applications/nanoparticleBuilder/nanorod_pentBuilder.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 4/5/12.
 *  @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 "shapedLatticePentRod.hpp"
#include "nanorod_pentBuilderCmd.h"
#include "shapedLatticeRod.hpp"
#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/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 */
  shapedLatticePentRod nanoRod(latticeConstant, latticeType,
                           rodRadius, rodLength);
  
  /* Build a lattice and get lattice points for this lattice constant */

  //Rotation angles for lattice
  RealType phi, theta, psi;

  // RealType cphi, sphi, ctheta, stheta, cpsi, spsi;

    
  /*cphi = cos(phi);
  sphi = sin(phi);
  ctheta = cos(theta);
  stheta = sin(theta);
  cpsi = cos(psi);
  spsi = sin(psi);*/

  //Rotates 45 degrees about z-axis
  RotMat3x3d rotation45( 45.0 * M_PI / 180.0, 0.0, 0.0);
 
  /*rotation45[0][0] = sqrt(2)/2;
  rotation45[0][1] = -sqrt(2)/2;
  rotation45[0][2] = 0;
  rotation45[1][0] = sqrt(2)/2;
  rotation45[1][1] = sqrt(2)/2;
  rotation45[1][2] = 0;
  rotation45[2][0] = 0;
  rotation45[2][1] = 0;
  rotation45[2][2] = 1;*/

  phi =  0.0;
  theta = 72 * M_PI / 180.0;
  psi = 0.0;

  //Rotates 72 degrees about y-axis
  RotMat3x3d rotation72(phi, theta, psi);

  /*rotation72[0][0] = sqrt(5)/4 - 0.25;
  rotation72[0][1] = 0;
  rotation72[0][2] = sqrt(2*(sqrt(5) + 5))/4;
  rotation72[1][0] = 0;
  rotation72[1][1] = 1;
  rotation72[1][2] = 0;
  rotation72[2][0] = -sqrt(2*(sqrt(5) + 5))/4;
  rotation72[2][1] = 0;
  rotation72[2][2] = sqrt(5)/4 - 0.25;*/

  vector<Vector3d> getsites = nanoRod.getSites();
  vector<Vector3d> getorientations = nanoRod.getOrientations();
  vector<Vector3d> sites;
  vector<Vector3d> orientations;

  for (unsigned int index = 0; index < getsites.size(); index++) {
    Vector3d mySite = getsites[index];
    Vector3d myOrient = getorientations[index];
    Vector3d mySite2 = rotation45 * mySite;
    Vector3d o2 = rotation45 * myOrient;
    sites.push_back(  mySite2 );
    orientations.push_back( o2 );

    mySite2 = rotation72 * mySite2;
    o2 = rotation72 * o2;
    sites.push_back( mySite2 );
    orientations.push_back( o2 );

    mySite2 = rotation72 * mySite2;
    o2 = rotation72 * o2;
    sites.push_back( mySite2 );
    orientations.push_back( o2 );

    mySite2 = rotation72 * mySite2;
    o2 = rotation72 * o2;
    sites.push_back( mySite2 );
    orientations.push_back( o2 );

    mySite2 = rotation72 * mySite2;
    o2 = rotation72 * o2;
    sites.push_back( mySite2 );
    orientations.push_back( o2 );
  }

  int nCenter = int( (rodLength + 1.154700538*rodRadius)/2.88 );

  for (unsigned int index = 0; index <= 0.5*nCenter; index++) {
    Vector3d myLoc_top(2.88*index, 0.0, 0.0);
    sites.push_back(myLoc_top);
    orientations.push_back(Vector3d(0.0));
  }

  for (unsigned int index = 1; index <= 0.5*nCenter; index++) {
    Vector3d myLoc_bottom(-2.88*index, 0.0, 0.0);
    sites.push_back(myLoc_bottom);
    orientations.push_back(Vector3d(0.0));
  }

