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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 |
| 12 |
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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 |
| 15 |
< |
* 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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> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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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 |
| 14 |
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* documentation and/or other materials provided with the |
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* distribution. |
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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 |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
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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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* SC_FF.cpp |
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* OOPSE-2.0 |
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* |
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* Created by Charles F. Vardeman II on 11/9/05. |
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* @author Charles F. Vardeman II |
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* @version $Id: SC_FF.cpp,v 1.4 2005-12-06 19:26:37 chuckv Exp $ |
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* @version $Id$ |
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* |
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*/ |
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|
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/DarkSide/suttonchen_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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> |
#include "io/OptionSectionParser.hpp" |
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> |
#include "io/BaseAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ChargeAtomTypesSectionParser.hpp" |
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#include "io/MultipoleAtomTypesSectionParser.hpp" |
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#include "io/EAMAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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– |
#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "io/SCAtomTypesSectionParser.hpp" |
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#include "io/OptionSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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SC_FF::SC_FF(){ |
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|
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//set default force field filename |
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setForceFieldFileName("SuttonChen.QSC.frc"); |
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|
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//the order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
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//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
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//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
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//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
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//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom type section parsers. |
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//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
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//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
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//not important. |
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spMan_.push_back(new OptionSectionParser(SCForceFieldOptions_)); |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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> |
setForceFieldFileName("SuttonChen.frc"); |
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> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new SCAtomTypesSectionParser()); |
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|
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> |
spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); |
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} |
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|
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void SC_FF::parse(const std::string& filename) { |
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// Set forcefield options |
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|
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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+ |
// useBase sets the responsibilities, and these have to be done |
| 84 |
+ |
// after the atomTypes and Base types have all been scanned: |
| 85 |
+ |
|
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+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
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+ |
if (ayb.size() > 1) { |
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+ |
for (int j = ayb.size()-1; j > 0; j--) { |
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+ |
|
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ayb[j-1]->useBase(ayb[j]); |
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+ |
|
| 92 |
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} |
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} |
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at->makeFortranAtomType(); |
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} |
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|
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// we try to create a second SC force field. |
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destroySCTypes(); |
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} |
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} //end namespace oopse |
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> |
} //end namespace OpenMD |
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|
