| 1 |
chuckv |
3154 |
/* |
| 2 |
|
|
* Copyright (c) 2007 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. Acknowledgement of the program authors must be made in any |
| 10 |
|
|
* publication of scientific results based in part on use of the |
| 11 |
|
|
* program. An acceptable form of acknowledgement is citation of |
| 12 |
|
|
* the article in which the program was described (Matthew |
| 13 |
|
|
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
|
|
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
|
|
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
|
|
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
|
|
* |
| 18 |
|
|
* 2. Redistributions of source code must retain the above copyright |
| 19 |
|
|
* notice, this list of conditions and the following disclaimer. |
| 20 |
|
|
* |
| 21 |
|
|
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
|
|
* notice, this list of conditions and the following disclaimer in the |
| 23 |
|
|
* documentation and/or other materials provided with the |
| 24 |
|
|
* distribution. |
| 25 |
|
|
* |
| 26 |
|
|
* This software is provided "AS IS," without a warranty of any |
| 27 |
|
|
* kind. All express or implied conditions, representations and |
| 28 |
|
|
* warranties, including any implied warranty of merchantability, |
| 29 |
|
|
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
|
|
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
|
|
* be liable for any damages suffered by licensee as a result of |
| 32 |
|
|
* using, modifying or distributing the software or its |
| 33 |
|
|
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
|
|
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
|
|
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
|
|
* damages, however caused and regardless of the theory of liability, |
| 37 |
|
|
* arising out of the use of or inability to use software, even if the |
| 38 |
|
|
* University of Notre Dame has been advised of the possibility of |
| 39 |
|
|
* such damages. |
| 40 |
|
|
*/ |
| 41 |
|
|
|
| 42 |
|
|
|
| 43 |
|
|
#include "UseTheForce/MnM_FF.hpp" |
| 44 |
|
|
#include "UseTheForce/DarkSide/lj_interface.h" |
| 45 |
|
|
#include "UseTheForce/DarkSide/sticky_interface.h" |
| 46 |
|
|
#include "UseTheForce/DarkSide/eam_interface.h" |
| 47 |
|
|
#include "UseTheForce/DarkSide/suttonchen_interface.h" |
| 48 |
|
|
#include "UseTheForce/ForceFieldFactory.hpp" |
| 49 |
|
|
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 50 |
|
|
#include "io/AtomTypesSectionParser.hpp" |
| 51 |
|
|
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 52 |
|
|
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 53 |
|
|
#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 54 |
|
|
#include "io/StickyAtomTypesSectionParser.hpp" |
| 55 |
|
|
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
| 56 |
|
|
#include "io/GayBerneAtomTypesSectionParser.hpp" |
| 57 |
|
|
#include "io/BondTypesSectionParser.hpp" |
| 58 |
|
|
#include "io/BendTypesSectionParser.hpp" |
| 59 |
|
|
#include "io/TorsionTypesSectionParser.hpp" |
| 60 |
|
|
#include "io/MetalNonMetalInteractionsSectionParser.hpp" |
| 61 |
|
|
#include "io/EAMAtomTypesSectionParser.hpp" |
| 62 |
|
|
#include "io/SCAtomTypesSectionParser.hpp" |
| 63 |
|
|
#include "io/OptionSectionParser.hpp" |
| 64 |
|
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 65 |
|
|
|
| 66 |
|
|
|
| 67 |
|
|
namespace oopse { |
| 68 |
|
|
|
| 69 |
|
|
MnM_FF::MnM_FF(){ |
| 70 |
|
|
|
| 71 |
|
|
//set default force field filename |
| 72 |
|
|
setForceFieldFileName("MnM.frc"); |
| 73 |
|
|
|
| 74 |
|
|
//The order of adding section parsers is important. |
| 75 |
|
|
//OptionSectionParser must come first to set options for other parsers |
| 76 |
|
|
//DirectionalAtomTypesSectionParser should be added before |
| 77 |
|
|
//AtomTypesSectionParser, and these two section parsers will actually |
| 78 |
|
|
//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and |
| 79 |
|
|
//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which |
| 80 |
|
|
//is a subclass of AtomType and should come first). Other AtomTypes Section |
| 81 |
|
|
//Parser will not create the "real" AtomType, they only add and set some |
| 82 |
|
|
//attribute of the AtomType. Thus their order are not important. |
| 83 |
|
|
//AtomTypesSectionParser should be added before other atom type section |
