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root/OpenMD/trunk/src/applications/randomBuilder/randomBuilder.cpp

Comparing trunk/src/applications/randomBuilder/randomBuilder.cpp (file contents):
Revision 1077 by gezelter, Wed Oct 18 19:35:07 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 5 | Line 5
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
8	>	* 1. Redistributions of source code must retain the above copyright
9		*    notice, this list of conditions and the following disclaimer.
10		*
11	<	* 3. Redistributions in binary form must reproduce the above copyright
11	>	* 2. Redistributions in binary form must reproduce the above copyright
12		*    notice, this list of conditions and the following disclaimer in the
13		*    documentation and/or other materials provided with the
14		*    distribution.
#	Line 37 | Line 28
28		* University of Notre Dame has been advised of the possibility of
29		* such damages.
30		*
31	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32	+	* research, please cite the appropriate papers when you publish your
33	+	* work.  Good starting points are:
34	+	*
35	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	+	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  randomBuilder.cpp
42		*
43		*  Created by Charles F. Vardeman II on 10 Apr 2006.
44		*  @author  Charles F. Vardeman II
45	<	*  @version $Id: randomBuilder.cpp,v 1.7 2006-10-18 19:35:07 gezelter Exp $
45	>	*  @version $Id$
46		*
47		*/
48
#	Line 69 | Line 69 | using namespace std;
69		#include "utils/StringUtils.hpp"
70
71		using namespace std;
72	<	using namespace oopse;
72	>	using namespace OpenMD;
73
74		void createMdFile(const std::string&oldMdFileName,
75		const std::string&newMdFileName,
#	Line 77 | Line 77 | int main(int argc, char *argv []) {
77
78		int main(int argc, char *argv []) {
79
80	–	// register force fields
81	–	registerForceFields();
80		registerLattice();
81
82		gengetopt_args_info args_info;
#	Line 233 | Line 231 | int main(int argc, char *argv []) {
231		for (int i=0; i < nComponents; i++) {
232		molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
233		totalMolecules += nMol.at(i);
234	<	molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
235	<	oldInfo->getForceField()));
234	>	molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i),
235	>	oldInfo->getForceField()));
236		totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
237		}
238		RealType avgMass = totalMass / (RealType) totalMolecules;
#	Line 285 | Line 283 | int main(int argc, char *argv []) {
283
284		createMdFile(inputFileName, outputFileName, nMol);
285
286	<	if (oldInfo != NULL)
289	<	delete oldInfo;
286	>	delete oldInfo;
287
288		// We need to read in the new SimInfo object, then Parse the
289		// md file and set up the system
#	Line 317 | Line 314 | int main(int argc, char *argv []) {
314		// Randomize a vector of ints:
315
316		vector<int> ids;
317	<	for (int i = 0; i < sites.size(); i++) ids.push_back(i);
317	>	for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i);
318		std::random_shuffle(ids.begin(), ids.end());
319
320		Molecule* mol;
#	Line 348 | Line 345 | int main(int argc, char *argv []) {
345
346		delete writer;
347
348	<	sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
348	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
349		"generated.\n", outputFileName.c_str());
350		painCave.isFatal = 0;
351		simError();
#	Line 370 | Line 367 | void createMdFile(const std::string&oldMdFileName,
367
368		oldMdFile.getline(buffer, MAXLEN);
369
370	<	int i = 0;
370	>	unsigned int i = 0;
371		while (!oldMdFile.eof()) {
372
373		//correct molecule number
374		if (strstr(buffer, "nMol") != NULL) {
375	<	if(i<nMol.size()){
375	>	if (i<nMol.size()){
376		sprintf(buffer, "\tnMol = %i;", nMol.at(i));
377		newMdFile << buffer << std::endl;
378		i++;

Comparing trunk/src/applications/randomBuilder/randomBuilder.cpp (property svn:keywords):
Revision 1077 by gezelter, Wed Oct 18 19:35:07 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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