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 "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;
  int curMolIndex;
  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);
  
  
  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
            latticeType.c_str());
    painCave.isFatal = 1;
    simError();
  }        
  
  //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(rodLength,rodDiameter);
#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
  
  curMolIndex = 0;
  
  //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
  latticeOrt = simpleLat->getLatticePointsOrt();
  
  
  /*
    void BaseLattice::getLatticePointsPos(std::vector<Vector3d>&
    latticePos, int nx, int ny, int nz){
    
    latticePos.resize(nCellSites);
                         
    for( int i=0;i < nCellSites;i++){
    
    latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
    latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
    latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);    
    }
    
  */
  
  
  
  
  numMol = 0;
  for(int i = 0; i < nx; i++) {
    for(int j = 0; j < ny; j++) {
      for(int k = 0; 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++;
          }
#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 = 0; i < nx; i++) {
    for(int j = 0; j < ny; j++) {
      for(int k = 0; k < nz; k++) {
        
        //get the position of the cell sites
        simpleLat->getLatticePointsPos(latticePos, i, j, k);
        
        for(int l = 0; l < numMolPerCell; l++) {
          if (mol != NULL) {

#ifdef HAVE_GCAL
            if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
              locator->placeMol(latticePos[l], latticeOrt[l], mol);
            }           
#else
            
            locator->placeMol(latticePos[l], latticeOrt[l], mol);
#endif
          } else {
            std::cerr << std::endl;                    
          }
          mol = NewInfo->nextMolecule(mi);
        }
      }
    }
  }
  
  
  
