38 |
|
* University of Notre Dame has been advised of the possibility of |
39 |
|
* such damages. |
40 |
|
*/ |
41 |
– |
|
42 |
– |
#include <stdlib.h> |
43 |
– |
#include <stdio.h> |
44 |
– |
#include <string.h> |
45 |
– |
#include <iostream> |
41 |
|
|
42 |
+ |
#include <functional> |
43 |
+ |
#include <iostream> |
44 |
+ |
#include <sstream> |
45 |
|
#include "types/MoleculeStamp.hpp" |
46 |
+ |
#include "utils/Tuple.hpp" |
47 |
|
|
48 |
|
namespace oopse { |
49 |
+ |
|
50 |
+ |
template<class ContainerType> |
51 |
+ |
std::string containerToString(ContainerType& cont) { |
52 |
+ |
std::ostringstream oss; |
53 |
+ |
oss << "("; |
54 |
+ |
typename ContainerType::iterator i = cont.begin(); |
55 |
+ |
if (i != cont.end()) { |
56 |
+ |
oss << *i; |
57 |
+ |
++i; |
58 |
+ |
} |
59 |
+ |
for (; i != cont.end();++i) { |
60 |
+ |
oss << ", "; |
61 |
+ |
oss << *i; |
62 |
+ |
} |
63 |
+ |
oss << ")"; |
64 |
+ |
return oss.str(); |
65 |
+ |
} |
66 |
+ |
|
67 |
|
MoleculeStamp::MoleculeStamp() { |
68 |
|
DefineParameter(Name, "name"); |
69 |
|
|
83 |
|
bool MoleculeStamp::addAtomStamp( AtomStamp* atom) { |
84 |
|
bool ret = addIndexSensitiveStamp(atomStamps_, atom); |
85 |
|
if (!ret) { |
86 |
< |
std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName() << " Molecule\n"; |
86 |
> |
std::cout<< "Error in Molecule " << getName() << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n"; |
87 |
|
} |
88 |
|
return ret; |
89 |
|
|
107 |
|
bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) { |
108 |
|
bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody); |
109 |
|
if (!ret) { |
110 |
< |
std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName() << " Molecule\n"; |
110 |
> |
std::cout<< "Error in Molecule " << getName() << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n"; |
111 |
|
} |
112 |
|
return ret; |
113 |
|
} |
124 |
|
void MoleculeStamp::validate() { |
125 |
|
DataHolder::validate(); |
126 |
|
|
127 |
+ |
atom2Rigidbody.resize(getNAtoms()); |
128 |
+ |
// negative number means atom is a free atom, does not belong to rigidbody |
129 |
+ |
//every element in atom2Rigidbody has unique negative number at the very beginning |
130 |
+ |
for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
131 |
+ |
atom2Rigidbody[i] = -1 - i; |
132 |
+ |
} |
133 |
+ |
for (int i = 0; i < getNRigidBodies(); ++i) { |
134 |
+ |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
135 |
+ |
std::vector<int> members = rbStamp->getMembers(); |
136 |
+ |
for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
137 |
+ |
atom2Rigidbody[*j] = i; |
138 |
+ |
} |
139 |
+ |
} |
140 |
+ |
|
141 |
+ |
checkAtoms(); |
142 |
+ |
checkBonds(); |
143 |
+ |
fillBondInfo(); |
144 |
+ |
checkBends(); |
145 |
+ |
checkTorsions(); |
146 |
+ |
checkRigidBodies(); |
147 |
+ |
checkCutoffGroups(); |
148 |
+ |
checkFragments(); |
149 |
+ |
|
150 |
+ |
int nrigidAtoms = 0; |
151 |
+ |
for (int i = 0; i < getNRigidBodies(); ++i) { |
152 |
+ |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
153 |
+ |
nrigidAtoms += rbStamp->getNMembers(); |
154 |
+ |
} |
155 |
+ |
nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
156 |
+ |
|
157 |
+ |
} |
158 |
+ |
|
159 |
+ |
void MoleculeStamp::checkAtoms() { |
160 |
|
std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL)); |
161 |
|
if (ai != atomStamps_.end()) { |
162 |
|
std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
163 |
|
} |
164 |
|
|
165 |
< |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
116 |
< |
if (ri != rigidBodyStamps_.end()) { |
117 |
< |
std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
118 |
< |
} |
119 |
