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;
  RealType rodRadius;
  RealType rodLength;
  Mat3x3d hmat;
  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 (unsigned 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 (unsigned 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 (unsigned int i = 0; i < sites.size(); i++) {
          bool vac = false;
          for (unsigned 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<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 (unsigned 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 (unsigned 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 (unsigned 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 (unsigned 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 (unsigned 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 (unsigned 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);

  unsigned int i = 0;
  while (!oldMdFile.eof()) {

    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      if(i<nMol.size()){
        sprintf(buffer, "\tnMol = %i;", nMol.at(i));
        newMdFile << buffer << std::endl;
        i++;
      }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();

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

Revision:	1876
Committed:	Fri May 17 17:10:11 2013 UTC (11 years, 11 months ago) by gezelter
File size:	16266 byte(s)
Log Message:	Compilation and portability fixes
#	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			MoLocator* locator;
86			int nComponents;
87			double latticeConstant;
88			RealType rodRadius;
89			RealType rodLength;
90			Mat3x3d hmat;
91			DumpWriter *writer;
92
93			// Parse Command Line Arguments
94			if (cmdline_parser(argc, argv, &args_info) != 0)
95			exit(1);
96
97			/* get lattice type */
98			latticeType = "FCC";
99
100			/* get input file name */
101			if (args_info.inputs_num)
102			inputFileName = args_info.inputs[0];
103			else {
104			sprintf(painCave.errMsg, "No input .md file name was specified "
105			"on the command line");
106			painCave.isFatal = 1;
107			cmdline_parser_print_help();
108			simError();
109			}
110
111			/* parse md file and set up the system */
112			SimCreator oldCreator;
113			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
114
115			latticeConstant = args_info.latticeConstant_arg;
116			rodRadius = args_info.radius_arg;
117			rodLength = args_info.length_arg;
118			Globals* simParams = oldInfo->getSimParams();
119
120	gezelter	1864	vector<Vector3d> sites;
121			vector<Vector3d> orientations;
122
123			if (args_info.ellipsoid_flag) {
124			shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
125			rodLength, rodRadius);
126			sites = nanoEllipsoid.getSites();
127			orientations = nanoEllipsoid.getOrientations();
128			} else {
129
130			/* Create nanorod */
131			shapedLatticeRod nanoRod(latticeConstant, latticeType,
132			rodRadius, rodLength);
133			/* Build a lattice and get lattice points for this lattice constant */
134			sites = nanoRod.getSites();
135			orientations = nanoRod.getOrientations();
136			}
137
138	kstocke1	1701	std::vector<int> vacancyTargets;
139			vector<bool> isVacancy;
140
141			Vector3d myLoc;
142			RealType myR;
143
144	gezelter	1876	for (unsigned int i = 0; i < sites.size(); i++)
145	kstocke1	1701	isVacancy.push_back(false);
146	gezelter	1876
147	kstocke1	1701	// cerr << "checking vacancyPercent" << "\n";
148			if (args_info.vacancyPercent_given) {
149			// cerr << "vacancyPercent given" << "\n";
150			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
151			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
152			painCave.isFatal = 1;
153			simError();
154			} else {
155			RealType vF = args_info.vacancyPercent_arg / 100.0;
156			// cerr << "vacancyPercent = " << vF << "\n";
157			RealType vIR;
158			RealType vOR;
159			if (args_info.vacancyInnerRadius_given) {
160			vIR = args_info.vacancyInnerRadius_arg;
161			} else {
162			vIR = 0.0;
163			}
164			if (args_info.vacancyOuterRadius_given) {
165			vOR = args_info.vacancyOuterRadius_arg;
166			} else {
167			vOR = rodRadius;
168			}
169			if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
170
171	gezelter	1876	for (unsigned int i = 0; i < sites.size(); i++) {
172	kstocke1	1701	myLoc = sites[i];
173			myR = myLoc.length();
174			if (myR >= vIR && myR <= vOR) {
175			vacancyTargets.push_back(i);
176			}
177			}
178			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
179
180			int nTargets = vacancyTargets.size();
181			vacancyTargets.resize((int)(vF * nTargets));
182
183
184			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
185			"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
186			vIR, vOR);
187			painCave.isFatal = 0;
188			simError();
189
190			isVacancy.clear();
191	gezelter	1876	for (unsigned int i = 0; i < sites.size(); i++) {
192	kstocke1	1701	bool vac = false;
193	gezelter	1876	for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
