, "box");
85			DefineOptionalParameter(BoxX, "boxX");
86			DefineOptionalParameter(BoxY, "boxY");
87			DefineOptionalParameter(BoxZ, "boxZ");
88			DefineOptionalParameter(SampleTime, "sampleTime");
89			DefineOptionalParameter(ResetTime, "resetTime");
90			DefineOptionalParameter(StatusTime, "statusTime");
91			DefineOptionalParameter(CutoffRadius, "cutoffRadius");
92			DefineOptionalParameter(SwitchingRadius, "switchingRadius");
93			DefineOptionalParameter(Dielectric, "dielectric");
94			DefineOptionalParameter(TempSet, "tempSet");
95			DefineOptionalParameter(ThermalTime, "thermalTime");
96			DefineOptionalParameter(TargetPressure, "targetPressure");
97			DefineOptionalParameter(TauThermostat, "tauThermostat");
98			DefineOptionalParameter(TauBarostat, "tauBarostat");
99			DefineOptionalParameter(ZconsTime, "zconsTime");
100			DefineOptionalParameter(NZconstraints, "nZconstraints");
101			DefineOptionalParameter(ZconsTol, "zconsTol");
102			DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
103			DefineOptionalParameter(Seed, "seed");
104			DefineOptionalParameter(Minimizer, "minimizer");
105			DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
106			DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
107			DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
108			DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
109			DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
110			DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
111			DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
112			DefineOptionalParameter(ZconsGap, "zconsGap");
113			DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
114			DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
115			DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
116			DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
117			DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
118			DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
119			DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
120			DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
121			DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
122			DefineOptionalParameter(SurfaceTension, "surfaceTension");
123			DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
124			DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
125			DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
126			DefineOptionalParameter(StatFileFormat, "statFileFormat");
127
128			DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
129			DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
130			DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
131			DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
132			DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
133			DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
134			DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
135	chrisfen	2365	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
136			DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
137			DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
138	tim	2364	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
139			DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
140			DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
141
142	gezelter	1490	}
143
144	tim	2364	int Globals::globalAssign( event* the_event ){
145	gezelter	1490
146	tim	2364	int key;
147			interface_assign_type the_type = the_event->evt.asmt.asmt_type;
148			char* lhs = the_event->evt.asmt.lhs;
149			std::string keyword(lhs);
150	chrisfen	2101
151	tim	2372	bool result = false;
152	gezelter	1490
153	tim	2364	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	tim	2372	sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %s.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.sval);
159	tim	2364	}
160			} else if( the_type == DOUBLE ){
161			result = i->second->setData(the_event->evt.asmt.rhs.dval);
162			if (!result )
163	tim	2372	sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %f.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.dval );
164	tim	2364	}
165			else if (the_type == INT ){
166			result = i->second->setData(the_event->evt.asmt.rhs.ival);