  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<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 (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 (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 (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:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (12 years, 7 months ago) by gezelter
File size:	18412 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 4/5/12.
42			* @author Kelsey M. Stocker
43			*
44			*/
45
46
47
48			#include <cstdlib>
49			#include <cstdio>
50			#include <cstring>
51			#include <cmath>
52			#include <iostream>
53			#include <string>
54			#include <map>
55			#include <fstream>
56			#include <algorithm>
57
58			#include "config.h"
59			#include "shapedLatticePentRod.hpp"
60			#include "nanorod_pentBuilderCmd.h"
61			#include "shapedLatticeRod.hpp"
62			#include "lattice/LatticeFactory.hpp"
63			#include "utils/MoLocator.hpp"
64			#include "lattice/Lattice.hpp"
65			#include "brains/Register.hpp"
66			#include "brains/SimInfo.hpp"
67			#include "brains/SimCreator.hpp"
68			#include "io/DumpWriter.hpp"
69			#include "math/SquareMatrix3.hpp"
70			#include "utils/StringUtils.hpp"
71
72			using namespace std;
73			using namespace OpenMD;
74			void createMdFile(const std::string&oldMdFileName,
75			const std::string&newMdFileName,
76			std::vector<int> numMol);
77
78			int main(int argc, char *argv []) {
79
80			registerLattice();
81
82			gengetopt_args_info args_info;
83			std::string latticeType;
84			std::string inputFileName;
85			std::string outputFileName;
86
87			MoLocator* locator;
88			int nComponents;
89			double latticeConstant;
90			std::vector<double> lc;
91
92			RealType rodRadius;
93			RealType rodLength;
94
95			Mat3x3d hmat;
96			std::vector<Vector3d> latticePos;
97			std::vector<Vector3d> latticeOrt;
98
99			DumpWriter *writer;
100
101			// Parse Command Line Arguments
102			if (cmdline_parser(argc, argv, &args_info) != 0)
103			exit(1);
104
105			/* get lattice type */
106			latticeType = "FCC";
107
108			/* get input file name */
109			if (args_info.inputs_num)
110			inputFileName = args_info.inputs[0];
111			else {
112			sprintf(painCave.errMsg, "No input .md file name was specified "
113			"on the command line");
114			painCave.isFatal = 1;
115			cmdline_parser_print_help();
116			simError();
117			}
118
119			/* parse md file and set up the system */
120			SimCreator oldCreator;
121			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
122
123			latticeConstant = args_info.latticeConstant_arg;
124			rodRadius = args_info.radius_arg;
125			rodLength = args_info.length_arg;
126			Globals* simParams = oldInfo->getSimParams();
127
128			/* Create nanorod */
129			shapedLatticePentRod nanoRod(latticeConstant, latticeType,
130			rodRadius, rodLength);
131
132			/* Build a lattice and get lattice points for this lattice constant */
133
134			//Rotation angles for lattice
135			RealType phi, theta, psi;
136
137	gezelter	1830	// RealType cphi, sphi, ctheta, stheta, cpsi, spsi;
138	kstocke1	1701
139
140			/*cphi = cos(phi);
141			sphi = sin(phi);
142			ctheta = cos(theta);
143			stheta = sin(theta);
144			cpsi = cos(psi);
145			spsi = sin(psi);*/
146
147			//Rotates 45 degrees about z-axis
148			RotMat3x3d rotation45( 45.0 * M_PI / 180.0, 0.0, 0.0);
149
150			/*rotation45[0][0] = sqrt(2)/2;
151			rotation45[0][1] = -sqrt(2)/2;
152			rotation45[0][2] = 0;
153			rotation45[1][0] = sqrt(2)/2;
154			rotation45[1][1] = sqrt(2)/2;
155			rotation45[1][2] = 0;
156			rotation45[2][0] = 0;
157			rotation45[2][1] = 0;
158			rotation45[2][2] = 1;*/
159
160			phi = 0.0;
161			theta = 72 * M_PI / 180.0;
162			psi = 0.0;
163
164			//Rotates 72 degrees about y-axis
165			RotMat3x3d rotation72(phi, theta, psi);
166
167			/*rotation72[0][0] = sqrt(5)/4 - 0.25;
168			rotation72[0][1] = 0;
169			rotation72[0][2] = sqrt(2*(sqrt(5) + 5))/4;
170			rotation72[1][0] = 0;
171			rotation72[1][1] = 1;
172			rotation72[1][2] = 0;
173			rotation72[2][0] = -sqrt(2*(sqrt(5) + 5))/4;
174			rotation72[2][1] = 0;
175			rotation72[2][2] = sqrt(5)/4 - 0.25;*/
176
177			vector<Vector3d> getsites = nanoRod.getSites();
178			vector<Vector3d> getorientations = nanoRod.getOrientations();
179			vector<Vector3d> sites;
180			vector<Vector3d> orientations;
181
