applications/nanoparticleBuilder/nanoparticleBuilder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

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

#include "config.h"
#include "shapedLatticeSpherical.hpp"
#include "nanoparticleBuilderCmd.h"
#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace oopse;
void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  std::vector<int> numMol);

int main(int argc, char *argv []) {
  
  //register force fields
  registerForceFields();
  registerLattice();
  
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outputFileName;

  MoLocator* locator;
  int nComponents;
  double latticeConstant;
  std::vector<double> lc;

  double particleRadius;

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

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

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

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

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

  if (args_info.molFraction_given && args_info.ShellRadius_given) {
    sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius "
            "arguments, but not both!");
    painCave.isFatal = 1;
    simError();
  }
  
  if (nComponents == 1) {
    molFractions.push_back(1.0);    
    shellRadii.push_back(particleRadius);
  } else if (args_info.molFraction_given) {
    if ((int)args_info.molFraction_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
      }
    } else if ((int)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();
    }
  } else if ((int)args_info.ShellRadius_given) {
    if ((int)args_info.ShellRadius_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        shellRadii.push_back(args_info.ShellRadius_arg[i]);
      }
    } else if ((int)args_info.ShellRadius_given == nComponents-1) {
      for (int i = 0; i < nComponents-1; i++) {
        shellRadii.push_back(args_info.ShellRadius_arg[i]);
      }
      shellRadii.push_back(particleRadius);
    } else {    
      sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the shell radii "
              "for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  } else {
    sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not "
            "specified either molFraction or ShellRadius arguments.");
    painCave.isFatal = 1;
    simError();
  }
    
  if (args_info.molFraction_given) {
    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;
    for (int i=0; i < nComponents; i++) {
      molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
      totalMolecules += nMol.at(i);
    }
    
    if (totalMolecules != nSites) {
      sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
              "to the number of lattice sites!");
      painCave.isFatal = 1;
      simError();
    }
  } else {

    for (int i = 0; i < shellRadii.size(); i++) {
      if (shellRadii.at(i) > particleRadius + 1e-6 ) {
        sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
        painCave.isFatal = 1;
        simError();
      } 
      if (shellRadii.at(i) <= 0.0 ) {
        sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
        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 ((int)args_info.molFraction_given){
    sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
    painCave.isFatal = 0;
    simError();
    std::random_shuffle(ids.begin(), ids.end());
  } else{ 
    sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
    painCave.isFatal = 0;
    simError();

    Vector3d myLoc;
    RealType myR;
    RealType smallestSoFar;
    int myComponent = -1;
    nMol.clear();
    nMol.resize(nComponents);

    for (int i = 0; i < sites.size(); i++) {
      myLoc = sites[i];
      myR = myLoc.length();
      smallestSoFar = particleRadius;
     
      for (int j = 0; j < nComponents; j++) {
        if (myR <= shellRadii[j]) {
          if (shellRadii[j] <= smallestSoFar) {
            smallestSoFar = shellRadii[j];
            myComponent = j;
          }
        }
      }
      componentFromSite[i] = myComponent;
      nMol[myComponent]++;
    }
  }   
  
  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;
  
  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());

    if (args_info.ShellRadius_given) {
      for (int n = 0; n < sites.size(); n++) {
        if (componentFromSite[n] == i) {
          mol = NewInfo->getMoleculeByGlobalIndex(l);
          locator->placeMol(sites[n], orientations[n], mol);
          l++;
        }
      }
    } else {
      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)=  10.0*particleRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) =  10.0*particleRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) =  10.0*particleRadius;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  writer = new DumpWriter(NewInfo, outputFileName);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
    painCave.isFatal = 1;
    simError();
  }
  
  writer->writeDump();

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

  delete writer;

