applications/simpleBuilder/simpleBuilder.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 "applications/simpleBuilder/simpleBuilderCmd.h"
#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();
    
    gengetopt_args_info args_info;
    std::string latticeType;
    std::string inputFileName;
    std::string outPrefix;
    std::string outMdFileName;
    std::string outInitFileName;
    BaseLattice *simpleLat;
    int numMol;
    double latticeConstant;
    std::vector<double> lc;
    double mass;
    const double rhoConvertConst = 1.661;
    double density;
    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);

    density = args_info.density_arg;

    //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 the number of unit cell
    nx = args_info.nx_arg;

    if (nx <= 0) {
        std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
        exit(1);
    }

    ny = args_info.ny_arg;

    if (ny <= 0) {
        std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
        exit(1);
    }

    nz = args_info.nz_arg;

    if (nz <= 0) {
        std::cerr << "The number of unit cell in k direction must be greater than 0" << 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()>= 2) {
        std::cerr << "can not build the system with more than two 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);

    //set lattice constant
    lc.push_back(latticeConstant);
    simpleLat->setLatticeConstant(lc);

    //calculate the total number of molecules
    numMol = nx * ny * nz * numMolPerCell;

    if (oldInfo->getNGlobalMolecules() != numMol) {
        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);
        std::cerr
            << "SimpleBuilder Error: the number of molecule and the density are not matched"
            << std::endl;
        std::cerr << "A new .md file: " << outMdFileName
            << " is generated, use it to rerun the simpleBuilder" << std::endl;
        exit(1);
    }

    //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());

    //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);

    //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);
                }
            }
        }
    }