| 84 |
|
|
//parsers. Make sure they are added after DirectionalAtomTypesSectionParser |
| 85 |
|
|
//and AtomTypesSectionParser. The order of BondTypesSectionParser, |
| 86 |
|
|
//BendTypesSectionParser and TorsionTypesSectionParser are not important. |
| 87 |
|
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 88 |
|
|
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 89 |
|
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 90 |
|
|
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 91 |
|
|
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 92 |
|
|
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 93 |
|
|
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
| 94 |
|
|
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
| 95 |
|
|
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
| 96 |
|
|
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 97 |
|
|
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 98 |
|
|
spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_)); |
| 99 |
|
|
spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); |
| 100 |
|
|
spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
| 101 |
|
|
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 102 |
|
|
|
| 103 |
|
|
} |
| 104 |
|
|
|
| 105 |
|
|
void MnM_FF::parse(const std::string& filename) { |
| 106 |
|
|
ifstrstream* ffStream; |
| 107 |
|
|
|
| 108 |
|
|
|
| 109 |
|
|
ffStream = openForceFieldFile(filename); |
| 110 |
|
|
|
| 111 |
|
|
spMan_.parse(*ffStream, *this); |
| 112 |
|
|
|
| 113 |
|
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 114 |
|
|
AtomType* at; |
| 115 |
|
|
|
| 116 |
|
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 117 |
|
|
at = atomTypeCont_.nextType(i)) { |
| 118 |
|
|
at->makeFortranAtomType(); |
| 119 |
|
|
} |
| 120 |
|
|
|
| 121 |
|
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 122 |
|
|
at = atomTypeCont_.nextType(i)) { |
| 123 |
|
|
at->complete(); |
| 124 |
|
|
} |
| 125 |
|
|
|
| 126 |
|
|
hasSCtypes_ = false; |
| 127 |
|
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 128 |
|
|
at = atomTypeCont_.nextType(i)) { |
| 129 |
|
|
if (at->isSC()) |
| 130 |
|
|
hasSCtypes_ = true; |
| 131 |
|
|
} |
| 132 |
|
|
|
| 133 |
|
|
hasEAMtypes_ = false; |
| 134 |
|
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 135 |
|
|
at = atomTypeCont_.nextType(i)) { |
| 136 |
|
|
if (at->isEAM()) |
| 137 |
|
|
hasEAMtypes_ = true; |
| 138 |
|
|
} |
| 139 |
|
|
|
| 140 |
|
|
|
| 141 |
|
|
|
| 142 |
|
|
|
| 143 |
|
|
if (hasEAMtypes_ && hasSCtypes_) { |
| 144 |
|
|
sprintf( painCave.errMsg, |
| 145 |
|
|
"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n"); |
| 146 |
|
|
painCave.severity = OOPSE_ERROR; |
| 147 |
|
|
painCave.isFatal = 1; |
| 148 |
|
|
simError(); |
| 149 |
|
|
} |
| 150 |
|
|
|
| 151 |
|
|
delete ffStream; |
| 152 |
|
|
|
| 153 |
|
|
} |
| 154 |
|
|
|
| 155 |
|
|
|
| 156 |
|
|
RealType MnM_FF::getRcutFromAtomType(AtomType* at) |
| 157 |
|
|
{ |
| 158 |
|
|
RealType rcut = 0.0; |
| 159 |
|
|
if (at->isEAM()) { |
| 160 |
|
|
GenericData* data = at->getPropertyByName("EAM"); |
| 161 |
|
|
if (data != NULL) { |
| 162 |
|
|
EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
| 163 |
|
|
|
| 164 |
|
|
if (eamData != NULL) { |
| 165 |
|
|
|
| 166 |
|
|
EAMParam& eamParam = eamData->getData(); |
| 167 |
|
|
rcut = eamParam.rcut; |
| 168 |
|
|
} |
| 169 |
|
|
else { |
| 170 |
|
|
sprintf(painCave.errMsg, |
| 171 |
|
|
"Can not cast GenericData to EAMParam\n"); |
| 172 |
|
|
painCave.severity = OOPSE_ERROR; |
| 173 |
|
|
painCave.isFatal = 1; |
| 174 |
|
|
simError(); |
| 175 |
|
|
} |
| 176 |
|
|
} |
| 177 |
|
|
else { |
| 178 |
|
|
sprintf(painCave.errMsg, "Can not find EAM Parameters\n"); |
| 179 |
|
|
painCave.severity = OOPSE_ERROR; |
| 180 |
|
|
painCave.isFatal = 1; |
| 181 |
|
|
simError(); |
| 182 |
|
|
} |
| 183 |
|
|
} |
| 184 |
|
|
else { |
| 185 |
|
|
rcut = ForceField::getRcutFromAtomType(at); |
| 186 |
|
|
} |
| 187 |
|
|
|
| 188 |
|
|
return rcut; |
| 189 |
|
|
} |
| 190 |
|
|
|
| 191 |
|
|
|
| 192 |
|
|
|
| 193 |
|
|
|
| 194 |
|
|
|
| 195 |
|
|
|
| 196 |
|
|
MnM_FF::~MnM_FF(){ |
| 197 |
|
|
destroyLJTypes(); |
| 198 |
|
|
destroyStickyTypes(); |
| 199 |
|
|
if (hasEAMtypes_) destroyEAMTypes(); |
| 200 |
|
|
if (hasSCtypes_) destroySCTypes(); |
| 201 |
|
|
} |
| 202 |
|
|
} //end namespace oopse |