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

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  std::vector<int> nMol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  
  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
  
  oldMdFile.getline(buffer, MAXLEN);
 
  int i = 0;
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      if(i<nMol.size()){
        sprintf(buffer, "\tnMol = %i;", nMol.at(i));                            
        newMdFile << buffer << std::endl;
        i++;
      }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	3051
Committed:	Tue Oct 17 17:51:52 2006 UTC (17 years, 11 months ago) by gezelter
File size:	12651 byte(s)
Log Message:	bug fixes
#	User	Rev	Content
1	chuckv	2352	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <cstdlib>
43			#include <cstdio>
44			#include <cstring>
45			#include <cmath>
46			#include <iostream>
47			#include <string>
48			#include <map>
49			#include <fstream>
50	chuckv	2657	#include <algorithm>
51	chuckv	2352
52			#include "config.h"
53	chuckv	2657	#include "shapedLatticeSpherical.hpp"
54	chuckv	2352	#include "nanoparticleBuilderCmd.h"
55			#include "lattice/LatticeFactory.hpp"
56			#include "utils/MoLocator.hpp"
57			#include "lattice/Lattice.hpp"
58			#include "brains/Register.hpp"
59			#include "brains/SimInfo.hpp"
60			#include "brains/SimCreator.hpp"
61			#include "io/DumpWriter.hpp"
62			#include "math/Vector3.hpp"
63			#include "math/SquareMatrix3.hpp"
64			#include "utils/StringUtils.hpp"
65
66			using namespace std;
67			using namespace oopse;
68			void createMdFile(const std::string&oldMdFileName,
69			const std::string&newMdFileName,
70	chuckv	3044	std::vector<int> numMol);
71	chuckv	2352
72			int main(int argc, char *argv []) {
73
74			//register force fields
75			registerForceFields();
76			registerLattice();
77
78			gengetopt_args_info args_info;
79			std::string latticeType;
80			std::string inputFileName;
81	chuckv	3044	std::string outputFileName;
82	chuckv	2352
83	chuckv	2657	MoLocator* locator;
84			int nComponents;
85	chuckv	2352	double latticeConstant;
86			std::vector<double> lc;
87	gezelter	3051
88	chuckv	2657	double particleRadius;
89	chuckv	2352
90			Mat3x3d hmat;
91			std::vector<Vector3d> latticePos;
92			std::vector<Vector3d> latticeOrt;
93	chuckv	3044
94	chuckv	2352	DumpWriter *writer;
95
96	chuckv	2574	// Parse Command Line Arguments
97	chuckv	2352	if (cmdline_parser(argc, argv, &args_info) != 0)
98			exit(1);
99	gezelter	3046
100	chuckv	2352	/* get lattice type */
101	chuckv	3044	latticeType = "FCC";
102
103	chuckv	2352	/* get input file name */
104			if (args_info.inputs_num)
105			inputFileName = args_info.inputs[0];
106			else {
107	gezelter	3051	sprintf(painCave.errMsg, "No input .md file name was specified"
108			"on the command line");
109	chuckv	3044	painCave.isFatal = 1;
110	chuckv	2352	cmdline_parser_print_help();
111	chuckv	3044	simError();
112	chuckv	2352	}
113
114			/* parse md file and set up the system */
115			SimCreator oldCreator;
116			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
117
118			latticeConstant = args_info.latticeCnst_arg;
119			particleRadius = args_info.radius_arg;
120	chuckv	2657	Globals* simParams = oldInfo->getSimParams();
121	chuckv	2352
122	chuckv	2657	/* Create nanoparticle */
123	gezelter	3046	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
124			particleRadius);
125	chuckv	2672
126	chuckv	2657	/* Build a lattice and get lattice points for this lattice constant */
127	gezelter	3046	vector<Vector3d> sites = nanoParticle.getSites();
128			vector<Vector3d> orientations = nanoParticle.getOrientations();
129	chuckv	3044
130			std::cout <<"nSites: " << sites.size() << std::endl;
131
132	chuckv	2657	/* Get number of lattice sites */
133	chuckv	3044	int nSites = sites.size();
134
135			std::vector<Component*> components = simParams->getComponents();
136			std::vector<RealType> molFractions;
