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 "applications/simpleBuilder/LatticeFactory.hpp"
#include "applications/simpleBuilder/MoLocator.hpp"
#include "applications/simpleBuilder/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();
    
    gengetopt_args_info args_info;
    std::string latticeType;
    std::string inputFileName;
    std::string outPrefix;
    std::string outMdFileName;
    std::string outInitFileName;
                std::string outGeomFileName;
                
                
    BaseLattice *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);

    if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) {
        std::cerr << latticeType << " is an invalid lattice type" << std::endl;
        std::cerr << LatticeFactory::getInstance()->toString() << std::endl;
        exit(1);
    }

    
    //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:	467
Committed:	Mon Apr 11 21:37:30 2005 UTC (20 years, 6 months ago) by chuckv
File size:	10721 byte(s)
Log Message:	Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
#	User	Rev	Content
1	chuckv	467	/*
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			#include "applications/simpleBuilder/LatticeFactory.hpp"
54			#include "applications/simpleBuilder/MoLocator.hpp"
55			#include "applications/simpleBuilder/Lattice.hpp"
56			#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
74			gengetopt_args_info args_info;
75			std::string latticeType;
76			std::string inputFileName;
77			std::string outPrefix;
78			std::string outMdFileName;
79			std::string outInitFileName;
80			std::string outGeomFileName;
81
82
83			BaseLattice *simpleLat;
84			int numMol;
85			double latticeConstant;
86			std::vector<double> lc;
87			double mass;
88			const double rhoConvertConst = 1.661;
89			double density;
90			double rodLength;
91			double rodDiameter;
92
93
94			int nx,
95			ny,
96			nz;
97			Mat3x3d hmat;
98			MoLocator *locator;
99			std::vector<Vector3d> latticePos;
100			std::vector<Vector3d> latticeOrt;
101			int numMolPerCell;
102			int curMolIndex;
103			DumpWriter *writer;
104
105			// parse command line arguments
106			if (cmdline_parser(argc, argv, &args_info) != 0)
107			exit(1);
108
109
110
111			//get lattice type
112			latticeType = UpperCase(args_info.latticetype_arg);
113
114			if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) {
115			std::cerr << latticeType << " is an invalid lattice type" << std::endl;
116			std::cerr << LatticeFactory::getInstance()->toString() << std::endl;
117			exit(1);
118			}
119
120
121			//get input file name
122			if (args_info.inputs_num)
123			inputFileName = args_info.inputs[0];
124			else {
125			std::cerr << "You must specify a input file name.\n" << std::endl;
126			cmdline_parser_print_help();
127			exit(1);
128			}
129
130			//parse md file and set up the system
131			SimCreator oldCreator;
132			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
133
134			if (oldInfo->getNMoleculeStamp()> 1) {
135			std::cerr << "can not build nanorod with more than one components"
136			<< std::endl;
137			exit(1);
138			}
139
140			//get mass of molecule.
141
142			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
143
144			//creat lattice
145			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
146
147			if (simpleLat == NULL) {
148			std::cerr << "Error in creating lattice" << std::endl;
149			exit(1);
150			}
151
152			numMolPerCell = simpleLat->getNumSitesPerCell();
153
154			//calculate lattice constant (in Angstrom)
155			//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
156			// 1.0 / 3.0);
157
158			latticeConstant = args_info.latticeCnst_arg;
159			rodLength = args_info.length_arg;
160			rodDiameter = args_info.width_arg;
161
162			//set lattice constant
163			lc.push_back(latticeConstant);
164			simpleLat->setLatticeConstant(lc);
165
166
167			//determine the output file names
168			if (args_info.output_given)
169			outInitFileName = args_info.output_arg;
170			else
171			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
172
173			//creat Molocator
174			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
175
176			/*
177			Assume we are carving nanorod out of a cublic block of material and that
178			the shape the material will fit within that block....
179			The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the
180			diameter of the particle.
181			*/
182			// Number of Unit Cells in Length first
183			ny = (int)(rodLength/latticeConstant);
184			// Number of unit cells in Width
185			nx = (int)(rodDiameter/latticeConstant);
