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, 234107 (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 "shapedLatticeEllipsoid.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();
  
  vector<Vector3d> sites;
  vector<Vector3d> orientations;

  if (args_info.ellipsoid_flag) {
    shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
                                         rodLength, rodRadius);
    sites = nanoEllipsoid.getSites();
    orientations = nanoEllipsoid.getOrientations();
  } else {
    
    /* Create nanorod */
    shapedLatticeRod nanoRod(latticeConstant, latticeType,
                             rodRadius, rodLength);
    /* Build a lattice and get lattice points for this lattice constant */
    sites = nanoRod.getSites();
    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);
  
  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:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	16309 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	kstocke1	1701	* [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	gezelter	1864	#include "shapedLatticeEllipsoid.hpp"
59	kstocke1	1701	#include "nanorodBuilderCmd.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			void createMdFile(const std::string&oldMdFileName,
74			const std::string&newMdFileName,
75			std::vector<int> numMol);
76
77			int main(int argc, char *argv []) {
78
79			registerLattice();
80
81			gengetopt_args_info args_info;
82			std::string latticeType;
83			std::string inputFileName;
84			std::string outputFileName;
85
86			MoLocator* locator;
87			int nComponents;
88			double latticeConstant;
89			std::vector<double> lc;
90
91			RealType rodRadius;
92			RealType rodLength;
93
94			Mat3x3d hmat;
95			std::vector<Vector3d> latticePos;
96			std::vector<Vector3d> latticeOrt;
97
98			DumpWriter *writer;
99
100			// Parse Command Line Arguments
101			if (cmdline_parser(argc, argv, &args_info) != 0)
102			exit(1);
103
104			/* get lattice type */
105			latticeType = "FCC";
106
107			/* get input file name */
108			if (args_info.inputs_num)
109			inputFileName = args_info.inputs[0];
110			else {
111			sprintf(painCave.errMsg, "No input .md file name was specified "
112			"on the command line");
113			painCave.isFatal = 1;
114			cmdline_parser_print_help();
115			simError();
116			}
117
118			/* parse md file and set up the system */
119			SimCreator oldCreator;
120			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
121
122			latticeConstant = args_info.latticeConstant_arg;
123			rodRadius = args_info.radius_arg;
124			rodLength = args_info.length_arg;
125			Globals* simParams = oldInfo->getSimParams();
126
127	gezelter	1864	vector<Vector3d> sites;
128			vector<Vector3d> orientations;
129
130			if (args_info.ellipsoid_flag) {
131			shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
132			rodLength, rodRadius);
133			sites = nanoEllipsoid.getSites();
134			orientations = nanoEllipsoid.getOrientations();
135			} else {
136
137			/* Create nanorod */
138			shapedLatticeRod nanoRod(latticeConstant, latticeType,
139			rodRadius, rodLength);
140			/* Build a lattice and get lattice points for this lattice constant */
141			sites = nanoRod.getSites();
142			orientations = nanoRod.getOrientations();
143			}
144
145	kstocke1	1701	std::vector<int> vacancyTargets;
146			vector<bool> isVacancy;
147
148			Vector3d myLoc;
149			RealType myR;
150
151			for (int i = 0; i < sites.size(); i++)
152			isVacancy.push_back(false);
153
154			// cerr << "checking vacancyPercent" << "\n";
155			if (args_info.vacancyPercent_given) {
156			// cerr << "vacancyPercent given" << "\n";
157			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
158			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
159			painCave.isFatal = 1;
160			simError();
161			} else {
162			RealType vF = args_info.vacancyPercent_arg / 100.0;
163			// cerr << "vacancyPercent = " << vF << "\n";
164			RealType vIR;
165			RealType vOR;
166			if (args_info.vacancyInnerRadius_given) {
167			vIR = args_info.vacancyInnerRadius_arg;
168			} else {
169			vIR = 0.0;
170			}
171			if (args_info.vacancyOuterRadius_given) {
172			vOR = args_info.vacancyOuterRadius_arg;
173			} else {
174			vOR = rodRadius;
175			}
176			if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
177
178			for (int i = 0; i < sites.size(); i++) {
179			myLoc = sites[i];
180			myR = myLoc.length();
181			if (myR >= vIR && myR <= vOR) {
182			vacancyTargets.push_back(i);
183			}
184			}
185			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
186
187			int nTargets = vacancyTargets.size();
188			vacancyTargets.resize((int)(vF * nTargets));
189
190
191			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
192			"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
193			vIR, vOR);
194			painCave.isFatal = 0;
195			simError();
196
197			isVacancy.clear();