194	kstocke1	1701	if (i == vacancyTargets[j]) vac = true;
195			}
196			isVacancy.push_back(vac);
197			}
198
199			} else {
200			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
201			"\tinner or outer radii. Check their values.");
202			painCave.isFatal = 1;
203			simError();
204			}
205			}
206			}
207
208			/* Get number of lattice sites */
209			int nSites = sites.size() - vacancyTargets.size();
210
211			// cerr << "sites.size() = " << sites.size() << "\n";
212			// cerr << "nSites = " << nSites << "\n";
213			// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";
214
215			std::vector<Component*> components = simParams->getComponents();
216			std::vector<RealType> molFractions;
217			std::vector<RealType> shellRadii;
218			std::vector<int> nMol;
219			std::map<int, int> componentFromSite;
220			nComponents = components.size();
221			// cerr << "nComponents = " << nComponents << "\n";
222
223			if (args_info.molFraction_given && args_info.shellRadius_given) {
224			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
225			"arguments, but not both!");
226			painCave.isFatal = 1;
227			simError();
228			}
229
230			if (nComponents == 1) {
231			molFractions.push_back(1.0);
232			shellRadii.push_back(rodRadius);
233			} else if (args_info.molFraction_given) {
234			if ((int)args_info.molFraction_given == nComponents) {
235			for (int i = 0; i < nComponents; i++) {
236			molFractions.push_back(args_info.molFraction_arg[i]);
237			}
238			} else if ((int)args_info.molFraction_given == nComponents-1) {
239			RealType remainingFraction = 1.0;
240			for (int i = 0; i < nComponents-1; i++) {
241			molFractions.push_back(args_info.molFraction_arg[i]);
242			remainingFraction -= molFractions[i];
243			}
244			molFractions.push_back(remainingFraction);
245			} else {
246			sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
247			"for all of the components in the <MetaData> block.");
248			painCave.isFatal = 1;
249			simError();
250			}
251			} else if ((int)args_info.shellRadius_given) {
252			if ((int)args_info.shellRadius_given == nComponents) {
253			for (int i = 0; i < nComponents; i++) {
254			shellRadii.push_back(args_info.shellRadius_arg[i]);
255			}
256			} else if ((int)args_info.shellRadius_given == nComponents-1) {
257			for (int i = 0; i < nComponents-1; i++) {
258			shellRadii.push_back(args_info.shellRadius_arg[i]);
259			}
260			shellRadii.push_back(rodRadius);
261			} else {
262			sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
263			"\tshell radii for all of the components in the <MetaData> block.");
264			painCave.isFatal = 1;
265			simError();
266			}
267			} else {
268			sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
269			"\tbut have not specified either molFraction or shellRadius arguments.");
270			painCave.isFatal = 1;
271			simError();
272			}
273
274			if (args_info.molFraction_given) {
275			RealType totalFraction = 0.0;
276
277			/* Do some simple sanity checking*/
278
279			for (int i = 0; i < nComponents; i++) {
280			if (molFractions.at(i) < 0.0) {
281			sprintf(painCave.errMsg, "One of the requested molFractions was"
282			" less than zero!");
283			painCave.isFatal = 1;
284			simError();
285			}
286			if (molFractions.at(i) > 1.0) {
287			sprintf(painCave.errMsg, "One of the requested molFractions was"
288			" greater than one!");
289			painCave.isFatal = 1;
290			simError();
291			}
292			totalFraction += molFractions.at(i);
293			}
294			if (abs(totalFraction - 1.0) > 1e-6) {
295			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
296			painCave.isFatal = 1;
297			simError();
298			}
299
300			int remaining = nSites;
301			for (int i=0; i < nComponents-1; i++) {
302			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
303			remaining -= nMol.at(i);
304			}
305			nMol.push_back(remaining);
306
307			// recompute actual mol fractions and perform final sanity check:
308
309			int totalMolecules = 0;
310			for (int i=0; i < nComponents; i++) {
311			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
312			totalMolecules += nMol.at(i);
313			}
314			if (totalMolecules != nSites) {
315			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
316			"to the number of lattice sites!");
317			painCave.isFatal = 1;
318			simError();
319			}
320			} else {
321
322	gezelter	1876	for (unsigned int i = 0; i < shellRadii.size(); i++) {
323	kstocke1	1701	if (shellRadii.at(i) > rodRadius + 1e-6 ) {
324			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius.");
325			painCave.isFatal = 1;
326			simError();
327			}
328			if (shellRadii.at(i) <= 0.0 ) {
329			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
330			painCave.isFatal = 1;
331			simError();
332			}
333			}
334			}
335
336			vector<int> ids;
337			if ((int)args_info.molFraction_given){
338			// cerr << "molFraction given 2" << "\n";
339			sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod.");
