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;
  Lattice *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);

  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
    
  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
            latticeType.c_str());
    painCave.isFatal = 1;
    simError();
  }

  //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;
    
  delete simpleLat;

  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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 3 months ago) by gezelter
File size:	8738 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	2204	//register force fields
71			registerForceFields();
72			registerLattice();
73	gezelter	1930
74	gezelter	2204	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			Lattice *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	gezelter	1930	ny,
89			nz;
90	gezelter	2204	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	tim	1501
98	gezelter	2204	// parse command line arguments
99			if (cmdline_parser(argc, argv, &args_info) != 0)
100			exit(1);
101	tim	1501
102	gezelter	2204	density = args_info.density_arg;
103	tim	1501
104	gezelter	2204	//get lattice type
105			latticeType = UpperCase(args_info.latticetype_arg);
106	tim	1501
107	gezelter	2204	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
108	tim	2184
109	gezelter	2204	if (simpleLat == NULL) {
110			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
111			latticeType.c_str());
112			painCave.isFatal = 1;
113			simError();
114			}
115	tim	1501
116	gezelter	2204	//get the number of unit cell
117			nx = args_info.nx_arg;
118	tim	1501
119	gezelter	2204	if (nx <= 0) {
120			std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
121			exit(1);
122			}
123	tim	1501
124	gezelter	2204	ny = args_info.ny_arg;
125	tim	1501
126	gezelter	2204	if (ny <= 0) {
127			std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
128			exit(1);
129			}
130	tim	1501
131	gezelter	2204	nz = args_info.nz_arg;
132	tim	1501
133	gezelter	2204	if (nz <= 0) {
134			std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl;
135			exit(1);
136			}
137	tim	1501
138	gezelter	2204	//get input file name
139			if (args_info.inputs_num)
140			inputFileName = args_info.inputs[0];
141			else {
142			std::cerr << "You must specify a input file name.\n" << std::endl;
143			cmdline_parser_print_help();
144			exit(1);
145			}
146	tim	1501
147	gezelter	2204	//parse md file and set up the system
148			SimCreator oldCreator;
149			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
150	tim	1501
151	gezelter	2204	if (oldInfo->getNMoleculeStamp()>= 2) {
152			std::cerr << "can not build the system with more than two components"
153			<< std::endl;
154			exit(1);
155			}
156	tim	1501
157	gezelter	2204	//get mass of molecule.
158	tim	1501
159	gezelter	2204	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
160	tim	1501
161	gezelter	2204	//creat lattice
162			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
163	tim	1501
164	gezelter	2204	if (simpleLat == NULL) {
165			std::cerr << "Error in creating lattice" << std::endl;
166			exit(1);
167			}
168	tim	1501
169	gezelter	2204	numMolPerCell = simpleLat->getNumSitesPerCell();
170	tim	1501
171	gezelter	2204	//calculate lattice constant (in Angstrom)
172			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
173			1.0 / 3.0);
174	tim	1501
175	gezelter	2204	//set lattice constant
176			lc.push_back(latticeConstant);
177			simpleLat->setLatticeConstant(lc);
178	tim	1501
179	gezelter	2204	//calculate the total number of molecules
180			numMol = nx * ny * nz * numMolPerCell;
181	tim	1501
182	gezelter	2204	if (oldInfo->getNGlobalMolecules() != numMol) {
183			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
184			outMdFileName = outPrefix + ".md";
185	gezelter	1930
186	gezelter	2204	//creat new .md file on fly which corrects the number of molecule
