45 |
|
* Phys Rev B, 28,784,1983 |
46 |
|
* |
47 |
|
*/ |
48 |
< |
|
48 |
> |
|
49 |
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#include "applications/staticProps/BondOrderParameter.hpp" |
50 |
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#include "utils/simError.h" |
51 |
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#include "io/DumpReader.hpp" |
52 |
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#include "primitives/Molecule.hpp" |
53 |
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#include "utils/NumericConstant.hpp" |
54 |
< |
#include "math/RealSphericalHarmonic.hpp" |
54 |
> |
#include "math/SphericalHarmonic.hpp" |
55 |
> |
|
56 |
|
namespace oopse { |
57 |
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|
58 |
+ |
BondOrderParameter::BondOrderParameter(SimInfo* info, |
59 |
+ |
const std::string& filename, |
60 |
+ |
const std::string& sele, |
61 |
+ |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
62 |
+ |
|
63 |
+ |
setOutputName(getPrefix(filename) + ".bo"); |
64 |
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|
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), |
61 |
< |
selectionScript1_(sele1), evaluator1_(info), |
62 |
< |
seleMan1_(info){ |
63 |
< |
|
64 |
< |
setOutputName(getPrefix(filename) + ".obo"); |
65 |
< |
|
66 |
< |
evaluator1_.loadScriptString(sele1); |
67 |
< |
evaluator2_.loadScriptString(sele2); |
68 |
< |
|
69 |
< |
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(); |
65 |
> |
evaluator_.loadScriptString(sele); |
66 |
> |
if (!evaluator_.isDynamic()) { |
67 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
68 |
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} |
69 |
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|
70 |
< |
/* Set up cutoff radius and type of order parameter we are calcuating*/ |
70 |
> |
// Set up cutoff radius and order of the Legendre Polynomial: |
71 |
> |
|
72 |
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lNumber_ = lNumber; |
73 |
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rCut_ = rCut; |
74 |
< |
mSize_ = 2*lNumber_+1; |
74 |
> |
mSize_ = 2*lNumber_+1; |
75 |
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|
76 |
< |
int i; |
85 |
< |
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 |
< |
} |
76 |
> |
// Q can take values from 0 to 1 |
77 |
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|
78 |
+ |
MinQ_ = 0.0; |
79 |
+ |
MaxQ_ = 1.0; |
80 |
+ |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
81 |
+ |
Q_histogram_.resize(nbins); |
82 |
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|
83 |
< |
} |
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 |
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|
86 |
< |
void BondOrderParameter::process |
87 |
< |
() { |
88 |
< |
Molecule* mol; |
89 |
< |
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; |
86 |
> |
MinW_ = -0.18; |
87 |
> |
MaxW_ = 0.18; |
88 |
> |
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
> |
W_histogram_.resize(nbins); |
90 |
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|
91 |
+ |
} |
92 |
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|
93 |
< |
DumpReader reader(info_, dumpFilename_); |
94 |
< |
int nFrames = reader.getNFrames(); |
93 |
> |
BondOrderParameter::~BondOrderParameter() { |
94 |
> |
Q_histogram_.clear(); |
95 |
> |
W_histogram_.clear(); |
96 |
> |
} |
97 |
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|
98 |
< |
/*Set the l for the spherical harmonic, it doesn't change*/ |
99 |
< |
sphericalHarmonic.setL(lNumber_); |
98 |
> |
void BondOrderParameter::initalizeHistogram() { |
99 |
> |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
100 |
> |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
