applications/randomBuilder/randomBuilder.cpp

/* Copyright (c) 2006 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  randomBuilder.cpp
 *
 *  Created by Charles F. Vardeman II on 10 Apr 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id$
 *
 */


#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "applications/randomBuilder/randomBuilderCmd.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 OpenMD;

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  std::vector<int> nMol);

int main(int argc, char *argv []) {

  registerLattice();
    
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outputFileName;
  Lattice *simpleLat;
  RealType latticeConstant;
  std::vector<RealType> lc;
  const RealType rhoConvertConst = 1.661;
  RealType density;
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator *locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int nMolPerCell;
  DumpWriter *writer;

  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);

  density = args_info.density_arg;

  //get lattice type
  latticeType = "FCC";

  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
    
  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
            latticeType.c_str());
    painCave.isFatal = 1;
    simError();
  }
  nMolPerCell = simpleLat->getNumSitesPerCell();

  //get the number of unit cells in each direction:

  nx = args_info.nx_arg;

  if (nx <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the x direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  ny = args_info.ny_arg;

  if (ny <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the y direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  nz = args_info.nz_arg;

  if (nz <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the z direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  int nSites = nMolPerCell * nx * ny * nz;

  //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;
    simError();
  }

  //parse md file and set up the system

  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  Globals* simParams = oldInfo->getSimParams();

  // Calculate lattice constant (in Angstroms)

  std::vector<Component*> components = simParams->getComponents();
  std::vector<RealType> molFractions;
  std::vector<RealType> molecularMasses;
  std::vector<int> nMol;
  int 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, "randomBuilder can't figure out molFractions "
              "for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  }

  // do some sanity checking:
  
  RealType totalFraction = 0.0;

  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(MoLocator::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();
  }
     
  latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
                        (RealType)(1.0 / 3.0));
  
  // Set the lattice constant
  
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
  
  // Calculate the lattice sites and fill the lattice vector.

  // Get the standard orientations of the cell sites

  latticeOrt = simpleLat->getLatticePointsOrt();

  vector<Vector3d> sites;
  vector<Vector3d> orientations;
  
  for(int i = 0; i < nx; i++) {
    for(int j = 0; j < ny; j++) {
      for(int k = 0; k < nz; k++) {

        // Get the position of the cell sites

        simpleLat->getLatticePointsPos(latticePos, i, j, k);

        for(int l = 0; l < nMolPerCell; l++) {
          sites.push_back(latticePos[l]);
          orientations.push_back(latticeOrt[l]);
        }
      }
    }
  }
  
  outputFileName = args_info.output_arg;

  // create a new .md file on the fly which corrects the number of molecules

  createMdFile(inputFileName, outputFileName, nMol);

  delete oldInfo;

  // We need to read in the new SimInfo object, then Parse the 
  // md file and set up the system

  SimCreator newCreator;
  SimInfo* newInfo = newCreator.createSim(outputFileName, false);

  // 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);

  // place the molecules

  // Randomize a vector of ints:

  vector<int> ids;
  for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
  std::random_shuffle(ids.begin(), ids.end());

  Molecule* mol;
  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++;
    }
  }
  
  // Create DumpWriter and write out the coordinates

  writer = new DumpWriter(newInfo, outputFileName);

  if (writer == NULL) {
    sprintf(painCave.errMsg, "error in creating DumpWriter");
    painCave.isFatal = 1;
    simError();
  }

  writer->writeDump();

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

  delete writer;

  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  painCave.severity = OPENMD_INFO;
  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);
 
  unsigned 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();

  if (i != nMol.size()) {
    sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
            "\tstatements in component blocks.  Make sure that all\n"
            "\tcomponents in the template file have nMol=1");
    painCave.isFatal = 1;
    simError();
  }

