src/brains/ForceField.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.
 */
 
/**
 * @file ForceField.cpp
 * @author tlin
 * @date 11/04/2004
 * @time 22:51am
 * @version 1.0
 */
  
#include <algorithm>
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
#include "utils/Tuple.hpp"
#include "UseTheForce/DarkSide/atype_interface.h"
#include "UseTheForce/DarkSide/fForceOptions_interface.h"
#include "UseTheForce/DarkSide/switcheroo_interface.h"
namespace oopse {

  ForceField::ForceField() { 
    char* tempPath; 
    tempPath = getenv("FORCE_PARAM_PATH");

    if (tempPath == NULL) {
      //convert a macro from compiler to a string in c++
      STR_DEFINE(ffPath_, FRC_PATH );
    } else {
      ffPath_ = tempPath;
    }
  }


  ForceField::~ForceField() {
    deleteAtypes();
    deleteSwitch();
  }

  AtomType* ForceField::getAtomType(const std::string &at) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.find(keys);
  }

  BondType* ForceField::getBondType(const std::string &at1, 
                                    const std::string &at2) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    

    //try exact match first
    BondType* bondType = bondTypeCont_.find(keys);
    if (bondType) {
      return bondType;
    } else {
      AtomType* atype1;
      AtomType* atype2;
      std::vector<std::string> at1key;
      at1key.push_back(at1);
      atype1 = atomTypeCont_.find(at1key);
  
      std::vector<std::string> at2key;
      at2key.push_back(at2);
      atype2 = atomTypeCont_.find(at2key);

      // query atom types for their chains of responsibility
      std::vector<AtomType*> at1Chain = atype1->allYourBase();
      std::vector<AtomType*> at2Chain = atype2->allYourBase();

      std::vector<AtomType*>::iterator i;
      std::vector<AtomType*>::iterator j;

      int ii = 0;
      int jj = 0;
      int bondTypeScore;

      std::vector<std::pair<int, std::vector<std::string> > > foundBonds;

      for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
        jj = 0;
        for (j = at2Chain.begin(); j != at2Chain.end(); j++) {

          bondTypeScore = ii + jj;

          std::vector<std::string> myKeys;
          myKeys.push_back((*i)->getName());
          myKeys.push_back((*j)->getName());

          BondType* bondType = bondTypeCont_.find(myKeys);
          if (bondType) {
            foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
          }
          jj++;
        }
        ii++;
      }


      if (foundBonds.size() > 0) {
        // sort the foundBonds by the score:
        std::sort(foundBonds.begin(), foundBonds.end());
     
        int bestScore = foundBonds[0].first;
        std::vector<std::string> theKeys = foundBonds[0].second;
        
        BondType* bestType = bondTypeCont_.find(theKeys);
        
        return bestType;
      } else {
        //if no exact match found, try wild card match
        return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
      }
    }
  }
  
  BendType* ForceField::getBendType(const std::string &at1, 
                                    const std::string &at2,
                                    const std::string &at3) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    

    //try exact match first
    BendType* bendType = bendTypeCont_.find(keys);
    if (bendType) {
      return bendType;
    } else {

      AtomType* atype1;
      AtomType* atype2;
      AtomType* atype3;
      std::vector<std::string> at1key;
      at1key.push_back(at1);
      atype1 = atomTypeCont_.find(at1key);
  
      std::vector<std::string> at2key;
      at2key.push_back(at2);
      atype2 = atomTypeCont_.find(at2key);

      std::vector<std::string> at3key;
      at3key.push_back(at3);
      atype3 = atomTypeCont_.find(at3key);

      // query atom types for their chains of responsibility
      std::vector<AtomType*> at1Chain = atype1->allYourBase();
      std::vector<AtomType*> at2Chain = atype2->allYourBase();
      std::vector<AtomType*> at3Chain = atype3->allYourBase();

      std::vector<AtomType*>::iterator i;
      std::vector<AtomType*>::iterator j;
      std::vector<AtomType*>::iterator k;

      int ii = 0;
      int jj = 0;
      int kk = 0;
      int IKscore;

      std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;

      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
        ii = 0;
        for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
          kk = 0;
          for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
          
