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 1.4 2006-10-10 02:44:13 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 outputFileName;
  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 cells in each direction:

  nx = args_info.nx_arg;

  if (nx <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the x direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  ny = args_info.ny_arg;

  if (ny <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the y direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  nz = args_info.nz_arg;

  if (nz <= 0) {
    sprintf(painCave.errMsg, "The number of unit cells in the z direction "
            "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }

  //get input file name
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    sprintf(painCave.errMsg, "No input .md file name was specified "
            "on the command line");
    painCave.isFatal = 1;
    simError();
  }

  //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) {
    sprintf(painCave.errMsg, "randomBuilder can't yet build a system with "
            "more than two components.");
    painCave.isFatal = 1;
    simError();
  }

  //get mass of molecule. 

  mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());

  // Create the lattice

  simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);

  if (simpleLat == NULL) {
    sprintf(painCave.errMsg, "Error in creating lattice.");
    painCave.isFatal = 1;
    simError();
  }

  numMolPerCell = simpleLat->getNumSitesPerCell();

  // Calculate lattice constant (in Angstroms)

  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
                        (RealType)(1.0 / 3.0));

  // Set the 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 the lattice vector.

  // Get the standard orientations of the cell sites

  latticeOrt = simpleLat->getLatticePointsOrt();

  vector<Vector3d> sites;
  vector<Vector3d> orientations;
  
  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++) {
          sites.push_back(latticePos[l]);
          orientations.push_back(latticeOrt[l]);
        }
      }
    }
  }

  int numSites = sites.size();

  numMol = new int[nComponents];
  if (nComponents != args_info.molFraction_given && nComponents != 1){
    sprintf(painCave.errMsg, "There needs to be the same number of "
            "molFraction arguments as there are components in the "
            "<MetaData> block.");
    painCave.isFatal = 1;
    simError();
  }
  int totComponents = 0;
  for (int i = 0;i<nComponents-1;i++){
    numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]);
    std::cout<<numMol[i]<<std::endl;
    totComponents += numMol[i];
  }
  numMol[nComponents-1] = numSites - totComponents;
  
  outputFileName = args_info.output_arg;

  // create a new .md file on the fly which corrects the number of molecules

  createMdFile(inputFileName, outputFileName, nComponents, numMol);

  if (oldInfo != NULL)
    delete oldInfo;

  // We need to read in the new SimInfo object, then Parse the 
  // md file and set up the system

  SimCreator newCreator;
  SimInfo* newInfo = newCreator.createSim(outputFileName, false);

  // 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

  newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);

  // place the molecules

  curMolIndex = 0;

  // Randomize a vector of ints:

  vector<int> ids;
  for (int i = 0; i < sites.size(); i++) ids.push_back(i);
  std::random_shuffle(ids.begin(), ids.end());

  Molecule* mol;
  int l = 0;
  for (int i = 0; i < nComponents; i++){
    locator = new MoLocator(newInfo->getMoleculeStamp(i), 
                            newInfo->getForceField());
    for (int n = 0; n < numMol[i]; n++) {
      mol = newInfo->getMoleculeByGlobalIndex(l);
      locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
      l++;
    }
  }
  
  // Create DumpWriter and write out the coordinates

  writer = new DumpWriter(newInfo, outputFileName);

  if (writer == NULL) {
    sprintf(painCave.errMsg, "error in creating DumpWriter");
    painCave.isFatal = 1;
    simError();
  }

  writer->writeDump();

  // deleting the writer will put the closing at the end of the dump file.

  delete writer;

