1 |
tim |
1719 |
/* |
2 |
|
|
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
|
|
* |
4 |
|
|
* Contact: oopse@oopse.org |
5 |
|
|
* |
6 |
|
|
* This program is free software; you can redistribute it and/or |
7 |
|
|
* modify it under the terms of the GNU Lesser General Public License |
8 |
|
|
* as published by the Free Software Foundation; either version 2.1 |
9 |
|
|
* of the License, or (at your option) any later version. |
10 |
|
|
* All we ask is that proper credit is given for our work, which includes |
11 |
|
|
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
|
|
* of your source code files, and to any copyright notice that you may distribute |
13 |
|
|
* with programs based on this work. |
14 |
|
|
* |
15 |
|
|
* This program is distributed in the hope that it will be useful, |
16 |
|
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
|
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
|
|
* GNU Lesser General Public License for more details. |
19 |
|
|
* |
20 |
|
|
* You should have received a copy of the GNU Lesser General Public License |
21 |
|
|
* along with this program; if not, write to the Free Software |
22 |
|
|
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
|
|
* |
24 |
|
|
*/ |
25 |
|
|
|
26 |
|
|
/** |
27 |
|
|
* @file MoleculeCreator.cpp |
28 |
|
|
* @author tlin |
29 |
|
|
* @date 11/04/2004 |
30 |
|
|
* @time 13:44am |
31 |
|
|
* @version 1.0 |
32 |
|
|
*/ |
33 |
|
|
|
34 |
|
|
#include <cassert> |
35 |
|
|
|
36 |
tim |
1805 |
#include "brains/MoleculeCreator.hpp" |
37 |
|
|
#include "primitives/GhostBend.hpp" |
38 |
tim |
1832 |
#include "types/DirectionalAtomType.hpp" |
39 |
tim |
1805 |
#include "utils/simError.h" |
40 |
|
|
#include "utils/StringUtils.hpp" |
41 |
|
|
|
42 |
tim |
1719 |
namespace oopse { |
43 |
|
|
|
44 |
tim |
1805 |
Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
45 |
|
|
int stampId, int globalIndex, LocalIndexManager* localIndexMan) { |
46 |
|
|
|
47 |
tim |
1733 |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID()); |
48 |
tim |
1719 |
|
49 |
|
|
//create atoms |
50 |
|
|
Atom* atom; |
51 |
|
|
AtomStamp* currentAtomStamp; |
52 |
|
|
int nAtom = molStamp->getNAtoms(); |
53 |
|
|
for (int i = 0; i < nAtom; ++i) { |
54 |
|
|
currentAtomStamp = molStamp->getAtom(i); |
55 |
tim |
1805 |
atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
56 |
tim |
1719 |
mol->addAtom(atom); |
57 |
|
|
} |
58 |
|
|
|
59 |
|
|
//create rigidbodies |
60 |
|
|
RigidBody* rb; |
61 |
|
|
RigidBodyStamp * currentRigidBodyStamp; |
62 |
|
|
int nRigidbodies = molStamp->getNRigidBodies(); |
63 |
|
|
|
64 |
|
|
for (int i = 0; i < nRigidbodies; ++i) { |
65 |
|
|
currentRigidBodyStamp = molStamp->getRigidBody(i); |
66 |
tim |
1805 |
rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan); |
67 |
tim |
1719 |
mol->addRigidBody(rb); |
68 |
|
|
} |
69 |
|
|
|
70 |
|
|
//create bonds |
71 |
|
|
Bond* bond; |
72 |
|
|
BondStamp* currentBondStamp; |
73 |
|
|
int nBonds = molStamp->getNBends(); |
74 |
|
|
|
75 |
|
|
for (int i = 0; i < nBonds; ++i) { |
76 |
tim |
1805 |
currentBondStamp = molStamp->getBond(i); |
