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, 24107 (2008). |
39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 |
+ |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
41 |
+ |
* Created by J. Daniel Gezelter on 09/26/06. |
42 |
+ |
* @author J. Daniel Gezelter |
43 |
+ |
* @version $Id$ |
44 |
+ |
* |
45 |
|
*/ |
41 |
– |
|
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 |
– |
*/ |
46 |
|
|
47 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
48 |
|
#include "utils/simError.h" |
49 |
|
#include "io/DumpReader.hpp" |
50 |
|
#include "primitives/Molecule.hpp" |
51 |
|
#include "utils/NumericConstant.hpp" |
52 |
< |
#include "math/RealSphericalHarmonic.hpp" |
52 |
> |
#include "math/Wigner3jm.hpp" |
53 |
|
|
54 |
< |
namespace oopse { |
54 |
> |
using namespace MATPACK; |
55 |
> |
namespace OpenMD { |
56 |
|
|
57 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
58 |
|
const std::string& filename, |
59 |
|
const std::string& sele, |
60 |
< |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
60 |
> |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
61 |
|
|
62 |
|
setOutputName(getPrefix(filename) + ".bo"); |
63 |
|
|
68 |
|
|
69 |
|
// Set up cutoff radius and order of the Legendre Polynomial: |
70 |
|
|
72 |
– |
lNumber_ = lNumber; |
71 |
|
rCut_ = rCut; |
72 |
< |
mSize_ = 2*lNumber_+1; |
72 |
> |
nBins_ = nbins; |
73 |
> |
Qcount_.resize(lMax_+1); |
74 |
> |
Wcount_.resize(lMax_+1); |
75 |
|
|
76 |
|
// Q can take values from 0 to 1 |
77 |
|
|
78 |
|
MinQ_ = 0.0; |
79 |
< |
MaxQ_ = 1.0; |
79 |
> |
MaxQ_ = 1.1; |
80 |
|
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
81 |
– |
Q_histogram_.resize(nbins); |
81 |
|
|
82 |
|
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
83 |
|
// use values for MinW_ and MaxW_ that are slightly larger than this: |
84 |
|
|
85 |
< |
MinW_ = -0.18; |
86 |
< |
MaxW_ = 0.18; |
85 |
> |
MinW_ = -1.1; |
86 |
> |
MaxW_ = 1.1; |
87 |
|
deltaW_ = (MaxW_ - MinW_) / nbins; |
89 |
– |
W_histogram_.resize(nbins); |
88 |
|
|
89 |
< |
} |
89 |
> |
// Make arrays for Wigner3jm |
90 |
> |
RealType* THRCOF = new RealType[2*lMax_+1]; |
91 |
> |
// Variables for Wigner routine |
92 |
> |
RealType lPass, m1Pass, m2m, m2M; |
93 |
> |
int error, mSize; |
94 |
> |
mSize = 2*lMax_+1; |
95 |
|
|
96 |
+ |
for (int l = 0; l <= lMax_; l++) { |
97 |
+ |
lPass = (RealType)l; |
98 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
99 |
+ |
m1Pass = (RealType)m1; |
100 |
+ |
|
101 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
102 |
+ |
|
103 |
+ |
// Zero work array |
104 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
105 |
+ |
THRCOF[ii] = 0.0; |
106 |
+ |
} |
107 |
+ |
|
108 |
+ |
// Get Wigner coefficients |
109 |
+ |
Wigner3jm(lPass, lPass, lPass, |
110 |
+ |
m1Pass, m2m, m2M, |
111 |
+ |
THRCOF, mSize, error); |
112 |
+ |
|
113 |
+ |
m2Min[lm] = (int)floor(m2m); |
114 |
+ |
m2Max[lm] = (int)floor(m2M); |
115 |
+ |
|
116 |
+ |
for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { |
117 |
+ |
w3j[lm].push_back(THRCOF[mmm]); |
118 |
+ |
} |
119 |
+ |
} |
120 |
+ |
} |
121 |
+ |
delete [] THRCOF; |
122 |
+ |
THRCOF = NULL; |
123 |
+ |
} |
124 |
+ |
|
125 |
|
BondOrderParameter::~BondOrderParameter() { |
126 |
|
Q_histogram_.clear(); |
127 |
|
W_histogram_.clear(); |
128 |
+ |
for (int l = 0; l <= lMax_; l++) { |
129 |
+ |
for (int m = -l; m <= l; m++) { |
130 |
+ |
w3j[std::make_pair(l,m)].clear(); |
131 |
+ |
} |
132 |
+ |
} |
133 |
+ |
w3j.clear(); |
134 |
+ |
m2Min.clear(); |
135 |
+ |
m2Max.clear(); |
136 |
|
} |
137 |
< |
|
138 |
< |
void BondOrderParameter::initalizeHistogram() { |