182	gezelter	1830	for (unsigned int index = 0; index < getsites.size(); index++) {
183	kstocke1	1701	Vector3d mySite = getsites[index];
184			Vector3d myOrient = getorientations[index];
185			Vector3d mySite2 = rotation45 * mySite;
186			Vector3d o2 = rotation45 * myOrient;
187			sites.push_back( mySite2 );
188			orientations.push_back( o2 );
189
190			mySite2 = rotation72 * mySite2;
191			o2 = rotation72 * o2;
192			sites.push_back( mySite2 );
193			orientations.push_back( o2 );
194
195			mySite2 = rotation72 * mySite2;
196			o2 = rotation72 * o2;
197			sites.push_back( mySite2 );
198			orientations.push_back( o2 );
199
200			mySite2 = rotation72 * mySite2;
201			o2 = rotation72 * o2;
202			sites.push_back( mySite2 );
203			orientations.push_back( o2 );
204
205			mySite2 = rotation72 * mySite2;
206			o2 = rotation72 * o2;
207			sites.push_back( mySite2 );
208			orientations.push_back( o2 );
209			}
210
211	gezelter	1830	int nCenter = int( (rodLength + 1.154700538*rodRadius)/2.88 );
212	kstocke1	1701
213	gezelter	1830	for (unsigned int index = 0; index <= 0.5*nCenter; index++) {
214	kstocke1	1701	Vector3d myLoc_top(2.88*index, 0.0, 0.0);
215			sites.push_back(myLoc_top);
216			orientations.push_back(Vector3d(0.0));
217			}
218
219	gezelter	1830	for (unsigned int index = 1; index <= 0.5*nCenter; index++) {
220	kstocke1	1701	Vector3d myLoc_bottom(-2.88*index, 0.0, 0.0);
221			sites.push_back(myLoc_bottom);
222			orientations.push_back(Vector3d(0.0));
223			}
224
225			std::vector<int> vacancyTargets;
226			vector<bool> isVacancy;
227
228			Vector3d myLoc;
229			RealType myR;
230
231	gezelter	1830	for (unsigned int i = 0; i < sites.size(); i++)
232	kstocke1	1701	isVacancy.push_back(false);
233
234			// cerr << "checking vacancyPercent" << "\n";
235			if (args_info.vacancyPercent_given) {
236			// cerr << "vacancyPercent given" << "\n";
237			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
238			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
239			painCave.isFatal = 1;
240			simError();
241			} else {
242			RealType vF = args_info.vacancyPercent_arg / 100.0;
243			// cerr << "vacancyPercent = " << vF << "\n";
244			RealType vIR;
245			RealType vOR;
246			if (args_info.vacancyInnerRadius_given) {
247			vIR = args_info.vacancyInnerRadius_arg;
248			} else {
249			vIR = 0.0;
250			}
251			if (args_info.vacancyOuterRadius_given) {
252			vOR = args_info.vacancyOuterRadius_arg;
253			} else {
254			vOR = rodRadius;
255			}
256			if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
257
258	gezelter	1830	for (unsigned int i = 0; i < sites.size(); i++) {
259	kstocke1	1701	myLoc = sites[i];
260			myR = myLoc.length();
261			if (myR >= vIR && myR <= vOR) {
262			vacancyTargets.push_back(i);
263			}
264			}
265			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
266
267			int nTargets = vacancyTargets.size();
268			vacancyTargets.resize((int)(vF * nTargets));
269
270
271			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
272			"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
273			vIR, vOR);
274			painCave.isFatal = 0;
275			simError();
276
277			isVacancy.clear();
278	gezelter	1830	for (unsigned int i = 0; i < sites.size(); i++) {
279	kstocke1	1701	bool vac = false;
280	gezelter	1830	for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
281	kstocke1	1701	if (i == vacancyTargets[j]) vac = true;
282			}
283			isVacancy.push_back(vac);
284			}
285
286			} else {
287			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
288			"\tinner or outer radii. Check their values.");
289			painCave.isFatal = 1;
290			simError();
291			}
292			}
293			}
294
295			/* Get number of lattice sites */
296			int nSites = sites.size() - vacancyTargets.size();
297
298			// cerr << "sites.size() = " << sites.size() << "\n";
299			// cerr << "nSites = " << nSites << "\n";
300			// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";
301
302			std::vector<Component*> components = simParams->getComponents();
303			std::vector<RealType> molFractions;
304			std::vector<RealType> shellRadii;
305			std::vector<RealType> molecularMasses;
306			std::vector<int> nMol;
307			std::map<int, int> componentFromSite;
308			nComponents = components.size();
309			// cerr << "nComponents = " << nComponents << "\n";
310
311			if (args_info.molFraction_given && args_info.shellRadius_given) {
