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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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* @file ForceField.cpp |
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* @author tlin |
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* @date 11/04/2004 |
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* @time 22:51am |
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* @version 1.0 |
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*/ |
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|
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#include <algorithm> |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/simError.h" |
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#include "utils/Tuple.hpp" |
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namespace OpenMD { |
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|
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ForceField::ForceField() { |
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|
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char* tempPath; |
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tempPath = getenv("FORCE_PARAM_PATH"); |
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|
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if (tempPath == NULL) { |
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//convert a macro from compiler to a string in c++ |
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STR_DEFINE(ffPath_, FRC_PATH ); |
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} else { |
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ffPath_ = tempPath; |
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} |
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} |
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|
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/** |
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* getAtomType by string |
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* |
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* finds the requested atom type in this force field using the string |
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* name of the atom type. |
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*/ |
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AtomType* ForceField::getAtomType(const std::string &at) { |
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std::vector<std::string> keys; |
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keys.push_back(at); |
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return atomTypeCont_.find(keys); |
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} |
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|
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/** |
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* getAtomType by ident |
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* |
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* finds the requested atom type in this force field using the |
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* integer ident instead of the string name of the atom type. |
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*/ |
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AtomType* ForceField::getAtomType(int ident) { |
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std::string at = atypeIdentToName.find(ident)->second; |
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return getAtomType(at); |
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} |
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|
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BondType* ForceField::getBondType(const std::string &at1, |
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const std::string &at2) { |
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std::vector<std::string> keys; |
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keys.push_back(at1); |
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keys.push_back(at2); |
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|
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//try exact match first |
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BondType* bondType = bondTypeCont_.find(keys); |
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if (bondType) { |
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return bondType; |
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} else { |
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AtomType* atype1; |
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AtomType* atype2; |
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std::vector<std::string> at1key; |
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at1key.push_back(at1); |
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atype1 = atomTypeCont_.find(at1key); |
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|
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std::vector<std::string> at2key; |
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at2key.push_back(at2); |
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atype2 = atomTypeCont_.find(at2key); |
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|
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// query atom types for their chains of responsibility |
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std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
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std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
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|
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std::vector<AtomType*>::iterator i; |
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std::vector<AtomType*>::iterator j; |
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|
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int ii = 0; |
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int jj = 0; |
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int bondTypeScore; |
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|
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std::vector<std::pair<int, std::vector<std::string> > > foundBonds; |
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|
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for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
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jj = 0; |
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for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
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|
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bondTypeScore = ii + jj; |
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|
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std::vector<std::string> myKeys; |
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myKeys.push_back((*i)->getName()); |
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myKeys.push_back((*j)->getName()); |
