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, 24107 (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(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);

  if (oldInfo != NULL)
    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;
  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:	1767
Committed:	Fri Jul 6 22:01:58 2012 UTC (12 years, 9 months ago) by gezelter
File size:	11573 byte(s)
Log Message:	Various fixes required to compile OpenMD with the MS Visual C++ compiler
#	User	Rev	Content
1	chuckv	950	/* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	950	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	950	* 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	gezelter	1390	* 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, 24107 (2008).
38	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	950	*
41			* randomBuilder.cpp
42			*
43			* Created by Charles F. Vardeman II on 10 Apr 2006.
44			* @author Charles F. Vardeman II
45	gezelter	1442	* @version $Id$
46	chuckv	950	*
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	gezelter	1390	using namespace OpenMD;
73	chuckv	950
74			void createMdFile(const std::string&oldMdFileName,
75			const std::string&newMdFileName,
76	gezelter	1065	std::vector<int> nMol);
77	chuckv	950
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	gezelter	1062	std::string outputFileName;
86	chuckv	950	Lattice *simpleLat;
87	tim	963	RealType latticeConstant;
88			std::vector<RealType> lc;
89			const RealType rhoConvertConst = 1.661;
90			RealType density;
91	gezelter	1062	int nx, ny, nz;
92	chuckv	950	Mat3x3d hmat;
93			MoLocator *locator;
94			std::vector<Vector3d> latticePos;
95			std::vector<Vector3d> latticeOrt;
96	gezelter	1065	int nMolPerCell;
97	chuckv	950	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	gezelter	1067	latticeType = "FCC";
107	chuckv	950
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	gezelter	1065	nMolPerCell = simpleLat->getNumSitesPerCell();
117	chuckv	950
118	gezelter	1062	//get the number of unit cells in each direction:
119
120	chuckv	950	nx = args_info.nx_arg;
121
122			if (nx <= 0) {
123	gezelter	1062	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	chuckv	950	}
128
129			ny = args_info.ny_arg;
130
131			if (ny <= 0) {
132	gezelter	1062	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	chuckv	950	}
137
138			nz = args_info.nz_arg;
139
140			if (nz <= 0) {
141	gezelter	1062	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	chuckv	950	}
146
147	gezelter	1065	int nSites = nMolPerCell * nx * ny * nz;
148
149	chuckv	950	//get input file name
150			if (args_info.inputs_num)
151			inputFileName = args_info.inputs[0];
152			else {
153	gezelter	1062	sprintf(painCave.errMsg, "No input .md file name was specified "
154			"on the command line");
155			painCave.isFatal = 1;
156			simError();
157	chuckv	950	}
158
159			//parse md file and set up the system
160	gezelter	1062
161	chuckv	950	SimCreator oldCreator;
162			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
163			Globals* simParams = oldInfo->getSimParams();
164
165	gezelter	1065	// 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	gezelter	1062	painCave.isFatal = 1;
217			simError();
218	chuckv	950	}
219
220	gezelter	1065	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	chuckv	950
227	gezelter	1065	// recompute actual mol fractions and perform final sanity check:
228	chuckv	950
229	gezelter	1065	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(getMolMass(oldInfo->getMoleculeStamp(i),
235			oldInfo->getForceField()));
236			totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
237			}
238			RealType avgMass = totalMass / (RealType) totalMolecules;
239	gezelter	1062
240	gezelter	1065	if (totalMolecules != nSites) {
241			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
242			"to the number of lattice sites!");
243	gezelter	1062	painCave.isFatal = 1;
244			simError();
245	chuckv	950	}
