51 |
|
#include "io/DumpReader.hpp" |
52 |
|
#include "primitives/Molecule.hpp" |
53 |
|
#include "utils/NumericConstant.hpp" |
54 |
< |
#include "math/RealSphericalHarmonic.hpp" |
54 |
> |
|
55 |
|
namespace oopse { |
56 |
|
|
57 |
– |
|
57 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
58 |
|
const std::string& filename, |
59 |
|
const std::string& sele, |
60 |
< |
double rCut, int lNumber, int nbins) |
62 |
< |
: StaticAnalyser(info, filename), selectionScript_(sele), |
63 |
< |
evaluator_(info), seleMan_(info){ |
60 |
> |
double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
61 |
|
|
62 |
< |
setOutputName(getPrefix(filename) + ".obo"); |
62 |
> |
setOutputName(getPrefix(filename) + ".bo"); |
63 |
|
|
64 |
|
evaluator_.loadScriptString(sele); |
65 |
|
if (!evaluator_.isDynamic()) { |
68 |
|
|
69 |
|
// Set up cutoff radius and order of the Legendre Polynomial: |
70 |
|
|
71 |
< |
lNumber_ = lNumber; |
71 |
> |
lMax_ = lMax; |
72 |
|
rCut_ = rCut; |
73 |
< |
mSize_ = 2*lNumber_+1; |
73 |
> |
nBins_ = nbins; |
74 |
> |
Qcount_.resize(lMax_+1); |
75 |
> |
Wcount_.resize(lMax_+1); |
76 |
|
|
77 |
< |
// Set the l for the spherical harmonic, it doesn't change |
77 |
> |
// Q can take values from 0 to 1 |
78 |
|
|
79 |
< |
sphericalHarmonic.setL(lNumber_); |
79 |
> |
MinQ_ = 0.0; |
80 |
> |
MaxQ_ = 1.1; |
81 |
> |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
82 |
|
|
83 |
< |
delta_Q = 1.0 / nbins; |
84 |
< |
delta_W = 2.0 / nbins; |
83 |
> |
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
84 |
> |
// use values for MinW_ and MaxW_ that are slightly larger than this: |
85 |
|
|
86 |
< |
Q_histogram_.resize(nbins); |
87 |
< |
W_histogram_.resize(nbins); |
86 |
> |
MinW_ = -0.18; |
87 |
> |
MaxW_ = 0.18; |
88 |
> |
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
> |
} |
90 |
|
|
91 |
+ |
BondOrderParameter::~BondOrderParameter() { |
92 |
+ |
Q_histogram_.clear(); |
93 |
+ |
W_histogram_.clear(); |
94 |
|
} |
95 |
|
|
96 |
|
void BondOrderParameter::initalizeHistogram() { |
97 |
< |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
98 |
< |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
97 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
98 |
> |
for (int l = 0; l <= lMax_; l++) { |
99 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
100 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
101 |
> |
} |
102 |
> |
} |
103 |
|
} |
104 |
|
|
105 |
|
void BondOrderParameter::process() { |
106 |
|
Molecule* mol; |
107 |
|
Atom* atom; |
108 |
|
RigidBody* rb; |
109 |
+ |
int myIndex; |
110 |
|
SimInfo::MoleculeIterator mi; |
111 |
|
Molecule::RigidBodyIterator rbIter; |
112 |
|
Molecule::AtomIterator ai; |
113 |
|
StuntDouble* sd; |
114 |
< |
RealType theta; |
114 |
> |
Vector3d vec; |
115 |
> |
RealType costheta; |
116 |
|
RealType phi; |
117 |
|
RealType r; |
118 |
|
RealType dist; |
119 |
< |
std::map<int, RealType> QBar_lm; |
120 |
< |
RealType QSq_l; |
121 |
< |
RealType Q_l; |
122 |
< |
int nBonds; |
123 |
< |
RealSphericalHarmonic sphericalHarmonic; |
119 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
120 |
> |
std::vector<RealType> q_l; |
121 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
122 |
> |
std::vector<RealType> Q2; |
123 |
> |
std::vector<RealType> Q; |
124 |
> |
std::vector<ComplexType> W; |
125 |
> |
std::vector<ComplexType> W_hat; |
126 |
> |
int nBonds, Nbonds; |
127 |
> |
SphericalHarmonic sphericalHarmonic; |
128 |
|
int i, j; |
129 |
< |
|
130 |
< |
|
129 |
> |
// Make arrays for Wigner3jm |
