applications/nanoparticleBuilder/nanoparticleBuilder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "config.h"

#include "nanoparticleBuilderCmd.h"
#include "sphericalNanoparticle.hpp"
#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace oopse;
void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  int numMol);

int main(int argc, char *argv []) {
  
  //register force fields
  registerForceFields();
  registerLattice();
  
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outPrefix;
  std::string outMdFileName;
  std::string outInitFileName;

  
  Lattice *simpleLat;
  int numMol;
  double latticeConstant;
  std::vector<double> lc;
  double mass;
  const double rhoConvertConst = 1.661;
  double density;
  
  
  Mat3x3d hmat;
  MoLocator *locator;
  sphericalNanoparticle *nanoparticle;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int nShells; /* Number of shells in nanoparticle*/
  int numSites;
  
  DumpWriter *writer;
  
  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
  
        
  /* get lattice type */
  latticeType = UpperCase(args_info.latticetype_arg);
    
  /* get input file name */
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    std::cerr << "You must specify a input file name.\n" << std::endl;
    cmdline_parser_print_help();
    exit(1);
  }
  
  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  nShells = 0;
  if (args_info.coreShellRadius_given){
    nShells = args_info.coreShellRadius_given;
  }
  
  nComponents = oldInfo->getNMoleculeStamp();
  
  /* Check to see if we have enough components to build that many shells. */
  if (nShells){
    if (oldInfo->getNMoleculeStamp() != nShells) {
      std::cerr << "Not enough components present in MD file to build specified number of shells"
      << std::endl;
      exit(1);
    }
  }
  
  
  //creat lattice
  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
  
  if (simpleLat == NULL) {
    std::cerr << "Error in creating lattice" << std::endl;
    exit(1);
  }
  
  numMolPerCell = simpleLat->getNumSitesPerCell();
  
  /*calculate lattice constant (in Angstrom)
  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
                        1.0 / 3.0);*/
  
  latticeConstant = args_info.latticeCnst_arg;
  particleRadius = args_info.radius_arg;
  particleDiameter = 2.0 * particleRadius;
  
  /* set lattice constant */
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
  
  
  /*determine the output file names*/
  if (args_info.output_given)
    outInitFileName = args_info.output_arg;
  else
    outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
  
  
  /* create Molocators */
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /* create a new spherical nanoparticle */
  nanoparticle = new sphericalNanoparticle(particleRadius,latticeConstant);
  /* Build a nanoparticle to see how many sites are there */
  numSites = new int[nComponents]
  nanoparticle.getNMol(numSites);
  
  numMol = new int[nComponents];
  /* Random particle is the default case*/
  if (!args_info.ShellRadius_given){
    std::cout << "Creating a random nanoparticle" << std::endl;
    /* Check to see if we have enough components */
    if (nComponents != args_info.molFraction_given + 1){
      std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
      exit 1;
    }
    int totComponents = 0;
    for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
      numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
      totComponents += numMol[i];
    }
    numMol[nComponents-1] = numSites - totComponents;

  } else{ /*Handle core-shell with multiple components.*/
    std::cout << "Creating a core-shell nanoparticle." << std::endl;
    if (nComponents != args_info.ShellRadius_given + 1){
      std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
      exit 1;
    }
    
    
  }

   //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
   latticeOrt = simpleLat->getLatticePointsOrt();
  
  
  // needed for writing out new md file.
  
    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
    outMdFileName = outPrefix + ".md";
  
    //creat new .md file on fly which corrects the number of molecule     
    createMdFile(inputFileName, outMdFileName, numcomponents,numMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  
  SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
  
  // This was so much fun the first time, lets do it again.
  
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);


  for(int i = -nx; i < nx; i++) {
     for(int j = -ny; j < ny; j++) {
        for(int k = -nz; k < nz; k++) {
           
           //get the position of the cell sites
           simpleLat->getLatticePointsPos(latticePos, i, j, k);
           
           for(int l = 0; l < numMolPerCell; l++) {
#ifdef HAVE_CGAL              
              if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
#endif                              
                 if (mol != NULL) {
                    locator->placeMol(latticePos[l], latticeOrt[l], mol);
                 } else {
                    std::cerr<<"Error in placing molecule " << std::endl;                    
                 }
                 mol = NewInfo->nextMolecule(mi);
#ifdef HAVE_CGAL                
              }
#endif              
           }
        }
     }
  }
  

  //fill Hmat
  hmat(0, 0)= nx * latticeConstant;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) = ny * latticeConstant;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) = nz * latticeConstant;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  NewInfo->setFinalConfigFileName(outInitFileName);
  writer = new DumpWriter(NewInfo);
  
  if (writer == NULL) {
    std::cerr << "error in creating DumpWriter" << std::endl;
    exit(1);
  }
  
  writer->writeDump();
  std::cout << "new initial configuration file: " << outInitFileName
            << " is generated." << std::endl;
  
