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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	8347 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	tim	12	#include <cstdlib>
44			#include <cstdio>
45			#include <cstring>
46			#include <cmath>
47			#include <iostream>
48			#include <string>
49			#include <map>
50			#include <fstream>
51
52			#include "applications/simpleBuilder/simpleBuilderCmd.h"
53	gezelter	481	#include "lattice/LatticeFactory.hpp"
54			#include "utils/MoLocator.hpp"
55			#include "lattice/Lattice.hpp"
56	gezelter	246	#include "brains/Register.hpp"
57			#include "brains/SimInfo.hpp"
58			#include "brains/SimCreator.hpp"
59			#include "io/DumpWriter.hpp"
60			#include "math/Vector3.hpp"
61			#include "math/SquareMatrix3.hpp"
62			#include "utils/StringUtils.hpp"
63	tim	12
64			using namespace std;
65	gezelter	1390	using namespace OpenMD;
66	tim	12
67	gezelter	1067	void createMdFile(const std::string&oldMdFileName,
68			const std::string&newMdFileName,
69			int nMol);
70
71	gezelter	246	int main(int argc, char *argv []) {
72	tim	12
73	gezelter	1067	// register force fields
74	gezelter	507	registerForceFields();
75			registerLattice();
76	gezelter	246
77	gezelter	507	gengetopt_args_info args_info;
78			std::string latticeType;
79			std::string inputFileName;
80	gezelter	1067	std::string outputFileName;
81	gezelter	507	Lattice *simpleLat;
82	gezelter	1067	RealType latticeConstant;
83			std::vector<RealType> lc;
84			const RealType rhoConvertConst = 1.661;
85			RealType density;
86			int nx, ny, nz;
87	gezelter	507	Mat3x3d hmat;
88			MoLocator *locator;
89			std::vector<Vector3d> latticePos;
90			std::vector<Vector3d> latticeOrt;
91	gezelter	1067	int nMolPerCell;
92	gezelter	507	DumpWriter *writer;
93	tim	12
94	gezelter	507	// parse command line arguments
95			if (cmdline_parser(argc, argv, &args_info) != 0)
96			exit(1);
97	tim	12
98	gezelter	507	density = args_info.density_arg;
99	tim	12
100	gezelter	507	//get lattice type
101	gezelter	1067	latticeType = "FCC";
102	tim	12
103	gezelter	507	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
104	tim	487
105	gezelter	507	if (simpleLat == NULL) {
106			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
107			latticeType.c_str());
108			painCave.isFatal = 1;
109			simError();
110			}
111	gezelter	1067	nMolPerCell = simpleLat->getNumSitesPerCell();
112	tim	12
113	gezelter	1067	//get the number of unit cells in each direction:
114
115	gezelter	507	nx = args_info.nx_arg;
116	tim	12
117	gezelter	507	if (nx <= 0) {
118	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the x direction "
119			"must be greater than 0.");
120			painCave.isFatal = 1;
121			simError();
122	gezelter	507	}
123	tim	12
124	gezelter	507	ny = args_info.ny_arg;
125	tim	12
126	gezelter	507	if (ny <= 0) {
127	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the y direction "
128			"must be greater than 0.");
129			painCave.isFatal = 1;
130			simError();
131	gezelter	507	}
132	tim	12
133	gezelter	507	nz = args_info.nz_arg;
134	tim	12
135	gezelter	507	if (nz <= 0) {
136	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the z direction "
137			"must be greater than 0.");
138			painCave.isFatal = 1;
139			simError();
140	gezelter	507	}
141	tim	12
142	gezelter	1067	int nSites = nMolPerCell * nx * ny * nz;
143
144	gezelter	507	//get input file name
145			if (args_info.inputs_num)
146			inputFileName = args_info.inputs[0];
147			else {
148	gezelter	1067	sprintf(painCave.errMsg, "No input .md file name was specified "
149			"on the command line");
150			painCave.isFatal = 1;
151			simError();
152	gezelter	507	}
153	tim	12
154	gezelter	507	//parse md file and set up the system
155	gezelter	1067
156	gezelter	507	SimCreator oldCreator;
157			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
158	gezelter	1067	Globals* simParams = oldInfo->getSimParams();
159	tim	12
160	gezelter	1067	// Calculate lattice constant (in Angstroms)
161	tim	12
162	gezelter	1067	RealType avgMass = getMolMass(oldInfo->getMoleculeStamp(0),
163			oldInfo->getForceField());
164	tim	12
165	gezelter	1067	latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
166			(RealType)(1.0 / 3.0));
167
168			// Set the lattice constant
169
170			lc.push_back(latticeConstant);
171			simpleLat->setLatticeConstant(lc);
172	tim	12
173	gezelter	1067	// Calculate the lattice sites and fill the lattice vector.
