src/UseTheForce/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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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"
namespace OpenMD {

  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;
    }
  }

  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 = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }            
      } else {
        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
        painCave.severity = OPENMD_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 = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    }  
    return ffStream;
  }

} //end namespace OpenMD
Revision:	1532
Committed:	Wed Dec 29 19:59:21 2010 UTC (14 years, 4 months ago) by gezelter
File size:	19179 byte(s)
Log Message:	Added MAW to the C++ side, removed a whole bunch more fortran.
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
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	gezelter	1390	namespace OpenMD {
55	gezelter	206
56	gezelter	507	ForceField::ForceField() {
57	gezelter	1460
58	gezelter	246	char* tempPath;
59			tempPath = getenv("FORCE_PARAM_PATH");
60	gezelter	1460
61	gezelter	246	if (tempPath == NULL) {
62	gezelter	1460	//convert a macro from compiler to a string in c++
63			STR_DEFINE(ffPath_, FRC_PATH );
64	gezelter	246	} else {
65	gezelter	507	ffPath_ = tempPath;
66	gezelter	246	}
67	gezelter	507	}
68	gezelter	206
69	gezelter	507	AtomType* ForceField::getAtomType(const std::string &at) {
70	gezelter	246	std::vector<std::string> keys;
71			keys.push_back(at);
72			return atomTypeCont_.find(keys);
73	gezelter	507	}
74	gezelter	206
75	cpuglis	1195	BondType* ForceField::getBondType(const std::string &at1,
76			const std::string &at2) {
77	gezelter	246	std::vector<std::string> keys;
78			keys.push_back(at1);
79			keys.push_back(at2);
80	gezelter	206
81	gezelter	246	//try exact match first
82			BondType* bondType = bondTypeCont_.find(keys);
83			if (bondType) {
84	gezelter	507	return bondType;
85	gezelter	246	} else {
86	gezelter	1269	AtomType* atype1;
87			AtomType* atype2;
88			std::vector<std::string> at1key;
89			at1key.push_back(at1);
90			atype1 = atomTypeCont_.find(at1key);
91
92			std::vector<std::string> at2key;
93			at2key.push_back(at2);
94			atype2 = atomTypeCont_.find(at2key);
95
96			// query atom types for their chains of responsibility
97			std::vector<AtomType*> at1Chain = atype1->allYourBase();
98			std::vector<AtomType*> at2Chain = atype2->allYourBase();
99
100			std::vector<AtomType*>::iterator i;
101			std::vector<AtomType*>::iterator j;
102
103			int ii = 0;
104			int jj = 0;
105			int bondTypeScore;
106
107			std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
108
109			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
110			jj = 0;
111			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
112
113			bondTypeScore = ii + jj;
114
115			std::vector<std::string> myKeys;
116			myKeys.push_back((*i)->getName());
117			myKeys.push_back((*j)->getName());
118
119			BondType* bondType = bondTypeCont_.find(myKeys);
120			if (bondType) {
121			foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
122			}
123			jj++;
124			}
125			ii++;
126			}
127
128
129	gezelter	1277	if (foundBonds.size() > 0) {
130			// sort the foundBonds by the score:
131			std::sort(foundBonds.begin(), foundBonds.end());
132
133			int bestScore = foundBonds[0].first;
134			std::vector<std::string> theKeys = foundBonds[0].second;
135
136			BondType* bestType = bondTypeCont_.find(theKeys);
137
138			return bestType;
139			} else {
140			//if no exact match found, try wild card match
141			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
142	gezelter	1269	}
143	gezelter	246	}
144	gezelter	507	}
145	gezelter	1269
146	cpuglis	1195	BendType* ForceField::getBendType(const std::string &at1,