< |
|
120 |
< |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
121 |
< |
if (fi != fragmentStamps_.end()) { |
122 |
< |
std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
123 |
< |
} |
165 |
> |
} |
166 |
|
|
167 |
+ |
void MoleculeStamp::checkBonds() { |
168 |
|
//make sure index is not out of range |
169 |
|
int natoms = getNAtoms(); |
170 |
|
for(int i = 0; i < getNBonds(); ++i) { |
171 |
|
BondStamp* bondStamp = getBondStamp(i); |
172 |
|
if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) { |
173 |
< |
std::cout << "Error in Molecule " << getName() << ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n"; |
173 |
> |
std::cout << "Error in Molecule " << getName() << ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n"; |
174 |
|
} |
175 |
|
} |
176 |
< |
for(int i = 0; i < getNBends(); ++i) { |
177 |
< |
BendStamp* bendStamp = getBendStamp(i); |
178 |
< |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
179 |
< |
std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
180 |
< |
if (j != bendAtoms.end()) { |
181 |
< |
std::cout << "Error in Molecule " << getName(); |
176 |
> |
|
177 |
> |
//make sure bonds are unique |
178 |
> |
std::set<std::pair<int, int> > allBonds; |
179 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
180 |
> |
BondStamp* bondStamp= getBondStamp(i); |
181 |
> |
std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB()); |
182 |
> |
//make sure bondTuple.first is always less than or equal to bondTuple.third |
183 |
> |
if (bondPair.first > bondPair.second) { |
184 |
> |
std::swap(bondPair.first, bondPair.second); |
185 |
|
} |
186 |
< |
|
187 |
< |
if (bendAtoms.size() == 2 && !bendStamp->haveGhostVectorSource()) { |
188 |
< |
std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing"; |
186 |
> |
|
187 |
> |
std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
188 |
> |
if ( iter != allBonds.end()) { |
189 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ")appears multiple times\n"; |
190 |
> |
} else { |
191 |
> |
allBonds.insert(bondPair); |
192 |
|
} |
144 |
– |
} |
145 |
– |
for(int i = 0; i < getNBends(); ++i) { |
146 |
– |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
147 |
– |
std::vector<int> torsionAtoms = torsionStamp ->getMembers(); |
148 |
– |
std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
149 |
– |
if (j != torsionAtoms.end()) { |
150 |
– |
std::cout << "Error in Molecule " << getName(); |
151 |
– |
} |
193 |
|
} |
194 |
< |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
195 |
< |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
196 |
< |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
197 |
< |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
198 |
< |
if (j != cutoffGroupAtoms.end()) { |
199 |
< |
std::cout << "Error in Molecule " << getName(); |
194 |
> |
|
195 |
> |
//make sure atoms belong to same rigidbody do not bond to each other |
196 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
197 |
> |
BondStamp* bondStamp = getBondStamp(i); |
198 |
> |
if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) { |
199 |
> |
std::cout << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
200 |
|
} |
201 |
|
} |
202 |
< |
|
203 |
< |
atom2Rigidbody.resize(natoms); |
204 |
< |
// negative number means atom is a free atom, does not belong to rigidbody |
205 |
< |
//every element in atom2Rigidbody has unique negative number at the very beginning |
206 |
< |
for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
207 |
< |
atom2Rigidbody[i] = -1 - i; |
202 |
> |
|
203 |
> |
} |
204 |
> |
|
205 |
> |
struct BendLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
