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. 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"
#include "UseTheForce/DarkSide/fForceOptions_interface.h"
#include "UseTheForce/DarkSide/switcheroo_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();
    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 = 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;
  }

  void ForceField::setFortranForceOptions(){
    ForceOptions theseFortranOptions;
    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
    setfForceOptions(&theseFortranOptions);
  }
} //end namespace OpenMD
Revision:	1460
Committed:	Wed Jul 7 15:04:32 2010 UTC (14 years, 9 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/ForceField.cpp*
File size:	19613 byte(s)
Log Message:	changed ORNULL
#	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	chuckv	821	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56	gezelter	939	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	gezelter	1390	namespace OpenMD {
58	gezelter	206
59	gezelter	507	ForceField::ForceField() {
60	gezelter	1460
61	gezelter	246	char* tempPath;
62			tempPath = getenv("FORCE_PARAM_PATH");
63	gezelter	1460
64	gezelter	246	if (tempPath == NULL) {
65	gezelter	1460	//convert a macro from compiler to a string in c++
66			STR_DEFINE(ffPath_, FRC_PATH );
67	gezelter	246	} else {
68	gezelter	507	ffPath_ = tempPath;
69	gezelter	246	}
70	gezelter	507	}
71	gezelter	206
72	tim	475
73	gezelter	507	ForceField::~ForceField() {
74	tim	475	deleteAtypes();
75	gezelter	939	deleteSwitch();
76	gezelter	507	}
77	tim	475
78	gezelter	507	AtomType* ForceField::getAtomType(const std::string &at) {
79	gezelter	246	std::vector<std::string> keys;
80			keys.push_back(at);
81			return atomTypeCont_.find(keys);
82	gezelter	507	}
83	gezelter	206
84	cpuglis	1195	BondType* ForceField::getBondType(const std::string &at1,
85			const std::string &at2) {
86	gezelter	246	std::vector<std::string> keys;
87			keys.push_back(at1);
88			keys.push_back(at2);
89	gezelter	206
90	gezelter	246	//try exact match first
91			BondType* bondType = bondTypeCont_.find(keys);
92			if (bondType) {
93	gezelter	507	return bondType;
94	gezelter	246	} else {
95	gezelter	1269	AtomType* atype1;
96			AtomType* atype2;
97			std::vector<std::string> at1key;
98			at1key.push_back(at1);
99			atype1 = atomTypeCont_.find(at1key);
100
101			std::vector<std::string> at2key;
102			at2key.push_back(at2);
103			atype2 = atomTypeCont_.find(at2key);
104
105			// query atom types for their chains of responsibility
106			std::vector<AtomType*> at1Chain = atype1->allYourBase();
107			std::vector<AtomType*> at2Chain = atype2->allYourBase();
108
109			std::vector<AtomType*>::iterator i;
110			std::vector<AtomType*>::iterator j;
111
112			int ii = 0;
113			int jj = 0;
114			int bondTypeScore;
115
116			std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
117
118			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
119			jj = 0;
120			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
121
122			bondTypeScore = ii + jj;
123
124			std::vector<std::string> myKeys;
125			myKeys.push_back((*i)->getName());
126			myKeys.push_back((*j)->getName());
127
128			BondType* bondType = bondTypeCont_.find(myKeys);
129			if (bondType) {
130			foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
131			}
132			jj++;
133			}
134			ii++;
135			}
136
137
138	gezelter	1277	if (foundBonds.size() > 0) {
139			// sort the foundBonds by the score:
140			std::sort(foundBonds.begin(), foundBonds.end());
141
142			int bestScore = foundBonds[0].first;
143			std::vector<std::string> theKeys = foundBonds[0].second;
144
145			BondType* bestType = bondTypeCont_.find(theKeys);
146
147			return bestType;
148			} else {
149			//if no exact match found, try wild card match
150			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
151	gezelter	1269	}
152	gezelter	246	}
153	gezelter	507	}
