applications/nanoparticleBuilder/icosahedralBuilder.cpp

/*
 * Copyright (c) 2013 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).
 */

#include "config.h"
#include "icosahedralBuilderCmd.h"
#include "utils/MoLocator.hpp"
#include "utils/Tuple.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "clusters/Icosahedron.hpp"
#include "clusters/Decahedron.hpp"

using namespace OpenMD;
using namespace std;

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  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);

  while (!oldMdFile.eof()) {

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

int main(int argc, char *argv []) {
  
  gengetopt_args_info args_info;
  std::string inputFileName;
  std::string outputFileName;
  
  MoLocator* locator;
  RealType latticeConstant;
  int nShells;

  DumpWriter *writer;
  
  // Parse Command Line Arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
         
  /* 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();
  }

  if (args_info.shells_given) {   
    nShells = args_info.shells_arg;    
    if( nShells < 0 ) {
      sprintf(painCave.errMsg, "icosahedralBuilder:  The number of shells\n"
              "\tmust be greater than or equal to zero.");
      painCave.isFatal = 1;
      cmdline_parser_print_help();
      simError();
    }
  } else {
    sprintf(painCave.errMsg, "icosahedralBuilder:  The number of shells\n"
            "\tis required to build a Mackay Icosahedron.");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }

  if (args_info.latticeConstant_given) {    
    latticeConstant = args_info.latticeConstant_arg;
  } else  {   
    sprintf(painCave.errMsg, "icosahedralBuilder:  No lattice constant\n"
            "\tgiven.");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }

  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  Globals* simParams = oldInfo->getSimParams();

  vector<Vector3d> Points;
  if (args_info.ico_given){
    Icosahedron* ico = new Icosahedron();
    Points = ico->getPoints(nShells);
  } else if (args_info.deca_given) {
    RegularDecahedron* deca = new RegularDecahedron(nShells);
    Points = deca->getPoints();
  } else if (args_info.ino_given) {
    int columnAtoms = args_info.columnAtoms_arg;    
    InoDecahedron* ino = new InoDecahedron(columnAtoms, nShells);
    Points = ino->getPoints();
  } else if (args_info.marks_given) {
    int columnAtoms = args_info.columnAtoms_arg;    
    int twinAtoms = args_info.twinAtoms_arg;
    Decahedron* marks = new Decahedron(columnAtoms, nShells, twinAtoms);
    Points = marks->getPoints();
  }
  else if (args_info.stone_given) {
    int columnAtoms = args_info.columnAtoms_arg;    
    int twinAtoms = args_info.twinAtoms_arg;
    int truncatedPlanes = args_info.truncatedPlanes_arg;
    CurlingStoneDecahedron* csd = new CurlingStoneDecahedron(columnAtoms, nShells, twinAtoms, truncatedPlanes);
    Points = csd->getPoints();
  }

  outputFileName = args_info.output_arg;
   
  // create a new .md file on fly which corrects the number of
  // molecules

  createMdFile(inputFileName, outputFileName, Points.size());
  
  delete oldInfo;
  
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
    
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);

  int l = 0;

  locator = new MoLocator(NewInfo->getMoleculeStamp(0), 
                          NewInfo->getForceField());
    
  Vector3d boxMax;
  Vector3d boxMin;

  for (unsigned int n = 0; n < Points.size(); n++) {
    mol = NewInfo->getMoleculeByGlobalIndex(l);
    Vector3d location = Points[n] * latticeConstant;
    Vector3d orientation = Vector3d(0, 0, 1.0);
    
    if (n == 0) {
      boxMax = location;
      boxMin = location;
    } else {
      for (int i = 0; i < 3; i++) {
        boxMax[i] = max(boxMax[i], location[i]);
        boxMin[i] = min(boxMin[i], location[i]);
      }
    }
    
    locator->placeMol(location, orientation, mol);
    l++;
  }

  Mat3x3d boundingBox;
  boundingBox(0,0) = 10.0*(boxMax[0] - boxMin[0]);
  boundingBox(1,1) = 10.0*(boxMax[1] - boxMin[1]);
  boundingBox(2,2) = 10.0*(boxMax[2] - boxMin[2]);
 