            IKscore = ii + kk;

            std::vector<std::string> myKeys;
            myKeys.push_back((*i)->getName());
            myKeys.push_back((*j)->getName());
            myKeys.push_back((*k)->getName());

            BendType* bendType = bendTypeCont_.find(myKeys);
            if (bendType) { 
              foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
            }
            kk++;
          }
          ii++;
        }
        jj++;
      }
      
      if (foundBends.size() > 0) {
        std::sort(foundBends.begin(), foundBends.end());
        int jscore = foundBends[0].first;
        int ikscore = foundBends[0].second;
        std::vector<std::string> theKeys = foundBends[0].third;       
        
        BendType* bestType = bendTypeCont_.find(theKeys);  
        return bestType;
      } else {        
        //if no exact match found, try wild card match
        return bendTypeCont_.find(keys, wildCardAtomTypeName_);      
      }
    }
  }

  TorsionType* ForceField::getTorsionType(const std::string &at1, 
                                          const std::string &at2,
                                          const std::string &at3, 
                                          const std::string &at4) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    


    //try exact match first
    TorsionType* torsionType = torsionTypeCont_.find(keys);
    if (torsionType) {
      return torsionType;
    } else {

      AtomType* atype1;
      AtomType* atype2;
      AtomType* atype3;
      AtomType* atype4;
      std::vector<std::string> at1key;
      at1key.push_back(at1);
      atype1 = atomTypeCont_.find(at1key);
  
      std::vector<std::string> at2key;
      at2key.push_back(at2);
      atype2 = atomTypeCont_.find(at2key);

      std::vector<std::string> at3key;
      at3key.push_back(at3);
      atype3 = atomTypeCont_.find(at3key);

      std::vector<std::string> at4key;
      at4key.push_back(at4);
      atype4 = atomTypeCont_.find(at4key);

      // query atom types for their chains of responsibility
      std::vector<AtomType*> at1Chain = atype1->allYourBase();
      std::vector<AtomType*> at2Chain = atype2->allYourBase();
      std::vector<AtomType*> at3Chain = atype3->allYourBase();
      std::vector<AtomType*> at4Chain = atype4->allYourBase();

      std::vector<AtomType*>::iterator i;
      std::vector<AtomType*>::iterator j;
      std::vector<AtomType*>::iterator k;
      std::vector<AtomType*>::iterator l;

      int ii = 0;
      int jj = 0;
      int kk = 0;
      int ll = 0;
      int ILscore;
      int JKscore;

      std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;

      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
        kk = 0;
        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
          ii = 0;       
          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
            ll = 0;
            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
          
              ILscore = ii + ll;
              JKscore = jj + kk;

              std::vector<std::string> myKeys;
              myKeys.push_back((*i)->getName());
              myKeys.push_back((*j)->getName());
              myKeys.push_back((*k)->getName());
              myKeys.push_back((*l)->getName());

              TorsionType* torsionType = torsionTypeCont_.find(myKeys);
              if (torsionType) { 
                foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
              }
              ll++;
            }
            ii++;
          }
          kk++;
        }
        jj++;
      }
      
      if (foundTorsions.size() > 0) {
        std::sort(foundTorsions.begin(), foundTorsions.end());
        int jkscore = foundTorsions[0].first;
        int ilscore = foundTorsions[0].second;
        std::vector<std::string> theKeys = foundTorsions[0].third;
        
        TorsionType* bestType = torsionTypeCont_.find(theKeys);
        return bestType;
      } else {
        //if no exact match found, try wild card match
        return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
      }
    }
  }

  InversionType* ForceField::getInversionType(const std::string &at1, 
                                              const std::string &at2,
                                              const std::string &at3, 
                                              const std::string &at4) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    

    //try exact match first
    InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
    if (inversionType) {
      return inversionType;
    } else {
      
      AtomType* atype1;
      AtomType* atype2;
      AtomType* atype3;
      AtomType* atype4;
      std::vector<std::string> at1key;
      at1key.push_back(at1);
      atype1 = atomTypeCont_.find(at1key);
      
      std::vector<std::string> at2key;
      at2key.push_back(at2);
      atype2 = atomTypeCont_.find(at2key);
      
      std::vector<std::string> at3key;
      at3key.push_back(at3);
      atype3 = atomTypeCont_.find(at3key);
      
      std::vector<std::string> at4key;
      at4key.push_back(at4);
      atype4 = atomTypeCont_.find(at4key);

