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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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 OpenMD;
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.", (int) vacancyTargets.size(), 
                vIR, vOR); 
        painCave.isFatal = 0;
        simError();

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

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

  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 OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}

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

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

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

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

Revision:	1704
Committed:	Tue Apr 24 20:40:04 2012 UTC (13 years ago) by gezelter
File size:	15236 byte(s)
Log Message:	qhull modifications for compilation
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	653	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	653	* 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	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	653	*/
42
43			#include <cstdlib>
44			#include <cstdio>
45			#include <cstring>
46			#include <cmath>
47			#include <iostream>
48			#include <string>
49			#include <map>
50			#include <fstream>
51	chuckv	911	#include <algorithm>
52	chuckv	653
53			#include "config.h"
54	chuckv	911	#include "shapedLatticeSpherical.hpp"
55	chuckv	653	#include "nanoparticleBuilderCmd.h"
56			#include "lattice/LatticeFactory.hpp"
57			#include "utils/MoLocator.hpp"
58			#include "lattice/Lattice.hpp"
59			#include "brains/Register.hpp"
60			#include "brains/SimInfo.hpp"
61			#include "brains/SimCreator.hpp"
62			#include "io/DumpWriter.hpp"
63			#include "math/Vector3.hpp"
64			#include "math/SquareMatrix3.hpp"
65			#include "utils/StringUtils.hpp"
66
67			using namespace std;
68	gezelter	1390	using namespace OpenMD;
69	chuckv	653	void createMdFile(const std::string&oldMdFileName,
70			const std::string&newMdFileName,
71	chuckv	1069	std::vector<int> numMol);
72	chuckv	653
73			int main(int argc, char *argv []) {
74
75			//register force fields
76			registerForceFields();
77			registerLattice();
78
79			gengetopt_args_info args_info;
80			std::string latticeType;
81			std::string inputFileName;
82	chuckv	1069	std::string outputFileName;
83	chuckv	653
84	chuckv	911	MoLocator* locator;
85			int nComponents;
86	chuckv	653	double latticeConstant;
87			std::vector<double> lc;
88	gezelter	1075
89	gezelter	1077	RealType particleRadius;
90	chuckv	653
91			Mat3x3d hmat;
92			std::vector<Vector3d> latticePos;
93			std::vector<Vector3d> latticeOrt;
94	chuckv	1069
95	chuckv	653	DumpWriter *writer;
96
97	chuckv	875	// Parse Command Line Arguments
98	chuckv	653	if (cmdline_parser(argc, argv, &args_info) != 0)
99			exit(1);
100	gezelter	1070
101	chuckv	653	/* get lattice type */
102	chuckv	1069	latticeType = "FCC";
103
104	chuckv	653	/* get input file name */
105			if (args_info.inputs_num)
106			inputFileName = args_info.inputs[0];
107			else {
108	gezelter	1077	sprintf(painCave.errMsg, "No input .md file name was specified "
109	gezelter	1075	"on the command line");
110	chuckv	1069	painCave.isFatal = 1;
111	chuckv	653	cmdline_parser_print_help();
112	chuckv	1069	simError();
113	chuckv	653	}
114
115			/* parse md file and set up the system */
116			SimCreator oldCreator;
117			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
118
119	gezelter	1077	latticeConstant = args_info.latticeConstant_arg;
120	chuckv	653	particleRadius = args_info.radius_arg;
121	chuckv	911	Globals* simParams = oldInfo->getSimParams();
122	chuckv	653
123	chuckv	911	/* Create nanoparticle */
124	gezelter	1070	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
125			particleRadius);
126	chuckv	918
127	chuckv	911	/* Build a lattice and get lattice points for this lattice constant */
