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 1.3 2006-10-09 22:16:44 gezelter 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;
  Lattice *simpleLat;
  int* numMol;
  RealType latticeConstant;
  std::vector<RealType> lc;
  RealType mass;
  const RealType rhoConvertConst = 1.661;
  RealType 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,
                        (RealType)(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((RealType)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);

  //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;
  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
  newInfo->setFinalConfigFileName(outMdFileName);
  writer = new DumpWriter(newInfo);

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

  writer->writeEor();
  std::cout << "new OOPSE MD file: " << outMdFileName
            << " has been generated." << std::endl;
  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:	3035
Committed:	Mon Oct 9 22:16:44 2006 UTC (17 years, 10 months ago) by gezelter
File size:	9494 byte(s)
Log Message:	Fixing the builders to prepare for OOPSE-4 release
#	User	Rev	Content
1	chuckv	2738	/* 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	gezelter	3035	* @version $Id: randomBuilder.cpp,v 1.3 2006-10-09 22:16:44 gezelter Exp $
46	chuckv	2738	*
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			Lattice *simpleLat;
90			int* numMol;
91	tim	2759	RealType latticeConstant;
92			std::vector<RealType> lc;
93			RealType mass;
94			const RealType rhoConvertConst = 1.661;
95			RealType density;
96	chuckv	2738	int nx,
97			ny,
98			nz;
99			Mat3x3d hmat;
100			MoLocator *locator;
101			std::vector<Vector3d> latticePos;
102			std::vector<Vector3d> latticeOrt;
103			int numMolPerCell;
104			int curMolIndex;
105			DumpWriter *writer;
106
107			// parse command line arguments
108			if (cmdline_parser(argc, argv, &args_info) != 0)
109			exit(1);
110
111			density = args_info.density_arg;
112
113			//get lattice type
114			latticeType = UpperCase(args_info.latticetype_arg);
115
116			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
117
118			if (simpleLat == NULL) {
119			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
120			latticeType.c_str());
121			painCave.isFatal = 1;
122			simError();
123			}
124
125			//get the number of unit cell
126			nx = args_info.nx_arg;
127
128			if (nx <= 0) {
129			std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl;
130			exit(1);
131			}
132
133			ny = args_info.ny_arg;
134
135			if (ny <= 0) {
136			std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl;
137			exit(1);
138			}
139
140			nz = args_info.nz_arg;
141
142			if (nz <= 0) {
143			std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl;
144			exit(1);
145			}
146
147			//get input file name
148			if (args_info.inputs_num)
149			inputFileName = args_info.inputs[0];
150			else {
151			std::cerr << "You must specify a input file name.\n" << std::endl;
152			cmdline_parser_print_help();
153			exit(1);
154			}
155
156			//parse md file and set up the system
157			SimCreator oldCreator;
158			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
159			Globals* simParams = oldInfo->getSimParams();
160
161			int nComponents =simParams->getNComponents();
162	gezelter	3035	if (oldInfo->getNMoleculeStamp() > 2) {
163	chuckv	2738	std::cerr << "can not build the system with more than two components"
164			<< std::endl;
165			exit(1);
166			}
167
168			//get mass of molecule.
169
170			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
171
172			//creat lattice
173			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
174
175			if (simpleLat == NULL) {
176			std::cerr << "Error in creating lattice" << std::endl;
177			exit(1);
178			}
179
180			numMolPerCell = simpleLat->getNumSitesPerCell();
181
182			//calculate lattice constant (in Angstrom)
183			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
184	tim	2759	(RealType)(1.0 / 3.0));
185	chuckv	2738
186			//set lattice constant
187			lc.push_back(latticeConstant);
188			simpleLat->setLatticeConstant(lc);
189
190			//calculate the total number of molecules
191			int totMol = nx * ny * nz * numMolPerCell;