186			nz = (int)(rodDiameter/latticeConstant);
187
188
189
190			// Create geometry for nanocrystal
191			//GeometryBuilder myGeometry(rodLength,rodDiameter);
192
193			/*
194			We have to build the system first to figure out how many molecules there are
195			then create a md file and then actually build the system.
196			*/
197
198			//place the molecules
199
200			curMolIndex = 0;
201
202			//get the orientation of the cell sites
203			//for the same type of molecule in same lattice, it will not change
204			latticeOrt = simpleLat->getLatticePointsOrt();
205
206
207			/*
208			void BaseLattice::getLatticePointsPos(std::vector<Vector3d>& latticePos, int nx, int ny, int nz){
209
210			latticePos.resize(nCellSites);
211
212			for( int i=0;i < nCellSites;i++){
213
214			latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5);
215			latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5);
216			latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5);
217			}
218
219			*/
220
221
222
223
224			numMol = 0;
225			for(int i = 0; i < nx; i++) {
226			for(int j = 0; j < ny; j++) {
227			for(int k = 0; k < nz; k++) {
228			//if (oldInfo->getNGlobalMolecules() != numMol) {
229
230
231
232			//get the position of the cell sites
233			simpleLat->getLatticePointsPos(latticePos, i, j, k);
234
235			for(int l = 0; l < numMolPerCell; l++) {
236			/*
237			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
238			numMol++;
239			}
240			*/
241			numMol++;
242			}
243			}
244			}
245			}
246
247
248			// needed for writing out new md file.
249
250			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
251			outMdFileName = outPrefix + ".md";
252
253			//creat new .md file on fly which corrects the number of molecule
254			createMdFile(inputFileName, outMdFileName, numMol);
255
256			if (oldInfo != NULL)
257			delete oldInfo;
258
259
260			// We need to read in new siminfo object.
261			//parse md file and set up the system
262			//SimCreator NewCreator;
263
264			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
265
266			// This was so much fun the first time, lets do it again.
267
268			Molecule* mol;
269			SimInfo::MoleculeIterator mi;
270			mol = NewInfo->beginMolecule(mi);
271
272			for(int i = 0; i < nx; i++) {
273			for(int j = 0; j < ny; j++) {
274			for(int k = 0; k < nz; k++) {
275
276			//get the position of the cell sites
277			simpleLat->getLatticePointsPos(latticePos, i, j, k);
278
279			for(int l = 0; l < numMolPerCell; l++) {
280			if (mol != NULL) {
281			/*
282			if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
283			locator->placeMol(latticePos[l], latticeOrt[l], mol);
284			}
285			*/
286			locator->placeMol(latticePos[l], latticeOrt[l], mol);
287			} else {
288			std::cerr << std::endl;
289			}
290			mol = NewInfo->nextMolecule(mi);
291			}
292			}
293			}
294			}
295
296
297
298			//fill Hmat
299			hmat(0, 0)= nx * latticeConstant;
300			hmat(0, 1) = 0.0;
301			hmat(0, 2) = 0.0;
302
303			hmat(1, 0) = 0.0;
304			hmat(1, 1) = ny * latticeConstant;
305			hmat(1, 2) = 0.0;
306
307			hmat(2, 0) = 0.0;
308			hmat(2, 1) = 0.0;
309			hmat(2, 2) = nz * latticeConstant;
310
311			//set Hmat
312			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
313
314
315			//create dumpwriter and write out the coordinates
316			NewInfo->setFinalConfigFileName(outInitFileName);
317			writer = new DumpWriter(NewInfo);
318
319			if (writer == NULL) {
320			std::cerr << "error in creating DumpWriter" << std::endl;
321			exit(1);
322			}
323
324			writer->writeDump();
325			std::cout << "new initial configuration file: " << outInitFileName
326			<< " is generated." << std::endl;
327
328			//delete objects
329
330			//delete oldInfo and oldSimSetup
331
332			if (NewInfo != NULL)
333			delete NewInfo;
334
335			if (writer != NULL)
336			delete writer;
337
338			return 0;
339			}
340
341			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
342			int numMol) {
343			ifstream oldMdFile;
344			ofstream newMdFile;
345			const int MAXLEN = 65535;
346			char buffer[MAXLEN];
347
348			//create new .md file based on old .md file
349			oldMdFile.open(oldMdFileName.c_str());
350			newMdFile.open(newMdFileName.c_str());
351
352			oldMdFile.getline(buffer, MAXLEN);
353
354			while (!oldMdFile.eof()) {
355
356			//correct molecule number
357			if (strstr(buffer, "nMol") != NULL) {
358			sprintf(buffer, "\tnMol = %i;", numMol);
359			newMdFile << buffer << std::endl;
360			} else
361			newMdFile << buffer << std::endl;
362
363			oldMdFile.getline(buffer, MAXLEN);
364			}
365
366			oldMdFile.close();
367			newMdFile.close();
368			}
369