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Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 1077 by gezelter, Wed Oct 18 19:35:07 2006 UTC vs.
Revision 1977 by gezelter, Wed Mar 12 21:35:23 2014 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 37 | Line 28
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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <cstdlib>
# Line 64 | Line 65 | using namespace std;
65   #include "utils/StringUtils.hpp"
66  
67   using namespace std;
68 < using namespace oopse;
68 > using namespace OpenMD;
69   void createMdFile(const std::string&oldMdFileName,
70                    const std::string&newMdFileName,
71                    std::vector<int> numMol);
72  
73   int main(int argc, char *argv []) {
74    
74 –  //register force fields
75 –  registerForceFields();
75    registerLattice();
76    
77    gengetopt_args_info args_info;
78    std::string latticeType;
79    std::string inputFileName;
80    std::string outputFileName;
82 –
81    MoLocator* locator;
82    int nComponents;
83    double latticeConstant;
86 –  std::vector<double> lc;
87 –
84    RealType particleRadius;
89 –
85    Mat3x3d hmat;
91 –  std::vector<Vector3d> latticePos;
92 –  std::vector<Vector3d> latticeOrt;
93 –
86    DumpWriter *writer;
87    
88    // Parse Command Line Arguments
# Line 126 | Line 118 | int main(int argc, char *argv []) {
118    /* Build a lattice and get lattice points for this lattice constant */
119    vector<Vector3d> sites = nanoParticle.getSites();
120    vector<Vector3d> orientations = nanoParticle.getOrientations();
121 +
122 +
123    std::vector<int> vacancyTargets;
124    vector<bool> isVacancy;
125    
126    Vector3d myLoc;
127    RealType myR;
128  
129 <  for (int i = 0; i < sites.size(); i++)
129 >  for (unsigned int i = 0; i < sites.size(); i++)
130      isVacancy.push_back(false);
131  
132    if (args_info.vacancyPercent_given) {
# Line 156 | Line 150 | int main(int argc, char *argv []) {
150        }
151        if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
152          
153 <        for (int i = 0; i < sites.size(); i++) {
153 >        for (unsigned int i = 0; i < sites.size(); i++) {
154            myLoc = sites[i];
155            myR = myLoc.length();
156            if (myR >= vIR && myR <= vOR) {
# Line 170 | Line 164 | int main(int argc, char *argv []) {
164          
165                    
166          sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
167 <                "\tsites between %lf and %lf.", vacancyTargets.size(),
167 >                "\tsites between %lf and %lf.", (int) vacancyTargets.size(),
168                  vIR, vOR);
169          painCave.isFatal = 0;
170 +        painCave.severity = OPENMD_INFO;
171          simError();
172  
173          isVacancy.clear();
174 <        for (int i = 0; i < sites.size(); i++) {
174 >        for (unsigned int i = 0; i < sites.size(); i++) {
175            bool vac = false;
176 <          for (int j = 0; j < vacancyTargets.size(); j++) {
176 >          for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
177              if (i == vacancyTargets[j]) vac = true;
178            }
179            isVacancy.push_back(vac);
# Line 199 | Line 194 | int main(int argc, char *argv []) {
194    std::vector<Component*> components = simParams->getComponents();
195    std::vector<RealType> molFractions;
196    std::vector<RealType> shellRadii;
202 –  std::vector<RealType> molecularMasses;
197    std::vector<int> nMol;
198    std::map<int, int> componentFromSite;
199    nComponents = components.size();
# Line 304 | Line 298 | int main(int argc, char *argv []) {
298      }
299    } else {
300  
301 <    for (int i = 0; i < shellRadii.size(); i++) {
301 >    for (unsigned int i = 0; i < shellRadii.size(); i++) {
302        if (shellRadii.at(i) > particleRadius + 1e-6 ) {
303          sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
304          painCave.isFatal = 1;
# Line 322 | Line 316 | int main(int argc, char *argv []) {
316    if ((int)args_info.molFraction_given){
317      sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
318      painCave.isFatal = 0;
319 +    painCave.severity = OPENMD_INFO;
320      simError();
321      /* Random particle is the default case*/
322  
323 <    for (int i = 0; i < sites.size(); i++)
323 >    for (unsigned int i = 0; i < sites.size(); i++)
324        if (!isVacancy[i]) ids.push_back(i);
325      
326      std::random_shuffle(ids.begin(), ids.end());
# Line 333 | Line 328 | int main(int argc, char *argv []) {
328    } else{
329      sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
330      painCave.isFatal = 0;
331 +    painCave.severity = OPENMD_INFO;
332      simError();
333  
334      RealType smallestSoFar;
# Line 340 | Line 336 | int main(int argc, char *argv []) {
336      nMol.clear();
337      nMol.resize(nComponents);
338  
339 <    for (int i = 0; i < sites.size(); i++) {
339 >    for (unsigned int i = 0; i < sites.size(); i++) {
340        myLoc = sites[i];
341        myR = myLoc.length();
342        smallestSoFar = particleRadius;      
# Line 364 | Line 360 | int main(int argc, char *argv []) {
360    //creat new .md file on fly which corrects the number of molecule    
361    createMdFile(inputFileName, outputFileName, nMol);
362    
363 <  if (oldInfo != NULL)
368 <    delete oldInfo;
363 >  delete oldInfo;
364    
365    SimCreator newCreator;
366    SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
# Line 376 | Line 371 | int main(int argc, char *argv []) {
371    mol = NewInfo->beginMolecule(mi);
372  
373    int l = 0;
379 –  int whichSite = 0;
374  
375    for (int i = 0; i < nComponents; i++){
376      locator = new MoLocator(NewInfo->getMoleculeStamp(i),
377                              NewInfo->getForceField());
378      
379      if (!args_info.molFraction_given) {
380 <      for (int n = 0; n < sites.size(); n++) {
380 >      for (unsigned int n = 0; n < sites.size(); n++) {
381          if (!isVacancy[n]) {
382            if (componentFromSite[n] == i) {
383              mol = NewInfo->getMoleculeByGlobalIndex(l);
# Line 434 | Line 428 | int main(int argc, char *argv []) {
428    delete writer;
429  
430    // cleanup a by calling sim error.....
431 <  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
431 >  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
432            "generated.\n", outputFileName.c_str());
433    painCave.isFatal = 0;
434 +  painCave.severity = OPENMD_INFO;
435    simError();
436    return 0;
437   }
# Line 454 | Line 449 | void createMdFile(const std::string&oldMdFileName,
449    newMdFile.open(newMdFileName.c_str());
450    oldMdFile.getline(buffer, MAXLEN);
451  
452 <  int i = 0;
452 >  unsigned int i = 0;
453    while (!oldMdFile.eof()) {
454  
455      //correct molecule number

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords):
Revision 1077 by gezelter, Wed Oct 18 19:35:07 2006 UTC vs.
Revision 1977 by gezelter, Wed Mar 12 21:35:23 2014 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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