137	gezelter	3051	std::vector<RealType> shellRadii;
138	chuckv	3044	std::vector<RealType> molecularMasses;
139			std::vector<int> nMol;
140	gezelter	3051	std::map<int, int> componentFromSite;
141	chuckv	3044	nComponents = components.size();
142
143	gezelter	3051	if (args_info.molFraction_given && args_info.ShellRadius_given) {
144			sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius "
145			"arguments, but not both!");
146			painCave.isFatal = 1;
147			simError();
148			}
149
150			if (nComponents == 1) {
151	chuckv	3044	molFractions.push_back(1.0);
152	gezelter	3051	shellRadii.push_back(particleRadius);
153			} else if (args_info.molFraction_given) {
154			if ((int)args_info.molFraction_given == nComponents) {
155			for (int i = 0; i < nComponents; i++) {
156			molFractions.push_back(args_info.molFraction_arg[i]);
157			}
158			} else if ((int)args_info.molFraction_given == nComponents-1) {
159			RealType remainingFraction = 1.0;
160			for (int i = 0; i < nComponents-1; i++) {
161			molFractions.push_back(args_info.molFraction_arg[i]);
162			remainingFraction -= molFractions[i];
163			}
164			molFractions.push_back(remainingFraction);
165			} else {
166			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
167			"for all of the components in the <MetaData> block.");
168	chuckv	3044	painCave.isFatal = 1;
169			simError();
170			}
171	gezelter	3051	} else if ((int)args_info.ShellRadius_given) {
172			if ((int)args_info.ShellRadius_given == nComponents) {
173			for (int i = 0; i < nComponents; i++) {
174			shellRadii.push_back(args_info.ShellRadius_arg[i]);
175			}
176			} else if ((int)args_info.ShellRadius_given == nComponents-1) {
177			for (int i = 0; i < nComponents-1; i++) {
178			shellRadii.push_back(args_info.ShellRadius_arg[i]);
179			}
180			shellRadii.push_back(particleRadius);
181			} else {
182			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the shell radii "
183			"for all of the components in the <MetaData> block.");
184	chuckv	3044	painCave.isFatal = 1;
185			simError();
186			}
187	gezelter	3051	} else {
188			sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not "
189			"specified either molFraction or ShellRadius arguments.");
190	chuckv	3044	painCave.isFatal = 1;
191			simError();
192			}
193	gezelter	3051
194			if (args_info.molFraction_given) {
195			RealType totalFraction = 0.0;
196
197			/* Do some simple sanity checking*/
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			for (int i=0; i < nComponents; i++) {
231			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
232			totalMolecules += nMol.at(i);
233			}
234
235			if (totalMolecules != nSites) {
236			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
237			"to the number of lattice sites!");
238			painCave.isFatal = 1;
239			simError();
240			}
241			} else {
242	chuckv	3044
243	gezelter	3051	for (int i = 0; i < shellRadii.size(); i++) {
244			if (shellRadii.at(i) > particleRadius + 1e-6 ) {
245			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
246			painCave.isFatal = 1;
247			simError();
248			}
249			if (shellRadii.at(i) <= 0.0 ) {
250			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
251			painCave.isFatal = 1;
252			simError();
253			}
254			}
255	chuckv	3044	}
256	gezelter	3051
257	chuckv	3044	vector<int> ids;
258			for (int i = 0; i < sites.size(); i++) ids.push_back(i);
259	chuckv	2352	/* Random particle is the default case*/
260	gezelter	3051	if ((int)args_info.molFraction_given){
261			sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
262			painCave.isFatal = 0;
263			simError();
264	chuckv	3044	std::random_shuffle(ids.begin(), ids.end());
265	gezelter	3051	} else{
266			sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
267			painCave.isFatal = 0;
268			simError();
269	chuckv	2352
270	gezelter	3051	Vector3d myLoc;
271			RealType myR;
272			RealType smallestSoFar;
273			int myComponent = -1;
