applications/nanoparticleBuilder/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. 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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 *  Created by Kelsey M. Stocker on 2/9/12.
 *  @author  Kelsey M. Stocker 
 *
 */

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

#include "config.h"
#include "shapedLatticeRod.hpp"
#include "nanorodBuilderCmd.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> numMol);

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

  RealType rodRadius;
  RealType rodLength;

  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.latticeConstant_arg;
  rodRadius = args_info.radius_arg;
  rodLength = args_info.length_arg;
  Globals* simParams = oldInfo->getSimParams();
  
  /* Create nanorod */
  shapedLatticeRod nanoRod(latticeConstant, latticeType,
                           rodRadius, rodLength);
  
  /* Build a lattice and get lattice points for this lattice constant */
  vector<Vector3d> sites = nanoRod.getSites();
  vector<Vector3d> orientations = nanoRod.getOrientations();
  std::vector<int> vacancyTargets;
  vector<bool> isVacancy;
  
  Vector3d myLoc;
  RealType myR;
 
  for (int i = 0; i < sites.size(); i++) 
    isVacancy.push_back(false);

  // cerr << "checking vacancyPercent" << "\n";
  if (args_info.vacancyPercent_given) {
    // cerr << "vacancyPercent given" << "\n";
    if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
      sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
      painCave.isFatal = 1;
      simError();
    } else {
      RealType vF = args_info.vacancyPercent_arg / 100.0;
      //  cerr << "vacancyPercent = " << vF << "\n";
      RealType vIR;
      RealType vOR;
      if (args_info.vacancyInnerRadius_given) {
        vIR = args_info.vacancyInnerRadius_arg;
      } else {
        vIR = 0.0;
      }
      if (args_info.vacancyOuterRadius_given) {
        vOR = args_info.vacancyOuterRadius_arg;
      } else {
        vOR = rodRadius;
      }
      if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
        
        for (int i = 0; i < sites.size(); i++) {
          myLoc = sites[i];
          myR = myLoc.length();
          if (myR >= vIR && myR <= vOR) {
            vacancyTargets.push_back(i);
          }          
        }
        std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
        
        int nTargets = vacancyTargets.size();
        vacancyTargets.resize((int)(vF * nTargets));
        
                  
        sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
                "\tsites between %lf and %lf.", (int) vacancyTargets.size(), 
                vIR, vOR); 
        painCave.isFatal = 0;
        simError();

        isVacancy.clear();
        for (int i = 0; i < sites.size(); i++) {
          bool vac = false;
          for (int j = 0; j < vacancyTargets.size(); j++) {
            if (i == vacancyTargets[j]) vac = true;
          }
          isVacancy.push_back(vac);
        }
               
      } else {
        sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
                "\tinner or outer radii.  Check their values.");
        painCave.isFatal = 1;
        simError();
      }
    }
  }

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

  // cerr << "sites.size() = " << sites.size() << "\n";
  // cerr << "nSites = " << nSites << "\n";
  // cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";

  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();
  // cerr << "nComponents = " << nComponents << "\n";

  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(rodRadius);
  } 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, "nanorodBuilder 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(rodRadius);
    } else {    
      sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
              "\tshell 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,\n"
            "\tbut 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) > rodRadius + 1e-6 ) {
        sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod 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;           
  if ((int)args_info.molFraction_given){
    //  cerr << "molFraction given 2" << "\n";
    sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod.");
    painCave.isFatal = 0;
    simError();
    /* Random rod is the default case*/

    for (int i = 0; i < sites.size(); i++) 
      if (!isVacancy[i]) ids.push_back(i);
    
    std::random_shuffle(ids.begin(), ids.end());
    
  } else{ 
    sprintf(painCave.errMsg, "Creating an fcc nanorod.");
    painCave.isFatal = 0;
    simError();

    // RealType smallestSoFar;
    int myComponent = -1;
    nMol.clear();
    nMol.resize(nComponents);