101 |
> |
} |
102 |
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|
103 |
< |
for (int i = 0; i < nFrames; i += step_) { |
104 |
< |
reader.readFrame(i); |
105 |
< |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
106 |
< |
nBonds = 0; |
103 |
> |
void BondOrderParameter::process() { |
104 |
> |
Molecule* mol; |
105 |
> |
Atom* atom; |
106 |
> |
RigidBody* rb; |
107 |
> |
SimInfo::MoleculeIterator mi; |
108 |
> |
Molecule::RigidBodyIterator rbIter; |
109 |
> |
Molecule::AtomIterator ai; |
110 |
> |
StuntDouble* sd; |
111 |
> |
RealType costheta; |
112 |
> |
RealType phi; |
113 |
> |
RealType r; |
114 |
> |
RealType dist; |
115 |
> |
std::map<int, ComplexType> QBar_lm; |
116 |
> |
RealType QSq_l; |
117 |
> |
RealType Q_l; |
118 |
> |
int nBonds; |
119 |
> |
SphericalHarmonic sphericalHarmonic; |
120 |
> |
int i, j; |
121 |
> |
|
122 |
> |
// Set the l for the spherical harmonic, it doesn't change |
123 |
> |
sphericalHarmonic.setL(lNumber_); |
124 |
|
|
126 |
– |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
127 |
– |
//change the positions of atoms which belong to the rigidbodies |
128 |
– |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
129 |
– |
rb->updateAtoms(); |
130 |
– |
} |
125 |
|
|
126 |
< |
} |
126 |
> |
DumpReader reader(info_, dumpFilename_); |
127 |
> |
int nFrames = reader.getNFrames(); |
128 |
> |
frameCounter_ = 0; |
129 |
|
|
130 |
+ |
for (int istep = 0; istep < nFrames; istep += step_) { |
131 |
+ |
reader.readFrame(istep); |
132 |
+ |
frameCounter_++; |
133 |
+ |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
134 |
+ |
|
135 |
+ |
if (evaluator_.isDynamic()) { |
136 |
+ |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
137 |
+ |
} |
138 |
|
|
139 |
< |
/* Setup QBar */ |
136 |
< |
QBar_lm = new double[mSize_]; |
139 |
> |
// update the positions of atoms which belong to the rigidbodies |
140 |
|
|
141 |
< |
/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
142 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
143 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
144 |
< |
currentSnapshot_->wrapVector(vec); |
145 |
< |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
146 |
< |
* we choose standard spherical coordinates */ |
147 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
141 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
142 |
> |
mol = info_->nextMolecule(mi)) { |
143 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
144 |
> |
rb = mol->nextRigidBody(rbIter)) { |
145 |
> |
rb->updateAtoms(); |
146 |
> |
} |
147 |
> |
} |
148 |
> |
|
149 |
> |
// outer loop is over the selected StuntDoubles: |
150 |
|
|
151 |
< |
/* Check to see if neighbor is in bond cuttoff*/ |
152 |
< |
if (r<rCut_){ |
148 |
< |
theta = atan(vec.y()/vec.x()); |
149 |
< |
phi = acos(vec.z()/r); |
150 |
< |
for(int m_index = 0; m_index < mSize_; m_index++){ |
151 |
< |
sphericalHarmonic.setM(m_index-lNumber_); |
152 |
< |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
153 |
< |
} |
154 |
< |
nBonds++; |
155 |
< |
} |
156 |
< |
} |
151 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
152 |
> |
sd = seleMan_.nextSelected(i)) { |
153 |
|
|
154 |
< |
/*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 |
< |
} |
154 |
> |
// For this central atom, zero out nBonds and QBar_lm |
155 |
|
|
156 |
+ |
nBonds = 0; |
157 |
+ |
|
158 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++) { |
159 |
+ |
QBar_lm[m] = 0.0; |
160 |
+ |
} |
161 |
+ |
|
162 |
+ |
// inner loop is over all other atoms in the system: |
163 |
+ |
|
164 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; |
165 |
+ |
mol = info_->nextMolecule(mi)) { |
166 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; |
167 |
+ |