      // query atom types for their chains of responsibility
      std::vector<AtomType*> at1Chain = atype1->allYourBase();
      std::vector<AtomType*> at2Chain = atype2->allYourBase();
      std::vector<AtomType*> at3Chain = atype3->allYourBase();
      std::vector<AtomType*> at4Chain = atype4->allYourBase();

      std::vector<AtomType*>::iterator i;
      std::vector<AtomType*>::iterator j;
      std::vector<AtomType*>::iterator k;
      std::vector<AtomType*>::iterator l;

      int ii = 0;
      int jj = 0;
      int kk = 0;
      int ll = 0;
      int Iscore;
      int JKLscore;
      
      std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
      
      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
        kk = 0;
        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
          ii = 0;       
          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
            ll = 0;
            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
              
              Iscore = ii;
              JKLscore = jj + kk + ll;
              
              std::vector<std::string> myKeys;
              myKeys.push_back((*i)->getName());
              myKeys.push_back((*j)->getName());
              myKeys.push_back((*k)->getName());
              myKeys.push_back((*l)->getName());
              
              InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
              if (inversionType) { 
                foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
              }
              ll++;
            }
            ii++;
          }
          kk++;
        }
        jj++;
      }
         
      if (foundInversions.size() > 0) {
        std::sort(foundInversions.begin(), foundInversions.end());
        int iscore = foundInversions[0].first;
        int jklscore = foundInversions[0].second;
        std::vector<std::string> theKeys = foundInversions[0].third;
        
        InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
        return bestType;
      } else {
        //if no exact match found, try wild card match
        return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
      }
    }
  }
  
  NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    
    //try exact match first
    NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
    if (nbiType) {
      return nbiType;
    } else {
      //if no exact match found, try wild card match
      return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
    }    
  }
  
  BondType* ForceField::getExactBondType(const std::string &at1, 
                                         const std::string &at2){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.find(keys);
  }
  
  BendType* ForceField::getExactBendType(const std::string &at1, 
                                         const std::string &at2,
                                         const std::string &at3){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.find(keys);
  }
  
  TorsionType* ForceField::getExactTorsionType(const std::string &at1, 
                                               const std::string &at2,
                                               const std::string &at3, 
                                               const std::string &at4){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);   
    return torsionTypeCont_.find(keys);
  }
  
  InversionType* ForceField::getExactInversionType(const std::string &at1, 
                                                   const std::string &at2,
                                                   const std::string &at3, 
                                                   const std::string &at4){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);   
    return inversionTypeCont_.find(keys);
  }
  
  NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return nonBondedInteractionTypeCont_.find(keys);
  }
  

  bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.add(keys, atomType);
  }

  bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.replace(keys, atomType);
  }

  bool ForceField::addBondType(const std::string &at1, const std::string &at2,
                               BondType* bondType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.add(keys, bondType);    
  }
  
  bool ForceField::addBendType(const std::string &at1, const std::string &at2,
                               const std::string &at3, BendType* bendType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.add(keys, bendType);
  }
  
  bool ForceField::addTorsionType(const std::string &at1, 
                                  const std::string &at2,
                                  const std::string &at3, 
                                  const std::string &at4, 
                                  TorsionType* torsionType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    
    return torsionTypeCont_.add(keys, torsionType);
  }

  bool ForceField::addInversionType(const std::string &at1, 
                                    const std::string &at2,
                                    const std::string &at3, 
                                    const std::string &at4, 
                                    InversionType* inversionType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    
    return inversionTypeCont_.add(keys, inversionType);
  }
  
  bool ForceField::addNonBondedInteractionType(const std::string &at1, 
                                               const std::string &at2, 
                                               NonBondedInteractionType* nbiType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return nonBondedInteractionTypeCont_.add(keys, nbiType);
  }
  
  RealType ForceField::getRcutFromAtomType(AtomType* at) {
    /**@todo */
    GenericData* data;
    RealType rcut = 0.0;
    
    if (at->isLennardJones()) {
      data = at->getPropertyByName("LennardJones");
      if (data != NULL) {
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        
        if (ljData != NULL) {
          LJParam ljParam = ljData->getData();
          
