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Comparing trunk/src/applications/randomBuilder/randomBuilder.cpp (file contents):
Revision 1065 by gezelter, Tue Oct 10 14:52:20 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 5 | Line 5
5   * redistribute this software in source and binary code form, provided
6   * that the following conditions are met:
7   *
8 < * 1. Acknowledgement of the program authors must be made in any
9 < *    publication of scientific results based in part on use of the
10 < *    program.  An acceptable form of acknowledgement is citation of
11 < *    the article in which the program was described (Matthew
12 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14 < *    Parallel Simulation Engine for Molecular Dynamics,"
15 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
16 < *
17 < * 2. Redistributions of source code must retain the above copyright
8 > * 1. Redistributions of source code must retain the above copyright
9   *    notice, this list of conditions and the following disclaimer.
10   *
11 < * 3. Redistributions in binary form must reproduce the above copyright
11 > * 2. Redistributions in binary form must reproduce the above copyright
12   *    notice, this list of conditions and the following disclaimer in the
13   *    documentation and/or other materials provided with the
14   *    distribution.
# Line 37 | Line 28
28   * University of Notre Dame has been advised of the possibility of
29   * such damages.
30   *
31 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32 + * research, please cite the appropriate papers when you publish your
33 + * work.  Good starting points are:
34 + *                                                                      
35 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
36 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
37 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 + * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39 + * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40   *
41   *  randomBuilder.cpp
42   *
43   *  Created by Charles F. Vardeman II on 10 Apr 2006.
44   *  @author  Charles F. Vardeman II
45 < *  @version $Id: randomBuilder.cpp,v 1.5 2006-10-10 14:52:20 gezelter Exp $
45 > *  @version $Id$
46   *
47   */
48  
# Line 69 | Line 69 | using namespace std;
69   #include "utils/StringUtils.hpp"
70  
71   using namespace std;
72 < using namespace oopse;
72 > using namespace OpenMD;
73  
74   void createMdFile(const std::string&oldMdFileName,
75                    const std::string&newMdFileName,
# Line 77 | Line 77 | int main(int argc, char *argv []) {
77  
78   int main(int argc, char *argv []) {
79  
80 –  // register force fields
81 –  registerForceFields();
80    registerLattice();
81      
82    gengetopt_args_info args_info;
# Line 105 | Line 103 | int main(int argc, char *argv []) {
103    density = args_info.density_arg;
104  
105    //get lattice type
106 <  latticeType = UpperCase(args_info.latticetype_arg);
106 >  latticeType = "FCC";
107  
108    simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
109      
# Line 317 | Line 315 | int main(int argc, char *argv []) {
315    // Randomize a vector of ints:
316  
317    vector<int> ids;
318 <  for (int i = 0; i < sites.size(); i++) ids.push_back(i);
318 >  for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
319    std::random_shuffle(ids.begin(), ids.end());
320  
321    Molecule* mol;
# Line 348 | Line 346 | int main(int argc, char *argv []) {
346  
347    delete writer;
348  
349 <  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
349 >  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
350            "generated.\n", outputFileName.c_str());
351    painCave.isFatal = 0;
352    simError();
# Line 370 | Line 368 | void createMdFile(const std::string&oldMdFileName,
368    
369    oldMdFile.getline(buffer, MAXLEN);
370  
371 <  int i = 0;
371 >  unsigned int i = 0;
372    while (!oldMdFile.eof()) {
373      
374      //correct molecule number
375      if (strstr(buffer, "nMol") != NULL) {
376 <      if(i<nMol.size()){
376 >      if (i<nMol.size()){
377          sprintf(buffer, "\tnMol = %i;", nMol.at(i));
378          newMdFile << buffer << std::endl;
379          i++;
# Line 388 | Line 386 | void createMdFile(const std::string&oldMdFileName,
386    
387    oldMdFile.close();
388    newMdFile.close();
389 +
390 +  if (i != nMol.size()) {
391 +    sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
392 +            "\tstatements in component blocks.  Make sure that all\n"
393 +            "\tcomponents in the template file have nMol=1");
394 +    painCave.isFatal = 1;
395 +    simError();
396 +  }
397 +
398   }
399  

Comparing trunk/src/applications/randomBuilder/randomBuilder.cpp (property svn:keywords):
Revision 1065 by gezelter, Tue Oct 10 14:52:20 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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