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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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 OpenMD;

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  int nMol);

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;
  RealType latticeConstant;
  std::vector<RealType> lc;
  const RealType rhoConvertConst = 1.661;
  RealType density;
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator *locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int nMolPerCell;
  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 = "FCC";

  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();
  }
  nMolPerCell = simpleLat->getNumSitesPerCell();

  //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();
  }

  int nSites = nMolPerCell * nx * ny * nz;

  //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();

  // Calculate lattice constant (in Angstroms)

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

  latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
                        (RealType)(1.0 / 3.0));
  
  // Set the lattice constant
  
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);

  // 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 < nMolPerCell; l++) {
          sites.push_back(latticePos[l]);
          orientations.push_back(latticeOrt[l]);
        }
      }
    }
  }
  
  outputFileName = args_info.output_arg;
  
  // create a new .md file on the fly which corrects the number of molecules

  createMdFile(inputFileName, outputFileName, nSites);

  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
  
  Molecule* mol;
  locator = new MoLocator(newInfo->getMoleculeStamp(0), 
                          newInfo->getForceField());
  for (int n = 0; n < nSites; n++) {
    mol = newInfo->getMoleculeByGlobalIndex(n);
    locator->placeMol(sites[n], orientations[n], mol);
  }
   
  // 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 OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}

void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  int nMol) {
  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;", nMol);
      newMdFile << buffer << std::endl;
    } else
      newMdFile << buffer << std::endl;

