applications/nanoRodBuilder/nanorodBuilder.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 "nanorodBuilderCmd.h"
#ifdef HAVE_CGAL
#include "GeometryBuilder.hpp"
#endif
#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;
  std::string outGeomFileName;
  
  
  Lattice *simpleLat;
  int numMol;
  double latticeConstant;
  std::vector<double> lc;
  double mass;
  const double rhoConvertConst = 1.661;
  double density;
  double rodLength;
  double rodDiameter;
  
  
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator *locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  DumpWriter *writer;
  
  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
  
  
  // Check for lib CGAL, if we don't have it, we should exit....
        
#ifndef HAVE_CGAL
  std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
            << std::endl;
  exit(1);
#endif
        
        
  //get lattice type
  latticeType = UpperCase(args_info.latticetype_arg);
  
  
  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
            latticeType.c_str());
    painCave.isFatal = 1;
    simError();
  }        
  
  //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);
  
  if (oldInfo->getNMoleculeStamp()> 1) {
    std::cerr << "can not build nanorod with more than one components"
              << std::endl;
    exit(1);
  }
  
  //get mass of molecule. 
  
  mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  //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;
  rodLength = args_info.length_arg;
  rodDiameter = args_info.width_arg;
  
  //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";
  
  
  //creat Molocator
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /*
    Assume we are carving nanorod out of a cublic block of material and that
    the shape the material will fit within that block.... 
    The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the 
    diameter of the particle.            
  */
  // Number of Unit Cells in Length first
  ny = (int)(rodLength/latticeConstant);
  // Number of unit cells in Width
  nx = (int)(rodDiameter/latticeConstant);
  nz = (int)(rodDiameter/latticeConstant);
  
  
  // Create geometry for nanocrystal
#ifdef HAVE_CGAL
  GeometryBuilder *myGeometry;
  // GeometryBuilder myGeometry(rodLength,rodDiameter);
  if (args_info.twinnedCrystal_flag){
     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
  }
  else{
     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
  }
  
  if (args_info.genGeomview_given){
     if (args_info.genGeomview_flag){
        outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
        myGeometry->dumpGeometry(outGeomFileName);
     }
  }
  
#endif
  
  /*
    We have to build the system first to figure out how many molecules
    there are then create a md file and then actually build the
    system.
  */
  
  //place the molecules
  

  //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
  latticeOrt = simpleLat->getLatticePointsOrt();
  
  
  numMol = 0;
  for(int i = -nx; i < nx; i++) {     
    for(int j = -ny; j < ny; j++) {       
      for(int k = -nz; k < nz; k++) {
        //if (oldInfo->getNGlobalMolecules() != numMol) {
        
        
        //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])){
            numMol++;
          }
#else
           numMol++;
#endif
        }
      }
    }
  }