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|
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BondType* bondType = bondTypeCont_.find(myKeys); |
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if (bondType) { |
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foundBonds.push_back(std::make_pair(bondTypeScore, myKeys)); |
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} |
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jj++; |
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} |
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ii++; |
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} |
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|
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|
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if (foundBonds.size() > 0) { |
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// sort the foundBonds by the score: |
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std::sort(foundBonds.begin(), foundBonds.end()); |
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|
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int bestScore = foundBonds[0].first; |
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std::vector<std::string> theKeys = foundBonds[0].second; |
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|
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BondType* bestType = bondTypeCont_.find(theKeys); |
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|
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return bestType; |
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} else { |
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//if no exact match found, try wild card match |
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return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
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} |
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} |
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} |
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|
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BendType* ForceField::getBendType(const std::string &at1, |
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const std::string &at2, |
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const std::string &at3) { |
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std::vector<std::string> keys; |
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keys.push_back(at1); |
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keys.push_back(at2); |
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keys.push_back(at3); |
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|
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//try exact match first |
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BendType* bendType = bendTypeCont_.find(keys); |
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if (bendType) { |
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return bendType; |
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} else { |
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|
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AtomType* atype1; |
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AtomType* atype2; |
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AtomType* atype3; |
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std::vector<std::string> at1key; |
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at1key.push_back(at1); |
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atype1 = atomTypeCont_.find(at1key); |
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|
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std::vector<std::string> at2key; |
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at2key.push_back(at2); |
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atype2 = atomTypeCont_.find(at2key); |
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|
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std::vector<std::string> at3key; |
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at3key.push_back(at3); |
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atype3 = atomTypeCont_.find(at3key); |
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|
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// query atom types for their chains of responsibility |
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std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
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std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
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std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
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|
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std::vector<AtomType*>::iterator i; |
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std::vector<AtomType*>::iterator j; |
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std::vector<AtomType*>::iterator k; |
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|
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int ii = 0; |
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int jj = 0; |
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int kk = 0; |
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int IKscore; |
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|
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std::vector<tuple3<int, int, std::vector<std::string> > > foundBends; |
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|
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for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
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ii = 0; |
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for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
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kk = 0; |
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for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
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|
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IKscore = ii + kk; |
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|
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std::vector<std::string> myKeys; |
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myKeys.push_back((*i)->getName()); |
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myKeys.push_back((*j)->getName()); |
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myKeys.push_back((*k)->getName()); |
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|
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BendType* bendType = bendTypeCont_.find(myKeys); |
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if (bendType) { |
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foundBends.push_back( make_tuple3(jj, IKscore, myKeys) ); |
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} |
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kk++; |