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat( boundingBox );
  
  //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;

  // clean up by calling simError.....
  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  painCave.severity = OPENMD_INFO;
  simError();
  return 0;
}
Revision:	1942
Committed:	Tue Nov 5 18:33:42 2013 UTC (11 years, 7 months ago) by gezelter
File size:	7905 byte(s)
Log Message:	Fixed some warning messages and NanoVolume issues.
#	User	Rev	Content
1	gezelter	1860	/*
2			* Copyright (c) 2013 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "config.h"
44			#include "icosahedralBuilderCmd.h"
45			#include "utils/MoLocator.hpp"
46			#include "utils/Tuple.hpp"
47			#include "brains/SimInfo.hpp"
48			#include "brains/SimCreator.hpp"
49			#include "io/DumpWriter.hpp"
50	gezelter	1862	#include "clusters/Icosahedron.hpp"
51			#include "clusters/Decahedron.hpp"
52	gezelter	1860
53			using namespace OpenMD;
54			using namespace std;
55
56			void createMdFile(const std::string&oldMdFileName,
57			const std::string&newMdFileName,
58			int nMol) {
59			ifstream oldMdFile;
60			ofstream newMdFile;
61			const int MAXLEN = 65535;
62			char buffer[MAXLEN];
63
64			//create new .md file based on old .md file
65			oldMdFile.open(oldMdFileName.c_str());
66			newMdFile.open(newMdFileName.c_str());
67			oldMdFile.getline(buffer, MAXLEN);
68
69			while (!oldMdFile.eof()) {
70
71			//correct molecule number
72			if (strstr(buffer, "nMol") != NULL) {
73			sprintf(buffer, "\tnMol = %i;", nMol);
74			newMdFile << buffer << std::endl;
75			} else {
76			newMdFile << buffer << std::endl;
77			}
78
79			oldMdFile.getline(buffer, MAXLEN);
80			}
81
82			oldMdFile.close();
83			newMdFile.close();
84			}
85
86			int main(int argc, char *argv []) {
87
88			gengetopt_args_info args_info;
89			std::string inputFileName;
90			std::string outputFileName;
91
92			MoLocator* locator;
93			RealType latticeConstant;
94			int nShells;
95	gezelter	1862
96	gezelter	1860	DumpWriter *writer;
97
98			// Parse Command Line Arguments
99			if (cmdline_parser(argc, argv, &args_info) != 0)
100			exit(1);
101
102			/* get input file name */
103			if (args_info.inputs_num)
104			inputFileName = args_info.inputs[0];
105			else {
106			sprintf(painCave.errMsg, "No input .md file name was specified "
107			"on the command line");
108			painCave.isFatal = 1;
109			cmdline_parser_print_help();
110			simError();
111			}
112
113			if (args_info.shells_given) {
114			nShells = args_info.shells_arg;
115			if( nShells < 0 ) {
116			sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n"
117			"\tmust be greater than or equal to zero.");
118			painCave.isFatal = 1;
119			cmdline_parser_print_help();
120			simError();
121			}
122			} else {
123			sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n"
124			"\tis required to build a Mackay Icosahedron.");
125			painCave.isFatal = 1;
126			cmdline_parser_print_help();
127			simError();
128			}
129
130			if (args_info.latticeConstant_given) {
131			latticeConstant = args_info.latticeConstant_arg;
132	gezelter	1862	} else {
133	gezelter	1860	sprintf(painCave.errMsg, "icosahedralBuilder: No lattice constant\n"
134	gezelter	1862	"\tgiven.");
135	gezelter	1860	painCave.isFatal = 1;
136			cmdline_parser_print_help();
137			simError();
138			}
139
140			/* parse md file and set up the system */
141			SimCreator oldCreator;