          //by default use 2.5*sigma as cutoff radius
          rcut = 2.5 * ljParam.sigma;
          
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to LJParam\n");
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();          
        }            
      } else {
        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }
    return rcut;    
  }
  

  ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
    std::string forceFieldFilename(filename);
    ifstrstream* ffStream = new ifstrstream();
    
    //try to open the force filed file in current directory first    
    ffStream->open(forceFieldFilename.c_str());
    if(!ffStream->is_open()){

      forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
      ffStream->open( forceFieldFilename.c_str() );

      //if current directory does not contain the force field file,
      //try to open it in the path        
      if(!ffStream->is_open()){

        sprintf( painCave.errMsg,
                 "Error opening the force field parameter file:\n"
                 "\t%s\n"
                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
                 "variable?\n",
                 forceFieldFilename.c_str() );
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    }  
    return ffStream;
  }

  void ForceField::setFortranForceOptions(){
    ForceOptions theseFortranOptions;
    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
    setfForceOptions(&theseFortranOptions);
  }
} //end namespace oopse
Revision:	1303
Committed:	Mon Oct 13 21:35:22 2008 UTC (16 years, 6 months ago) by cli2
Original Path:	*trunk/src/UseTheForce/ForceField.cpp*
File size:	19562 byte(s)
Log Message:	Fixes for Inversions for use with Amber
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	507	/**
43			* @file ForceField.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49	gezelter	246
50	gezelter	1269	#include <algorithm>
51	gezelter	206	#include "UseTheForce/ForceField.hpp"
52	gezelter	246	#include "utils/simError.h"
53	gezelter	1269	#include "utils/Tuple.hpp"
54	tim	475	#include "UseTheForce/DarkSide/atype_interface.h"
55	chuckv	821	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56	gezelter	939	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	gezelter	246	namespace oopse {
58	gezelter	206
59	gezelter	507	ForceField::ForceField() {
60	gezelter	246	char* tempPath;
61			tempPath = getenv("FORCE_PARAM_PATH");
62	gezelter	206
63	gezelter	246	if (tempPath == NULL) {
64	gezelter	507	//convert a macro from compiler to a string in c++
65			STR_DEFINE(ffPath_, FRC_PATH );
66	gezelter	246	} else {
67	gezelter	507	ffPath_ = tempPath;
68	gezelter	246	}
69	gezelter	507	}
70	gezelter	206
71	tim	475
72	gezelter	507	ForceField::~ForceField() {
73	tim	475	deleteAtypes();
74	gezelter	939	deleteSwitch();
75	gezelter	507	}
76	tim	475
77	gezelter	507	AtomType* ForceField::getAtomType(const std::string &at) {
78	gezelter	246	std::vector<std::string> keys;
79			keys.push_back(at);
80			return atomTypeCont_.find(keys);
81	gezelter	507	}
82	gezelter	206
83	cpuglis	1195	BondType* ForceField::getBondType(const std::string &at1,
84			const std::string &at2) {
85	gezelter	246	std::vector<std::string> keys;
86			keys.push_back(at1);
87			keys.push_back(at2);
88	gezelter	206
89	gezelter	246	//try exact match first
90			BondType* bondType = bondTypeCont_.find(keys);
91			if (bondType) {
92	gezelter	507	return bondType;
93	gezelter	246	} else {
94	gezelter	1269	AtomType* atype1;
95			AtomType* atype2;
96			std::vector<std::string> at1key;
97			at1key.push_back(at1);
98			atype1 = atomTypeCont_.find(at1key);
99
100			std::vector<std::string> at2key;
101			at2key.push_back(at2);
102			atype2 = atomTypeCont_.find(at2key);
103
104			// query atom types for their chains of responsibility
105			std::vector<AtomType*> at1Chain = atype1->allYourBase();
106			std::vector<AtomType*> at2Chain = atype2->allYourBase();
107
108			std::vector<AtomType*>::iterator i;
109			std::vector<AtomType*>::iterator j;
110
111			int ii = 0;
112			int jj = 0;
113			int bondTypeScore;
114
115			std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
116