206 |
> |
bool operator()(IntTuple3 b1, IntTuple3 b2) { |
207 |
> |
return b1.first < b2.first |
208 |
> |
|| (!(b2.first < b1.first) && b1.second < b2.second) |
209 |
> |
|| (!(b2.first < b1.first) && !(b2.second < b2.second) && b1.third < b2.third); |
210 |
|
} |
211 |
+ |
}; |
212 |
|
|
213 |
< |
for (int i = 0; i < getNRigidBodies(); ++i) { |
214 |
< |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
215 |
< |
std::vector<int> members = rbStamp->getMembers(); |
216 |
< |
for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
217 |
< |
atom2Rigidbody[*j] = i; |
213 |
> |
void MoleculeStamp::checkBends() { |
214 |
> |
for(int i = 0; i < getNBends(); ++i) { |
215 |
> |
BendStamp* bendStamp = getBendStamp(i); |
216 |
> |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
217 |
> |
std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
218 |
> |
if (j != bendAtoms.end()) { |
219 |
> |
std::cout << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << "have invalid indices\n"; |
220 |
|
} |
221 |
< |
} |
222 |
< |
//make sure atoms belong to same rigidbody do not bond to each other |
223 |
< |
for(int i = 0; i < getNBonds(); ++i) { |
224 |
< |
BondStamp* bondStamp = getBondStamp(i); |
225 |
< |
if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) |
226 |
< |
std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << "belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
221 |
> |
|
222 |
> |
if (bendAtoms.size() == 2 ) { |
223 |
> |
if (!bendStamp->haveGhostVectorSource()) { |
224 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
225 |
> |
}else{ |
226 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
227 |
> |
if (ghostIndex < getNAtoms()) { |
228 |
> |
if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
229 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
230 |
> |
} |
231 |
> |
if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
232 |
> |
std::cout << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
233 |
> |
} |
234 |
> |
}else { |
235 |
> |
std::cout << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
236 |
> |
} |
237 |
> |
} |
238 |
> |
} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
239 |
> |
std::cout << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
240 |
|
} |
241 |
< |
|
241 |
> |
} |
242 |
> |
|
243 |
|
for(int i = 0; i < getNBends(); ++i) { |
244 |
|
BendStamp* bendStamp = getBendStamp(i); |
245 |
|
std::vector<int> bendAtoms = bendStamp->getMembers(); |
250 |
|
if (rigidbodyIndex >= 0) { |
251 |
|
++rigidSet[rigidbodyIndex]; |
252 |
|
if (rigidSet[rigidbodyIndex] > 1) { |
253 |
< |
std::cout << "Error in Molecule " << getName() << ": "; |
194 |
< |
//std::cout << "atoms of bend " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
253 |
> |
std::cout << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n"; |
254 |
|
} |
255 |
|
} |
256 |
|
} |
257 |
< |
} |
257 |
> |
} |
258 |
> |
|
259 |
> |
|
260 |
> |
std::set<IntTuple3, BendLessThan> allBends; |
261 |
> |
std::set<IntTuple3, BendLessThan>::iterator iter; |
262 |
> |
for(int i = 0; i < getNBends(); ++i) { |
263 |
> |
BendStamp* bendStamp= getBendStamp(i); |
264 |
> |
std::vector<int> bend = bendStamp->getMembers(); |
265 |
> |
if (bend.size() == 2) { |
266 |
> |
// in case we have two ghost bend. For example, |
267 |
> |
// bend { |
268 |
> |
// members (0, 1); |
269 |
> |
// ghostVectorSource = 0; |
270 |
> |
// } |
271 |
> |
// and |
272 |
> |
// bend { |
273 |
> |
// members (0, 1); |
274 |
> |
// ghostVectorSource = 0; |
275 |
> |
// } |
276 |
> |
// In order to distinguish them. we expand them to Tuple3. |
277 |
> |
// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
278 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
279 |
> |
std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
280 |
> |
if (j != bend.end()) { |
281 |
> |
bend.insert(j, ghostIndex); |
282 |
> |
} |
283 |
> |
} |
284 |
> |
|
285 |
> |
IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
286 |
> |
//make sure bendTuple.first is always less than or equal to bendTuple.third |
287 |
> |
if (bendTuple.first > bendTuple.third) { |
288 |
> |
std::swap(bendTuple.first, bendTuple.third); |
289 |
> |
} |
290 |
> |
|
291 |
> |
iter = allBends.find(bendTuple); |
292 |
> |
if ( iter != allBends.end()) { |
293 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n"; |
294 |
> |
} else { |
295 |
> |
allBends.insert(bendTuple); |
296 |
> |
} |
297 |
> |
} |
298 |
> |
|
299 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
300 |
> |
BondStamp* bondStamp = getBondStamp(i); |
301 |
> |
int a = bondStamp->getA(); |
302 |
> |
int b = bondStamp->getB(); |
303 |
> |
|
304 |
> |
AtomStamp* atomA = getAtomStamp(a); |
305 |
> |
AtomStamp* atomB = getAtomStamp(b); |
306 |
> |
|
307 |
> |
//find bend c--a--b |
308 |
> |
AtomStamp::AtomIter ai; |
309 |
> |
for(int c= atomA->getFirstBonedAtom(ai);c != -1;c = atomA->getNextBonedAtom(ai)) |
310 |
> |
{ |
311 |
> |
if(b == c) |
312 |
> |
continue; |
313 |
> |
|
314 |
> |
IntTuple3 newBend(c, a, b); |
315 |
> |
if (newBend.first > newBend.third) { |
316 |
> |
std::swap(newBend.first, newBend.third); |
317 |
> |
} |
318 |
> |
|
319 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
320 |
> |
allBends.insert(newBend); |
321 |
> |
BendStamp * newBendStamp = new BendStamp(); |
322 |
> |
newBendStamp->setMembers(newBend); |
323 |
> |
addBendStamp(newBendStamp); |
324 |
> |
} |
325 |
> |
} |
326 |
> |
|
327 |
> |
//find bend a--b--c |
328 |
> |
for(int c= atomB->getFirstBonedAtom(ai);c != -1;c = atomB->getNextBonedAtom(ai)) |
329 |
> |
{ |
330 |
> |
if(a == c) |
331 |
> |
continue; |
332 |
> |
|
333 |
> |
IntTuple3 newBend( a, b, c); |
334 |
> |
if (newBend.first > newBend.third) { |
335 |
> |
std::swap(newBend.first, newBend.third); |
336 |
> |
} |
337 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
338 |
> |
allBends.insert(newBend); |
339 |
> |
BendStamp * newBendStamp = new BendStamp(); |
340 |
> |
newBendStamp->setMembers(newBend); |
341 |
> |
addBendStamp(newBendStamp); |
342 |
> |
} |
343 |
> |
} |
344 |
> |
} |
345 |
> |
|
346 |
> |
} |
347 |
> |
|
348 |
> |
struct TorsionLessThan : public std::binary_function<IntTuple4, IntTuple4, bool> { |
349 |
> |
bool operator()(IntTuple4 t1, IntTuple4 t2) { |
350 |
> |
|
351 |
> |
return t1.first < t2.first |
352 |
> |
|| (!(t2.first < t1.first) && t1.second < t2.second) |
353 |
> |
|| (!(t2.first < t1.first) && !(t2.second < t2.second) && t1.third < t2.third) |
354 |
> |
||(!(t2.first < t1.first) && !(t2.second < t2.second) && !(t2.third < t1.third) && t1.fourth < t2.fourth); |
355 |
> |
} |
356 |
> |
|
357 |
> |
|
358 |
> |
|
359 |
> |
}; |
360 |
> |
|
361 |
> |
|
362 |
> |
void MoleculeStamp::checkTorsions() { |
363 |
|
for(int i = 0; i < getNTorsions(); ++i) { |
364 |
|
TorsionStamp* torsionStamp = getTorsionStamp(i); |
365 |
+ |
std::vector<int> torsionAtoms = torsionStamp ->getMembers(); |
366 |
+ |
std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
367 |
+ |
if (j != torsionAtoms.end()) { |
368 |
+ |
std::cout << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n"; |
369 |
+ |
} |
370 |
+ |
} |
371 |
+ |
|
372 |
+ |
for(int i = 0; i < getNTorsions(); ++i) { |
373 |
+ |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
