37 |
|
* arising out of the use of or inability to use software, even if the |
38 |
|
* University of Notre Dame has been advised of the possibility of |
39 |
|
* such damages. |
40 |
+ |
* |
41 |
+ |
* BondOrderParameter.cpp |
42 |
+ |
* OOPSE-4 |
43 |
+ |
* |
44 |
+ |
* Created by J. Daniel Gezelter on 09/26/06. |
45 |
+ |
* @author J. Daniel Gezelter |
46 |
+ |
* @version $Id: BondOrderParameter.cpp,v 1.20 2006-11-03 22:02:55 gezelter Exp $ |
47 |
+ |
* |
48 |
|
*/ |
49 |
< |
|
42 |
< |
|
43 |
< |
/* Creates orientational bond order parameters as outlined by |
44 |
< |
* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
45 |
< |
* Phys Rev B, 28,784,1983 |
46 |
< |
* |
47 |
< |
*/ |
48 |
< |
|
49 |
> |
|
50 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
51 |
|
#include "utils/simError.h" |
52 |
|
#include "io/DumpReader.hpp" |
53 |
|
#include "primitives/Molecule.hpp" |
54 |
|
#include "utils/NumericConstant.hpp" |
55 |
< |
#include "math/RealSphericalHarmonic.hpp" |
55 |
> |
|
56 |
|
namespace oopse { |
57 |
|
|
58 |
+ |
BondOrderParameter::BondOrderParameter(SimInfo* info, |
59 |
+ |
const std::string& filename, |
60 |
+ |
const std::string& sele, |
61 |
+ |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
62 |
+ |
|
63 |
+ |
setOutputName(getPrefix(filename) + ".bo"); |
64 |
|
|
65 |
< |
BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
66 |
< |
const std::string& sele2, double rCut, int lNumber) |
67 |
< |
: StaticAnalyser(info, filename), |
68 |
< |
selectionScript1_(sele1), evaluator1_(info), |
62 |
< |
seleMan1_(info){ |
65 |
> |
evaluator_.loadScriptString(sele); |
66 |
> |
if (!evaluator_.isDynamic()) { |
67 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
68 |
> |
} |
69 |
|
|
70 |
< |
setOutputName(getPrefix(filename) + ".obo"); |
70 |
> |
// Set up cutoff radius and order of the Legendre Polynomial: |
71 |
|
|
72 |
< |
evaluator1_.loadScriptString(sele1); |
73 |
< |
evaluator2_.loadScriptString(sele2); |
72 |
> |
rCut_ = rCut; |
73 |
> |
nBins_ = nbins; |
74 |
> |
Qcount_.resize(lMax_+1); |
75 |
> |
Wcount_.resize(lMax_+1); |
76 |
|
|
77 |
< |
if (!evaluator1_.isDynamic()) { |
70 |
< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
71 |
< |
}else { |
72 |
< |
sprintf( painCave.errMsg, |
73 |
< |
"--sele1 must be static selection\n"); |
74 |
< |
painCave.severity = OOPSE_ERROR; |
75 |
< |
painCave.isFatal = 1; |
76 |
< |
simError(); |
77 |
< |
} |
77 |
> |
// Q can take values from 0 to 1 |
78 |
|
|
79 |
< |
/* Set up cutoff radius and type of order parameter we are calcuating*/ |
80 |
< |
lNumber_ = lNumber; |
81 |
< |
rCut_ = rCut; |
82 |
< |
mSize_ = 2*lNumber_+1; |
79 |
> |
MinQ_ = 0.0; |
80 |
> |
MaxQ_ = 1.1; |
81 |
> |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
82 |
|
|
83 |
< |
int i; |
84 |
< |
int j; |
86 |
< |
StuntDouble* sd1; |
87 |
< |
StuntDouble* sd2; |
88 |
< |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j); |
89 |
< |
sd1 != NULL && sd2 != NULL; |
90 |
< |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
91 |
< |
for (sd2 = seleMan1_.beginSelected(j),sd2 |
92 |
< |
sdPairs_.push_back(std::make_pair(sd1, sd2)); |
93 |
< |
} |
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 |
+ |
MinW_ = -0.25; |
87 |
+ |