147			const std::string &at2,
148	gezelter	507	const std::string &at3) {
149	gezelter	246	std::vector<std::string> keys;
150			keys.push_back(at1);
151			keys.push_back(at2);
152			keys.push_back(at3);
153	gezelter	206
154	gezelter	246	//try exact match first
155			BendType* bendType = bendTypeCont_.find(keys);
156			if (bendType) {
157	gezelter	507	return bendType;
158	gezelter	246	} else {
159	gezelter	1269
160			AtomType* atype1;
161			AtomType* atype2;
162			AtomType* atype3;
163			std::vector<std::string> at1key;
164			at1key.push_back(at1);
165			atype1 = atomTypeCont_.find(at1key);
166
167			std::vector<std::string> at2key;
168			at2key.push_back(at2);
169			atype2 = atomTypeCont_.find(at2key);
170
171			std::vector<std::string> at3key;
172			at3key.push_back(at3);
173			atype3 = atomTypeCont_.find(at3key);
174
175			// query atom types for their chains of responsibility
176			std::vector<AtomType*> at1Chain = atype1->allYourBase();
177			std::vector<AtomType*> at2Chain = atype2->allYourBase();
178			std::vector<AtomType*> at3Chain = atype3->allYourBase();
179
180			std::vector<AtomType*>::iterator i;
181			std::vector<AtomType*>::iterator j;
182			std::vector<AtomType*>::iterator k;
183
184			int ii = 0;
185			int jj = 0;
186			int kk = 0;
187			int IKscore;
188
189			std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
190
191			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
192			ii = 0;
193			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
194			kk = 0;
195			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
196
197			IKscore = ii + kk;
198
199			std::vector<std::string> myKeys;
200			myKeys.push_back((*i)->getName());
201			myKeys.push_back((*j)->getName());
202			myKeys.push_back((*k)->getName());
203
204			BendType* bendType = bendTypeCont_.find(myKeys);
205			if (bendType) {
206			foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
207			}
208			kk++;
209			}
210			ii++;
211			}
212			jj++;
213			}
214
215	gezelter	1277	if (foundBends.size() > 0) {
216			std::sort(foundBends.begin(), foundBends.end());
217			int jscore = foundBends[0].first;
218			int ikscore = foundBends[0].second;
219	cli2	1289	std::vector<std::string> theKeys = foundBends[0].third;
220	gezelter	1277
221			BendType* bestType = bendTypeCont_.find(theKeys);
222			return bestType;
223			} else {
224	gezelter	1269	//if no exact match found, try wild card match
225			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
226			}
227	gezelter	246	}
228	gezelter	507	}
229	gezelter	206
230	cpuglis	1195	TorsionType* ForceField::getTorsionType(const std::string &at1,
231			const std::string &at2,
232			const std::string &at3,
233			const std::string &at4) {
234	gezelter	246	std::vector<std::string> keys;
235			keys.push_back(at1);
236			keys.push_back(at2);
237			keys.push_back(at3);
238			keys.push_back(at4);
239	gezelter	206
240	gezelter	1269
241			//try exact match first
242	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
243			if (torsionType) {
244	gezelter	507	return torsionType;
245	gezelter	246	} else {
246	gezelter	1269
247			AtomType* atype1;
248			AtomType* atype2;
249			AtomType* atype3;
250			AtomType* atype4;
251			std::vector<std::string> at1key;
252			at1key.push_back(at1);
253			atype1 = atomTypeCont_.find(at1key);
254
255			std::vector<std::string> at2key;
256			at2key.push_back(at2);
257			atype2 = atomTypeCont_.find(at2key);
258
259			std::vector<std::string> at3key;
260			at3key.push_back(at3);
261			atype3 = atomTypeCont_.find(at3key);
262
263			std::vector<std::string> at4key;
264			at4key.push_back(at4);
265			atype4 = atomTypeCont_.find(at4key);
266
267			// query atom types for their chains of responsibility
268			std::vector<AtomType*> at1Chain = atype1->allYourBase();
269			std::vector<AtomType*> at2Chain = atype2->allYourBase();