154	gezelter	1269
155	cpuglis	1195	BendType* ForceField::getBendType(const std::string &at1,
156			const std::string &at2,
157	gezelter	507	const std::string &at3) {
158	gezelter	246	std::vector<std::string> keys;
159			keys.push_back(at1);
160			keys.push_back(at2);
161			keys.push_back(at3);
162	gezelter	206
163	gezelter	246	//try exact match first
164			BendType* bendType = bendTypeCont_.find(keys);
165			if (bendType) {
166	gezelter	507	return bendType;
167	gezelter	246	} else {
168	gezelter	1269
169			AtomType* atype1;
170			AtomType* atype2;
171			AtomType* atype3;
172			std::vector<std::string> at1key;
173			at1key.push_back(at1);
174			atype1 = atomTypeCont_.find(at1key);
175
176			std::vector<std::string> at2key;
177			at2key.push_back(at2);
178			atype2 = atomTypeCont_.find(at2key);
179
180			std::vector<std::string> at3key;
181			at3key.push_back(at3);
182			atype3 = atomTypeCont_.find(at3key);
183
184			// query atom types for their chains of responsibility
185			std::vector<AtomType*> at1Chain = atype1->allYourBase();
186			std::vector<AtomType*> at2Chain = atype2->allYourBase();
187			std::vector<AtomType*> at3Chain = atype3->allYourBase();
188
189			std::vector<AtomType*>::iterator i;
190			std::vector<AtomType*>::iterator j;
191			std::vector<AtomType*>::iterator k;
192
193			int ii = 0;
194			int jj = 0;
195			int kk = 0;
196			int IKscore;
197
198			std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
199
200			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
201			ii = 0;
202			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
203			kk = 0;
204			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
205
206			IKscore = ii + kk;
207
208			std::vector<std::string> myKeys;
209			myKeys.push_back((*i)->getName());
210			myKeys.push_back((*j)->getName());
211			myKeys.push_back((*k)->getName());
212
213			BendType* bendType = bendTypeCont_.find(myKeys);
214			if (bendType) {
215			foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
216			}
217			kk++;
218			}
219			ii++;
220			}
221			jj++;
222			}
223
224	gezelter	1277	if (foundBends.size() > 0) {
225			std::sort(foundBends.begin(), foundBends.end());
226			int jscore = foundBends[0].first;
227			int ikscore = foundBends[0].second;
228	cli2	1289	std::vector<std::string> theKeys = foundBends[0].third;
229	gezelter	1277
230			BendType* bestType = bendTypeCont_.find(theKeys);
231			return bestType;
232			} else {
233	gezelter	1269	//if no exact match found, try wild card match
234			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
235			}
236	gezelter	246	}
237	gezelter	507	}
238	gezelter	206
239	cpuglis	1195	TorsionType* ForceField::getTorsionType(const std::string &at1,
240			const std::string &at2,
241			const std::string &at3,
242			const std::string &at4) {
243	gezelter	246	std::vector<std::string> keys;
244			keys.push_back(at1);
245			keys.push_back(at2);
246			keys.push_back(at3);
247			keys.push_back(at4);
248	gezelter	206
249	gezelter	1269
250			//try exact match first
251	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
252			if (torsionType) {
253	gezelter	507	return torsionType;
254	gezelter	246	} else {
255	gezelter	1269
256			AtomType* atype1;
257			AtomType* atype2;
258			AtomType* atype3;
259			AtomType* atype4;
260			std::vector<std::string> at1key;
261			at1key.push_back(at1);
262			atype1 = atomTypeCont_.find(at1key);
263
264			std::vector<std::string> at2key;
265			at2key.push_back(at2);
266			atype2 = atomTypeCont_.find(at2key);
267
268			std::vector<std::string> at3key;
269			at3key.push_back(at3);
270			atype3 = atomTypeCont_.find(at3key);
271
272			std::vector<std::string> at4key;
273			at4key.push_back(at4);
274			atype4 = atomTypeCont_.find(at4key);
275
276			// query atom types for their chains of responsibility
277			std::vector<AtomType*> at1Chain = atype1->allYourBase();
278			std::vector<AtomType*> at2Chain = atype2->allYourBase();
