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"
#include "UseTheForce/DarkSide/atype_interface.h"
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;
    }
  }


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

  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:	1530
Committed:	Tue Dec 28 21:47:55 2010 UTC (14 years, 4 months ago) by gezelter
File size:	19285 byte(s)
Log Message:	Moved switching functions and force options over to the C++ side, and removed them from 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	tim	475	#include "UseTheForce/DarkSide/atype_interface.h"
55	gezelter	1390	namespace OpenMD {
56	gezelter	206
57	gezelter	507	ForceField::ForceField() {
58	gezelter	1460
59	gezelter	246	char* tempPath;
60			tempPath = getenv("FORCE_PARAM_PATH");
61	gezelter	1460
62	gezelter	246	if (tempPath == NULL) {
63	gezelter	1460	//convert a macro from compiler to a string in c++
64			STR_DEFINE(ffPath_, FRC_PATH );
65	gezelter	246	} else {
66	gezelter	507	ffPath_ = tempPath;
67	gezelter	246	}
68	gezelter	507	}
69	gezelter	206
70	tim	475
71	gezelter	507	ForceField::~ForceField() {
72	tim	475	deleteAtypes();
73	gezelter	507	}
74	tim	475
75	gezelter	507	AtomType* ForceField::getAtomType(const std::string &at) {
76	gezelter	246	std::vector<std::string> keys;
77			keys.push_back(at);
78			return atomTypeCont_.find(keys);
79	gezelter	507	}
80	gezelter	206
81	cpuglis	1195	BondType* ForceField::getBondType(const std::string &at1,
82			const std::string &at2) {
83	gezelter	246	std::vector<std::string> keys;
84			keys.push_back(at1);
85			keys.push_back(at2);
86	gezelter	206
87	gezelter	246	//try exact match first
88			BondType* bondType = bondTypeCont_.find(keys);
89			if (bondType) {
90	gezelter	507	return bondType;
91	gezelter	246	} else {
92	gezelter	1269	AtomType* atype1;
93			AtomType* atype2;
94			std::vector<std::string> at1key;
95			at1key.push_back(at1);
96			atype1 = atomTypeCont_.find(at1key);
97
98			std::vector<std::string> at2key;
99			at2key.push_back(at2);
100			atype2 = atomTypeCont_.find(at2key);
101
102			// query atom types for their chains of responsibility
103			std::vector<AtomType*> at1Chain = atype1->allYourBase();
104			std::vector<AtomType*> at2Chain = atype2->allYourBase();
105
106			std::vector<AtomType*>::iterator i;
107			std::vector<AtomType*>::iterator j;
108
109			int ii = 0;
110			int jj = 0;
111			int bondTypeScore;
112
113			std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
114
115			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
116			jj = 0;
117			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
118
119			bondTypeScore = ii + jj;
120
121			std::vector<std::string> myKeys;
122			myKeys.push_back((*i)->getName());
123			myKeys.push_back((*j)->getName());
124
125			BondType* bondType = bondTypeCont_.find(myKeys);
126			if (bondType) {
127			foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
128			}
129			jj++;
130			}
131			ii++;
132			}
133
134
135	gezelter	1277	if (foundBonds.size() > 0) {
136			// sort the foundBonds by the score:
137			std::sort(foundBonds.begin(), foundBonds.end());
138
139			int bestScore = foundBonds[0].first;
140			std::vector<std::string> theKeys = foundBonds[0].second;
141
142			BondType* bestType = bondTypeCont_.find(theKeys);
143
144			return bestType;
145			} else {
146			//if no exact match found, try wild card match
147			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
148	gezelter	1269	}
149	gezelter	246	}
150	gezelter	507	}
151	gezelter	1269
152	cpuglis	1195	BendType* ForceField::getBendType(const std::string &at1,
153			const std::string &at2,
154	gezelter	507	const std::string &at3) {
155	gezelter	246	std::vector<std::string> keys;
156			keys.push_back(at1);
157			keys.push_back(at2);
158			keys.push_back(at3);