MaxW_ = 0.25; |
88 |
+ |
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
|
|
90 |
< |
} |
90 |
> |
// Make arrays for Wigner3jm |
91 |
> |
double* THRCOF = new double[2*lMax_+1]; |
92 |
> |
// Variables for Wigner routine |
93 |
> |
double lPass, m1Pass, m2m, m2M; |
94 |
> |
int error, mSize; |
95 |
> |
mSize = 2*lMax_+1; |
96 |
|
|
97 |
< |
void BondOrderParameter::process |
98 |
< |
() { |
99 |
< |
Molecule* mol; |
100 |
< |
RigidBody* rb; |
102 |
< |
SimInfo::MoleculeIterator mi; |
103 |
< |
Molecule::RigidBodyIterator rbIter; |
104 |
< |
RealType theta; |
105 |
< |
RealType phi; |
106 |
< |
RealType r; |
107 |
< |
RealType dist; |
108 |
< |
RealType* QBar_lm; |
109 |
< |
RealType QSq_l; |
110 |
< |
int nBonds; |
111 |
< |
int m, m_index; |
112 |
< |
RealSphericalHarmonic sphericalHarmonic; |
97 |
> |
for (int l = 0; l <= lMax_; l++) { |
98 |
> |
lPass = (double)l; |
99 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
100 |
> |
m1Pass = (double)m1; |
101 |
|
|
102 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
103 |
+ |
|
104 |
+ |
// Zero work array |
105 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
106 |
+ |
THRCOF[ii] = 0.0; |
107 |
+ |
} |
108 |
+ |
|
109 |
+ |
// Get Wigner coefficients |
110 |
+ |
Wigner3jm(&lPass, &lPass, &lPass, |
111 |
+ |
&m1Pass, &m2m, &m2M, |
112 |
+ |
THRCOF, &mSize, &error); |
113 |
+ |
|
114 |
+ |
m2Min[lm] = (int)floor(m2m); |
115 |
+ |
m2Max[lm] = (int)floor(m2M); |
116 |
+ |
|
117 |
+ |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
118 |
+ |
w3j[lm].push_back(THRCOF[mmm]); |
119 |
+ |
} |
120 |
+ |
} |
121 |
+ |
} |
122 |
+ |
delete [] THRCOF; |
123 |
+ |
THRCOF = NULL; |
124 |
+ |
} |
125 |
+ |
|
126 |
+ |
BondOrderParameter::~BondOrderParameter() { |
127 |
+ |
Q_histogram_.clear(); |
128 |
+ |
W_histogram_.clear(); |
129 |
+ |
for (int l = 0; l <= lMax_; l++) { |
130 |
+ |
for (int m = -l; m <= l; m++) { |
131 |
+ |
w3j[std::make_pair(l,m)].clear(); |
132 |
+ |
} |
133 |
+ |
} |
134 |
+ |
w3j.clear(); |
135 |
+ |
m2Min.clear(); |
136 |
+ |
m2Max.clear(); |
137 |
+ |
} |
138 |
+ |
|
139 |
+ |
void BondOrderParameter::initalizeHistogram() { |
140 |
+ |
for (int bin = 0; bin < nBins_; bin++) { |
141 |
+ |
for (int l = 0; l <= lMax_; l++) { |
142 |
+ |
Q_histogram_[std::make_pair(bin,l)] = 0; |
143 |
+ |
W_histogram_[std::make_pair(bin,l)] = 0; |
144 |
+ |
} |
145 |
+ |
} |
146 |
+ |
} |
147 |
|
|
148 |
< |
DumpReader reader(info_, dumpFilename_); |
149 |
< |
int nFrames = reader.getNFrames(); |
148 |
> |
void BondOrderParameter::process() { |
149 |
> |
Molecule* mol; |
150 |
> |
Atom* atom; |
151 |
> |
RigidBody* rb; |
152 |
> |
int myIndex; |
153 |
> |
SimInfo::MoleculeIterator mi; |
154 |
> |
Molecule::RigidBodyIterator rbIter; |
155 |
> |
Molecule::AtomIterator ai; |
156 |
> |
StuntDouble* sd; |
157 |
> |
Vector3d vec; |
158 |
> |
RealType costheta; |
159 |
> |
RealType phi; |
160 |
> |
RealType r; |
161 |
> |
RealType dist; |
162 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
163 |
> |
std::vector<RealType> q_l; |
164 |
> |
std::vector<RealType> q2; |
165 |
> |
std::vector<ComplexType> w; |
166 |
> |
std::vector<ComplexType> w_hat; |
167 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
168 |
> |