128	gezelter	1070	vector<Vector3d> sites = nanoParticle.getSites();
129			vector<Vector3d> orientations = nanoParticle.getOrientations();
130	gezelter	1704
131
132	gezelter	1077	std::vector<int> vacancyTargets;
133			vector<bool> isVacancy;
134
135			Vector3d myLoc;
136			RealType myR;
137
138			for (int i = 0; i < sites.size(); i++)
139			isVacancy.push_back(false);
140	chuckv	1069
141	gezelter	1077	if (args_info.vacancyPercent_given) {
142			if (args_info.vacancyPercent_arg < 0.0 \|\| args_info.vacancyPercent_arg > 100.0) {
143			sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
144			painCave.isFatal = 1;
145			simError();
146			} else {
147			RealType vF = args_info.vacancyPercent_arg / 100.0;
148			RealType vIR;
149			RealType vOR;
150			if (args_info.vacancyInnerRadius_given) {
151			vIR = args_info.vacancyInnerRadius_arg;
152			} else {
153			vIR = 0.0;
154			}
155			if (args_info.vacancyOuterRadius_given) {
156			vOR = args_info.vacancyOuterRadius_arg;
157			} else {
158			vOR = particleRadius;
159			}
160			if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
161
162			for (int i = 0; i < sites.size(); i++) {
163			myLoc = sites[i];
164			myR = myLoc.length();
165			if (myR >= vIR && myR <= vOR) {
166			vacancyTargets.push_back(i);
167			}
168			}
169			std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
170
171			int nTargets = vacancyTargets.size();
172			vacancyTargets.resize((int)(vF * nTargets));
173
174
175			sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
176	gezelter	1390	"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
177	gezelter	1077	vIR, vOR);
178			painCave.isFatal = 0;
179			simError();
180	chuckv	1069
181	gezelter	1077	isVacancy.clear();
182			for (int i = 0; i < sites.size(); i++) {
183			bool vac = false;
184			for (int j = 0; j < vacancyTargets.size(); j++) {
185			if (i == vacancyTargets[j]) vac = true;
186			}
187			isVacancy.push_back(vac);
188			}
189
190			} else {
191			sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
192			"\tinner or outer radii. Check their values.");
193			painCave.isFatal = 1;
194			simError();
195			}
196			}
197			}
198
199	chuckv	911	/* Get number of lattice sites */
200	gezelter	1077	int nSites = sites.size() - vacancyTargets.size();
201	chuckv	1069
202			std::vector<Component*> components = simParams->getComponents();
203			std::vector<RealType> molFractions;
204	gezelter	1075	std::vector<RealType> shellRadii;
205	chuckv	1069	std::vector<RealType> molecularMasses;
206			std::vector<int> nMol;
207	gezelter	1075	std::map<int, int> componentFromSite;
208	chuckv	1069	nComponents = components.size();
209
210	gezelter	1077	if (args_info.molFraction_given && args_info.shellRadius_given) {
211			sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
212	gezelter	1075	"arguments, but not both!");
213			painCave.isFatal = 1;
214			simError();
215			}
216
217			if (nComponents == 1) {
218	chuckv	1069	molFractions.push_back(1.0);
219	gezelter	1075	shellRadii.push_back(particleRadius);
220			} else if (args_info.molFraction_given) {
221			if ((int)args_info.molFraction_given == nComponents) {
222			for (int i = 0; i < nComponents; i++) {
223			molFractions.push_back(args_info.molFraction_arg[i]);
224			}
225			} else if ((int)args_info.molFraction_given == nComponents-1) {
226			RealType remainingFraction = 1.0;
227			for (int i = 0; i < nComponents-1; i++) {
228			molFractions.push_back(args_info.molFraction_arg[i]);
229			remainingFraction -= molFractions[i];
230			}
231			molFractions.push_back(remainingFraction);
232			} else {
233			sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
234			"for all of the components in the <MetaData> block.");
235	chuckv	1069	painCave.isFatal = 1;
236			simError();
237			}
238	gezelter	1077	} else if ((int)args_info.shellRadius_given) {
239			if ((int)args_info.shellRadius_given == nComponents) {
240	gezelter	1075	for (int i = 0; i < nComponents; i++) {
