| 1 |
/* |
| 2 |
* Copyright (c) 2005 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, 234107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include <cstring> |
| 44 |
#include "visitors/AtomVisitor.hpp" |
| 45 |
#include "primitives/DirectionalAtom.hpp" |
| 46 |
#include "primitives/RigidBody.hpp" |
| 47 |
#include "types/FixedChargeAdapter.hpp" |
| 48 |
#include "types/FluctuatingChargeAdapter.hpp" |
| 49 |
#include "types/MultipoleAdapter.hpp" |
| 50 |
#include "types/GayBerneAdapter.hpp" |
| 51 |
|
| 52 |
namespace OpenMD { |
| 53 |
|
| 54 |
BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() { |
| 55 |
storageLayout_ = info->getStorageLayout(); |
| 56 |
} |
| 57 |
|
| 58 |
void BaseAtomVisitor::visit(RigidBody *rb) { |
| 59 |
//vector<Atom*> myAtoms; |
| 60 |
//vector<Atom*>::iterator atomIter; |
| 61 |
|
| 62 |
//myAtoms = rb->getAtoms(); |
| 63 |
|
| 64 |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
| 65 |
// (*atomIter)->accept(this); |
| 66 |
} |
| 67 |
|
| 68 |
void BaseAtomVisitor::setVisited(Atom *atom) { |
| 69 |
GenericData *data; |
| 70 |
data = atom->getPropertyByName("VISITED"); |
| 71 |
|
| 72 |
//if visited property is not existed, add it as new property |
| 73 |
if (data == NULL) { |
| 74 |
data = new GenericData(); |
| 75 |
data->setID("VISITED"); |
| 76 |
atom->addProperty(data); |
| 77 |
} |
| 78 |
} |
| 79 |
|
| 80 |
bool BaseAtomVisitor::isVisited(Atom *atom) { |
| 81 |
GenericData *data; |
| 82 |
data = atom->getPropertyByName("VISITED"); |
| 83 |
return data == NULL ? false : true; |
| 84 |
} |
| 85 |
|
| 86 |
//------------------------------------------------------------------------// |
| 87 |
|
| 88 |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 89 |
AtomData *atomData; |
| 90 |
AtomInfo *atomInfo; |
| 91 |
AtomType* atype = atom->getAtomType(); |
| 92 |
|
| 93 |
if (isVisited(atom)) |
| 94 |
return; |
| 95 |
|
| 96 |
atomInfo = new AtomInfo; |
| 97 |
atomInfo->atomTypeName = atom->getType(); |
| 98 |
atomInfo->pos = atom->getPos(); |
| 99 |
atomInfo->vel = atom->getVel(); |
| 100 |
atomInfo->frc = atom->getFrc(); |
| 101 |
atomInfo->vec = V3Zero; |
| 102 |
atomInfo->hasVelocity = true; |
| 103 |
atomInfo->hasForce = true; |
| 104 |
|
| 105 |
FixedChargeAdapter fca = FixedChargeAdapter(atype); |
| 106 |
if ( fca.isFixedCharge() ) { |
| 107 |
atomInfo->hasCharge = true; |
| 108 |
atomInfo->charge = fca.getCharge(); |
| 109 |
} |
| 110 |
|
| 111 |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype); |
| 112 |
if ( fqa.isFluctuatingCharge() ) { |
| 113 |
atomInfo->hasCharge = true; |
| 114 |
atomInfo->charge += atom->getFlucQPos(); |
| 115 |
} |
| 116 |
|
| 117 |
if ((storageLayout_ & DataStorage::dslElectricField) && |
| 118 |
(atype->isElectrostatic())) { |
| 119 |
atomInfo->hasElectricField = true; |
| 120 |
atomInfo->eField = atom->getElectricField(); |
| 121 |
} |
| 122 |
|
| 123 |
atomData = new AtomData; |
| 124 |
atomData->setID("ATOMDATA"); |
| 125 |
atomData->addAtomInfo(atomInfo); |
| 126 |
|
| 127 |
atom->addProperty(atomData); |
| 128 |
|
| 129 |
setVisited(atom); |
| 130 |
} |
| 131 |
|
| 132 |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 133 |
AtomData *atomData; |
| 134 |
AtomInfo *atomInfo; |
| 135 |
AtomType* atype = datom->getAtomType(); |
| 136 |
|
| 137 |
if (isVisited(datom)) |
| 138 |
return; |
| 139 |
|
| 140 |
atomInfo = new AtomInfo; |
| 141 |
atomInfo->atomTypeName = datom->getType(); |
| 142 |
atomInfo->pos = datom->getPos(); |
| 143 |
atomInfo->vel = datom->getVel(); |
| 144 |
atomInfo->frc = datom->getFrc(); |
| 145 |
atomInfo->hasVelocity = true; |
| 146 |
atomInfo->hasForce = true; |
| 147 |
|
| 148 |
FixedChargeAdapter fca = FixedChargeAdapter(atype); |
| 149 |
if ( fca.isFixedCharge() ) { |
| 150 |
atomInfo->hasCharge = true; |
| 151 |
atomInfo->charge = fca.getCharge(); |
| 152 |
} |
| 153 |
|
| 154 |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype); |
| 155 |
if ( fqa.isFluctuatingCharge() ) { |
| 156 |
atomInfo->hasCharge = true; |
| 157 |
atomInfo->charge += datom->getFlucQPos(); |
| 158 |
} |
| 159 |
|
| 160 |
if ((storageLayout_ & DataStorage::dslElectricField) && |
| 161 |
(atype->isElectrostatic())) { |
| 162 |
atomInfo->hasElectricField = true; |
| 163 |
atomInfo->eField = datom->getElectricField(); |
| 164 |
} |
| 165 |
|
| 166 |
GayBerneAdapter gba = GayBerneAdapter(atype); |
| 167 |
MultipoleAdapter ma = MultipoleAdapter(atype); |
| 168 |
|
| 169 |
if (gba.isGayBerne()) { |
| 170 |
atomInfo->hasVector = true; |
| 171 |
atomInfo->vec = datom->getA().transpose()*V3Z; |
| 172 |
} else if (ma.isDipole()) { |
| 173 |
atomInfo->hasVector = true; |
| 174 |
atomInfo->vec = datom->getDipole(); |
| 175 |
} else if (ma.isQuadrupole()) { |
| 176 |
atomInfo->hasVector = true; |
| 177 |
atomInfo->vec = datom->getA().transpose()*V3Z; |
| 178 |
} |
| 179 |
|
| 180 |
atomData = new AtomData; |
| 181 |
atomData->setID("ATOMDATA"); |
| 182 |
atomData->addAtomInfo(atomInfo); |
| 183 |
|
| 184 |
datom->addProperty(atomData); |
| 185 |
|
| 186 |
setVisited(datom); |
| 187 |
} |
| 188 |
|
| 189 |
const std::string DefaultAtomVisitor::toString() { |
| 190 |
char buffer[65535]; |
| 191 |
std::string result; |
| 192 |
|
| 193 |
sprintf(buffer, |
| 194 |
"--------------------------------------------------------------\n"); |
| 195 |
result += buffer; |
| 196 |
|
| 197 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 198 |
result += buffer; |
| 199 |
|
| 200 |
sprintf(buffer, |
| 201 |
"Visitor Description: copy atom infomation into atom data\n"); |
| 202 |
result += buffer; |
| 203 |
|
| 204 |
sprintf(buffer, |
| 205 |
"--------------------------------------------------------------\n"); |
| 206 |
result += buffer; |
| 207 |
|
| 208 |
return result; |
| 209 |
} |
| 210 |
} //namespace OpenMD |
