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 <algorithm>

#include "config.h"
#include "shapedLatticeSpherical.hpp"
#include "nanoparticleBuilderCmd.h"
#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,
                  std::vector<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 outputFileName;

  Lattice *simpleLat;
  MoLocator* locator;
  int* numMol;
  int nComponents;
  double latticeConstant;
  std::vector<double> lc;
  double mass;                                                                          
  const double rhoConvertConst = 1.661;
  double density;
  double particleRadius;

  Mat3x3d hmat;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int nShells; /* Number of shells in nanoparticle*/
 
  DumpWriter *writer;
  
  // Parse Command Line Arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
         
  /* get lattice type */
  latticeType = "FCC";

  /* get input file name */
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
      sprintf(painCave.errMsg, "No input .md file name was specified"
              "on the command line");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }
  
  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  latticeConstant = args_info.latticeCnst_arg;
  particleRadius = args_info.radius_arg;
  Globals* simParams = oldInfo->getSimParams();
  
  /* Create nanoparticle */
  shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
                                      particleRadius);
  
  /* Build a lattice and get lattice points for this lattice constant */
  vector<Vector3d> sites = nanoParticle.getSites();
  vector<Vector3d> orientations = nanoParticle.getOrientations();

  std::cout <<"nSites: " << sites.size() << std::endl;

  /* Get number of lattice sites */
  int nSites = sites.size();

  std::vector<Component*> components = simParams->getComponents();
  std::vector<RealType> molFractions;
  std::vector<RealType> molecularMasses;
  std::vector<int> nMol;
  nComponents = components.size();

 if (nComponents == 1) {
    molFractions.push_back(1.0);    
  } else {
   if (args_info.molFraction_given == nComponents) {
     for (int i = 0; i < nComponents; i++) {
       molFractions.push_back(args_info.molFraction_arg[i]);
     }
    } else if (args_info.molFraction_given == nComponents-1) {
     RealType remainingFraction = 1.0;
     for (int i = 0; i < nComponents-1; i++) {
       molFractions.push_back(args_info.molFraction_arg[i]);
       remainingFraction -= molFractions[i];
     }
     molFractions.push_back(remainingFraction);
   } else {    
     sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
             "for all of the components in the <MetaData> block.");
     painCave.isFatal = 1;
     simError();
   }
 }
 
 RealType totalFraction = 0.0;
 
 /* Do some simple sanity checking*/

  for (int i = 0; i < nComponents; i++) {
    if (molFractions.at(i) < 0.0) {
      sprintf(painCave.errMsg, "One of the requested molFractions was"
              " less than zero!");
      painCave.isFatal = 1;
      simError();
    }
    if (molFractions.at(i) > 1.0) {
      sprintf(painCave.errMsg, "One of the requested molFractions was"
              " greater than one!");
      painCave.isFatal = 1;
      simError();
    }
    totalFraction += molFractions.at(i);
  }
  if (abs(totalFraction - 1.0) > 1e-6) {
    sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
    painCave.isFatal = 1;
    simError();
  }

  int remaining = nSites;
  for (int i=0; i < nComponents-1; i++) {    
    nMol.push_back(int((RealType)nSites * molFractions.at(i)));
    remaining -= nMol.at(i);
  }
  nMol.push_back(remaining);


// recompute actual mol fractions and perform final sanity check:

  int totalMolecules = 0;
  RealType totalMass = 0.0;
  for (int i=0; i < nComponents; i++) {
    molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
    totalMolecules += nMol.at(i);
    molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
                                         oldInfo->getForceField()));
    totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
  }
  RealType avgMass = totalMass / (RealType) totalMolecules;

  if (totalMolecules != nSites) {
    sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
            "to the number of lattice sites!");
    painCave.isFatal = 1;
    simError();
  }
     
  vector<int> ids;
  for (int i = 0; i < sites.size(); i++) ids.push_back(i);
  /* Random particle is the default case*/
  if (!args_info.ShellRadius_given){
    /* do the iPod thing, Shuffle da vector */
    std::random_shuffle(ids.begin(), ids.end());
  } else{ /*Handle core-shell with multiple components.*/
    std::cout << "Creating a core-shell nanoparticle." << std::endl;
    if (nComponents != args_info.ShellRadius_given + 1){
      sprintf(painCave.errMsg, "Number of .md components "
              "does not match the number of shell radius specifications");
      painCave.isFatal = 1;
      simError();
    }   
    
