applications/nanoRodBuilder/nanorodBuilder.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 "config.h"

#include "nanorodBuilderCmd.h"
#ifdef HAVE_CGAL
#include "GeometryBuilder.hpp"
#endif
#include "GeometryFactory.hpp"
#include "Geometry.hpp"
#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/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,
                  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 outPrefix;
  std::string outMdFileName;
  std::string outInitFileName;
  std::string outGeomFileName;
  
  
  Lattice *simpleLat;
  int numMol;
  double latticeConstant;
  std::vector<double> lc;
  double mass;
  const double rhoConvertConst = 1.661;
  double density;
  double rodLength;
  double rodDiameter;
  
  
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator *locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  DumpWriter *writer;
  
  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
  
  
  // Check for lib CGAL, if we don't have it, we should exit....
        
#ifndef HAVE_CGAL
  std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
            << std::endl;
  exit(1);
#endif
        
        
  //get lattice type
  latticeType = UpperCase(args_info.latticetype_arg);
    
  //get input file name
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    std::cerr << "You must specify a input file name.\n" << std::endl;
    cmdline_parser_print_help();
    exit(1);
  }
  
  //parse md file and set up the system
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  if (oldInfo->getNMoleculeStamp()> 1) {
    std::cerr << "can not build nanorod with more than one components"
              << std::endl;
    exit(1);
  }
  
  //get mass of molecule. 
  
  mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  //creat lattice
  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
  
  if (simpleLat == NULL) {
    std::cerr << "Error in creating lattice" << std::endl;
    exit(1);
  }
  
  numMolPerCell = simpleLat->getNumSitesPerCell();
  
  //calculate lattice constant (in Angstrom)
  //latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
  //                      1.0 / 3.0);
  
  latticeConstant = args_info.latticeCnst_arg;
  rodLength = args_info.length_arg;
  rodDiameter = args_info.width_arg;
  
  //set lattice constant
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
  
  
  //determine the output file names  
  if (args_info.output_given)
    outInitFileName = args_info.output_arg;
  else
    outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
  
  
  //creat Molocator
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /*
    Assume we are carving nanorod out of a cublic block of material and that
    the shape the material will fit within that block.... 
    The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the 
    diameter of the particle.            
  */
  // Number of Unit Cells in Length first
  ny = (int)(rodLength/latticeConstant);
  // Number of unit cells in Width
  nx = (int)(rodDiameter/latticeConstant);
  nz = (int)(rodDiameter/latticeConstant);
  
  
  // Create geometry for nanocrystal
#ifdef HAVE_CGAL
  GeometryBuilder *myGeometry;
  // GeometryBuilder myGeometry(rodLength,rodDiameter);
  if (args_info.twinnedCrystal_flag){
     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
  }
  else{
     myGeometry = new GeometryBuilder(rodLength,rodDiameter);
  }
  
  if (args_info.genGeomview_given){
     if (args_info.genGeomview_flag){
        outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
        myGeometry->dumpGeometry(outGeomFileName);
     }
  }
  
#endif
  
  /*
    We have to build the system first to figure out how many molecules
    there are then create a md file and then actually build the
    system.
  */
  
  //place the molecules
  

  //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
  latticeOrt = simpleLat->getLatticePointsOrt();
  
  
  numMol = 0;
  for(int i = -nx; i < nx; i++) {     
    for(int j = -ny; j < ny; j++) {       
      for(int k = -nz; k < nz; k++) {
        //if (oldInfo->getNGlobalMolecules() != numMol) {
        
        
        //get the position of the cell sites
        simpleLat->getLatticePointsPos(latticePos, i, j, k);
        
        for(int l = 0; l < numMolPerCell; l++) {

#ifdef HAVE_CGAL
          if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
            numMol++;
          }
#else
           numMol++;
#endif
        }
      }
    }
  }

  
  // needed for writing out new md file.
  
  outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
  outMdFileName = outPrefix + ".md";
  
  //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outMdFileName, numMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  
  SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
  
  // This was so much fun the first time, lets do it again.
  
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);


  for(int i = -nx; i < nx; i++) {
     for(int j = -ny; j < ny; j++) {
        for(int k = -nz; k < nz; k++) {
           
           //get the position of the cell sites
           simpleLat->getLatticePointsPos(latticePos, i, j, k);
           
           for(int l = 0; l < numMolPerCell; l++) {
#ifdef HAVE_CGAL              
              if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
#endif                              
                 if (mol != NULL) {
                    locator->placeMol(latticePos[l], latticeOrt[l], mol);
                 } else {
                    std::cerr<<"Error in placing molecule " << std::endl;                    
                 }
                 mol = NewInfo->nextMolecule(mi);
#ifdef HAVE_CGAL                
              }
#endif              
           }
        }
     }
  }
  

  //fill Hmat
  hmat(0, 0)= nx * latticeConstant;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) = ny * latticeConstant;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) = nz * latticeConstant;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  NewInfo->setFinalConfigFileName(outInitFileName);
  writer = new DumpWriter(NewInfo);
  
  if (writer == NULL) {
    std::cerr << "error in creating DumpWriter" << std::endl;
    exit(1);
  }
  
  writer->writeDump();
  std::cout << "new initial configuration file: " << outInitFileName
            << " is generated." << std::endl;
  
