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 "nanorodBuilderCmd.h"
//#include "GeometryBuilder.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;
    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
                //GeometryBuilder myGeometry(rodLength,rodDiameter);
                
                /*
                 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++) {
                                                /*
                                                if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
                                                        numMol++;
                                                }
                                                 */
                                                numMol++;
                                        }
                                        }
                                }
                        }
                
                        
                // 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) {
                                                        /*
                                                        if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
                                                                locator->placeMol(latticePos[l], latticeOrt[l], mol);
                                                        }               
                                                         */
                                                        locator->placeMol(latticePos[l], latticeOrt[l], mol);
                                                } 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;
                
    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:	2184
Committed:	Tue Apr 12 22:33:50 2005 UTC (19 years, 2 months ago) by tim
File size:	10705 byte(s)
Log Message:	refactory lattice
#	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
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 "nanorodBuilderCmd.h"
52			//#include "GeometryBuilder.hpp"
53	gezelter	2178	#include "lattice/LatticeFactory.hpp"
54			#include "utils/MoLocator.hpp"
55			#include "lattice/Lattice.hpp"
56	chuckv	2164	#include "brains/Register.hpp"
57			#include "brains/SimInfo.hpp"
58			#include "brains/SimCreator.hpp"
59			#include "io/DumpWriter.hpp"
60			#include "math/Vector3.hpp"
61			#include "math/SquareMatrix3.hpp"
62			#include "utils/StringUtils.hpp"
63
64			using namespace std;
65			using namespace oopse;
66			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
67			int numMol);
68
69			int main(int argc, char *argv []) {
70
71			//register force fields
72			registerForceFields();
73	tim	2181	registerLattice();
74	chuckv	2164
75			gengetopt_args_info args_info;
76			std::string latticeType;
77			std::string inputFileName;
78			std::string outPrefix;
79			std::string outMdFileName;
80			std::string outInitFileName;
81			std::string outGeomFileName;
82
83
84	tim	2184	Lattice *simpleLat;
85	chuckv	2164	int numMol;
86			double latticeConstant;
87			std::vector<double> lc;
88			double mass;
89			const double rhoConvertConst = 1.661;
90			double density;
91			double rodLength;
92			double rodDiameter;
93
94
95			int nx,
96			ny,
97			nz;
98			Mat3x3d hmat;
99			MoLocator *locator;
100			std::vector<Vector3d> latticePos;
101			std::vector<Vector3d> latticeOrt;
102			int numMolPerCell;
103			int curMolIndex;
104			DumpWriter *writer;
105
106			// parse command line arguments
107			if (cmdline_parser(argc, argv, &args_info) != 0)
108			exit(1);
109
110
111
112			//get lattice type
113			latticeType = UpperCase(args_info.latticetype_arg);
114
115
116	tim	2184	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
117			if (simpleLat == NULL) {
118			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
119			latticeType.c_str());
120			painCave.isFatal = 1;
121			simError();
122			}
123
124	chuckv	2164	//get input file name
125			if (args_info.inputs_num)
126			inputFileName = args_info.inputs[0];
127			else {
128			std::cerr << "You must specify a input file name.\n" << std::endl;
129			cmdline_parser_print_help();
130			exit(1);
131			}
132
133			//parse md file and set up the system
134			SimCreator oldCreator;
135			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
136
137			if (oldInfo->getNMoleculeStamp()> 1) {
138			std::cerr << "can not build nanorod with more than one components"
139			<< std::endl;
140			exit(1);
141			}
142
143			//get mass of molecule.
144
145			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
146
147			//creat lattice
148			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
149
150			if (simpleLat == NULL) {
151			std::cerr << "Error in creating lattice" << std::endl;
152			exit(1);
153			}
154
155			numMolPerCell = simpleLat->getNumSitesPerCell();
156
157			//calculate lattice constant (in Angstrom)
158			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
159			// 1.0 / 3.0);
160
161			latticeConstant = args_info.latticeCnst_arg;
162			rodLength = args_info.length_arg;
163			rodDiameter = args_info.width_arg;
164
165			//set lattice constant
166			lc.push_back(latticeConstant);
167			simpleLat->setLatticeConstant(lc);
168
169
170			//determine the output file names