279			std::vector<AtomType*> at3Chain = atype3->allYourBase();
280			std::vector<AtomType*> at4Chain = atype4->allYourBase();
281
282			std::vector<AtomType*>::iterator i;
283			std::vector<AtomType*>::iterator j;
284			std::vector<AtomType*>::iterator k;
285			std::vector<AtomType*>::iterator l;
286
287			int ii = 0;
288			int jj = 0;
289			int kk = 0;
290			int ll = 0;
291			int ILscore;
292			int JKscore;
293
294			std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
295
296			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
297			kk = 0;
298			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
299			ii = 0;
300			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
301			ll = 0;
302			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
303
304			ILscore = ii + ll;
305			JKscore = jj + kk;
306
307			std::vector<std::string> myKeys;
308			myKeys.push_back((*i)->getName());
309			myKeys.push_back((*j)->getName());
310			myKeys.push_back((*k)->getName());
311			myKeys.push_back((*l)->getName());
312
313			TorsionType* torsionType = torsionTypeCont_.find(myKeys);
314			if (torsionType) {
315			foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
316			}
317			ll++;
318			}
319			ii++;
320			}
321			kk++;
322			}
323			jj++;
324			}
325
326	gezelter	1277	if (foundTorsions.size() > 0) {
327			std::sort(foundTorsions.begin(), foundTorsions.end());
328			int jkscore = foundTorsions[0].first;
329			int ilscore = foundTorsions[0].second;
330			std::vector<std::string> theKeys = foundTorsions[0].third;
331
332			TorsionType* bestType = torsionTypeCont_.find(theKeys);
333			return bestType;
334	gezelter	1269	} else {
335			//if no exact match found, try wild card match
336			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
337			}
338	gezelter	246	}
339	gezelter	507	}
340	gezelter	206
341	cli2	1275	InversionType* ForceField::getInversionType(const std::string &at1,
342			const std::string &at2,
343			const std::string &at3,
344			const std::string &at4) {
345			std::vector<std::string> keys;
346			keys.push_back(at1);
347			keys.push_back(at2);
348			keys.push_back(at3);
349			keys.push_back(at4);
350
351			//try exact match first
352	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
353	cli2	1275	if (inversionType) {
354			return inversionType;
355			} else {
356
357			AtomType* atype1;
358			AtomType* atype2;
359			AtomType* atype3;
360			AtomType* atype4;
361			std::vector<std::string> at1key;
362			at1key.push_back(at1);
363			atype1 = atomTypeCont_.find(at1key);
364
365			std::vector<std::string> at2key;
366			at2key.push_back(at2);
367			atype2 = atomTypeCont_.find(at2key);
368
369			std::vector<std::string> at3key;
370			at3key.push_back(at3);
371			atype3 = atomTypeCont_.find(at3key);
372
373			std::vector<std::string> at4key;
374			at4key.push_back(at4);
375			atype4 = atomTypeCont_.find(at4key);
376
377			// query atom types for their chains of responsibility
378			std::vector<AtomType*> at1Chain = atype1->allYourBase();
379			std::vector<AtomType*> at2Chain = atype2->allYourBase();
380			std::vector<AtomType*> at3Chain = atype3->allYourBase();
381			std::vector<AtomType*> at4Chain = atype4->allYourBase();
382
383			std::vector<AtomType*>::iterator i;
384			std::vector<AtomType*>::iterator j;
385			std::vector<AtomType*>::iterator k;
386			std::vector<AtomType*>::iterator l;
387
388			int ii = 0;
389			int jj = 0;
390			int kk = 0;
391			int ll = 0;
392			int Iscore;
393			int JKLscore;
394
395			std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
396
397			for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
398			kk = 0;
399			for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
400			ii = 0;
401			for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
402			ll = 0;
403			for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
404
405			Iscore = ii;
406			JKLscore = jj + kk + ll;
407