270			std::vector<AtomType*> at3Chain = atype3->allYourBase();
271			std::vector<AtomType*> at4Chain = atype4->allYourBase();
272
273			std::vector<AtomType*>::iterator i;
274			std::vector<AtomType*>::iterator j;
275			std::vector<AtomType*>::iterator k;
276			std::vector<AtomType*>::iterator l;
277
278			int ii = 0;
279			int jj = 0;
280			int kk = 0;
281			int ll = 0;
282			int ILscore;
283			int JKscore;
284
285			std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
286
287			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
288			kk = 0;
289			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
290			ii = 0;
291			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
292			ll = 0;
293			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
294
295			ILscore = ii + ll;
296			JKscore = jj + kk;
297
298			std::vector<std::string> myKeys;
299			myKeys.push_back((*i)->getName());
300			myKeys.push_back((*j)->getName());
301			myKeys.push_back((*k)->getName());
302			myKeys.push_back((*l)->getName());
303
304			TorsionType* torsionType = torsionTypeCont_.find(myKeys);
305			if (torsionType) {
306			foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
307			}
308			ll++;
309			}
310			ii++;
311			}
312			kk++;
313			}
314			jj++;
315			}
316
317	gezelter	1277	if (foundTorsions.size() > 0) {
318			std::sort(foundTorsions.begin(), foundTorsions.end());
319			int jkscore = foundTorsions[0].first;
320			int ilscore = foundTorsions[0].second;
321			std::vector<std::string> theKeys = foundTorsions[0].third;
322
323			TorsionType* bestType = torsionTypeCont_.find(theKeys);
324			return bestType;
325	gezelter	1269	} else {
326			//if no exact match found, try wild card match
327			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
328			}
329	gezelter	246	}
330	gezelter	507	}
331	gezelter	206
332	cli2	1275	InversionType* ForceField::getInversionType(const std::string &at1,
333			const std::string &at2,
334			const std::string &at3,
335			const std::string &at4) {
336			std::vector<std::string> keys;
337			keys.push_back(at1);
338			keys.push_back(at2);
339			keys.push_back(at3);
340			keys.push_back(at4);
341
342			//try exact match first
343	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
344	cli2	1275	if (inversionType) {
345			return inversionType;
346			} else {
347
348			AtomType* atype1;
349			AtomType* atype2;
350			AtomType* atype3;
351			AtomType* atype4;
352			std::vector<std::string> at1key;
353			at1key.push_back(at1);
354			atype1 = atomTypeCont_.find(at1key);
355
356			std::vector<std::string> at2key;
357			at2key.push_back(at2);
358			atype2 = atomTypeCont_.find(at2key);
359
360			std::vector<std::string> at3key;
361			at3key.push_back(at3);
362			atype3 = atomTypeCont_.find(at3key);
363
364			std::vector<std::string> at4key;
365			at4key.push_back(at4);
366			atype4 = atomTypeCont_.find(at4key);
367
368			// query atom types for their chains of responsibility
369			std::vector<AtomType*> at1Chain = atype1->allYourBase();
370			std::vector<AtomType*> at2Chain = atype2->allYourBase();
371			std::vector<AtomType*> at3Chain = atype3->allYourBase();
372			std::vector<AtomType*> at4Chain = atype4->allYourBase();
373
374			std::vector<AtomType*>::iterator i;
375			std::vector<AtomType*>::iterator j;
376			std::vector<AtomType*>::iterator k;
377			std::vector<AtomType*>::iterator l;
378
379			int ii = 0;
380			int jj = 0;
381			int kk = 0;
382			int ll = 0;
383			int Iscore;
384			int JKLscore;
385
386			std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
387
388			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
389			kk = 0;
390			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
391			ii = 0;
392			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
393			ll = 0;
394			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
395