241	gezelter	1077	shellRadii.push_back(args_info.shellRadius_arg[i]);
242	gezelter	1075	}
243	gezelter	1077	} else if ((int)args_info.shellRadius_given == nComponents-1) {
244	gezelter	1075	for (int i = 0; i < nComponents-1; i++) {
245	gezelter	1077	shellRadii.push_back(args_info.shellRadius_arg[i]);
246	gezelter	1075	}
247			shellRadii.push_back(particleRadius);
248			} else {
249	gezelter	1077	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
250			"\tshell radii for all of the components in the <MetaData> block.");
251	chuckv	1069	painCave.isFatal = 1;
252			simError();
253			}
254	gezelter	1075	} else {
255	gezelter	1077	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
256			"\tbut have not specified either molFraction or shellRadius arguments.");
257	chuckv	1069	painCave.isFatal = 1;
258			simError();
259			}
260	gezelter	1075
261			if (args_info.molFraction_given) {
262			RealType totalFraction = 0.0;
263
264			/* Do some simple sanity checking*/
265
266			for (int i = 0; i < nComponents; i++) {
267			if (molFractions.at(i) < 0.0) {
268			sprintf(painCave.errMsg, "One of the requested molFractions was"
269			" less than zero!");
270			painCave.isFatal = 1;
271			simError();
272			}
273			if (molFractions.at(i) > 1.0) {
274			sprintf(painCave.errMsg, "One of the requested molFractions was"
275			" greater than one!");
276			painCave.isFatal = 1;
277			simError();
278			}
279			totalFraction += molFractions.at(i);
280			}
281			if (abs(totalFraction - 1.0) > 1e-6) {
282			sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
283			painCave.isFatal = 1;
284			simError();
285			}
286
287			int remaining = nSites;
288			for (int i=0; i < nComponents-1; i++) {
289			nMol.push_back(int((RealType)nSites * molFractions.at(i)));
290			remaining -= nMol.at(i);
291			}
292			nMol.push_back(remaining);
293
294			// recompute actual mol fractions and perform final sanity check:
295
296			int totalMolecules = 0;
297			for (int i=0; i < nComponents; i++) {
298			molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
299			totalMolecules += nMol.at(i);
300			}
301
302			if (totalMolecules != nSites) {
303			sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
304			"to the number of lattice sites!");
305			painCave.isFatal = 1;
306			simError();
307			}
308			} else {
309	chuckv	1069
310	gezelter	1075	for (int i = 0; i < shellRadii.size(); i++) {
311			if (shellRadii.at(i) > particleRadius + 1e-6 ) {
312			sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
313			painCave.isFatal = 1;
314			simError();
315			}
316			if (shellRadii.at(i) <= 0.0 ) {
317			sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
318			painCave.isFatal = 1;
319			simError();
320			}
321			}
322	chuckv	1069	}
323	gezelter	1077
324			vector<int> ids;
325	gezelter	1075	if ((int)args_info.molFraction_given){
326			sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
327			painCave.isFatal = 0;
328			simError();
329	gezelter	1077	/* Random particle is the default case*/
330
331			for (int i = 0; i < sites.size(); i++)
332			if (!isVacancy[i]) ids.push_back(i);
333
334	chuckv	1069	std::random_shuffle(ids.begin(), ids.end());
335	gezelter	1077
336	gezelter	1075	} else{
337			sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
338			painCave.isFatal = 0;
339			simError();
340	chuckv	653
341	gezelter	1075	RealType smallestSoFar;
342			int myComponent = -1;
343			nMol.clear();
344			nMol.resize(nComponents);
345
346			for (int i = 0; i < sites.size(); i++) {
347			myLoc = sites[i];
348			myR = myLoc.length();
349	gezelter	1077	smallestSoFar = particleRadius;
350			if (!isVacancy[i]) {
351			for (int j = 0; j < nComponents; j++) {
352			if (myR <= shellRadii[j]) {
353			if (shellRadii[j] <= smallestSoFar) {
354			smallestSoFar = shellRadii[j];
355			myComponent = j;
356			}
357	gezelter	1075	}
358			}
359	gezelter	1077	componentFromSite[i] = myComponent;
360			nMol[myComponent]++;