  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
          "generated.", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  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:	3036
Committed:	Tue Oct 10 02:44:13 2006 UTC (17 years, 8 months ago) by gezelter
File size:	10017 byte(s)
Log Message:	fixing bugs in randomBuilder
#	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	3036	* @version $Id: randomBuilder.cpp,v 1.4 2006-10-10 02:44:13 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	gezelter	3036	int components, int* numMol);
77	chuckv	2738
78			int main(int argc, char *argv []) {
79
80	gezelter	3036	// register force fields
81	chuckv	2738	registerForceFields();
82			registerLattice();
83
84			gengetopt_args_info args_info;
85			std::string latticeType;
86			std::string inputFileName;
87	gezelter	3036	std::string outputFileName;
88	chuckv	2738	Lattice *simpleLat;
89			int* numMol;
90	tim	2759	RealType latticeConstant;
91			std::vector<RealType> lc;
92			RealType mass;
93			const RealType rhoConvertConst = 1.661;
94			RealType density;
95	gezelter	3036	int nx, ny, nz;
96	chuckv	2738	Mat3x3d hmat;
97			MoLocator *locator;
98			std::vector<Vector3d> latticePos;
99			std::vector<Vector3d> latticeOrt;
100			int numMolPerCell;
101			int curMolIndex;
102			DumpWriter *writer;
103
104			// parse command line arguments
105			if (cmdline_parser(argc, argv, &args_info) != 0)
106			exit(1);
107
108			density = args_info.density_arg;
109
110			//get lattice type
111			latticeType = UpperCase(args_info.latticetype_arg);
112
113			simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
114
115			if (simpleLat == NULL) {
116			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
117			latticeType.c_str());
118			painCave.isFatal = 1;
119			simError();
120			}
121
122	gezelter	3036	//get the number of unit cells in each direction:
123
124	chuckv	2738	nx = args_info.nx_arg;
125
126			if (nx <= 0) {
127	gezelter	3036	sprintf(painCave.errMsg, "The number of unit cells in the x direction "
128			"must be greater than 0.");
129			painCave.isFatal = 1;
130			simError();
131	chuckv	2738	}
132
133			ny = args_info.ny_arg;
134
135			if (ny <= 0) {
136	gezelter	3036	sprintf(painCave.errMsg, "The number of unit cells in the y direction "
137			"must be greater than 0.");
138			painCave.isFatal = 1;
139			simError();
140	chuckv	2738	}
141
142			nz = args_info.nz_arg;
143
144			if (nz <= 0) {
145	gezelter	3036	sprintf(painCave.errMsg, "The number of unit cells in the z direction "
146			"must be greater than 0.");
147			painCave.isFatal = 1;
148			simError();
149	chuckv	2738	}
150
151			//get input file name
152			if (args_info.inputs_num)
153			inputFileName = args_info.inputs[0];
154			else {
155	gezelter	3036	sprintf(painCave.errMsg, "No input .md file name was specified "
156			"on the command line");
157			painCave.isFatal = 1;
158			simError();
159	chuckv	2738	}
160
161			//parse md file and set up the system
162	gezelter	3036
163	chuckv	2738	SimCreator oldCreator;
164			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
165			Globals* simParams = oldInfo->getSimParams();
166
167			int nComponents =simParams->getNComponents();
168	gezelter	3035	if (oldInfo->getNMoleculeStamp() > 2) {
169	gezelter	3036	sprintf(painCave.errMsg, "randomBuilder can't yet build a system with "
170			"more than two components.");
171			painCave.isFatal = 1;
172			simError();
173	chuckv	2738	}
174
175			//get mass of molecule.
176
177			mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
178
179	gezelter	3036	// Create the lattice
180
181	chuckv	2738	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
182
183			if (simpleLat == NULL) {
184	gezelter	3036	sprintf(painCave.errMsg, "Error in creating lattice.");
185			painCave.isFatal = 1;
186			simError();
187	chuckv	2738	}
188
189			numMolPerCell = simpleLat->getNumSitesPerCell();
190
191	gezelter	3036	// Calculate lattice constant (in Angstroms)
192
193	chuckv	2738	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
194	tim	2759	(RealType)(1.0 / 3.0));
195	chuckv	2738
196	gezelter	3036	// Set the lattice constant
197
198	chuckv	2738	lc.push_back(latticeConstant);
199			simpleLat->setLatticeConstant(lc);
200
201	gezelter	3036	// Calculate the total number of molecules
202
203	chuckv	2738	int totMol = nx * ny * nz * numMolPerCell;
204
205	gezelter	3036	// Calculate the lattice sites and fill the lattice vector.
206
207			// Get the standard orientations of the cell sites
208
209			latticeOrt = simpleLat->getLatticePointsOrt();
210
