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 ago) by chuckv
File size:	9903 byte(s)
Log Message:	Added random builder to cvs.
#	User	Rev	Content
1	chuckv	950	/* 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