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 |
|
#include "applications/staticProps/RippleOP.hpp" |
45 |
|
#include "io/DumpReader.hpp" |
46 |
|
#include "primitives/Molecule.hpp" |
47 |
|
#include "utils/NumericConstant.hpp" |
48 |
< |
namespace oopse { |
48 |
> |
#include "types/MultipoleAdapter.hpp" |
49 |
> |
namespace OpenMD { |
50 |
|
|
51 |
< |
|
52 |
< |
RippleOP::RippleOP(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
53 |
< |
: StaticAnalyser(info, filename), |
54 |
< |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
55 |
< |
seleMan1_(info), seleMan2_(info){ |
51 |
> |
|
52 |
> |
RippleOP::RippleOP(SimInfo* info, const std::string& filename, |
53 |
> |
const std::string& sele1, const std::string& sele2) |
54 |
> |
: StaticAnalyser(info, filename), |
55 |
> |
selectionScript1_(sele1), selectionScript2_(sele2), |
56 |
> |
seleMan1_(info), seleMan2_(info), evaluator1_(info), evaluator2_(info) { |
57 |
|
|
58 |
|
setOutputName(getPrefix(filename) + ".rp2"); |
59 |
|
|
65 |
|
}else { |
66 |
|
sprintf( painCave.errMsg, |
67 |
|
"--sele1 must be static selection\n"); |
68 |
< |
painCave.severity = OOPSE_ERROR; |
68 |
> |
painCave.severity = OPENMD_ERROR; |
69 |
|
painCave.isFatal = 1; |
70 |
|
simError(); |
71 |
|
} |
75 |
|
}else { |
76 |
|
sprintf( painCave.errMsg, |
77 |
|
"--sele2 must be static selection\n"); |
78 |
< |
painCave.severity = OOPSE_ERROR; |
78 |
> |
painCave.severity = OPENMD_ERROR; |
79 |
|
painCave.isFatal = 1; |
80 |
|
simError(); |
81 |
|
} |
83 |
|
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
84 |
|
sprintf( painCave.errMsg, |
85 |
|
"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
86 |
< |
painCave.severity = OOPSE_ERROR; |
86 |
> |
painCave.severity = OPENMD_ERROR; |
87 |
|
painCave.isFatal = 1; |
88 |
|
simError(); |
89 |
|
|
107 |
|
RigidBody* rb; |
108 |
|
SimInfo::MoleculeIterator mi; |
109 |
|
Molecule::RigidBodyIterator rbIter; |
110 |
+ |
|
111 |
+ |
StuntDouble* j1; |
112 |
+ |
StuntDouble* j2; |
113 |
+ |
StuntDouble* sd3; |
114 |
|
|
115 |
|
DumpReader reader(info_, dumpFilename_); |
116 |
|
int nFrames = reader.getNFrames(); |
117 |
< |
|
117 |
> |
|
118 |
|
for (int i = 0; i < nFrames; i += step_) { |
119 |
|
reader.readFrame(i); |
120 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
121 |
+ |
int nMolecules = info_->getNGlobalMolecules(); |
122 |
+ |
int i1; |
123 |
+ |
int nUpper=0; |
124 |
+ |
int nLower=0; |
125 |
+ |
int nTail=0; |
126 |
+ |
RealType sumZ = 0.0; |
127 |
|
|
128 |
< |
|
129 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
128 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
129 |
> |
mol = info_->nextMolecule(mi)) { |
130 |
|
//change the positions of atoms which belong to the rigidbodies |
131 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
131 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
132 |
> |
rb = mol->nextRigidBody(rbIter)) { |
133 |
|
rb->updateAtoms(); |
134 |
|
} |
135 |
|
} |
136 |
+ |
|
137 |
+ |
for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; |
138 |
+ |
sd3 = seleMan2_.nextSelected(i1)) { |
139 |
+ |
Vector3d pos1 = sd3->getPos(); |
140 |
+ |
if (usePeriodicBoundaryConditions_) |
141 |
+ |
currentSnapshot_->wrapVector(pos1); |
142 |
+ |
sd3->setPos(pos1); |
143 |
+ |
} |
144 |
+ |
|
145 |
+ |
for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; |
146 |
+ |
sd3 = seleMan2_.nextSelected(i1)) { |
147 |
+ |
Vector3d pos1 = sd3->getPos(); |
148 |
+ |
sumZ += pos1.z(); |
149 |
+ |
} |
150 |
+ |
RealType avgZ = sumZ / (RealType) nMolecules; |
151 |
|
|
152 |