396			Iscore = ii;
397			JKLscore = jj + kk + ll;
398
399			std::vector<std::string> myKeys;
400			myKeys.push_back((*i)->getName());
401			myKeys.push_back((*j)->getName());
402			myKeys.push_back((*k)->getName());
403			myKeys.push_back((*l)->getName());
404
405	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
406	cli2	1275	if (inversionType) {
407			foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
408			}
409			ll++;
410			}
411			ii++;
412			}
413			kk++;
414			}
415			jj++;
416			}
417	gezelter	1277
418			if (foundInversions.size() > 0) {
419			std::sort(foundInversions.begin(), foundInversions.end());
420			int iscore = foundInversions[0].first;
421			int jklscore = foundInversions[0].second;
422			std::vector<std::string> theKeys = foundInversions[0].third;
423
424	cli2	1303	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
425	gezelter	1277	return bestType;
426	cli2	1275	} else {
427			//if no exact match found, try wild card match
428			return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
429			}
430			}
431			}
432
433	chuckv	1151	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
434			std::vector<std::string> keys;
435			keys.push_back(at1);
436			keys.push_back(at2);
437	cpuglis	1195
438	chuckv	1151	//try exact match first
439			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
440			if (nbiType) {
441			return nbiType;
442			} else {
443			//if no exact match found, try wild card match
444			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
445	cpuglis	1195	}
446	chuckv	1151	}
447	cpuglis	1195
448			BondType* ForceField::getExactBondType(const std::string &at1,
449			const std::string &at2){
450	gezelter	246	std::vector<std::string> keys;
451			keys.push_back(at1);
452			keys.push_back(at2);
453			return bondTypeCont_.find(keys);
454	gezelter	507	}
455	cpuglis	1195
456			BendType* ForceField::getExactBendType(const std::string &at1,
457			const std::string &at2,
458	gezelter	507	const std::string &at3){
459	gezelter	246	std::vector<std::string> keys;
460			keys.push_back(at1);
461			keys.push_back(at2);
462			keys.push_back(at3);
463			return bendTypeCont_.find(keys);
464	gezelter	507	}
465	cpuglis	1195
466			TorsionType* ForceField::getExactTorsionType(const std::string &at1,
467			const std::string &at2,
468			const std::string &at3,
469			const std::string &at4){
470	gezelter	246	std::vector<std::string> keys;
471			keys.push_back(at1);
472			keys.push_back(at2);
473			keys.push_back(at3);
474			keys.push_back(at4);
475			return torsionTypeCont_.find(keys);
476	gezelter	507	}
477	cli2	1275
478			InversionType* ForceField::getExactInversionType(const std::string &at1,
479			const std::string &at2,
480			const std::string &at3,
481			const std::string &at4){
482			std::vector<std::string> keys;
483			keys.push_back(at1);
484			keys.push_back(at2);
485			keys.push_back(at3);
486			keys.push_back(at4);
487			return inversionTypeCont_.find(keys);
488			}
489
490	chuckv	1151	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
491			std::vector<std::string> keys;
492			keys.push_back(at1);
493			keys.push_back(at2);
494			return nonBondedInteractionTypeCont_.find(keys);
495			}
496	cli2	1275
497	chuckv	1151
498	gezelter	507	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
499	gezelter	246	std::vector<std::string> keys;
500			keys.push_back(at);
501			return atomTypeCont_.add(keys, atomType);
502	gezelter	507	}
503	gezelter	206
504	gezelter	1282	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
505			std::vector<std::string> keys;
506			keys.push_back(at);
507			return atomTypeCont_.replace(keys, atomType);
508			}
509
510	cpuglis	1195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
511			BondType* bondType) {
512	gezelter	246	std::vector<std::string> keys;
513			keys.push_back(at1);
514			keys.push_back(at2);