std::vector<RealType> Q2; |
169 |
> |
std::vector<RealType> Q; |
170 |
> |
std::vector<ComplexType> W; |
171 |
> |
std::vector<ComplexType> W_hat; |
172 |
> |
int nBonds, Nbonds; |
173 |
> |
SphericalHarmonic sphericalHarmonic; |
174 |
> |
int i, j; |
175 |
|
|
176 |
< |
/*Set the l for the spherical harmonic, it doesn't change*/ |
177 |
< |
sphericalHarmonic.setL(lNumber_); |
176 |
> |
DumpReader reader(info_, dumpFilename_); |
177 |
> |
int nFrames = reader.getNFrames(); |
178 |
> |
frameCounter_ = 0; |
179 |
|
|
180 |
< |
for (int i = 0; i < nFrames; i += step_) { |
181 |
< |
reader.readFrame(i); |
182 |
< |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
183 |
< |
nBonds = 0; |
180 |
> |
q_l.resize(lMax_+1); |
181 |
> |
q2.resize(lMax_+1); |
182 |
> |
w.resize(lMax_+1); |
183 |
> |
w_hat.resize(lMax_+1); |
184 |
|
|
185 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
186 |
< |
//change the positions of atoms which belong to the rigidbodies |
187 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
188 |
< |
rb->updateAtoms(); |
130 |
< |
} |
185 |
> |
Q2.resize(lMax_+1); |
186 |
> |
Q.resize(lMax_+1); |
187 |
> |
W.resize(lMax_+1); |
188 |
> |
W_hat.resize(lMax_+1); |
189 |
|
|
190 |
< |
} |
190 |
> |
for (int istep = 0; istep < nFrames; istep += step_) { |
191 |
> |
reader.readFrame(istep); |
192 |
> |
frameCounter_++; |
193 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
194 |
> |
|
195 |
> |
if (evaluator_.isDynamic()) { |
196 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
197 |
> |
} |
198 |
|
|
199 |
+ |
// update the positions of atoms which belong to the rigidbodies |
200 |
|
|
201 |
< |
/* Setup QBar */ |
202 |
< |
QBar_lm = new double[mSize_]; |
201 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
202 |
> |
mol = info_->nextMolecule(mi)) { |
203 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
204 |
> |
rb = mol->nextRigidBody(rbIter)) { |
205 |
> |
rb->updateAtoms(); |
206 |
> |
} |
207 |
> |
} |
208 |
> |
|
209 |
> |
// outer loop is over the selected StuntDoubles: |
210 |
|
|
211 |
< |
/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
212 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
140 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
141 |
< |
currentSnapshot_->wrapVector(vec); |
142 |
< |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
143 |
< |
* we choose standard spherical coordinates */ |
144 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
211 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
212 |
> |
sd = seleMan_.nextSelected(i)) { |
213 |
|
|
214 |
< |
/* Check to see if neighbor is in bond cuttoff*/ |
215 |
< |
if (r<rCut_){ |
216 |
< |
theta = atan(vec.y()/vec.x()); |
217 |
< |
phi = acos(vec.z()/r); |
218 |
< |
for(int m_index = 0; m_index < mSize_; m_index++){ |
219 |
< |
sphericalHarmonic.setM(m_index-lNumber_); |
220 |
< |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
221 |
< |
} |
222 |
< |
nBonds++; |
223 |
< |
} |
224 |
< |
} |
214 |
> |
myIndex = sd->getGlobalIndex(); |
215 |
> |
nBonds = 0; |
216 |
> |
|
217 |
> |
for (int l = 0; l <= lMax_; l++) { |
218 |
> |
for (int m = -l; m <= l; m++) { |
219 |
> |
q[std::make_pair(l,m)] = 0.0; |
220 |
> |
} |
221 |
> |
} |
222 |
> |
|
223 |
> |