< |
Mat3x3d orderTensorHead(0.0), orderTensorTail(0.0); |
153 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
154 |
< |
Vector3d vecHead = j->first->getElectroFrame().getColumn(2); |
155 |
< |
Vector3d vecTail = j->second->getA().getColumn(2); |
156 |
< |
orderTensorHead +=outProduct(vecHead, vecHead); |
152 |
> |
Mat3x3d orderTensorHeadUpper(0.0); |
153 |
> |
Mat3x3d orderTensorTail(0.0); |
154 |
> |
Mat3x3d orderTensorHeadLower(0.0); |
155 |
> |
for (j1 = seleMan1_.beginSelected(i1); j1 != NULL; |
156 |
> |
j1 = seleMan1_.nextSelected(i1)) { |
157 |
> |
Vector3d pos = j1->getPos(); |
158 |
> |
if (usePeriodicBoundaryConditions_) |
159 |
> |
currentSnapshot_->wrapVector(pos); |
160 |
> |
Vector3d vecHeadUpper; |
161 |
> |
if (pos.z() >= avgZ){ |
162 |
> |
AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType(); |
163 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
164 |
> |
if (ma1.isDipole()) |
165 |
> |
vecHeadUpper = j1->getDipole(); |
166 |
> |
else |
167 |
> |
vecHeadUpper = j1->getA().transpose()*V3Z; |
168 |
> |
nUpper++; |
169 |
> |
} |
170 |
> |
Vector3d vecHeadLower; |
171 |
> |
if (pos.z() <= avgZ){ |
172 |
> |
AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType(); |
173 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
174 |
> |
if (ma1.isDipole()) |
175 |
> |
vecHeadLower = j1->getDipole(); |
176 |
> |
else |
177 |
> |
vecHeadLower = j1->getA().transpose() * V3Z; |
178 |
> |
nLower++; |
179 |
> |
} |
180 |
> |
orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper); |
181 |
> |
orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower); |
182 |
> |
} |
183 |
> |
for (j2 = seleMan2_.beginSelected(i1); j2 != NULL; |
184 |
> |
j2 = seleMan2_.nextSelected(i1)) { |
185 |
> |
// The lab frame vector corresponding to the body-fixed |
186 |
> |
// z-axis is simply the second column of A.transpose() |
187 |
> |
// or, identically, the second row of A itself. |
188 |
> |
|
189 |
> |
Vector3d vecTail = j2->getA().getRow(2); |
190 |
|
orderTensorTail +=outProduct(vecTail, vecTail); |
191 |
+ |
nTail++; |
192 |
|
} |
130 |
– |
|
131 |
– |
orderTensorHead /= sdPairs_.size(); |
132 |
– |
orderTensorHead -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
193 |
|
|
194 |
< |
orderTensorTail /= sdPairs_.size(); |
194 |
> |
orderTensorHeadUpper /= (RealType) nUpper; |
195 |
> |
orderTensorHeadLower /= (RealType) nLower; |
196 |
> |
orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
197 |
> |
orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
198 |
> |
|
199 |
> |
orderTensorTail /= (RealType) nTail; |
200 |
|
orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
201 |
|
|
202 |
< |
Vector3d eigenvaluesHead, eigenvaluesTail; |
203 |
< |
Mat3x3d eigenvectorsHead, eigenvectorsTail; |
204 |
< |
Mat3x3d::diagonalize(orderTensorHead, eigenvaluesHead, eigenvectorsHead); |
205 |
< |
Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail); |
206 |
< |
|
207 |
< |
int which; |
208 |
< |
RealType maxEval = 0.0; |
202 |
> |
Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail; |
203 |
> |
Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail; |
204 |
> |
Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper, |
205 |
> |
eigenvectorsHeadUpper); |
206 |
> |
Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower, |
207 |
> |
eigenvectorsHeadLower); |
208 |
> |
Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail); |
209 |
> |
|
210 |
> |
int whichUpper(-1), whichLower(-1), whichTail(-1); |
211 |
> |
RealType maxEvalUpper = 0.0; |
212 |
> |
RealType maxEvalLower = 0.0; |