  }

  
  outputFileName = args_info.output_arg;
 
  
   //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outputFileName, nMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
  
  
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);
  int l = 0;

  for (int i = 0; i < nComponents; i++){
    locator = new MoLocator(NewInfo->getMoleculeStamp(i), 
                            NewInfo->getForceField());
    for (int n = 0; n < nMol.at(i); n++) {
      mol = NewInfo->getMoleculeByGlobalIndex(l);
      locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
      l++;
    }
  }
  

  //fill Hmat
  hmat(0, 0)=  2.0*particleRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) =  2.0*particleRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) =  2.0*particleRadius;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  writer = new DumpWriter(NewInfo, outputFileName);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
      painCave.isFatal = 1;
      simError();
  }
  
  writer->writeDump();

  // deleting the writer will put the closing at the end of the dump file

  delete writer;

  // cleanup a by calling sim error.....
  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}

void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
                  std::vector<int> nMol) {
  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);
 
  int i = 0;
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      if(i<nMol.size()){
        sprintf(buffer, "\tnMol = %i;", nMol.at(i));                            
        newMdFile << buffer << std::endl;
        i++;
      }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	3046
Committed:	Sat Oct 14 20:21:26 2006 UTC (17 years, 11 months ago) by gezelter
File size:	10588 byte(s)
Log Message:	fixed a few bugs
#	User	Rev	Content
1	chuckv	2352	/*
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	chuckv	2657	#include <algorithm>
51	chuckv	2352
52			#include "config.h"
53	chuckv	2657	#include "shapedLatticeSpherical.hpp"
54	chuckv	2352	#include "nanoparticleBuilderCmd.h"
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	chuckv	3044	std::vector<int> numMol);
71	chuckv	2352
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	chuckv	3044	std::string outputFileName;
82	chuckv	2352
83			Lattice *simpleLat;
84	chuckv	2657	MoLocator* locator;
85			int* numMol;
86			int nComponents;
87	chuckv	2352	double latticeConstant;
88			std::vector<double> lc;
89	chuckv	3044	double mass;
90	chuckv	2352	const double rhoConvertConst = 1.661;
91			double density;
92	chuckv	2657	double particleRadius;
93	chuckv	2352
94			Mat3x3d hmat;
95			std::vector<Vector3d> latticePos;
96			std::vector<Vector3d> latticeOrt;
97			int numMolPerCell;
98			int nShells; /* Number of shells in nanoparticle*/
99	chuckv	3044
100	chuckv	2352	DumpWriter *writer;
101
102	chuckv	2574	// Parse Command Line Arguments
103	chuckv	2352	if (cmdline_parser(argc, argv, &args_info) != 0)
104			exit(1);
105	gezelter	3046
106	chuckv	2352	/* get lattice type */
107	chuckv	3044	latticeType = "FCC";
108
109	chuckv	2352	/* get input file name */
110			if (args_info.inputs_num)
111			inputFileName = args_info.inputs[0];
112			else {
113	chuckv	3044	sprintf(painCave.errMsg, "No input .md file name was specified"
114			"on the command line");
115			painCave.isFatal = 1;
116	chuckv	2352	cmdline_parser_print_help();
117	chuckv	3044	simError();
118	chuckv	2352	}
119
120			/* parse md file and set up the system */
121			SimCreator oldCreator;
122			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
123
124			latticeConstant = args_info.latticeCnst_arg;
125			particleRadius = args_info.radius_arg;