312			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
313			"arguments, but not both!");
314			painCave.isFatal = 1;
315			simError();
316			}
317
318			if (nComponents == 1) {
319			molFractions.push_back(1.0);
320			shellRadii.push_back(rodRadius);
321			} else if (args_info.molFraction_given) {
322			if ((int)args_info.molFraction_given == nComponents) {
323			for (int i = 0; i < nComponents; i++) {
324			molFractions.push_back(args_info.molFraction_arg[i]);
325			}
326			} else if ((int)args_info.molFraction_given == nComponents-1) {
327			RealType remainingFraction = 1.0;
328			for (int i = 0; i < nComponents-1; i++) {
329			molFractions.push_back(args_info.molFraction_arg[i]);
330			remainingFraction -= molFractions[i];
331			}
332			molFractions.push_back(remainingFraction);
333			} else {
334			sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
335			"for all of the components in the <MetaData> block.");
336			painCave.isFatal = 1;
337			simError();
338			}
339			} else if ((int)args_info.shellRadius_given) {
340			if ((int)args_info.shellRadius_given == nComponents) {
341			for (int i = 0; i < nComponents; i++) {
342			shellRadii.push_back(args_info.shellRadius_arg[i]);
343			}
344			} else if ((int)args_info.shellRadius_given == nComponents-1) {
345			for (int i = 0; i < nComponents-1; i++) {
346			shellRadii.push_back(args_info.shellRadius_arg[i]);
347			}
348			shellRadii.push_back(rodRadius);
349			} else {
350			sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
351			"\tshell radii for all of the components in the <MetaData> block.");
352			painCave.isFatal = 1;
353			simError();
354			}
355			} else {
356			sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
357			"\tbut have not specified either molFraction or shellRadius arguments.");
358			painCave.isFatal = 1;
359			simError();
360			}
361
362			if (args_info.molFraction_given) {
363			RealType totalFraction = 0.0;
364
365			/* Do some simple sanity checking*/
366
367			for (int i = 0; i < nComponents; i++) {
368			if (molFractions.at(i) < 0.0) {
369			sprintf(painCave.errMsg, "One of the requested molFractions was"
370			" less than zero!");
371			painCave.isFatal = 1;
372			simError();
373			}
374			if (molFractions.at(i) > 1.0) {
375			sprintf(painCave.errMsg, "One of the requested molFractions was"
376			" greater than one!");
377			painCave.isFatal = 1;
378			simError();
379			}
380			totalFraction += molFractions.at(i);
381			}
382			if (abs(totalFraction - 1.0) > 1e-6) {
383			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
384			painCave.isFatal = 1;
385			simError();
386			}
387
388			int remaining = nSites;
389			for (int i=0; i < nComponents-1; i++) {
390			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
391			remaining -= nMol.at(i);
392			}
393			nMol.push_back(remaining);
394
395			// recompute actual mol fractions and perform final sanity check:
396
397			int totalMolecules = 0;
398			for (int i=0; i < nComponents; i++) {
399			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
400			totalMolecules += nMol.at(i);
401			}
402			if (totalMolecules != nSites) {
403			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
404			"to the number of lattice sites!");
405			painCave.isFatal = 1;
406			simError();
407			}
408			} else {
409
410	gezelter	1830	for (unsigned int i = 0; i < shellRadii.size(); i++) {
411	kstocke1	1701	if (shellRadii.at(i) > rodRadius + 1e-6 ) {
412			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius.");
413			painCave.isFatal = 1;
414			simError();
415			}
416			if (shellRadii.at(i) <= 0.0 ) {
417			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
418			painCave.isFatal = 1;
419			simError();
420			}
421			}
422			}
423
424			vector<int> ids;
425			if ((int)args_info.molFraction_given){
426			// cerr << "molFraction given 2" << "\n";
427			sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod.");
428			painCave.isFatal = 0;
429			simError();
430			/* Random rod is the default case*/
431
432	gezelter	1830	for (unsigned int i = 0; i < sites.size(); i++)
433	kstocke1	1701	if (!isVacancy[i]) ids.push_back(i);
434
435			std::random_shuffle(ids.begin(), ids.end());
436
437			} else{
438			sprintf(painCave.errMsg, "Creating an fcc nanorod.");
439			painCave.isFatal = 0;
440			simError();
441
442	gezelter	1798	// RealType smallestSoFar;