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} |
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ii++; |
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} |
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jj++; |
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} |
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|
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if (foundBends.size() > 0) { |
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std::sort(foundBends.begin(), foundBends.end()); |
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int jscore = foundBends[0].first; |
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int ikscore = foundBends[0].second; |
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std::vector<std::string> theKeys = foundBends[0].third; |
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|
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BendType* bestType = bendTypeCont_.find(theKeys); |
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return bestType; |
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} else { |
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//if no exact match found, try wild card match |
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return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
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} |
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} |
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} |
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|
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TorsionType* ForceField::getTorsionType(const std::string &at1, |
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const std::string &at2, |
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const std::string &at3, |
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const std::string &at4) { |
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std::vector<std::string> keys; |
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keys.push_back(at1); |
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keys.push_back(at2); |
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keys.push_back(at3); |
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keys.push_back(at4); |
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|
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|
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//try exact match first |
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TorsionType* torsionType = torsionTypeCont_.find(keys); |
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if (torsionType) { |
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return torsionType; |
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} else { |
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|
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AtomType* atype1; |
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AtomType* atype2; |
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AtomType* atype3; |
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AtomType* atype4; |
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std::vector<std::string> at1key; |
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at1key.push_back(at1); |
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atype1 = atomTypeCont_.find(at1key); |
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|
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std::vector<std::string> at2key; |
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at2key.push_back(at2); |
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atype2 = atomTypeCont_.find(at2key); |
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|
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std::vector<std::string> at3key; |
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at3key.push_back(at3); |
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atype3 = atomTypeCont_.find(at3key); |
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|
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std::vector<std::string> at4key; |
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at4key.push_back(at4); |
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atype4 = atomTypeCont_.find(at4key); |
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|
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// query atom types for their chains of responsibility |
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std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
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std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
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std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
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std::vector<AtomType*> at4Chain = atype4->allYourBase(); |
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|
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std::vector<AtomType*>::iterator i; |
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std::vector<AtomType*>::iterator j; |
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std::vector<AtomType*>::iterator k; |
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std::vector<AtomType*>::iterator l; |
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|
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int ii = 0; |
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int jj = 0; |
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int kk = 0; |
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int ll = 0; |
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int ILscore; |
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int JKscore; |
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|
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std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions; |
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|
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for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
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kk = 0; |
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for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
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ii = 0; |
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for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
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ll = 0; |
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for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
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|
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ILscore = ii + ll; |
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JKscore = jj + kk; |
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|
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std::vector<std::string> myKeys; |
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myKeys.push_back((*i)->getName()); |