274			nMol.clear();
275			nMol.resize(nComponents);
276
277			for (int i = 0; i < sites.size(); i++) {
278			myLoc = sites[i];
279			myR = myLoc.length();
280			smallestSoFar = particleRadius;
281
282			for (int j = 0; j < nComponents; j++) {
283			if (myR <= shellRadii[j]) {
284			if (shellRadii[j] <= smallestSoFar) {
285			smallestSoFar = shellRadii[j];
286			myComponent = j;
287			}
288			}
289			}
290			componentFromSite[i] = myComponent;
291			nMol[myComponent]++;
292			}
293			}
294	chuckv	2737
295	chuckv	3044	outputFileName = args_info.output_arg;
296
297	chuckv	2737
298	gezelter	3051	//creat new .md file on fly which corrects the number of molecule
299	chuckv	3044	createMdFile(inputFileName, outputFileName, nMol);
300	chuckv	2352
301			if (oldInfo != NULL)
302			delete oldInfo;
303
304	chuckv	2737	SimCreator newCreator;
305	chuckv	3044	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
306	gezelter	3051
307	chuckv	2657	// Place molecules
308	chuckv	2352	Molecule* mol;
309			SimInfo::MoleculeIterator mi;
310			mol = NewInfo->beginMolecule(mi);
311	chuckv	2737	int l = 0;
312	chuckv	3044
313			for (int i = 0; i < nComponents; i++){
314			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
315			NewInfo->getForceField());
316	gezelter	3051
317			if (args_info.ShellRadius_given) {
318			for (int n = 0; n < sites.size(); n++) {
319			if (componentFromSite[n] == i) {
320			mol = NewInfo->getMoleculeByGlobalIndex(l);
321			locator->placeMol(sites[n], orientations[n], mol);
322			l++;
323			}
324			}
325			} else {
326			for (int n = 0; n < nMol.at(i); n++) {
327			mol = NewInfo->getMoleculeByGlobalIndex(l);
328			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
329			l++;
330			}
331	chuckv	3044	}
332	gezelter	3051	}
333	chuckv	2352
334			//fill Hmat
335	gezelter	3051	hmat(0, 0)= 10.0*particleRadius;
336	chuckv	2352	hmat(0, 1) = 0.0;
337			hmat(0, 2) = 0.0;
338
339			hmat(1, 0) = 0.0;
340	gezelter	3051	hmat(1, 1) = 10.0*particleRadius;
341	chuckv	2352	hmat(1, 2) = 0.0;
342
343			hmat(2, 0) = 0.0;
344			hmat(2, 1) = 0.0;
345	gezelter	3051	hmat(2, 2) = 10.0*particleRadius;
346	chuckv	2352
347			//set Hmat
348			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
349
350
351			//create dumpwriter and write out the coordinates
352	gezelter	3046	writer = new DumpWriter(NewInfo, outputFileName);
353	chuckv	2352
354			if (writer == NULL) {
355	chuckv	3044	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
356	gezelter	3051	painCave.isFatal = 1;
357			simError();
358	chuckv	2352	}
359
360			writer->writeDump();
361	chuckv	3044
362			// deleting the writer will put the closing at the end of the dump file
363	gezelter	3046
364	chuckv	3044	delete writer;
365
366			// cleanup a by calling sim error.....
367			sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
368			"generated.\n", outputFileName.c_str());
369			painCave.isFatal = 0;
370			simError();
371	chuckv	2352	return 0;
372			}
373
374	gezelter	3051	void createMdFile(const std::string&oldMdFileName,
375			const std::string&newMdFileName,
376	chuckv	3044	std::vector<int> nMol) {
377	chuckv	2352	ifstream oldMdFile;
378			ofstream newMdFile;
379			const int MAXLEN = 65535;
380			char buffer[MAXLEN];
381
382			//create new .md file based on old .md file
383			oldMdFile.open(oldMdFileName.c_str());
384			newMdFile.open(newMdFileName.c_str());
385
386			oldMdFile.getline(buffer, MAXLEN);
387	chuckv	2657
388			int i = 0;
389	chuckv	2352	while (!oldMdFile.eof()) {
390
391			//correct molecule number
392			if (strstr(buffer, "nMol") != NULL) {
393	chuckv	3044	if(i<nMol.size()){
394			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
395	chuckv	2737	newMdFile << buffer << std::endl;
396			i++;
397			}
398	chuckv	2352	} else
399			newMdFile << buffer << std::endl;
400
401			oldMdFile.getline(buffer, MAXLEN);
402			}
403
404			oldMdFile.close();
405			newMdFile.close();
406			}
407