130 |
> |
double* THRCOF = new double[2*lMax_+1]; |
131 |
> |
// Variables for Wigner routine |
132 |
> |
double lPass, m1Pass, m2Min, m2Max; |
133 |
> |
int error, m1, m2, m3, mSize; |
134 |
> |
mSize = 2*lMax_+1; |
135 |
> |
|
136 |
|
DumpReader reader(info_, dumpFilename_); |
137 |
|
int nFrames = reader.getNFrames(); |
138 |
+ |
frameCounter_ = 0; |
139 |
|
|
140 |
+ |
q_l.resize(lMax_+1); |
141 |
+ |
Q2.resize(lMax_+1); |
142 |
+ |
Q.resize(lMax_+1); |
143 |
+ |
W.resize(lMax_+1); |
144 |
+ |
W_hat.resize(lMax_+1); |
145 |
|
|
146 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
147 |
|
reader.readFrame(istep); |
148 |
+ |
frameCounter_++; |
149 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
150 |
|
|
151 |
|
if (evaluator_.isDynamic()) { |
160 |
|
rb = mol->nextRigidBody(rbIter)) { |
161 |
|
rb->updateAtoms(); |
162 |
|
} |
163 |
< |
} |
164 |
< |
|
163 |
> |
} |
164 |
> |
|
165 |
|
// outer loop is over the selected StuntDoubles: |
166 |
|
|
167 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
168 |
|
sd = seleMan_.nextSelected(i)) { |
169 |
|
|
170 |
< |
// For this central atom, zero out nBonds and QBar_lm |
143 |
< |
|
170 |
> |
myIndex = sd->getGlobalIndex(); |
171 |
|
nBonds = 0; |
172 |
< |
|
173 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
174 |
< |
QBar_lm[m] = 0.0; |
172 |
> |
|
173 |
> |
for (int l = 0; l <= lMax_; l++) { |
174 |
> |
for (int m = -l; m <= l; m++) { |
175 |
> |
q[std::make_pair(l,m)] = 0.0; |
176 |
> |
} |
177 |
|
} |
178 |
|
|
179 |
|
// inner loop is over all other atoms in the system: |
183 |
|
for (atom = mol->beginAtom(ai); atom != NULL; |
184 |
|
atom = mol->nextAtom(ai)) { |
185 |
|
|
186 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
187 |
|
|
188 |
< |
Vector3d vec = sd->getPos() - atom->getPos(); |
189 |
< |
currentSnapshot_->wrapVector(vec); |
190 |
< |
|
191 |
< |
// Calculate "bonds" and build Q_lm(r) where |
192 |
< |
// Q_lm = Y_lm(theta(r),phi(r)) |
193 |
< |
// The spherical harmonics are wrt any arbitrary coordinate |
194 |
< |
// system, we choose standard spherical coordinates |
195 |
< |
|
196 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
197 |
< |
|
198 |
< |
// Check to see if neighbor is in bond cutoff |
199 |
< |
|
200 |
< |
if (r < rCut_) { |
201 |
< |
theta = atan2(vec.y(), vec.x()); |
202 |
< |
phi = acos(vec.z()/r); |
203 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
204 |
< |
sphericalHarmonic.setM(m); |
205 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
206 |
< |
} |
207 |
< |
nBonds++; |
208 |
< |
} |
188 |
> |
vec = sd->getPos() - atom->getPos(); |
189 |
> |
currentSnapshot_->wrapVector(vec); |
190 |
> |
|
191 |
> |
// Calculate "bonds" and build Q_lm(r) where |
192 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
193 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
194 |
> |
// system, we choose standard spherical coordinates |
195 |
> |
|
196 |
> |
r = vec.length(); |
197 |
> |
|
198 |
> |
// Check to see if neighbor is in bond cutoff |
199 |
> |
|
200 |
> |
if (r < rCut_) { |
201 |
> |
costheta = vec.z() / r; |
202 |
> |
phi = atan2(vec.y(), vec.x()); |
203 |
> |
|
204 |
> |
for (int l = 0; l <= lMax_; l++) { |
205 |
> |
sphericalHarmonic.setL(l); |
206 |
> |
for(int m = -l; m <= l; m++){ |
207 |
> |
sphericalHarmonic.setM(m); |
208 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
209 |
> |
} |
210 |
> |
} |
211 |
> |
nBonds++; |
212 |
> |
} |
213 |
> |
} |
214 |
|
} |
215 |
|
} |
216 |
|
|
217 |
< |
// Normalize Qbar |
