applications/simpleBuilder/simpleBuilder.cpp

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "io/Globals.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimSetup.hpp"
#include "applications/simpleBuilder/simpleBuilderCmd.h"
#include "utils/StringUtils.hpp"
#include "applications/simpleBuilder/LatticeFactory.hpp"
#include "math/Vector3.hpp"
#include "applications/simpleBuilder/MoLocator.hpp"
#include "applications/simpleBuilder/Lattice.hpp"

using namespace std;

void createMdFile(const string&oldMdFileName, const string&newMdFileName,
                  int numMol);
double getMolMass(MoleculeStamp * molStamp, ForceFields * myFF);

int main(int argc, char *argv []) {
    gengetopt_args_info args_info;
    string latticeType;
    string inputFileName;
    string outPrefix;
    string outMdFileName;
    string outInitFileName;
    SimInfo *oldInfo;
    SimSetup *oldSimSetup;
    BaseLattice *simpleLat;
    int numMol;
    double latticeConstant;
    vector < double > lc;
    double mass;
    const double rhoConvertConst = 1.661;
    double density;
    int nx,
    ny,
    nz;
    double Hmat[3][3];
    MoLocator *locator;
    vector < Vector3d > latticePos;
    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)) {
        cerr << latticeType << " is an invalid lattice type" << endl;
        cerr << LatticeFactory::getInstance()->toString() << endl;
        exit(1);
    }

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

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

    ny = args_info.ny_arg;

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

    nz = args_info.nz_arg;

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

    //get input file name
    if (args_info.inputs_num)
        inputFileName = args_info.inputs[0];
    else {
        cerr << "You must specify a input file name.\n" << endl;
        cmdline_parser_print_help();
        exit(1);
    }

    //parse md file and set up the system
    oldInfo = new SimInfo;

    if (oldInfo == NULL) {
        cerr << "error in creating SimInfo" << endl;
        exit(1);
    }

    oldSimSetup = new SimSetup();

    if (oldSimSetup == NULL) {
        cerr << "error in creating SimSetup" << endl;
        exit(1);
    }

    oldSimSetup->suspendInit();
    oldSimSetup->setSimInfo(oldInfo);
    oldSimSetup->parseFile(&inputFileName[0]);
    oldSimSetup->createSim();

    if (oldInfo->nComponents >= 2) {
        cerr << "can not build the system with more than two components"
            << endl;
        exit(1);
    }

    //get mass of molecule. 
    //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
    mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());

    //creat lattice
    simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);

    if (simpleLat == NULL) {
        cerr << "Error in creating lattice" << 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->n_mol != 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);
        cerr
            << "SimpleBuilder Error: the number of molecule and the density are not matched"
            << endl;
        cerr << "A new .md file: " << outMdFileName
            << " is generated, use it to rerun the simpleBuilder" << 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";

    //allocat memory for storing pos, vel and etc
    oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);

    for(int i = 0; i < oldInfo->n_atoms; i++)
oldInfo->atoms[i]->setCoords();

    //creat Molocator
    locator = new MoLocator(oldInfo->compStamps[0],
                            oldSimSetup->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->setBoxM(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();

    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++)
            locator->placeMol(latticePos[l], latticeOrt[l],
                              &(oldInfo->molecules[curMolIndex++]));
            }
        }
    }

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

    if (writer == NULL) {
        cerr << "error in creating DumpWriter" << endl;
        exit(1);
    }

    writer->writeFinal(0);
    cout << "new initial configuration file: " << outInitFileName
        << " is generated." << endl;

    //delete objects

    //delete oldInfo and oldSimSetup
    if (oldInfo != NULL)
        delete oldInfo;

    if (oldSimSetup != NULL)
        delete oldSimSetup;

    if (writer != NULL)
        delete writer;

    return 0;
}

void createMdFile(const string&oldMdFileName, const 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 << endl;
        } else
            newMdFile << buffer << endl;

        oldMdFile.getline(buffer, MAXLEN);
    }

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

double getMolMass(MoleculeStamp *molStamp, ForceFields *myFF) {
    int nAtoms;
    AtomStamp *currAtomStamp;
    double totMass;

    totMass = 0;
    nAtoms = molStamp->getNAtoms();

    for(size_t i = 0; i < nAtoms; i++) {
        currAtomStamp = molStamp->getAtom(i);
        totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
    }