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myKeys.push_back((*j)->getName()); |
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myKeys.push_back((*k)->getName()); |
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myKeys.push_back((*l)->getName()); |
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|
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TorsionType* torsionType = torsionTypeCont_.find(myKeys); |
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if (torsionType) { |
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foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) ); |
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} |
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ll++; |
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} |
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ii++; |
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} |
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kk++; |
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} |
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jj++; |
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} |
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|
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if (foundTorsions.size() > 0) { |
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std::sort(foundTorsions.begin(), foundTorsions.end()); |
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int jkscore = foundTorsions[0].first; |
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int ilscore = foundTorsions[0].second; |
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std::vector<std::string> theKeys = foundTorsions[0].third; |
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|
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TorsionType* bestType = torsionTypeCont_.find(theKeys); |
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return bestType; |
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} else { |
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//if no exact match found, try wild card match |
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return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
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} |
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} |
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} |
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|
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InversionType* ForceField::getInversionType(const std::string &at1, |
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const std::string &at2, |
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const std::string &at3, |
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const std::string &at4) { |
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std::vector<std::string> keys; |
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keys.push_back(at1); |
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keys.push_back(at2); |
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keys.push_back(at3); |
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keys.push_back(at4); |
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|
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//try exact match first |
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InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
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if (inversionType) { |
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return inversionType; |
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} else { |
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|
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AtomType* atype1; |
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AtomType* atype2; |
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AtomType* atype3; |
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AtomType* atype4; |
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std::vector<std::string> at1key; |
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at1key.push_back(at1); |
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atype1 = atomTypeCont_.find(at1key); |
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|
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std::vector<std::string> at2key; |
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at2key.push_back(at2); |
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atype2 = atomTypeCont_.find(at2key); |
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|
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std::vector<std::string> at3key; |
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at3key.push_back(at3); |
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atype3 = atomTypeCont_.find(at3key); |
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|
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std::vector<std::string> at4key; |
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at4key.push_back(at4); |
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atype4 = atomTypeCont_.find(at4key); |
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|
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// query atom types for their chains of responsibility |
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std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 387 |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 388 |
std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
| 389 |
std::vector<AtomType*> at4Chain = atype4->allYourBase(); |
| 390 |
|
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std::vector<AtomType*>::iterator i; |
| 392 |
std::vector<AtomType*>::iterator j; |
| 393 |
std::vector<AtomType*>::iterator k; |
| 394 |
std::vector<AtomType*>::iterator l; |
| 395 |
|
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int ii = 0; |
| 397 |
int jj = 0; |
| 398 |
int kk = 0; |
| 399 |
int ll = 0; |
| 400 |
int Iscore; |
| 401 |
int JKLscore; |
| 402 |
|
| 403 |
std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions; |
| 404 |
|
| 405 |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 406 |
kk = 0; |
| 407 |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 408 |
ii = 0; |
| 409 |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 410 |
ll = 0; |
| 411 |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 412 |
|
| 413 |
Iscore = ii; |
| 414 |
JKLscore = jj + kk + ll; |
| 415 |
|
| 416 |
std::vector<std::string> myKeys; |
| 417 |
myKeys.push_back((*i)->getName()); |
| 418 |
myKeys.push_back((*j)->getName()); |
| 419 |
myKeys.push_back((*k)->getName()); |
| 420 |
myKeys.push_back((*l)->getName()); |
| 421 |
|
| 422 |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 423 |
if (inversionType) { |
| 424 |
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 425 |
} |
| 426 |
ll++; |
| 427 |
} |
| 428 |
ii++; |
| 429 |
} |
| 430 |
kk++; |
| 431 |
} |
| 432 |
jj++; |
| 433 |
} |
| 434 |
|
| 435 |
if (foundInversions.size() > 0) { |