    // cerr << "shellRadii[0] " << shellRadii[0] << "\n";
    // cerr << "rodRadius " << rodRadius << "\n";

    for (int i = 0; i < sites.size(); i++) {
      myLoc = sites[i];
      myR = myLoc.length();
      // smallestSoFar = rodRadius;  
      // cerr << "vac = " << isVacancy[i]<< "\n";
    
      if (!isVacancy[i]) {


        // for (int j = 0; j < nComponents; j++) {
        //   if (myR <= shellRadii[j]) {
        //     if (shellRadii[j] <= smallestSoFar) {
        //       smallestSoFar = shellRadii[j];
        //       myComponent = j;
        //     }
        //   }
        // }
        myComponent = 0;
        componentFromSite[i] = myComponent;
        nMol[myComponent]++;
        //      cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
      }
    }       
  }
  //     cerr << "nMol = " << nMol.at(0) << "\n";

  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());
    
    //   cerr << "nMol = " << nMol.at(i) << "\n";
    if (!args_info.molFraction_given) {
      for (int n = 0; n < sites.size(); n++) {
        if (!isVacancy[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*rodRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) = 10.0*rodRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) = 5.0*rodLength + 2.0*rodRadius;
  
  //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 dumpwriter 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 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);

  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:	1828
Committed:	Wed Jan 9 19:59:00 2013 UTC (12 years, 3 months ago) by gezelter
File size:	15959 byte(s)
Log Message:	Fixed some cruft
#	User	Rev	Content
1	kstocke1	1701	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			* Created by Kelsey M. Stocker on 2/9/12.
42			* @author Kelsey M. Stocker
43			*
44			*/
45
46			#include <cstdlib>
47			#include <cstdio>
48			#include <cstring>
49			#include <cmath>
50			#include <iostream>
51			#include <string>
52			#include <map>
53			#include <fstream>
54			#include <algorithm>
55
56			#include "config.h"
57			#include "shapedLatticeRod.hpp"
58			#include "nanorodBuilderCmd.h"
59			#include "lattice/LatticeFactory.hpp"
60			#include "utils/MoLocator.hpp"
61			#include "lattice/Lattice.hpp"
62			#include "brains/Register.hpp"
63			#include "brains/SimInfo.hpp"
64			#include "brains/SimCreator.hpp"
65			#include "io/DumpWriter.hpp"
66			#include "math/Vector3.hpp"
67			#include "math/SquareMatrix3.hpp"
68			#include "utils/StringUtils.hpp"
69
70			using namespace std;
71			using namespace OpenMD;
72			void createMdFile(const std::string&oldMdFileName,
73			const std::string&newMdFileName,
74			std::vector<int> numMol);
75
76			int main(int argc, char *argv []) {
77
78			registerLattice();
79
80			gengetopt_args_info args_info;
81			std::string latticeType;
82			std::string inputFileName;
83			std::string outputFileName;
84
85			MoLocator* locator;
86			int nComponents;
87			double latticeConstant;
88			std::vector<double> lc;
89
90			RealType rodRadius;
91			RealType rodLength;
92
93			Mat3x3d hmat;
94			std::vector<Vector3d> latticePos;
95			std::vector<Vector3d> latticeOrt;
96
97			DumpWriter *writer;
98
99			// Parse Command Line Arguments
100			if (cmdline_parser(argc, argv, &args_info) != 0)
101			exit(1);
102
103			/* get lattice type */
104			latticeType = "FCC";
105
106			/* get input file name */
107			if (args_info.inputs_num)
108			inputFileName = args_info.inputs[0];
109			else {
110			sprintf(painCave.errMsg, "No input .md file name was specified "
111			"on the command line");
112			painCave.isFatal = 1;
113			cmdline_parser_print_help();
114			simError();
115			}
116
117			/* parse md file and set up the system */
118			SimCreator oldCreator;
119			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
120
121			latticeConstant = args_info.latticeConstant_arg;
122			rodRadius = args_info.radius_arg;