// inner loop is over all other atoms in the system: |
224 |
> |
|
225 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
226 |
> |
mol = info_->nextMolecule(mi)) { |
227 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
228 |
> |
atom = mol->nextAtom(ai)) { |
229 |
|
|
230 |
< |
/*Normalize Qbar by number of Bonds*/ |
159 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
160 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nBonds; |
161 |
< |
} |
230 |
> |
if (atom->getGlobalIndex() != myIndex) { |
231 |
|
|
232 |
+ |
vec = sd->getPos() - atom->getPos(); |
233 |
|
|
234 |
< |
} |
234 |
> |
if (usePeriodicBoundaryConditions_) |
235 |
> |
currentSnapshot_->wrapVector(vec); |
236 |
> |
|
237 |
> |
// Calculate "bonds" and build Q_lm(r) where |
238 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
239 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
240 |
> |
// system, we choose standard spherical coordinates |
241 |
> |
|
242 |
> |
r = vec.length(); |
243 |
> |
|
244 |
> |
// Check to see if neighbor is in bond cutoff |
245 |
> |
|
246 |
> |
if (r < rCut_) { |
247 |
> |
costheta = vec.z() / r; |
248 |
> |
phi = atan2(vec.y(), vec.x()); |
249 |
|
|
250 |
< |
/*Normalize by number of frames*/ |
251 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
252 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
253 |
< |
} |
250 |
> |
for (int l = 0; l <= lMax_; l++) { |
251 |
> |
sphericalHarmonic.setL(l); |
252 |
> |
for(int m = -l; m <= l; m++){ |
253 |
> |
sphericalHarmonic.setM(m); |
254 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
255 |
> |
} |
256 |
> |
} |
257 |
> |
nBonds++; |
258 |
> |
} |
259 |
> |
} |
260 |
> |
} |
261 |
> |
} |
262 |
> |
|
263 |
> |
|
264 |
> |
for (int l = 0; l <= lMax_; l++) { |
265 |
> |
q_l[l] = 0.0; |
266 |
> |
for(int m = -l; m <= l; m++) { |
267 |
> |
q_l[l] += norm(q[std::make_pair(l,m)]); |
268 |
> |
} |
269 |
> |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
270 |
> |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
271 |
> |
} |
272 |
|
|
273 |
+ |
// Find second order invariant Q_l |
274 |
+ |
|
275 |
+ |
for (int l = 0; l <= lMax_; l++) { |
276 |
+ |
q2[l] = 0.0; |
277 |
+ |
for (int m = -l; m <= l; m++){ |
278 |
+ |
q2[l] += norm(q[std::make_pair(l,m)]); |
279 |
+ |
} |
280 |
+ |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
281 |
+ |
(RealType)(2*l + 1))/(RealType)nBonds; |
282 |
+ |
} |
283 |
|
|
284 |
+ |
// Find Third Order Invariant W_l |
285 |
+ |
|
286 |
+ |
for (int l = 0; l <= lMax_; l++) { |
287 |
+ |
w[l] = 0.0; |
288 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
289 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
290 |
+ |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
291 |
+ |
int m2 = m2Min[lm] + mmm; |
292 |
+ |
int m3 = -m1-m2; |
293 |
+ |
w[l] += w3j[lm][mmm] * q[lm] * |
294 |
+ |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
295 |
+ |
} |
296 |
+ |
} |
297 |
+ |
|
298 |
+ |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
299 |
+ |
} |
300 |
|
|
301 |
< |
/* Find second order invariant Q_l*/ |
302 |
< |
|
303 |
< |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
304 |
< |
QSq_l += pow(QBar_lm(m),2); |
301 |
> |
collectHistogram(q_l, w_hat); |