167			if (!result )
168	tim	2372	sprintf(the_event->err_msg, "Error in parsing %s: expect %s, but get %d.\n", keyword.c_str(), i->second->getParamType(), the_event->evt.asmt.rhs.ival );
169	tim	2364
170			} else {
171	tim	2372	sprintf(the_event->err_msg, "%s is an unrecognized keyword\n", keyword.c_str() );
172	tim	2364	}
173			}
174
175			if (keyword == "nComponents" && getNComponents() > 0) {
176			components = new Component*[getNComponents()];
177			}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
178			zConstraints = new ZconStamp*[getNZconstraints()];
179			}
180	gezelter	1490
181	tim	2364	return result;
182	gezelter	1490	}
183
184			int Globals::newComponent( event* the_event ){
185
186			current_component = new Component;
187			int index = the_event->evt.blk_index;
188			char err[200];
189
190	tim	2364	if( haveNComponents() && index < getNComponents() )
191	gezelter	1490	components[index] = current_component;
192			else{
193	tim	2364	if( haveNComponents() ){
194	gezelter	1490	sprintf( err, "meta-data parsing error: %d out of nComponents range",
195			index );
196			the_event->err_msg = strdup( err );
197			return 0;
198			}
199			else{
200			the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
201			" first component declaration." );
202			return 0;
203			}
204			}
205
206			return 1;
207			}
208
209
210
211			int Globals::componentAssign( event* the_event ){
212
213			switch( the_event->evt.asmt.asmt_type ){
214
215			case STRING:
216			return current_component->assignString( the_event->evt.asmt.lhs,
217			the_event->evt.asmt.rhs.sval,
218			&(the_event->err_msg));
219			break;
220
221			case DOUBLE:
222			return current_component->assignDouble( the_event->evt.asmt.lhs,
223			the_event->evt.asmt.rhs.dval,
224			&(the_event->err_msg));
225			break;
226
227			case INT:
228			return current_component->assignInt( the_event->evt.asmt.lhs,
229			the_event->evt.asmt.rhs.ival,
230			&(the_event->err_msg));
231			break;
232
233			default:
234			the_event->err_msg = strdup( "Globals error. Invalid component"
235			" assignment type" );
236			return 0;
237			break;
238			}
239			return 0;
240			}
241
242			int Globals::componentEnd( event* the_event ){
243
244			the_event->err_msg = current_component->checkMe();
245			if( the_event->err_msg != NULL ) return 0;
246
247			return 1;
248			}
249
250			int Globals::newZconstraint( event* the_event ){
251
252
253			int index = the_event->evt.blk_index;
254			char err[200];
255			current_zConstraint = new ZconStamp( index );
256
257	tim	2364	if( haveNZconstraints() && index < getNZconstraints() )
258	gezelter	1490	zConstraints[index] = current_zConstraint;
259			else{
260	tim	2364	if( haveNZconstraints() ){
261	gezelter	1490	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
262			index );
263			the_event->err_msg = strdup( err );
264			return 0;
265			}
266			else{
267			the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
268			" not given before"
269			" first zConstraint declaration." );
270			return 0;
271			}
272			}
273	tim	2364
274	gezelter	1490	return 1;
275			}
276
277
278
279			int Globals::zConstraintAssign( event* the_event ){
280
281			switch( the_event->evt.asmt.asmt_type ){
282
283			case STRING:
284			return current_zConstraint->assignString( the_event->evt.asmt.lhs,
285			the_event->evt.asmt.rhs.sval,
286			&(the_event->err_msg));
287			break;
288
289			case DOUBLE:
290			return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
291			the_event->evt.asmt.rhs.dval,
292			&(the_event->err_msg));
293			break;
294
295			case INT:
296			return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
297			the_event->evt.asmt.rhs.ival,
298			&(the_event->err_msg));
299			break;
300
301			default:
302			the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
303			" assignment type" );
304			return 0;
305			break;
306			}
307			return 0;
308			}
309
310			int Globals::zConstraintEnd( event* the_event ){
311
312			the_event->err_msg = current_zConstraint->checkMe();
313			if( the_event->err_msg != NULL ) return 0;
314
315			return 1;
316			}
317
318	tim	2364	char* Globals::checkMe( void ){
319	tim	2109