77 |
tim |
1719 |
bond = createBond(ff, mol, currentBondStamp); |
78 |
|
|
mol->addBond(bond); |
79 |
|
|
} |
80 |
|
|
|
81 |
|
|
//create bends |
82 |
|
|
Bend* bend; |
83 |
|
|
BendStamp* currentBendStamp; |
84 |
|
|
int nBends = molStamp->getNBends(); |
85 |
|
|
for (int i = 0; i < nBends; ++i) { |
86 |
|
|
currentBendStamp = molStamp->getBend(i); |
87 |
|
|
bend = createBend(ff, mol, currentBendStamp); |
88 |
|
|
mol->addBend(bend); |
89 |
|
|
} |
90 |
|
|
|
91 |
|
|
//create torsions |
92 |
|
|
Torsion* torsion; |
93 |
|
|
TorsionStamp* currentTorsionStamp; |
94 |
|
|
int nTorsions = molStamp->getNTorsions(); |
95 |
|
|
for (int i = 0; i < nTorsions; ++i) { |
96 |
|
|
currentTorsionStamp = molStamp->getTorsion(i); |
97 |
|
|
torsion = createTorsion(ff, mol, currentTorsionStamp); |
98 |
|
|
mol->addTorsion(torsion); |
99 |
|
|
} |
100 |
|
|
|
101 |
|
|
//create cutoffGroups |
102 |
|
|
CutoffGroup* cutoffGroup; |
103 |
|
|
CutoffGroupStamp* currentCutoffGroupStamp; |
104 |
|
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
105 |
|
|
for (int i = 0; i < nCutoffGroups; ++i) { |
106 |
|
|
currentCutoffGroupStamp = molStamp->getCutoffGroup(i); |
107 |
tim |
1805 |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
108 |
tim |
1719 |
mol->addCutoffGroup(cutoffGroup); |
109 |
|
|
} |
110 |
|
|
|
111 |
tim |
1734 |
//every free atom is a cutoff group |
112 |
|
|
std::set<Atom*> allAtoms; |
113 |
tim |
1805 |
Molecule::AtomIterator ai; |
114 |
tim |
1734 |
|
115 |
|
|
//add all atoms into allAtoms set |
116 |
|
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
117 |
|
|
allAtoms.insert(atom); |
118 |
|
|
} |
119 |
|
|
|
120 |
tim |
1805 |
Molecule::CutoffGroupIterator ci; |
121 |
tim |
1734 |
CutoffGroup* cg; |
122 |
|
|
std::set<Atom*> cutoffAtoms; |
123 |
|
|
|
124 |
|
|
//add all of the atoms belong to cutoff groups into cutoffAtoms set |
125 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
126 |
|
|
|
127 |
|
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
128 |
|
|
cutoffAtoms.insert(atom); |
129 |
|
|
} |
130 |
|
|
|
131 |
|
|
} |
132 |
|
|
|
133 |
|
|
//find all free atoms (which do not belong to cutoff groups) |
134 |
|
|
//performs the "difference" operation from set theory, the output range contains a copy of every |
135 |
|
|
//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
136 |
|
|
//[cutoffAtoms.begin(), cutoffAtoms.end()). |
137 |
|
|
std::vector<Atom*> freeAtoms; |
138 |
|
|
std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(), |
139 |
tim |
1805 |
std::back_inserter(freeAtoms)); |
140 |
tim |
1734 |
|
141 |
|
|
if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) { |
142 |
|
|
//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
143 |
|
|
sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule"); |
144 |
|
|
|
145 |
|
|
painCave.isFatal = 1; |
146 |
|
|
simError(); |
147 |
|
|
} |
148 |
|
|
|
149 |
|
|
//loop over the free atoms and then create one cutoff group for every single free atom |
150 |
|
|
std::vector<Atom*>::iterator fai; |
151 |
|
|
|
152 |
|
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