123			rodLength = args_info.length_arg;
124			Globals* simParams = oldInfo->getSimParams();
125
126			/* Create nanorod */
127			shapedLatticeRod nanoRod(latticeConstant, latticeType,
128			rodRadius, rodLength);
129
130			/* Build a lattice and get lattice points for this lattice constant */
131			vector<Vector3d> sites = nanoRod.getSites();
132			vector<Vector3d> orientations = nanoRod.getOrientations();
133			std::vector<int> vacancyTargets;
134			vector<bool> isVacancy;
135
136			Vector3d myLoc;
137			RealType myR;
138
139			for (int i = 0; i < sites.size(); i++)
140			isVacancy.push_back(false);
141
142			// cerr << "checking vacancyPercent" << "\n";
143			if (args_info.vacancyPercent_given) {
144			// cerr << "vacancyPercent given" << "\n";
145			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
146			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
147			painCave.isFatal = 1;
148			simError();
149			} else {
150			RealType vF = args_info.vacancyPercent_arg / 100.0;
151			// cerr << "vacancyPercent = " << vF << "\n";
152			RealType vIR;
153			RealType vOR;
154			if (args_info.vacancyInnerRadius_given) {
155			vIR = args_info.vacancyInnerRadius_arg;
156			} else {
157			vIR = 0.0;
158			}
159			if (args_info.vacancyOuterRadius_given) {
160			vOR = args_info.vacancyOuterRadius_arg;
161			} else {
162			vOR = rodRadius;
163			}
164			if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
165
166			for (int i = 0; i < sites.size(); i++) {
167			myLoc = sites[i];
168			myR = myLoc.length();
169			if (myR >= vIR && myR <= vOR) {
170			vacancyTargets.push_back(i);
171			}
172			}
173			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
174
175			int nTargets = vacancyTargets.size();
176			vacancyTargets.resize((int)(vF * nTargets));
177
178
179			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
180			"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
181			vIR, vOR);
182			painCave.isFatal = 0;
183			simError();
184
185			isVacancy.clear();
186			for (int i = 0; i < sites.size(); i++) {
187			bool vac = false;
188			for (int j = 0; j < vacancyTargets.size(); j++) {
189			if (i == vacancyTargets[j]) vac = true;
190			}
191			isVacancy.push_back(vac);
192			}
193
194			} else {
195			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
196			"\tinner or outer radii. Check their values.");
197			painCave.isFatal = 1;
198			simError();
199			}
200			}
201			}
202
203			/* Get number of lattice sites */
204			int nSites = sites.size() - vacancyTargets.size();
205
206			// cerr << "sites.size() = " << sites.size() << "\n";
207			// cerr << "nSites = " << nSites << "\n";
208			// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";
209
210			std::vector<Component*> components = simParams->getComponents();
211			std::vector<RealType> molFractions;
212			std::vector<RealType> shellRadii;
213			std::vector<RealType> molecularMasses;
214			std::vector<int> nMol;
215			std::map<int, int> componentFromSite;
216			nComponents = components.size();
217			// cerr << "nComponents = " << nComponents << "\n";
218
219			if (args_info.molFraction_given && args_info.shellRadius_given) {
220			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
221			"arguments, but not both!");
222			painCave.isFatal = 1;
223			simError();
224			}
225
226			if (nComponents == 1) {
227			molFractions.push_back(1.0);
228			shellRadii.push_back(rodRadius);
229			} else if (args_info.molFraction_given) {
230			if ((int)args_info.molFraction_given == nComponents) {
231			for (int i = 0; i < nComponents; i++) {
232			molFractions.push_back(args_info.molFraction_arg[i]);
233			}
234			} else if ((int)args_info.molFraction_given == nComponents-1) {
235			RealType remainingFraction = 1.0;
236			for (int i = 0; i < nComponents-1; i++) {
237			molFractions.push_back(args_info.molFraction_arg[i]);
238			remainingFraction -= molFractions[i];
239			}