213 |
> |
RealType maxEvalTail = 0.0; |
214 |
|
for(int k = 0; k< 3; k++){ |
215 |
< |
if(fabs(eigenvaluesHead[k]) > maxEval){ |
216 |
< |
which = k; |
217 |
< |
maxEval = fabs(eigenvaluesHead[k]); |
215 |
> |
if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){ |
216 |
> |
whichUpper = k; |
217 |
> |
maxEvalUpper = fabs(eigenvaluesHeadUpper[k]); |
218 |
|
} |
219 |
|
} |
220 |
< |
RealType p2Head = 1.5 * maxEval; |
151 |
< |
maxEval = 0.0; |
220 |
> |
RealType p2HeadUpper = 1.5 * maxEvalUpper; |
221 |
|
for(int k = 0; k< 3; k++){ |
222 |
< |
if(fabs(eigenvaluesTail[k]) > maxEval){ |
223 |
< |
which = k; |
224 |
< |
maxEval = fabs(eigenvaluesTail[k]); |
222 |
> |
if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){ |
223 |
> |
whichLower = k; |
224 |
> |
maxEvalLower = fabs(eigenvaluesHeadLower[k]); |
225 |
|
} |
226 |
|
} |
227 |
< |
RealType p2Tail = 1.5 * maxEval; |
227 |
> |
RealType p2HeadLower = 1.5 * maxEvalLower; |
228 |
> |
for(int k = 0; k< 3; k++){ |
229 |
> |
if(fabs(eigenvaluesTail[k]) > maxEvalTail){ |
230 |
> |
whichTail = k; |
231 |
> |
maxEvalTail = fabs(eigenvaluesTail[k]); |
232 |
> |
} |
233 |
> |
} |
234 |
> |
RealType p2Tail = 1.5 * maxEvalTail; |
235 |
|
|
236 |
< |
//the eigen vector is already normalized in SquareMatrix3::diagonalize |
237 |
< |
Vector3d directorHead = eigenvectorsHead.getColumn(which); |
238 |
< |
if (directorHead[0] < 0) { |
239 |
< |
directorHead.negate(); |
236 |
> |
//the eigenvector is already normalized in SquareMatrix3::diagonalize |
237 |
> |
Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper); |
238 |
> |
if (directorHeadUpper[0] < 0) { |
239 |
> |
directorHeadUpper.negate(); |
240 |
|
} |
241 |
< |
Vector3d directorTail = eigenvectorsTail.getColumn(which); |
241 |
> |
Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower); |
242 |
> |
if (directorHeadLower[0] < 0) { |
243 |
> |
directorHeadLower.negate(); |
244 |
> |
} |
245 |
> |
Vector3d directorTail = eigenvectorsTail.getColumn(whichTail); |
246 |
|
if (directorTail[0] < 0) { |
247 |
|
directorTail.negate(); |
248 |
|
} |
249 |
|
|
250 |
< |
OrderParam paramHead, paramTail; |
251 |
< |
paramHead.p2 = p2Head; |
252 |
< |
paramHead.director = directorHead; |
250 |
> |
OrderParam paramHeadUpper, paramHeadLower, paramTail; |
251 |
> |
paramHeadUpper.p2 = p2HeadUpper; |
252 |
> |
paramHeadUpper.director = directorHeadUpper; |
253 |
> |
paramHeadLower.p2 = p2HeadLower; |
254 |
> |
paramHeadLower.director = directorHeadLower; |
255 |
|
paramTail.p2 = p2Tail; |
256 |
|
paramTail.director = directorTail; |
257 |
|
|
258 |
< |
orderParamsHead_.push_back(paramHead); |
258 |
> |
orderParamsHeadUpper_.push_back(paramHeadUpper); |
259 |
> |
orderParamsHeadLower_.push_back(paramHeadLower); |
260 |
|
orderParamsTail_.push_back(paramTail); |
261 |
|
|
262 |
|
} |
263 |
|
|
264 |
< |
OrderParam sumOPHead, errsumOPHead; |
264 |
> |
OrderParam sumOPHeadUpper, errsumOPHeadUpper; |
265 |
> |
OrderParam sumOPHeadLower, errsumOPHeadLower; |
266 |
|
OrderParam sumOPTail, errsumOPTail; |
267 |
|
|
268 |
< |
sumOPHead.p2 = 0.0; |
269 |
< |
errsumOPHead.p2 = 0.0; |
270 |
< |
for (std::size_t i = 0; i < orderParamsHead_.size(); ++i) { |
271 |
< |
sumOPHead.p2 += orderParamsHead_[i].p2; |
272 |
< |
sumOPHead.director[0] += orderParamsHead_[i].director[0]; |
273 |
< |
sumOPHead.director[1] += orderParamsHead_[i].director[1]; |
274 |
< |
sumOPHead.director[2] += orderParamsHead_[i].director[2]; |
268 |
> |
sumOPHeadUpper.p2 = 0.0; |
269 |
> |
errsumOPHeadUpper.p2 = 0.0; |
270 |
> |
sumOPHeadLower.p2 = 0.0; |
