| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 |
|
/** |
| 44 |
|
* @file MoleculeCreator.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/04/2004 |
| 46 |
– |
* @time 13:44am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 50 |
|
#include <cassert> |
| 51 |
+ |
#include <typeinfo> |
| 52 |
|
#include <set> |
| 53 |
|
|
| 54 |
|
#include "brains/MoleculeCreator.hpp" |
| 55 |
|
#include "primitives/GhostBend.hpp" |
| 56 |
|
#include "primitives/GhostTorsion.hpp" |
| 57 |
< |
#include "types/DirectionalAtomType.hpp" |
| 57 |
> |
#include "types/AtomType.hpp" |
| 58 |
|
#include "types/FixedBondType.hpp" |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "utils/StringUtils.hpp" |
| 61 |
|
|
| 62 |
< |
namespace oopse { |
| 62 |
> |
namespace OpenMD { |
| 63 |
|
|
| 64 |
< |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
| 65 |
< |
int stampId, int globalIndex, LocalIndexManager* localIndexMan) { |
| 64 |
> |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
| 65 |
> |
MoleculeStamp *molStamp, |
| 66 |
> |
int stampId, int globalIndex, |
| 67 |
> |
LocalIndexManager* localIndexMan) { |
| 68 |
> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
| 69 |
> |
molStamp->getRegion() ); |
| 70 |
|
|
| 66 |
– |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID()); |
| 67 |
– |
|
| 71 |
|
//create atoms |
| 72 |
|
Atom* atom; |
| 73 |
|
AtomStamp* currentAtomStamp; |
| 74 |
|
int nAtom = molStamp->getNAtoms(); |
| 75 |
|
for (int i = 0; i < nAtom; ++i) { |
| 76 |
< |
currentAtomStamp = molStamp->getAtom(i); |
| 76 |
> |
currentAtomStamp = molStamp->getAtomStamp(i); |
| 77 |
|
atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
| 78 |
|
mol->addAtom(atom); |
| 79 |
|
} |
| 84 |
|
int nRigidbodies = molStamp->getNRigidBodies(); |
| 85 |
|
|
| 86 |
|
for (int i = 0; i < nRigidbodies; ++i) { |
| 87 |
< |
currentRigidBodyStamp = molStamp->getRigidBody(i); |
| 88 |
< |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan); |
| 87 |
> |
currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
| 88 |
> |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, |
| 89 |
> |
localIndexMan); |
| 90 |
|
mol->addRigidBody(rb); |
| 91 |
|
} |
| 92 |
< |
|
| 92 |
> |
|
| 93 |
|
//create bonds |
| 94 |
|
Bond* bond; |
| 95 |
|
BondStamp* currentBondStamp; |
| 96 |
|
int nBonds = molStamp->getNBonds(); |
| 97 |
|
|
| 98 |
|
for (int i = 0; i < nBonds; ++i) { |
| 99 |
< |
currentBondStamp = molStamp->getBond(i); |
| 99 |
> |
currentBondStamp = molStamp->getBondStamp(i); |
| 100 |
|
bond = createBond(ff, mol, currentBondStamp); |
| 101 |
|
mol->addBond(bond); |
| 102 |
|
} |
| 106 |
|
BendStamp* currentBendStamp; |
| 107 |
|
int nBends = molStamp->getNBends(); |
| 108 |
|
for (int i = 0; i < nBends; ++i) { |
| 109 |
< |
currentBendStamp = molStamp->getBend(i); |
| 109 |
> |
currentBendStamp = molStamp->getBendStamp(i); |
| 110 |
|
bend = createBend(ff, mol, currentBendStamp); |
| 111 |
|
mol->addBend(bend); |
| 112 |
|
} |
| 116 |
|
TorsionStamp* currentTorsionStamp; |
| 117 |
|
int nTorsions = molStamp->getNTorsions(); |
| 118 |
|
for (int i = 0; i < nTorsions; ++i) { |
| 119 |
< |
currentTorsionStamp = molStamp->getTorsion(i); |
| 119 |
> |
currentTorsionStamp = molStamp->getTorsionStamp(i); |
| 120 |
|
torsion = createTorsion(ff, mol, currentTorsionStamp); |
| 121 |
|
mol->addTorsion(torsion); |
| 122 |
|
} |
| 123 |
|
|
