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 outputFileName;
  std::string outGeomFileName;
  
  
  Lattice *simpleLat;
  int numMol;
  RealType latticeConstant;
  std::vector<RealType> lc;
  RealType mass;
  const RealType rhoConvertConst = 1.661;
  RealType density;
  RealType rodLength;
  RealType rodDiameter;
  
  
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator *locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int nComponents;
  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 {
    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);
  Globals* simParams = oldInfo->getSimParams();

  nComponents = simParams->getNComponents();
  if (nComponents> 1) {
    sprintf(painCave.errMsg, "Nanorods can only contain a single component ");
    painCave.isFatal = 1;
    simError();
  }
  
  //get mass of molecule. 
  
  mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  //creat lattice
  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
  
  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Error in creating lattice. ");
    painCave.isFatal = 1;
    simError();
  }
  
  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){
    outputFileName = args_info.output_arg;
  }else{
    sprintf(painCave.errMsg, "No output file name was specified "
            "on the command line");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }
  
  
  //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.
  

  //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outputFileName, 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 = newCreator.createSim(outputFileName, 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 {
                   sprintf(painCave.errMsg, "Error in placing molecule onto lattice ");
                   painCave.isFatal = 1;
                   simError();
                 }
                 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(outputFileName);
  writer = new DumpWriter(newInfo);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating DumpWrite object. ");
    painCave.isFatal = 1;
    simError();
  }
  
  writer->writeEor();
  std::cout << "new initial configuration file: " << outputFileName
            << " is generated." << std::endl;
  