374 |
|
std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
375 |
|
std::vector<int> rigidSet(getNRigidBodies(), 0); |
376 |
|
std::vector<int>::iterator j; |
379 |
|
if (rigidbodyIndex >= 0) { |
380 |
|
++rigidSet[rigidbodyIndex]; |
381 |
|
if (rigidSet[rigidbodyIndex] > 1) { |
382 |
< |
std::cout << "Error in Molecule " << getName() << ": "; |
210 |
< |
//std::cout << "atoms of torsion " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
382 |
> |
std::cout << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n"; |
383 |
|
} |
384 |
|
} |
385 |
|
} |
386 |
< |
} |
386 |
> |
} |
387 |
|
|
388 |
+ |
std::set<IntTuple4, TorsionLessThan> allTorsions; |
389 |
+ |
std::set<IntTuple4, TorsionLessThan>::iterator iter; |
390 |
+ |
for(int i = 0; i < getNTorsions(); ++i) { |
391 |
+ |
TorsionStamp* torsionStamp= getTorsionStamp(i); |
392 |
+ |
std::vector<int> torsion = torsionStamp->getMembers(); |
393 |
+ |
if (torsion.size() == 3) { |
394 |
+ |
int ghostIndex = torsionStamp->getGhostVectorSource(); |
395 |
+ |
std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
396 |
+ |
if (j != torsion.end()) { |
397 |
+ |
torsion.insert(j, ghostIndex); |
398 |
+ |
} |
399 |
+ |
} |
400 |
|
|
401 |
< |
//fill in bond information into atom |
402 |
< |
fillBondInfo(); |
403 |
< |
findBends(); |
404 |
< |
findTorsions(); |
401 |
> |
IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
402 |
> |
if (torsionTuple.first > torsionTuple.fourth) { |
403 |
> |
std::swap(torsionTuple.first, torsionTuple.fourth); |
404 |
> |
std::swap(torsionTuple.second, torsionTuple.third); |
405 |
> |
} |
406 |
|
|
407 |
< |
int nrigidAtoms = 0; |
407 |
> |
iter = allTorsions.find(torsionTuple); |
408 |
> |
if ( iter == allTorsions.end()) { |
409 |
> |
allTorsions.insert(torsionTuple); |
410 |
> |
} else { |
411 |
> |
std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n"; |
412 |
> |
} |
413 |
> |
} |
414 |
> |
|
415 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
416 |
> |
BondStamp* bondStamp = getBondStamp(i); |
417 |
> |
int b = bondStamp->getA(); |
418 |
> |
int c = bondStamp->getB(); |
419 |
> |
|
420 |
> |
AtomStamp* atomB = getAtomStamp(b); |
421 |
> |
AtomStamp* atomC = getAtomStamp(c); |
422 |
> |
|
423 |
> |
AtomStamp::AtomIter ai2; |
424 |
> |
AtomStamp::AtomIter ai3; |
425 |
> |
|
426 |
> |
for(int a = atomB->getFirstBonedAtom(ai2);a != -1;a = atomB->getNextBonedAtom(ai2)) |
427 |
> |
{ |
428 |
> |
if(a == c) |
429 |
> |
continue; |
430 |
> |
|
431 |
> |
for(int d = atomC->getFirstBonedAtom(ai3);d != -1;d = atomC->getNextBonedAtom(ai3)) |
432 |
> |
{ |
433 |
> |
if(d == b) |
434 |
> |
continue; |
435 |
> |
|
436 |
> |
IntTuple4 newTorsion(a, b, c, d); |
437 |
> |
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
438 |
> |
if (newTorsion.first > newTorsion.fourth) { |
439 |
> |
std::swap(newTorsion.first, newTorsion.fourth); |
440 |
> |
std::swap(newTorsion.second, newTorsion.third); |
441 |
> |
} |
442 |
> |
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
443 |
> |
allTorsions.insert(newTorsion); |
444 |
> |
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
445 |
> |
newTorsionStamp->setMembers(newTorsion); |
446 |
> |
addTorsionStamp(newTorsionStamp); |
447 |
> |
} |
448 |
> |
} |
449 |
> |
} |
450 |
> |
} |
451 |
> |
|
452 |
> |
} |
453 |
> |
|
454 |
> |
void MoleculeStamp::checkRigidBodies() { |
455 |
> |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
456 |
> |
if (ri != rigidBodyStamps_.end()) { |
457 |
> |
std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
458 |
> |
} |
459 |
> |
|
460 |
|
for (int i = 0; i < getNRigidBodies(); ++i) { |
461 |