}

Revision:	1978
Committed:	Thu Mar 13 13:03:11 2014 UTC (11 years, 1 month ago) by gezelter
File size:	11606 byte(s)
Log Message:	More error message clarifications, added a few steps to the builders sample
#	Content
1	/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
2	*
3	* The University of Notre Dame grants you ("Licensee") a
4	* non-exclusive, royalty free, license to use, modify and
5	* redistribute this software in source and binary code form, provided
6	* that the following conditions are met:
7	*
8	* 1. Redistributions of source code must retain the above copyright
9	* notice, this list of conditions and the following disclaimer.
10	*
11	* 2. Redistributions in binary form must reproduce the above copyright
12	* notice, this list of conditions and the following disclaimer in the
13	* documentation and/or other materials provided with the
14	* distribution.
15	*
16	* This software is provided "AS IS," without a warranty of any
17	* kind. All express or implied conditions, representations and
18	* warranties, including any implied warranty of merchantability,
19	* fitness for a particular purpose or non-infringement, are hereby
20	* excluded. The University of Notre Dame and its licensors shall not
21	* be liable for any damages suffered by licensee as a result of
22	* using, modifying or distributing the software or its
23	* derivatives. In no event will the University of Notre Dame or its
24	* licensors be liable for any lost revenue, profit or data, or for
25	* direct, indirect, special, consequential, incidental or punitive
26	* damages, however caused and regardless of the theory of liability,
27	* arising out of the use of or inability to use software, even if the
28	* University of Notre Dame has been advised of the possibility of
29	* such damages.
30	*
31	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32	* research, please cite the appropriate papers when you publish your
33	* work. Good starting points are:
34	*
35	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	*
41	* randomBuilder.cpp
42	*
43	* Created by Charles F. Vardeman II on 10 Apr 2006.
44	* @author Charles F. Vardeman II
45	* @version $Id$
46	*
47	*/
48
49
50	#include <cstdlib>
51	#include <cstdio>
52	#include <cstring>
53	#include <cmath>
54	#include <iostream>
55	#include <string>
56	#include <map>
57	#include <fstream>
58
59	#include "applications/randomBuilder/randomBuilderCmd.h"
60	#include "lattice/LatticeFactory.hpp"
61	#include "utils/MoLocator.hpp"
62	#include "lattice/Lattice.hpp"
63	#include "brains/Register.hpp"
64	#include "brains/SimInfo.hpp"
65	#include "brains/SimCreator.hpp"
66	#include "io/DumpWriter.hpp"
67	#include "math/Vector3.hpp"
68	#include "math/SquareMatrix3.hpp"
69	#include "utils/StringUtils.hpp"
70
71	using namespace std;
72	using namespace OpenMD;
73
74	void createMdFile(const std::string&oldMdFileName,
75	const std::string&newMdFileName,
76	std::vector<int> nMol);
77
78	int main(int argc, char *argv []) {
79
80	registerLattice();
81
82	gengetopt_args_info args_info;
83	std::string latticeType;
84	std::string inputFileName;
85	std::string outputFileName;
86	Lattice *simpleLat;
87	RealType latticeConstant;
88	std::vector<RealType> lc;
89	const RealType rhoConvertConst = 1.661;
90	RealType density;
91	int nx, ny, nz;
92	Mat3x3d hmat;
93	MoLocator *locator;
94	std::vector<Vector3d> latticePos;
95	std::vector<Vector3d> latticeOrt;
96	int nMolPerCell;
97	DumpWriter *writer;
98
99	// parse command line arguments
100	if (cmdline_parser(argc, argv, &args_info) != 0)
101	exit(1);
102
103	density = args_info.density_arg;
104
105	//get lattice type
106	latticeType = "FCC";
107
108	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
109
110	if (simpleLat == NULL) {
111	sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
112	latticeType.c_str());