408			std::vector<std::string> myKeys;
409			myKeys.push_back((*i)->getName());
410			myKeys.push_back((*j)->getName());
411			myKeys.push_back((*k)->getName());
412			myKeys.push_back((*l)->getName());
413
414	cli2	1303	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
415	cli2	1275	if (inversionType) {
416			foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
417			}
418			ll++;
419			}
420			ii++;
421			}
422			kk++;
423			}
424			jj++;
425			}
426	gezelter	1277
427			if (foundInversions.size() > 0) {
428			std::sort(foundInversions.begin(), foundInversions.end());
429			int iscore = foundInversions[0].first;
430			int jklscore = foundInversions[0].second;
431			std::vector<std::string> theKeys = foundInversions[0].third;
432
433	cli2	1303	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
434	gezelter	1277	return bestType;
435	cli2	1275	} else {
436			//if no exact match found, try wild card match
437			return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
438			}
439			}
440			}
441
442	chuckv	1151	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
443			std::vector<std::string> keys;
444			keys.push_back(at1);
445			keys.push_back(at2);
446	cpuglis	1195
447	chuckv	1151	//try exact match first
448			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
449			if (nbiType) {
450			return nbiType;
451			} else {
452			//if no exact match found, try wild card match
453			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
454	cpuglis	1195	}
455	chuckv	1151	}
456	cpuglis	1195
457			BondType* ForceField::getExactBondType(const std::string &at1,
458			const std::string &at2){
459	gezelter	246	std::vector<std::string> keys;
460			keys.push_back(at1);
461			keys.push_back(at2);
462			return bondTypeCont_.find(keys);
463	gezelter	507	}
464	cpuglis	1195
465			BendType* ForceField::getExactBendType(const std::string &at1,
466			const std::string &at2,
467	gezelter	507	const std::string &at3){
468	gezelter	246	std::vector<std::string> keys;
469			keys.push_back(at1);
470			keys.push_back(at2);
471			keys.push_back(at3);
472			return bendTypeCont_.find(keys);
473	gezelter	507	}
474	cpuglis	1195
475			TorsionType* ForceField::getExactTorsionType(const std::string &at1,
476			const std::string &at2,
477			const std::string &at3,
478			const std::string &at4){
479	gezelter	246	std::vector<std::string> keys;
480			keys.push_back(at1);
481			keys.push_back(at2);
482			keys.push_back(at3);
483			keys.push_back(at4);
484			return torsionTypeCont_.find(keys);
485	gezelter	507	}
486	cli2	1275
487			InversionType* ForceField::getExactInversionType(const std::string &at1,
488			const std::string &at2,
489			const std::string &at3,
490			const std::string &at4){
491			std::vector<std::string> keys;
492			keys.push_back(at1);
493			keys.push_back(at2);
494			keys.push_back(at3);
495			keys.push_back(at4);
496			return inversionTypeCont_.find(keys);
497			}
498
499	chuckv	1151	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
500			std::vector<std::string> keys;
501			keys.push_back(at1);
502			keys.push_back(at2);
503			return nonBondedInteractionTypeCont_.find(keys);
504			}
505	cli2	1275
506	chuckv	1151
507	gezelter	507	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
508	gezelter	246	std::vector<std::string> keys;
509			keys.push_back(at);
510			return atomTypeCont_.add(keys, atomType);
511	gezelter	507	}
512	gezelter	206
513	gezelter	1282	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
514			std::vector<std::string> keys;
515			keys.push_back(at);
516			return atomTypeCont_.replace(keys, atomType);
517			}
518
519	cpuglis	1195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
520			BondType* bondType) {
521	gezelter	246	std::vector<std::string> keys;
522			keys.push_back(at1);
523			keys.push_back(at2);
524	cpuglis	1195	return bondTypeCont_.add(keys, bondType);
525	gezelter	507	}
526	cpuglis	1195
527	gezelter	507	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