    oldMdFile.getline(buffer, MAXLEN);
  }

  oldMdFile.close();
  newMdFile.close();
}

Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	8281 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	tim	12	#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	gezelter	481	#include "lattice/LatticeFactory.hpp"
53			#include "utils/MoLocator.hpp"
54			#include "lattice/Lattice.hpp"
55	gezelter	246	#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	tim	12
63			using namespace std;
64	gezelter	1390	using namespace OpenMD;
65	tim	12
66	gezelter	1067	void createMdFile(const std::string&oldMdFileName,
67			const std::string&newMdFileName,
68			int nMol);
69
70	gezelter	246	int main(int argc, char *argv []) {
71	tim	12
72	gezelter	1067	// register force fields
73	gezelter	507	registerForceFields();
74			registerLattice();
75	gezelter	246
76	gezelter	507	gengetopt_args_info args_info;
77			std::string latticeType;
78			std::string inputFileName;
79	gezelter	1067	std::string outputFileName;
80	gezelter	507	Lattice *simpleLat;
81	gezelter	1067	RealType latticeConstant;
82			std::vector<RealType> lc;
83			const RealType rhoConvertConst = 1.661;
84			RealType density;
85			int nx, ny, nz;
86	gezelter	507	Mat3x3d hmat;
87			MoLocator *locator;
88			std::vector<Vector3d> latticePos;
89			std::vector<Vector3d> latticeOrt;
90	gezelter	1067	int nMolPerCell;
91	gezelter	507	DumpWriter *writer;
92	tim	12
93	gezelter	507	// parse command line arguments
94			if (cmdline_parser(argc, argv, &args_info) != 0)
95			exit(1);
96	tim	12
97	gezelter	507	density = args_info.density_arg;
98	tim	12
99	gezelter	507	//get lattice type
100	gezelter	1067	latticeType = "FCC";
101	tim	12
102	gezelter	507	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
103	tim	487
104	gezelter	507	if (simpleLat == NULL) {
105			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
106			latticeType.c_str());
107			painCave.isFatal = 1;
108			simError();
109			}
110	gezelter	1067	nMolPerCell = simpleLat->getNumSitesPerCell();
111	tim	12
112	gezelter	1067	//get the number of unit cells in each direction:
113
114	gezelter	507	nx = args_info.nx_arg;
115	tim	12
116	gezelter	507	if (nx <= 0) {
117	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the x direction "
118			"must be greater than 0.");
119			painCave.isFatal = 1;
120			simError();
121	gezelter	507	}
122	tim	12
123	gezelter	507	ny = args_info.ny_arg;
124	tim	12
125	gezelter	507	if (ny <= 0) {
126	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the y direction "
127			"must be greater than 0.");
128			painCave.isFatal = 1;
129			simError();
130	gezelter	507	}
131	tim	12
132	gezelter	507	nz = args_info.nz_arg;
133	tim	12
134	gezelter	507	if (nz <= 0) {
135	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the z direction "
136			"must be greater than 0.");
137			painCave.isFatal = 1;
138			simError();
139	gezelter	507	}
140	tim	12
141	gezelter	1067	int nSites = nMolPerCell * nx * ny * nz;
142
143	gezelter	507	//get input file name
144			if (args_info.inputs_num)
145			inputFileName = args_info.inputs[0];
146			else {
147	gezelter	1067	sprintf(painCave.errMsg, "No input .md file name was specified "
148			"on the command line");
149			painCave.isFatal = 1;
150			simError();
151	gezelter	507	}
152	tim	12
153	gezelter	507	//parse md file and set up the system
154	gezelter	1067
155	gezelter	507	SimCreator oldCreator;
156			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
157	gezelter	1067	Globals* simParams = oldInfo->getSimParams();
158	tim	12
159	gezelter	1067	// Calculate lattice constant (in Angstroms)
160	tim	12
161	gezelter	1067	RealType avgMass = getMolMass(oldInfo->getMoleculeStamp(0),
162			oldInfo->getForceField());
163	tim	12
164	gezelter	1067	latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
165			(RealType)(1.0 / 3.0));
166
167			// Set the lattice constant
168
169			lc.push_back(latticeConstant);
170			simpleLat->setLatticeConstant(lc);
171	tim	12
172	gezelter	1067	// Calculate the lattice sites and fill the lattice vector.
173	tim	12
174	gezelter	1067	// Get the standard orientations of the cell sites
175	tim	12
176	gezelter	1067	latticeOrt = simpleLat->getLatticePointsOrt();
177	tim	12
178	gezelter	1067	vector<Vector3d> sites;
179			vector<Vector3d> orientations;
180
181			for(int i = 0; i < nx; i++) {
182			for(int j = 0; j < ny; j++) {
183			for(int k = 0; k < nz; k++) {
184	tim	12
185	gezelter	1067	// Get the position of the cell sites
186
187			simpleLat->getLatticePointsPos(latticePos, i, j, k);
188
189			for(int l = 0; l < nMolPerCell; l++) {
190			sites.push_back(latticePos[l]);
191			orientations.push_back(latticeOrt[l]);
192			}
193			}
194			}
195			}
196
197			outputFileName = args_info.output_arg;
198
199			// create a new .md file on the fly which corrects the number of molecules
200	tim	12
201	gezelter	1067	createMdFile(inputFileName, outputFileName, nSites);
202	tim	12
203	gezelter	1067	if (oldInfo != NULL)
204			delete oldInfo;
205	gezelter	246
206	gezelter	1067	// We need to read in the new SimInfo object, then Parse the
207			// md file and set up the system
208	tim	12
209	gezelter	1067	SimCreator newCreator;
210			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
211	tim	12
212	gezelter	1067	// fill Hmat
213
214			hmat(0, 0) = nx * latticeConstant;
215	gezelter	507	hmat(0, 1) = 0.0;
216			hmat(0, 2) = 0.0;
217	tim	12
218	gezelter	507	hmat(1, 0) = 0.0;
219			hmat(1, 1) = ny * latticeConstant;
220			hmat(1, 2) = 0.0;
221	tim	12
222	gezelter	507	hmat(2, 0) = 0.0;
223			hmat(2, 1) = 0.0;
224			hmat(2, 2) = nz * latticeConstant;
225	tim	12
226	gezelter	1067	// Set Hmat
227	tim	12
228	gezelter	1067	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
229	gezelter	246
230	gezelter	1067	// place the molecules
231
232	gezelter	507	Molecule* mol;
233	gezelter	1067	locator = new MoLocator(newInfo->getMoleculeStamp(0),
234			newInfo->getForceField());
235			for (int n = 0; n < nSites; n++) {
236			mol = newInfo->getMoleculeByGlobalIndex(n);
237			locator->placeMol(sites[n], orientations[n], mol);
238	gezelter	507	}
239	gezelter	1067
240			// Create DumpWriter and write out the coordinates
241	tim	12
242	gezelter	1067	writer = new DumpWriter(newInfo, outputFileName);
243
244	gezelter	507	if (writer == NULL) {
245	gezelter	1067	sprintf(painCave.errMsg, "error in creating DumpWriter");
246			painCave.isFatal = 1;
247			simError();
248	gezelter	507	}
249	tim	12
250	gezelter	507	writer->writeDump();
251	gezelter	246
252	gezelter	1067	// deleting the writer will put the closing at the end of the dump file.
253	gezelter	246
254	gezelter	1067	delete writer;
255	gezelter	246
256	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
257	gezelter	1067	"generated.\n", outputFileName.c_str());
258			painCave.isFatal = 0;
259			simError();
260	gezelter	507	return 0;
261	tim	12	}
262
263	gezelter	1067	void createMdFile(const std::string&oldMdFileName,
264			const std::string&newMdFileName,
265			int nMol) {
266	gezelter	507	ifstream oldMdFile;
267			ofstream newMdFile;
268			const int MAXLEN = 65535;
269			char buffer[MAXLEN];
270	tim	12
271	gezelter	507	//create new .md file based on old .md file
272			oldMdFile.open(oldMdFileName.c_str());
273			newMdFile.open(newMdFileName.c_str());
274	tim	12
275	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
276	gezelter	246
277	gezelter	507	while (!oldMdFile.eof()) {
278	gezelter	246
279	gezelter	507	//correct molecule number
280			if (strstr(buffer, "nMol") != NULL) {
281	gezelter	1067	sprintf(buffer, "\t\tnMol = %d;", nMol);
282	gezelter	507	newMdFile << buffer << std::endl;
283			} else
284			newMdFile << buffer << std::endl;
285	gezelter	246
286	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
287			}
288	gezelter	246
289	gezelter	507	oldMdFile.close();
290			newMdFile.close();
291	tim	12	}
292	gezelter	246