113	painCave.isFatal = 1;
114	simError();
115	}
116	nMolPerCell = simpleLat->getNumSitesPerCell();
117
118	//get the number of unit cells in each direction:
119
120	nx = args_info.nx_arg;
121
122	if (nx <= 0) {
123	sprintf(painCave.errMsg, "The number of unit cells in the x direction "
124	"must be greater than 0.");
125	painCave.isFatal = 1;
126	simError();
127	}
128
129	ny = args_info.ny_arg;
130
131	if (ny <= 0) {
132	sprintf(painCave.errMsg, "The number of unit cells in the y direction "
133	"must be greater than 0.");
134	painCave.isFatal = 1;
135	simError();
136	}
137
138	nz = args_info.nz_arg;
139
140	if (nz <= 0) {
141	sprintf(painCave.errMsg, "The number of unit cells in the z direction "
142	"must be greater than 0.");
143	painCave.isFatal = 1;
144	simError();
145	}
146
147	int nSites = nMolPerCell * nx * ny * nz;
148
149	//get input file name
150	if (args_info.inputs_num)
151	inputFileName = args_info.inputs[0];
152	else {
153	sprintf(painCave.errMsg, "No input .md file name was specified "
154	"on the command line");
155	painCave.isFatal = 1;
156	simError();
157	}
158
159	//parse md file and set up the system
160
161	SimCreator oldCreator;
162	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
163	Globals* simParams = oldInfo->getSimParams();
164
165	// Calculate lattice constant (in Angstroms)
166
167	std::vector<Component*> components = simParams->getComponents();
168	std::vector<RealType> molFractions;
169	std::vector<RealType> molecularMasses;
170	std::vector<int> nMol;
171	int nComponents = components.size();
172
173	if (nComponents == 1) {
174	molFractions.push_back(1.0);
175	} else {
176	if (args_info.molFraction_given == nComponents) {
177	for (int i = 0; i < nComponents; i++) {
178	molFractions.push_back(args_info.molFraction_arg[i]);
179	}
180	} else if (args_info.molFraction_given == nComponents-1) {
181	RealType remainingFraction = 1.0;
182	for (int i = 0; i < nComponents-1; i++) {
183	molFractions.push_back(args_info.molFraction_arg[i]);
184	remainingFraction -= molFractions[i];
185	}
186	molFractions.push_back(remainingFraction);
187	} else {
188	sprintf(painCave.errMsg, "randomBuilder can't figure out molFractions "
189	"for all of the components in the <MetaData> block.");
190	painCave.isFatal = 1;
191	simError();
192	}
193	}
194
195	// do some sanity checking:
196
197	RealType totalFraction = 0.0;
198
199	for (int i = 0; i < nComponents; i++) {
200	if (molFractions.at(i) < 0.0) {
201	sprintf(painCave.errMsg, "One of the requested molFractions was"
202	" less than zero!");
203	painCave.isFatal = 1;
204	simError();
205	}
206	if (molFractions.at(i) > 1.0) {
207	sprintf(painCave.errMsg, "One of the requested molFractions was"
208	" greater than one!");
209	painCave.isFatal = 1;
210	simError();
211	}
212	totalFraction += molFractions.at(i);
213	}
214	if (abs(totalFraction - 1.0) > 1e-6) {
215	sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
216	painCave.isFatal = 1;
217	simError();
218	}
219
220	int remaining = nSites;
221	for (int i=0; i < nComponents-1; i++) {
222	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
223	remaining -= nMol.at(i);
224	}
225	nMol.push_back(remaining);
226
227	// recompute actual mol fractions and perform final sanity check:
228
229	int totalMolecules = 0;
230	RealType totalMass = 0.0;
231	for (int i=0; i < nComponents; i++) {
232	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
233	totalMolecules += nMol.at(i);
234	molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i),
235	oldInfo->getForceField()));
236	totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
237	}
238	RealType avgMass = totalMass / (RealType) totalMolecules;
239
240	if (totalMolecules != nSites) {
241	sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
242	"to the number of lattice sites!");
243	painCave.isFatal = 1;
244	simError();
