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);
  
  
  
  //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_GCAL
  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_GCAL
          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 = 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:	2190
Committed:	Wed Apr 13 22:30:22 2005 UTC (19 years, 2 months ago) by gezelter
File size:	10704 byte(s)
Log Message:	added CGAL checks
#	User	Rev	Content
1	chuckv	2164	/*
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	gezelter	2190
42	chuckv	2164	#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	gezelter	2190	#include "config.h"
52
53	chuckv	2164	#include "nanorodBuilderCmd.h"
54	gezelter	2190	#ifdef HAVE_CGAL
55			#include "GeometryBuilder.hpp"
56			#endif
57	gezelter	2178	#include "lattice/LatticeFactory.hpp"
58			#include "utils/MoLocator.hpp"
59			#include "lattice/Lattice.hpp"
60	chuckv	2164	#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	gezelter	2190	void createMdFile(const std::string&oldMdFileName,
71			const std::string&newMdFileName,
72	chuckv	2164	int numMol);
73
74			int main(int argc, char *argv []) {
75	gezelter	2190
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
115			//get lattice type
116			latticeType = UpperCase(args_info.latticetype_arg);
117
118
119			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
120			if (simpleLat == NULL) {
121			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
122			latticeType.c_str());
123			painCave.isFatal = 1;
124			simError();
125			}
126
127			//get input file name
128			if (args_info.inputs_num)
129			inputFileName = args_info.inputs[0];
130			else {
131			std::cerr << "You must specify a input file name.\n" << std::endl;
132			cmdline_parser_print_help();
133			exit(1);
134			}
135
136			//parse md file and set up the system
137			SimCreator oldCreator;
138			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
139
140			if (oldInfo->getNMoleculeStamp()> 1) {
141			std::cerr << "can not build nanorod with more than one components"
142			<< std::endl;
143			exit(1);
144			}
145
146			//get mass of molecule.
147
148			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
149
150			//creat lattice
151			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
152
153			if (simpleLat == NULL) {
154			std::cerr << "Error in creating lattice" << std::endl;
155			exit(1);
156			}
157
158			numMolPerCell = simpleLat->getNumSitesPerCell();
159
160			//calculate lattice constant (in Angstrom)
161			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
162			// 1.0 / 3.0);
163
164			latticeConstant = args_info.latticeCnst_arg;
165			rodLength = args_info.length_arg;
166			rodDiameter = args_info.width_arg;
167
168			//set lattice constant
169			lc.push_back(latticeConstant);
170			simpleLat->setLatticeConstant(lc);
171
172
173			//determine the output file names
174			if (args_info.output_given)
175			outInitFileName = args_info.output_arg;
176			else
177			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
178
179			//creat Molocator
180			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
181
182			/*
183			Assume we are carving nanorod out of a cublic block of material and that
184			the shape the material will fit within that block....
185			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
186			diameter of the particle.
187			*/
188			// Number of Unit Cells in Length first
189			ny = (int)(rodLength/latticeConstant);
190			// Number of unit cells in Width
191			nx = (int)(rodDiameter/latticeConstant);
192			nz = (int)(rodDiameter/latticeConstant);
193
194
195
196			// Create geometry for nanocrystal
197			#ifdef HAVE_GCAL
198			GeometryBuilder myGeometry(rodLength,rodDiameter);
199			#endif
200
201			/*
202			We have to build the system first to figure out how many molecules
203			there are then create a md file and then actually build the
204			system.
205			*/
206
207			//place the molecules
208
209			curMolIndex = 0;
210
211			//get the orientation of the cell sites
212			//for the same type of molecule in same lattice, it will not change
213			latticeOrt = simpleLat->getLatticePointsOrt();
214
215
216			/*
217			void BaseLattice::getLatticePointsPos(std::vector<Vector3d>&
218			latticePos, int nx, int ny, int nz){
219	chuckv	2164
220	gezelter	2190	latticePos.resize(nCellSites);
221
222			for( int i=0;i < nCellSites;i++){
223	chuckv	2164
224	gezelter	2190	latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
225			latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
226			latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);
227	chuckv	2164	}
228
229	gezelter	2190	*/
230
231
232
233
234			numMol = 0;
235			for(int i = 0; i < nx; i++) {
236			for(int j = 0; j < ny; j++) {
237			for(int k = 0; k < nz; k++) {
238			//if (oldInfo->getNGlobalMolecules() != numMol) {
239	chuckv	2164
240	gezelter	2190
241
242			//get the position of the cell sites
243			simpleLat->getLatticePointsPos(latticePos, i, j, k);
244
245			for(int l = 0; l < numMolPerCell; l++) {
246	chuckv	2164
247	gezelter	2190	#ifdef HAVE_GCAL
248			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
249			numMol++;
250			}
251			#else
252			numMol++;
253			#endif
254			}
255			}
256	chuckv	2164	}
257	gezelter	2190	}
258
259
260			// needed for writing out new md file.