| 436 |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 437 |
int iscore = foundInversions[0].first; |
| 438 |
int jklscore = foundInversions[0].second; |
| 439 |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 440 |
|
| 441 |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 442 |
return bestType; |
| 443 |
} else { |
| 444 |
//if no exact match found, try wild card match |
| 445 |
return inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 446 |
} |
| 447 |
} |
| 448 |
} |
| 449 |
|
| 450 |
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 451 |
std::vector<std::string> keys; |
| 452 |
keys.push_back(at1); |
| 453 |
keys.push_back(at2); |
| 454 |
|
| 455 |
//try exact match first |
| 456 |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); |
| 457 |
if (nbiType) { |
| 458 |
return nbiType; |
| 459 |
} else { |
| 460 |
//if no exact match found, try wild card match |
| 461 |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 462 |
} |
| 463 |
} |
| 464 |
|
| 465 |
BondType* ForceField::getExactBondType(const std::string &at1, |
| 466 |
const std::string &at2){ |
| 467 |
std::vector<std::string> keys; |
| 468 |
keys.push_back(at1); |
| 469 |
keys.push_back(at2); |
| 470 |
return bondTypeCont_.find(keys); |
| 471 |
} |
| 472 |
|
| 473 |
BendType* ForceField::getExactBendType(const std::string &at1, |
| 474 |
const std::string &at2, |
| 475 |
const std::string &at3){ |
| 476 |
std::vector<std::string> keys; |
| 477 |
keys.push_back(at1); |
| 478 |
keys.push_back(at2); |
| 479 |
keys.push_back(at3); |
| 480 |
return bendTypeCont_.find(keys); |
| 481 |
} |
| 482 |
|
| 483 |
TorsionType* ForceField::getExactTorsionType(const std::string &at1, |
| 484 |
const std::string &at2, |
| 485 |
const std::string &at3, |
| 486 |
const std::string &at4){ |
| 487 |
std::vector<std::string> keys; |
| 488 |
keys.push_back(at1); |
| 489 |
keys.push_back(at2); |
| 490 |
keys.push_back(at3); |
| 491 |
keys.push_back(at4); |
| 492 |
return torsionTypeCont_.find(keys); |
| 493 |
} |
| 494 |
|
| 495 |
InversionType* ForceField::getExactInversionType(const std::string &at1, |
| 496 |
const std::string &at2, |
| 497 |
const std::string &at3, |
| 498 |
const std::string &at4){ |
| 499 |
std::vector<std::string> keys; |
| 500 |
keys.push_back(at1); |
| 501 |
keys.push_back(at2); |
| 502 |
keys.push_back(at3); |
| 503 |
keys.push_back(at4); |
| 504 |
return inversionTypeCont_.find(keys); |
| 505 |
} |
| 506 |
|
| 507 |
NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ |
| 508 |
std::vector<std::string> keys; |
| 509 |
keys.push_back(at1); |
| 510 |
keys.push_back(at2); |
| 511 |
return nonBondedInteractionTypeCont_.find(keys); |
| 512 |
} |
| 513 |
|
| 514 |
|
| 515 |
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 516 |
std::vector<std::string> keys; |
| 517 |
keys.push_back(at); |
| 518 |
atypeIdentToName[atomType->getIdent()] = at; |
| 519 |
return atomTypeCont_.add(keys, atomType); |
| 520 |
} |
| 521 |
|
| 522 |
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 523 |
std::vector<std::string> keys; |
| 524 |
keys.push_back(at); |
| 525 |
atypeIdentToName[atomType->getIdent()] = at; |
| 526 |
return atomTypeCont_.replace(keys, atomType); |
| 527 |
} |
| 528 |
|
| 529 |
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
| 530 |
BondType* bondType) { |
| 531 |
std::vector<std::string> keys; |
| 532 |
keys.push_back(at1); |
| 533 |
keys.push_back(at2); |
| 534 |
return bondTypeCont_.add(keys, bondType); |
| 535 |
} |
| 536 |
|
| 537 |
bool ForceField::addBendType(const std::string &at1, const std::string &at2, |
| 538 |
const std::string &at3, BendType* bendType) { |
| 539 |
std::vector<std::string> keys; |
| 540 |
keys.push_back(at1); |
| 541 |
keys.push_back(at2); |
| 542 |
keys.push_back(at3); |
| 543 |
return bendTypeCont_.add(keys, bendType); |
| 544 |
} |
| 545 |
|
| 546 |
bool ForceField::addTorsionType(const std::string &at1, |
| 547 |
const std::string &at2, |
| 548 |
const std::string &at3, |
| 549 |
const std::string &at4, |
| 550 |
TorsionType* torsionType) { |
| 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 torsionTypeCont_.add(keys, torsionType); |
| 557 |
} |
| 558 |
|
| 559 |
bool ForceField::addInversionType(const std::string &at1, |
| 560 |
const std::string &at2, |
| 561 |
const std::string &at3, |
| 562 |
const std::string &at4, |
| 563 |
InversionType* inversionType) { |
| 564 |
std::vector<std::string> keys; |
| 565 |
keys.push_back(at1); |
| 566 |
keys.push_back(at2); |
| 567 |
keys.push_back(at3); |
| 568 |
keys.push_back(at4); |
| 569 |
return inversionTypeCont_.add(keys, inversionType); |
| 570 |
} |
| 571 |
|
| 572 |
bool ForceField::addNonBondedInteractionType(const std::string &at1, |
| 573 |
const std::string &at2, |
| 574 |
NonBondedInteractionType* nbiType) { |
| 575 |
std::vector<std::string> keys; |
| 576 |
keys.push_back(at1); |
| 577 |
keys.push_back(at2); |
| 578 |
return nonBondedInteractionTypeCont_.add(keys, nbiType); |
| 579 |
} |
| 580 |
|
| 581 |
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 582 |
/**@todo */ |
| 583 |
GenericData* data; |
| 584 |
RealType rcut = 0.0; |
| 585 |
|
| 586 |
if (at->isLennardJones()) { |
| 587 |
data = at->getPropertyByName("LennardJones"); |
| 588 |
if (data != NULL) { |
| 589 |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 590 |
|
| 591 |
if (ljData != NULL) { |
| 592 |
LJParam ljParam = ljData->getData(); |
| 593 |
|
| 594 |
//by default use 2.5*sigma as cutoff radius |
| 595 |
rcut = 2.5 * ljParam.sigma; |
| 596 |
|
| 597 |
} else { |
| 598 |
sprintf( painCave.errMsg, |
| 599 |
"Can not cast GenericData to LJParam\n"); |
| 600 |
painCave.severity = OPENMD_ERROR; |
| 601 |
painCave.isFatal = 1; |
| 602 |
simError(); |
| 603 |
} |
| 604 |
} else { |
| 605 |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 606 |
painCave.severity = OPENMD_ERROR; |
| 607 |
painCave.isFatal = 1; |
| 608 |
simError(); |
| 609 |
} |
| 610 |
} |
| 611 |
return rcut; |
| 612 |
} |
| 613 |
|
| 614 |
|
| 615 |
ifstrstream* ForceField::openForceFieldFile(const std::string& filename) { |
| 616 |
std::string forceFieldFilename(filename); |
| 617 |
ifstrstream* ffStream = new ifstrstream(); |
| 618 |
|
| 619 |
//try to open the force filed file in current directory first |
| 620 |
ffStream->open(forceFieldFilename.c_str()); |
| 621 |
if(!ffStream->is_open()){ |
| 622 |
|
| 623 |
forceFieldFilename = ffPath_ + "/" + forceFieldFilename; |
| 624 |
ffStream->open( forceFieldFilename.c_str() ); |
| 625 |
|
| 626 |
//if current directory does not contain the force field file, |
| 627 |
//try to open it in the path |
| 628 |
if(!ffStream->is_open()){ |
| 629 |
|
| 630 |
sprintf( painCave.errMsg, |
| 631 |
"Error opening the force field parameter file:\n" |
| 632 |
"\t%s\n" |
| 633 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 634 |
"variable?\n", |
| 635 |
forceFieldFilename.c_str() ); |
| 636 |
painCave.severity = OPENMD_ERROR; |
| 637 |
painCave.isFatal = 1; |
| 638 |
simError(); |
| 639 |
} |
| 640 |
} |
| 641 |
return ffStream; |
| 642 |
} |
| 643 |
|
| 644 |
} //end namespace OpenMD |