159	gezelter	206
160	gezelter	246	//try exact match first
161			BendType* bendType = bendTypeCont_.find(keys);
162			if (bendType) {
163	gezelter	507	return bendType;
164	gezelter	246	} else {
165	gezelter	1269
166			AtomType* atype1;
167			AtomType* atype2;
168			AtomType* atype3;
169			std::vector<std::string> at1key;
170			at1key.push_back(at1);
171			atype1 = atomTypeCont_.find(at1key);
172
173			std::vector<std::string> at2key;
174			at2key.push_back(at2);
175			atype2 = atomTypeCont_.find(at2key);
176
177			std::vector<std::string> at3key;
178			at3key.push_back(at3);
179			atype3 = atomTypeCont_.find(at3key);
180
181			// query atom types for their chains of responsibility
182			std::vector<AtomType*> at1Chain = atype1->allYourBase();
183			std::vector<AtomType*> at2Chain = atype2->allYourBase();
184			std::vector<AtomType*> at3Chain = atype3->allYourBase();
185
186			std::vector<AtomType*>::iterator i;
187			std::vector<AtomType*>::iterator j;
188			std::vector<AtomType*>::iterator k;
189
190			int ii = 0;
191			int jj = 0;
192			int kk = 0;
193			int IKscore;
194
195			std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
196
197			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
198			ii = 0;
199			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
200			kk = 0;
201			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
202
203			IKscore = ii + kk;
204
205			std::vector<std::string> myKeys;
206			myKeys.push_back((*i)->getName());
207			myKeys.push_back((*j)->getName());
208			myKeys.push_back((*k)->getName());
209
210			BendType* bendType = bendTypeCont_.find(myKeys);
211			if (bendType) {
212			foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
213			}
214			kk++;
215			}
216			ii++;
217			}
218			jj++;
219			}
220
221	gezelter	1277	if (foundBends.size() > 0) {
222			std::sort(foundBends.begin(), foundBends.end());
223			int jscore = foundBends[0].first;
224			int ikscore = foundBends[0].second;
225	cli2	1289	std::vector<std::string> theKeys = foundBends[0].third;
226	gezelter	1277
227			BendType* bestType = bendTypeCont_.find(theKeys);
228			return bestType;
229			} else {
230	gezelter	1269	//if no exact match found, try wild card match
231			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
232			}
233	gezelter	246	}
234	gezelter	507	}
235	gezelter	206
236	cpuglis	1195	TorsionType* ForceField::getTorsionType(const std::string &at1,
237			const std::string &at2,
238			const std::string &at3,
239			const std::string &at4) {
240	gezelter	246	std::vector<std::string> keys;
241			keys.push_back(at1);
242			keys.push_back(at2);
243			keys.push_back(at3);
244			keys.push_back(at4);
245	gezelter	206
246	gezelter	1269
247			//try exact match first
248	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
249			if (torsionType) {
250	gezelter	507	return torsionType;
251	gezelter	246	} else {
252	gezelter	1269
253			AtomType* atype1;
254			AtomType* atype2;
255			AtomType* atype3;
256			AtomType* atype4;
257			std::vector<std::string> at1key;
258			at1key.push_back(at1);
259			atype1 = atomTypeCont_.find(at1key);
260
261			std::vector<std::string> at2key;
262			at2key.push_back(at2);
263			atype2 = atomTypeCont_.find(at2key);
264
265			std::vector<std::string> at3key;
266			at3key.push_back(at3);
267			atype3 = atomTypeCont_.find(at3key);
268
269			std::vector<std::string> at4key;
270			at4key.push_back(at4);
271			atype4 = atomTypeCont_.find(at4key);
272
273			// query atom types for their chains of responsibility
274			std::vector<AtomType*> at1Chain = atype1->allYourBase();
275			std::vector<AtomType*> at2Chain = atype2->allYourBase();
276			std::vector<AtomType*> at3Chain = atype3->allYourBase();
277			std::vector<AtomType*> at4Chain = atype4->allYourBase();
278
