applications/randomBuilder/randomBuilder.cpp

/* Copyright (c) 2006 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.
 *
 *
 *  randomBuilder.cpp
 *
 *  Created by Charles F. Vardeman II on 10 Apr 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: randomBuilder.cpp,v 1.1 2006-04-25 22:59:27 chuckv Exp $
 *
 */


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

#include "applications/randomBuilder/randomBuilderCmd.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 components,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);
  Globals* simParams = oldInfo->getSimParams();

  int nComponents =simParams->getNComponents();
  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
  int totMol = nx * ny * nz * numMolPerCell;

  // Calculate the lattice sites and fill lattice vector.
  vector<Vector3d> latticeSites;
  
  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++) {
          latticeSites.push_back(latticePos[l]);
        }
      }
    }
  }

  int numSites = latticeSites.size();

  numMol = new int[nComponents];
  if (nComponents != args_info.molFraction_given && nComponents != 1){
    std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
    exit(1);
  }
  int totComponents = 0;
  for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */
    numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
    std::cout<<numMol[i]<<std::endl;
    totComponents += numMol[i];
  }
  numMol[nComponents-1] = numSites - totComponents;
  

  outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
  outMdFileName = outPrefix + ".md";

  //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outMdFileName, nComponents,numMol);


  //determine the output file names  
  if (args_info.output_given){
    outInitFileName = args_info.output_arg;
  }else{
    outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
  }

  //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();

 
  /* Randomize position vector */
  std::random_shuffle(latticeSites.begin(), latticeSites.end());


  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outMdFileName, false);
  
  /* create Molocators */
  locator = new MoLocator(NewInfo->getMoleculeStamp(0), NewInfo->getForceField());
  
  
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);
  int l = 0;
  for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
    locator->placeMol(latticeSites[l], latticeOrt[l], mol);
    l++;
  }


  //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 components,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);
 