117			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
118			jj = 0;
119			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
120
121			bondTypeScore = ii + jj;
122
123			std::vector<std::string> myKeys;
124			myKeys.push_back((*i)->getName());
125			myKeys.push_back((*j)->getName());
126
127			BondType* bondType = bondTypeCont_.find(myKeys);
128			if (bondType) {
129			foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
130			}
131			jj++;
132			}
133			ii++;
134			}
135
136
137	gezelter	1277	if (foundBonds.size() > 0) {
138			// sort the foundBonds by the score:
139			std::sort(foundBonds.begin(), foundBonds.end());
140
141			int bestScore = foundBonds[0].first;
142			std::vector<std::string> theKeys = foundBonds[0].second;
143
144			BondType* bestType = bondTypeCont_.find(theKeys);
145
146			return bestType;
147			} else {
148			//if no exact match found, try wild card match
149			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
150	gezelter	1269	}
151	gezelter	246	}
152	gezelter	507	}
153	gezelter	1269
154	cpuglis	1195	BendType* ForceField::getBendType(const std::string &at1,
155			const std::string &at2,
156	gezelter	507	const std::string &at3) {
157	gezelter	246	std::vector<std::string> keys;
158			keys.push_back(at1);
159			keys.push_back(at2);
160			keys.push_back(at3);
161	gezelter	206
162	gezelter	246	//try exact match first
163			BendType* bendType = bendTypeCont_.find(keys);
164			if (bendType) {
165	gezelter	507	return bendType;
166	gezelter	246	} else {
167	gezelter	1269
168			AtomType* atype1;
169			AtomType* atype2;
170			AtomType* atype3;
171			std::vector<std::string> at1key;
172			at1key.push_back(at1);
173			atype1 = atomTypeCont_.find(at1key);
174
175			std::vector<std::string> at2key;
176			at2key.push_back(at2);
177			atype2 = atomTypeCont_.find(at2key);
178
179			std::vector<std::string> at3key;
180			at3key.push_back(at3);
181			atype3 = atomTypeCont_.find(at3key);
182
183			// query atom types for their chains of responsibility
184			std::vector<AtomType*> at1Chain = atype1->allYourBase();
185			std::vector<AtomType*> at2Chain = atype2->allYourBase();
186			std::vector<AtomType*> at3Chain = atype3->allYourBase();
187
188			std::vector<AtomType*>::iterator i;
189			std::vector<AtomType*>::iterator j;
190			std::vector<AtomType*>::iterator k;
191
192			int ii = 0;
193			int jj = 0;
194			int kk = 0;
195			int IKscore;
196
197			std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
198
199			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
200			ii = 0;
201			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
202			kk = 0;
203			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
204
205			IKscore = ii + kk;
206
207			std::vector<std::string> myKeys;
208			myKeys.push_back((*i)->getName());
209			myKeys.push_back((*j)->getName());
210			myKeys.push_back((*k)->getName());
211
212			BendType* bendType = bendTypeCont_.find(myKeys);
213			if (bendType) {
214			foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
215			}
216			kk++;
217			}
218			ii++;
219			}
220			jj++;
221			}
222
223	gezelter	1277	if (foundBends.size() > 0) {
224			std::sort(foundBends.begin(), foundBends.end());
225			int jscore = foundBends[0].first;
226			int ikscore = foundBends[0].second;
227	cli2	1289	std::vector<std::string> theKeys = foundBends[0].third;
228	gezelter	1277
229			BendType* bestType = bendTypeCont_.find(theKeys);
230			return bestType;
231			} else {
232	gezelter	1269	//if no exact match found, try wild card match
233			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
234			}
235	gezelter	246	}
236	gezelter	507	}
237	gezelter	206
238	cpuglis	1195	TorsionType* ForceField::getTorsionType(const std::string &at1,
239			const std::string &at2,
240			const std::string &at3,
241			const std::string &at4) {
242	gezelter	246	std::vector<std::string> keys;
243			keys.push_back(at1);
244			keys.push_back(at2);
245			keys.push_back(at3);
246			keys.push_back(at4);
247	gezelter	206
248	gezelter	1269
249			//try exact match first
250	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
251			if (torsionType) {
252	gezelter	507	return torsionType;
