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, 234107 (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 []) {

  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 = MoLocator::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);

  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:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	8291 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	507	registerLattice();
74	gezelter	246
75	gezelter	507	gengetopt_args_info args_info;
76			std::string latticeType;
77			std::string inputFileName;
78	gezelter	1067	std::string outputFileName;
79	gezelter	507	Lattice *simpleLat;
80	gezelter	1067	RealType latticeConstant;
81			std::vector<RealType> lc;
82			const RealType rhoConvertConst = 1.661;
83			RealType density;
84			int nx, ny, nz;
85	gezelter	507	Mat3x3d hmat;
86			MoLocator *locator;
87			std::vector<Vector3d> latticePos;
88			std::vector<Vector3d> latticeOrt;
89	gezelter	1067	int nMolPerCell;
90	gezelter	507	DumpWriter *writer;
91	tim	12
92	gezelter	507	// parse command line arguments
93			if (cmdline_parser(argc, argv, &args_info) != 0)
94			exit(1);
95	tim	12
96	gezelter	507	density = args_info.density_arg;
97	tim	12
98	gezelter	507	//get lattice type
99	gezelter	1067	latticeType = "FCC";
100	tim	12
101	gezelter	507	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
102	tim	487
103	gezelter	507	if (simpleLat == NULL) {
104			sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n",
105			latticeType.c_str());
106			painCave.isFatal = 1;
107			simError();
108			}
109	gezelter	1067	nMolPerCell = simpleLat->getNumSitesPerCell();
110	tim	12
111	gezelter	1067	//get the number of unit cells in each direction:
112
113	gezelter	507	nx = args_info.nx_arg;
114	tim	12
115	gezelter	507	if (nx <= 0) {
116	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the x direction "
117			"must be greater than 0.");
118			painCave.isFatal = 1;
119			simError();
120	gezelter	507	}
121	tim	12
122	gezelter	507	ny = args_info.ny_arg;
123	tim	12
124	gezelter	507	if (ny <= 0) {
125	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the y direction "
126			"must be greater than 0.");
127			painCave.isFatal = 1;
128			simError();
129	gezelter	507	}
130	tim	12
131	gezelter	507	nz = args_info.nz_arg;
132	tim	12
133	gezelter	507	if (nz <= 0) {
134	gezelter	1067	sprintf(painCave.errMsg, "The number of unit cells in the z direction "
135			"must be greater than 0.");
136			painCave.isFatal = 1;
137			simError();
138	gezelter	507	}
139	tim	12
140	gezelter	1067	int nSites = nMolPerCell * nx * ny * nz;
141
142	gezelter	507	//get input file name
143			if (args_info.inputs_num)
144			inputFileName = args_info.inputs[0];
145			else {
146	gezelter	1067	sprintf(painCave.errMsg, "No input .md file name was specified "
147			"on the command line");
148			painCave.isFatal = 1;
149			simError();
150	gezelter	507	}
151	tim	12
152	gezelter	507	//parse md file and set up the system
153	gezelter	1067
154	gezelter	507	SimCreator oldCreator;
155			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
156	gezelter	1067	Globals* simParams = oldInfo->getSimParams();
157	tim	12
158	gezelter	1067	// Calculate lattice constant (in Angstroms)
159	tim	12
160	gezelter	1808	RealType avgMass = MoLocator::getMolMass(oldInfo->getMoleculeStamp(0),
161			oldInfo->getForceField());
162	tim	12
163	gezelter	1067	latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
164			(RealType)(1.0 / 3.0));
165
166			// Set the lattice constant
167
168			lc.push_back(latticeConstant);
169			simpleLat->setLatticeConstant(lc);
170	tim	12
171	gezelter	1067	// Calculate the lattice sites and fill the lattice vector.
