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, 2 months ago) by gezelter
File size:	8738 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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	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	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	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
108
109	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
116	//get the number of unit cell
117	nx = args_info.nx_arg;
118
119	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
124	ny = args_info.ny_arg;
125
126	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
131	nz = args_info.nz_arg;
132
133	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
138	//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
147	//parse md file and set up the system
148	SimCreator oldCreator;
149	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
150
151	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
157	//get mass of molecule.
158
159	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
160
161	//creat lattice
162	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
163
164	if (simpleLat == NULL) {
165	std::cerr << "Error in creating lattice" << std::endl;
166	exit(1);
167	}
168
169	numMolPerCell = simpleLat->getNumSitesPerCell();
170
171	//calculate lattice constant (in Angstrom)
172	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
173	1.0 / 3.0);
174
175	//set lattice constant
176	lc.push_back(latticeConstant);
177	simpleLat->setLatticeConstant(lc);
178
179	//calculate the total number of molecules
180	numMol = nx * ny * nz * numMolPerCell;
181
182	if (oldInfo->getNGlobalMolecules() != numMol) {
183	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
184	outMdFileName = outPrefix + ".md";
185
186	//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
196	//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
202	//creat Molocator
203	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
204
205	//fill Hmat
206	hmat(0, 0)= nx * latticeConstant;
207	hmat(0, 1) = 0.0;
208	hmat(0, 2) = 0.0;
209
210	hmat(1, 0) = 0.0;
211	hmat(1, 1) = ny * latticeConstant;
212	hmat(1, 2) = 0.0;
213
214	hmat(2, 0) = 0.0;
215	hmat(2, 1) = 0.0;
216	hmat(2, 2) = nz * latticeConstant;
217
218	//set Hmat
219	oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
220
221	//place the molecules
222
223	curMolIndex = 0;
224
225	//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
229	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
236	//get the position of the cell sites
237	simpleLat->getLatticePointsPos(latticePos, i, j, k);
238
239	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	}
249	}
250
251	//create dumpwriter and write out the coordinates
252	oldInfo->setFinalConfigFileName(outInitFileName);
253	writer = new DumpWriter(oldInfo);
254
255	if (writer == NULL) {
256	std::cerr << "error in creating DumpWriter" << std::endl;
257	exit(1);
258	}
259
260	writer->writeDump();
261	std::cout << "new initial configuration file: " << outInitFileName
262	<< " is generated." << std::endl;
263
264	//delete objects
265
266	//delete oldInfo and oldSimSetup
267	if (oldInfo != NULL)
268	delete oldInfo;
269
270	if (writer != NULL)
271	delete writer;
272
273	delete simpleLat;
274
275	return 0;
276	}
277
278	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
279	int numMol) {
280	ifstream oldMdFile;
281	ofstream newMdFile;
282	const int MAXLEN = 65535;
283	char buffer[MAXLEN];
284
285	//create new .md file based on old .md file
286	oldMdFile.open(oldMdFileName.c_str());
287	newMdFile.open(newMdFileName.c_str());
288
289	oldMdFile.getline(buffer, MAXLEN);
290
291	while (!oldMdFile.eof()) {
292
293	//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
300	oldMdFile.getline(buffer, MAXLEN);
301	}
302
303	oldMdFile.close();
304	newMdFile.close();
305	}
306