279			std::vector<AtomType*>::iterator i;
280			std::vector<AtomType*>::iterator j;
281			std::vector<AtomType*>::iterator k;
282			std::vector<AtomType*>::iterator l;
283
284			int ii = 0;
285			int jj = 0;
286			int kk = 0;
287			int ll = 0;
288			int ILscore;
289			int JKscore;
290
291			std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
292
293			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
294			kk = 0;
295			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
296			ii = 0;
297			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
298			ll = 0;
299			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
300
301			ILscore = ii + ll;
302			JKscore = jj + kk;
303
304			std::vector<std::string> myKeys;
305			myKeys.push_back((*i)->getName());
306			myKeys.push_back((*j)->getName());
307			myKeys.push_back((*k)->getName());
308			myKeys.push_back((*l)->getName());
309
310			TorsionType* torsionType = torsionTypeCont_.find(myKeys);
311			if (torsionType) {
312			foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
313			}
314			ll++;
315			}
316			ii++;
317			}
318			kk++;
319			}
320			jj++;
321			}
322
323	gezelter	1277	if (foundTorsions.size() > 0) {
324			std::sort(foundTorsions.begin(), foundTorsions.end());
325			int jkscore = foundTorsions[0].first;
326			int ilscore = foundTorsions[0].second;
327			std::vector<std::string> theKeys = foundTorsions[0].third;
328
329			TorsionType* bestType = torsionTypeCont_.find(theKeys);
330			return bestType;
331	gezelter	1269	} else {
332			//if no exact match found, try wild card match
333			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
334			}
335	gezelter	246	}
336	gezelter	507	}
337	gezelter	206
338	cli2	1275	InversionType* ForceField::getInversionType(const std::string &at1,
339			const std::string &at2,
340			const std::string &at3,
341			const std::string &at4) {
342			std::vector<std::string> keys;
343			keys.push_back(at1);
344			keys.push_back(at2);
345			keys.push_back(at3);
346			keys.push_back(at4);
347
348			//try exact match first
349	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
350	cli2	1275	if (inversionType) {
351			return inversionType;
352			} else {
353
354			AtomType* atype1;
355			AtomType* atype2;
356			AtomType* atype3;
357			AtomType* atype4;
358			std::vector<std::string> at1key;
359			at1key.push_back(at1);
360			atype1 = atomTypeCont_.find(at1key);
361
362			std::vector<std::string> at2key;
363			at2key.push_back(at2);
364			atype2 = atomTypeCont_.find(at2key);
365
366			std::vector<std::string> at3key;
367			at3key.push_back(at3);
368			atype3 = atomTypeCont_.find(at3key);
369
370			std::vector<std::string> at4key;
371			at4key.push_back(at4);
372			atype4 = atomTypeCont_.find(at4key);
373
374			// query atom types for their chains of responsibility
375			std::vector<AtomType*> at1Chain = atype1->allYourBase();
376			std::vector<AtomType*> at2Chain = atype2->allYourBase();
377			std::vector<AtomType*> at3Chain = atype3->allYourBase();
378			std::vector<AtomType*> at4Chain = atype4->allYourBase();
379
380			std::vector<AtomType*>::iterator i;
381			std::vector<AtomType*>::iterator j;
382			std::vector<AtomType*>::iterator k;
383			std::vector<AtomType*>::iterator l;
384
385			int ii = 0;
386			int jj = 0;
387			int kk = 0;
388			int ll = 0;
389			int Iscore;
390			int JKLscore;
391
392			std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
393
394			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
395			kk = 0;
396			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
397			ii = 0;
398			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
399			ll = 0;
400			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
401
402			Iscore = ii;
403			JKLscore = jj + kk + ll;
404
405			std::vector<std::string> myKeys;