| 124 |
+ |
//create inversions |
| 125 |
+ |
Inversion* inversion; |
| 126 |
+ |
InversionStamp* currentInversionStamp; |
| 127 |
+ |
int nInversions = molStamp->getNInversions(); |
| 128 |
+ |
for (int i = 0; i < nInversions; ++i) { |
| 129 |
+ |
currentInversionStamp = molStamp->getInversionStamp(i); |
| 130 |
+ |
inversion = createInversion(ff, mol, currentInversionStamp); |
| 131 |
+ |
if (inversion != NULL ) { |
| 132 |
+ |
mol->addInversion(inversion); |
| 133 |
+ |
} |
| 134 |
+ |
} |
| 135 |
+ |
|
| 136 |
|
//create cutoffGroups |
| 137 |
|
CutoffGroup* cutoffGroup; |
| 138 |
|
CutoffGroupStamp* currentCutoffGroupStamp; |
| 139 |
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 140 |
|
for (int i = 0; i < nCutoffGroups; ++i) { |
| 141 |
< |
currentCutoffGroupStamp = molStamp->getCutoffGroup(i); |
| 142 |
< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 141 |
> |
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 142 |
> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan); |
| 143 |
|
mol->addCutoffGroup(cutoffGroup); |
| 144 |
|
} |
| 145 |
|
|
| 156 |
|
Molecule::CutoffGroupIterator ci; |
| 157 |
|
CutoffGroup* cg; |
| 158 |
|
|
| 159 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 160 |
< |
|
| 159 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 160 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 161 |
> |
|
| 162 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 163 |
< |
//erase the atoms belong to cutoff groups from freeAtoms vector |
| 164 |
< |
freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end()); |
| 165 |
< |
} |
| 166 |
< |
|
| 163 |
> |
//erase the atoms belong to cutoff groups from freeAtoms vector |
| 164 |
> |
freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), |
| 165 |
> |
freeAtoms.end()); |
| 166 |
> |
} |
| 167 |
|
} |
| 168 |
|
|
| 169 |
< |
//loop over the free atoms and then create one cutoff group for every single free atom |
| 169 |
> |
// loop over the free atoms and then create one cutoff group for |
| 170 |
> |
// every single free atom |
| 171 |
|
|
| 172 |
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 173 |
< |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 173 |
> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
| 174 |
|
mol->addCutoffGroup(cutoffGroup); |
| 175 |
|
} |
| 176 |
|
//create constraints |
| 177 |
|
createConstraintPair(mol); |
| 178 |
|
createConstraintElem(mol); |
| 179 |
|
|
| 180 |
+ |
// Does this molecule stamp define a total constrained charge value? |
| 181 |
+ |
// If so, let the created molecule know about it. |
| 182 |
+ |
|
| 183 |
+ |
if (molStamp->haveConstrainTotalCharge() ) { |
| 184 |
+ |
mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
| 185 |
+ |
} |
| 186 |
+ |
|
| 187 |
|
//the construction of this molecule is finished |
| 188 |
|
mol->complete(); |
| 189 |
< |
|
| 189 |
> |
|
| 190 |
|
return mol; |
| 191 |
|
} |
| 192 |
|
|
| 193 |
|
|
| 194 |
< |
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
| 195 |
< |
LocalIndexManager* localIndexMan) { |
| 194 |
> |
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, |
| 195 |
> |
AtomStamp* stamp, |
| 196 |
> |
LocalIndexManager* localIndexMan) { |
| 197 |
|
AtomType * atomType; |
| 198 |
|
Atom* atom; |
| 199 |
|
|
| 200 |
|
atomType = ff->getAtomType(stamp->getType()); |
| 201 |
< |
|
| 201 |
> |
|
| 202 |
|
if (atomType == NULL) { |