153 |
tim |
1842 |
cutoffGroup = createCutoffGroup(mol, *fai); |
154 |
tim |
1734 |
mol->addCutoffGroup(cutoffGroup); |
155 |
|
|
} |
156 |
tim |
1719 |
//create constraints |
157 |
|
|
|
158 |
|
|
//the construction of this molecule is finished |
159 |
|
|
mol->complete(); |
160 |
|
|
|
161 |
|
|
return mol; |
162 |
|
|
} |
163 |
|
|
|
164 |
|
|
|
165 |
|
|
Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
166 |
|
|
LocalIndexManager* localIndexMan) { |
167 |
|
|
AtomType * atomType; |
168 |
|
|
Atom* atom; |
169 |
|
|
|
170 |
|
|
atomType = ff->getAtomType(stamp->getType()); |
171 |
|
|
|
172 |
tim |
1804 |
if (atomType == NULL) { |
173 |
tim |
1733 |
sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]", |
174 |
|
|
stamp->getType()); |
175 |
|
|
|
176 |
|
|
painCave.isFatal = 1; |
177 |
|
|
simError(); |
178 |
|
|
} |
179 |
|
|
|
180 |
tim |
1719 |
//below code still have some kind of hard-coding smell |
181 |
tim |
1813 |
if (atomType->isDirectional()){ |
182 |
|
|
|
183 |
tim |
1804 |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
184 |
tim |
1813 |
|
185 |
tim |
1804 |
if (dAtomType == NULL) { |
186 |
|
|
sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
187 |
|
|
|
188 |
|
|
painCave.isFatal = 1; |
189 |
|
|
simError(); |
190 |
|
|
} |
191 |
tim |
1813 |
|
192 |
|
|
DirectionalAtom* dAtom; |
193 |
tim |
1804 |
dAtom = new DirectionalAtom(dAtomType); |
194 |
tim |
1719 |
atom = dAtom; |
195 |
|
|
} |
196 |
|
|
else{ |
197 |
|
|
atom = new Atom(atomType); |
198 |
|
|
} |
199 |
|
|
|
200 |
|
|
atom->setLocalIndex(localIndexMan->getNextAtomIndex()); |
201 |
tim |
1805 |
|
202 |
|
|
return atom; |
203 |
tim |
1719 |
} |
204 |
|
|
|
205 |
|
|
RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol, |
206 |
|
|
RigidBodyStamp* rbStamp, |
207 |
|
|
LocalIndexManager* localIndexMan) { |
208 |
|
|
Atom* atom; |
209 |
|
|
int nAtoms; |
210 |
|
|
Vector3d refCoor; |
211 |
|
|
AtomStamp* atomStamp; |
212 |
|
|
|
213 |
|
|
RigidBody* rb = new RigidBody(); |
214 |
tim |
1805 |
nAtoms = rbStamp->getNMembers(); |
215 |
tim |
1719 |
for (int i = 0; i < nAtoms; ++i) { |
216 |
|
|
//rbStamp->getMember(i) return the local index of current atom inside the molecule. |
217 |
|
|
//It is not the same as local index of atom which is the index of atom at DataStorage class |
218 |
|
|
atom = mol->getAtomAt(rbStamp->getMember(i)); |
219 |
tim |
1805 |
atomStamp= molStamp->getAtom(rbStamp->getMember(i)); |
220 |
tim |
1719 |
rb->addAtom(atom, atomStamp); |
221 |
|
|
} |
222 |
tim |
1733 |
|
223 |
|
|
//after all of the atoms are added, we need to calculate the reference coordinates |
224 |
tim |
1719 |
rb->calcRefCoords(); |
225 |
tim |
1733 |
|
226 |
|
|
//set the local index of this rigid body, global index will be set later |
227 |
tim |
1719 |
rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
228 |
tim |
1733 |
|
229 |
|
|
//the rule for naming rigidbody MoleculeName_RB_Integer |
230 |
|
|
//The first part is the name of the molecule |
231 |
|
|
//The second part is alway fixed as "RB" |
232 |
|
|