  //delete objects
  
  //delete oldInfo and oldSimSetup
  
  if (NewInfo != NULL)
    delete NewInfo;
  
  if (writer != NULL)
    delete writer;
  delete simpleLat;     
  cmdline_parser_free(&args_info);
  return 0;
}

void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
                  int components,int &nummol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  
  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
  
  oldMdFile.getline(buffer, MAXLEN);
  
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      sprintf(buffer, "\tnMol = %i;", numMol);                          
      newMdFile << buffer << std::endl;
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	653
Committed:	Tue Oct 11 21:57:22 2005 UTC (20 years ago) by chuckv
File size:	10207 byte(s)
Log Message:	Added code for nanoparticle builder to cvs.
#	User	Rev	Content
1	chuckv	653	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <cstdlib>
43			#include <cstdio>
44			#include <cstring>
45			#include <cmath>
46			#include <iostream>
47			#include <string>
48			#include <map>
49			#include <fstream>
50
51			#include "config.h"
52
53			#include "nanoparticleBuilderCmd.h"
54			#include "sphericalNanoparticle.hpp"
55			#include "lattice/LatticeFactory.hpp"
56			#include "utils/MoLocator.hpp"
57			#include "lattice/Lattice.hpp"
58			#include "brains/Register.hpp"
59			#include "brains/SimInfo.hpp"
60			#include "brains/SimCreator.hpp"
61			#include "io/DumpWriter.hpp"
62			#include "math/Vector3.hpp"
63			#include "math/SquareMatrix3.hpp"
64			#include "utils/StringUtils.hpp"
65
66			using namespace std;
67			using namespace oopse;
68			void createMdFile(const std::string&oldMdFileName,
69			const std::string&newMdFileName,
70			int numMol);
71
72			int main(int argc, char *argv []) {
73
74			//register force fields
75			registerForceFields();
76			registerLattice();
77
78			gengetopt_args_info args_info;
79			std::string latticeType;
80			std::string inputFileName;
81			std::string outPrefix;
82			std::string outMdFileName;
83			std::string outInitFileName;
84
85
86
87			Lattice *simpleLat;
88			int numMol;
89			double latticeConstant;
90			std::vector<double> lc;
91			double mass;
92			const double rhoConvertConst = 1.661;
93			double density;
94
95
96
97			Mat3x3d hmat;
98			MoLocator *locator;
99			sphericalNanoparticle *nanoparticle;
100			std::vector<Vector3d> latticePos;
101			std::vector<Vector3d> latticeOrt;
102			int numMolPerCell;
103			int nShells; /* Number of shells in nanoparticle*/
104			int numSites;
105
106			DumpWriter *writer;
107
108			// parse command line arguments
109			if (cmdline_parser(argc, argv, &args_info) != 0)
110			exit(1);
111
112
113
114			/* get lattice type */
115			latticeType = UpperCase(args_info.latticetype_arg);
116
117			/* get input file name */
118			if (args_info.inputs_num)
119			inputFileName = args_info.inputs[0];
120			else {
121			std::cerr << "You must specify a input file name.\n" << std::endl;
122			cmdline_parser_print_help();
123			exit(1);
124			}
125
126			/* parse md file and set up the system */
127			SimCreator oldCreator;
128			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
129
130			nShells = 0;
131			if (args_info.coreShellRadius_given){
132			nShells = args_info.coreShellRadius_given;
133			}
134
135			nComponents = oldInfo->getNMoleculeStamp();
136
137			/* Check to see if we have enough components to build that many shells. */
138			if (nShells){
139			if (oldInfo->getNMoleculeStamp() != nShells) {
140			std::cerr << "Not enough components present in MD file to build specified number of shells"
141			<< std::endl;
142			exit(1);
143			}
144			}
145
146
147			//creat lattice
148			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
149
150			if (simpleLat == NULL) {
151			std::cerr << "Error in creating lattice" << std::endl;
152			exit(1);
153			}
154
155			numMolPerCell = simpleLat->getNumSitesPerCell();
156
157			/*calculate lattice constant (in Angstrom)
158			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
159			1.0 / 3.0);*/
160
161			latticeConstant = args_info.latticeCnst_arg;
162			particleRadius = args_info.radius_arg;
163			particleDiameter = 2.0 * particleRadius;
164
165			/* set lattice constant */
166			lc.push_back(latticeConstant);
167			simpleLat->setLatticeConstant(lc);
168
169
170			/determine the output file names/
171			if (args_info.output_given)
172			outInitFileName = args_info.output_arg;
173			else
174			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
175
176
177
178
179
180
181			/* create Molocators */
182			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