  //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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	10897 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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 "lattice/LatticeFactory.hpp"
58	#include "utils/MoLocator.hpp"
59	#include "lattice/Lattice.hpp"
60	#include "brains/Register.hpp"
61	#include "brains/SimInfo.hpp"
62	#include "brains/SimCreator.hpp"
63	#include "io/DumpWriter.hpp"
64	#include "math/Vector3.hpp"
65	#include "math/SquareMatrix3.hpp"
66	#include "utils/StringUtils.hpp"
67
68	using namespace std;
69	using namespace oopse;
70	void createMdFile(const std::string&oldMdFileName,
71	const std::string&newMdFileName,
72	int numMol);
73
74	int main(int argc, char *argv []) {
75
76	//register force fields
77	registerForceFields();
78	registerLattice();
79
80	gengetopt_args_info args_info;
81	std::string latticeType;
82	std::string inputFileName;
83	std::string outPrefix;
84	std::string outMdFileName;
85	std::string outInitFileName;
86	std::string outGeomFileName;
87
88
89	Lattice *simpleLat;
90	int numMol;
91	double latticeConstant;
92	std::vector<double> lc;
93	double mass;
94	const double rhoConvertConst = 1.661;
95	double density;
96	double rodLength;
97	double rodDiameter;
98
99
100	int nx, ny, nz;
101	Mat3x3d hmat;
102	MoLocator *locator;
103	std::vector<Vector3d> latticePos;
104	std::vector<Vector3d> latticeOrt;
105	int numMolPerCell;
106	int curMolIndex;
107	DumpWriter *writer;
108
109	// parse command line arguments
110	if (cmdline_parser(argc, argv, &args_info) != 0)
111	exit(1);
112
113
114	// Check for lib CGAL, if we don't have it, we should exit....
115
116	#ifndef HAVE_CGAL
117	std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL."
118	<< std::endl;
119	exit(1);
120	#endif
121
122
123
124	//get lattice type
125	latticeType = UpperCase(args_info.latticetype_arg);
126
127
128	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
129	if (simpleLat == NULL) {
130	sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
131	latticeType.c_str());
132	painCave.isFatal = 1;
133	simError();
134	}
135
136	//get input file name
137	if (args_info.inputs_num)
138	inputFileName = args_info.inputs[0];
139	else {
140	std::cerr << "You must specify a input file name.\n" << std::endl;
141	cmdline_parser_print_help();
142	exit(1);
143	}
144
145	//parse md file and set up the system
146	SimCreator oldCreator;
147	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
148
149	if (oldInfo->getNMoleculeStamp()> 1) {
150	std::cerr << "can not build nanorod with more than one components"
151	<< std::endl;
152	exit(1);
153	}
154
155	//get mass of molecule.
156
157	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
158
159	//creat lattice
160	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
161
162	if (simpleLat == NULL) {
163	std::cerr << "Error in creating lattice" << std::endl;
164	exit(1);
165	}
166
167	numMolPerCell = simpleLat->getNumSitesPerCell();
168
169	//calculate lattice constant (in Angstrom)
170	//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
171	// 1.0 / 3.0);
172
173	latticeConstant = args_info.latticeCnst_arg;
174	rodLength = args_info.length_arg;
175	rodDiameter = args_info.width_arg;
176
177	//set lattice constant
178	lc.push_back(latticeConstant);
179	simpleLat->setLatticeConstant(lc);
180
181
182	//determine the output file names
183	if (args_info.output_given)
184	outInitFileName = args_info.output_arg;
185	else
186	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
187
188	//creat Molocator
189	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
190
191	/*
192	Assume we are carving nanorod out of a cublic block of material and that
193	the shape the material will fit within that block....
194	The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
195	diameter of the particle.
196	*/
197	// Number of Unit Cells in Length first
198	ny = (int)(rodLength/latticeConstant);
199	// Number of unit cells in Width
200	nx = (int)(rodDiameter/latticeConstant);
201	nz = (int)(rodDiameter/latticeConstant);
202
203
204
205	// Create geometry for nanocrystal
206	#ifdef HAVE_CGAL
207	GeometryBuilder myGeometry(rodLength,rodDiameter);
208	#endif
209
210	/*
211	We have to build the system first to figure out how many molecules
212	there are then create a md file and then actually build the
213	system.
214	*/
215
216	//place the molecules
217
218	curMolIndex = 0;
219
220	//get the orientation of the cell sites
221	//for the same type of molecule in same lattice, it will not change
222	latticeOrt = simpleLat->getLatticePointsOrt();
223
224
225	/*
226	void BaseLattice::getLatticePointsPos(std::vector<Vector3d>&
227	latticePos, int nx, int ny, int nz){
228
229	latticePos.resize(nCellSites);
230
231	for( int i=0;i < nCellSites;i++){
232
233	latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
234	latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
235	latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);
236	}
237
238	*/
239
240
241
242
243	numMol = 0;
244	for(int i = 0; i < nx; i++) {
245	for(int j = 0; j < ny; j++) {
246	for(int k = 0; k < nz; k++) {
247	//if (oldInfo->getNGlobalMolecules() != numMol) {
248
249
250
251	//get the position of the cell sites
252	simpleLat->getLatticePointsPos(latticePos, i, j, k);
253
254	for(int l = 0; l < numMolPerCell; l++) {
255
256	#ifdef HAVE_CGAL
257	if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
258	numMol++;
259	}
260	#endif
261	}
262	}
263	}
264	}
265
266
267	// needed for writing out new md file.
268
269	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
270	outMdFileName = outPrefix + ".md";
271
272	//creat new .md file on fly which corrects the number of molecule
273	createMdFile(inputFileName, outMdFileName, numMol);
274
275	if (oldInfo != NULL)
276	delete oldInfo;
277
278
279	// We need to read in new siminfo object.
280	//parse md file and set up the system
281	//SimCreator NewCreator;
282
283	SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
284
285	// This was so much fun the first time, lets do it again.
286
287	Molecule* mol;
288	SimInfo::MoleculeIterator mi;
289	mol = NewInfo->beginMolecule(mi);
290
291	for(int i = 0; i < nx; i++) {
292	for(int j = 0; j < ny; j++) {
293	for(int k = 0; k < nz; k++) {
294
295	//get the position of the cell sites
296	simpleLat->getLatticePointsPos(latticePos, i, j, k);
297
298	for(int l = 0; l < numMolPerCell; l++) {
299	if (mol != NULL) {
300
301	#ifdef HAVE_GCAL
302	if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
303	locator->placeMol(latticePos[l], latticeOrt[l], mol);
304	}
305	#else
306
307	locator->placeMol(latticePos[l], latticeOrt[l], mol);
308	#endif
309	} else {
310	std::cerr << std::endl;
311	}
312	mol = NewInfo->nextMolecule(mi);
313	}
314	}
315	}
316	}
317
318
319
320	//fill Hmat
321	hmat(0, 0)= nx * latticeConstant;
322	hmat(0, 1) = 0.0;
323	hmat(0, 2) = 0.0;
324
325	hmat(1, 0) = 0.0;
326	hmat(1, 1) = ny * latticeConstant;
327	hmat(1, 2) = 0.0;
328
329	hmat(2, 0) = 0.0;
330	hmat(2, 1) = 0.0;
331	hmat(2, 2) = nz * latticeConstant;
332
333	//set Hmat
334	NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
335
336
337	//create dumpwriter and write out the coordinates
338	NewInfo->setFinalConfigFileName(outInitFileName);
339	writer = new DumpWriter(NewInfo);
340
341	if (writer == NULL) {
342	std::cerr << "error in creating DumpWriter" << std::endl;
343	exit(1);
344	}
345
346	writer->writeDump();
347	std::cout << "new initial configuration file: " << outInitFileName
348	<< " is generated." << std::endl;
349
350	//delete objects
351
352	//delete oldInfo and oldSimSetup
353
354	if (NewInfo != NULL)
355	delete NewInfo;
356
357	if (writer != NULL)
358	delete writer;
359	delete simpleLat;
360	cmdline_parser_free(&args_info);
361	return 0;
362	}
363
364	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
365	int numMol) {
366	ifstream oldMdFile;
367	ofstream newMdFile;
368	const int MAXLEN = 65535;
369	char buffer[MAXLEN];
370
371	//create new .md file based on old .md file
372	oldMdFile.open(oldMdFileName.c_str());
373	newMdFile.open(newMdFileName.c_str());
374
375	oldMdFile.getline(buffer, MAXLEN);
376
377	while (!oldMdFile.eof()) {
378
379	//correct molecule number
380	if (strstr(buffer, "nMol") != NULL) {
381	sprintf(buffer, "\tnMol = %i;", numMol);
382	newMdFile << buffer << std::endl;
383	} else
384	newMdFile << buffer << std::endl;
385
386	oldMdFile.getline(buffer, MAXLEN);
387	}
388
389	oldMdFile.close();
390	newMdFile.close();
391	}
392