  //delete objects
  
  //delete oldInfo and oldSimSetup
  
  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:	1085
Committed:	Mon Oct 23 18:11:06 2006 UTC (18 years, 6 months ago) by chuckv
File size:	10926 byte(s)
Log Message:	Changes to nanorod builder for new dump format. Changes to configure to test for new version of cgal.
#	User	Rev	Content
1	gezelter	507	/*
2	chuckv	467	* 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	493
42	chuckv	467	#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	493	#include "config.h"
52
53	chuckv	467	#include "nanorodBuilderCmd.h"
54	gezelter	493	#ifdef HAVE_CGAL
55			#include "GeometryBuilder.hpp"
56			#endif
57	gezelter	481	#include "lattice/LatticeFactory.hpp"
58			#include "utils/MoLocator.hpp"
59			#include "lattice/Lattice.hpp"
60	chuckv	467	#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	493	void createMdFile(const std::string&oldMdFileName,
71			const std::string&newMdFileName,
72	chuckv	467	int numMol);
73
74			int main(int argc, char *argv []) {
75	gezelter	493
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	chuckv	1085	std::string outputFileName;
85	gezelter	493	std::string outGeomFileName;
86
87
88			Lattice *simpleLat;
89			int numMol;
90	tim	963	RealType latticeConstant;
91			std::vector<RealType> lc;
92			RealType mass;
93			const RealType rhoConvertConst = 1.661;
94			RealType density;
95			RealType rodLength;
96			RealType rodDiameter;
97	gezelter	493
98
99			int nx, ny, nz;
100			Mat3x3d hmat;
101			MoLocator *locator;
102			std::vector<Vector3d> latticePos;
103			std::vector<Vector3d> latticeOrt;
104			int numMolPerCell;
105	chuckv	1085	int nComponents;
106	gezelter	493	DumpWriter *writer;
107
108			// parse command line arguments
109			if (cmdline_parser(argc, argv, &args_info) != 0)
110			exit(1);
111
112
113	gezelter	507	// Check for lib CGAL, if we don't have it, we should exit....
114	chuckv	499
115			#ifndef HAVE_CGAL
116	gezelter	507	std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
117			<< std::endl;
118			exit(1);
119	chuckv	499	#endif
120
121
122
123	gezelter	493	//get lattice type
124			latticeType = UpperCase(args_info.latticetype_arg);
125	chuckv	542
126	chuckv	1085	/* get input file name */
127	gezelter	493	if (args_info.inputs_num)
128			inputFileName = args_info.inputs[0];
129			else {
130	chuckv	1085	sprintf(painCave.errMsg, "No input .md file name was specified "
131			"on the command line");
132			painCave.isFatal = 1;
133	gezelter	493	cmdline_parser_print_help();
134	chuckv	1085	simError();
135	gezelter	493	}
136	chuckv	1085
137	gezelter	493	//parse md file and set up the system
138			SimCreator oldCreator;
139			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
140	chuckv	1085	Globals* simParams = oldInfo->getSimParams();
141
142			nComponents = simParams->getNComponents();
143			if (nComponents> 1) {
144			sprintf(painCave.errMsg, "Nanorods can only contain a single component ");
145			painCave.isFatal = 1;
146			simError();
147	gezelter	493	}
148
149			//get mass of molecule.
150
151			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
152
153			//creat lattice
154			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
155
156			if (simpleLat == NULL) {
157	chuckv	1085	sprintf(painCave.errMsg, "Error in creating lattice. ");
158			painCave.isFatal = 1;
159			simError();
160	gezelter	493	}
161
162			numMolPerCell = simpleLat->getNumSitesPerCell();
163
164			//calculate lattice constant (in Angstrom)
165			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
166			// 1.0 / 3.0);
167
168			latticeConstant = args_info.latticeCnst_arg;
169			rodLength = args_info.length_arg;
170			rodDiameter = args_info.width_arg;
171
172			//set lattice constant
173			lc.push_back(latticeConstant);
174			simpleLat->setLatticeConstant(lc);
175
176
177			//determine the output file names
178	chuckv	1085	if (args_info.output_given){
179			outputFileName = args_info.output_arg;
180			}else{
181			sprintf(painCave.errMsg, "No output file name was specified "
182			"on the command line");
183			painCave.isFatal = 1;
184			cmdline_parser_print_help();
185			simError();
186			}
187	gezelter	493
188	chuckv	518
189
190
191
192
193	gezelter	493	//creat Molocator
194			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
195
196			/*
197			Assume we are carving nanorod out of a cublic block of material and that
198			the shape the material will fit within that block....
199			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
200			diameter of the particle.
201			*/
202			// Number of Unit Cells in Length first
203			ny = (int)(rodLength/latticeConstant);
204			// Number of unit cells in Width