126	chuckv	2657	Globals* simParams = oldInfo->getSimParams();
127	chuckv	2352
128	chuckv	2657	/* Create nanoparticle */
129	gezelter	3046	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
130			particleRadius);
131	chuckv	2672
132	chuckv	2657	/* Build a lattice and get lattice points for this lattice constant */
133	gezelter	3046	vector<Vector3d> sites = nanoParticle.getSites();
134			vector<Vector3d> orientations = nanoParticle.getOrientations();
135	chuckv	3044
136			std::cout <<"nSites: " << sites.size() << std::endl;
137
138	chuckv	2657	/* Get number of lattice sites */
139	chuckv	3044	int nSites = sites.size();
140
141			std::vector<Component*> components = simParams->getComponents();
142			std::vector<RealType> molFractions;
143			std::vector<RealType> molecularMasses;
144			std::vector<int> nMol;
145			nComponents = components.size();
146
147			if (nComponents == 1) {
148			molFractions.push_back(1.0);
149			} else {
150	gezelter	3046	if (args_info.molFraction_given == nComponents) {
151			for (int i = 0; i < nComponents; i++) {
152			molFractions.push_back(args_info.molFraction_arg[i]);
153			}
154	chuckv	3044	} else if (args_info.molFraction_given == nComponents-1) {
155	gezelter	3046	RealType remainingFraction = 1.0;
156			for (int i = 0; i < nComponents-1; i++) {
157			molFractions.push_back(args_info.molFraction_arg[i]);
158			remainingFraction -= molFractions[i];
159			}
160			molFractions.push_back(remainingFraction);
161			} else {
162			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
163			"for all of the components in the <MetaData> block.");
164			painCave.isFatal = 1;
165			simError();
166			}
167			}
168
169	chuckv	3044	RealType totalFraction = 0.0;
170	gezelter	3046
171	chuckv	3044	/* Do some simple sanity checking*/
172
173			for (int i = 0; i < nComponents; i++) {
174			if (molFractions.at(i) < 0.0) {
175			sprintf(painCave.errMsg, "One of the requested molFractions was"
176			" less than zero!");
177			painCave.isFatal = 1;
178			simError();
179			}
180			if (molFractions.at(i) > 1.0) {
181			sprintf(painCave.errMsg, "One of the requested molFractions was"
182			" greater than one!");
183			painCave.isFatal = 1;
184			simError();
185			}
186			totalFraction += molFractions.at(i);
187			}
188			if (abs(totalFraction - 1.0) > 1e-6) {
189			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
190			painCave.isFatal = 1;
191			simError();
192			}
193
194			int remaining = nSites;
195			for (int i=0; i < nComponents-1; i++) {
196			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
197			remaining -= nMol.at(i);
198			}
199			nMol.push_back(remaining);
200
201
202
203			// recompute actual mol fractions and perform final sanity check:
204
205			int totalMolecules = 0;
206			RealType totalMass = 0.0;
207			for (int i=0; i < nComponents; i++) {
208			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
209			totalMolecules += nMol.at(i);
210			molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
211			oldInfo->getForceField()));
212			totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
213			}
214			RealType avgMass = totalMass / (RealType) totalMolecules;
215
216			if (totalMolecules != nSites) {
217			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
218			"to the number of lattice sites!");
219			painCave.isFatal = 1;
220			simError();
221			}
222
223			vector<int> ids;
224			for (int i = 0; i < sites.size(); i++) ids.push_back(i);
225	chuckv	2352	/* Random particle is the default case*/
226			if (!args_info.ShellRadius_given){
227	chuckv	2737	/* do the iPod thing, Shuffle da vector */
228	chuckv	3044	std::random_shuffle(ids.begin(), ids.end());