253	gezelter	246	} else {
254	gezelter	1269
255			AtomType* atype1;
256			AtomType* atype2;
257			AtomType* atype3;
258			AtomType* atype4;
259			std::vector<std::string> at1key;
260			at1key.push_back(at1);
261			atype1 = atomTypeCont_.find(at1key);
262
263			std::vector<std::string> at2key;
264			at2key.push_back(at2);
265			atype2 = atomTypeCont_.find(at2key);
266
267			std::vector<std::string> at3key;
268			at3key.push_back(at3);
269			atype3 = atomTypeCont_.find(at3key);
270
271			std::vector<std::string> at4key;
272			at4key.push_back(at4);
273			atype4 = atomTypeCont_.find(at4key);
274
275			// query atom types for their chains of responsibility
276			std::vector<AtomType*> at1Chain = atype1->allYourBase();
277			std::vector<AtomType*> at2Chain = atype2->allYourBase();
278			std::vector<AtomType*> at3Chain = atype3->allYourBase();
279			std::vector<AtomType*> at4Chain = atype4->allYourBase();
280
281			std::vector<AtomType*>::iterator i;
282			std::vector<AtomType*>::iterator j;
283			std::vector<AtomType*>::iterator k;
284			std::vector<AtomType*>::iterator l;
285
286			int ii = 0;
287			int jj = 0;
288			int kk = 0;
289			int ll = 0;
290			int ILscore;
291			int JKscore;
292
293			std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
294
295			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
296			kk = 0;
297			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
298			ii = 0;
299			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
300			ll = 0;
301			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
302
303			ILscore = ii + ll;
304			JKscore = jj + kk;
305
306			std::vector<std::string> myKeys;
307			myKeys.push_back((*i)->getName());
308			myKeys.push_back((*j)->getName());
309			myKeys.push_back((*k)->getName());
310			myKeys.push_back((*l)->getName());
311
312			TorsionType* torsionType = torsionTypeCont_.find(myKeys);
313			if (torsionType) {
314			foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
315			}
316			ll++;
317			}
318			ii++;
319			}
320			kk++;
321			}
322			jj++;
323			}
324
325	gezelter	1277	if (foundTorsions.size() > 0) {
326			std::sort(foundTorsions.begin(), foundTorsions.end());
327			int jkscore = foundTorsions[0].first;
328			int ilscore = foundTorsions[0].second;
329			std::vector<std::string> theKeys = foundTorsions[0].third;
330
331			TorsionType* bestType = torsionTypeCont_.find(theKeys);
332			return bestType;
333	gezelter	1269	} else {
334			//if no exact match found, try wild card match
335			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
336			}
337	gezelter	246	}
338	gezelter	507	}
339	gezelter	206
340	cli2	1275	InversionType* ForceField::getInversionType(const std::string &at1,
341			const std::string &at2,
342			const std::string &at3,
343			const std::string &at4) {
344			std::vector<std::string> keys;
345			keys.push_back(at1);
346			keys.push_back(at2);
347			keys.push_back(at3);
348			keys.push_back(at4);
349
350			//try exact match first
351	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
352	cli2	1275	if (inversionType) {
353			return inversionType;
354			} else {
355
356			AtomType* atype1;
357			AtomType* atype2;
358			AtomType* atype3;
359			AtomType* atype4;
360			std::vector<std::string> at1key;
361			at1key.push_back(at1);
362			atype1 = atomTypeCont_.find(at1key);
363
364			std::vector<std::string> at2key;
365			at2key.push_back(at2);
366			atype2 = atomTypeCont_.find(at2key);
367
368			std::vector<std::string> at3key;
369			at3key.push_back(at3);
370			atype3 = atomTypeCont_.find(at3key);
371
372			std::vector<std::string> at4key;
373			at4key.push_back(at4);
374			atype4 = atomTypeCont_.find(at4key);
375
376			// query atom types for their chains of responsibility
377			std::vector<AtomType*> at1Chain = atype1->allYourBase();
378			std::vector<AtomType*> at2Chain = atype2->allYourBase();
379			std::vector<AtomType*> at3Chain = atype3->allYourBase();
380			std::vector<AtomType*> at4Chain = atype4->allYourBase();
381
382			std::vector<AtomType*>::iterator i;
383			std::vector<AtomType*>::iterator j;
384			std::vector<AtomType*>::iterator k;
385			std::vector<AtomType*>::iterator l;