245	}
246
247	latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
248	(RealType)(1.0 / 3.0));
249
250	// Set the lattice constant
251
252	lc.push_back(latticeConstant);
253	simpleLat->setLatticeConstant(lc);
254
255	// Calculate the lattice sites and fill the lattice vector.
256
257	// Get the standard orientations of the cell sites
258
259	latticeOrt = simpleLat->getLatticePointsOrt();
260
261	vector<Vector3d> sites;
262	vector<Vector3d> orientations;
263
264	for(int i = 0; i < nx; i++) {
265	for(int j = 0; j < ny; j++) {
266	for(int k = 0; k < nz; k++) {
267
268	// Get the position of the cell sites
269
270	simpleLat->getLatticePointsPos(latticePos, i, j, k);
271
272	for(int l = 0; l < nMolPerCell; l++) {
273	sites.push_back(latticePos[l]);
274	orientations.push_back(latticeOrt[l]);
275	}
276	}
277	}
278	}
279
280	outputFileName = args_info.output_arg;
281
282	// create a new .md file on the fly which corrects the number of molecules
283
284	createMdFile(inputFileName, outputFileName, nMol);
285
286	delete oldInfo;
287
288	// We need to read in the new SimInfo object, then Parse the
289	// md file and set up the system
290
291	SimCreator newCreator;
292	SimInfo* newInfo = newCreator.createSim(outputFileName, false);
293
294	// fill Hmat
295
296	hmat(0, 0) = nx * latticeConstant;
297	hmat(0, 1) = 0.0;
298	hmat(0, 2) = 0.0;
299
300	hmat(1, 0) = 0.0;
301	hmat(1, 1) = ny * latticeConstant;
302	hmat(1, 2) = 0.0;
303
304	hmat(2, 0) = 0.0;
305	hmat(2, 1) = 0.0;
306	hmat(2, 2) = nz * latticeConstant;
307
308	// Set Hmat
309
310	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
311
312	// place the molecules
313
314	// Randomize a vector of ints:
315
316	vector<int> ids;
317	for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
318	std::random_shuffle(ids.begin(), ids.end());
319
320	Molecule* mol;
321	int l = 0;
322	for (int i = 0; i < nComponents; i++){
323	locator = new MoLocator(newInfo->getMoleculeStamp(i),
324	newInfo->getForceField());
325	for (int n = 0; n < nMol.at(i); n++) {
326	mol = newInfo->getMoleculeByGlobalIndex(l);
327	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
328	l++;
329	}
330	}
331
332	// Create DumpWriter and write out the coordinates
333
334	writer = new DumpWriter(newInfo, outputFileName);
335
336	if (writer == NULL) {
337	sprintf(painCave.errMsg, "error in creating DumpWriter");
338	painCave.isFatal = 1;
339	simError();
340	}
341
342	writer->writeDump();
343
344	// deleting the writer will put the closing at the end of the dump file.
345
346	delete writer;
347
348	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
349	"generated.\n", outputFileName.c_str());
350	painCave.isFatal = 0;
351	painCave.severity = OPENMD_INFO;
352	simError();
353	return 0;
354	}
355
356	void createMdFile(const std::string&oldMdFileName,
357	const std::string&newMdFileName,
358	std::vector<int> nMol) {
359	ifstream oldMdFile;
360	ofstream newMdFile;
361	const int MAXLEN = 65535;
362	char buffer[MAXLEN];
363
364	//create new .md file based on old .md file
365
366	oldMdFile.open(oldMdFileName.c_str());
367	newMdFile.open(newMdFileName.c_str());
368
369	oldMdFile.getline(buffer, MAXLEN);
370
371	unsigned int i = 0;
372	while (!oldMdFile.eof()) {
373
374	//correct molecule number
375	if (strstr(buffer, "nMol") != NULL) {
376	if (i<nMol.size()){
377	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
378	newMdFile << buffer << std::endl;
379	i++;
380	}
381	} else
382	newMdFile << buffer << std::endl;
383
384	oldMdFile.getline(buffer, MAXLEN);
385	}
386
387	oldMdFile.close();
388	newMdFile.close();
389
390	if (i != nMol.size()) {
391	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
392	"\tstatements in component blocks. Make sure that all\n"
393	"\tcomponents in the template file have nMol=1");
394	painCave.isFatal = 1;
395	simError();
396	}
397
398	}
399