205			nx = (int)(rodDiameter/latticeConstant);
206			nz = (int)(rodDiameter/latticeConstant);
207
208
209
210			// Create geometry for nanocrystal
211	chuckv	499	#ifdef HAVE_CGAL
212	chuckv	521	GeometryBuilder *myGeometry;
213			// GeometryBuilder myGeometry(rodLength,rodDiameter);
214			if (args_info.twinnedCrystal_flag){
215			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
216			}
217			else{
218			myGeometry = new GeometryBuilder(rodLength,rodDiameter);
219			}
220
221	chuckv	518	if (args_info.genGeomview_given){
222			if (args_info.genGeomview_flag){
223			outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
224	chuckv	521	myGeometry->dumpGeometry(outGeomFileName);
225	chuckv	518	}
226			}
227	chuckv	521
228	gezelter	493	#endif
229
230			/*
231			We have to build the system first to figure out how many molecules
232			there are then create a md file and then actually build the
233			system.
234			*/
235
236			//place the molecules
237
238	chuckv	521
239	gezelter	493
240			//get the orientation of the cell sites
241			//for the same type of molecule in same lattice, it will not change
242			latticeOrt = simpleLat->getLatticePointsOrt();
243
244
245
246			numMol = 0;
247	chuckv	518	for(int i = -nx; i < nx; i++) {
248			for(int j = -ny; j < ny; j++) {
249			for(int k = -nz; k < nz; k++) {
250	gezelter	493	//if (oldInfo->getNGlobalMolecules() != numMol) {
251	chuckv	467
252	gezelter	493
253
254			//get the position of the cell sites
255			simpleLat->getLatticePointsPos(latticePos, i, j, k);
256
257			for(int l = 0; l < numMolPerCell; l++) {
258	chuckv	467
259	chuckv	499	#ifdef HAVE_CGAL
260	chuckv	521	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
261	gezelter	493	numMol++;
262			}
263	chuckv	521	#else
264			numMol++;
265	gezelter	493	#endif
266			}
267			}
268	chuckv	467	}
269	gezelter	493	}
270	chuckv	521
271	gezelter	493
272			// needed for writing out new md file.
273
274	chuckv	1085
275
276	gezelter	493
277			//creat new .md file on fly which corrects the number of molecule
278	chuckv	1085	createMdFile(inputFileName, outputFileName, numMol);
279	gezelter	493
280			if (oldInfo != NULL)
281			delete oldInfo;
282
283
284			// We need to read in new siminfo object.
285			//parse md file and set up the system
286	chuckv	1085	SimCreator newCreator;
287			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
288	gezelter	493
289			// This was so much fun the first time, lets do it again.
290
291			Molecule* mol;
292			SimInfo::MoleculeIterator mi;
293	chuckv	1085	mol = newInfo->beginMolecule(mi);
294	chuckv	521
295
296	chuckv	518	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	521	#ifdef HAVE_CGAL
305			if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
306			#endif
307	chuckv	518	if (mol != NULL) {
308			locator->placeMol(latticePos[l], latticeOrt[l], mol);
309			} else {
310	chuckv	1085	sprintf(painCave.errMsg, "Error in placing molecule onto lattice ");
311			painCave.isFatal = 1;
312			simError();
313	chuckv	518	}
314	chuckv	1085	mol = newInfo->nextMolecule(mi);
315	chuckv	521	#ifdef HAVE_CGAL
316	chuckv	518	}
317	chuckv	521	#endif
318	chuckv	518	}
319	gezelter	493	}
320	chuckv	518	}
321	gezelter	493	}
322
323	chuckv	521
324	gezelter	493
325			//fill Hmat
326			hmat(0, 0)= nx * latticeConstant;
327			hmat(0, 1) = 0.0;
328			hmat(0, 2) = 0.0;
329
330			hmat(1, 0) = 0.0;
331			hmat(1, 1) = ny * latticeConstant;
332			hmat(1, 2) = 0.0;
333
334			hmat(2, 0) = 0.0;
335			hmat(2, 1) = 0.0;
336			hmat(2, 2) = nz * latticeConstant;
337
338			//set Hmat
339	chuckv	1085	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
340	gezelter	493
341
342			//create dumpwriter and write out the coordinates
343	chuckv	1085	newInfo->setFinalConfigFileName(outputFileName);
344			writer = new DumpWriter(newInfo);
345	gezelter	493
346			if (writer == NULL) {
347	chuckv	1085	sprintf(painCave.errMsg, "Error in creating DumpWrite object. ");
348			painCave.isFatal = 1;
349			simError();
350	gezelter	507	}
351	gezelter	493
352	chuckv	792	writer->writeEor();
353	chuckv	1085	std::cout << "new initial configuration file: " << outputFileName
354	gezelter	493	<< " is generated." << std::endl;
355
356			//delete objects
357
358			//delete oldInfo and oldSimSetup
359
360			if (writer != NULL)
361			delete writer;
362			delete simpleLat;
363			cmdline_parser_free(&args_info);
364			return 0;
365	chuckv	467	}
366
367			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
368			int numMol) {
369	gezelter	493	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	467	oldMdFile.getline(buffer, MAXLEN);
390	gezelter	493	}
391
392			oldMdFile.close();
393			newMdFile.close();
394	chuckv	1085
395	chuckv	467	}
396