198			for (int i = 0; i < sites.size(); i++) {
199			bool vac = false;
200			for (int j = 0; j < vacancyTargets.size(); j++) {
201			if (i == vacancyTargets[j]) vac = true;
202			}
203			isVacancy.push_back(vac);
204			}
205
206			} else {
207			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
208			"\tinner or outer radii. Check their values.");
209			painCave.isFatal = 1;
210			simError();
211			}
212			}
213			}
214
215			/* Get number of lattice sites */
216			int nSites = sites.size() - vacancyTargets.size();
217
218			// cerr << "sites.size() = " << sites.size() << "\n";
219			// cerr << "nSites = " << nSites << "\n";
220			// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";
221
222			std::vector<Component*> components = simParams->getComponents();
223			std::vector<RealType> molFractions;
224			std::vector<RealType> shellRadii;
225			std::vector<RealType> molecularMasses;
226			std::vector<int> nMol;
227			std::map<int, int> componentFromSite;
228			nComponents = components.size();
229			// cerr << "nComponents = " << nComponents << "\n";
230
231			if (args_info.molFraction_given && args_info.shellRadius_given) {
232			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
233			"arguments, but not both!");
234			painCave.isFatal = 1;
235			simError();
236			}
237
238			if (nComponents == 1) {
239			molFractions.push_back(1.0);
240			shellRadii.push_back(rodRadius);
241			} else if (args_info.molFraction_given) {
242			if ((int)args_info.molFraction_given == nComponents) {
243			for (int i = 0; i < nComponents; i++) {
244			molFractions.push_back(args_info.molFraction_arg[i]);
245			}
246			} else if ((int)args_info.molFraction_given == nComponents-1) {
247			RealType remainingFraction = 1.0;
248			for (int i = 0; i < nComponents-1; i++) {
249			molFractions.push_back(args_info.molFraction_arg[i]);
250			remainingFraction -= molFractions[i];
251			}
252			molFractions.push_back(remainingFraction);
253			} else {
254			sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
255			"for all of the components in the <MetaData> block.");
256			painCave.isFatal = 1;
257			simError();
258			}
259			} else if ((int)args_info.shellRadius_given) {
260			if ((int)args_info.shellRadius_given == nComponents) {
261			for (int i = 0; i < nComponents; i++) {
262			shellRadii.push_back(args_info.shellRadius_arg[i]);
263			}
264			} else if ((int)args_info.shellRadius_given == nComponents-1) {
265			for (int i = 0; i < nComponents-1; i++) {
266			shellRadii.push_back(args_info.shellRadius_arg[i]);
267			}
268			shellRadii.push_back(rodRadius);
269			} else {
270			sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
271			"\tshell radii for all of the components in the <MetaData> block.");
272			painCave.isFatal = 1;
273			simError();
274			}
275			} else {
276			sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
277			"\tbut have not specified either molFraction or shellRadius arguments.");
278			painCave.isFatal = 1;
279			simError();
280			}
281
282			if (args_info.molFraction_given) {
283			RealType totalFraction = 0.0;
284
285			/* Do some simple sanity checking*/
286
287			for (int i = 0; i < nComponents; i++) {
288			if (molFractions.at(i) < 0.0) {
289			sprintf(painCave.errMsg, "One of the requested molFractions was"
290			" less than zero!");
291			painCave.isFatal = 1;
292			simError();
293			}
294			if (molFractions.at(i) > 1.0) {
295			sprintf(painCave.errMsg, "One of the requested molFractions was"
296			" greater than one!");
297			painCave.isFatal = 1;
298			simError();
299			}
300			totalFraction += molFractions.at(i);
301			}
302			if (abs(totalFraction - 1.0) > 1e-6) {
303			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
304			painCave.isFatal = 1;
305			simError();
306			}
307
308			int remaining = nSites;
309			for (int i=0; i < nComponents-1; i++) {
310			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
311			remaining -= nMol.at(i);
312			}
313			nMol.push_back(remaining);
314
315			// recompute actual mol fractions and perform final sanity check:
316
317			int totalMolecules = 0;
318			for (int i=0; i < nComponents; i++) {
319			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
320			totalMolecules += nMol.at(i);
321			}
322			if (totalMolecules != nSites) {
323			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
324			"to the number of lattice sites!");
325			painCave.isFatal = 1;
326			simError();
327			}
328			} else {
329
330			for (int i = 0; i < shellRadii.size(); i++) {
331			if (shellRadii.at(i) > rodRadius + 1e-6 ) {
332			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius.");
333			painCave.isFatal = 1;
334			simError();
335			}
336			if (shellRadii.at(i) <= 0.0 ) {
337			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
338			painCave.isFatal = 1;
339			simError();
340			}
341			}
342			}
343
