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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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|
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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 "UseTheForce/ForceField.hpp" |
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#include "utils/simError.h" |
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#include "UseTheForce/DarkSide/atype_interface.h" |
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#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
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namespace oopse { |
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|
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< |
AtomType* ForceField::getMatchingAtomType(const string &at) { |
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> |
ForceField::ForceField() { |
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char* tempPath; |
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> |
tempPath = getenv("FORCE_PARAM_PATH"); |
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|
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< |
map<string, AtomType*>::iterator iter; |
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< |
|
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< |
iter = atomTypeMap.find(at); |
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< |
if (iter != atomTypeMap.end()) { |
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< |
return iter->second; |
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< |
} else { |
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return NULL; |
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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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|
| 15 |
– |
BondType* ForceField::getMatchingBondType(const string &at1, |
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– |
const string &at2) { |
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|
|
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< |
map<pair<string,string>, BondType*>::iterator iter; |
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< |
vector<BondType*> foundTypes; |
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> |
ForceField::~ForceField() { |
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> |
deleteAtypes(); |
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deleteSwitch(); |
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> |
} |
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|
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< |
iter = bondTypeMap.find(pair<at1, at2>); |
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< |
if (iter != bondTypeMap.end()) { |
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< |
// exact match, so just return it |
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< |
return iter->second; |
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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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< |
iter = bondTypeMap.find(pair<at2, at1>); |
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< |
if (iter != bondTypeMap.end()) { |
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< |
// exact match in reverse order, so just return it |
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< |
return iter->second; |
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< |
} |
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> |
BondType* ForceField::getBondType(const std::string &at1, 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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< |
iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>); |
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< |
if (iter != bondTypeMap.end()) { |
| 88 |
< |
foundTypes.push_back(iter->second); |
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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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> |
//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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< |
iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>); |
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< |
if (iter != bondTypeMap.end()) { |
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< |
foundTypes.push_back(iter->second); |
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> |
BendType* ForceField::getBendType(const std::string &at1, 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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> |
//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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< |
iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>); |
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< |
if (iter != bondTypeMap.end()) { |
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< |
foundTypes.push_back(iter->second); |
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> |
TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2, |
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const std::string &at3, 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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> |
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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> |
//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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> |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
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> |
|
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|
} |
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|
|
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< |
iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>); |
| 135 |
< |
if (iter != bondTypeMap.end()) { |
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< |
foundTypes.push_back(iter->second); |
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> |
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, 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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NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); |
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if (nbiType) { |
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return nbiType; |
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} else { |
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//if no exact match found, try wild card match |
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> |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
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} |
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> |
|
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|
} |
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|
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if (foundTypes.empty()) { |
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return NULL; |
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} else { |
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|
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|
|
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< |