  //delete objects
  
  //delete oldInfo and oldSimSetup
  
  if (NewInfo != NULL)
    delete NewInfo;
  
  if (writer != NULL)
    delete writer;
  delete simpleLat;     
  cmdline_parser_free(&args_info);
  return 0;
}

void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
                  int numMol) {
  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;", numMol);                          
      newMdFile << buffer << std::endl;
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	2252
Committed:	Mon May 30 14:01:52 2005 UTC (19 years, 2 months ago) by chuckv
File size:	10773 byte(s)
Log Message:	Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
#	Content
1	/*
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
51	#include "config.h"
52
53	#include "nanorodBuilderCmd.h"
54	#ifdef HAVE_CGAL
55	#include "GeometryBuilder.hpp"
56	#endif
57	#include "GeometryFactory.hpp"
58	#include "Geometry.hpp"
59	#include "lattice/LatticeFactory.hpp"
60	#include "utils/MoLocator.hpp"
61	#include "lattice/Lattice.hpp"
62	#include "brains/Register.hpp"
63	#include "brains/SimInfo.hpp"
64	#include "brains/SimCreator.hpp"
65	#include "io/DumpWriter.hpp"
66	#include "math/Vector3.hpp"
67	#include "math/SquareMatrix3.hpp"
68	#include "utils/StringUtils.hpp"
69
70	using namespace std;
71	using namespace oopse;
72	void createMdFile(const std::string&oldMdFileName,
73	const std::string&newMdFileName,
74	int numMol);
75
76	int main(int argc, char *argv []) {
77
78	//register force fields
79	registerForceFields();
80	registerLattice();
81
82	gengetopt_args_info args_info;
83	std::string latticeType;
84	std::string inputFileName;
85	std::string outPrefix;
86	std::string outMdFileName;
87	std::string outInitFileName;
88	std::string outGeomFileName;
89
90
91	Lattice *simpleLat;
92	int numMol;
93	double latticeConstant;
94	std::vector<double> lc;
95	double mass;
96	const double rhoConvertConst = 1.661;
97	double density;
98	double rodLength;
99	double rodDiameter;
100
101
102	int nx, ny, nz;
103	Mat3x3d hmat;
104	MoLocator *locator;
105	std::vector<Vector3d> latticePos;
106	std::vector<Vector3d> latticeOrt;
107	int numMolPerCell;
108	DumpWriter *writer;
109
110	// parse command line arguments
111	if (cmdline_parser(argc, argv, &args_info) != 0)
112	exit(1);
113
114
115	// Check for lib CGAL, if we don't have it, we should exit....
116
117	#ifndef HAVE_CGAL
118	std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
119	<< std::endl;
120	exit(1);
121	#endif
122
123
124
125	//get lattice type
126	latticeType = UpperCase(args_info.latticetype_arg);
127
128	//get input file name
129	if (args_info.inputs_num)
130	inputFileName = args_info.inputs[0];
131	else {
132	std::cerr << "You must specify a input file name.\n" << std::endl;
133	cmdline_parser_print_help();
134	exit(1);
135	}
136
137	//parse md file and set up the system
138	SimCreator oldCreator;
139	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
140
141	if (oldInfo->getNMoleculeStamp()> 1) {
142	std::cerr << "can not build nanorod with more than one components"
143	<< std::endl;
144	exit(1);
145	}
146
147	//get mass of molecule.
148
149	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
150
151	//creat lattice
152	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
153
154	if (simpleLat == NULL) {
155	std::cerr << "Error in creating lattice" << std::endl;
156	exit(1);
157	}
158
159	numMolPerCell = simpleLat->getNumSitesPerCell();
160
161	//calculate lattice constant (in Angstrom)
162	//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
163	// 1.0 / 3.0);
164
165	latticeConstant = args_info.latticeCnst_arg;
166	rodLength = args_info.length_arg;
167	rodDiameter = args_info.width_arg;
168
169	//set lattice constant
170	lc.push_back(latticeConstant);
171	simpleLat->setLatticeConstant(lc);
172
173
174	//determine the output file names
175	if (args_info.output_given)
176	outInitFileName = args_info.output_arg;
177	else
178	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
179
180
181
182
183
184
185	//creat Molocator
186	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
187
188	/*
189	Assume we are carving nanorod out of a cublic block of material and that
190	the shape the material will fit within that block....
191	The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
192	diameter of the particle.
193	*/
194	// Number of Unit Cells in Length first
195	ny = (int)(rodLength/latticeConstant);
196	// Number of unit cells in Width
197	nx = (int)(rodDiameter/latticeConstant);