//The third part is the index of the rigidbody defined in meta-data file |
233 |
|
|
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
234 |
tim |
1805 |
/**@todo replace itoa by lexi_cast */ |
235 |
|
|
rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies())); |
236 |
tim |
1719 |
|
237 |
|
|
return rb; |
238 |
|
|
} |
239 |
|
|
|
240 |
|
|
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) { |
241 |
|
|
BondType* bondType; |
242 |
|
|
Atom* atomA; |
243 |
|
|
Atom* atomB; |
244 |
|
|
|
245 |
|
|
atomA = mol->getAtomAt(stamp->getA()); |
246 |
|
|
atomB = mol->getAtomAt(stamp->getB()); |
247 |
|
|
|
248 |
|
|
assert( atomA && atomB); |
249 |
|
|
|
250 |
tim |
1805 |
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
251 |
tim |
1719 |
|
252 |
tim |
1733 |
if (bondType == NULL) { |
253 |
|
|
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
254 |
|
|
atomA->getType().c_str(), |
255 |
|
|
atomB->getType().c_str()); |
256 |
|
|
|
257 |
|
|
painCave.isFatal = 1; |
258 |
|
|
simError(); |
259 |
|
|
} |
260 |
tim |
1719 |
return new Bond(atomA, atomB, bondType); |
261 |
|
|
} |
262 |
|
|
|
263 |
|
|
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
264 |
tim |
1774 |
bool isGhostBend = false; |
265 |
|
|
int ghostIndex; |
266 |
tim |
1719 |
|
267 |
|
|
|
268 |
tim |
1774 |
// |
269 |
|
|
if (stamp->haveExtras()){ |
270 |
tim |
1805 |
LinkedAssign* extras = stamp->getExtras(); |
271 |
tim |
1774 |
LinkedAssign* currentExtra = extras; |
272 |
tim |
1719 |
|
273 |
tim |
1774 |
while (currentExtra != NULL){ |
274 |
|
|
if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){ |
275 |
|
|
switch (currentExtra->getType()){ |
276 |
|
|
case 0: |
277 |
|
|
ghostIndex = currentExtra->getInt(); |
278 |
|
|
isGhostBend = true; |
279 |
|
|
break; |
280 |
tim |
1719 |
|
281 |
tim |
1774 |
default: |
282 |
|
|
sprintf(painCave.errMsg, |
283 |
|
|
"SimSetup Error: ghostVectorSource must be an int.\n"); |
284 |
|
|
painCave.isFatal = 1; |
285 |
|
|
simError(); |
286 |
|
|
} |
287 |
|
|
} else{ |
288 |
|
|
sprintf(painCave.errMsg, |
289 |
|
|
"SimSetup Error: unhandled bend assignment:\n"); |
290 |
|
|
painCave.isFatal = 1; |
291 |
|
|
simError(); |
292 |
|
|
} |
293 |
|
|
currentExtra = currentExtra->getNext(); |
294 |
|
|
} |
295 |
|
|
|
296 |
tim |
1733 |
} |
297 |
|
|
|
298 |
tim |
1774 |
if (isGhostBend) { |
299 |
tim |
1733 |
|
300 |
tim |
1774 |
int indexA = stamp->getA(); |
301 |
|
|
int indexB= stamp->getB(); |
302 |
|
|
|
303 |
|
|
assert(indexA != indexB); |
304 |
|
|
|
305 |
|
|
int normalIndex; |
306 |
|
|
if (indexA == ghostIndex) { |
307 |
|
|
normalIndex = indexB; |
308 |
|
|
} else if (indexB == ghostIndex) { |
309 |
|
|
normalIndex = indexA; |
310 |
|
|
} |
311 |
|
|
|
312 |
tim |
1805 |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
313 |
|
|
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
314 |
|
|
if (ghostAtom == NULL) { |
315 |
|
|
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
316 |
|
|
painCave.isFatal = 1; |
317 |
|
|
simError(); |
318 |
|
|
} |
319 |
|
|
|
320 |
tim |
1774 |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
321 |
|