|
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> |
BondType* ForceField::getExactBondType(const std::string &at1, 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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> |
return bondTypeCont_.find(keys); |
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> |
} |
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|
|
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+ |
BendType* ForceField::getExactBendType(const std::string &at1, 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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return bendTypeCont_.find(keys); |
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} |
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|
|
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TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2, |
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const std::string &at3, 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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+ |
return torsionTypeCont_.find(keys); |
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+ |
} |
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|
|
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< |
|
| 176 |
> |
NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, 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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> |
return nonBondedInteractionTypeCont_.find(keys); |
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> |
} |
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|
|
| 183 |
|
|
| 184 |
< |
BendType* ForceField::getMatchingBendType(const string &at1, const string &at2, |
| 185 |
< |
const string &at3); |
| 186 |
< |
TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2, |
| 187 |
< |
const string &at3, const string &at4); |
| 184 |
> |
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 185 |
> |
std::vector<std::string> keys; |
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> |
keys.push_back(at); |
| 187 |
> |
return atomTypeCont_.add(keys, atomType); |
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> |
} |
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|
|
| 190 |
< |
double ForceField::getRcutForAtomType(AtomType* at); |
| 190 |
> |
bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) { |
| 191 |
> |
std::vector<std::string> keys; |
| 192 |
> |
keys.push_back(at1); |
| 193 |
> |
keys.push_back(at2); |
| 194 |
> |
return bondTypeCont_.add(keys, bondType); |
| 195 |
|
|
| 196 |
+ |
} |
| 197 |
|
|
| 198 |
< |
vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) { |
| 199 |
< |
|
| 200 |
< |
vector<vector<string> > results; |
| 198 |
> |
bool ForceField::addBendType(const std::string &at1, const std::string &at2, |
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> |
const std::string &at3, BendType* bendType) { |
| 200 |
> |
std::vector<std::string> keys; |
| 201 |
> |
keys.push_back(at1); |
| 202 |
> |
keys.push_back(at2); |
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> |
keys.push_back(at3); |
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> |
return bendTypeCont_.add(keys, bendType); |
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> |
} |
| 206 |
|
|
| 207 |
< |
|
| 207 |
> |
bool ForceField::addTorsionType(const std::string &at1, const std::string &at2, |
| 208 |
> |
const std::string &at3, const std::string &at4, TorsionType* torsionType) { |
| 209 |
> |
std::vector<std::string> keys; |
| 210 |
> |
keys.push_back(at1); |
| 211 |
> |
keys.push_back(at2); |
| 212 |
> |
keys.push_back(at3); |
| 213 |
> |
keys.push_back(at4); |
| 214 |
> |
return torsionTypeCont_.add(keys, torsionType); |
| 215 |
> |
} |
| 216 |
|
|
| 217 |
+ |
bool ForceField::addNonBondedInteractionType(const std::string &at1, const std::string &at2, NonBondedInteractionType* nbiType) { |
| 218 |
+ |
std::vector<std::string> keys; |
| 219 |
+ |
keys.push_back(at1); |
| 220 |
+ |
keys.push_back(at2); |
| 221 |
+ |
return nonBondedInteractionTypeCont_.add(keys, nbiType); |
| 222 |
|
|
| 223 |
< |
vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) { |
| 81 |
< |
|
| 82 |
< |
int nStrings; |
| 83 |
< |
vector<string> oneResult; |
| 84 |
< |
vector<vector<string> > allResults; |
| 223 |
> |
} |
| 224 |
|
|
| 225 |
< |
nStrings = myAts.size(); |
| 225 |
> |
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 226 |
> |
/**@todo */ |
| 227 |
> |
GenericData* data; |
| 228 |
> |
RealType rcut = 0.0; |
| 229 |
|
|
| 230 |
< |
if (nStrings == 1) { |
| 231 |
< |
oneResult.push_back(wildcardCharacter); |
| 232 |
< |
allResults.push_back(oneResult); |
| 233 |
< |
return allResults; |
| 234 |
< |
} else { |
| 235 |
< |
|
| 236 |
< |
for (i=0; i < nStrings; i++) { |
| 237 |
< |
oneResult = myAts; |
| 238 |
< |
replace(oneResult.begin(), oneResult.end(), |
| 230 |
> |
if (at->isLennardJones()) { |
| 231 |
> |
data = at->getPropertyByName("LennardJones"); |
| 232 |
> |
if (data != NULL) { |
| 233 |
> |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 234 |
> |
|
| 235 |
> |
if (ljData != NULL) { |
| 236 |
> |
LJParam ljParam = ljData->getData(); |
| 237 |
> |
|
| 238 |
> |
//by default use 2.5*sigma as cutoff radius |
| 239 |
> |
rcut = 2.5 * ljParam.sigma; |
| 240 |
> |
|
| 241 |
> |
} else { |
| 242 |
> |
sprintf( painCave.errMsg, |
| 243 |
> |
"Can not cast GenericData to LJParam\n"); |
| 244 |
> |
painCave.severity = OOPSE_ERROR; |
| 245 |
> |
painCave.isFatal = 1; |
| 246 |
> |
simError(); |
| 247 |
> |
} |
| 248 |
> |
} else { |
| 249 |
> |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 250 |
> |
painCave.severity = OOPSE_ERROR; |
| 251 |
> |
painCave.isFatal = 1; |
| 252 |
> |
simError(); |
| 253 |
> |
} |
| 254 |
> |
} |
| 255 |
> |
|
| 256 |
> |
return rcut; |
| 257 |
> |
} |
| 258 |
> |
|
| 259 |
> |
|
| 260 |
> |
ifstrstream* ForceField::openForceFieldFile(const std::string& filename) { |
| 261 |
> |
std::string forceFieldFilename(filename); |
| 262 |
> |
ifstrstream* ffStream = new ifstrstream(); |
| 263 |
> |
|
| 264 |
> |
//try to open the force filed file in current directory first |
| 265 |
> |
ffStream->open(forceFieldFilename.c_str()); |
| 266 |
> |
if(!ffStream->is_open()){ |
| 267 |
> |
|
| 268 |
> |
forceFieldFilename = ffPath_ + "/" + forceFieldFilename; |
| 269 |
> |
ffStream->open( forceFieldFilename.c_str() ); |
| 270 |
> |
|
| 271 |
> |
//if current directory does not contain the force field file, |
| 272 |
> |
//try to open it in the path |
| 273 |
> |
if(!ffStream->is_open()){ |
| 274 |
> |
|
| 275 |
> |
sprintf( painCave.errMsg, |
| 276 |
> |
"Error opening the force field parameter file:\n" |
| 277 |
> |
"\t%s\n" |
| 278 |
> |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 279 |
> |
"variable?\n", |
| 280 |
> |
forceFieldFilename.c_str() ); |
| 281 |
> |
painCave.severity = OOPSE_ERROR; |
| 282 |
> |
painCave.isFatal = 1; |
| 283 |
> |
simError(); |
| 284 |
> |
} |
| 285 |
> |
} |
| 286 |
> |
|
| 287 |
> |
return ffStream; |
| 288 |
> |
|
| 289 |
> |
} |
| 290 |
> |
|
| 291 |
> |
void ForceField::setFortranForceOptions(){ |
| 292 |
> |
ForceOptions theseFortranOptions; |
| 293 |
> |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 294 |
> |
setfForceOptions(&theseFortranOptions); |
| 295 |
> |
} |
| 296 |
> |
} //end namespace oopse |