| 203 |
|
sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]", |
| 204 |
< |
stamp->getType()); |
| 204 |
> |
stamp->getType().c_str()); |
| 205 |
|
|
| 206 |
|
painCave.isFatal = 1; |
| 207 |
|
simError(); |
| 208 |
|
} |
| 209 |
< |
|
| 209 |
> |
|
| 210 |
|
//below code still have some kind of hard-coding smell |
| 211 |
|
if (atomType->isDirectional()){ |
| 186 |
– |
|
| 187 |
– |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 188 |
– |
|
| 189 |
– |
if (dAtomType == NULL) { |
| 190 |
– |
sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
| 212 |
|
|
| 192 |
– |
painCave.isFatal = 1; |
| 193 |
– |
simError(); |
| 194 |
– |
} |
| 195 |
– |
|
| 213 |
|
DirectionalAtom* dAtom; |
| 214 |
< |
dAtom = new DirectionalAtom(dAtomType); |
| 214 |
> |
dAtom = new DirectionalAtom(atomType); |
| 215 |
|
atom = dAtom; |
| 216 |
|
} |
| 217 |
|
else{ |
| 222 |
|
|
| 223 |
|
return atom; |
| 224 |
|
} |
| 225 |
< |
|
| 226 |
< |
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol, |
| 225 |
> |
|
| 226 |
> |
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
| 227 |
> |
Molecule* mol, |
| 228 |
|
RigidBodyStamp* rbStamp, |
| 229 |
|
LocalIndexManager* localIndexMan) { |
| 230 |
|
Atom* atom; |
| 235 |
|
RigidBody* rb = new RigidBody(); |
| 236 |
|
nAtoms = rbStamp->getNMembers(); |
| 237 |
|
for (int i = 0; i < nAtoms; ++i) { |
| 238 |
< |
//rbStamp->getMember(i) return the local index of current atom inside the molecule. |
| 239 |
< |
//It is not the same as local index of atom which is the index of atom at DataStorage class |
| 240 |
< |
atom = mol->getAtomAt(rbStamp->getMember(i)); |
| 241 |
< |
atomStamp= molStamp->getAtom(rbStamp->getMember(i)); |
| 238 |
> |
//rbStamp->getMember(i) return the local index of current atom |
| 239 |
> |
//inside the molecule. It is not the same as local index of |
| 240 |
> |
//atom which is the index of atom at DataStorage class |
| 241 |
> |
atom = mol->getAtomAt(rbStamp->getMemberAt(i)); |
| 242 |
> |
atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i)); |
| 243 |
|
rb->addAtom(atom, atomStamp); |
| 244 |
|
} |
| 245 |
|
|
| 246 |
< |
//after all of the atoms are added, we need to calculate the reference coordinates |
| 246 |
> |
//after all of the atoms are added, we need to calculate the |
| 247 |
> |
//reference coordinates |
| 248 |
|
rb->calcRefCoords(); |
| 249 |
|
|
| 250 |
|
//set the local index of this rigid body, global index will be set later |
| 256 |
|
//The third part is the index of the rigidbody defined in meta-data file |
| 257 |
|
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 258 |
|
/**@todo replace itoa by lexi_cast */ |
| 259 |
< |
std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
| 259 |
> |
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 260 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 261 |
|
|
| 262 |
|
return rb; |
| 263 |
|
} |
| 264 |
|
|
| 265 |
< |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) { |
| 265 |
> |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
| 266 |
> |
BondStamp* stamp) { |
| 267 |
|
BondType* bondType; |
| 268 |
|
Atom* atomA; |
| 269 |
|
Atom* atomB; |
| 270 |
< |
|
| 270 |
> |
|
| 271 |
|
atomA = mol->getAtomAt(stamp->getA()); |
| 272 |
|
atomB = mol->getAtomAt(stamp->getB()); |
| 273 |
< |
|
| 273 |
> |
|
| 274 |
|
assert( atomA && atomB); |
| 275 |
|
|
| 276 |
|