386
387			int ii = 0;
388			int jj = 0;
389			int kk = 0;
390			int ll = 0;
391			int Iscore;
392			int JKLscore;
393
394			std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
395
396			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
397			kk = 0;
398			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
399			ii = 0;
400			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
401			ll = 0;
402			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
403
404			Iscore = ii;
405			JKLscore = jj + kk + ll;
406
407			std::vector<std::string> myKeys;
408			myKeys.push_back((*i)->getName());
409			myKeys.push_back((*j)->getName());
410			myKeys.push_back((*k)->getName());
411			myKeys.push_back((*l)->getName());
412
413	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
414	cli2	1275	if (inversionType) {
415			foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
416			}
417			ll++;
418			}
419			ii++;
420			}
421			kk++;
422			}
423			jj++;
424			}
425	gezelter	1277
426			if (foundInversions.size() > 0) {
427			std::sort(foundInversions.begin(), foundInversions.end());
428			int iscore = foundInversions[0].first;
429			int jklscore = foundInversions[0].second;
430			std::vector<std::string> theKeys = foundInversions[0].third;
431
432	cli2	1303	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
433	gezelter	1277	return bestType;
434	cli2	1275	} else {
435			//if no exact match found, try wild card match
436			return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
437			}
438			}
439			}
440
441	chuckv	1151	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
442			std::vector<std::string> keys;
443			keys.push_back(at1);
444			keys.push_back(at2);
445	cpuglis	1195
446	chuckv	1151	//try exact match first
447			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
448			if (nbiType) {
449			return nbiType;
450			} else {
451			//if no exact match found, try wild card match
452			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
453	cpuglis	1195	}
454	chuckv	1151	}
455	cpuglis	1195
456			BondType* ForceField::getExactBondType(const std::string &at1,
457			const std::string &at2){
458	gezelter	246	std::vector<std::string> keys;
459			keys.push_back(at1);
460			keys.push_back(at2);
461			return bondTypeCont_.find(keys);
462	gezelter	507	}
463	cpuglis	1195
464			BendType* ForceField::getExactBendType(const std::string &at1,
465			const std::string &at2,
466	gezelter	507	const std::string &at3){
467	gezelter	246	std::vector<std::string> keys;
468			keys.push_back(at1);
469			keys.push_back(at2);
470			keys.push_back(at3);
471			return bendTypeCont_.find(keys);
472	gezelter	507	}
473	cpuglis	1195
474			TorsionType* ForceField::getExactTorsionType(const std::string &at1,
475			const std::string &at2,
476			const std::string &at3,
477			const std::string &at4){
478	gezelter	246	std::vector<std::string> keys;
479			keys.push_back(at1);
480			keys.push_back(at2);
481			keys.push_back(at3);
482			keys.push_back(at4);
483			return torsionTypeCont_.find(keys);
484	gezelter	507	}
485	cli2	1275
486			InversionType* ForceField::getExactInversionType(const std::string &at1,
487			const std::string &at2,
488			const std::string &at3,
489			const std::string &at4){
490			std::vector<std::string> keys;
491			keys.push_back(at1);
492			keys.push_back(at2);
493			keys.push_back(at3);
494			keys.push_back(at4);
495			return inversionTypeCont_.find(keys);
496			}
497
498	chuckv	1151	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
499			std::vector<std::string> keys;
500			keys.push_back(at1);
501			keys.push_back(at2);
502			return nonBondedInteractionTypeCont_.find(keys);
503			}
504	cli2	1275
505	chuckv	1151
506	gezelter	507	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
507	gezelter	246	std::vector<std::string> keys;
508			keys.push_back(at);
509			return atomTypeCont_.add(keys, atomType);
510	gezelter	507	}
511	gezelter	206
512	gezelter	1282	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
513			std::vector<std::string> keys;
514			keys.push_back(at);
515			return atomTypeCont_.replace(keys, atomType);
516			}
517