183
184			/* create a new spherical nanoparticle */
185			nanoparticle = new sphericalNanoparticle(particleRadius,latticeConstant);
186			/* Build a nanoparticle to see how many sites are there */
187			numSites = new int[nComponents]
188			nanoparticle.getNMol(numSites);
189
190			numMol = new int[nComponents];
191			/* Random particle is the default case*/
192			if (!args_info.ShellRadius_given){
193			std::cout << "Creating a random nanoparticle" << std::endl;
194			/* Check to see if we have enough components */
195			if (nComponents != args_info.molFraction_given + 1){
196			std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
197			exit 1;
198			}
199			int totComponents = 0;
200			for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
201			numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
202			totComponents += numMol[i];
203			}
204			numMol[nComponents-1] = numSites - totComponents;
205
206			} else{ /Handle core-shell with multiple components./
207			std::cout << "Creating a core-shell nanoparticle." << std::endl;
208			if (nComponents != args_info.ShellRadius_given + 1){
209			std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
210			exit 1;
211			}
212
213
214
215			}
216
217			//get the orientation of the cell sites
218			//for the same type of molecule in same lattice, it will not change
219			latticeOrt = simpleLat->getLatticePointsOrt();
220
221
222
223			// needed for writing out new md file.
224
225			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
226			outMdFileName = outPrefix + ".md";
227
228			//creat new .md file on fly which corrects the number of molecule
229			createMdFile(inputFileName, outMdFileName, numcomponents,numMol);
230
231			if (oldInfo != NULL)
232			delete oldInfo;
233
234
235			// We need to read in new siminfo object.
236			//parse md file and set up the system
237			//SimCreator NewCreator;
238
239			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
240
241			// This was so much fun the first time, lets do it again.
242
243			Molecule* mol;
244			SimInfo::MoleculeIterator mi;
245			mol = NewInfo->beginMolecule(mi);
246
247
248			for(int i = -nx; i < nx; i++) {
249			for(int j = -ny; j < ny; j++) {
250			for(int k = -nz; k < nz; k++) {
251
252			//get the position of the cell sites
253			simpleLat->getLatticePointsPos(latticePos, i, j, k);
254
255			for(int l = 0; l < numMolPerCell; l++) {
256			#ifdef HAVE_CGAL
257			if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
258			#endif
259			if (mol != NULL) {
260			locator->placeMol(latticePos[l], latticeOrt[l], mol);
261			} else {
262			std::cerr<<"Error in placing molecule " << std::endl;
263			}
264			mol = NewInfo->nextMolecule(mi);
265			#ifdef HAVE_CGAL
266			}
267			#endif
268			}
269			}
270			}
271			}
272
273
274
275			//fill Hmat
276			hmat(0, 0)= nx * latticeConstant;
277			hmat(0, 1) = 0.0;
278			hmat(0, 2) = 0.0;
279
280			hmat(1, 0) = 0.0;
281			hmat(1, 1) = ny * latticeConstant;
282			hmat(1, 2) = 0.0;
283
284			hmat(2, 0) = 0.0;
285			hmat(2, 1) = 0.0;
286			hmat(2, 2) = nz * latticeConstant;
287
288			//set Hmat
289			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
290
291
292			//create dumpwriter and write out the coordinates
293			NewInfo->setFinalConfigFileName(outInitFileName);
294			writer = new DumpWriter(NewInfo);
295
296			if (writer == NULL) {
297			std::cerr << "error in creating DumpWriter" << std::endl;
298			exit(1);
299			}
300
301			writer->writeDump();
302			std::cout << "new initial configuration file: " << outInitFileName
303			<< " is generated." << std::endl;
304
305			//delete objects
306
307			//delete oldInfo and oldSimSetup
308
309			if (NewInfo != NULL)
310			delete NewInfo;
311
312			if (writer != NULL)
313			delete writer;
314			delete simpleLat;
315			cmdline_parser_free(&args_info);
316			return 0;
317			}
318
319			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
320			int components,int &nummol) {
321			ifstream oldMdFile;
322			ofstream newMdFile;
323			const int MAXLEN = 65535;
324			char buffer[MAXLEN];
325
326			//create new .md file based on old .md file
327			oldMdFile.open(oldMdFileName.c_str());
328			newMdFile.open(newMdFileName.c_str());
329
330			oldMdFile.getline(buffer, MAXLEN);
331
332			while (!oldMdFile.eof()) {
333
334			//correct molecule number
335			if (strstr(buffer, "nMol") != NULL) {
336			sprintf(buffer, "\tnMol = %i;", numMol);
337			newMdFile << buffer << std::endl;
338			} else
339			newMdFile << buffer << std::endl;
340
341			oldMdFile.getline(buffer, MAXLEN);
342			}
343
344			oldMdFile.close();
345			newMdFile.close();
346			}
347