218 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
219 |
< |
QBar_lm[m] /= nBonds; |
217 |
> |
|
218 |
> |
for (int l = 0; l <= lMax_; l++) { |
219 |
> |
q_l[l] = 0.0; |
220 |
> |
for(int m = -l; m <= l; m++) { |
221 |
> |
q_l[l] += norm(q[std::make_pair(l,m)]); |
222 |
> |
} |
223 |
> |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
224 |
> |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
225 |
|
} |
226 |
< |
|
187 |
< |
// Find second order invariant Q_l |
188 |
< |
|
189 |
< |
QSq_l = 0.0; |
190 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
191 |
< |
QSq_l += pow(QBar_lm[m], 2); |
192 |
< |
} |
193 |
< |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
194 |
< |
|
195 |
< |
// Find Third Order Invariant W_l |
196 |
< |
|
197 |
< |
// Make arrays for Wigner3jm |
198 |
< |
double* THRCOF = new double[mSize_]; |
199 |
< |
// Variables for Wigner routine |
200 |
< |
double l_ = (double)lNumber_; |
201 |
< |
double m2Min, m2Max; |
202 |
< |
int error, m1, m2, m3; |
226 |
> |
collectHistogram(q_l); |
227 |
|
|
228 |
< |
W_l_ = 0.0; |
229 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
230 |
< |
// Zero work array |
231 |
< |
for (int ii = 0; ii < mSize_; ii+){ |
208 |
< |
THRCOF[i] = 0.0; |
228 |
> |
Nbonds += nBonds; |
229 |
> |
for (int l = 0; l <= lMax_; l++) { |
230 |
> |
for (int m = -l; m <= l; m++) { |
231 |
> |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
232 |
|
} |
210 |
– |
// Get Wigner coefficients |
211 |
– |
Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
212 |
– |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
213 |
– |
m2 = floor(m2Min) + m_index - 1; |
214 |
– |
m3 = -m1-m2; |
215 |
– |
W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
216 |
– |
} |
233 |
|
} |
218 |
– |
|
219 |
– |
W_l_hat = W_l_ / pow(QSq_l, 1.5); |
220 |
– |
|
221 |
– |
// accumulate histogram data for Q_l and W_l_hat: |
222 |
– |
|
223 |
– |
collectHistogram(Q_l, W_l_hat); |
224 |
– |
|
234 |
|
} |
235 |
|
} |
236 |
< |
|
237 |
< |
// Normalize by number of frames |
238 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
239 |
< |
QBar_lm[m] /= nFrames; |
236 |
> |
|
237 |
> |
// Normalize Qbar2 |
238 |
> |
for (int l = 0; l <= lMax_; l++) { |
239 |
> |
for (int m = -l; m <= l; m++){ |
240 |
> |
QBar[std::make_pair(l,m)] /= Nbonds; |
241 |
> |
} |
242 |
|
} |
243 |
|
|
244 |
< |
|
234 |
< |
|
235 |
< |
|
236 |
< |
|
237 |
< |
writeOrderParameter(); |
244 |
> |
// Find second order invariant Q_l |
245 |
|
|
246 |
< |
} |
247 |
< |
|
248 |
< |
|
249 |
< |
void BondOrderParameter::processHistogram() { |
246 |
> |
for (int l = 0; l <= lMax_; l++) { |
247 |
> |
Q2[l] = 0.0; |
248 |
> |
for (int m = -l; m <= l; m++){ |
249 |
> |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
250 |
> |
} |
251 |
> |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
252 |
> |
} |
253 |
|
|
244 |
– |
int nPairs = getNPairs(); |
245 |
– |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
246 |
– |
RealType pairDensity = nPairs /volume * 2.0; |
247 |
– |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
254 |
|
|
255 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
256 |
< |
|
257 |
< |
RealType rLower = i * deltaR_; |
258 |
< |
RealType rUpper = rLower + deltaR_; |
259 |
< |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
260 |
< |
RealType nIdeal = volSlice * pairConstant; |
261 |
< |
|
262 |
< |
avgGofr_[i] += histogram_[i] / nIdeal; |
255 |
> |
|
256 |
> |
// Find Third Order Invariant W_l |
257 |
> |
|
258 |
> |
for (int l = 0; l <= lMax_; l++) { |