302 |
> |
|
303 |
> |
Nbonds += nBonds; |
304 |
> |
for (int l = 0; l <= lMax_; l++) { |
305 |
> |
for (int m = -l; m <= l; m++) { |
306 |
> |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
307 |
> |
} |
308 |
> |
} |
309 |
|
} |
310 |
< |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
310 |
> |
} |
311 |
> |
|
312 |
> |
// Normalize Qbar2 |
313 |
> |
for (int l = 0; l <= lMax_; l++) { |
314 |
> |
for (int m = -l; m <= l; m++){ |
315 |
> |
QBar[std::make_pair(l,m)] /= Nbonds; |
316 |
> |
} |
317 |
> |
} |
318 |
> |
|
319 |
> |
// Find second order invariant Q_l |
320 |
> |
|
321 |
> |
for (int l = 0; l <= lMax_; l++) { |
322 |
> |
Q2[l] = 0.0; |
323 |
> |
for (int m = -l; m <= l; m++){ |
324 |
> |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
325 |
> |
} |
326 |
> |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
327 |
> |
} |
328 |
> |
|
329 |
> |
// Find Third Order Invariant W_l |
330 |
> |
|
331 |
> |
for (int l = 0; l <= lMax_; l++) { |
332 |
> |
W[l] = 0.0; |
333 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
334 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
335 |
> |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
336 |
> |
int m2 = m2Min[lm] + mmm; |
337 |
> |
int m3 = -m1-m2; |
338 |
> |
W[l] += w3j[lm][mmm] * QBar[lm] * |
339 |
> |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
340 |
> |
} |
341 |
> |
} |
342 |
> |
|
343 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
344 |
> |
} |
345 |
> |
|
346 |
> |
writeOrderParameter(Q, W_hat); |
347 |
> |
} |
348 |
|
|
349 |
< |
/* Find Third Order Invariant W_l*/ |
349 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
350 |
> |
std::vector<ComplexType> what) { |
351 |
|
|
352 |
< |
/* Make arrays for Wigner3jm */ |
353 |
< |
double* THRCOF = new double[mSize_]; |
354 |
< |
/* Variables for Wigner routine */ |
355 |
< |
double l_ = (double)lNumber_; |
356 |
< |
double m2Min; |
357 |
< |
double m2Max; |
358 |
< |
int error; |
359 |
< |
int m1; |
360 |
< |
int m2; |
361 |
< |
int m3; |
352 |
> |
for (int l = 0; l <= lMax_; l++) { |
353 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
354 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
355 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
356 |
> |
Qcount_[l]++; |
357 |
> |
} else { |
358 |
> |
sprintf( painCave.errMsg, |
359 |
> |
"q_l value outside reasonable range\n"); |
360 |
> |
painCave.severity = OOPSE_ERROR; |
361 |
> |
painCave.isFatal = 1; |
362 |
> |
simError(); |
363 |
> |
} |
364 |
> |
} |
365 |
|
|
366 |
< |
for (int m1 = -lNumber_;m <= lNumber_;m1++){ |
367 |
< |
/* Zero work array */ |
368 |
< |
for (i=0; i<mSize_;i++){ |
369 |
< |
THRCOF[i] = 0.0; |
370 |
< |
} |
371 |
< |
/* Get wigner coefficients */ |
372 |
< |
Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error); |
373 |
< |
for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){ |
374 |
< |
m2 = floor(m2Min) + m_index - 1; |
375 |
< |
m3 = -m1-m2; |
376 |
< |
W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_); |
204 |
< |
} |
366 |
> |
for (int l = 0; l <= lMax_; l++) { |
367 |
> |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
368 |
> |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
369 |
> |
W_histogram_[std::make_pair(wbin,l)] += 1; |