139 |
< |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
140 |
< |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
137 |
> |
|
138 |
> |
void BondOrderParameter::initializeHistogram() { |
139 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
140 |
> |
for (int l = 0; l <= lMax_; l++) { |
141 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
142 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
143 |
> |
} |
144 |
> |
} |
145 |
|
} |
146 |
|
|
147 |
|
void BondOrderParameter::process() { |
148 |
|
Molecule* mol; |
149 |
|
Atom* atom; |
150 |
|
RigidBody* rb; |
151 |
+ |
int myIndex; |
152 |
|
SimInfo::MoleculeIterator mi; |
153 |
|
Molecule::RigidBodyIterator rbIter; |
154 |
|
Molecule::AtomIterator ai; |
155 |
|
StuntDouble* sd; |
156 |
< |
RealType theta; |
156 |
> |
Vector3d vec; |
157 |
> |
RealType costheta; |
158 |
|
RealType phi; |
159 |
|
RealType r; |
160 |
< |
RealType dist; |
161 |
< |
std::map<int, RealType> QBar_lm; |
162 |
< |
RealType QSq_l; |
163 |
< |
RealType Q_l; |
164 |
< |
int nBonds; |
165 |
< |
RealSphericalHarmonic sphericalHarmonic; |
166 |
< |
int i, j; |
167 |
< |
|
168 |
< |
// Set the l for the spherical harmonic, it doesn't change |
169 |
< |
sphericalHarmonic.setL(lNumber_); |
160 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
161 |
> |
std::vector<RealType> q_l; |
162 |
> |
std::vector<RealType> q2; |
163 |
> |
std::vector<ComplexType> w; |
164 |
> |
std::vector<ComplexType> w_hat; |
165 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
166 |
> |
std::vector<RealType> Q2; |
167 |
> |
std::vector<RealType> Q; |
168 |
> |
std::vector<ComplexType> W; |
169 |
> |
std::vector<ComplexType> W_hat; |
170 |
> |
int nBonds, Nbonds; |
171 |
> |
SphericalHarmonic sphericalHarmonic; |
172 |
> |
int i; |
173 |
|
|
125 |
– |
|
174 |
|
DumpReader reader(info_, dumpFilename_); |
175 |
|
int nFrames = reader.getNFrames(); |
176 |
|
frameCounter_ = 0; |
177 |
|
|
178 |
+ |
q_l.resize(lMax_+1); |
179 |
+ |
q2.resize(lMax_+1); |
180 |
+ |
w.resize(lMax_+1); |
181 |
+ |
w_hat.resize(lMax_+1); |
182 |
+ |
|
183 |
+ |
Q2.resize(lMax_+1); |
184 |
+ |
Q.resize(lMax_+1); |
185 |
+ |
W.resize(lMax_+1); |
186 |
+ |
W_hat.resize(lMax_+1); |
187 |
+ |
Nbonds = 0; |
188 |
+ |
|
189 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
190 |
|
reader.readFrame(istep); |
191 |
|
frameCounter_++; |
203 |
|
rb = mol->nextRigidBody(rbIter)) { |
204 |
|
rb->updateAtoms(); |
205 |
|
} |
206 |
< |
} |
207 |
< |
|
206 |
> |
} |
207 |
> |
|
208 |
|
// outer loop is over the selected StuntDoubles: |
209 |
|
|
210 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
211 |
|
sd = seleMan_.nextSelected(i)) { |
212 |
|
|
213 |
< |
// For this central atom, zero out nBonds and QBar_lm |
155 |
< |
|
213 |
> |
myIndex = sd->getGlobalIndex(); |
214 |
|
nBonds = 0; |
215 |
< |
|
216 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
217 |
< |
QBar_lm[m] = 0.0; |
215 |
> |
|
216 |
> |
for (int l = 0; l <= lMax_; l++) { |
217 |
> |
for (int m = -l; m <= l; m++) { |
218 |
> |
q[std::make_pair(l,m)] = 0.0; |
219 |
> |
} |
220 |
|
} |
221 |
|
|
222 |
|
// inner loop is over all other atoms in the system: |
226 |
|
for (atom = mol->beginAtom(ai); atom != NULL; |
227 |
|
atom = mol->nextAtom(ai)) { |
228 |
|
|
229 |
+ |
if (atom->getGlobalIndex() != myIndex) { |
230 |
|
|
231 |
< |
Vector3d vec = sd->getPos() - atom->getPos(); |
232 |
< |
currentSnapshot_->wrapVector(vec); |
233 |
< |
|
234 |
< |
// Calculate "bonds" and build Q_lm(r) where |
235 |
< |
// Q_lm = Y_lm(theta(r),phi(r)) |
236 |
< |
