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 "GeometryFactory.hpp"
#include "Geometry.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;
  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);
    
  //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:	2252
Committed:	Mon May 30 14:01:52 2005 UTC (19 years, 1 month ago) by chuckv
File size:	10773 byte(s)
Log Message:	Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
#	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	chuckv	2252	#include "GeometryFactory.hpp"
58			#include "Geometry.hpp"
59	gezelter	2178	#include "lattice/LatticeFactory.hpp"
60			#include "utils/MoLocator.hpp"
61			#include "lattice/Lattice.hpp"
62	chuckv	2164	#include "brains/Register.hpp"
63			#include "brains/SimInfo.hpp"
64			#include "brains/SimCreator.hpp"
65			#include "io/DumpWriter.hpp"
66			#include "math/Vector3.hpp"
67			#include "math/SquareMatrix3.hpp"
68			#include "utils/StringUtils.hpp"
69
70			using namespace std;
71			using namespace oopse;
72	gezelter	2190	void createMdFile(const std::string&oldMdFileName,
73			const std::string&newMdFileName,
74	chuckv	2164	int numMol);
75
76			int main(int argc, char *argv []) {
77	gezelter	2190
78			//register force fields
79			registerForceFields();
80			registerLattice();
81
82			gengetopt_args_info args_info;
83			std::string latticeType;
84			std::string inputFileName;
85			std::string outPrefix;
86			std::string outMdFileName;
87			std::string outInitFileName;
88			std::string outGeomFileName;
89
90
91			Lattice *simpleLat;
92			int numMol;
93			double latticeConstant;
94			std::vector<double> lc;
95			double mass;
96			const double rhoConvertConst = 1.661;
97			double density;
98			double rodLength;
99			double rodDiameter;
100
101
102			int nx, ny, nz;
103			Mat3x3d hmat;
104			MoLocator *locator;
105			std::vector<Vector3d> latticePos;
106			std::vector<Vector3d> latticeOrt;
107			int numMolPerCell;
108			DumpWriter *writer;
109
110			// parse command line arguments
111			if (cmdline_parser(argc, argv, &args_info) != 0)
112			exit(1);
113
114
115	gezelter	2204	// Check for lib CGAL, if we don't have it, we should exit....
116	chuckv	2196
117			#ifndef HAVE_CGAL
118	gezelter	2204	std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
119			<< std::endl;
120			exit(1);
121	chuckv	2196	#endif
122
123
124
125	gezelter	2190	//get lattice type
126			latticeType = UpperCase(args_info.latticetype_arg);
127	chuckv	2239
128	gezelter	2190	//get input file name
129			if (args_info.inputs_num)
130			inputFileName = args_info.inputs[0];
131			else {
132			std::cerr << "You must specify a input file name.\n" << std::endl;
133			cmdline_parser_print_help();
134			exit(1);
135			}
136
137			//parse md file and set up the system
138			SimCreator oldCreator;
139			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
140
141			if (oldInfo->getNMoleculeStamp()> 1) {
142			std::cerr << "can not build nanorod with more than one components"
143			<< std::endl;
144			exit(1);
145			}
146
147			//get mass of molecule.
148
149			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
150
151			//creat lattice
152			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
153
154			if (simpleLat == NULL) {
155			std::cerr << "Error in creating lattice" << std::endl;
156			exit(1);
157			}
158
159			numMolPerCell = simpleLat->getNumSitesPerCell();
160
161			//calculate lattice constant (in Angstrom)
162			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
163			// 1.0 / 3.0);
164
165			latticeConstant = args_info.latticeCnst_arg;
166			rodLength = args_info.length_arg;
167			rodDiameter = args_info.width_arg;
168
169			//set lattice constant
170			lc.push_back(latticeConstant);
171			simpleLat->setLatticeConstant(lc);
172
173
174			//determine the output file names
175			if (args_info.output_given)
176			outInitFileName = args_info.output_arg;
177			else
178			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
179
180	chuckv	2215
181
182
183
184
185	gezelter	2190	//creat Molocator
186			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
187
188			/*
189			Assume we are carving nanorod out of a cublic block of material and that
190			the shape the material will fit within that block....
191			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
192			diameter of the particle.
193			*/
194			// Number of Unit Cells in Length first
195			ny = (int)(rodLength/latticeConstant);
196			// Number of unit cells in Width
197			nx = (int)(rodDiameter/latticeConstant);
198			nz = (int)(rodDiameter/latticeConstant);
199
200
201
202			// Create geometry for nanocrystal
203	chuckv	2196	#ifdef HAVE_CGAL
204	chuckv	2218	GeometryBuilder *myGeometry;
205			// GeometryBuilder myGeometry(rodLength,rodDiameter);
206			if (args_info.twinnedCrystal_flag){
207			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
208			}
209			else{
210			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
211			}
212
213	chuckv	2215	if (args_info.genGeomview_given){
214			if (args_info.genGeomview_flag){
215			outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
216	chuckv	2218	myGeometry->dumpGeometry(outGeomFileName);
217	chuckv	2215	}
218			}
219	chuckv	2218
220	gezelter	2190	#endif
221
222			/*
223			We have to build the system first to figure out how many molecules
224			there are then create a md file and then actually build the
225			system.