198	nz = (int)(rodDiameter/latticeConstant);
199
200
201
202	// Create geometry for nanocrystal
203	#ifdef HAVE_CGAL
204	GeometryBuilder *myGeometry;
205	// GeometryBuilder myGeometry(rodLength,rodDiameter);
206	if (args_info.twinnedCrystal_flag){
207	myGeometry = new GeometryBuilder(rodLength,rodDiameter);
208	}
209	else{
210	myGeometry = new GeometryBuilder(rodLength,rodDiameter);
211	}
212
213	if (args_info.genGeomview_given){
214	if (args_info.genGeomview_flag){
215	outGeomFileName = getPrefix(inputFileName.c_str()) + ".off";
216	myGeometry->dumpGeometry(outGeomFileName);
217	}
218	}
219
220	#endif
221
222	/*
223	We have to build the system first to figure out how many molecules
224	there are then create a md file and then actually build the
225	system.
226	*/
227
228	//place the molecules
229
230
231
232	//get the orientation of the cell sites
233	//for the same type of molecule in same lattice, it will not change
234	latticeOrt = simpleLat->getLatticePointsOrt();
235
236
237
238	numMol = 0;
239	for(int i = -nx; i < nx; i++) {
240	for(int j = -ny; j < ny; j++) {
241	for(int k = -nz; k < nz; k++) {
242	//if (oldInfo->getNGlobalMolecules() != numMol) {
243
244
245
246	//get the position of the cell sites
247	simpleLat->getLatticePointsPos(latticePos, i, j, k);
248
249	for(int l = 0; l < numMolPerCell; l++) {
250
251	#ifdef HAVE_CGAL
252	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
253	numMol++;
254	}
255	#else
256	numMol++;
257	#endif
258	}
259	}
260	}
261	}
262
263
264	// needed for writing out new md file.
265
266	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
267	outMdFileName = outPrefix + ".md";
268
269	//creat new .md file on fly which corrects the number of molecule
270	createMdFile(inputFileName, outMdFileName, numMol);
271
272	if (oldInfo != NULL)
273	delete oldInfo;
274
275
276	// We need to read in new siminfo object.
277	//parse md file and set up the system
278	//SimCreator NewCreator;
279
280	SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
281
282	// This was so much fun the first time, lets do it again.
283
284	Molecule* mol;
285	SimInfo::MoleculeIterator mi;
286	mol = NewInfo->beginMolecule(mi);
287
288
289	for(int i = -nx; i < nx; i++) {
290	for(int j = -ny; j < ny; j++) {
291	for(int k = -nz; k < nz; k++) {
292
293	//get the position of the cell sites
294	simpleLat->getLatticePointsPos(latticePos, i, j, k);
295
296	for(int l = 0; l < numMolPerCell; l++) {
297	#ifdef HAVE_CGAL
298	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
299	#endif
300	if (mol != NULL) {
301	locator->placeMol(latticePos[l], latticeOrt[l], mol);
302	} else {
303	std::cerr<<"Error in placing molecule " << std::endl;
304	}
305	mol = NewInfo->nextMolecule(mi);
306	#ifdef HAVE_CGAL
307	}
308	#endif
309	}
310	}
311	}
312	}
313
314
315
316	//fill Hmat
317	hmat(0, 0)= nx * latticeConstant;
318	hmat(0, 1) = 0.0;
319	hmat(0, 2) = 0.0;
320
321	hmat(1, 0) = 0.0;
322	hmat(1, 1) = ny * latticeConstant;
323	hmat(1, 2) = 0.0;
324
325	hmat(2, 0) = 0.0;
326	hmat(2, 1) = 0.0;
327	hmat(2, 2) = nz * latticeConstant;
328
329	//set Hmat
330	NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
331
332
333	//create dumpwriter and write out the coordinates
334	NewInfo->setFinalConfigFileName(outInitFileName);
335	writer = new DumpWriter(NewInfo);
336
337	if (writer == NULL) {
338	std::cerr << "error in creating DumpWriter" << std::endl;
339	exit(1);
340	}
341
342	writer->writeDump();
343	std::cout << "new initial configuration file: " << outInitFileName
344	<< " is generated." << std::endl;
345
346	//delete objects
347
348	//delete oldInfo and oldSimSetup
349
350	if (NewInfo != NULL)
351	delete NewInfo;
352
353	if (writer != NULL)
354	delete writer;
355	delete simpleLat;
356	cmdline_parser_free(&args_info);
357	return 0;
358	}
359
360	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
361	int numMol) {
362	ifstream oldMdFile;
363	ofstream newMdFile;
364	const int MAXLEN = 65535;
365	char buffer[MAXLEN];
366
367	//create new .md file based on old .md file
368	oldMdFile.open(oldMdFileName.c_str());
369	newMdFile.open(newMdFileName.c_str());
370
371	oldMdFile.getline(buffer, MAXLEN);
372
373	while (!oldMdFile.eof()) {
374
375	//correct molecule number
376	if (strstr(buffer, "nMol") != NULL) {
377	sprintf(buffer, "\tnMol = %i;", numMol);
378	newMdFile << buffer << std::endl;
379	} else
380	newMdFile << buffer << std::endl;
381
382	oldMdFile.getline(buffer, MAXLEN);
383	}
384
385	oldMdFile.close();
386	newMdFile.close();
387	}
388