370 |
> |
Wcount_[l]++; |
371 |
> |
} else { |
372 |
> |
sprintf( painCave.errMsg, |
373 |
> |
"Re[w_hat] value outside reasonable range\n"); |
374 |
> |
painCave.severity = OOPSE_ERROR; |
375 |
> |
painCave.isFatal = 1; |
376 |
> |
simError(); |
377 |
|
} |
378 |
+ |
} |
379 |
|
|
380 |
+ |
} |
381 |
|
|
208 |
– |
writeOrderParameter(); |
382 |
|
|
383 |
< |
} |
383 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
384 |
> |
std::vector<ComplexType> What) { |
385 |
> |
|
386 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
387 |
|
|
388 |
+ |
if (osq.is_open()) { |
389 |
+ |
|
390 |
+ |
osq << "# Bond Order Parameters\n"; |
391 |
+ |
osq << "# selection: (" << selectionScript_ << ")\n"; |
392 |
+ |
osq << "# \n"; |
393 |
+ |
for (int l = 0; l <= lMax_; l++) { |
394 |
+ |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
395 |
+ |
} |
396 |
+ |
// Normalize by number of frames and write it out: |
397 |
+ |
for (int i = 0; i < nBins_; ++i) { |
398 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
399 |
+ |
osq << Qval; |
400 |
+ |
for (int l = 0; l <= lMax_; l++) { |
401 |
+ |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]*deltaQ_/ |
402 |
+ |
(RealType)Qcount_[l]; |
403 |
+ |
} |
404 |
+ |
osq << "\n"; |
405 |
+ |
} |
406 |
|
|
407 |
< |
void BondOrderParameter::writeOrderParameter() { |
407 |
> |
osq.close(); |
408 |
|
|
409 |
< |
std::ofstream os(getOutputFileName().c_str()); |
410 |
< |
os << "#radial distribution function\n"; |
411 |
< |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
412 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
413 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
409 |
> |
} else { |
410 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
411 |
> |
(getOutputFileName() + "q").c_str()); |
412 |
> |
painCave.isFatal = 1; |
413 |
> |
simError(); |
414 |
> |
} |
415 |
|
|
416 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
222 |
< |
os << orderParams_[i].p2 << "\t" |
223 |
< |
<< orderParams_[i].director[0] << "\t" |
224 |
< |
<< orderParams_[i].director[1] << "\t" |
225 |
< |
<< orderParams_[i].director[2] << "\t" |
226 |
< |
<< orderParams_[i].angle << "\n"; |
416 |
> |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
417 |
|
|
418 |
+ |
if (osw.is_open()) { |
419 |
+ |
osw << "# Bond Order Parameters\n"; |
420 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
421 |
+ |
osw << "# \n"; |
422 |
+ |
for (int l = 0; l <= lMax_; l++) { |
423 |
+ |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
424 |
|
} |
425 |
+ |
// Normalize by number of frames and write it out: |
426 |
+ |
for (int i = 0; i < nBins_; ++i) { |
427 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
428 |
+ |
osw << Wval; |
429 |
+ |
for (int l = 0; l <= lMax_; l++) { |
430 |
+ |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]*deltaW_/ |
431 |
+ |
(RealType)Wcount_[l]; |
432 |
+ |
} |
433 |
+ |
osw << "\n"; |
434 |
+ |
} |
435 |
|
|
436 |
+ |
osw.close(); |
437 |
+ |
} else { |
438 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
439 |
+ |
(getOutputFileName() + "w").c_str()); |
440 |
+ |
painCave.isFatal = 1; |
441 |
+ |
simError(); |
442 |
|
} |
443 |
< |
|
443 |
> |
|
444 |
|
} |
445 |
< |
|
445 |
> |
} |