applications/nanoparticleBuilder/nanoparticleBuilder.cpp

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

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

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

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

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

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

  RealType particleRadius;

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

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

  if (args_info.vacancyPercent_given) {
    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;
      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 = particleRadius;
      }
      if (vIR >= 0.0 && vOR <= particleRadius && 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.", 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();

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

  if (args_info.molFraction_given && args_info.shellRadius_given) {
    sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
            "arguments, but not both!");
    painCave.isFatal = 1;
    simError();
  }
  
  if (nComponents == 1) {
    molFractions.push_back(1.0);    
    shellRadii.push_back(particleRadius);
  } else if (args_info.molFraction_given) {
    if ((int)args_info.molFraction_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
      }
    } else if ((int)args_info.molFraction_given == nComponents-1) {
      RealType remainingFraction = 1.0;
      for (int i = 0; i < nComponents-1; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
        remainingFraction -= molFractions[i];
      }
      molFractions.push_back(remainingFraction);
    } else {    
      sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
              "for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  } else if ((int)args_info.shellRadius_given) {
    if ((int)args_info.shellRadius_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        shellRadii.push_back(args_info.shellRadius_arg[i]);
      }
    } else if ((int)args_info.shellRadius_given == nComponents-1) {
      for (int i = 0; i < nComponents-1; i++) {
        shellRadii.push_back(args_info.shellRadius_arg[i]);
      }
      shellRadii.push_back(particleRadius);
    } else {    
      sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\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) > particleRadius + 1e-6 ) {
        sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
        painCave.isFatal = 1;
        simError();
      } 
      if (shellRadii.at(i) <= 0.0 ) {
        sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
        painCave.isFatal = 1;
        simError();
      }
    }
  }

  vector<int> ids;           
  if ((int)args_info.molFraction_given){
    sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
    painCave.isFatal = 0;
    simError();
    /* Random particle 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 a core-shell spherical nanoparticle.");
    painCave.isFatal = 0;
    simError();

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

    for (int i = 0; i < sites.size(); i++) {
      myLoc = sites[i];
      myR = myLoc.length();
      smallestSoFar = particleRadius;      
      if (!isVacancy[i]) {
        for (int j = 0; j < nComponents; j++) {
          if (myR <= shellRadii[j]) {
            if (shellRadii[j] <= smallestSoFar) {
              smallestSoFar = shellRadii[j];
              myComponent = j;
            }
          }
        }
        componentFromSite[i] = myComponent;
        nMol[myComponent]++;
      }
    }       
  }
  
  outputFileName = args_info.output_arg;
   
  //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outputFileName, nMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
    
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);

  int l = 0;
  int whichSite = 0;

  for (int i = 0; i < nComponents; i++){
    locator = new MoLocator(NewInfo->getMoleculeStamp(i), 
                            NewInfo->getForceField());
    
    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*particleRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) =  10.0*particleRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) =  10.0*particleRadius;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  writer = new DumpWriter(NewInfo, outputFileName);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating 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 OOPSE MD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  std::vector<int> nMol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  
  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
  oldMdFile.getline(buffer, MAXLEN);