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
| 279 |
|
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
| 280 |
|
atomA->getType().c_str(), |
| 281 |
|
atomB->getType().c_str()); |
| 282 |
< |
|
| 282 |
> |
|
| 283 |
|
painCave.isFatal = 1; |
| 284 |
|
simError(); |
| 285 |
|
} |
| 286 |
|
return new Bond(atomA, atomB, bondType); |
| 287 |
|
} |
| 288 |
< |
|
| 289 |
< |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
| 290 |
< |
bool isGhostBend = false; |
| 291 |
< |
int ghostIndex; |
| 292 |
< |
|
| 293 |
< |
|
| 294 |
< |
// |
| 295 |
< |
if (stamp->haveExtras()){ |
| 296 |
< |
LinkedAssign* extras = stamp->getExtras(); |
| 297 |
< |
LinkedAssign* currentExtra = extras; |
| 298 |
< |
|
| 299 |
< |
while (currentExtra != NULL){ |
| 300 |
< |
if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){ |
| 301 |
< |
switch (currentExtra->getType()){ |
| 302 |
< |
case 0: |
| 303 |
< |
ghostIndex = currentExtra->getInt(); |
| 304 |
< |
isGhostBend = true; |
| 305 |
< |
break; |
| 306 |
< |
|
| 307 |
< |
default: |
| 308 |
< |
sprintf(painCave.errMsg, |
| 288 |
< |
"SimSetup Error: ghostVectorSource must be an int.\n"); |
| 289 |
< |
painCave.isFatal = 1; |
| 290 |
< |
simError(); |
| 291 |
< |
} |
| 292 |
< |
} else{ |
| 293 |
< |
sprintf(painCave.errMsg, |
| 294 |
< |
"SimSetup Error: unhandled bend assignment:\n"); |
| 295 |
< |
painCave.isFatal = 1; |
| 296 |
< |
simError(); |
| 297 |
< |
} |
| 298 |
< |
currentExtra = currentExtra->getNext(); |
| 299 |
< |
} |
| 288 |
> |
|
| 289 |
> |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
| 290 |
> |
BendStamp* stamp) { |
| 291 |
> |
Bend* bend = NULL; |
| 292 |
> |
std::vector<int> bendAtoms = stamp->getMembers(); |
| 293 |
> |
if (bendAtoms.size() == 3) { |
| 294 |
> |
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
| 295 |
> |
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
| 296 |
> |
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
| 297 |
> |
|
| 298 |
> |
assert( atomA && atomB && atomC); |
| 299 |
> |
|
| 300 |
> |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), |
| 301 |
> |
atomB->getType().c_str(), |
| 302 |
> |
atomC->getType().c_str()); |
| 303 |
> |
|
| 304 |
> |
if (bendType == NULL) { |
| 305 |
> |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 306 |
> |
atomA->getType().c_str(), |
| 307 |
> |
atomB->getType().c_str(), |
| 308 |
> |
atomC->getType().c_str()); |
| 309 |
|
|
| 310 |
< |
} |
| 311 |
< |
|
| 303 |
< |
if (isGhostBend) { |
| 304 |
< |
|
| 305 |
< |
int indexA = stamp->getA(); |
| 306 |
< |
int indexB= stamp->getB(); |
| 307 |
< |
|
| 308 |
< |
assert(indexA != indexB); |
| 309 |
< |
|
| 310 |
< |
int normalIndex; |
| 311 |
< |
if (indexA == ghostIndex) { |
| 312 |
< |
normalIndex = indexB; |
| 313 |
< |
} else if (indexB == ghostIndex) { |
| 314 |
< |
normalIndex = indexA; |
| 310 |
> |
painCave.isFatal = 1; |
| 311 |
> |
simError(); |
| 312 |
|
} |
| 313 |
< |
|
| 313 |
> |
|
| 314 |
> |
bend = new Bend(atomA, atomB, atomC, bendType); |
| 315 |
> |
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
| 316 |
> |
int ghostIndex = stamp->getGhostVectorSource(); |
| 317 |
> |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
| 318 |
|
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
| 319 |
|
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
| 320 |
|
if (ghostAtom == NULL) { |
| 334 |
|
painCave.isFatal = 1; |
| 335 |
|