226			*/
227
228			//place the molecules
229
230	chuckv	2218
231	gezelter	2190
232			//get the orientation of the cell sites
233			//for the same type of molecule in same lattice, it will not change
234			latticeOrt = simpleLat->getLatticePointsOrt();
235
236
237
238			numMol = 0;
239	chuckv	2215	for(int i = -nx; i < nx; i++) {
240			for(int j = -ny; j < ny; j++) {
241			for(int k = -nz; k < nz; k++) {
242	gezelter	2190	//if (oldInfo->getNGlobalMolecules() != numMol) {
243	chuckv	2164
244	gezelter	2190
245
246			//get the position of the cell sites
247			simpleLat->getLatticePointsPos(latticePos, i, j, k);
248
249			for(int l = 0; l < numMolPerCell; l++) {
250	chuckv	2164
251	chuckv	2196	#ifdef HAVE_CGAL
252	chuckv	2218	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
253	gezelter	2190	numMol++;
254			}
255	chuckv	2218	#else
256			numMol++;
257	gezelter	2190	#endif
258			}
259			}
260	chuckv	2164	}
261	gezelter	2190	}
262	chuckv	2218
263	gezelter	2190
264			// needed for writing out new md file.
265
266			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
267			outMdFileName = outPrefix + ".md";
268
269			//creat new .md file on fly which corrects the number of molecule
270			createMdFile(inputFileName, outMdFileName, numMol);
271
272			if (oldInfo != NULL)
273			delete oldInfo;
274
275
276			// We need to read in new siminfo object.
277			//parse md file and set up the system
278			//SimCreator NewCreator;
279
280			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
281
282			// This was so much fun the first time, lets do it again.
283
284			Molecule* mol;
285			SimInfo::MoleculeIterator mi;
286			mol = NewInfo->beginMolecule(mi);
287	chuckv	2218
288
289	chuckv	2215	for(int i = -nx; i < nx; i++) {
290			for(int j = -ny; j < ny; j++) {
291			for(int k = -nz; k < nz; k++) {
292
293			//get the position of the cell sites
294			simpleLat->getLatticePointsPos(latticePos, i, j, k);
295
296			for(int l = 0; l < numMolPerCell; l++) {
297	chuckv	2218	#ifdef HAVE_CGAL
298			if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
299			#endif
300	chuckv	2215	if (mol != NULL) {
301			locator->placeMol(latticePos[l], latticeOrt[l], mol);
302			} else {
303	chuckv	2218	std::cerr<<"Error in placing molecule " << std::endl;
304	chuckv	2215	}
305			mol = NewInfo->nextMolecule(mi);
306	chuckv	2218	#ifdef HAVE_CGAL
307	chuckv	2215	}
308	chuckv	2218	#endif
309	chuckv	2215	}
310	gezelter	2190	}
311	chuckv	2215	}
312	gezelter	2190	}
313
314	chuckv	2218
315	gezelter	2190
316			//fill Hmat
317			hmat(0, 0)= nx * latticeConstant;
318			hmat(0, 1) = 0.0;
319			hmat(0, 2) = 0.0;
320
321			hmat(1, 0) = 0.0;
322			hmat(1, 1) = ny * latticeConstant;
323			hmat(1, 2) = 0.0;
324
325			hmat(2, 0) = 0.0;
326			hmat(2, 1) = 0.0;
327			hmat(2, 2) = nz * latticeConstant;
328
329			//set Hmat
330			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
331
332
333			//create dumpwriter and write out the coordinates
334			NewInfo->setFinalConfigFileName(outInitFileName);
335			writer = new DumpWriter(NewInfo);
336
337			if (writer == NULL) {
338			std::cerr << "error in creating DumpWriter" << std::endl;
339			exit(1);
340	gezelter	2204	}
341	gezelter	2190
342			writer->writeDump();
343			std::cout << "new initial configuration file: " << outInitFileName
344			<< " is generated." << std::endl;
345
346			//delete objects
347
348			//delete oldInfo and oldSimSetup
349
350			if (NewInfo != NULL)
351			delete NewInfo;
352
353			if (writer != NULL)
354			delete writer;
355			delete simpleLat;
356			cmdline_parser_free(&args_info);
357			return 0;
358	chuckv	2164	}
359
360			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
361			int numMol) {
362	gezelter	2190	ifstream oldMdFile;
363			ofstream newMdFile;
364			const int MAXLEN = 65535;
365			char buffer[MAXLEN];
366
367			//create new .md file based on old .md file
368			oldMdFile.open(oldMdFileName.c_str());
369			newMdFile.open(newMdFileName.c_str());
370
371			oldMdFile.getline(buffer, MAXLEN);
372
373			while (!oldMdFile.eof()) {
374
375			//correct molecule number
376			if (strstr(buffer, "nMol") != NULL) {
377			sprintf(buffer, "\tnMol = %i;", numMol);
378			newMdFile << buffer << std::endl;
379			} else
380			newMdFile << buffer << std::endl;
381
382	chuckv	2164	oldMdFile.getline(buffer, MAXLEN);
383	gezelter	2190	}
384
385			oldMdFile.close();
386			newMdFile.close();
387	chuckv	2164	}
388