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

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

  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:	1077
Committed:	Wed Oct 18 19:35:07 2006 UTC (19 years ago) by gezelter
Original Path:	*trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp*
File size:	15122 byte(s)
Log Message:	bug fixes for vacancies
#	User	Rev	Content
1	chuckv	653	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <cstdlib>
43			#include <cstdio>
44			#include <cstring>
45			#include <cmath>
46			#include <iostream>
47			#include <string>
48			#include <map>
49			#include <fstream>
50	chuckv	911	#include <algorithm>
51	chuckv	653
52			#include "config.h"
53	chuckv	911	#include "shapedLatticeSpherical.hpp"
54	chuckv	653	#include "nanoparticleBuilderCmd.h"
55			#include "lattice/LatticeFactory.hpp"
56			#include "utils/MoLocator.hpp"
57			#include "lattice/Lattice.hpp"
58			#include "brains/Register.hpp"
59			#include "brains/SimInfo.hpp"
60			#include "brains/SimCreator.hpp"
61			#include "io/DumpWriter.hpp"
62			#include "math/Vector3.hpp"
63			#include "math/SquareMatrix3.hpp"
64			#include "utils/StringUtils.hpp"
65
66			using namespace std;
67			using namespace oopse;
68			void createMdFile(const std::string&oldMdFileName,
69			const std::string&newMdFileName,
70	chuckv	1069	std::vector<int> numMol);
71	chuckv	653
72			int main(int argc, char *argv []) {
73
74			//register force fields
75			registerForceFields();
76			registerLattice();
77
78			gengetopt_args_info args_info;
79			std::string latticeType;
80			std::string inputFileName;
81	chuckv	1069	std::string outputFileName;
82	chuckv	653
83	chuckv	911	MoLocator* locator;
84			int nComponents;
85	chuckv	653	double latticeConstant;
86			std::vector<double> lc;
87	gezelter	1075
88	gezelter	1077	RealType particleRadius;
89	chuckv	653
90			Mat3x3d hmat;
91			std::vector<Vector3d> latticePos;
92			std::vector<Vector3d> latticeOrt;
93	chuckv	1069
94	chuckv	653	DumpWriter *writer;
95
96	chuckv	875	// Parse Command Line Arguments
97	chuckv	653	if (cmdline_parser(argc, argv, &args_info) != 0)
98			exit(1);
99	gezelter	1070
100	chuckv	653	/* get lattice type */
101	chuckv	1069	latticeType = "FCC";
102
103	chuckv	653	/* get input file name */
104			if (args_info.inputs_num)
105			inputFileName = args_info.inputs[0];
106			else {
107	gezelter	1077	sprintf(painCave.errMsg, "No input .md file name was specified "
108	gezelter	1075	"on the command line");
109	chuckv	1069	painCave.isFatal = 1;
110	chuckv	653	cmdline_parser_print_help();
111	chuckv	1069	simError();
112	chuckv	653	}
113
114			/* parse md file and set up the system */
115			SimCreator oldCreator;
116			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
117
118	gezelter	1077	latticeConstant = args_info.latticeConstant_arg;
119	chuckv	653	particleRadius = args_info.radius_arg;
120	chuckv	911	Globals* simParams = oldInfo->getSimParams();
121	chuckv	653
122	chuckv	911	/* Create nanoparticle */
123	gezelter	1070	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
124			particleRadius);
125	chuckv	918
126	chuckv	911	/* Build a lattice and get lattice points for this lattice constant */
127	gezelter	1070	vector<Vector3d> sites = nanoParticle.getSites();
128			vector<Vector3d> orientations = nanoParticle.getOrientations();
129	gezelter	1077	std::vector<int> vacancyTargets;
130			vector<bool> isVacancy;
131
132			Vector3d myLoc;
133			RealType myR;
134
135			for (int i = 0; i < sites.size(); i++)
136			isVacancy.push_back(false);
137	chuckv	1069
138	gezelter	1077	if (args_info.vacancyPercent_given) {
139			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
140			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
141			painCave.isFatal = 1;
142			simError();
143			} else {
144			RealType vF = args_info.vacancyPercent_arg / 100.0;
145			RealType vIR;
146			RealType vOR;
147			if (args_info.vacancyInnerRadius_given) {
148			vIR = args_info.vacancyInnerRadius_arg;
149			} else {
150			vIR = 0.0;
151			}
152			if (args_info.vacancyOuterRadius_given) {
153			vOR = args_info.vacancyOuterRadius_arg;
154			} else {
155			vOR = particleRadius;
156			}
157			if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
158
159			for (int i = 0; i < sites.size(); i++) {
160			myLoc = sites[i];
161			myR = myLoc.length();
162			if (myR >= vIR && myR <= vOR) {
163			vacancyTargets.push_back(i);
164			}
165			}
166			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
167
168			int nTargets = vacancyTargets.size();
169			vacancyTargets.resize((int)(vF * nTargets));
170
171
172			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
173			"\tsites between %lf and %lf.", vacancyTargets.size(),
174			vIR, vOR);
175			painCave.isFatal = 0;
176			simError();
177	chuckv	1069
178	gezelter	1077	isVacancy.clear();
179			for (int i = 0; i < sites.size(); i++) {
180			bool vac = false;
181			for (int j = 0; j < vacancyTargets.size(); j++) {