229	chuckv	2352	} else{ /Handle core-shell with multiple components./
230			std::cout << "Creating a core-shell nanoparticle." << std::endl;
231			if (nComponents != args_info.ShellRadius_given + 1){
232	chuckv	3044	sprintf(painCave.errMsg, "Number of .md components "
233			"does not match the number of shell radius specifications");
234			painCave.isFatal = 1;
235			simError();
236	chuckv	2657	}
237	chuckv	2352
238			}
239
240	chuckv	2737
241	chuckv	2352
242	chuckv	2737
243	chuckv	3044	outputFileName = args_info.output_arg;
244
245	chuckv	2737
246	chuckv	3044	//creat new .md file on fly which corrects the number of molecule
247			createMdFile(inputFileName, outputFileName, nMol);
248	chuckv	2352
249			if (oldInfo != NULL)
250			delete oldInfo;
251
252
253			// We need to read in new siminfo object.
254			//parse md file and set up the system
255			//SimCreator NewCreator;
256	chuckv	2737	SimCreator newCreator;
257	chuckv	3044	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
258	chuckv	2352
259
260	chuckv	2657	// Place molecules
261	chuckv	2352	Molecule* mol;
262			SimInfo::MoleculeIterator mi;
263			mol = NewInfo->beginMolecule(mi);
264	chuckv	2737	int l = 0;
265	chuckv	3044
266			for (int i = 0; i < nComponents; i++){
267			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
268			NewInfo->getForceField());
269			for (int n = 0; n < nMol.at(i); n++) {
270			mol = NewInfo->getMoleculeByGlobalIndex(l);
271			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
272			l++;
273			}
274	chuckv	2657	}
275	chuckv	2352
276	chuckv	3044
277
278	chuckv	2352	//fill Hmat
279	chuckv	3044	hmat(0, 0)= 2.0*particleRadius;
280	chuckv	2352	hmat(0, 1) = 0.0;
281			hmat(0, 2) = 0.0;
282
283			hmat(1, 0) = 0.0;
284	chuckv	3044	hmat(1, 1) = 2.0*particleRadius;
285	chuckv	2352	hmat(1, 2) = 0.0;
286
287			hmat(2, 0) = 0.0;
288			hmat(2, 1) = 0.0;
289	chuckv	3044	hmat(2, 2) = 2.0*particleRadius;
290	chuckv	2352
291			//set Hmat
292			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
293
294
295			//create dumpwriter and write out the coordinates
296	gezelter	3046	writer = new DumpWriter(NewInfo, outputFileName);
297	chuckv	2352
298			if (writer == NULL) {
299	chuckv	3044	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
300			painCave.isFatal = 1;
301			simError();
302	chuckv	2352	}
303
304			writer->writeDump();
305	chuckv	3044
306			// deleting the writer will put the closing at the end of the dump file
307	gezelter	3046
308	chuckv	3044	delete writer;
309
310			// cleanup a by calling sim error.....
311			sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
312			"generated.\n", outputFileName.c_str());
313			painCave.isFatal = 0;
314			simError();
315	chuckv	2352	return 0;
316			}
317
318			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
319	chuckv	3044	std::vector<int> nMol) {
320	chuckv	2352	ifstream oldMdFile;
321			ofstream newMdFile;
322			const int MAXLEN = 65535;
323			char buffer[MAXLEN];
324
325			//create new .md file based on old .md file
326			oldMdFile.open(oldMdFileName.c_str());
327			newMdFile.open(newMdFileName.c_str());
328
329			oldMdFile.getline(buffer, MAXLEN);
330	chuckv	2657
331			int i = 0;
332	chuckv	2352	while (!oldMdFile.eof()) {
333
334			//correct molecule number
335			if (strstr(buffer, "nMol") != NULL) {
336	chuckv	3044	if(i<nMol.size()){
337			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
338	chuckv	2737	newMdFile << buffer << std::endl;
339			i++;
340			}
341	chuckv	2352	} else
342			newMdFile << buffer << std::endl;
343
344			oldMdFile.getline(buffer, MAXLEN);
345			}
346
347			oldMdFile.close();
348			newMdFile.close();
349			}
350