  
  // 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, 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 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:	2218
Committed:	Tue May 3 17:55:28 2005 UTC (19 years, 2 months ago) by chuckv
File size:	10982 byte(s)
Log Message:	More changes to nanoRodBuilder....
#	User	Rev	Content
1	gezelter	2204	/*
2	chuckv	2164	* 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	gezelter	2190
42	chuckv	2164	#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	gezelter	2190	#include "config.h"
52
53	chuckv	2164	#include "nanorodBuilderCmd.h"
54	gezelter	2190	#ifdef HAVE_CGAL
55			#include "GeometryBuilder.hpp"
56			#endif
57	gezelter	2178	#include "lattice/LatticeFactory.hpp"
58			#include "utils/MoLocator.hpp"
59			#include "lattice/Lattice.hpp"
60	chuckv	2164	#include "brains/Register.hpp"
61			#include "brains/SimInfo.hpp"
62			#include "brains/SimCreator.hpp"
63			#include "io/DumpWriter.hpp"
64			#include "math/Vector3.hpp"
65			#include "math/SquareMatrix3.hpp"
66			#include "utils/StringUtils.hpp"
67
68			using namespace std;
69			using namespace oopse;
70	gezelter	2190	void createMdFile(const std::string&oldMdFileName,
71			const std::string&newMdFileName,
72	chuckv	2164	int numMol);
73
74			int main(int argc, char *argv []) {
75	gezelter	2190
76			//register force fields
77			registerForceFields();
78			registerLattice();
79
80			gengetopt_args_info args_info;
81			std::string latticeType;
82			std::string inputFileName;
83			std::string outPrefix;
84			std::string outMdFileName;
85			std::string outInitFileName;
86			std::string outGeomFileName;
87
88
89			Lattice *simpleLat;
90			int numMol;
91			double latticeConstant;
92			std::vector<double> lc;
93			double mass;
94			const double rhoConvertConst = 1.661;
95			double density;
96			double rodLength;
97			double rodDiameter;
98
99
100			int nx, ny, nz;
101			Mat3x3d hmat;
102			MoLocator *locator;
103			std::vector<Vector3d> latticePos;
104			std::vector<Vector3d> latticeOrt;
105			int numMolPerCell;
106			DumpWriter *writer;
107
108			// parse command line arguments
109			if (cmdline_parser(argc, argv, &args_info) != 0)
110			exit(1);
111
112
113	gezelter	2204	// Check for lib CGAL, if we don't have it, we should exit....
114	chuckv	2196
115			#ifndef HAVE_CGAL
116	gezelter	2204	std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
117			<< std::endl;
118			exit(1);
119	chuckv	2196	#endif
120
121
122
123	gezelter	2190	//get lattice type
124			latticeType = UpperCase(args_info.latticetype_arg);
125
126
127			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
128			if (simpleLat == NULL) {
129			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
130			latticeType.c_str());
131			painCave.isFatal = 1;
132			simError();
133			}
134
135			//get input file name
136			if (args_info.inputs_num)
137			inputFileName = args_info.inputs[0];
138			else {
139			std::cerr << "You must specify a input file name.\n" << std::endl;
140			cmdline_parser_print_help();
141			exit(1);
142			}
143
144			//parse md file and set up the system
145			SimCreator oldCreator;
146			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
147
148			if (oldInfo->getNMoleculeStamp()> 1) {
149			std::cerr << "can not build nanorod with more than one components"
150			<< std::endl;
151			exit(1);
152			}
153
154			//get mass of molecule.
155
156			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
157
158			//creat lattice
159			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
160
161			if (simpleLat == NULL) {
162			std::cerr << "Error in creating lattice" << std::endl;
163			exit(1);
164			}
165
166			numMolPerCell = simpleLat->getNumSitesPerCell();
167
168			//calculate lattice constant (in Angstrom)
169			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
170			// 1.0 / 3.0);
171
172			latticeConstant = args_info.latticeCnst_arg;
173			rodLength = args_info.length_arg;
174			rodDiameter = args_info.width_arg;
175
176			//set lattice constant
177			lc.push_back(latticeConstant);
178			simpleLat->setLatticeConstant(lc);
179
180
181			//determine the output file names
182			if (args_info.output_given)
183			outInitFileName = args_info.output_arg;
184			else
185			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
186
187	chuckv	2215
188
189
190
191
192	gezelter	2190	//creat Molocator
193			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
194
195			/*
196			Assume we are carving nanorod out of a cublic block of material and that
197			the shape the material will fit within that block....
198			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
199			diameter of the particle.
200			*/
201			// Number of Unit Cells in Length first
202			ny = (int)(rodLength/latticeConstant);
203			// Number of unit cells in Width
204			nx = (int)(rodDiameter/latticeConstant);
205			nz = (int)(rodDiameter/latticeConstant);
206
207
208
209			// Create geometry for nanocrystal
210	chuckv	2196	#ifdef HAVE_CGAL
211	chuckv	2218	GeometryBuilder *myGeometry;
212			// GeometryBuilder myGeometry(rodLength,rodDiameter);