192
193			// Calculate the lattice sites and fill lattice vector.
194			vector<Vector3d> latticeSites;
195
196			for(int i = 0; i < nx; i++) {
197			for(int j = 0; j < ny; j++) {
198			for(int k = 0; k < nz; k++) {
199
200			//get the position of the cell sites
201			simpleLat->getLatticePointsPos(latticePos, i, j, k);
202
203			for(int l = 0; l < numMolPerCell; l++) {
204			latticeSites.push_back(latticePos[l]);
205			}
206			}
207			}
208			}
209
210			int numSites = latticeSites.size();
211
212			numMol = new int[nComponents];
213			if (nComponents != args_info.molFraction_given && nComponents != 1){
214			std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
215			exit(1);
216			}
217			int totComponents = 0;
218			for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */
219	tim	2759	numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]);
220	chuckv	2738	std::cout<<numMol[i]<<std::endl;
221			totComponents += numMol[i];
222			}
223			numMol[nComponents-1] = numSites - totComponents;
224
225
226			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
227			outMdFileName = outPrefix + ".md";
228
229			//creat new .md file on fly which corrects the number of molecule
230	gezelter	3035	createMdFile(inputFileName, outMdFileName, nComponents, numMol);
231	chuckv	2738
232			//fill Hmat
233			hmat(0, 0)= nx * latticeConstant;
234			hmat(0, 1) = 0.0;
235			hmat(0, 2) = 0.0;
236
237			hmat(1, 0) = 0.0;
238			hmat(1, 1) = ny * latticeConstant;
239			hmat(1, 2) = 0.0;
240
241			hmat(2, 0) = 0.0;
242			hmat(2, 1) = 0.0;
243			hmat(2, 2) = nz * latticeConstant;
244
245			//set Hmat
246			oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
247
248			//place the molecules
249
250			curMolIndex = 0;
251
252			//get the orientation of the cell sites
253			//for the same type of molecule in same lattice, it will not change
254			latticeOrt = simpleLat->getLatticePointsOrt();
255
256
257			/* Randomize position vector */
258			std::random_shuffle(latticeSites.begin(), latticeSites.end());
259
260			if (oldInfo != NULL)
261			delete oldInfo;
262	gezelter	3035
263	chuckv	2738	// We need to read in new siminfo object.
264	gezelter	3035	// parse md file and set up the system
265
266	chuckv	2738	SimCreator newCreator;
267	gezelter	3035	SimInfo* newInfo = newCreator.createSim(outMdFileName, false);
268	chuckv	2738
269			/* create Molocators */
270	gezelter	3035	locator = new MoLocator(newInfo->getMoleculeStamp(0), newInfo->getForceField());
271	chuckv	2738
272
273
274			Molecule* mol;
275			SimInfo::MoleculeIterator mi;
276	gezelter	3035	mol = newInfo->beginMolecule(mi);
277	chuckv	2738	int l = 0;
278	gezelter	3035	for (mol = newInfo->beginMolecule(mi); mol != NULL; mol = newInfo->nextMolecule(mi)) {
279	chuckv	2738	locator->placeMol(latticeSites[l], latticeOrt[l], mol);
280			l++;
281			}
282
283			//create dumpwriter and write out the coordinates
284	gezelter	3035	newInfo->setFinalConfigFileName(outMdFileName);
285			writer = new DumpWriter(newInfo);
286	chuckv	2738
287			if (writer == NULL) {
288			std::cerr << "error in creating DumpWriter" << std::endl;
289			exit(1);
290			}
291
292	gezelter	3035	writer->writeEor();
293			std::cout << "new OOPSE MD file: " << outMdFileName
294			<< " has been generated." << std::endl;
295	chuckv	2738	return 0;
296			}
297
298			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
299			int components,int* numMol) {
300			ifstream oldMdFile;
301			ofstream newMdFile;
302			const int MAXLEN = 65535;
303			char buffer[MAXLEN];
304
305			//create new .md file based on old .md file
306			oldMdFile.open(oldMdFileName.c_str());
307			newMdFile.open(newMdFileName.c_str());
308
309			oldMdFile.getline(buffer, MAXLEN);
310
311			int i = 0;
312			while (!oldMdFile.eof()) {
313
314			//correct molecule number
315			if (strstr(buffer, "nMol") != NULL) {
316			if(i<components){
317			sprintf(buffer, "\tnMol = %i;", numMol[i]);
318			newMdFile << buffer << std::endl;
319			i++;
320			}
321			} else
322			newMdFile << buffer << std::endl;
323
324			oldMdFile.getline(buffer, MAXLEN);
325			}
326
327			oldMdFile.close();
328			newMdFile.close();
329			}
330