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 outPrefix;
  std::string outputFileName;
  std::string outInitFileName;

  
  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 Molocators */
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /* Create nanoparticle */
  shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
  
  /* Build a lattice and get lattice points for this lattice constant */
  vector<Vector3d> sites = nanoParticle.getPoints();
  vector<Vector3d> orientations = nanoParticle.getPointsOrt();

  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();
  std::cout << "new initial configuration file: " << outInitFileName
            << " is generated." << std::endl;
 

  // 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:	3044
Committed:	Fri Oct 13 20:16:59 2006 UTC (17 years, 10 months ago) by chuckv
File size:	10881 byte(s)
Log Message:	Changed nanoparticle builder for new dump syntax.
#	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			std::string outPrefix;
82	chuckv	3044	std::string outputFileName;
83	chuckv	2352	std::string outInitFileName;
84
85
86
87			Lattice *simpleLat;
88	chuckv	2657	MoLocator* locator;
89			int* numMol;
90			int nComponents;
91	chuckv	2352	double latticeConstant;
92			std::vector<double> lc;
93	chuckv	3044	double mass;
94
95	chuckv	2352	const double rhoConvertConst = 1.661;
96			double density;
97	chuckv	2657	double particleRadius;
98	chuckv	2352
99
100
101			Mat3x3d hmat;
102			std::vector<Vector3d> latticePos;
103			std::vector<Vector3d> latticeOrt;
104			int numMolPerCell;
105			int nShells; /* Number of shells in nanoparticle*/
106	chuckv	3044
107	chuckv	2352
108			DumpWriter *writer;
109
110	chuckv	2574	// Parse Command Line Arguments
111	chuckv	2352	if (cmdline_parser(argc, argv, &args_info) != 0)
112			exit(1);
113
114
115
116			/* get lattice type */
117	chuckv	3044	latticeType = "FCC";
118
119	chuckv	2352	/* get input file name */
120			if (args_info.inputs_num)
121			inputFileName = args_info.inputs[0];
122			else {
123	chuckv	3044	sprintf(painCave.errMsg, "No input .md file name was specified"
124			"on the command line");
125			painCave.isFatal = 1;
126	chuckv	2352	cmdline_parser_print_help();
127	chuckv	3044	simError();
128	chuckv	2352	}
129
130			/* parse md file and set up the system */
131			SimCreator oldCreator;
132			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
133
134
135			latticeConstant = args_info.latticeCnst_arg;
136			particleRadius = args_info.radius_arg;
137	chuckv	2657	Globals* simParams = oldInfo->getSimParams();
138	chuckv	2352
139	chuckv	3044
140	chuckv	2352	/* create Molocators */
141			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
142
143	chuckv	2657	/* Create nanoparticle */
144			shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
145	chuckv	2672
146	chuckv	2657	/* Build a lattice and get lattice points for this lattice constant */
147	chuckv	3044	vector<Vector3d> sites = nanoParticle.getPoints();
148			vector<Vector3d> orientations = nanoParticle.getPointsOrt();
149
150			std::cout <<"nSites: " << sites.size() << std::endl;
151
152	chuckv	2657	/* Get number of lattice sites */
153	chuckv	3044	int nSites = sites.size();
154	chuckv	2657
155	chuckv	3044
156
157
158			std::vector<Component*> components = simParams->getComponents();
159			std::vector<RealType> molFractions;
160			std::vector<RealType> molecularMasses;
161			std::vector<int> nMol;
162			nComponents = components.size();
163	chuckv	2352
164	chuckv	3044
165
166			if (nComponents == 1) {
167			molFractions.push_back(1.0);
168			} else {
169			if (args_info.molFraction_given == nComponents) {
170			for (int i = 0; i < nComponents; i++) {
171			molFractions.push_back(args_info.molFraction_arg[i]);
172			}
173			} else if (args_info.molFraction_given == nComponents-1) {
174			RealType remainingFraction = 1.0;
175			for (int i = 0; i < nComponents-1; i++) {
176			molFractions.push_back(args_info.molFraction_arg[i]);
177			remainingFraction -= molFractions[i];
178			}
179			molFractions.push_back(remainingFraction);
180			} else {
181			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
182			"for all of the components in the <MetaData> block.");
183			painCave.isFatal = 1;
184			simError();
185			}
186			}
187
188			RealType totalFraction = 0.0;
189
190			/* Do some simple sanity checking*/
191
192
193
194			for (int i = 0; i < nComponents; i++) {
195			if (molFractions.at(i) < 0.0) {
196			sprintf(painCave.errMsg, "One of the requested molFractions was"
197			" less than zero!");
198			painCave.isFatal = 1;
199			simError();
200			}
201			if (molFractions.at(i) > 1.0) {
202			sprintf(painCave.errMsg, "One of the requested molFractions was"
203			" greater than one!");
204			painCave.isFatal = 1;
205			simError();
206			}
207			totalFraction += molFractions.at(i);
208			}
209			if (abs(totalFraction - 1.0) > 1e-6) {
210			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
211			painCave.isFatal = 1;
212			simError();