246	gezelter	1065
247			latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
248	tim	963	(RealType)(1.0 / 3.0));
249	gezelter	1065
250	gezelter	1062	// Set the lattice constant
251	gezelter	1065
252	chuckv	950	lc.push_back(latticeConstant);
253			simpleLat->setLatticeConstant(lc);
254	gezelter	1065
255	gezelter	1062	// 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	chuckv	950
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	gezelter	1062	// Get the position of the cell sites
269
270	chuckv	950	simpleLat->getLatticePointsPos(latticePos, i, j, k);
271
272	gezelter	1065	for(int l = 0; l < nMolPerCell; l++) {
273	gezelter	1062	sites.push_back(latticePos[l]);
274			orientations.push_back(latticeOrt[l]);
275	chuckv	950	}
276			}
277			}
278			}
279
280	gezelter	1062	outputFileName = args_info.output_arg;
281	chuckv	950
282	gezelter	1062	// create a new .md file on the fly which corrects the number of molecules
283	chuckv	950
284	gezelter	1065	createMdFile(inputFileName, outputFileName, nMol);
285	chuckv	950
286	gezelter	1062	if (oldInfo != NULL)
287			delete oldInfo;
288
289			// We need to read in the new SimInfo object, then Parse the
290			// md file and set up the system
291
292			SimCreator newCreator;
293			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
294
295			// fill Hmat
296
297			hmat(0, 0) = nx * latticeConstant;
298	chuckv	950	hmat(0, 1) = 0.0;
299			hmat(0, 2) = 0.0;
300
301			hmat(1, 0) = 0.0;
302			hmat(1, 1) = ny * latticeConstant;
303			hmat(1, 2) = 0.0;
304
305			hmat(2, 0) = 0.0;
306			hmat(2, 1) = 0.0;
307			hmat(2, 2) = nz * latticeConstant;
308
309	gezelter	1062	// Set Hmat
310	chuckv	950
311	gezelter	1062	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
312	chuckv	950
313	gezelter	1062	// place the molecules
314
315			// Randomize a vector of ints:
316	chuckv	950
317	gezelter	1062	vector<int> ids;
318	gezelter	1767	for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
319	gezelter	1062	std::random_shuffle(ids.begin(), ids.end());
320	chuckv	950
321			Molecule* mol;
322			int l = 0;
323	gezelter	1062	for (int i = 0; i < nComponents; i++){
324			locator = new MoLocator(newInfo->getMoleculeStamp(i),
325			newInfo->getForceField());
326	gezelter	1065	for (int n = 0; n < nMol.at(i); n++) {
327	gezelter	1062	mol = newInfo->getMoleculeByGlobalIndex(l);
328			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
329			l++;
330			}
331	chuckv	950	}
332	gezelter	1062
333			// Create DumpWriter and write out the coordinates
334	chuckv	950
335	gezelter	1062	writer = new DumpWriter(newInfo, outputFileName);
336	chuckv	950
337			if (writer == NULL) {
338	gezelter	1062	sprintf(painCave.errMsg, "error in creating DumpWriter");
339			painCave.isFatal = 1;
340			simError();
341	chuckv	950	}
342
343	gezelter	1062	writer->writeDump();
344
345			// deleting the writer will put the closing at the end of the dump file.
346
347			delete writer;
348
349	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
350	gezelter	1065	"generated.\n", outputFileName.c_str());
351	gezelter	1062	painCave.isFatal = 0;
352			simError();
353	chuckv	950	return 0;
354			}
355
356	gezelter	1062	void createMdFile(const std::string&oldMdFileName,
357			const std::string&newMdFileName,
358	gezelter	1065	std::vector<int> nMol) {
359	chuckv	950	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	gezelter	1062
366	chuckv	950	oldMdFile.open(oldMdFileName.c_str());
367			newMdFile.open(newMdFileName.c_str());
368
369			oldMdFile.getline(buffer, MAXLEN);
370
371	gezelter	1767	unsigned int i = 0;
372	chuckv	950	while (!oldMdFile.eof()) {
373
374			//correct molecule number
375			if (strstr(buffer, "nMol") != NULL) {
376	gezelter	1767	if (i<nMol.size()){
377	gezelter	1065	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
378	chuckv	950	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	gezelter	1077
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	chuckv	950	}
399