simError(); |
| 336 |
|
} |
| 337 |
< |
|
| 338 |
< |
return new GhostBend(normalAtom, ghostAtom, bendType); |
| 337 |
> |
|
| 338 |
> |
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 339 |
> |
|
| 340 |
> |
} |
| 341 |
> |
|
| 342 |
> |
return bend; |
| 343 |
> |
} |
| 344 |
|
|
| 345 |
< |
} else { |
| 346 |
< |
|
| 341 |
< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
| 342 |
< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
| 343 |
< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
| 345 |
> |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
| 346 |
> |
TorsionStamp* stamp) { |
| 347 |
|
|
| 348 |
< |
assert( atomA && atomB && atomC); |
| 349 |
< |
|
| 350 |
< |
BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
| 351 |
< |
|
| 349 |
< |
if (bendType == NULL) { |
| 350 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
| 351 |
< |
atomA->getType().c_str(), |
| 352 |
< |
atomB->getType().c_str(), |
| 353 |
< |
atomC->getType().c_str()); |
| 354 |
< |
|
| 355 |
< |
painCave.isFatal = 1; |
| 356 |
< |
simError(); |
| 357 |
< |
} |
| 358 |
< |
|
| 359 |
< |
return new Bend(atomA, atomB, atomC, bendType); |
| 348 |
> |
Torsion* torsion = NULL; |
| 349 |
> |
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 350 |
> |
if (torsionAtoms.size() < 3) { |
| 351 |
> |
return torsion; |
| 352 |
|
} |
| 361 |
– |
} |
| 353 |
|
|
| 354 |
< |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
| 354 |
> |
Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
| 355 |
> |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
| 356 |
> |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
| 357 |
|
|
| 358 |
< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
| 359 |
< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
| 367 |
< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
| 368 |
< |
Torsion* torsion; |
| 358 |
> |
if (torsionAtoms.size() == 4) { |
| 359 |
> |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
| 360 |
|
|
| 370 |
– |
if (stamp->getD() != -1) { |
| 371 |
– |
Atom* atomD = mol->getAtomAt(stamp->getD()); |
| 372 |
– |
|
| 361 |
|
assert(atomA && atomB && atomC && atomD); |
| 362 |
|
|
| 363 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 364 |
< |
atomC->getType(), atomD->getType()); |
| 365 |
< |
|
| 363 |
> |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
| 364 |
> |
atomB->getType(), |
| 365 |
> |
atomC->getType(), |
| 366 |
> |
atomD->getType()); |
| 367 |
|
if (torsionType == NULL) { |
| 368 |
|
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 369 |
|
atomA->getType().c_str(), |
| 370 |
|
atomB->getType().c_str(), |
| 371 |
|
atomC->getType().c_str(), |
| 372 |
|
atomD->getType().c_str()); |
| 373 |
< |
|
| 373 |
> |
|
| 374 |
|
painCave.isFatal = 1; |
| 375 |
|
simError(); |
| 376 |
|
} |
| 377 |
< |
|
| 377 |
> |
|
| 378 |
|
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 379 |
|
} |
| 380 |
|
else { |
| 381 |
< |
|
| 382 |
< |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC); |
| 381 |
> |
|
| 382 |
> |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
| 383 |
|
if (dAtom == NULL) { |
| 384 |
|
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
| 385 |
|
painCave.isFatal = 1; |
| 386 |
|
simError(); |
| 387 |
|
} |
| 388 |
< |
|
| 388 |
> |
|
| 389 |
|
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 390 |
|
atomC->getType(), "GHOST"); |