// The spherical harmonics are wrt any arbitrary coordinate |
237 |
< |
// system, we choose standard spherical coordinates |
238 |
< |
|
239 |
< |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
240 |
< |
|
241 |
< |
// Check to see if neighbor is in bond cutoff |
242 |
< |
|
243 |
< |
if (r < rCut_) { |
244 |
< |
theta = atan2(vec.y(), vec.x()); |
245 |
< |
phi = acos(vec.z()/r); |
246 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
247 |
< |
sphericalHarmonic.setM(m); |
248 |
< |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
249 |
< |
} |
250 |
< |
nBonds++; |
251 |
< |
} |
231 |
> |
vec = sd->getPos() - atom->getPos(); |
232 |
> |
|
233 |
> |
if (usePeriodicBoundaryConditions_) |
234 |
> |
currentSnapshot_->wrapVector(vec); |
235 |
> |
|
236 |
> |
// Calculate "bonds" and build Q_lm(r) where |
237 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
238 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
239 |
> |
// system, we choose standard spherical coordinates |
240 |
> |
|
241 |
> |
r = vec.length(); |
242 |
> |
|
243 |
> |
// Check to see if neighbor is in bond cutoff |
244 |
> |
|
245 |
> |
if (r < rCut_) { |
246 |
> |
costheta = vec.z() / r; |
247 |
> |
phi = atan2(vec.y(), vec.x()); |
248 |
> |
|
249 |
> |
for (int l = 0; l <= lMax_; l++) { |
250 |
> |
sphericalHarmonic.setL(l); |
251 |
> |
for(int m = -l; m <= l; m++){ |
252 |
> |
sphericalHarmonic.setM(m); |
253 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
254 |
> |
|
255 |
> |
} |
256 |
> |
} |
257 |
> |
nBonds++; |
258 |
> |
} |
259 |
> |
} |
260 |
|
} |
261 |
|
} |
262 |
|
|
263 |
< |
// Normalize Qbar |
264 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
265 |
< |
QBar_lm[m] /= nBonds; |
266 |
< |
} |
267 |
< |
|
268 |
< |
// Find second order invariant Q_l |
269 |
< |
|
270 |
< |
QSq_l = 0.0; |
271 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
203 |
< |
QSq_l += pow(QBar_lm[m], 2); |
263 |
> |
|
264 |
> |
for (int l = 0; l <= lMax_; l++) { |
265 |
> |
q2[l] = 0.0; |
266 |
> |
for (int m = -l; m <= l; m++){ |
267 |
> |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
268 |
> |
|
269 |
> |
q2[l] += norm(q[std::make_pair(l,m)]); |
270 |
> |
} |
271 |
> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
272 |
|
} |
273 |
< |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
206 |
< |
|
273 |
> |
|
274 |
|
// Find Third Order Invariant W_l |
275 |
< |
|
276 |
< |
// Make arrays for Wigner3jm |
277 |
< |
double* THRCOF = new double[mSize_]; |
278 |
< |
// Variables for Wigner routine |
279 |
< |
double l_ = (double)lNumber_; |
280 |
< |
double m1Pass, m2Min, m2Max; |
281 |
< |
int error, m1, m2, m3; |
282 |
< |
|
283 |
< |
RealType W_l; |
284 |
< |
RealType W_l_hat; |
285 |
< |
W_l = 0.0; |
219 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
220 |
< |
// Zero work array |
221 |
< |
for (int ii = 0; ii < mSize_; ii++){ |
222 |
< |
THRCOF[i] = 0.0; |
275 |
> |
|
276 |
> |
for (int l = 0; l <= lMax_; l++) { |
277 |
> |
w[l] = 0.0; |
278 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
279 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
280 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
281 |
> |
int m2 = m2Min[lm] + mmm; |
282 |
> |
int m3 = -m1-m2; |
283 |
> |
w[l] += w3j[lm][mmm] * q[lm] * |
284 |
> |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
285 |
> |
} |
286 |
|
} |
287 |
< |
// Get Wigner coefficients |
288 |
< |
m1Pass = (double)m1; |
226 |
< |
Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
227 |
< |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
228 |
< |
m2 = floor(m2Min) + m_index - 1; |