261
262			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
263			outMdFileName = outPrefix + ".md";
264
265			//creat new .md file on fly which corrects the number of molecule
266			createMdFile(inputFileName, outMdFileName, numMol);
267
268			if (oldInfo != NULL)
269			delete oldInfo;
270
271
272			// We need to read in new siminfo object.
273			//parse md file and set up the system
274			//SimCreator NewCreator;
275
276			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
277
278			// This was so much fun the first time, lets do it again.
279
280			Molecule* mol;
281			SimInfo::MoleculeIterator mi;
282			mol = NewInfo->beginMolecule(mi);
283
284			for(int i = 0; i < nx; i++) {
285			for(int j = 0; j < ny; j++) {
286			for(int k = 0; k < nz; k++) {
287
288			//get the position of the cell sites
289			simpleLat->getLatticePointsPos(latticePos, i, j, k);
290
291			for(int l = 0; l < numMolPerCell; l++) {
292			if (mol != NULL) {
293	chuckv	2164
294	gezelter	2190	#ifdef HAVE_GCAL
295			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
296			locator->placeMol(latticePos[l], latticeOrt[l], mol);
297			}
298			#else
299
300			locator->placeMol(latticePos[l], latticeOrt[l], mol);
301			#endif
302			} else {
303			std::cerr << std::endl;
304			}
305			mol = NewInfo->nextMolecule(mi);
306			}
307			}
308	chuckv	2164	}
309	gezelter	2190	}
310
311
312
313			//fill Hmat
314			hmat(0, 0)= nx * latticeConstant;
315			hmat(0, 1) = 0.0;
316			hmat(0, 2) = 0.0;
317
318			hmat(1, 0) = 0.0;
319			hmat(1, 1) = ny * latticeConstant;
320			hmat(1, 2) = 0.0;
321
322			hmat(2, 0) = 0.0;
323			hmat(2, 1) = 0.0;
324			hmat(2, 2) = nz * latticeConstant;
325
326			//set Hmat
327			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
328
329
330			//create dumpwriter and write out the coordinates
331			NewInfo->setFinalConfigFileName(outInitFileName);
332			writer = new DumpWriter(NewInfo);
333
334			if (writer == NULL) {
335			std::cerr << "error in creating DumpWriter" << std::endl;
336			exit(1);
337			}
338
339			writer->writeDump();
340			std::cout << "new initial configuration file: " << outInitFileName
341			<< " is generated." << std::endl;
342
343			//delete objects
344
345			//delete oldInfo and oldSimSetup
346
347			if (NewInfo != NULL)
348			delete NewInfo;
349
350			if (writer != NULL)
351			delete writer;
352			delete simpleLat;
353			cmdline_parser_free(&args_info);
354			return 0;
355	chuckv	2164	}
356
357			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
358			int numMol) {
359	gezelter	2190	ifstream oldMdFile;
360			ofstream newMdFile;
361			const int MAXLEN = 65535;
362			char buffer[MAXLEN];
363
364			//create new .md file based on old .md file
365			oldMdFile.open(oldMdFileName.c_str());
366			newMdFile.open(newMdFileName.c_str());
367
368			oldMdFile.getline(buffer, MAXLEN);
369
370			while (!oldMdFile.eof()) {
371
372			//correct molecule number
373			if (strstr(buffer, "nMol") != NULL) {
374			sprintf(buffer, "\tnMol = %i;", numMol);
375			newMdFile << buffer << std::endl;
376			} else
377			newMdFile << buffer << std::endl;
378
379	chuckv	2164	oldMdFile.getline(buffer, MAXLEN);
380	gezelter	2190	}
381
382			oldMdFile.close();
383			newMdFile.close();
384	chuckv	2164	}
385