320	gezelter	1490
321	tim	2364	std::string err("The following required keywords are missing:\n");
322			short int have_err = 0;
323	gezelter	1490
324	tim	2364	ParamMap::iterator i;
325			for (i = parameters_.begin(); i != parameters_.end(); ++i) {
326			if (!i->second->isOptional() && i->second->empty()) {
327			err += i->second->getKeyword() + "\n";
328	gezelter	1490	}
329			}
330
331	tim	2371	CheckParameter(ForceField, isNotEmpty());
332			CheckParameter(NComponents,isPositive());
333			CheckParameter(TargetTemp, isPositive());
334			CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) \|\| isEqualIgnoreCase(std::string("NVT")) \|\|
335			isEqualIgnoreCase(std::string("NPTi")) \|\| isEqualIgnoreCase(std::string("NPTf"))\|\|
336			isEqualIgnoreCase(std::string("NPTxyz")) );
337
338			CheckParameter(Dt, isPositive());
339			CheckParameter(RunTime, isPositive());
340			CheckParameter(InitialConfig, isNotEmpty());
341			CheckParameter(FinalConfig, isNotEmpty());
342			CheckParameter(NMol, isPositive());
343			CheckParameter(Density, isPositive());
344			CheckParameter(Box, isPositive());
345			CheckParameter(BoxX, isPositive());
346			CheckParameter(BoxY, isPositive());
347			CheckParameter(BoxZ, isPositive());
348			CheckParameter(SampleTime, isNonNegative());
349			CheckParameter(ResetTime, isNonNegative());
350			CheckParameter(StatusTime, isNonNegative());
351			CheckParameter(CutoffRadius, isPositive());
352			CheckParameter(SwitchingRadius, isNonNegative());
353			CheckParameter(Dielectric, isPositive());
354			CheckParameter(ThermalTime, isNonNegative());
355			CheckParameter(TargetPressure, isPositive());
356			CheckParameter(TauThermostat, isPositive());
357			CheckParameter(TauBarostat, isPositive());
358			CheckParameter(ZconsTime, isPositive());
359			CheckParameter(NZconstraints, isPositive());
360			CheckParameter(ZconsTol, isPositive());
361			//CheckParameter(ZconsForcePolicy,);
362			CheckParameter(Seed, isPositive());
363			CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) \|\| isEqualIgnoreCase(std::string("CG")));
364			CheckParameter(MinimizerMaxIter, isPositive());
365			CheckParameter(MinimizerWriteFrq, isPositive());
366			CheckParameter(MinimizerStepSize, isPositive());
367			CheckParameter(MinimizerFTol, isPositive());
368			CheckParameter(MinimizerGTol, isPositive());
369			CheckParameter(MinimizerLSTol, isPositive());
370			CheckParameter(MinimizerLSMaxIter, isPositive());
371			CheckParameter(ZconsGap, isPositive());
372			CheckParameter(ZconsFixtime, isPositive());
373			CheckParameter(ThermodynamicIntegrationLambda, isPositive());
374			CheckParameter(ThermodynamicIntegrationK, isPositive());
375			CheckParameter(ForceFieldVariant, isNotEmpty());
376			CheckParameter(ForceFieldFileName, isNotEmpty());
377			CheckParameter(ThermIntDistSpringConst, isPositive());
378			CheckParameter(ThermIntThetaSpringConst, isPositive());
379			CheckParameter(ThermIntOmegaSpringConst, isPositive());
380			CheckParameter(SurfaceTension, isPositive());
381			CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) \|\| isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) \|\| isEqualIgnoreCase(std::string("DAMPED_WOLF")) \|\| isEqualIgnoreCase(std::string("REACTION_FIELD")) );
382			CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) \|\| isEqualIgnoreCase(std::string("MAX")) \|\| isEqualIgnoreCase(std::string("TRADITIONAL")));
383			//CheckParameter(StatFileFormat,);
384			//CheckParameter(MixingRule,);
385			CheckParameter(OrthoBoxTolerance, isPositive());
386			CheckParameter(ThermIntDistSpringConst, isPositive());
387			CheckParameter(ThermIntThetaSpringConst, isPositive());
388			CheckParameter(ThermIntOmegaSpringConst, isPositive());
389			CheckParameter(DampingAlpha,isPositive());
390			CheckParameter(SkinThickness, isPositive());
391
392	tim	2364	//@todo memory leak
393			if( have_err )
394			return strdup( err.c_str() );
395	gezelter	1490
396	tim	2364	return NULL;
397	gezelter	1490
398
399			}
400
401			int Globals::globalEnd( event* the_event ){
402
403			the_event->err_msg = checkMe();
404			if( the_event->err_msg != NULL ) return 0;
405
406			return 1;
407			}