211			vector<Vector3d> sites;
212			vector<Vector3d> orientations;
213	chuckv	2738
214			for(int i = 0; i < nx; i++) {
215			for(int j = 0; j < ny; j++) {
216			for(int k = 0; k < nz; k++) {
217
218	gezelter	3036	// Get the position of the cell sites
219
220	chuckv	2738	simpleLat->getLatticePointsPos(latticePos, i, j, k);
221
222			for(int l = 0; l < numMolPerCell; l++) {
223	gezelter	3036	sites.push_back(latticePos[l]);
224			orientations.push_back(latticeOrt[l]);
225	chuckv	2738	}
226			}
227			}
228			}
229
230	gezelter	3036	int numSites = sites.size();
231	chuckv	2738
232			numMol = new int[nComponents];
233			if (nComponents != args_info.molFraction_given && nComponents != 1){
234	gezelter	3036	sprintf(painCave.errMsg, "There needs to be the same number of "
235			"molFraction arguments as there are components in the "
236			"<MetaData> block.");
237			painCave.isFatal = 1;
238			simError();
239	chuckv	2738	}
240			int totComponents = 0;
241	gezelter	3036	for (int i = 0;i<nComponents-1;i++){
242	tim	2759	numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]);
243	chuckv	2738	std::cout<<numMol[i]<<std::endl;
244			totComponents += numMol[i];
245			}
246			numMol[nComponents-1] = numSites - totComponents;
247
248	gezelter	3036	outputFileName = args_info.output_arg;
249	chuckv	2738
250	gezelter	3036	// create a new .md file on the fly which corrects the number of molecules
251	chuckv	2738
252	gezelter	3036	createMdFile(inputFileName, outputFileName, nComponents, numMol);
253	chuckv	2738
254	gezelter	3036	if (oldInfo != NULL)
255			delete oldInfo;
256
257			// We need to read in the new SimInfo object, then Parse the
258			// md file and set up the system
259
260			SimCreator newCreator;
261			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
262
263			// fill Hmat
264
265			hmat(0, 0) = nx * latticeConstant;
266	chuckv	2738	hmat(0, 1) = 0.0;
267			hmat(0, 2) = 0.0;
268
269			hmat(1, 0) = 0.0;
270			hmat(1, 1) = ny * latticeConstant;
271			hmat(1, 2) = 0.0;
272
273			hmat(2, 0) = 0.0;
274			hmat(2, 1) = 0.0;
275			hmat(2, 2) = nz * latticeConstant;
276
277	gezelter	3036	// Set Hmat
278	chuckv	2738
279	gezelter	3036	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
280	chuckv	2738
281	gezelter	3036	// place the molecules
282
283	chuckv	2738	curMolIndex = 0;
284
285	gezelter	3036	// Randomize a vector of ints:
286	chuckv	2738
287	gezelter	3036	vector<int> ids;
288			for (int i = 0; i < sites.size(); i++) ids.push_back(i);
289			std::random_shuffle(ids.begin(), ids.end());
290	chuckv	2738
291			Molecule* mol;
292			int l = 0;
293	gezelter	3036	for (int i = 0; i < nComponents; i++){
294			locator = new MoLocator(newInfo->getMoleculeStamp(i),
295			newInfo->getForceField());
296			for (int n = 0; n < numMol[i]; n++) {
297			mol = newInfo->getMoleculeByGlobalIndex(l);
298			locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
299			l++;
300			}
301	chuckv	2738	}
302	gezelter	3036
303			// Create DumpWriter and write out the coordinates
304	chuckv	2738
305	gezelter	3036	writer = new DumpWriter(newInfo, outputFileName);
306	chuckv	2738
307			if (writer == NULL) {
308	gezelter	3036	sprintf(painCave.errMsg, "error in creating DumpWriter");
309			painCave.isFatal = 1;
310			simError();
311	chuckv	2738	}
312
313	gezelter	3036	writer->writeDump();
314
315			// deleting the writer will put the closing at the end of the dump file.
316
317			delete writer;
318
319			sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
320			"generated.", outputFileName.c_str());
321			painCave.isFatal = 0;
322			simError();
323	chuckv	2738	return 0;
324			}
325
326	gezelter	3036	void createMdFile(const std::string&oldMdFileName,
327			const std::string&newMdFileName,
328			int components, int* numMol) {
329	chuckv	2738	ifstream oldMdFile;
330			ofstream newMdFile;
331			const int MAXLEN = 65535;
332			char buffer[MAXLEN];
333
334			//create new .md file based on old .md file
335	gezelter	3036
336	chuckv	2738	oldMdFile.open(oldMdFileName.c_str());
337			newMdFile.open(newMdFileName.c_str());
338
339			oldMdFile.getline(buffer, MAXLEN);
340
341			int i = 0;
342			while (!oldMdFile.eof()) {
343
344			//correct molecule number
345			if (strstr(buffer, "nMol") != NULL) {
346			if(i<components){
347	gezelter	3036	sprintf(buffer, "\tnMol = %i;", numMol[i]);
348	chuckv	2738	newMdFile << buffer << std::endl;
349			i++;
350			}
351			} else
352			newMdFile << buffer << std::endl;
353
354			oldMdFile.getline(buffer, MAXLEN);
355			}
356
357			oldMdFile.close();
358			newMdFile.close();
359			}
360