172	tim	12
173	gezelter	1067	// Get the standard orientations of the cell sites
174	tim	12
175	gezelter	1067	latticeOrt = simpleLat->getLatticePointsOrt();
176	tim	12
177	gezelter	1067	vector<Vector3d> sites;
178			vector<Vector3d> orientations;
179
180			for(int i = 0; i < nx; i++) {
181			for(int j = 0; j < ny; j++) {
182			for(int k = 0; k < nz; k++) {
183	tim	12
184	gezelter	1067	// Get the position of the cell sites
185
186			simpleLat->getLatticePointsPos(latticePos, i, j, k);
187
188			for(int l = 0; l < nMolPerCell; l++) {
189			sites.push_back(latticePos[l]);
190			orientations.push_back(latticeOrt[l]);
191			}
192			}
193			}
194			}
195
196			outputFileName = args_info.output_arg;
197
198			// create a new .md file on the fly which corrects the number of molecules
199	tim	12
200	gezelter	1067	createMdFile(inputFileName, outputFileName, nSites);
201	tim	12
202	gezelter	1874	delete oldInfo;
203	gezelter	246
204	gezelter	1067	// We need to read in the new SimInfo object, then Parse the
205			// md file and set up the system
206	tim	12
207	gezelter	1067	SimCreator newCreator;
208			SimInfo* newInfo = newCreator.createSim(outputFileName, false);
209	tim	12
210	gezelter	1067	// fill Hmat
211
212			hmat(0, 0) = nx * latticeConstant;
213	gezelter	507	hmat(0, 1) = 0.0;
214			hmat(0, 2) = 0.0;
215	tim	12
216	gezelter	507	hmat(1, 0) = 0.0;
217			hmat(1, 1) = ny * latticeConstant;
218			hmat(1, 2) = 0.0;
219	tim	12
220	gezelter	507	hmat(2, 0) = 0.0;
221			hmat(2, 1) = 0.0;
222			hmat(2, 2) = nz * latticeConstant;
223	tim	12
224	gezelter	1067	// Set Hmat
225	tim	12
226	gezelter	1067	newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
227	gezelter	246
228	gezelter	1067	// place the molecules
229
230	gezelter	507	Molecule* mol;
231	gezelter	1067	locator = new MoLocator(newInfo->getMoleculeStamp(0),
232			newInfo->getForceField());
233			for (int n = 0; n < nSites; n++) {
234			mol = newInfo->getMoleculeByGlobalIndex(n);
235			locator->placeMol(sites[n], orientations[n], mol);
236	gezelter	507	}
237	gezelter	1067
238			// Create DumpWriter and write out the coordinates
239	tim	12
240	gezelter	1067	writer = new DumpWriter(newInfo, outputFileName);
241
242	gezelter	507	if (writer == NULL) {
243	gezelter	1067	sprintf(painCave.errMsg, "error in creating DumpWriter");
244			painCave.isFatal = 1;
245			simError();
246	gezelter	507	}
247	tim	12
248	gezelter	507	writer->writeDump();
249	gezelter	246
250	gezelter	1067	// deleting the writer will put the closing at the end of the dump file.
251	gezelter	246
252	gezelter	1067	delete writer;
253	gezelter	246
254	gezelter	1390	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
255	gezelter	1067	"generated.\n", outputFileName.c_str());
256			painCave.isFatal = 0;
257			simError();
258	gezelter	507	return 0;
259	tim	12	}
260
261	gezelter	1067	void createMdFile(const std::string&oldMdFileName,
262			const std::string&newMdFileName,
263			int nMol) {
264	gezelter	507	ifstream oldMdFile;
265			ofstream newMdFile;
266			const int MAXLEN = 65535;
267			char buffer[MAXLEN];
268	tim	12
269	gezelter	507	//create new .md file based on old .md file
270			oldMdFile.open(oldMdFileName.c_str());
271			newMdFile.open(newMdFileName.c_str());
272	tim	12
273	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
274	gezelter	246
275	gezelter	507	while (!oldMdFile.eof()) {
276	gezelter	246
277	gezelter	507	//correct molecule number
278			if (strstr(buffer, "nMol") != NULL) {
279	gezelter	1067	sprintf(buffer, "\t\tnMol = %d;", nMol);
280	gezelter	507	newMdFile << buffer << std::endl;
281			} else
282			newMdFile << buffer << std::endl;
283	gezelter	246
284	gezelter	507	oldMdFile.getline(buffer, MAXLEN);
285			}
286	gezelter	246
287	gezelter	507	oldMdFile.close();
288			newMdFile.close();
289	tim	12	}
290	gezelter	246