344			vector<int> ids;
345			if ((int)args_info.molFraction_given){
346			// cerr << "molFraction given 2" << "\n";
347			sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod.");
348			painCave.isFatal = 0;
349			simError();
350			/* Random rod is the default case*/
351
352			for (int i = 0; i < sites.size(); i++)
353			if (!isVacancy[i]) ids.push_back(i);
354
355			std::random_shuffle(ids.begin(), ids.end());
356
357			} else{
358			sprintf(painCave.errMsg, "Creating an fcc nanorod.");
359			painCave.isFatal = 0;
360			simError();
361
362	gezelter	1828	// RealType smallestSoFar;
363	kstocke1	1701	int myComponent = -1;
364			nMol.clear();
365			nMol.resize(nComponents);
366
367			// cerr << "shellRadii[0] " << shellRadii[0] << "\n";
368	gezelter	1828	// cerr << "rodRadius " << rodRadius << "\n";
369	kstocke1	1701
370			for (int i = 0; i < sites.size(); i++) {
371			myLoc = sites[i];
372			myR = myLoc.length();
373	gezelter	1828	// smallestSoFar = rodRadius;
374			// cerr << "vac = " << isVacancy[i]<< "\n";
375	kstocke1	1701
376			if (!isVacancy[i]) {
377
378
379			// for (int j = 0; j < nComponents; j++) {
380			// if (myR <= shellRadii[j]) {
381			// if (shellRadii[j] <= smallestSoFar) {
382			// smallestSoFar = shellRadii[j];
383			// myComponent = j;
384			// }
385			// }
386			// }
387			myComponent = 0;
388			componentFromSite[i] = myComponent;
389			nMol[myComponent]++;
390			// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
391			}
392			}
393			}
394			// cerr << "nMol = " << nMol.at(0) << "\n";
395
396			outputFileName = args_info.output_arg;
397
398			//creat new .md file on fly which corrects the number of molecule
399
400			createMdFile(inputFileName, outputFileName, nMol);
401
402	gezelter	1874	delete oldInfo;
403	kstocke1	1701
404			SimCreator newCreator;
405			SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
406
407			// Place molecules
408			Molecule* mol;
409			SimInfo::MoleculeIterator mi;
410			mol = NewInfo->beginMolecule(mi);
411
412			int l = 0;
413
414			for (int i = 0; i < nComponents; i++){
415			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
416			NewInfo->getForceField());
417
418			// cerr << "nMol = " << nMol.at(i) << "\n";
419			if (!args_info.molFraction_given) {
420			for (int n = 0; n < sites.size(); n++) {
421			if (!isVacancy[n]) {
422			if (componentFromSite[n] == i) {
423			mol = NewInfo->getMoleculeByGlobalIndex(l);
424			locator->placeMol(sites[n], orientations[n], mol);
425			l++;
426			}
427			}
428			}
429			} else {
430			for (int n = 0; n < nMol.at(i); n++) {
431			mol = NewInfo->getMoleculeByGlobalIndex(l);
432			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
433			l++;
434			}
435			}
436			}
437
438			//fill Hmat
439			hmat(0, 0)= 10.0*rodRadius;
440			hmat(0, 1) = 0.0;
441			hmat(0, 2) = 0.0;
442
443			hmat(1, 0) = 0.0;
444			hmat(1, 1) = 10.0*rodRadius;
445			hmat(1, 2) = 0.0;
446
447			hmat(2, 0) = 0.0;
448			hmat(2, 1) = 0.0;
449			hmat(2, 2) = 5.0rodLength + 2.0rodRadius;
450
451			//set Hmat
452			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
453
454
455			//create dumpwriter and write out the coordinates
456			writer = new DumpWriter(NewInfo, outputFileName);
457
458			if (writer == NULL) {
459			sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
460			painCave.isFatal = 1;
461			simError();
462			}
463
464			writer->writeDump();
465
466			// deleting the writer will put the closing at the end of the dump file
467
468			delete writer;
469
470			// cleanup a by calling sim error.....
471			sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
472			"generated.\n", outputFileName.c_str());
473			painCave.isFatal = 0;
474			simError();
475			return 0;
476			}
477
478			void createMdFile(const std::string&oldMdFileName,
479			const std::string&newMdFileName,
480			std::vector<int> nMol) {
481			ifstream oldMdFile;
482			ofstream newMdFile;
483			const int MAXLEN = 65535;
484			char buffer[MAXLEN];
485
486			//create new .md file based on old .md file
487			oldMdFile.open(oldMdFileName.c_str());
488			newMdFile.open(newMdFileName.c_str());
489			oldMdFile.getline(buffer, MAXLEN);
490
491			int i = 0;
492			while (!oldMdFile.eof()) {
493
494			//correct molecule number
495			if (strstr(buffer, "nMol") != NULL) {
496			if(i<nMol.size()){
497			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
498			newMdFile << buffer << std::endl;
499			i++;
500			}
501			} else
502			newMdFile << buffer << std::endl;
503
504			oldMdFile.getline(buffer, MAXLEN);
505			}
506
507			oldMdFile.close();
508			newMdFile.close();
509
510			if (i != nMol.size()) {
511			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
512			"\tstatements in component blocks. Make sure that all\n"
513			"\tcomponents in the template file have nMol=1");
514			painCave.isFatal = 1;
515			simError();
516			}
517
518			}
519