187			createMdFile(inputFileName, outMdFileName, numMol);
188			std::cerr
189			<< "SimpleBuilder Error: the number of molecule and the density are not matched"
190			<< std::endl;
191			std::cerr << "A new .md file: " << outMdFileName
192			<< " is generated, use it to rerun the simpleBuilder" << std::endl;
193			exit(1);
194			}
195	tim	1501
196	gezelter	2204	//determine the output file names
197			if (args_info.output_given)
198			outInitFileName = args_info.output_arg;
199			else
200			outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
201	gezelter	1930
202	gezelter	2204	//creat Molocator
203			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
204	tim	1501
205	gezelter	2204	//fill Hmat
206			hmat(0, 0)= nx * latticeConstant;
207			hmat(0, 1) = 0.0;
208			hmat(0, 2) = 0.0;
209	tim	1501
210	gezelter	2204	hmat(1, 0) = 0.0;
211			hmat(1, 1) = ny * latticeConstant;
212			hmat(1, 2) = 0.0;
213	tim	1501
214	gezelter	2204	hmat(2, 0) = 0.0;
215			hmat(2, 1) = 0.0;
216			hmat(2, 2) = nz * latticeConstant;
217	tim	1501
218	gezelter	2204	//set Hmat
219			oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
220	tim	1501
221	gezelter	2204	//place the molecules
222	gezelter	1930
223	gezelter	2204	curMolIndex = 0;
224	gezelter	1930
225	gezelter	2204	//get the orientation of the cell sites
226			//for the same type of molecule in same lattice, it will not change
227			latticeOrt = simpleLat->getLatticePointsOrt();
228	gezelter	1930
229	gezelter	2204	Molecule* mol;
230			SimInfo::MoleculeIterator mi;
231			mol = oldInfo->beginMolecule(mi);
232			for(int i = 0; i < nx; i++) {
233			for(int j = 0; j < ny; j++) {
234			for(int k = 0; k < nz; k++) {
235	gezelter	1930
236	gezelter	2204	//get the position of the cell sites
237			simpleLat->getLatticePointsPos(latticePos, i, j, k);
238	gezelter	1930
239	gezelter	2204	for(int l = 0; l < numMolPerCell; l++) {
240			if (mol != NULL) {
241			locator->placeMol(latticePos[l], latticeOrt[l], mol);
242			} else {
243			std::cerr << std::endl;
244			}
245			mol = oldInfo->nextMolecule(mi);
246			}
247			}
248	tim	1501	}
249	gezelter	2204	}
250	tim	1501
251	gezelter	2204	//create dumpwriter and write out the coordinates
252			oldInfo->setFinalConfigFileName(outInitFileName);
253			writer = new DumpWriter(oldInfo);
254	tim	1501
255	gezelter	2204	if (writer == NULL) {
256			std::cerr << "error in creating DumpWriter" << std::endl;
257			exit(1);
258			}
259	tim	1501
260	gezelter	2204	writer->writeDump();
261			std::cout << "new initial configuration file: " << outInitFileName
262			<< " is generated." << std::endl;
263	gezelter	1930
264	gezelter	2204	//delete objects
265	gezelter	1930
266	gezelter	2204	//delete oldInfo and oldSimSetup
267			if (oldInfo != NULL)
268			delete oldInfo;
269	gezelter	1930
270	gezelter	2204	if (writer != NULL)
271			delete writer;
272	tim	2185
273	gezelter	2204	delete simpleLat;
274	gezelter	1930
275	gezelter	2204	return 0;
276	tim	1501	}
277
278	gezelter	1930	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
279			int numMol) {
280	gezelter	2204	ifstream oldMdFile;
281			ofstream newMdFile;
282			const int MAXLEN = 65535;
283			char buffer[MAXLEN];
284	tim	1501
285	gezelter	2204	//create new .md file based on old .md file
286			oldMdFile.open(oldMdFileName.c_str());
287			newMdFile.open(newMdFileName.c_str());
288	tim	1501
289	gezelter	2204	oldMdFile.getline(buffer, MAXLEN);
290	gezelter	1930
291	gezelter	2204	while (!oldMdFile.eof()) {
292	gezelter	1930
293	gezelter	2204	//correct molecule number
294			if (strstr(buffer, "nMol") != NULL) {
295			sprintf(buffer, "\t\tnMol = %d;", numMol);
296			newMdFile << buffer << std::endl;
297			} else
298			newMdFile << buffer << std::endl;
299	gezelter	1930
300	gezelter	2204	oldMdFile.getline(buffer, MAXLEN);
301			}
302	gezelter	1930
303	gezelter	2204	oldMdFile.close();
304			newMdFile.close();
305	tim	1501	}
306	gezelter	1930