start/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....
                
                
                
                // Create geometry for nanocrystal
                GeometryBuilder myGeometry(rodLength,rodDiameter);
                
                
                
                
                //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();
                
    Molecule* mol;
    SimInfo::MoleculeIterator mi;
    mol = oldInfo->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) {
                                                        locator->placeMol(latticePos[l], latticeOrt[l], mol);
                                                } else {
                                                        std::cerr << std::endl;                    
                                                }
                                                mol = oldInfo->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
    oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);

    
    //create dumpwriter and write out the coordinates
    oldInfo->setFinalConfigFileName(outInitFileName);
    writer = new DumpWriter(oldInfo);

    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 (oldInfo != NULL)
        delete oldInfo;

    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, "\t\tnMol = %d;", numMol);
            newMdFile << buffer << std::endl;
        } else
            newMdFile << buffer << std::endl;

        oldMdFile.getline(buffer, MAXLEN);
    }

    oldMdFile.close();
    newMdFile.close();
}

Revision:	3484
Committed:	Tue Jan 13 14:39:51 2009 UTC (15 years, 7 months ago)
File size:	8443 byte(s)
Log Message:	This commit was manufactured by cvs2svn to create tag 'start'.
#	User	Rev	Content
1	chuckv	2148	/*
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
180
181
182			// Create geometry for nanocrystal
183			GeometryBuilder myGeometry(rodLength,rodDiameter);
184
185
186
187
188			//place the molecules
189
190			curMolIndex = 0;
191
192			//get the orientation of the cell sites
193			//for the same type of molecule in same lattice, it will not change
194			latticeOrt = simpleLat->getLatticePointsOrt();
195
196			Molecule* mol;
197			SimInfo::MoleculeIterator mi;
198			mol = oldInfo->beginMolecule(mi);
199			for(int i = 0; i < nx; i++) {
200			for(int j = 0; j < ny; j++) {
201			for(int k = 0; k < nz; k++) {
202
203			//get the position of the cell sites
204			simpleLat->getLatticePointsPos(latticePos, i, j, k);
205
206			for(int l = 0; l < numMolPerCell; l++) {
207			if (mol != NULL) {
208			locator->placeMol(latticePos[l], latticeOrt[l], mol);
209			} else {
210			std::cerr << std::endl;
211			}
212			mol = oldInfo->nextMolecule(mi);
213			}
214			}
215			}
216			}
217
218
219
220
221
222
223
224			//fill Hmat
225			hmat(0, 0)= nx * latticeConstant;
226			hmat(0, 1) = 0.0;
227			hmat(0, 2) = 0.0;
228
229			hmat(1, 0) = 0.0;
230			hmat(1, 1) = ny * latticeConstant;
231			hmat(1, 2) = 0.0;
232
233			hmat(2, 0) = 0.0;
234			hmat(2, 1) = 0.0;
235			hmat(2, 2) = nz * latticeConstant;
236
237			//set Hmat
238			oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
239
240
241			//create dumpwriter and write out the coordinates
242			oldInfo->setFinalConfigFileName(outInitFileName);
243			writer = new DumpWriter(oldInfo);
244
245			if (writer == NULL) {
246			std::cerr << "error in creating DumpWriter" << std::endl;
247			exit(1);
248			}
249
250			writer->writeDump();
251			std::cout << "new initial configuration file: " << outInitFileName
252			<< " is generated." << std::endl;
253
254			//delete objects
255
256			//delete oldInfo and oldSimSetup
257			if (oldInfo != NULL)
258			delete oldInfo;
259
260			if (writer != NULL)
261			delete writer;
262
263			return 0;
264			}
265
266			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
267			int numMol) {
268			ifstream oldMdFile;
269			ofstream newMdFile;
270			const int MAXLEN = 65535;
271			char buffer[MAXLEN];
272
273			//create new .md file based on old .md file
274			oldMdFile.open(oldMdFileName.c_str());
275			newMdFile.open(newMdFileName.c_str());
276
277			oldMdFile.getline(buffer, MAXLEN);
278
279			while (!oldMdFile.eof()) {
280
281			//correct molecule number
282			if (strstr(buffer, "nMol") != NULL) {
283			sprintf(buffer, "\t\tnMol = %d;", numMol);
284			newMdFile << buffer << std::endl;
285			} else
286			newMdFile << buffer << std::endl;
287
288			oldMdFile.getline(buffer, MAXLEN);
289			}
290
291			oldMdFile.close();
292			newMdFile.close();
293			}
294