229 |
< |
m3 = -m1-m2; |
230 |
< |
W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
231 |
< |
} |
287 |
> |
|
288 |
> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
289 |
|
} |
290 |
|
|
291 |
< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
292 |
< |
|
293 |
< |
// accumulate histogram data for Q_l and W_l_hat: |
294 |
< |
|
295 |
< |
collectHistogram(Q_l, W_l_hat); |
296 |
< |
|
291 |
> |
collectHistogram(q_l, w_hat); |
292 |
> |
|
293 |
> |
Nbonds += nBonds; |
294 |
> |
for (int l = 0; l <= lMax_; l++) { |
295 |
> |
for (int m = -l; m <= l; m++) { |
296 |
> |
QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
297 |
> |
} |
298 |
> |
} |
299 |
|
} |
300 |
|
} |
301 |
+ |
|
302 |
+ |
// Normalize Qbar2 |
303 |
+ |
for (int l = 0; l <= lMax_; l++) { |
304 |
+ |
for (int m = -l; m <= l; m++){ |
305 |
+ |
QBar[std::make_pair(l,m)] /= Nbonds; |
306 |
+ |
} |
307 |
+ |
} |
308 |
|
|
309 |
< |
writeOrderParameter(); |
309 |
> |
// Find second order invariant Q_l |
310 |
|
|
311 |
+ |
for (int l = 0; l <= lMax_; l++) { |
312 |
+ |
Q2[l] = 0.0; |
313 |
+ |
for (int m = -l; m <= l; m++){ |
314 |
+ |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
315 |
+ |
} |
316 |
+ |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
317 |
+ |
} |
318 |
+ |
|
319 |
+ |
// Find Third Order Invariant W_l |
320 |
+ |
|
321 |
+ |
for (int l = 0; l <= lMax_; l++) { |
322 |
+ |
W[l] = 0.0; |
323 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
324 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
325 |
+ |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
326 |
+ |
int m2 = m2Min[lm] + mmm; |
327 |
+ |
int m3 = -m1-m2; |
328 |
+ |
W[l] += w3j[lm][mmm] * QBar[lm] * |
329 |
+ |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
330 |
+ |
} |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
W_hat[l] = W[l] / pow(Q2[l], RealType(1.5)); |
334 |
+ |
} |
335 |
+ |
|
336 |
+ |
writeOrderParameter(Q, W_hat); |
337 |
|
} |
338 |
|
|
339 |
+ |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
340 |
+ |
std::vector<ComplexType> what) { |
341 |
|
|
342 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
343 |
< |
|
344 |
< |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
345 |
< |
int qbin = (Q_l - MinQ_) / deltaQ_; |
346 |
< |
Q_histogram_[qbin] += 1; |
347 |
< |
Qcount_++; |
348 |
< |
sumQ_ += Q_l; |
349 |
< |
sumQ2_ += Q_l * Q_l; |
350 |
< |
} else { |
351 |
< |
sprintf( painCave.errMsg, |
352 |
< |
"Q_l value outside reasonable range\n"); |
353 |
< |
painCave.severity = OOPSE_ERROR; |
260 |
< |
painCave.isFatal = 1; |
261 |
< |
simError(); |
342 |
> |
for (int l = 0; l <= lMax_; l++) { |
343 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
344 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
345 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
346 |
> |
Qcount_[l]++; |
347 |
> |
} else { |
348 |
> |
sprintf( painCave.errMsg, |
349 |
> |
"q_l value outside reasonable range\n"); |
350 |
> |
painCave.severity = OPENMD_ERROR; |
351 |
> |
painCave.isFatal = 1; |
352 |
> |
simError(); |
353 |
> |
} |
354 |
|
} |
355 |
|
|
356 |
< |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
357 |
< |
int wbin = (W_l_hat - MinW_) / deltaW_; |
358 |
< |
W_histogram_[wbin] += 1; |
359 |
< |
Wcount_++; |
360 |
< |
sumW_ += W_l_hat; |
361 |
< |
sumW2_ += W_l_hat*W_l_hat; |
362 |
< |
} else { |
363 |
< |
sprintf( painCave.errMsg, |
364 |
< |
"W_l_hat value outside reasonable range\n"); |
365 |
< |
painCave.severity = OOPSE_ERROR; |
366 |
< |
painCave.isFatal = 1; |
367 |
< |
simError(); |
356 |
> |
for (int l = 0; l <= lMax_; l++) { |