406			myKeys.push_back((*i)->getName());
407			myKeys.push_back((*j)->getName());
408			myKeys.push_back((*k)->getName());
409			myKeys.push_back((*l)->getName());
410
411	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
412	cli2	1275	if (inversionType) {
413			foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
414			}
415			ll++;
416			}
417			ii++;
418			}
419			kk++;
420			}
421			jj++;
422			}
423	gezelter	1277
424			if (foundInversions.size() > 0) {
425			std::sort(foundInversions.begin(), foundInversions.end());
426			int iscore = foundInversions[0].first;
427			int jklscore = foundInversions[0].second;
428			std::vector<std::string> theKeys = foundInversions[0].third;
429
430	cli2	1303	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
431	gezelter	1277	return bestType;
432	cli2	1275	} else {
433			//if no exact match found, try wild card match
434			return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
435			}
436			}
437			}
438
439	chuckv	1151	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
440			std::vector<std::string> keys;
441			keys.push_back(at1);
442			keys.push_back(at2);
443	cpuglis	1195
444	chuckv	1151	//try exact match first
445			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
446			if (nbiType) {
447			return nbiType;
448			} else {
449			//if no exact match found, try wild card match
450			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
451	cpuglis	1195	}
452	chuckv	1151	}
453	cpuglis	1195
454			BondType* ForceField::getExactBondType(const std::string &at1,
455			const std::string &at2){
456	gezelter	246	std::vector<std::string> keys;
457			keys.push_back(at1);
458			keys.push_back(at2);
459			return bondTypeCont_.find(keys);
460	gezelter	507	}
461	cpuglis	1195
462			BendType* ForceField::getExactBendType(const std::string &at1,
463			const std::string &at2,
464	gezelter	507	const std::string &at3){
465	gezelter	246	std::vector<std::string> keys;
466			keys.push_back(at1);
467			keys.push_back(at2);
468			keys.push_back(at3);
469			return bendTypeCont_.find(keys);
470	gezelter	507	}
471	cpuglis	1195
472			TorsionType* ForceField::getExactTorsionType(const std::string &at1,
473			const std::string &at2,
474			const std::string &at3,
475			const std::string &at4){
476	gezelter	246	std::vector<std::string> keys;
477			keys.push_back(at1);
478			keys.push_back(at2);
479			keys.push_back(at3);
480			keys.push_back(at4);
481			return torsionTypeCont_.find(keys);
482	gezelter	507	}
483	cli2	1275
484			InversionType* ForceField::getExactInversionType(const std::string &at1,
485			const std::string &at2,
486			const std::string &at3,
487			const std::string &at4){
488			std::vector<std::string> keys;
489			keys.push_back(at1);
490			keys.push_back(at2);
491			keys.push_back(at3);
492			keys.push_back(at4);
493			return inversionTypeCont_.find(keys);
494			}
495
496	chuckv	1151	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
497			std::vector<std::string> keys;
498			keys.push_back(at1);
499			keys.push_back(at2);
500			return nonBondedInteractionTypeCont_.find(keys);
501			}
502	cli2	1275
503	chuckv	1151
504	gezelter	507	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
505	gezelter	246	std::vector<std::string> keys;
506			keys.push_back(at);
507			return atomTypeCont_.add(keys, atomType);
508	gezelter	507	}
509	gezelter	206
510	gezelter	1282	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
511			std::vector<std::string> keys;
512			keys.push_back(at);
513			return atomTypeCont_.replace(keys, atomType);
514			}
515
516	cpuglis	1195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
517			BondType* bondType) {
518	gezelter	246	std::vector<std::string> keys;
519			keys.push_back(at1);
520			keys.push_back(at2);
521	cpuglis	1195	return bondTypeCont_.add(keys, bondType);
