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);

  unsigned int i = 0;
  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;
   
  //creat new .md file on fly which corrects the number of molecule    

  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;

  // 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;
  painCave.severity = OPENMD_INFO;
  simError();
  return 0;
}
Revision:	1876
Committed:	Fri May 17 17:10:11 2013 UTC (11 years, 11 months ago) by gezelter
File size:	7931 byte(s)
Log Message:	Compilation and portability fixes
#	Content
1	/*
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	#include "clusters/Icosahedron.hpp"
51	#include "clusters/Decahedron.hpp"
52
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	unsigned int i = 0;
70	while (!oldMdFile.eof()) {
71
72	//correct molecule number
73	if (strstr(buffer, "nMol") != NULL) {
74	sprintf(buffer, "\tnMol = %i;", nMol);
75	newMdFile << buffer << std::endl;
76	} else {
77	newMdFile << buffer << std::endl;
78	}
79
80	oldMdFile.getline(buffer, MAXLEN);
81	}
82
83	oldMdFile.close();
84	newMdFile.close();
85	}
86
87	int main(int argc, char *argv []) {
88
89	gengetopt_args_info args_info;
90	std::string inputFileName;
91	std::string outputFileName;
92
93	MoLocator* locator;
94	RealType latticeConstant;
95	int nShells;
96
97	DumpWriter *writer;
98
99	// Parse Command Line Arguments
100	if (cmdline_parser(argc, argv, &args_info) != 0)
101	exit(1);
102
103	/* get input file name */
104	if (args_info.inputs_num)
105	inputFileName = args_info.inputs[0];
106	else {
107	sprintf(painCave.errMsg, "No input .md file name was specified "
108	"on the command line");
109	painCave.isFatal = 1;
110	cmdline_parser_print_help();
111	simError();
112	}
113
114	if (args_info.shells_given) {
115	nShells = args_info.shells_arg;
116	if( nShells < 0 ) {
117	sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n"
118	"\tmust be greater than or equal to zero.");
119	painCave.isFatal = 1;
120	cmdline_parser_print_help();
121	simError();
122	}
123	} else {
124	sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n"
125	"\tis required to build a Mackay Icosahedron.");
126	painCave.isFatal = 1;
127	cmdline_parser_print_help();
128	simError();
129	}
130
131	if (args_info.latticeConstant_given) {
132	latticeConstant = args_info.latticeConstant_arg;
133	} else {
134	sprintf(painCave.errMsg, "icosahedralBuilder: No lattice constant\n"
135	"\tgiven.");
136	painCave.isFatal = 1;
137	cmdline_parser_print_help();
138	simError();
139	}
140
141	/* parse md file and set up the system */
142	SimCreator oldCreator;
143	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
144	Globals* simParams = oldInfo->getSimParams();
145
146	vector<Vector3d> Points;
147	if (args_info.ico_given){
148	Icosahedron* ico = new Icosahedron();
149	Points = ico->getPoints(nShells);
150	} else if (args_info.deca_given) {
151	RegularDecahedron* deca = new RegularDecahedron(nShells);
152	Points = deca->getPoints();
153	} else if (args_info.ino_given) {
154	int columnAtoms = args_info.columnAtoms_arg;
155	InoDecahedron* ino = new InoDecahedron(columnAtoms, nShells);
156	Points = ino->getPoints();
157	} else if (args_info.marks_given) {
158	int columnAtoms = args_info.columnAtoms_arg;
159	int twinAtoms = args_info.twinAtoms_arg;
160	Decahedron* marks = new Decahedron(columnAtoms, nShells, twinAtoms);
161	Points = marks->getPoints();
162	}
163	else if (args_info.stone_given) {
164	int columnAtoms = args_info.columnAtoms_arg;
165	int twinAtoms = args_info.twinAtoms_arg;
166	int truncatedPlanes = args_info.truncatedPlanes_arg;
167	CurlingStoneDecahedron* csd = new CurlingStoneDecahedron(columnAtoms, nShells, twinAtoms, truncatedPlanes);
168	Points = csd->getPoints();
169	}
170
171
172
173	outputFileName = args_info.output_arg;
174
175	//creat new .md file on fly which corrects the number of molecule
176
177	createMdFile(inputFileName, outputFileName, Points.size());
178
179	delete oldInfo;
180
181	SimCreator newCreator;
182	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
183
184	// Place molecules
185	Molecule* mol;
186	SimInfo::MoleculeIterator mi;
187	mol = NewInfo->beginMolecule(mi);
188
189	int l = 0;
190
191	locator = new MoLocator(NewInfo->getMoleculeStamp(0),
192	NewInfo->getForceField());
193
194	Vector3d boxMax;
195	Vector3d boxMin;
196
197	for (unsigned int n = 0; n < Points.size(); n++) {
198	mol = NewInfo->getMoleculeByGlobalIndex(l);
199	Vector3d location = Points[n] * latticeConstant;
200	Vector3d orientation = Vector3d(0, 0, 1.0);
201
202	if (n == 0) {
203	boxMax = location;
204	boxMin = location;
205	} else {
206	for (int i = 0; i < 3; i++) {
207	boxMax[i] = max(boxMax[i], location[i]);
208	boxMin[i] = min(boxMin[i], location[i]);
209	}
210	}
211
212	locator->placeMol(location, orientation, mol);
213	l++;
214	}
215
216	Mat3x3d boundingBox;
217	boundingBox(0,0) = 10.0*(boxMax[0] - boxMin[0]);
218	boundingBox(1,1) = 10.0*(boxMax[1] - boxMin[1]);
219	boundingBox(2,2) = 10.0*(boxMax[2] - boxMin[2]);
220
221	//set Hmat
222	NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat( boundingBox );
223
224	//create dumpwriter and write out the coordinates
225	writer = new DumpWriter(NewInfo, outputFileName);
226
227	if (writer == NULL) {
228	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
229	painCave.isFatal = 1;
230	simError();
231	}
232
233	writer->writeDump();
234
235	// deleting the writer will put the closing at the end of the dump file
236
237	delete writer;
238
239	// cleanup a by calling sim error.....
240	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
241	"generated.\n", outputFileName.c_str());
242	painCave.isFatal = 0;
243	painCave.severity = OPENMD_INFO;
244	simError();
245	return 0;
246	}