528			const std::string &at3, BendType* bendType) {
529	gezelter	246	std::vector<std::string> keys;
530			keys.push_back(at1);
531			keys.push_back(at2);
532			keys.push_back(at3);
533			return bendTypeCont_.add(keys, bendType);
534	gezelter	507	}
535	cpuglis	1195
536			bool ForceField::addTorsionType(const std::string &at1,
537			const std::string &at2,
538			const std::string &at3,
539			const std::string &at4,
540			TorsionType* torsionType) {
541	gezelter	246	std::vector<std::string> keys;
542			keys.push_back(at1);
543			keys.push_back(at2);
544			keys.push_back(at3);
545			keys.push_back(at4);
546			return torsionTypeCont_.add(keys, torsionType);
547	gezelter	507	}
548	gezelter	206
549	cli2	1275	bool ForceField::addInversionType(const std::string &at1,
550			const std::string &at2,
551			const std::string &at3,
552			const std::string &at4,
553			InversionType* inversionType) {
554			std::vector<std::string> keys;
555			keys.push_back(at1);
556			keys.push_back(at2);
557			keys.push_back(at3);
558			keys.push_back(at4);
559			return inversionTypeCont_.add(keys, inversionType);
560			}
561
562	cpuglis	1195	bool ForceField::addNonBondedInteractionType(const std::string &at1,
563			const std::string &at2,
564			NonBondedInteractionType* nbiType) {
565	chuckv	1151	std::vector<std::string> keys;
566			keys.push_back(at1);
567			keys.push_back(at2);
568			return nonBondedInteractionTypeCont_.add(keys, nbiType);
569			}
570	cpuglis	1195
571	tim	963	RealType ForceField::getRcutFromAtomType(AtomType* at) {
572	gezelter	246	/*@todo /
573			GenericData* data;
574	tim	963	RealType rcut = 0.0;
575	cpuglis	1195
576	gezelter	246	if (at->isLennardJones()) {
577	gezelter	507	data = at->getPropertyByName("LennardJones");
578			if (data != NULL) {
579			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
580	cpuglis	1195
581	gezelter	507	if (ljData != NULL) {
582			LJParam ljParam = ljData->getData();
583	cpuglis	1195
584	gezelter	507	//by default use 2.5*sigma as cutoff radius
585			rcut = 2.5 * ljParam.sigma;
586	cpuglis	1195
587	gezelter	507	} else {
588			sprintf( painCave.errMsg,
589			"Can not cast GenericData to LJParam\n");
590	gezelter	1390	painCave.severity = OPENMD_ERROR;
591	gezelter	507	painCave.isFatal = 1;
592			simError();
593			}
594			} else {
595			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
596	gezelter	1390	painCave.severity = OPENMD_ERROR;
597	gezelter	507	painCave.isFatal = 1;
598			simError();
599			}
600	gezelter	246	}
601			return rcut;
602	gezelter	507	}
603	cpuglis	1195
604	gezelter	206
605	gezelter	507	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
606	gezelter	246	std::string forceFieldFilename(filename);
607			ifstrstream* ffStream = new ifstrstream();
608
609			//try to open the force filed file in current directory first
610			ffStream->open(forceFieldFilename.c_str());
611			if(!ffStream->is_open()){
612
613	gezelter	507	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
614			ffStream->open( forceFieldFilename.c_str() );
615	gezelter	246
616	gezelter	507	//if current directory does not contain the force field file,
617			//try to open it in the path
618			if(!ffStream->is_open()){
619	gezelter	246
620	gezelter	507	sprintf( painCave.errMsg,
621			"Error opening the force field parameter file:\n"
622			"\t%s\n"
623			"\tHave you tried setting the FORCE_PARAM_PATH environment "
624			"variable?\n",
625			forceFieldFilename.c_str() );
626	gezelter	1390	painCave.severity = OPENMD_ERROR;
627	gezelter	507	painCave.isFatal = 1;
628			simError();
629			}
630	gezelter	246	}
631			return ffStream;
632	gezelter	507	}
633	gezelter	246
634	chuckv	821	void ForceField::setFortranForceOptions(){
635			ForceOptions theseFortranOptions;
636			forceFieldOptions_.makeFortranOptions(theseFortranOptions);
637			setfForceOptions(&theseFortranOptions);
638			}
639	gezelter	1390	} //end namespace OpenMD