atom = mol->nextAtom(ai)) { |
168 |
|
|
164 |
– |
} |
169 |
|
|
170 |
< |
/*Normalize by number of frames*/ |
171 |
< |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
172 |
< |
QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
173 |
< |
} |
170 |
> |
Vector3d vec = sd->getPos() - atom->getPos(); |
171 |
> |
currentSnapshot_->wrapVector(vec); |
172 |
> |
|
173 |
> |
// Calculate "bonds" and build Q_lm(r) where |
174 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
175 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
176 |
> |
// system, we choose standard spherical coordinates |
177 |
> |
|
178 |
> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
179 |
> |
|
180 |
> |
// Check to see if neighbor is in bond cutoff |
181 |
> |
|
182 |
> |
if (r < rCut_) { |
183 |
> |
costheta = vec.z() / r; |
184 |
> |
phi = atan2(vec.y(), vec.x()); |
185 |
> |
|
186 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
187 |
> |
sphericalHarmonic.setM(m); |
188 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); |
189 |
> |
} |
190 |
> |
nBonds++; |
191 |
> |
} |
192 |
> |
} |
193 |
> |
} |
194 |
> |
|
195 |
> |
// Normalize Qbar2 |
196 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
197 |
> |
QBar_lm[m] /= nBonds; |
198 |
> |
} |
199 |
|
|
200 |
+ |
// Find second order invariant Q_l |
201 |
|
|
202 |
+ |
QSq_l = 0.0; |
203 |
+ |
for (int m = -lNumber_; m <= lNumber_; m++){ |
204 |
+ |
QSq_l += norm(QBar_lm[m]); |
205 |
+ |
} |
206 |
+ |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
207 |
+ |
|
208 |
+ |
// Find Third Order Invariant W_l |
209 |
|
|
210 |
< |
/* Find second order invariant Q_l*/ |
210 |
> |
// Make arrays for Wigner3jm |
211 |
> |
double* THRCOF = new double[mSize_]; |
212 |
> |
// Variables for Wigner routine |
213 |
> |
double l_ = (double)lNumber_; |
214 |
> |
double m1Pass, m2Min, m2Max; |
215 |
> |
int error, m1, m2, m3; |
216 |
|
|
217 |
< |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
218 |
< |
QSq_l += pow(QBar_lm(m),2); |
219 |
< |
} |
220 |
< |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
217 |
> |
ComplexType W_l; |
218 |
> |
ComplexType W_l_hat; |
219 |
> |
W_l = 0.0; |
220 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
221 |
> |
// Zero work array |
222 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
223 |
> |
THRCOF[i] = 0.0; |
224 |
> |
} |
225 |
> |
// Get Wigner coefficients |
226 |
> |
m1Pass = (double)m1; |
227 |
> |
Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
228 |
> |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
229 |
> |
m2 = floor(m2Min) + m_index - 1; |
230 |
> |
m3 = -m1-m2; |
231 |
> |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
232 |
> |
} |
233 |
> |
} |
234 |
|
|
235 |
< |
/* Find Third Order Invariant W_l*/ |
235 |
> |
W_l_hat = W_l / pow(QSq_l, 1.5); |
236 |
|
|
237 |
< |
/* Make arrays for Wigner3jm */ |
183 |
< |
double* THRCOF = new double[mSize_]; |
184 |
< |
/* Variables for Wigner routine */ |
185 |
< |
double l_ = (double)lNumber_; |
186 |
< |
double m2Min; |
187 |
< |
double m2Max; |
188 |
< |
int error; |
189 |
< |
int m1; |
190 |
< |
int m2; |
191 |
< |
int m3; |
237 |
> |
// accumulate histogram data for Q_l and W_l_hat: |
238 |
|
|
239 |
< |
for (int m1 = -lNumber_;m <= lNumber_;m1++){ |
240 |
< |
/* Zero work array */ |
195 |
< |
for (i=0; i<mSize_;i++){ |
196 |
< |
THRCOF[i] = 0.0; |
197 |
< |
} |
198 |
< |
/* Get wigner coefficients */ |
199 |
< |
Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error); |
200 |
< |
for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){ |
201 |
< |
m2 = floor(m2Min) + m_index - 1; |
202 |
< |
m3 = -m1-m2; |
203 |
< |
W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_); |
204 |
< |
} |
239 |
> |