182			if (i == vacancyTargets[j]) vac = true;
183			}
184			isVacancy.push_back(vac);
185			}
186
187			} else {
188			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
189			"\tinner or outer radii. Check their values.");
190			painCave.isFatal = 1;
191			simError();
192			}
193			}
194			}
195
196	chuckv	911	/* Get number of lattice sites */
197	gezelter	1077	int nSites = sites.size() - vacancyTargets.size();
198	chuckv	1069
199			std::vector<Component*> components = simParams->getComponents();
200			std::vector<RealType> molFractions;
201	gezelter	1075	std::vector<RealType> shellRadii;
202	chuckv	1069	std::vector<RealType> molecularMasses;
203			std::vector<int> nMol;
204	gezelter	1075	std::map<int, int> componentFromSite;
205	chuckv	1069	nComponents = components.size();
206
207	gezelter	1077	if (args_info.molFraction_given && args_info.shellRadius_given) {
208			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
209	gezelter	1075	"arguments, but not both!");
210			painCave.isFatal = 1;
211			simError();
212			}
213
214			if (nComponents == 1) {
215	chuckv	1069	molFractions.push_back(1.0);
216	gezelter	1075	shellRadii.push_back(particleRadius);
217			} else if (args_info.molFraction_given) {
218			if ((int)args_info.molFraction_given == nComponents) {
219			for (int i = 0; i < nComponents; i++) {
220			molFractions.push_back(args_info.molFraction_arg[i]);
221			}
222			} else if ((int)args_info.molFraction_given == nComponents-1) {
223			RealType remainingFraction = 1.0;
224			for (int i = 0; i < nComponents-1; i++) {
225			molFractions.push_back(args_info.molFraction_arg[i]);
226			remainingFraction -= molFractions[i];
227			}
228			molFractions.push_back(remainingFraction);
229			} else {
230			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
231			"for all of the components in the <MetaData> block.");
232	chuckv	1069	painCave.isFatal = 1;
233			simError();
234			}
235	gezelter	1077	} else if ((int)args_info.shellRadius_given) {
236			if ((int)args_info.shellRadius_given == nComponents) {
237	gezelter	1075	for (int i = 0; i < nComponents; i++) {
238	gezelter	1077	shellRadii.push_back(args_info.shellRadius_arg[i]);
239	gezelter	1075	}
240	gezelter	1077	} else if ((int)args_info.shellRadius_given == nComponents-1) {
241	gezelter	1075	for (int i = 0; i < nComponents-1; i++) {
242	gezelter	1077	shellRadii.push_back(args_info.shellRadius_arg[i]);
243	gezelter	1075	}
244			shellRadii.push_back(particleRadius);
245			} else {
246	gezelter	1077	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
247			"\tshell radii for all of the components in the <MetaData> block.");
248	chuckv	1069	painCave.isFatal = 1;
249			simError();
250			}
251	gezelter	1075	} else {
252	gezelter	1077	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
253			"\tbut have not specified either molFraction or shellRadius arguments.");
254	chuckv	1069	painCave.isFatal = 1;
255			simError();
256			}
257	gezelter	1075
258			if (args_info.molFraction_given) {
259			RealType totalFraction = 0.0;
260
261			/* Do some simple sanity checking*/
262
263			for (int i = 0; i < nComponents; i++) {
264			if (molFractions.at(i) < 0.0) {
265			sprintf(painCave.errMsg, "One of the requested molFractions was"
266			" less than zero!");
267			painCave.isFatal = 1;
268			simError();
269			}
270			if (molFractions.at(i) > 1.0) {
271			sprintf(painCave.errMsg, "One of the requested molFractions was"
272			" greater than one!");
273			painCave.isFatal = 1;
274			simError();
275			}
276			totalFraction += molFractions.at(i);
277			}
278			if (abs(totalFraction - 1.0) > 1e-6) {
279			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
280			painCave.isFatal = 1;
281			simError();
282			}
283
284			int remaining = nSites;
285			for (int i=0; i < nComponents-1; i++) {
286			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
287			remaining -= nMol.at(i);
288			}
289			nMol.push_back(remaining);
290
291			// recompute actual mol fractions and perform final sanity check:
292
293			int totalMolecules = 0;
294			for (int i=0; i < nComponents; i++) {
295			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
296			totalMolecules += nMol.at(i);
297			}
298
299			if (totalMolecules != nSites) {
300			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
301			"to the number of lattice sites!");
302			painCave.isFatal = 1;
303			simError();
304			}
305			} else {
306	chuckv	1069
307	gezelter	1075	for (int i = 0; i < shellRadii.size(); i++) {
308			if (shellRadii.at(i) > particleRadius + 1e-6 ) {
309			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
310			painCave.isFatal = 1;
311			simError();
312			}
313			if (shellRadii.at(i) <= 0.0 ) {
314			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
315			painCave.isFatal = 1;
316			simError();
317			}
318			}
319	chuckv	1069	}
320	gezelter	1077
321			vector<int> ids;
322	gezelter	1075	if ((int)args_info.molFraction_given){
323			sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
