| 1 |
/* |
| 2 |
* Copyright (c) 2008 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 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* 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 |
* |
| 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 |
*/ |
| 41 |
|
| 42 |
|
| 43 |
#include "UseTheForce/Amber_FF.hpp" |
| 44 |
#include "UseTheForce/ForceFieldFactory.hpp" |
| 45 |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 46 |
#include "io/AtomTypesSectionParser.hpp" |
| 47 |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 48 |
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 49 |
#include "io/BondTypesSectionParser.hpp" |
| 50 |
#include "io/BendTypesSectionParser.hpp" |
| 51 |
#include "io/TorsionTypesSectionParser.hpp" |
| 52 |
#include "io/InversionTypesSectionParser.hpp" |
| 53 |
#include "io/OptionSectionParser.hpp" |
| 54 |
#include "UseTheForce/ForceFieldCreator.hpp" |
| 55 |
|
| 56 |
namespace OpenMD { |
| 57 |
|
| 58 |
Amber_FF::Amber_FF(){ |
| 59 |
|
| 60 |
//set default force field filename |
| 61 |
setForceFieldFileName("Amber.frc"); |
| 62 |
|
| 63 |
//The order of adding section parsers is important. |
| 64 |
|
| 65 |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 66 |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 67 |
spMan_.push_back(new AtomTypesSectionParser()); |
| 68 |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 69 |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 70 |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 71 |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 72 |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 73 |
spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); |
| 74 |
} |
| 75 |
|
| 76 |
void Amber_FF::parse(const std::string& filename) { |
| 77 |
ifstrstream* ffStream; |
| 78 |
|
| 79 |
ffStream = openForceFieldFile(filename); |
| 80 |
spMan_.parse(*ffStream, *this); |
| 81 |
|
| 82 |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 83 |
AtomType* at; |
| 84 |
|
| 85 |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 86 |
at = atomTypeCont_.nextType(i)) { |
| 87 |
|
| 88 |
// useBase sets the responsibilities, and these have to be done |
| 89 |
// after the atomTypes and Base types have all been scanned: |
| 90 |
|
| 91 |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 92 |
if (ayb.size() > 1) { |
| 93 |
for (int j = ayb.size()-1; j > 0; j--) { |
| 94 |
|
| 95 |
ayb[j-1]->useBase(ayb[j]); |
| 96 |
|
| 97 |
} |
| 98 |
} |
| 99 |
at->makeFortranAtomType(); |
| 100 |
} |
| 101 |
|
| 102 |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 103 |
at = atomTypeCont_.nextType(i)) { |
| 104 |
at->complete(); |
| 105 |
} |
| 106 |
|
| 107 |
delete ffStream; |
| 108 |
|
| 109 |
} |
| 110 |
|
| 111 |
Amber_FF::~Amber_FF(){ |
| 112 |
} |
| 113 |
} //end namespace OpenMD |