171			if (args_info.output_given)
172			outInitFileName = args_info.output_arg;
173			else
174			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
175
176			//creat Molocator
177			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
178
179			/*
180			Assume we are carving nanorod out of a cublic block of material and that
181			the shape the material will fit within that block....
182			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
183			diameter of the particle.
184			*/
185			// Number of Unit Cells in Length first
186			ny = (int)(rodLength/latticeConstant);
187			// Number of unit cells in Width
188			nx = (int)(rodDiameter/latticeConstant);
189			nz = (int)(rodDiameter/latticeConstant);
190
191
192
193			// Create geometry for nanocrystal
194			//GeometryBuilder myGeometry(rodLength,rodDiameter);
195
196			/*
197			We have to build the system first to figure out how many molecules there are
198			then create a md file and then actually build the system.
199			*/
200
201			//place the molecules
202
203			curMolIndex = 0;
204
205			//get the orientation of the cell sites
206			//for the same type of molecule in same lattice, it will not change
207			latticeOrt = simpleLat->getLatticePointsOrt();
208
209
210			/*
211			void BaseLattice::getLatticePointsPos(std::vector<Vector3d>& latticePos, int nx, int ny, int nz){
212
213			latticePos.resize(nCellSites);
214
215			for( int i=0;i < nCellSites;i++){
216
217			latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
218			latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
219			latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);
220			}
221
222			*/
223
224
225
226
227			numMol = 0;
228			for(int i = 0; i < nx; i++) {
229			for(int j = 0; j < ny; j++) {
230			for(int k = 0; k < nz; k++) {
231			//if (oldInfo->getNGlobalMolecules() != numMol) {
232
233
234
235			//get the position of the cell sites
236			simpleLat->getLatticePointsPos(latticePos, i, j, k);
237
238			for(int l = 0; l < numMolPerCell; l++) {
239			/*
240			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
241			numMol++;
242			}
243			*/
244			numMol++;
245			}
246			}
247			}
248			}
249
250
251			// needed for writing out new md file.
252
253			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
254			outMdFileName = outPrefix + ".md";
255
256			//creat new .md file on fly which corrects the number of molecule
257			createMdFile(inputFileName, outMdFileName, numMol);
258
259			if (oldInfo != NULL)
260			delete oldInfo;
261
262
263			// We need to read in new siminfo object.
264			//parse md file and set up the system
265			//SimCreator NewCreator;
266
267			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
268
269			// This was so much fun the first time, lets do it again.
270
271			Molecule* mol;
272			SimInfo::MoleculeIterator mi;
273			mol = NewInfo->beginMolecule(mi);
274
275			for(int i = 0; i < nx; i++) {
276			for(int j = 0; j < ny; j++) {
277			for(int k = 0; k < nz; k++) {
278
279			//get the position of the cell sites
280			simpleLat->getLatticePointsPos(latticePos, i, j, k);
281
282			for(int l = 0; l < numMolPerCell; l++) {
283			if (mol != NULL) {
284			/*
285			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
286			locator->placeMol(latticePos[l], latticeOrt[l], mol);
287			}
288			*/
289			locator->placeMol(latticePos[l], latticeOrt[l], mol);
290			} else {
291			std::cerr << std::endl;
292			}
293			mol = NewInfo->nextMolecule(mi);
294			}
295			}
296			}
297			}
298
299
300
301			//fill Hmat
302			hmat(0, 0)= nx * latticeConstant;
303			hmat(0, 1) = 0.0;
304			hmat(0, 2) = 0.0;
305
306			hmat(1, 0) = 0.0;
307			hmat(1, 1) = ny * latticeConstant;
308			hmat(1, 2) = 0.0;
309
310			hmat(2, 0) = 0.0;
311			hmat(2, 1) = 0.0;
312			hmat(2, 2) = nz * latticeConstant;
313
314			//set Hmat
315			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
316
317
318			//create dumpwriter and write out the coordinates
319			NewInfo->setFinalConfigFileName(outInitFileName);
320			writer = new DumpWriter(NewInfo);
321
322			if (writer == NULL) {
323			std::cerr << "error in creating DumpWriter" << std::endl;
324			exit(1);
325			}
326
327			writer->writeDump();
328			std::cout << "new initial configuration file: " << outInitFileName
329			<< " is generated." << std::endl;
330
331			//delete objects
332
333			//delete oldInfo and oldSimSetup
334
335			if (NewInfo != NULL)
336			delete NewInfo;
337
338			if (writer != NULL)
339			delete writer;
340
341			return 0;
342			}
343
344			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
345			int numMol) {
346			ifstream oldMdFile;
347			ofstream newMdFile;
348			const int MAXLEN = 65535;
349			char buffer[MAXLEN];
350
351			//create new .md file based on old .md file
352			oldMdFile.open(oldMdFileName.c_str());
353			newMdFile.open(newMdFileName.c_str());
354
355			oldMdFile.getline(buffer, MAXLEN);
356
357			while (!oldMdFile.eof()) {
358
359			//correct molecule number
360			if (strstr(buffer, "nMol") != NULL) {
361			sprintf(buffer, "\tnMol = %i;", numMol);
362			newMdFile << buffer << std::endl;
363			} else
364			newMdFile << buffer << std::endl;
365
366			oldMdFile.getline(buffer, MAXLEN);
367			}
368
369			oldMdFile.close();
370			newMdFile.close();
371			}
372