271 |
> |
errsumOPHeadLower.p2 = 0.0; |
272 |
> |
for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
273 |
> |
sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2; |
274 |
> |
sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0]; |
275 |
> |
sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1]; |
276 |
> |
sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2]; |
277 |
|
} |
278 |
|
|
279 |
< |
avgOPHead.p2 = sumOPHead.p2 / (RealType)orderParamsHead_.size(); |
280 |
< |
avgOPHead.director[0] = sumOPHead.director[0] / (RealType)orderParamsHead_.size(); |
281 |
< |
avgOPHead.director[1] = sumOPHead.director[1] / (RealType)orderParamsHead_.size(); |
282 |
< |
avgOPHead.director[2] = sumOPHead.director[2] / (RealType)orderParamsHead_.size(); |
283 |
< |
for (std::size_t i = 0; i < orderParamsHead_.size(); ++i) { |
284 |
< |
errsumOPHead.p2 += pow((orderParamsHead_[i].p2 - avgOPHead.p2), 2); |
279 |
> |
avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size(); |
280 |
> |
avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size(); |
281 |
> |
avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size(); |
282 |
> |
avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size(); |
283 |
> |
for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) { |
284 |
> |
errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2); |
285 |
|
} |
286 |
< |
errOPHead.p2 = sqrt(errsumOPHead.p2 / (RealType)orderParamsHead_.size()); |
286 |
> |
errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size()); |
287 |
> |
for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
288 |
> |
sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2; |
289 |
> |
sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0]; |
290 |
> |
sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1]; |
291 |
> |
sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2]; |
292 |
> |
} |
293 |
|
|
294 |
+ |
avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size(); |
295 |
+ |
avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size(); |
296 |
+ |
avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size(); |
297 |
+ |
avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size(); |
298 |
+ |
for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) { |
299 |
+ |
errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2); |
300 |
+ |
} |
301 |
+ |
errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size()); |
302 |
+ |
|
303 |
|
sumOPTail.p2 = 0.0; |
304 |
|
errsumOPTail.p2 = 0.0; |
305 |
|
for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) { |
328 |
|
os<< "#selection1: (" << selectionScript1_ << ")\n"; |
329 |
|
os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |
330 |
|
|
331 |
< |
os << avgOPHead.p2 << "\t" |
332 |
< |
<< errOPHead.p2 << "\t" |
333 |
< |
<< avgOPHead.director[0] << "\t" |
334 |
< |
<< avgOPHead.director[1] << "\t" |
335 |
< |
<< avgOPHead.director[2] << "\n"; |
331 |
> |
os << avgOPHeadUpper.p2 << "\t" |
332 |
> |
<< errOPHeadUpper.p2 << "\t" |
333 |
> |
<< avgOPHeadUpper.director[0] << "\t" |
334 |
> |
<< avgOPHeadUpper.director[1] << "\t" |
335 |
> |
<< avgOPHeadUpper.director[2] << "\n"; |
336 |
> |
|
337 |
> |
os << avgOPHeadLower.p2 << "\t" |
338 |
> |
<< errOPHeadLower.p2 << "\t" |
339 |
> |
<< avgOPHeadLower.director[0] << "\t" |
340 |
> |
<< avgOPHeadLower.director[1] << "\t" |
341 |
> |
<< avgOPHeadLower.director[2] << "\n"; |
342 |
|
|
343 |
|
os << "selection2: (" << selectionScript2_ << ")\n"; |
344 |
|
os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n"; |