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Comparing trunk/src/applications/staticProps/BondOrderParameter.cpp (file contents):
Revision 1094 by gezelter, Tue Nov 21 20:44:54 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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.
# Line 38 | Line 29
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31   *
32 < *  BondOrderParameter.cpp
33 < *  OOPSE-4
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]  Vardeman & Gezelter, in progress (2009).                        
40   *
41   *  Created by J. Daniel Gezelter on 09/26/06.
42   *  @author  J. Daniel Gezelter
43 < *  @version $Id: BondOrderParameter.cpp,v 1.21 2006-11-21 20:44:54 gezelter Exp $
43 > *  @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $
44   *
45   */
46  
# Line 53 | Line 50
50   #include "primitives/Molecule.hpp"
51   #include "utils/NumericConstant.hpp"
52  
53 < namespace oopse {
53 > namespace OpenMD {
54  
55    BondOrderParameter::BondOrderParameter(SimInfo* info,
56                                           const std::string& filename,
# Line 83 | Line 80 | namespace oopse {
80      // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll
81      // use values for MinW_ and MaxW_ that are slightly larger than this:
82  
83 <    MinW_ = -0.25;
84 <    MaxW_ = 0.25;
83 >    MinW_ = -1.1;
84 >    MaxW_ = 1.1;
85      deltaW_ = (MaxW_ - MinW_) / nbins;
86  
87      // Make arrays for Wigner3jm
# Line 105 | Line 102 | namespace oopse {
102          for (int ii = 0; ii < 2*l + 1; ii++){
103            THRCOF[ii] = 0.0;
104          }
105 <            
105 >
106          // Get Wigner coefficients
107          Wigner3jm(&lPass, &lPass, &lPass,
108                    &m1Pass, &m2m, &m2M,
# Line 114 | Line 111 | namespace oopse {
111          m2Min[lm] = (int)floor(m2m);
112          m2Max[lm] = (int)floor(m2M);
113          
114 <        for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) {
114 >        for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) {
115            w3j[lm].push_back(THRCOF[mmm]);
116          }
117        }
# Line 277 | Line 274 | namespace oopse {
274            w[l] = 0.0;
275            for (int m1 = -l; m1 <= l; m1++) {
276              std::pair<int,int> lm = std::make_pair(l, m1);
277 <            for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
277 >            for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
278                int m2 = m2Min[lm] + mmm;
279                int m3 = -m1-m2;
280                w[l] += w3j[lm][mmm] * q[lm] *
# Line 322 | Line 319 | namespace oopse {
319        W[l] = 0.0;
320        for (int m1 = -l; m1 <= l; m1++) {
321          std::pair<int,int> lm = std::make_pair(l, m1);
322 <        for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) {
322 >        for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) {
323            int m2 = m2Min[lm] + mmm;
324            int m3 = -m1-m2;
325            W[l] += w3j[lm][mmm] * QBar[lm] *
# Line 347 | Line 344 | namespace oopse {
344        } else {
345          sprintf( painCave.errMsg,
346                   "q_l value outside reasonable range\n");
347 <        painCave.severity = OOPSE_ERROR;
347 >        painCave.severity = OPENMD_ERROR;
348          painCave.isFatal = 1;
349          simError();  
350        }
# Line 361 | Line 358 | namespace oopse {
358        } else {
359          sprintf( painCave.errMsg,
360                   "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l]));
361 <        painCave.severity = OOPSE_ERROR;
361 >        painCave.severity = OPENMD_ERROR;
362          painCave.isFatal = 1;
363          simError();  
364        }

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