| 391 |
< |
|
| 391 |
> |
|
| 392 |
|
if (torsionType == NULL) { |
| 393 |
|
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 394 |
|
atomA->getType().c_str(), |
| 395 |
|
atomB->getType().c_str(), |
| 396 |
|
atomC->getType().c_str(), |
| 397 |
|
"GHOST"); |
| 398 |
< |
|
| 398 |
> |
|
| 399 |
|
painCave.isFatal = 1; |
| 400 |
|
simError(); |
| 401 |
|
} |
| 402 |
< |
|
| 402 |
> |
|
| 403 |
|
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 404 |
|
} |
| 405 |
< |
|
| 405 |
> |
|
| 406 |
|
return torsion; |
| 407 |
|
} |
| 408 |
|
|
| 409 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 409 |
> |
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
| 410 |
> |
InversionStamp* stamp) { |
| 411 |
> |
|
| 412 |
> |
Inversion* inversion = NULL; |
| 413 |
> |
int center = stamp->getCenter(); |
| 414 |
> |
std::vector<int> satellites = stamp->getSatellites(); |
| 415 |
> |
if (satellites.size() != 3) { |
| 416 |
> |
return inversion; |
| 417 |
> |
} |
| 418 |
> |
|
| 419 |
> |
Atom* atomA = mol->getAtomAt(center); |
| 420 |
> |
Atom* atomB = mol->getAtomAt(satellites[0]); |
| 421 |
> |
Atom* atomC = mol->getAtomAt(satellites[1]); |
| 422 |
> |
Atom* atomD = mol->getAtomAt(satellites[2]); |
| 423 |
> |
|
| 424 |
> |
assert(atomA && atomB && atomC && atomD); |
| 425 |
> |
|
| 426 |
> |
InversionType* inversionType = ff->getInversionType(atomA->getType(), |
| 427 |
> |
atomB->getType(), |
| 428 |
> |
atomC->getType(), |
| 429 |
> |
atomD->getType()); |
| 430 |
> |
|
| 431 |
> |
if (inversionType == NULL) { |
| 432 |
> |
sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n" |
| 433 |
> |
"\t(May not be a problem: not all inversions are parametrized)\n", |
| 434 |
> |
atomA->getType().c_str(), |
| 435 |
> |
atomB->getType().c_str(), |
| 436 |
> |
atomC->getType().c_str(), |
| 437 |
> |
atomD->getType().c_str()); |
| 438 |
> |
|
| 439 |
> |
painCave.isFatal = 0; |
| 440 |
> |
painCave.severity = OPENMD_INFO; |
| 441 |
> |
simError(); |
| 442 |
> |
return NULL; |
| 443 |
> |
} else { |
| 444 |
> |
|
| 445 |
> |
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
| 446 |
> |
return inversion; |
| 447 |
> |
} |
| 448 |
> |
} |
| 449 |
> |
|
| 450 |
> |
|
| 451 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 452 |
> |
CutoffGroupStamp* stamp, |
| 453 |
> |
LocalIndexManager* localIndexMan) { |
| 454 |
|
int nAtoms; |
| 455 |
|
CutoffGroup* cg; |
| 456 |
|
Atom* atom; |
| 458 |
|
|
| 459 |
|
nAtoms = stamp->getNMembers(); |
| 460 |
|
for (int i =0; i < nAtoms; ++i) { |
| 461 |
< |
atom = mol->getAtomAt(stamp->getMember(i)); |
| 461 |
> |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
| 462 |
|
assert(atom); |
| 463 |
|
cg->addAtom(atom); |
| 464 |
|
} |
| 465 |
< |
|
| 465 |
> |
|
| 466 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 467 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 468 |
> |
|
| 469 |
|
return cg; |
| 470 |
|
} |
| 471 |
< |
|
| 472 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 471 |
> |
|
| 472 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 473 |
> |
LocalIndexManager* localIndexMan) { |
| 474 |
|
CutoffGroup* cg; |
| 475 |
|
cg = new CutoffGroup(); |
| 476 |
|
cg->addAtom(atom); |
| 477 |
+ |
|
| 478 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 479 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 480 |
+ |
|
| 481 |
|
return cg; |
| 482 |
|
} |
| 483 |
|
|