357 |
> |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
358 |
> |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
359 |
> |
W_histogram_[std::make_pair(wbin,l)] += 1; |
360 |
> |
Wcount_[l]++; |
361 |
> |
} else { |
362 |
> |
sprintf( painCave.errMsg, |
363 |
> |
"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
364 |
> |
painCave.severity = OPENMD_ERROR; |
365 |
> |
painCave.isFatal = 1; |
366 |
> |
simError(); |
367 |
> |
} |
368 |
|
} |
369 |
+ |
|
370 |
|
} |
371 |
|
|
279 |
– |
void BondOrderParameter::writeOrderParameter() { |
372 |
|
|
373 |
+ |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
374 |
+ |
std::vector<ComplexType> What) { |
375 |
+ |
|
376 |
|
std::ofstream osq((getOutputFileName() + "q").c_str()); |
377 |
|
|
378 |
|
if (osq.is_open()) { |
284 |
– |
|
285 |
– |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
286 |
– |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
379 |
|
|
380 |
< |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
380 |
> |
osq << "# Bond Order Parameters\n"; |
381 |
|
osq << "# selection: (" << selectionScript_ << ")\n"; |
382 |
< |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
383 |
< |
osq << "# std. dev.: " << qStdDev << "\n"; |
384 |
< |
|
382 |
> |
osq << "# \n"; |
383 |
> |
for (int l = 0; l <= lMax_; l++) { |
384 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
385 |
> |
} |
386 |
|
// Normalize by number of frames and write it out: |
387 |
< |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
388 |
< |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
389 |
< |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
387 |
> |
for (int i = 0; i < nBins_; ++i) { |
388 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
389 |
> |
osq << Qval; |
390 |
> |
for (int l = 0; l <= lMax_; l++) { |
391 |
> |
|
392 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
393 |
> |
} |
394 |
> |
osq << "\n"; |
395 |
|
} |
396 |
< |
|
396 |
> |
|
397 |
|
osq.close(); |
398 |
+ |
|
399 |
|
} else { |
400 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
401 |
|
(getOutputFileName() + "q").c_str()); |
406 |
|
std::ofstream osw((getOutputFileName() + "w").c_str()); |
407 |
|
|
408 |
|
if (osw.is_open()) { |
409 |
< |
|
311 |
< |
RealType wAvg = sumW_ / (RealType) Wcount_; |
312 |
< |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
313 |
< |
|
314 |
< |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
409 |
> |
osw << "# Bond Order Parameters\n"; |
410 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
411 |
< |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
412 |
< |
osw << "# std. dev.: " << wStdDev << "\n"; |
413 |
< |
|
411 |
> |
osw << "# \n"; |
412 |
> |
for (int l = 0; l <= lMax_; l++) { |
413 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
414 |
> |
} |
415 |
|
// Normalize by number of frames and write it out: |
416 |
< |
for (int i = 0; i < W_histogram_.size(); ++i) { |
417 |
< |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
418 |
< |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
416 |
> |
for (int i = 0; i < nBins_; ++i) { |
417 |
> |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
418 |
> |
osw << Wval; |
419 |
> |
for (int l = 0; l <= lMax_; l++) { |
420 |
> |
|
421 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
422 |
> |
} |
423 |
> |
osw << "\n"; |
424 |
|
} |
425 |
< |
|
425 |
> |
|
426 |
|
osw.close(); |
427 |
|
} else { |
428 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
430 |
|
painCave.isFatal = 1; |
431 |
|
simError(); |
432 |
|
} |
433 |
+ |
|
434 |
|
} |
435 |
|
} |