142			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
143			Globals* simParams = oldInfo->getSimParams();
144
145	gezelter	1862	vector<Vector3d> Points;
146			if (args_info.ico_given){
147			Icosahedron* ico = new Icosahedron();
148			Points = ico->getPoints(nShells);
149			} else if (args_info.deca_given) {
150			RegularDecahedron* deca = new RegularDecahedron(nShells);
151			Points = deca->getPoints();
152			} else if (args_info.ino_given) {
153			int columnAtoms = args_info.columnAtoms_arg;
154			InoDecahedron* ino = new InoDecahedron(columnAtoms, nShells);
155			Points = ino->getPoints();
156			} else if (args_info.marks_given) {
157			int columnAtoms = args_info.columnAtoms_arg;
158			int twinAtoms = args_info.twinAtoms_arg;
159			Decahedron* marks = new Decahedron(columnAtoms, nShells, twinAtoms);
160			Points = marks->getPoints();
161			}
162			else if (args_info.stone_given) {
163			int columnAtoms = args_info.columnAtoms_arg;
164			int twinAtoms = args_info.twinAtoms_arg;
165			int truncatedPlanes = args_info.truncatedPlanes_arg;
166			CurlingStoneDecahedron* csd = new CurlingStoneDecahedron(columnAtoms, nShells, twinAtoms, truncatedPlanes);
167			Points = csd->getPoints();
168			}
169	gezelter	1860
170			outputFileName = args_info.output_arg;
171
172	gezelter	1942	// create a new .md file on fly which corrects the number of
173			// molecules
174	gezelter	1860
175			createMdFile(inputFileName, outputFileName, Points.size());
176
177	gezelter	1874	delete oldInfo;
178	gezelter	1860
179			SimCreator newCreator;
180			SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
181
182			// Place molecules
183			Molecule* mol;
184			SimInfo::MoleculeIterator mi;
185			mol = NewInfo->beginMolecule(mi);
186
187			int l = 0;
188
189			locator = new MoLocator(NewInfo->getMoleculeStamp(0),
190			NewInfo->getForceField());
191
192			Vector3d boxMax;
193			Vector3d boxMin;
194
195	gezelter	1876	for (unsigned int n = 0; n < Points.size(); n++) {
196	gezelter	1860	mol = NewInfo->getMoleculeByGlobalIndex(l);
197			Vector3d location = Points[n] * latticeConstant;
198			Vector3d orientation = Vector3d(0, 0, 1.0);
199	gezelter	1876
200	gezelter	1860	if (n == 0) {
201			boxMax = location;
202			boxMin = location;
203			} else {
204			for (int i = 0; i < 3; i++) {
205			boxMax[i] = max(boxMax[i], location[i]);
206			boxMin[i] = min(boxMin[i], location[i]);
207			}
208			}
209
210			locator->placeMol(location, orientation, mol);
211			l++;
212			}
213
214			Mat3x3d boundingBox;
215			boundingBox(0,0) = 10.0*(boxMax[0] - boxMin[0]);
216			boundingBox(1,1) = 10.0*(boxMax[1] - boxMin[1]);
217			boundingBox(2,2) = 10.0*(boxMax[2] - boxMin[2]);
218
219			//set Hmat
220			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat( boundingBox );
221
222			//create dumpwriter and write out the coordinates
223			writer = new DumpWriter(NewInfo, outputFileName);
224
225			if (writer == NULL) {
226			sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
227			painCave.isFatal = 1;
228			simError();
229			}
230
231			writer->writeDump();
232
233			// deleting the writer will put the closing at the end of the dump file
234
235			delete writer;
236
237	gezelter	1942	// clean up by calling simError.....
238	gezelter	1860	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
239			"generated.\n", outputFileName.c_str());
240			painCave.isFatal = 0;
241			painCave.severity = OPENMD_INFO;
242			simError();
243			return 0;
244			}