|
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
462 |
< |
nrigidAtoms += rbStamp->getNMembers(); |
463 |
< |
} |
464 |
< |
nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
462 |
> |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
463 |
> |
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
464 |
> |
if (j != rigidAtoms.end()) { |
465 |
> |
std::cout << "Error in Molecule " << getName(); |
466 |
> |
} |
467 |
> |
|
468 |
> |
} |
469 |
> |
} |
470 |
|
|
471 |
< |
} |
471 |
> |
void MoleculeStamp::checkCutoffGroups() { |
472 |
|
|
473 |
< |
void MoleculeStamp::fillBondInfo() { |
473 |
> |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
474 |
> |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
475 |
> |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
476 |
> |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
477 |
> |
if (j != cutoffGroupAtoms.end()) { |
478 |
> |
std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
479 |
> |
} |
480 |
> |
} |
481 |
|
} |
482 |
|
|
483 |
< |
void MoleculeStamp::findBends() { |
483 |
> |
void MoleculeStamp::checkFragments() { |
484 |
|
|
485 |
+ |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
486 |
+ |
if (fi != fragmentStamps_.end()) { |
487 |
+ |
std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
488 |
+ |
} |
489 |
+ |
|
490 |
|
} |
491 |
|
|
492 |
< |
void MoleculeStamp::findTorsions() { |
492 |
> |
void MoleculeStamp::fillBondInfo() { |
493 |
|
|
494 |
+ |
for (int i = 0; i < getNBonds(); ++i) { |
495 |
+ |
BondStamp* bondStamp = getBondStamp(i); |
496 |
+ |
int a = bondStamp->getA(); |
497 |
+ |
int b = bondStamp->getB(); |
498 |
+ |
AtomStamp* atomA = getAtomStamp(a); |
499 |
+ |
AtomStamp* atomB = getAtomStamp(b); |
500 |
+ |
atomA->addBond(i); |
501 |
+ |
atomA->addBondedAtom(b); |
502 |
+ |
atomB->addBond(i); |
503 |
+ |
atomB->addBondedAtom(a); |
504 |
+ |
|
505 |
+ |
} |
506 |
|
} |
507 |
|
|
508 |
+ |
|
509 |
+ |
|
510 |
|
//Function Name: isBondInSameRigidBody |
511 |
|
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
512 |
|
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
530 |
|
// Function Name: isAtomInRigidBody |
531 |
|
//return false if atom does not belong to a rigid body, otherwise return true |
532 |
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
533 |
< |
int whichRigidBody; |
266 |
< |
int consAtomIndex; |
267 |
< |
|
268 |
< |
return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
533 |
> |
return atom2Rigidbody[atomIndex] >=0 ; |
534 |
|
|
535 |
|
} |
536 |
|
|
541 |
|
//whichRigidBody: the index of rigidbody in component |
542 |
|
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
543 |
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
279 |
– |
RigidBodyStamp* rbStamp; |
280 |
– |
int numRb; |
281 |
– |
int numAtom; |
544 |
|
|
545 |
+ |
|
546 |
+ |
|
547 |
|
whichRigidBody = -1; |
548 |
|
consAtomIndex = -1; |
549 |
|
|
550 |
< |
numRb = this->getNRigidBodies(); |
551 |
< |
|
552 |
< |
for(int i = 0 ; i < numRb; i++){ |
553 |
< |
rbStamp = this->getRigidBodyStamp(i); |
554 |
< |
numAtom = rbStamp->getNMembers(); |
291 |
< |
for(int j = 0; j < numAtom; j++) |
550 |
> |
if (atom2Rigidbody[atomIndex] >=0) { |
551 |
> |
whichRigidBody = atom2Rigidbody[atomIndex]; |
552 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody); |
553 |
> |
int numAtom = rbStamp->getNMembers(); |
554 |
> |
for(int j = 0; j < numAtom; j++) { |
555 |
|
if (rbStamp->getMemberAt(j) == atomIndex){ |
293 |
– |
whichRigidBody = i; |
556 |
|
consAtomIndex = j; |
557 |
|
return true; |
558 |
|
} |
559 |
+ |
} |
560 |
|
} |
561 |
|
|
562 |
|
return false; |