259 |
> |
W[l] = 0.0; |
260 |
> |
lPass = (double)l; |
261 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
262 |
> |
// Zero work array |
263 |
> |
for (int ii = 0; ii < 2*l + 1; ii++){ |
264 |
> |
THRCOF[ii] = 0.0; |
265 |
> |
} |
266 |
> |
// Get Wigner coefficients |
267 |
> |
m1Pass = (double)m1; |
268 |
> |
|
269 |
> |
Wigner3jm(&lPass, &lPass, &lPass, |
270 |
> |
&m1Pass, &m2Min, &m2Max, |
271 |
> |
THRCOF, &mSize, &error); |
272 |
> |
|
273 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
274 |
> |
m2 = (int)floor(m2Min) + mmm; |
275 |
> |
m3 = -m1-m2; |
276 |
> |
W[l] += THRCOF[mmm] * |
277 |
> |
QBar[std::make_pair(l,m1)] * |
278 |
> |
QBar[std::make_pair(l,m2)] * |
279 |
> |
QBar[std::make_pair(l,m3)]; |
280 |
> |
} |
281 |
> |
} |
282 |
> |
|
283 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
284 |
|
} |
285 |
< |
|
285 |
> |
|
286 |
> |
writeOrderParameter(Q, W_hat); |
287 |
|
} |
288 |
|
|
289 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
289 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q) { |
290 |
|
|
291 |
< |
if (Q_l < Max_Q) { |
292 |
< |
int whichBin = Q_l / deltaQ_; |
293 |
< |
Q_histogram_[whichBin] += 1; |
291 |
> |
for (int l = 0; l <= lMax_; l++) { |
292 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
293 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
294 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
295 |
> |
Qcount_[l]++; |
296 |
> |
} else { |
297 |
> |
sprintf( painCave.errMsg, |
298 |
> |
"q_l value outside reasonable range\n"); |
299 |
> |
painCave.severity = OOPSE_ERROR; |
300 |
> |
painCave.isFatal = 1; |
301 |
> |
simError(); |
302 |
> |
} |
303 |
|
} |
267 |
– |
if (W_l_hat < Max_W) { |
268 |
– |
int whichBin = W_l_hat / deltaW_; |
269 |
– |
W_histogram_[whichBin] += 1; |
270 |
– |
} |
271 |
– |
} |
272 |
– |
|
304 |
|
|
305 |
< |
void BondOrderParameter::writeOrderParameter() { |
305 |
> |
} |
306 |
|
|
307 |
+ |
|
308 |
+ |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) { |
309 |
+ |
|
310 |
|
std::ofstream os(getOutputFileName().c_str()); |
311 |
< |
os << "#Bond Order Parameter\n"; |
312 |
< |
os << "#selection: (" << selectionScript_ << ")\n"; |
311 |
> |
|
312 |
> |
if (os.is_open()) { |
313 |
> |
|
314 |
> |
os << "# Bond Order Parameters\n"; |
315 |
> |
os << "# selection: (" << selectionScript_ << ")\n"; |
316 |
> |
for (int l = 0; l <= lMax_; l++) { |
317 |
> |
os << "# \n"; |
318 |
> |
os << "# <Q_" << l << ">: " << Q[l] << "\n"; |
319 |
> |
os << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
320 |
> |
} |
321 |
> |
// Normalize by number of frames and write it out: |
322 |
> |
for (int i = 0; i < nBins_; ++i) { |
323 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
324 |
> |
os << Qval; |
325 |
> |
for (int l = 0; l <= lMax_; l++) { |
326 |
> |
os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
327 |
> |
} |
328 |
> |
os << "\n"; |
329 |
> |
} |
330 |
|
|
331 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
281 |
< |
os << orderParams_[i].p2 << "\t" |
282 |
< |
<< orderParams_[i].director[0] << "\t" |
283 |
< |
<< orderParams_[i].director[1] << "\t" |
284 |
< |
<< orderParams_[i].director[2] << "\t" |
285 |
< |
<< orderParams_[i].angle << "\n"; |
331 |
> |
os.close(); |
332 |
|
|
333 |
+ |
} else { |
334 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
335 |
+ |
getOutputFileName().c_str()); |
336 |
+ |
painCave.isFatal = 1; |
337 |
+ |
simError(); |
338 |
|
} |
339 |
|
} |
289 |
– |
|
290 |
– |
|
291 |
– |
|
340 |
|
} |