213			}
214
215			int remaining = nSites;
216			for (int i=0; i < nComponents-1; i++) {
217			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
218			remaining -= nMol.at(i);
219			}
220			nMol.push_back(remaining);
221
222
223
224			// recompute actual mol fractions and perform final sanity check:
225
226			int totalMolecules = 0;
227			RealType totalMass = 0.0;
228			for (int i=0; i < nComponents; i++) {
229			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
230			totalMolecules += nMol.at(i);
231			molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
232			oldInfo->getForceField()));
233			totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
234			}
235			RealType avgMass = totalMass / (RealType) totalMolecules;
236
237			if (totalMolecules != nSites) {
238			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
239			"to the number of lattice sites!");
240			painCave.isFatal = 1;
241			simError();
242			}
243
244
245
246
247			vector<int> ids;
248			for (int i = 0; i < sites.size(); i++) ids.push_back(i);
249	chuckv	2352	/* Random particle is the default case*/
250			if (!args_info.ShellRadius_given){
251	chuckv	2737	/* do the iPod thing, Shuffle da vector */
252	chuckv	3044	std::random_shuffle(ids.begin(), ids.end());
253	chuckv	2352	} else{ /Handle core-shell with multiple components./
254			std::cout << "Creating a core-shell nanoparticle." << std::endl;
255			if (nComponents != args_info.ShellRadius_given + 1){
256	chuckv	3044	sprintf(painCave.errMsg, "Number of .md components "
257			"does not match the number of shell radius specifications");
258			painCave.isFatal = 1;
259			simError();
260	chuckv	2657	}
261	chuckv	2352
262			}
263
264	chuckv	2737
265	chuckv	2352
266	chuckv	2737
267	chuckv	3044	outputFileName = args_info.output_arg;
268
269	chuckv	2737
270	chuckv	3044	//creat new .md file on fly which corrects the number of molecule
271			createMdFile(inputFileName, outputFileName, nMol);
272	chuckv	2352
273			if (oldInfo != NULL)
274			delete oldInfo;
275
276
277			// We need to read in new siminfo object.
278			//parse md file and set up the system
279			//SimCreator NewCreator;
280	chuckv	2737	SimCreator newCreator;
281	chuckv	3044	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
282	chuckv	2352
283
284	chuckv	2657	// Place molecules
285	chuckv	2352	Molecule* mol;
286			SimInfo::MoleculeIterator mi;
287			mol = NewInfo->beginMolecule(mi);
288	chuckv	2737	int l = 0;
289	chuckv	3044
290			for (int i = 0; i < nComponents; i++){
291			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
292			NewInfo->getForceField());
293			for (int n = 0; n < nMol.at(i); n++) {
294			mol = NewInfo->getMoleculeByGlobalIndex(l);
295			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
296			l++;
297			}
298	chuckv	2657	}
299	chuckv	2352
300	chuckv	3044
301
302	chuckv	2352	//fill Hmat
303	chuckv	3044	hmat(0, 0)= 2.0*particleRadius;
304	chuckv	2352	hmat(0, 1) = 0.0;
305			hmat(0, 2) = 0.0;
306
307			hmat(1, 0) = 0.0;
308	chuckv	3044	hmat(1, 1) = 2.0*particleRadius;
309	chuckv	2352	hmat(1, 2) = 0.0;
310
311			hmat(2, 0) = 0.0;
312			hmat(2, 1) = 0.0;
313	chuckv	3044	hmat(2, 2) = 2.0*particleRadius;
314	chuckv	2352
315			//set Hmat
316			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
317
318
319			//create dumpwriter and write out the coordinates
320	chuckv	3044	writer = new DumpWriter(NewInfo,outputFileName);
321	chuckv	2352
322			if (writer == NULL) {
323	chuckv	3044	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
324			painCave.isFatal = 1;
325			simError();
326	chuckv	2352	}
327
328			writer->writeDump();
329			std::cout << "new initial configuration file: " << outInitFileName
330			<< " is generated." << std::endl;
331	chuckv	3044
332
333			// deleting the writer will put the closing at the end of the dump file
334			delete writer;
335
336			// cleanup a by calling sim error.....
337			sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
338			"generated.\n", outputFileName.c_str());
339			painCave.isFatal = 0;
340			simError();
341	chuckv	2352	return 0;
342			}
343
344			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
345	chuckv	3044	std::vector<int> nMol) {
346	chuckv	2352	ifstream oldMdFile;
347			ofstream newMdFile;
348			const int MAXLEN = 65535;
349			char buffer[MAXLEN];
350
351			//create new .md file based on old .md file
352			oldMdFile.open(oldMdFileName.c_str());
353			newMdFile.open(newMdFileName.c_str());
354
355			oldMdFile.getline(buffer, MAXLEN);
356	chuckv	2657
357			int i = 0;
358	chuckv	2352	while (!oldMdFile.eof()) {
359
360			//correct molecule number
361			if (strstr(buffer, "nMol") != NULL) {
362	chuckv	3044	if(i<nMol.size()){
363			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
364	chuckv	2737	newMdFile << buffer << std::endl;
365			i++;
366			}
367	chuckv	2352	} else
368			newMdFile << buffer << std::endl;
369
370			oldMdFile.getline(buffer, MAXLEN);
371			}
372
373			oldMdFile.close();
374			newMdFile.close();
375			}
376