|
|
322 |
|
|
if (bendType == NULL) { |
323 |
|
|
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
324 |
|
|
normalAtom->getType().c_str(), |
325 |
|
|
ghostAtom->getType().c_str(), |
326 |
|
|
"GHOST"); |
327 |
|
|
|
328 |
|
|
painCave.isFatal = 1; |
329 |
|
|
simError(); |
330 |
|
|
} |
331 |
tim |
1805 |
|
332 |
tim |
1774 |
return new GhostBend(normalAtom, ghostAtom, bendType); |
333 |
|
|
|
334 |
|
|
} else { |
335 |
|
|
|
336 |
|
|
Atom* atomA = mol->getAtomAt(stamp->getA()); |
337 |
|
|
Atom* atomB = mol->getAtomAt(stamp->getB()); |
338 |
|
|
Atom* atomC = mol->getAtomAt(stamp->getC()); |
339 |
|
|
|
340 |
|
|
assert( atomA && atomB && atomC); |
341 |
|
|
|
342 |
|
|
BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
343 |
|
|
|
344 |
|
|
if (bendType == NULL) { |
345 |
|
|
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
346 |
|
|
atomA->getType().c_str(), |
347 |
|
|
atomB->getType().c_str(), |
348 |
|
|
atomC->getType().c_str()); |
349 |
|
|
|
350 |
|
|
painCave.isFatal = 1; |
351 |
|
|
simError(); |
352 |
|
|
} |
353 |
|
|
|
354 |
|
|
return new Bend(atomA, atomB, atomC, bendType); |
355 |
|
|
} |
356 |
tim |
1719 |
} |
357 |
|
|
|
358 |
|
|
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
359 |
|
|
TorsionType* torsionType; |
360 |
|
|
Atom* atomA; |
361 |
|
|
Atom* atomB; |
362 |
|
|
Atom* atomC; |
363 |
|
|
Atom* atomD; |
364 |
|
|
|
365 |
|
|
atomA = mol->getAtomAt(stamp->getA()); |
366 |
|
|
atomB = mol->getAtomAt(stamp->getB()); |
367 |
|
|
atomC = mol->getAtomAt(stamp->getC()); |
368 |
|
|
atomD = mol->getAtomAt(stamp->getD()); |
369 |
|
|
|
370 |
|
|
assert(atomA && atomB && atomC && atomD); |
371 |
|
|
|
372 |
tim |
1805 |
torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
373 |
tim |
1719 |
atomC->getType(), atomD->getType()); |
374 |
|
|
|
375 |
tim |
1733 |
if (torsionType == NULL) { |
376 |
|
|
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
377 |
|
|
atomA->getType().c_str(), |
378 |
|
|
atomB->getType().c_str(), |
379 |
|
|
atomC->getType().c_str(), |
380 |
|
|
atomD->getType().c_str()); |
381 |
|
|
|
382 |
|
|
painCave.isFatal = 1; |
383 |
|
|
simError(); |
384 |
|
|
} |
385 |
|
|
|
386 |
tim |
1805 |
return new Torsion(atomA, atomB, atomC, atomD, torsionType); |
387 |
tim |
1719 |
} |
388 |
|
|
|
389 |
|
|
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
390 |
|
|
int nAtoms; |
391 |
|
|
CutoffGroup* cg; |
392 |
|
|
Atom* atom; |
393 |
|
|
cg = new CutoffGroup(); |
394 |
|
|
|
395 |
|
|
nAtoms = stamp->getNMembers(); |
396 |
|
|
for (int i =0; i < nAtoms; ++i) { |
397 |
|
|
atom = mol->getAtomAt(stamp->getMember(i)); |
398 |
|
|
assert(atom); |
399 |
|
|
cg->addAtom(atom); |
400 |
|
|
} |
401 |
|
|
|
402 |
|
|
return cg; |
403 |
|
|
} |
404 |
|
|
|
405 |
tim |
1734 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
406 |
|
|
CutoffGroup* cg; |
407 |
|
|
cg = new CutoffGroup(); |
408 |
tim |
1805 |
cg->addAtom(atom); |
409 |
tim |
1734 |
return cg; |
410 |
|
|
} |
411 |
tim |
1719 |
//Constraint* MoleculeCreator::createConstraint() { |
412 |
|
|
|
413 |
|
|
//} |
414 |
|
|
|
415 |
|
|
} |