    return totMass;
}
Revision:	1770
Committed:	Tue Nov 23 17:53:43 2004 UTC (19 years, 9 months ago) by tim
File size:	7826 byte(s)
Log Message:	add Electrostatic AtomType Section Parser
#	User	Rev	Content
1	tim	1770	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
4			#include <cmath>
5			#include <iostream>
6			#include <string>
7			#include <map>
8			#include <fstream>
9
10			#include "io/Globals.hpp"
11			#include "brains/SimInfo.hpp"
12			#include "brains/SimSetup.hpp"
13			#include "applications/simpleBuilder/simpleBuilderCmd.h"
14			#include "utils/StringUtils.hpp"
15			#include "applications/simpleBuilder/LatticeFactory.hpp"
16			#include "math/Vector3.hpp"
17			#include "applications/simpleBuilder/MoLocator.hpp"
18			#include "applications/simpleBuilder/Lattice.hpp"
19
20			using namespace std;
21
22			void createMdFile(const string&oldMdFileName, const string&newMdFileName,
23			int numMol);
24			double getMolMass(MoleculeStamp * molStamp, ForceFields * myFF);
25
26			int main(int argc, char *argv []) {
27			gengetopt_args_info args_info;
28			string latticeType;
29			string inputFileName;
30			string outPrefix;
31			string outMdFileName;
32			string outInitFileName;
33			SimInfo *oldInfo;
34			SimSetup *oldSimSetup;
35			BaseLattice *simpleLat;
36			int numMol;
37			double latticeConstant;
38			vector < double > lc;
39			double mass;
40			const double rhoConvertConst = 1.661;
41			double density;
42			int nx,
43			ny,
44			nz;
45			double Hmat[3][3];
46			MoLocator *locator;
47			vector < Vector3d > latticePos;
48			vector < Vector3d > latticeOrt;
49			int numMolPerCell;
50			int curMolIndex;
51			DumpWriter *writer;
52
53			// parse command line arguments
54			if (cmdline_parser(argc, argv, &args_info) != 0)
55			exit(1);
56
57			density = args_info.density_arg;
58
59			//get lattice type
60			latticeType = UpperCase(args_info.latticetype_arg);
61
62			if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) {
63			cerr << latticeType << " is an invalid lattice type" << endl;
64			cerr << LatticeFactory::getInstance()->toString() << endl;
65			exit(1);
66			}
67
68			//get the number of unit cell
69			nx = args_info.nx_arg;
70
71			if (nx <= 0) {
72			cerr << "The number of unit cell in h direction must be greater than 0"
73			<< endl;
74			exit(1);
75			}
76
77			ny = args_info.ny_arg;
78
79			if (ny <= 0) {
80			cerr << "The number of unit cell in l direction must be greater than 0"
81			<< endl;
82			exit(1);
83			}
84
85			nz = args_info.nz_arg;
86
87			if (nz <= 0) {
88			cerr << "The number of unit cell in k direction must be greater than 0"
89			<< endl;
90			exit(1);
91			}
92
93			//get input file name
94			if (args_info.inputs_num)
95			inputFileName = args_info.inputs[0];
96			else {
97			cerr << "You must specify a input file name.\n" << endl;
98			cmdline_parser_print_help();
99			exit(1);
100			}
101
102			//parse md file and set up the system
103			oldInfo = new SimInfo;
104
105			if (oldInfo == NULL) {
106			cerr << "error in creating SimInfo" << endl;
107			exit(1);
108			}
109
110			oldSimSetup = new SimSetup();
111
112			if (oldSimSetup == NULL) {
113			cerr << "error in creating SimSetup" << endl;
114			exit(1);
115			}
116
117			oldSimSetup->suspendInit();
118			oldSimSetup->setSimInfo(oldInfo);
119			oldSimSetup->parseFile(&inputFileName[0]);
120			oldSimSetup->createSim();
121
122			if (oldInfo->nComponents >= 2) {
123			cerr << "can not build the system with more than two components"
124			<< endl;
125			exit(1);
126			}
127
128			//get mass of molecule.
129			//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
130			mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());
131
132			//creat lattice
133			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
134
135			if (simpleLat == NULL) {
136			cerr << "Error in creating lattice" << endl;
137			exit(1);
138			}
139
140			numMolPerCell = simpleLat->getNumSitesPerCell();
141
142			//calculate lattice constant (in Angstrom)