515	cpuglis	1195	return bondTypeCont_.add(keys, bondType);
516	gezelter	507	}
517	cpuglis	1195
518	gezelter	507	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
519			const std::string &at3, BendType* bendType) {
520	gezelter	246	std::vector<std::string> keys;
521			keys.push_back(at1);
522			keys.push_back(at2);
523			keys.push_back(at3);
524			return bendTypeCont_.add(keys, bendType);
525	gezelter	507	}
526	cpuglis	1195
527			bool ForceField::addTorsionType(const std::string &at1,
528			const std::string &at2,
529			const std::string &at3,
530			const std::string &at4,
531			TorsionType* torsionType) {
532	gezelter	246	std::vector<std::string> keys;
533			keys.push_back(at1);
534			keys.push_back(at2);
535			keys.push_back(at3);
536			keys.push_back(at4);
537			return torsionTypeCont_.add(keys, torsionType);
538	gezelter	507	}
539	gezelter	206
540	cli2	1275	bool ForceField::addInversionType(const std::string &at1,
541			const std::string &at2,
542			const std::string &at3,
543			const std::string &at4,
544			InversionType* inversionType) {
545			std::vector<std::string> keys;
546			keys.push_back(at1);
547			keys.push_back(at2);
548			keys.push_back(at3);
549			keys.push_back(at4);
550			return inversionTypeCont_.add(keys, inversionType);
551			}
552
553	cpuglis	1195	bool ForceField::addNonBondedInteractionType(const std::string &at1,
554			const std::string &at2,
555			NonBondedInteractionType* nbiType) {
556	chuckv	1151	std::vector<std::string> keys;
557			keys.push_back(at1);
558			keys.push_back(at2);
559			return nonBondedInteractionTypeCont_.add(keys, nbiType);
560			}
561	cpuglis	1195
562	tim	963	RealType ForceField::getRcutFromAtomType(AtomType* at) {
563	gezelter	246	/*@todo /
564			GenericData* data;
565	tim	963	RealType rcut = 0.0;
566	cpuglis	1195
567	gezelter	246	if (at->isLennardJones()) {
568	gezelter	507	data = at->getPropertyByName("LennardJones");
569			if (data != NULL) {
570			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
571	cpuglis	1195
572	gezelter	507	if (ljData != NULL) {
573			LJParam ljParam = ljData->getData();
574	cpuglis	1195
575	gezelter	507	//by default use 2.5*sigma as cutoff radius
576			rcut = 2.5 * ljParam.sigma;
577	cpuglis	1195
578	gezelter	507	} else {
579			sprintf( painCave.errMsg,
580			"Can not cast GenericData to LJParam\n");
581	gezelter	1390	painCave.severity = OPENMD_ERROR;
582	gezelter	507	painCave.isFatal = 1;
583			simError();
584			}
585			} else {
586			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
587	gezelter	1390	painCave.severity = OPENMD_ERROR;
588	gezelter	507	painCave.isFatal = 1;
589			simError();
590			}
591	gezelter	246	}
592			return rcut;
593	gezelter	507	}
594	cpuglis	1195
595	gezelter	206
596	gezelter	507	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
597	gezelter	246	std::string forceFieldFilename(filename);
598			ifstrstream* ffStream = new ifstrstream();
599
600			//try to open the force filed file in current directory first
601			ffStream->open(forceFieldFilename.c_str());
602			if(!ffStream->is_open()){
603
604	gezelter	507	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
605			ffStream->open( forceFieldFilename.c_str() );
606	gezelter	246
607	gezelter	507	//if current directory does not contain the force field file,
608			//try to open it in the path
609			if(!ffStream->is_open()){
610	gezelter	246
611	gezelter	507	sprintf( painCave.errMsg,
612			"Error opening the force field parameter file:\n"
613			"\t%s\n"
614			"\tHave you tried setting the FORCE_PARAM_PATH environment "
615			"variable?\n",
616			forceFieldFilename.c_str() );
617	gezelter	1390	painCave.severity = OPENMD_ERROR;
618	gezelter	507	painCave.isFatal = 1;
619			simError();
620			}
621	gezelter	246	}
622			return ffStream;
623	gezelter	507	}
624	gezelter	246
625	gezelter	1390	} //end namespace OpenMD