240			molFractions.push_back(remainingFraction);
241			} else {
242			sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
243			"for all of the components in the <MetaData> block.");
244			painCave.isFatal = 1;
245			simError();
246			}
247			} else if ((int)args_info.shellRadius_given) {
248			if ((int)args_info.shellRadius_given == nComponents) {
249			for (int i = 0; i < nComponents; i++) {
250			shellRadii.push_back(args_info.shellRadius_arg[i]);
251			}
252			} else if ((int)args_info.shellRadius_given == nComponents-1) {
253			for (int i = 0; i < nComponents-1; i++) {
254			shellRadii.push_back(args_info.shellRadius_arg[i]);
255			}
256			shellRadii.push_back(rodRadius);
257			} else {
258			sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
259			"\tshell radii for all of the components in the <MetaData> block.");
260			painCave.isFatal = 1;
261			simError();
262			}
263			} else {
264			sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
265			"\tbut have not specified either molFraction or shellRadius arguments.");
266			painCave.isFatal = 1;
267			simError();
268			}
269
270			if (args_info.molFraction_given) {
271			RealType totalFraction = 0.0;
272
273			/* Do some simple sanity checking*/
274
275			for (int i = 0; i < nComponents; i++) {
276			if (molFractions.at(i) < 0.0) {
277			sprintf(painCave.errMsg, "One of the requested molFractions was"
278			" less than zero!");
279			painCave.isFatal = 1;
280			simError();
281			}
282			if (molFractions.at(i) > 1.0) {
283			sprintf(painCave.errMsg, "One of the requested molFractions was"
284			" greater than one!");
285			painCave.isFatal = 1;
286			simError();
287			}
288			totalFraction += molFractions.at(i);
289			}
290			if (abs(totalFraction - 1.0) > 1e-6) {
291			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
292			painCave.isFatal = 1;
293			simError();
294			}
295
296			int remaining = nSites;
297			for (int i=0; i < nComponents-1; i++) {
298			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
299			remaining -= nMol.at(i);
300			}
301			nMol.push_back(remaining);
302
303			// recompute actual mol fractions and perform final sanity check:
304
305			int totalMolecules = 0;
306			for (int i=0; i < nComponents; i++) {
307			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
308			totalMolecules += nMol.at(i);
309			}
310			if (totalMolecules != nSites) {
311			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
312			"to the number of lattice sites!");
313			painCave.isFatal = 1;
314			simError();
315			}
316			} else {
317
318			for (int i = 0; i < shellRadii.size(); i++) {
319			if (shellRadii.at(i) > rodRadius + 1e-6 ) {
320			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius.");
321			painCave.isFatal = 1;
322			simError();
323			}
324			if (shellRadii.at(i) <= 0.0 ) {
325			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
326			painCave.isFatal = 1;
327			simError();
328			}
329			}
330			}
331
332			vector<int> ids;
333			if ((int)args_info.molFraction_given){
334			// cerr << "molFraction given 2" << "\n";
335			sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod.");
336			painCave.isFatal = 0;
337			simError();
338			/* Random rod is the default case*/
339
340			for (int i = 0; i < sites.size(); i++)
341			if (!isVacancy[i]) ids.push_back(i);
342
343			std::random_shuffle(ids.begin(), ids.end());
344
345			} else{
346			sprintf(painCave.errMsg, "Creating an fcc nanorod.");
347			painCave.isFatal = 0;
348			simError();
349
350	gezelter	1828	// RealType smallestSoFar;
351	kstocke1	1701	int myComponent = -1;
352			nMol.clear();
353			nMol.resize(nComponents);
354
355			// cerr << "shellRadii[0] " << shellRadii[0] << "\n";
356	gezelter	1828	// cerr << "rodRadius " << rodRadius << "\n";
357	kstocke1	1701
358			for (int i = 0; i < sites.size(); i++) {
359			myLoc = sites[i];
360			myR = myLoc.length();
361	gezelter	1828	// smallestSoFar = rodRadius;