143			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
144			1.0 / 3.0);
145
146			//set lattice constant
147			lc.push_back(latticeConstant);
148			simpleLat->setLatticeConstant(lc);
149
150			//calculate the total number of molecules
151			numMol = nx * ny * nz * numMolPerCell;
152
153			if (oldInfo->n_mol != numMol) {
154			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
155			outMdFileName = outPrefix + ".md";
156
157			//creat new .md file on fly which corrects the number of molecule
158			createMdFile(inputFileName, outMdFileName, numMol);
159			cerr
160			<< "SimpleBuilder Error: the number of molecule and the density are not matched"
161			<< endl;
162			cerr << "A new .md file: " << outMdFileName
163			<< " is generated, use it to rerun the simpleBuilder" << endl;
164			exit(1);
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			//allocat memory for storing pos, vel and etc
174			oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
175
176			for(int i = 0; i < oldInfo->n_atoms; i++)
177			oldInfo->atoms[i]->setCoords();
178
179			//creat Molocator
180			locator = new MoLocator(oldInfo->compStamps[0],
181			oldSimSetup->getForceField());
182
183			//fill Hmat
184			Hmat[0][0] = nx * latticeConstant;
185			Hmat[0][1] = 0.0;
186			Hmat[0][2] = 0.0;
187
188			Hmat[1][0] = 0.0;
189			Hmat[1][1] = ny * latticeConstant;
190			Hmat[1][2] = 0.0;
191
192			Hmat[2][0] = 0.0;
193			Hmat[2][1] = 0.0;
194			Hmat[2][2] = nz * latticeConstant;
195
196			//set Hmat
197			oldInfo->setBoxM(Hmat);
198
199			//place the molecules
200
201			curMolIndex = 0;
202
203			//get the orientation of the cell sites
204			//for the same type of molecule in same lattice, it will not change
205			latticeOrt = simpleLat->getLatticePointsOrt();
206
207			for(int i = 0; i < nx; i++) {
208			for(int j = 0; j < ny; j++) {
209			for(int k = 0; k < nz; k++) {
210
211			//get the position of the cell sites
212			simpleLat->getLatticePointsPos(latticePos, i, j, k);
213
214			for(int l = 0; l < numMolPerCell; l++)
215			locator->placeMol(latticePos[l], latticeOrt[l],
216			&(oldInfo->molecules[curMolIndex++]));
217			}
218			}
219			}
220
221			//create dumpwriter and write out the coordinates
222			oldInfo->finalName = outInitFileName;
223			writer = new DumpWriter(oldInfo);
224
225			if (writer == NULL) {
226			cerr << "error in creating DumpWriter" << endl;
227			exit(1);
228			}
229
230			writer->writeFinal(0);
231			cout << "new initial configuration file: " << outInitFileName
232			<< " is generated." << endl;
233
234			//delete objects
235
236			//delete oldInfo and oldSimSetup
237			if (oldInfo != NULL)
238			delete oldInfo;
239
240			if (oldSimSetup != NULL)
241			delete oldSimSetup;
242
243			if (writer != NULL)
244			delete writer;
245
246			return 0;
247			}
248
249			void createMdFile(const string&oldMdFileName, const string&newMdFileName,
250			int numMol) {
251			ifstream oldMdFile;
252			ofstream newMdFile;
253			const int MAXLEN = 65535;
254			char buffer[MAXLEN];
255
256			//create new .md file based on old .md file
257			oldMdFile.open(oldMdFileName.c_str());
258			newMdFile.open(newMdFileName.c_str());
259
260			oldMdFile.getline(buffer, MAXLEN);
261
262			while (!oldMdFile.eof()) {
263
264			//correct molecule number
265			if (strstr(buffer, "nMol") != NULL) {
266			sprintf(buffer, "\t\tnMol = %d;", numMol);
267			newMdFile << buffer << endl;
268			} else
269			newMdFile << buffer << endl;
270
271			oldMdFile.getline(buffer, MAXLEN);
272			}
273
274			oldMdFile.close();
275			newMdFile.close();
276			}
277
278			double getMolMass(MoleculeStamp molStamp, ForceFields myFF) {
279			int nAtoms;
280			AtomStamp *currAtomStamp;
281			double totMass;
282
283			totMass = 0;
284			nAtoms = molStamp->getNAtoms();
285
286			for(size_t i = 0; i < nAtoms; i++) {
287			currAtomStamp = molStamp->getAtom(i);
288			totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
289			}
290
291			return totMass;
292			}