213			if (args_info.twinnedCrystal_flag){
214			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
215			}
216			else{
217			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
218			}
219
220	chuckv	2215	if (args_info.genGeomview_given){
221			if (args_info.genGeomview_flag){
222			outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
223	chuckv	2218	myGeometry->dumpGeometry(outGeomFileName);
224	chuckv	2215	}
225			}
226	chuckv	2218
227	gezelter	2190	#endif
228
229			/*
230			We have to build the system first to figure out how many molecules
231			there are then create a md file and then actually build the
232			system.
233			*/
234
235			//place the molecules
236
237	chuckv	2218
238	gezelter	2190
239			//get the orientation of the cell sites
240			//for the same type of molecule in same lattice, it will not change
241			latticeOrt = simpleLat->getLatticePointsOrt();
242
243
244
245			numMol = 0;
246	chuckv	2215	for(int i = -nx; i < nx; i++) {
247			for(int j = -ny; j < ny; j++) {
248			for(int k = -nz; k < nz; k++) {
249	gezelter	2190	//if (oldInfo->getNGlobalMolecules() != numMol) {
250	chuckv	2164
251	gezelter	2190
252
253			//get the position of the cell sites
254			simpleLat->getLatticePointsPos(latticePos, i, j, k);
255
256			for(int l = 0; l < numMolPerCell; l++) {
257	chuckv	2164
258	chuckv	2196	#ifdef HAVE_CGAL
259	chuckv	2218	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
260	gezelter	2190	numMol++;
261			}
262	chuckv	2218	#else
263			numMol++;
264	gezelter	2190	#endif
265			}
266			}
267	chuckv	2164	}
268	gezelter	2190	}
269	chuckv	2218
270	gezelter	2190
271			// needed for writing out new md file.
272
273			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
274			outMdFileName = outPrefix + ".md";
275
276			//creat new .md file on fly which corrects the number of molecule
277			createMdFile(inputFileName, outMdFileName, numMol);
278
279			if (oldInfo != NULL)
280			delete oldInfo;
281
282
283			// We need to read in new siminfo object.
284			//parse md file and set up the system
285			//SimCreator NewCreator;
286
287			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
288
289			// This was so much fun the first time, lets do it again.
290
291			Molecule* mol;
292			SimInfo::MoleculeIterator mi;
293			mol = NewInfo->beginMolecule(mi);
294	chuckv	2218
295
296	chuckv	2215	for(int i = -nx; i < nx; i++) {
297			for(int j = -ny; j < ny; j++) {
298			for(int k = -nz; k < nz; k++) {
299
300			//get the position of the cell sites
301			simpleLat->getLatticePointsPos(latticePos, i, j, k);
302
303			for(int l = 0; l < numMolPerCell; l++) {
304	chuckv	2218	#ifdef HAVE_CGAL
305			if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
306			#endif
307	chuckv	2215	if (mol != NULL) {
308			locator->placeMol(latticePos[l], latticeOrt[l], mol);
309			} else {
310	chuckv	2218	std::cerr<<"Error in placing molecule " << std::endl;
311	chuckv	2215	}
312			mol = NewInfo->nextMolecule(mi);
313	chuckv	2218	#ifdef HAVE_CGAL
314	chuckv	2215	}
315	chuckv	2218	#endif
316	chuckv	2215	}
317	gezelter	2190	}
318	chuckv	2215	}
319	gezelter	2190	}
320
321	chuckv	2218
322	gezelter	2190
323			//fill Hmat
324			hmat(0, 0)= nx * latticeConstant;
325			hmat(0, 1) = 0.0;
326			hmat(0, 2) = 0.0;
327
328			hmat(1, 0) = 0.0;
329			hmat(1, 1) = ny * latticeConstant;
330			hmat(1, 2) = 0.0;
331
332			hmat(2, 0) = 0.0;
333			hmat(2, 1) = 0.0;
334			hmat(2, 2) = nz * latticeConstant;
335
336			//set Hmat
337			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
338
339
340			//create dumpwriter and write out the coordinates
341			NewInfo->setFinalConfigFileName(outInitFileName);
342			writer = new DumpWriter(NewInfo);
343
344			if (writer == NULL) {
345			std::cerr << "error in creating DumpWriter" << std::endl;
346			exit(1);
347	gezelter	2204	}
348	gezelter	2190
349			writer->writeDump();
350			std::cout << "new initial configuration file: " << outInitFileName
351			<< " is generated." << std::endl;
352
353			//delete objects
354
355			//delete oldInfo and oldSimSetup
356
357			if (NewInfo != NULL)
358			delete NewInfo;
359
360			if (writer != NULL)
361			delete writer;
362			delete simpleLat;
363			cmdline_parser_free(&args_info);
364			return 0;
365	chuckv	2164	}
366
367			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
368			int numMol) {
369	gezelter	2190	ifstream oldMdFile;
370			ofstream newMdFile;
371			const int MAXLEN = 65535;
372			char buffer[MAXLEN];
373
374			//create new .md file based on old .md file
375			oldMdFile.open(oldMdFileName.c_str());
376			newMdFile.open(newMdFileName.c_str());
377
378			oldMdFile.getline(buffer, MAXLEN);
379
380			while (!oldMdFile.eof()) {
381
382			//correct molecule number
383			if (strstr(buffer, "nMol") != NULL) {
384			sprintf(buffer, "\tnMol = %i;", numMol);
385			newMdFile << buffer << std::endl;
386			} else
387			newMdFile << buffer << std::endl;
388
389	chuckv	2164	oldMdFile.getline(buffer, MAXLEN);
390	gezelter	2190	}
391
392			oldMdFile.close();
393			newMdFile.close();
394	chuckv	2164	}
395