362			// cerr << "vac = " << isVacancy[i]<< "\n";
363	kstocke1	1701
364			if (!isVacancy[i]) {
365
366
367			// for (int j = 0; j < nComponents; j++) {
368			// if (myR <= shellRadii[j]) {
369			// if (shellRadii[j] <= smallestSoFar) {
370			// smallestSoFar = shellRadii[j];
371			// myComponent = j;
372			// }
373			// }
374			// }
375			myComponent = 0;
376			componentFromSite[i] = myComponent;
377			nMol[myComponent]++;
378			// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
379			}
380			}
381			}
382			// cerr << "nMol = " << nMol.at(0) << "\n";
383
384			outputFileName = args_info.output_arg;
385
386			//creat new .md file on fly which corrects the number of molecule
387
388			createMdFile(inputFileName, outputFileName, nMol);
389
390			if (oldInfo != NULL)
391			delete oldInfo;
392
393			SimCreator newCreator;
394			SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
395
396			// Place molecules
397			Molecule* mol;
398			SimInfo::MoleculeIterator mi;
399			mol = NewInfo->beginMolecule(mi);
400
401			int l = 0;
402
403			for (int i = 0; i < nComponents; i++){
404			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
405			NewInfo->getForceField());
406
407			// cerr << "nMol = " << nMol.at(i) << "\n";
408			if (!args_info.molFraction_given) {
409			for (int n = 0; n < sites.size(); n++) {
410			if (!isVacancy[n]) {
411			if (componentFromSite[n] == i) {
412			mol = NewInfo->getMoleculeByGlobalIndex(l);
413			locator->placeMol(sites[n], orientations[n], mol);
414			l++;
415			}
416			}
417			}
418			} else {
419			for (int n = 0; n < nMol.at(i); n++) {
420			mol = NewInfo->getMoleculeByGlobalIndex(l);
421			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
422			l++;
423			}
424			}
425			}
426
427			//fill Hmat
428			hmat(0, 0)= 10.0*rodRadius;
429			hmat(0, 1) = 0.0;
430			hmat(0, 2) = 0.0;
431
432			hmat(1, 0) = 0.0;
433			hmat(1, 1) = 10.0*rodRadius;
434			hmat(1, 2) = 0.0;
435
436			hmat(2, 0) = 0.0;
437			hmat(2, 1) = 0.0;
438			hmat(2, 2) = 5.0rodLength + 2.0rodRadius;
439
440			//set Hmat
441			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
442
443
444			//create dumpwriter and write out the coordinates
445			writer = new DumpWriter(NewInfo, outputFileName);
446
447			if (writer == NULL) {
448			sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
449			painCave.isFatal = 1;
450			simError();
451			}
452
453			writer->writeDump();
454
455			// deleting the writer will put the closing at the end of the dump file
456
457			delete writer;
458
459			// cleanup a by calling sim error.....
460			sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
461			"generated.\n", outputFileName.c_str());
462			painCave.isFatal = 0;
463			simError();
464			return 0;
465			}
466
467			void createMdFile(const std::string&oldMdFileName,
468			const std::string&newMdFileName,
469			std::vector<int> nMol) {
470			ifstream oldMdFile;
471			ofstream newMdFile;
472			const int MAXLEN = 65535;
473			char buffer[MAXLEN];
474
475			//create new .md file based on old .md file
476			oldMdFile.open(oldMdFileName.c_str());
477			newMdFile.open(newMdFileName.c_str());
478			oldMdFile.getline(buffer, MAXLEN);
479
480			int i = 0;
481			while (!oldMdFile.eof()) {
482
483			//correct molecule number
484			if (strstr(buffer, "nMol") != NULL) {
485			if(i<nMol.size()){
486			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
487			newMdFile << buffer << std::endl;
488			i++;
489			}
490			} else
491			newMdFile << buffer << std::endl;
492
493			oldMdFile.getline(buffer, MAXLEN);
494			}
495
496			oldMdFile.close();
497			newMdFile.close();
498
499			if (i != nMol.size()) {
500			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
501			"\tstatements in component blocks. Make sure that all\n"
502			"\tcomponents in the template file have nMol=1");
503			painCave.isFatal = 1;
504			simError();
505			}
506
507			}
508