518	cpuglis	1195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
519			BondType* bondType) {
520	gezelter	246	std::vector<std::string> keys;
521			keys.push_back(at1);
522			keys.push_back(at2);
523	cpuglis	1195	return bondTypeCont_.add(keys, bondType);
524	gezelter	507	}
525	cpuglis	1195
526	gezelter	507	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
527			const std::string &at3, BendType* bendType) {
528	gezelter	246	std::vector<std::string> keys;
529			keys.push_back(at1);
530			keys.push_back(at2);
531			keys.push_back(at3);
532			return bendTypeCont_.add(keys, bendType);
533	gezelter	507	}
534	cpuglis	1195
535			bool ForceField::addTorsionType(const std::string &at1,
536			const std::string &at2,
537			const std::string &at3,
538			const std::string &at4,
539			TorsionType* torsionType) {
540	gezelter	246	std::vector<std::string> keys;
541			keys.push_back(at1);
542			keys.push_back(at2);
543			keys.push_back(at3);
544			keys.push_back(at4);
545			return torsionTypeCont_.add(keys, torsionType);
546	gezelter	507	}
547	gezelter	206
548	cli2	1275	bool ForceField::addInversionType(const std::string &at1,
549			const std::string &at2,
550			const std::string &at3,
551			const std::string &at4,
552			InversionType* inversionType) {
553			std::vector<std::string> keys;
554			keys.push_back(at1);
555			keys.push_back(at2);
556			keys.push_back(at3);
557			keys.push_back(at4);
558			return inversionTypeCont_.add(keys, inversionType);
559			}
560
561	cpuglis	1195	bool ForceField::addNonBondedInteractionType(const std::string &at1,
562			const std::string &at2,
563			NonBondedInteractionType* nbiType) {
564	chuckv	1151	std::vector<std::string> keys;
565			keys.push_back(at1);
566			keys.push_back(at2);
567			return nonBondedInteractionTypeCont_.add(keys, nbiType);
568			}
569	cpuglis	1195
570	tim	963	RealType ForceField::getRcutFromAtomType(AtomType* at) {
571	gezelter	246	/*@todo /
572			GenericData* data;
573	tim	963	RealType rcut = 0.0;
574	cpuglis	1195
575	gezelter	246	if (at->isLennardJones()) {
576	gezelter	507	data = at->getPropertyByName("LennardJones");
577			if (data != NULL) {
578			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
579	cpuglis	1195
580	gezelter	507	if (ljData != NULL) {
581			LJParam ljParam = ljData->getData();
582	cpuglis	1195
583	gezelter	507	//by default use 2.5*sigma as cutoff radius
584			rcut = 2.5 * ljParam.sigma;
585	cpuglis	1195
586	gezelter	507	} else {
587			sprintf( painCave.errMsg,
588			"Can not cast GenericData to LJParam\n");
589			painCave.severity = OOPSE_ERROR;
590			painCave.isFatal = 1;
591			simError();
592			}
593			} else {
594			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
595			painCave.severity = OOPSE_ERROR;
596			painCave.isFatal = 1;
597			simError();
598			}
599	gezelter	246	}
600			return rcut;
601	gezelter	507	}
602	cpuglis	1195
603	gezelter	206
604	gezelter	507	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
605	gezelter	246	std::string forceFieldFilename(filename);
606			ifstrstream* ffStream = new ifstrstream();
607
608			//try to open the force filed file in current directory first
609			ffStream->open(forceFieldFilename.c_str());
610			if(!ffStream->is_open()){
611
612	gezelter	507	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
613			ffStream->open( forceFieldFilename.c_str() );
614	gezelter	246
615	gezelter	507	//if current directory does not contain the force field file,
616			//try to open it in the path
617			if(!ffStream->is_open()){
618	gezelter	246
619	gezelter	507	sprintf( painCave.errMsg,
620			"Error opening the force field parameter file:\n"
621			"\t%s\n"
622			"\tHave you tried setting the FORCE_PARAM_PATH environment "
623			"variable?\n",
624			forceFieldFilename.c_str() );
625			painCave.severity = OOPSE_ERROR;
626			painCave.isFatal = 1;
627			simError();
628			}
629	gezelter	246	}
630			return ffStream;
631	gezelter	507	}
632	gezelter	246
633	chuckv	821	void ForceField::setFortranForceOptions(){
634			ForceOptions theseFortranOptions;
635			forceFieldOptions_.makeFortranOptions(theseFortranOptions);
636			setfForceOptions(&theseFortranOptions);
637			}
638	gezelter	246	} //end namespace oopse