361	gezelter	1075	}
362	gezelter	1077	}
363			}
364	chuckv	949
365	chuckv	1069	outputFileName = args_info.output_arg;
366	gezelter	1077
367	gezelter	1075	//creat new .md file on fly which corrects the number of molecule
368	chuckv	1069	createMdFile(inputFileName, outputFileName, nMol);
369	chuckv	653
370			if (oldInfo != NULL)
371			delete oldInfo;
372
373	chuckv	949	SimCreator newCreator;
374	chuckv	1069	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
375	gezelter	1075
376	chuckv	911	// Place molecules
377	chuckv	653	Molecule* mol;
378			SimInfo::MoleculeIterator mi;
379			mol = NewInfo->beginMolecule(mi);
380	gezelter	1077
381	chuckv	949	int l = 0;
382	gezelter	1077	int whichSite = 0;
383	chuckv	1069
384			for (int i = 0; i < nComponents; i++){
385			locator = new MoLocator(NewInfo->getMoleculeStamp(i),
386			NewInfo->getForceField());
387	gezelter	1077
388			if (!args_info.molFraction_given) {
389	gezelter	1075	for (int n = 0; n < sites.size(); n++) {
390	gezelter	1077	if (!isVacancy[n]) {
391			if (componentFromSite[n] == i) {
392			mol = NewInfo->getMoleculeByGlobalIndex(l);
393			locator->placeMol(sites[n], orientations[n], mol);
394			l++;
395			}
396	gezelter	1075	}
397			}
398			} else {
399			for (int n = 0; n < nMol.at(i); n++) {
400			mol = NewInfo->getMoleculeByGlobalIndex(l);
401			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
402			l++;
403			}
404	chuckv	1069	}
405	gezelter	1077	}
406	chuckv	653
407			//fill Hmat
408	gezelter	1075	hmat(0, 0)= 10.0*particleRadius;
409	chuckv	653	hmat(0, 1) = 0.0;
410			hmat(0, 2) = 0.0;
411
412			hmat(1, 0) = 0.0;
413	gezelter	1075	hmat(1, 1) = 10.0*particleRadius;
414	chuckv	653	hmat(1, 2) = 0.0;
415
416			hmat(2, 0) = 0.0;
417			hmat(2, 1) = 0.0;
418	gezelter	1075	hmat(2, 2) = 10.0*particleRadius;
419	chuckv	653
420			//set Hmat
421			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
422
423
424			//create dumpwriter and write out the coordinates
425	gezelter	1070	writer = new DumpWriter(NewInfo, outputFileName);
426	chuckv	653
427			if (writer == NULL) {
428	gezelter	1077	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
429	gezelter	1075	painCave.isFatal = 1;
430			simError();
431	chuckv	653	}
432
433			writer->writeDump();
434	chuckv	1069
435			// deleting the writer will put the closing at the end of the dump file
436	gezelter	1070
437	chuckv	1069	delete writer;
438
439			// cleanup a by calling sim error.....
440	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
441	chuckv	1069	"generated.\n", outputFileName.c_str());
442			painCave.isFatal = 0;
443			simError();
444	chuckv	653	return 0;
445			}
446
447	gezelter	1075	void createMdFile(const std::string&oldMdFileName,
448			const std::string&newMdFileName,
449	chuckv	1069	std::vector<int> nMol) {
450	chuckv	653	ifstream oldMdFile;
451			ofstream newMdFile;
452			const int MAXLEN = 65535;
453			char buffer[MAXLEN];
454
455			//create new .md file based on old .md file
456			oldMdFile.open(oldMdFileName.c_str());
457			newMdFile.open(newMdFileName.c_str());
458			oldMdFile.getline(buffer, MAXLEN);
459	gezelter	1077
460	chuckv	911	int i = 0;
461	chuckv	653	while (!oldMdFile.eof()) {
462	gezelter	1077
463	chuckv	653	//correct molecule number
464			if (strstr(buffer, "nMol") != NULL) {
465	chuckv	1069	if(i<nMol.size()){
466	gezelter	1077	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
467	chuckv	949	newMdFile << buffer << std::endl;
468			i++;
469			}
470	chuckv	653	} else
471			newMdFile << buffer << std::endl;
472
473			oldMdFile.getline(buffer, MAXLEN);
474			}
475
476			oldMdFile.close();
477			newMdFile.close();
478	gezelter	1077
479			if (i != nMol.size()) {
480			sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
481			"\tstatements in component blocks. Make sure that all\n"
482			"\tcomponents in the template file have nMol=1");
483			painCave.isFatal = 1;
484			simError();
485			}
486
487	chuckv	653	}
488