340			painCave.isFatal = 0;
341			simError();
342			/* Random rod is the default case*/
343
344	gezelter	1876	for (unsigned int i = 0; i < sites.size(); i++)
345	kstocke1	1701	if (!isVacancy[i]) ids.push_back(i);
346
347			std::random_shuffle(ids.begin(), ids.end());
348
349			} else{
350			sprintf(painCave.errMsg, "Creating an fcc nanorod.");
351			painCave.isFatal = 0;
352			simError();
353
354	gezelter	1828	// RealType smallestSoFar;
355	kstocke1	1701	int myComponent = -1;
356			nMol.clear();
357			nMol.resize(nComponents);
358
359			// cerr << "shellRadii[0] " << shellRadii[0] << "\n";
360	gezelter	1828	// cerr << "rodRadius " << rodRadius << "\n";
361	kstocke1	1701
362	gezelter	1876	for (unsigned int i = 0; i < sites.size(); i++) {
363	kstocke1	1701	myLoc = sites[i];
364			myR = myLoc.length();
365	gezelter	1828	// smallestSoFar = rodRadius;
366			// cerr << "vac = " << isVacancy[i]<< "\n";
367	kstocke1	1701
368			if (!isVacancy[i]) {
369
370
371			// for (int j = 0; j < nComponents; j++) {
372			// if (myR <= shellRadii[j]) {
373			// if (shellRadii[j] <= smallestSoFar) {
374			// smallestSoFar = shellRadii[j];
375			// myComponent = j;
376			// }
377			// }
378			// }
379			myComponent = 0;
380			componentFromSite[i] = myComponent;
381			nMol[myComponent]++;
382			// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
383			}
384			}
385			}
386			// cerr << "nMol = " << nMol.at(0) << "\n";
387
388			outputFileName = args_info.output_arg;
389
390			//creat new .md file on fly which corrects the number of molecule
391
392			createMdFile(inputFileName, outputFileName, nMol);
393
394	gezelter	1874	delete oldInfo;
395	kstocke1	1701
396			SimCreator newCreator;
397			SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
398
399			// Place molecules
400			Molecule* mol;
401			SimInfo::MoleculeIterator mi;
402			mol = NewInfo->beginMolecule(mi);
403
404			int l = 0;
405
406	gezelter	1876	for (unsigned int i = 0; i < nComponents; i++){
407	kstocke1	1701	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
408			NewInfo->getForceField());
409
410			// cerr << "nMol = " << nMol.at(i) << "\n";
411			if (!args_info.molFraction_given) {
412	gezelter	1876	for (unsigned int n = 0; n < sites.size(); n++) {
413	kstocke1	1701	if (!isVacancy[n]) {
414			if (componentFromSite[n] == i) {
415			mol = NewInfo->getMoleculeByGlobalIndex(l);
416			locator->placeMol(sites[n], orientations[n], mol);
417			l++;
418			}
419			}
420			}
421			} else {
422	gezelter	1876	for (unsigned int n = 0; n < nMol.at(i); n++) {
423	kstocke1	1701	mol = NewInfo->getMoleculeByGlobalIndex(l);
424			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
425			l++;
426			}
427			}
428			}
429
430			//fill Hmat
431			hmat(0, 0)= 10.0*rodRadius;
432			hmat(0, 1) = 0.0;
433			hmat(0, 2) = 0.0;
434
435			hmat(1, 0) = 0.0;
436			hmat(1, 1) = 10.0*rodRadius;
437			hmat(1, 2) = 0.0;
438
439			hmat(2, 0) = 0.0;
440			hmat(2, 1) = 0.0;
441			hmat(2, 2) = 5.0rodLength + 2.0rodRadius;
442
443			//set Hmat
444			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
445
446
447			//create dumpwriter and write out the coordinates
448			writer = new DumpWriter(NewInfo, outputFileName);
449
450			if (writer == NULL) {
451			sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
452			painCave.isFatal = 1;
453			simError();
454			}
455
456			writer->writeDump();
457
458			// deleting the writer will put the closing at the end of the dump file
459
460			delete writer;
461
462			// cleanup a by calling sim error.....
463			sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
464			"generated.\n", outputFileName.c_str());
465			painCave.isFatal = 0;
466			simError();
467			return 0;
468			}
469
470			void createMdFile(const std::string&oldMdFileName,
471			const std::string&newMdFileName,
472			std::vector<int> nMol) {
473			ifstream oldMdFile;
474			ofstream newMdFile;
475			const int MAXLEN = 65535;
476			char buffer[MAXLEN];
477
478			//create new .md file based on old .md file
479			oldMdFile.open(oldMdFileName.c_str());
480			newMdFile.open(newMdFileName.c_str());
481			oldMdFile.getline(buffer, MAXLEN);
482
483	gezelter	1876	unsigned int i = 0;
484	kstocke1	1701	while (!oldMdFile.eof()) {
485
486			//correct molecule number
487			if (strstr(buffer, "nMol") != NULL) {
488			if(i<nMol.size()){
489			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
490			newMdFile << buffer << std::endl;
491			i++;
492			}
493			} else
494			newMdFile << buffer << std::endl;
495
496			oldMdFile.getline(buffer, MAXLEN);
497			}
498
499			oldMdFile.close();
500			newMdFile.close();
501
502			if (i != nMol.size()) {
503			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
504			"\tstatements in component blocks. Make sure that all\n"
505			"\tcomponents in the template file have nMol=1");
506			painCave.isFatal = 1;
507			simError();
508			}
509
510			}
511