collectHistogram(Q_l, real(W_l_hat)); |
240 |
> |
|
241 |
|
} |
242 |
+ |
} |
243 |
+ |
|
244 |
+ |
writeOrderParameter(); |
245 |
+ |
|
246 |
+ |
} |
247 |
|
|
248 |
|
|
249 |
< |
writeOrderParameter(); |
249 |
> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
250 |
|
|
251 |
+ |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
252 |
+ |
int qbin = (Q_l - MinQ_) / deltaQ_; |
253 |
+ |
Q_histogram_[qbin] += 1; |
254 |
+ |
Qcount_++; |
255 |
+ |
sumQ_ += Q_l; |
256 |
+ |
sumQ2_ += Q_l * Q_l; |
257 |
+ |
} else { |
258 |
+ |
sprintf( painCave.errMsg, |
259 |
+ |
"Q_l value outside reasonable range\n"); |
260 |
+ |
painCave.severity = OOPSE_ERROR; |
261 |
+ |
painCave.isFatal = 1; |
262 |
+ |
simError(); |
263 |
|
} |
264 |
|
|
265 |
+ |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
266 |
+ |
int wbin = (W_l_hat - MinW_) / deltaW_; |
267 |
+ |
W_histogram_[wbin] += 1; |
268 |
+ |
Wcount_++; |
269 |
+ |
sumW_ += W_l_hat; |
270 |
+ |
sumW2_ += W_l_hat*W_l_hat; |
271 |
+ |
} else { |
272 |
+ |
sprintf( painCave.errMsg, |
273 |
+ |
"W_l_hat value outside reasonable range\n"); |
274 |
+ |
painCave.severity = OOPSE_ERROR; |
275 |
+ |
painCave.isFatal = 1; |
276 |
+ |
simError(); |
277 |
+ |
} |
278 |
+ |
} |
279 |
|
|
280 |
< |
void BondOrderParameter::writeOrderParameter() { |
280 |
> |
void BondOrderParameter::writeOrderParameter() { |
281 |
|
|
282 |
< |
std::ofstream os(getOutputFileName().c_str()); |
216 |
< |
os << "#radial distribution function\n"; |
217 |
< |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
218 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
219 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
282 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
283 |
|
|
284 |
< |
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"; |
284 |
> |
if (osq.is_open()) { |
285 |
|
|
286 |
+ |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
287 |
+ |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
288 |
+ |
|
289 |
+ |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
290 |
+ |
osq << "# selection: (" << selectionScript_ << ")\n"; |
291 |
+ |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
292 |
+ |
osq << "# std. dev.: " << qStdDev << "\n"; |
293 |
+ |
|
294 |
+ |
// Normalize by number of frames and write it out: |
295 |
+ |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
296 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
297 |
+ |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
298 |
|
} |
299 |
< |
|
299 |
> |
|
300 |
> |
osq.close(); |
301 |
> |
} else { |
302 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
303 |
> |
(getOutputFileName() + "q").c_str()); |
304 |
> |
painCave.isFatal = 1; |
305 |
> |
simError(); |
306 |
|
} |
307 |
|
|
308 |
< |
} |
308 |
> |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
309 |
|
|
310 |
+ |
if (osw.is_open()) { |
311 |
+ |
|
312 |
+ |
RealType wAvg = sumW_ / (RealType) Wcount_; |
313 |
+ |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
314 |
+ |
|
315 |
+ |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
316 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
317 |
+ |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
318 |
+ |
osw << "# std. dev.: " << wStdDev << "\n"; |
319 |
+ |
|
320 |
+ |
// Normalize by number of frames and write it out: |
321 |
+ |
for (int i = 0; i < W_histogram_.size(); ++i) { |
322 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
323 |
+ |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
osw.close(); |
327 |
+ |
} else { |
328 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
329 |
+ |
(getOutputFileName() + "w").c_str()); |
330 |
+ |
painCave.isFatal = 1; |
331 |
+ |
simError(); |
332 |
+ |
} |
333 |
+ |
} |
334 |
+ |
} |