522	gezelter	507	}
523	cpuglis	1195
524	gezelter	507	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
525			const std::string &at3, BendType* bendType) {
526	gezelter	246	std::vector<std::string> keys;
527			keys.push_back(at1);
528			keys.push_back(at2);
529			keys.push_back(at3);
530			return bendTypeCont_.add(keys, bendType);
531	gezelter	507	}
532	cpuglis	1195
533			bool ForceField::addTorsionType(const std::string &at1,
534			const std::string &at2,
535			const std::string &at3,
536			const std::string &at4,
537			TorsionType* torsionType) {
538	gezelter	246	std::vector<std::string> keys;
539			keys.push_back(at1);
540			keys.push_back(at2);
541			keys.push_back(at3);
542			keys.push_back(at4);
543			return torsionTypeCont_.add(keys, torsionType);
544	gezelter	507	}
545	gezelter	206
546	cli2	1275	bool ForceField::addInversionType(const std::string &at1,
547			const std::string &at2,
548			const std::string &at3,
549			const std::string &at4,
550			InversionType* inversionType) {
551			std::vector<std::string> keys;
552			keys.push_back(at1);
553			keys.push_back(at2);
554			keys.push_back(at3);
555			keys.push_back(at4);
556			return inversionTypeCont_.add(keys, inversionType);
557			}
558
559	cpuglis	1195	bool ForceField::addNonBondedInteractionType(const std::string &at1,
560			const std::string &at2,
561			NonBondedInteractionType* nbiType) {
562	chuckv	1151	std::vector<std::string> keys;
563			keys.push_back(at1);
564			keys.push_back(at2);
565			return nonBondedInteractionTypeCont_.add(keys, nbiType);
566			}
567	cpuglis	1195
568	tim	963	RealType ForceField::getRcutFromAtomType(AtomType* at) {
569	gezelter	246	/*@todo /
570			GenericData* data;
571	tim	963	RealType rcut = 0.0;
572	cpuglis	1195
573	gezelter	246	if (at->isLennardJones()) {
574	gezelter	507	data = at->getPropertyByName("LennardJones");
575			if (data != NULL) {
576			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
577	cpuglis	1195
578	gezelter	507	if (ljData != NULL) {
579			LJParam ljParam = ljData->getData();
580	cpuglis	1195
581	gezelter	507	//by default use 2.5*sigma as cutoff radius
582			rcut = 2.5 * ljParam.sigma;
583	cpuglis	1195
584	gezelter	507	} else {
585			sprintf( painCave.errMsg,
586			"Can not cast GenericData to LJParam\n");
587	gezelter	1390	painCave.severity = OPENMD_ERROR;
588	gezelter	507	painCave.isFatal = 1;
589			simError();
590			}
591			} else {
592			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
593	gezelter	1390	painCave.severity = OPENMD_ERROR;
594	gezelter	507	painCave.isFatal = 1;
595			simError();
596			}
597	gezelter	246	}
598			return rcut;
599	gezelter	507	}
600	cpuglis	1195
601	gezelter	206
602	gezelter	507	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
603	gezelter	246	std::string forceFieldFilename(filename);
604			ifstrstream* ffStream = new ifstrstream();
605
606			//try to open the force filed file in current directory first
607			ffStream->open(forceFieldFilename.c_str());
608			if(!ffStream->is_open()){
609
610	gezelter	507	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
611			ffStream->open( forceFieldFilename.c_str() );
612	gezelter	246
613	gezelter	507	//if current directory does not contain the force field file,
614			//try to open it in the path
615			if(!ffStream->is_open()){
616	gezelter	246
617	gezelter	507	sprintf( painCave.errMsg,
618			"Error opening the force field parameter file:\n"
619			"\t%s\n"
620			"\tHave you tried setting the FORCE_PARAM_PATH environment "
621			"variable?\n",
622			forceFieldFilename.c_str() );
623	gezelter	1390	painCave.severity = OPENMD_ERROR;
624	gezelter	507	painCave.isFatal = 1;
625			simError();
626			}
627	gezelter	246	}
628			return ffStream;
629	gezelter	507	}
630	gezelter	246
631	gezelter	1390	} //end namespace OpenMD