  int i = 0;
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      if(i<components){
        sprintf(buffer, "\tnMol = %i;", numMol[i]);                             
        newMdFile << buffer << std::endl;
        i++;
      }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	950
Committed:	Tue Apr 25 22:59:27 2006 UTC (19 years, 6 months ago) by chuckv
File size:	9903 byte(s)
Log Message:	Added random builder to cvs.
#	Content
1	/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
2	*
3	* The University of Notre Dame grants you ("Licensee") a
4	* non-exclusive, royalty free, license to use, modify and
5	* redistribute this software in source and binary code form, provided
6	* that the following conditions are met:
7	*
8	* 1. Acknowledgement of the program authors must be made in any
9	* publication of scientific results based in part on use of the
10	* program. An acceptable form of acknowledgement is citation of
11	* the article in which the program was described (Matthew
12	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14	* Parallel Simulation Engine for Molecular Dynamics,"
15	* J. Comput. Chem. 26, pp. 252-271 (2005))
16	*
17	* 2. Redistributions of source code must retain the above copyright
18	* notice, this list of conditions and the following disclaimer.
19	*
20	* 3. Redistributions in binary form must reproduce the above copyright
21	* notice, this list of conditions and the following disclaimer in the
22	* documentation and/or other materials provided with the
23	* distribution.
24	*
25	* This software is provided "AS IS," without a warranty of any
26	* kind. All express or implied conditions, representations and
27	* warranties, including any implied warranty of merchantability,
28	* fitness for a particular purpose or non-infringement, are hereby
29	* excluded. The University of Notre Dame and its licensors shall not
30	* be liable for any damages suffered by licensee as a result of
31	* using, modifying or distributing the software or its
32	* derivatives. In no event will the University of Notre Dame or its
33	* licensors be liable for any lost revenue, profit or data, or for
34	* direct, indirect, special, consequential, incidental or punitive
35	* damages, however caused and regardless of the theory of liability,
36	* arising out of the use of or inability to use software, even if the
37	* University of Notre Dame has been advised of the possibility of
38	* such damages.
39	*
40	*
41	* randomBuilder.cpp
42	*
43	* Created by Charles F. Vardeman II on 10 Apr 2006.
44	* @author Charles F. Vardeman II
45	* @version $Id: randomBuilder.cpp,v 1.1 2006-04-25 22:59:27 chuckv Exp $
46	*
47	*/
48
49
50	#include <cstdlib>
51	#include <cstdio>
52	#include <cstring>
53	#include <cmath>
54	#include <iostream>
55	#include <string>
56	#include <map>
57	#include <fstream>
58
59	#include "applications/randomBuilder/randomBuilderCmd.h"
60	#include "lattice/LatticeFactory.hpp"
61	#include "utils/MoLocator.hpp"
62	#include "lattice/Lattice.hpp"
63	#include "brains/Register.hpp"
64	#include "brains/SimInfo.hpp"
65	#include "brains/SimCreator.hpp"
66	#include "io/DumpWriter.hpp"
67	#include "math/Vector3.hpp"
68	#include "math/SquareMatrix3.hpp"
69	#include "utils/StringUtils.hpp"
70
71	using namespace std;
72	using namespace oopse;
73
74	void createMdFile(const std::string&oldMdFileName,
75	const std::string&newMdFileName,
76	int components,int* numMol);
77
78	int main(int argc, char *argv []) {
79
80	//register force fields
81	registerForceFields();
82	registerLattice();
83
84	gengetopt_args_info args_info;
85	std::string latticeType;
86	std::string inputFileName;
87	std::string outPrefix;
88	std::string outMdFileName;
89	std::string outInitFileName;
90	Lattice *simpleLat;
91	int* numMol;
92	double latticeConstant;
93	std::vector<double> lc;
94	double mass;
95	const double rhoConvertConst = 1.661;
96	double density;
97	int nx,
98	ny,
99	nz;
100	Mat3x3d hmat;
101	MoLocator *locator;
102	std::vector<Vector3d> latticePos;
103	std::vector<Vector3d> latticeOrt;
104	int numMolPerCell;
105	int curMolIndex;
106	DumpWriter *writer;
107
108	// parse command line arguments
109	if (cmdline_parser(argc, argv, &args_info) != 0)
110	exit(1);
111
112	density = args_info.density_arg;
113
114	//get lattice type
115	latticeType = UpperCase(args_info.latticetype_arg);
116
117	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
118
119	if (simpleLat == NULL) {
120	sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
121	latticeType.c_str());
122	painCave.isFatal = 1;
123	simError();
124	}
125
126	//get the number of unit cell
127	nx = args_info.nx_arg;
128
129	if (nx <= 0) {
130	std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
131	exit(1);
132	}
133
134	ny = args_info.ny_arg;
135
136	if (ny <= 0) {
137	std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
138	exit(1);
139	}
140
141	nz = args_info.nz_arg;
142
143	if (nz <= 0) {
144	std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl;
145	exit(1);
146	}
147
148	//get input file name
149	if (args_info.inputs_num)
150	inputFileName = args_info.inputs[0];
151	else {
152	std::cerr << "You must specify a input file name.\n" << std::endl;
153	cmdline_parser_print_help();