    //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:	2178
Committed:	Tue Apr 12 21:27:27 2005 UTC (19 years, 3 months ago) by gezelter
File size:	9305 byte(s)
Log Message:	added lattice directory, so all of these files are now redundant
#	User	Rev	Content
1	gezelter	1930	/*
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	tim	1501	#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 "applications/simpleBuilder/simpleBuilderCmd.h"
52	gezelter	2178	#include "lattice/LatticeFactory.hpp"
53			#include "utils/MoLocator.hpp"
54			#include "lattice/Lattice.hpp"
55	gezelter	1930	#include "brains/Register.hpp"
56			#include "brains/SimInfo.hpp"
57			#include "brains/SimCreator.hpp"
58			#include "io/DumpWriter.hpp"
59			#include "math/Vector3.hpp"
60			#include "math/SquareMatrix3.hpp"
61			#include "utils/StringUtils.hpp"
62	tim	1501
63			using namespace std;
64	gezelter	1930	using namespace oopse;
65			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
66			int numMol);
67	tim	1501
68	gezelter	1930	int main(int argc, char *argv []) {
69	tim	1501
70	gezelter	1930	//register force fields
71			registerForceFields();
72
73			gengetopt_args_info args_info;
74			std::string latticeType;
75			std::string inputFileName;
76			std::string outPrefix;
77			std::string outMdFileName;
78			std::string outInitFileName;
79			BaseLattice *simpleLat;
80			int numMol;
81			double latticeConstant;
82			std::vector<double> lc;
83			double mass;
84			const double rhoConvertConst = 1.661;
85			double density;
86			int nx,
87			ny,
88			nz;
89			Mat3x3d hmat;
90			MoLocator *locator;
91			std::vector<Vector3d> latticePos;
92			std::vector<Vector3d> latticeOrt;
93			int numMolPerCell;
94			int curMolIndex;
95			DumpWriter *writer;
96	tim	1501
97	gezelter	1930	// parse command line arguments
98			if (cmdline_parser(argc, argv, &args_info) != 0)
99			exit(1);
100	tim	1501
101	gezelter	1930	density = args_info.density_arg;
102	tim	1501
103	gezelter	1930	//get lattice type
104			latticeType = UpperCase(args_info.latticetype_arg);
105	tim	1501
106	gezelter	1930	if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) {
107			std::cerr << latticeType << " is an invalid lattice type" << std::endl;
108			std::cerr << LatticeFactory::getInstance()->toString() << std::endl;
109			exit(1);
110			}
111	tim	1501
112	gezelter	1930	//get the number of unit cell
113			nx = args_info.nx_arg;
114	tim	1501
115	gezelter	1930	if (nx <= 0) {
116			std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
117			exit(1);
118			}
119	tim	1501
120	gezelter	1930	ny = args_info.ny_arg;
121	tim	1501
122	gezelter	1930	if (ny <= 0) {
123			std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
124			exit(1);
125			}
126	tim	1501
127	gezelter	1930	nz = args_info.nz_arg;
128	tim	1501
129	gezelter	1930	if (nz <= 0) {
130			std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl;
131			exit(1);
132			}
133	tim	1501
134	gezelter	1930	//get input file name
135			if (args_info.inputs_num)
136			inputFileName = args_info.inputs[0];
137			else {
138			std::cerr << "You must specify a input file name.\n" << std::endl;
139			cmdline_parser_print_help();
140			exit(1);
141			}
142	tim	1501
143	gezelter	1930	//parse md file and set up the system
144			SimCreator oldCreator;
145			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
146	tim	1501
147	gezelter	1930	if (oldInfo->getNMoleculeStamp()>= 2) {
148			std::cerr << "can not build the system with more than two components"
149			<< std::endl;
150			exit(1);
151			}
152	tim	1501
153	gezelter	1930	//get mass of molecule.
154	tim	1501
155	gezelter	1930	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
156	tim	1501
157	gezelter	1930	//creat lattice
158			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
159	tim	1501
160	gezelter	1930	if (simpleLat == NULL) {
161			std::cerr << "Error in creating lattice" << std::endl;
162			exit(1);
163			}
164	tim	1501
165	gezelter	1930	numMolPerCell = simpleLat->getNumSitesPerCell();
166	tim	1501
167	gezelter	1930	//calculate lattice constant (in Angstrom)
168			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
169			1.0 / 3.0);
170	tim	1501
171	gezelter	1930	//set lattice constant
172			lc.push_back(latticeConstant);
173			simpleLat->setLatticeConstant(lc);
174	tim	1501
175	gezelter	1930	//calculate the total number of molecules
176			numMol = nx * ny * nz * numMolPerCell;
177	tim	1501
178	gezelter	1930	if (oldInfo->getNGlobalMolecules() != numMol) {
179			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
180			outMdFileName = outPrefix + ".md";
181
182			//creat new .md file on fly which corrects the number of molecule
183			createMdFile(inputFileName, outMdFileName, numMol);
184			std::cerr
185			<< "SimpleBuilder Error: the number of molecule and the density are not matched"
186			<< std::endl;
187			std::cerr << "A new .md file: " << outMdFileName
188			<< " is generated, use it to rerun the simpleBuilder" << std::endl;
189			exit(1);
190	tim	1501	}
191
192	gezelter	1930	//determine the output file names
193			if (args_info.output_given)
194			outInitFileName = args_info.output_arg;
195			else
196			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
197
198			//creat Molocator
199			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
200	tim	1501
201	gezelter	1930	//fill Hmat
202			hmat(0, 0)= nx * latticeConstant;
203			hmat(0, 1) = 0.0;
204			hmat(0, 2) = 0.0;
205	tim	1501
206	gezelter	1930	hmat(1, 0) = 0.0;
207			hmat(1, 1) = ny * latticeConstant;
208			hmat(1, 2) = 0.0;
209	tim	1501
210	gezelter	1930	hmat(2, 0) = 0.0;
211			hmat(2, 1) = 0.0;
212			hmat(2, 2) = nz * latticeConstant;
213	tim	1501
214	gezelter	1930	//set Hmat
215			oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
216	tim	1501
217	gezelter	1930	//place the molecules
218
219			curMolIndex = 0;
220
221			//get the orientation of the cell sites
222			//for the same type of molecule in same lattice, it will not change
223			latticeOrt = simpleLat->getLatticePointsOrt();
224
225			Molecule* mol;
226			SimInfo::MoleculeIterator mi;
227			mol = oldInfo->beginMolecule(mi);
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
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			if (mol != NULL) {
237			locator->placeMol(latticePos[l], latticeOrt[l], mol);
238			} else {
239			std::cerr << std::endl;
240			}
241			mol = oldInfo->nextMolecule(mi);
242			}
243			}
244			}
245	tim	1501	}
246
247	gezelter	1930	//create dumpwriter and write out the coordinates
248			oldInfo->setFinalConfigFileName(outInitFileName);
249	tim	2060	writer = new DumpWriter(oldInfo);
250	tim	1501
251	gezelter	1930	if (writer == NULL) {
252			std::cerr << "error in creating DumpWriter" << std::endl;
253			exit(1);
254			}
255	tim	1501
256	gezelter	1930	writer->writeDump();
257			std::cout << "new initial configuration file: " << outInitFileName
258			<< " is generated." << std::endl;
259
260			//delete objects
261
262			//delete oldInfo and oldSimSetup
263			if (oldInfo != NULL)
264			delete oldInfo;
265
266			if (writer != NULL)
267			delete writer;
268
269			return 0;
270	tim	1501	}
271
272	gezelter	1930	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
273			int numMol) {
274			ifstream oldMdFile;
275			ofstream newMdFile;
276			const int MAXLEN = 65535;
277			char buffer[MAXLEN];
278	tim	1501
279	gezelter	1930	//create new .md file based on old .md file
280			oldMdFile.open(oldMdFileName.c_str());
281			newMdFile.open(newMdFileName.c_str());
282	tim	1501
283	gezelter	1930	oldMdFile.getline(buffer, MAXLEN);
284
285			while (!oldMdFile.eof()) {
286
287			//correct molecule number
288			if (strstr(buffer, "nMol") != NULL) {
289			sprintf(buffer, "\t\tnMol = %d;", numMol);
290			newMdFile << buffer << std::endl;
291			} else
292			newMdFile << buffer << std::endl;
293
294			oldMdFile.getline(buffer, MAXLEN);
295			}
296
297			oldMdFile.close();
298			newMdFile.close();
299	tim	1501	}
300	gezelter	1930