443	kstocke1	1701	int myComponent = -1;
444			nMol.clear();
445			nMol.resize(nComponents);
446
447			// cerr << "shellRadii[0] " << shellRadii[0] << "\n";
448			// cerr << "rodRadius " << rodRadius << "\n";
449
450	gezelter	1830	for (unsigned int i = 0; i < sites.size(); i++) {
451	kstocke1	1701	myLoc = sites[i];
452			myR = myLoc.length();
453	gezelter	1798	// smallestSoFar = rodRadius;
454			// cerr << "vac = " << isVacancy[i]<< "\n";
455	kstocke1	1701
456			if (!isVacancy[i]) {
457
458
459			// for (int j = 0; j < nComponents; j++) {
460			// if (myR <= shellRadii[j]) {
461			// if (shellRadii[j] <= smallestSoFar) {
462			// smallestSoFar = shellRadii[j];
463			// myComponent = j;
464			// }
465			// }
466			// }
467			myComponent = 0;
468			componentFromSite[i] = myComponent;
469			nMol[myComponent]++;
470			// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
471			}
472			}
473			}
474			// cerr << "nMol = " << nMol.at(0) << "\n";
475
476			outputFileName = args_info.output_arg;
477
478			//creat new .md file on fly which corrects the number of molecule
479
480			createMdFile(inputFileName, outputFileName, nMol);
481
482	gezelter	1874	delete oldInfo;
483	kstocke1	1701
484			SimCreator newCreator;
485			SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
486
487			// Place molecules
488			Molecule* mol;
489			SimInfo::MoleculeIterator mi;
490			mol = NewInfo->beginMolecule(mi);
491
492			int l = 0;
493
494			for (int i = 0; i < nComponents; i++){
495			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
496			NewInfo->getForceField());
497
498			// cerr << "nMol = " << nMol.at(i) << "\n";
499			if (!args_info.molFraction_given) {
500	gezelter	1830	for (unsigned int n = 0; n < sites.size(); n++) {
501	kstocke1	1701	if (!isVacancy[n]) {
502			if (componentFromSite[n] == i) {
503			mol = NewInfo->getMoleculeByGlobalIndex(l);
504			locator->placeMol(sites[n], orientations[n], mol);
505			l++;
506			}
507			}
508			}
509			} else {
510			for (int n = 0; n < nMol.at(i); n++) {
511			mol = NewInfo->getMoleculeByGlobalIndex(l);
512			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
513			l++;
514			}
515			}
516			}
517
518			//fill Hmat
519			hmat(0, 0)= 10.0*rodRadius;
520			hmat(0, 1) = 0.0;
521			hmat(0, 2) = 0.0;
522
523			hmat(1, 0) = 0.0;
524			hmat(1, 1) = 10.0*rodRadius;
525			hmat(1, 2) = 0.0;
526
527			hmat(2, 0) = 0.0;
528			hmat(2, 1) = 0.0;
529			hmat(2, 2) = 5.0rodLength + 2.0rodRadius;
530
531			//set Hmat
532			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
533
534
535			//create dumpwriter and write out the coordinates
536			writer = new DumpWriter(NewInfo, outputFileName);
537
538			if (writer == NULL) {
539			sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
540			painCave.isFatal = 1;
541			simError();
542			}
543
544			writer->writeDump();
545
546			// deleting the writer will put the closing at the end of the dump file
547
548			delete writer;
549
550			// cleanup a by calling sim error.....
551			sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
552			"generated.\n", outputFileName.c_str());
553			painCave.isFatal = 0;
554			simError();
555			return 0;
556			}
557
558			void createMdFile(const std::string&oldMdFileName,
559			const std::string&newMdFileName,
560			std::vector<int> nMol) {
561			ifstream oldMdFile;
562			ofstream newMdFile;
563			const int MAXLEN = 65535;
564			char buffer[MAXLEN];
565
566			//create new .md file based on old .md file
567			oldMdFile.open(oldMdFileName.c_str());
568			newMdFile.open(newMdFileName.c_str());
569			oldMdFile.getline(buffer, MAXLEN);
570
571	gezelter	1830	unsigned int i = 0;
572	kstocke1	1701	while (!oldMdFile.eof()) {
573
574			//correct molecule number
575			if (strstr(buffer, "nMol") != NULL) {
576			if(i<nMol.size()){
577			sprintf(buffer, "\tnMol = %i;", nMol.at(i));
578			newMdFile << buffer << std::endl;
579			i++;
580			}
581			} else
582			newMdFile << buffer << std::endl;
583
584			oldMdFile.getline(buffer, MAXLEN);
585			}
586
587			oldMdFile.close();
588			newMdFile.close();
589
590			if (i != nMol.size()) {
591			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
592			"\tstatements in component blocks. Make sure that all\n"
593			"\tcomponents in the template file have nMol=1");
594			painCave.isFatal = 1;
595			simError();
596			}
597
598			}
599