324			painCave.isFatal = 0;
325			simError();
326	gezelter	1077	/* Random particle is the default case*/
327
328			for (int i = 0; i < sites.size(); i++)
329			if (!isVacancy[i]) ids.push_back(i);
330
331	chuckv	1069	std::random_shuffle(ids.begin(), ids.end());
332	gezelter	1077
333	gezelter	1075	} else{
334			sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
335			painCave.isFatal = 0;
336			simError();
337	chuckv	653
338	gezelter	1075	RealType smallestSoFar;
339			int myComponent = -1;
340			nMol.clear();
341			nMol.resize(nComponents);
342
343			for (int i = 0; i < sites.size(); i++) {
344			myLoc = sites[i];
345			myR = myLoc.length();
346	gezelter	1077	smallestSoFar = particleRadius;
347			if (!isVacancy[i]) {
348			for (int j = 0; j < nComponents; j++) {
349			if (myR <= shellRadii[j]) {
350			if (shellRadii[j] <= smallestSoFar) {
351			smallestSoFar = shellRadii[j];
352			myComponent = j;
353			}
354	gezelter	1075	}
355			}
356	gezelter	1077	componentFromSite[i] = myComponent;
357			nMol[myComponent]++;
358	gezelter	1075	}
359	gezelter	1077	}
360			}
361	chuckv	949
362	chuckv	1069	outputFileName = args_info.output_arg;
363	gezelter	1077
364	gezelter	1075	//creat new .md file on fly which corrects the number of molecule
365	chuckv	1069	createMdFile(inputFileName, outputFileName, nMol);
366	chuckv	653
367			if (oldInfo != NULL)
368			delete oldInfo;
369
370	chuckv	949	SimCreator newCreator;
371	chuckv	1069	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
372	gezelter	1075
373	chuckv	911	// Place molecules
374	chuckv	653	Molecule* mol;
375			SimInfo::MoleculeIterator mi;
376			mol = NewInfo->beginMolecule(mi);
377	gezelter	1077
378	chuckv	949	int l = 0;
379	gezelter	1077	int whichSite = 0;
380	chuckv	1069
381			for (int i = 0; i < nComponents; i++){
382			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
383			NewInfo->getForceField());
384	gezelter	1077
385			if (!args_info.molFraction_given) {
386	gezelter	1075	for (int n = 0; n < sites.size(); n++) {
387	gezelter	1077	if (!isVacancy[n]) {
388			if (componentFromSite[n] == i) {
389			mol = NewInfo->getMoleculeByGlobalIndex(l);
390			locator->placeMol(sites[n], orientations[n], mol);
391			l++;
392			}
393	gezelter	1075	}
394			}
395			} else {
396			for (int n = 0; n < nMol.at(i); n++) {
397			mol = NewInfo->getMoleculeByGlobalIndex(l);
398			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
399			l++;
400			}
401	chuckv	1069	}
402	gezelter	1077	}
403	chuckv	653
404			//fill Hmat
405	gezelter	1075	hmat(0, 0)= 10.0*particleRadius;
406	chuckv	653	hmat(0, 1) = 0.0;
407			hmat(0, 2) = 0.0;
408
409			hmat(1, 0) = 0.0;
410	gezelter	1075	hmat(1, 1) = 10.0*particleRadius;
411	chuckv	653	hmat(1, 2) = 0.0;
412
413			hmat(2, 0) = 0.0;
414			hmat(2, 1) = 0.0;
415	gezelter	1075	hmat(2, 2) = 10.0*particleRadius;
416	chuckv	653
417			//set Hmat
418			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
419
420
421			//create dumpwriter and write out the coordinates
422	gezelter	1070	writer = new DumpWriter(NewInfo, outputFileName);
423	chuckv	653
424			if (writer == NULL) {
425	gezelter	1077	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
426	gezelter	1075	painCave.isFatal = 1;
427			simError();
428	chuckv	653	}
429
430			writer->writeDump();
431	chuckv	1069
432			// deleting the writer will put the closing at the end of the dump file
433	gezelter	1070
434	chuckv	1069	delete writer;
435
436			// cleanup a by calling sim error.....
437			sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
438			"generated.\n", outputFileName.c_str());
439			painCave.isFatal = 0;
440			simError();
441	chuckv	653	return 0;
442			}
443
444	gezelter	1075	void createMdFile(const std::string&oldMdFileName,
445			const std::string&newMdFileName,
446	chuckv	1069	std::vector<int> nMol) {
447	chuckv	653	ifstream oldMdFile;
448			ofstream newMdFile;
449			const int MAXLEN = 65535;
450			char buffer[MAXLEN];
451
452			//create new .md file based on old .md file
453			oldMdFile.open(oldMdFileName.c_str());
454			newMdFile.open(newMdFileName.c_str());
455			oldMdFile.getline(buffer, MAXLEN);
456	gezelter	1077
457	chuckv	911	int i = 0;
458	chuckv	653	while (!oldMdFile.eof()) {
459	gezelter	1077
460	chuckv	653	//correct molecule number
461			if (strstr(buffer, "nMol") != NULL) {
462	chuckv	1069	if(i<nMol.size()){
463	gezelter	1077	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
464	chuckv	949	newMdFile << buffer << std::endl;
465			i++;
466			}
467	chuckv	653	} else
468			newMdFile << buffer << std::endl;
469
470			oldMdFile.getline(buffer, MAXLEN);
471			}
472
473			oldMdFile.close();
474			newMdFile.close();
475	gezelter	1077
476			if (i != nMol.size()) {
477			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
478			"\tstatements in component blocks. Make sure that all\n"
479			"\tcomponents in the template file have nMol=1");
480			painCave.isFatal = 1;
481			simError();
482			}
483
484	chuckv	653	}
485