154	exit(1);
155	}
156
157	//parse md file and set up the system
158	SimCreator oldCreator;
159	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
160	Globals* simParams = oldInfo->getSimParams();
161
162	int nComponents =simParams->getNComponents();
163	if (oldInfo->getNMoleculeStamp()>= 2) {
164	std::cerr << "can not build the system with more than two components"
165	<< std::endl;
166	exit(1);
167	}
168
169	//get mass of molecule.
170
171	mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
172
173	//creat lattice
174	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
175
176	if (simpleLat == NULL) {
177	std::cerr << "Error in creating lattice" << std::endl;
178	exit(1);
179	}
180
181	numMolPerCell = simpleLat->getNumSitesPerCell();
182
183	//calculate lattice constant (in Angstrom)
184	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
185	1.0 / 3.0);
186
187	//set lattice constant
188	lc.push_back(latticeConstant);
189	simpleLat->setLatticeConstant(lc);
190
191	//calculate the total number of molecules
192	int totMol = nx * ny * nz * numMolPerCell;
193
194	// Calculate the lattice sites and fill lattice vector.
195	vector<Vector3d> latticeSites;
196
197	for(int i = 0; i < nx; i++) {
198	for(int j = 0; j < ny; j++) {
199	for(int k = 0; k < nz; k++) {
200
201	//get the position of the cell sites
202	simpleLat->getLatticePointsPos(latticePos, i, j, k);
203
204	for(int l = 0; l < numMolPerCell; l++) {
205	latticeSites.push_back(latticePos[l]);
206	}
207	}
208	}
209	}
210
211	int numSites = latticeSites.size();
212
213	numMol = new int[nComponents];
214	if (nComponents != args_info.molFraction_given && nComponents != 1){
215	std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
216	exit(1);
217	}
218	int totComponents = 0;
219	for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */
220	numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
221	std::cout<<numMol[i]<<std::endl;
222	totComponents += numMol[i];
223	}
224	numMol[nComponents-1] = numSites - totComponents;
225
226
227	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
228	outMdFileName = outPrefix + ".md";
229
230	//creat new .md file on fly which corrects the number of molecule
231	createMdFile(inputFileName, outMdFileName, nComponents,numMol);
232
233
234
235	//determine the output file names
236	if (args_info.output_given){
237	outInitFileName = args_info.output_arg;
238	}else{
239	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
240	}
241
242	//fill Hmat
243	hmat(0, 0)= nx * latticeConstant;
244	hmat(0, 1) = 0.0;
245	hmat(0, 2) = 0.0;
246
247	hmat(1, 0) = 0.0;
248	hmat(1, 1) = ny * latticeConstant;
249	hmat(1, 2) = 0.0;
250
251	hmat(2, 0) = 0.0;
252	hmat(2, 1) = 0.0;
253	hmat(2, 2) = nz * latticeConstant;
254
255	//set Hmat
256	oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
257
258	//place the molecules
259
260	curMolIndex = 0;
261
262	//get the orientation of the cell sites
263	//for the same type of molecule in same lattice, it will not change
264	latticeOrt = simpleLat->getLatticePointsOrt();
265
266
267	/* Randomize position vector */
268	std::random_shuffle(latticeSites.begin(), latticeSites.end());
269
270
271	if (oldInfo != NULL)
272	delete oldInfo;
273
274
275	// We need to read in new siminfo object.
276	//parse md file and set up the system
277	//SimCreator NewCreator;
278	SimCreator newCreator;
279	SimInfo* NewInfo = newCreator.createSim(outMdFileName, false);
280
281	/* create Molocators */
282	locator = new MoLocator(NewInfo->getMoleculeStamp(0), NewInfo->getForceField());
283
284
285
286	Molecule* mol;
287	SimInfo::MoleculeIterator mi;
288	mol = NewInfo->beginMolecule(mi);
289	int l = 0;
290	for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
291	locator->placeMol(latticeSites[l], latticeOrt[l], mol);
292	l++;
293	}
294
295
296
297	//create dumpwriter and write out the coordinates
298	oldInfo->setFinalConfigFileName(outInitFileName);
299	writer = new DumpWriter(oldInfo);
300
301	if (writer == NULL) {
302	std::cerr << "error in creating DumpWriter" << std::endl;
303	exit(1);
304	}
305
306	writer->writeDump();
307	std::cout << "new initial configuration file: " << outInitFileName
308	<< " is generated." << std::endl;
309
310	//delete objects
311
312	//delete oldInfo and oldSimSetup
313	if (oldInfo != NULL)
314	delete oldInfo;
315
316	if (writer != NULL)
317	delete writer;
318
319	delete simpleLat;
320
321	return 0;
322	}
323
324	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
325	int components,int* numMol) {
326	ifstream oldMdFile;
327	ofstream newMdFile;
328	const int MAXLEN = 65535;
329	char buffer[MAXLEN];
330
331	//create new .md file based on old .md file
332	oldMdFile.open(oldMdFileName.c_str());
333	newMdFile.open(newMdFileName.c_str());
334
335	oldMdFile.getline(buffer, MAXLEN);
336
337	int i = 0;
338	while (!oldMdFile.eof()) {
339
340	//correct molecule number
341	if (strstr(buffer, "nMol") != NULL) {
342	if(i<components){
343	sprintf(buffer, "\tnMol = %i;", numMol[i]);
344	newMdFile << buffer << std::endl;
345	i++;
346	}
347	} else
348	newMdFile << buffer << std::endl;
349
350	oldMdFile.getline(buffer, MAXLEN);
351	}
352
353	oldMdFile.close();
354	newMdFile.close();
355	}
356