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();
    registerLattice();
    
    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:	2181
Committed:	Tue Apr 12 21:58:09 2005 UTC (19 years, 3 months ago) by tim
File size:	9328 byte(s)
Log Message:	refactory LatticeFactory and LatticeCreator
#	Content
1	/*
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 "applications/simpleBuilder/simpleBuilderCmd.h"
52	#include "lattice/LatticeFactory.hpp"
53	#include "utils/MoLocator.hpp"
54	#include "lattice/Lattice.hpp"
55	#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
63	using namespace std;
64	using namespace oopse;
65	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
66	int numMol);
67
68	int main(int argc, char *argv []) {
69
70	//register force fields
71	registerForceFields();
72	registerLattice();
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	BaseLattice *simpleLat;
81	int numMol;
82	double latticeConstant;
83	std::vector<double> lc;
84	double mass;
85	const double rhoConvertConst = 1.661;
86	double density;
87	int nx,
88	ny,
89	nz;
90	Mat3x3d hmat;
91	MoLocator *locator;
92	std::vector<Vector3d> latticePos;
93	std::vector<Vector3d> latticeOrt;
94	int numMolPerCell;
95	int curMolIndex;
96	DumpWriter *writer;
97
98	// parse command line arguments
99	if (cmdline_parser(argc, argv, &args_info) != 0)
100	exit(1);
101
102	density = args_info.density_arg;
103
104	//get lattice type
105	latticeType = UpperCase(args_info.latticetype_arg);
106
107	if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) {
108	std::cerr << latticeType << " is an invalid lattice type" << std::endl;
109	std::cerr << LatticeFactory::getInstance()->toString() << std::endl;
110	exit(1);
111	}
112
113	//get the number of unit cell
114	nx = args_info.nx_arg;
115
116	if (nx <= 0) {
117	std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
118	exit(1);
119	}
120
121	ny = args_info.ny_arg;
122
123	if (ny <= 0) {
124	std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
125	exit(1);
126	}
127
128	nz = args_info.nz_arg;
129
130	if (nz <= 0) {
131	std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl;
132	exit(1);
133	}
134
135	//get input file name
136	if (args_info.inputs_num)
137	inputFileName = args_info.inputs[0];
138	else {
139	std::cerr << "You must specify a input file name.\n" << std::endl;
140	cmdline_parser_print_help();
141	exit(1);
142	}
143
144	//parse md file and set up the system
145	SimCreator oldCreator;
146	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
147
148	if (oldInfo->getNMoleculeStamp()>= 2) {
149	std::cerr << "can not build the system with more than two components"
150	<< std::endl;
151	exit(1);
152	}
153
154	//get mass of molecule.
155
156	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
157
158	//creat lattice
159	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
160
161	if (simpleLat == NULL) {
162	std::cerr << "Error in creating lattice" << std::endl;
163	exit(1);
164	}
165
166	numMolPerCell = simpleLat->getNumSitesPerCell();
167
168	//calculate lattice constant (in Angstrom)
169	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
170	1.0 / 3.0);
171
172	//set lattice constant
173	lc.push_back(latticeConstant);
174	simpleLat->setLatticeConstant(lc);
175
176	//calculate the total number of molecules
177	numMol = nx * ny * nz * numMolPerCell;
178
179	if (oldInfo->getNGlobalMolecules() != numMol) {
180	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
181	outMdFileName = outPrefix + ".md";
182
183	//creat new .md file on fly which corrects the number of molecule
184	createMdFile(inputFileName, outMdFileName, numMol);
185	std::cerr
186	<< "SimpleBuilder Error: the number of molecule and the density are not matched"
187	<< std::endl;
188	std::cerr << "A new .md file: " << outMdFileName
189	<< " is generated, use it to rerun the simpleBuilder" << std::endl;
190	exit(1);
191	}
192
193	//determine the output file names
194	if (args_info.output_given)
195	outInitFileName = args_info.output_arg;
196	else
197	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
198
199	//creat Molocator
200	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
201
202	//fill Hmat
203	hmat(0, 0)= nx * latticeConstant;
204	hmat(0, 1) = 0.0;
205	hmat(0, 2) = 0.0;
206
207	hmat(1, 0) = 0.0;
208	hmat(1, 1) = ny * latticeConstant;
209	hmat(1, 2) = 0.0;
210
211	hmat(2, 0) = 0.0;
212	hmat(2, 1) = 0.0;
213	hmat(2, 2) = nz * latticeConstant;
214
215	//set Hmat
216	oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
217
218	//place the molecules
219
220	curMolIndex = 0;
221
222	//get the orientation of the cell sites
223	//for the same type of molecule in same lattice, it will not change
224	latticeOrt = simpleLat->getLatticePointsOrt();
225
226	Molecule* mol;
227	SimInfo::MoleculeIterator mi;
228	mol = oldInfo->beginMolecule(mi);
229	for(int i = 0; i < nx; i++) {
230	for(int j = 0; j < ny; j++) {
231	for(int k = 0; k < nz; k++) {
232
233	//get the position of the cell sites
234	simpleLat->getLatticePointsPos(latticePos, i, j, k);
235
236	for(int l = 0; l < numMolPerCell; l++) {
237	if (mol != NULL) {
238	locator->placeMol(latticePos[l], latticeOrt[l], mol);
239	} else {
240	std::cerr << std::endl;
241	}
242	mol = oldInfo->nextMolecule(mi);
243	}
244	}
245	}
246	}
247
248	//create dumpwriter and write out the coordinates
249	oldInfo->setFinalConfigFileName(outInitFileName);
250	writer = new DumpWriter(oldInfo);
251
252	if (writer == NULL) {
253	std::cerr << "error in creating DumpWriter" << std::endl;
254	exit(1);
255	}
256
257	writer->writeDump();
258	std::cout << "new initial configuration file: " << outInitFileName
259	<< " is generated." << std::endl;
260
261	//delete objects
262
263	//delete oldInfo and oldSimSetup
264	if (oldInfo != NULL)
265	delete oldInfo;
266
267	if (writer != NULL)
268	delete writer;
269
270	return 0;
271	}
272
273	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
274	int numMol) {
275	ifstream oldMdFile;
276	ofstream newMdFile;
277	const int MAXLEN = 65535;
278	char buffer[MAXLEN];
279
280	//create new .md file based on old .md file
281	oldMdFile.open(oldMdFileName.c_str());
282	newMdFile.open(newMdFileName.c_str());
283
284	oldMdFile.getline(buffer, MAXLEN);
285
286	while (!oldMdFile.eof()) {
287
288	//correct molecule number
289	if (strstr(buffer, "nMol") != NULL) {
290	sprintf(buffer, "\t\tnMol = %d;", numMol);
291	newMdFile << buffer << std::endl;
292	} else
293	newMdFile << buffer << std::endl;
294
295	oldMdFile.getline(buffer, MAXLEN);
296	}
297
298	oldMdFile.close();
299	newMdFile.close();
300	}
301