174	tim	12
175	gezelter	1067	// Get the standard orientations of the cell sites
176	tim	12
177	gezelter	1067	latticeOrt = simpleLat->getLatticePointsOrt();
178	tim	12
179	gezelter	1067	vector<Vector3d> sites;
180			vector<Vector3d> orientations;
181
182			for(int i = 0; i < nx; i++) {
183			for(int j = 0; j < ny; j++) {
184			for(int k = 0; k < nz; k++) {
185	tim	12
186	gezelter	1067	// Get the position of the cell sites
187
188			simpleLat->getLatticePointsPos(latticePos, i, j, k);
189
190			for(int l = 0; l < nMolPerCell; l++) {
191			sites.push_back(latticePos[l]);
192			orientations.push_back(latticeOrt[l]);
193			}
194			}
195			}
196			}
197
198			outputFileName = args_info.output_arg;
199
200			// create a new .md file on the fly which corrects the number of molecules
201	tim	12
202	gezelter	1067	createMdFile(inputFileName, outputFileName, nSites);
203	tim	12
204	gezelter	1067	if (oldInfo != NULL)
205			delete oldInfo;
206	gezelter	246
207	gezelter	1067	// We need to read in the new SimInfo object, then Parse the
208			// md file and set up the system
209	tim	12
210	gezelter	1067	SimCreator newCreator;
211			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
212	tim	12
213	gezelter	1067	// fill Hmat
214
215			hmat(0, 0) = nx * latticeConstant;
216	gezelter	507	hmat(0, 1) = 0.0;
217			hmat(0, 2) = 0.0;
218	tim	12
219	gezelter	507	hmat(1, 0) = 0.0;
220			hmat(1, 1) = ny * latticeConstant;
221			hmat(1, 2) = 0.0;
222	tim	12
223	gezelter	507	hmat(2, 0) = 0.0;
224			hmat(2, 1) = 0.0;
225			hmat(2, 2) = nz * latticeConstant;
226	tim	12
227	gezelter	1067	// Set Hmat
228	tim	12
229	gezelter	1067	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
230	gezelter	246
231	gezelter	1067	// place the molecules
232
233	gezelter	507	Molecule* mol;
234	gezelter	1067	locator = new MoLocator(newInfo->getMoleculeStamp(0),
235			newInfo->getForceField());
236			for (int n = 0; n < nSites; n++) {
237			mol = newInfo->getMoleculeByGlobalIndex(n);
238			locator->placeMol(sites[n], orientations[n], mol);
239	gezelter	507	}
240	gezelter	1067
241			// Create DumpWriter and write out the coordinates
242	tim	12
243	gezelter	1067	writer = new DumpWriter(newInfo, outputFileName);
244
245	gezelter	507	if (writer == NULL) {
246	gezelter	1067	sprintf(painCave.errMsg, "error in creating DumpWriter");
247			painCave.isFatal = 1;
248			simError();
249	gezelter	507	}
250	tim	12
251	gezelter	507	writer->writeDump();
252	gezelter	246
253	gezelter	1067	// deleting the writer will put the closing at the end of the dump file.
254	gezelter	246
255	gezelter	1067	delete writer;
256	gezelter	246
257	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
258	gezelter	1067	"generated.\n", outputFileName.c_str());
259			painCave.isFatal = 0;
260			simError();
261	gezelter	507	return 0;
262	tim	12	}
263
264	gezelter	1067	void createMdFile(const std::string&oldMdFileName,
265			const std::string&newMdFileName,
266			int nMol) {
267	gezelter	507	ifstream oldMdFile;
268			ofstream newMdFile;
269			const int MAXLEN = 65535;
270			char buffer[MAXLEN];
271	tim	12
272	gezelter	507	//create new .md file based on old .md file
273			oldMdFile.open(oldMdFileName.c_str());
274			newMdFile.open(newMdFileName.c_str());
275	tim	12
276	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
277	gezelter	246
278	gezelter	507	while (!oldMdFile.eof()) {
279	gezelter	246
280	gezelter	507	//correct molecule number
281			if (strstr(buffer, "nMol") != NULL) {
282	gezelter	1067	sprintf(buffer, "\t\tnMol = %d;", nMol);
283	gezelter	507	newMdFile << buffer << std::endl;
284			} else
285			newMdFile << buffer << std::endl;
286	gezelter	246
287	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
288			}
289	gezelter	246
290	gezelter	507	oldMdFile.close();
291			newMdFile.close();
292	tim	12	}
293	gezelter	246