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Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents), Revision 1704 by gezelter, Tue Apr 24 20:40:04 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <cstdlib>
#	Line 47 | Line 48
48		#include <string>
49		#include <map>
50		#include <fstream>
51	+	#include <algorithm>
52
53		#include "config.h"
54	<
54	>	#include "shapedLatticeSpherical.hpp"
55		#include "nanoparticleBuilderCmd.h"
54	–	#include "sphericalNanoparticle.hpp"
56		#include "lattice/LatticeFactory.hpp"
57		#include "utils/MoLocator.hpp"
58		#include "lattice/Lattice.hpp"
#	Line 64 | Line 65 | using namespace std;
65		#include "utils/StringUtils.hpp"
66
67		using namespace std;
68	<	using namespace oopse;
68	>	using namespace OpenMD;
69		void createMdFile(const std::string&oldMdFileName,
70		const std::string&newMdFileName,
71	<	int numMol);
71	>	std::vector<int> numMol);
72
73		int main(int argc, char *argv []) {
74
#	Line 78 | Line 79 | int main(int argc, char *argv []) {
79		gengetopt_args_info args_info;
80		std::string latticeType;
81		std::string inputFileName;
82	<	std::string outPrefix;
82	<	std::string outMdFileName;
83	<	std::string outInitFileName;
82	>	std::string outputFileName;
83
84	<
85	<
87	<	Lattice *simpleLat;
88	<	int numMol;
84	>	MoLocator* locator;
85	>	int nComponents;
86		double latticeConstant;
87		std::vector<double> lc;
91	–	double mass;
92	–	const double rhoConvertConst = 1.661;
93	–	double density;
94	–
95	–
88
89	+	RealType particleRadius;
90	+
91		Mat3x3d hmat;
98	–	MoLocator *locator;
99	–	sphericalNanoparticle *nanoparticle;
92		std::vector<Vector3d> latticePos;
93		std::vector<Vector3d> latticeOrt;
94	<	int numMolPerCell;
103	<	int nShells; /* Number of shells in nanoparticle*/
104	<	int numSites;
105	<
94	>
95		DumpWriter *writer;
96
97	<	// parse command line arguments
97	>	// Parse Command Line Arguments
98		if (cmdline_parser(argc, argv, &args_info) != 0)
99		exit(1);
100	<
112	<
113	<
100	>
101		/* get lattice type */
102	<	latticeType = UpperCase(args_info.latticetype_arg);
103	<
102	>	latticeType = "FCC";
103	>
104		/* get input file name */
105		if (args_info.inputs_num)
106		inputFileName = args_info.inputs[0];
107		else {
108	<	std::cerr << "You must specify a input file name.\n" << std::endl;
108	>	sprintf(painCave.errMsg, "No input .md file name was specified "
109	>	"on the command line");
110	>	painCave.isFatal = 1;
111		cmdline_parser_print_help();
112	<	exit(1);
112	>	simError();
113		}
114
115		/* parse md file and set up the system */
116		SimCreator oldCreator;
117		SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
118
119	<	nShells = 0;
120	<	if (args_info.coreShellRadius_given){
121	<	nShells = args_info.coreShellRadius_given;
133	<	}
119	>	latticeConstant = args_info.latticeConstant_arg;
120	>	particleRadius = args_info.radius_arg;
121	>	Globals* simParams = oldInfo->getSimParams();
122
123	<	nComponents = oldInfo->getNMoleculeStamp();
123	>	/* Create nanoparticle */
124	>	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
125	>	particleRadius);
126
127	<	/* Check to see if we have enough components to build that many shells. */
128	<	if (nShells){
129	<	if (oldInfo->getNMoleculeStamp() != nShells) {
130	<	std::cerr << "Not enough components present in MD file to build specified number of shells"
131	<	<< std::endl;
132	<	exit(1);
127	>	/* Build a lattice and get lattice points for this lattice constant */
128	>	vector<Vector3d> sites = nanoParticle.getSites();
129	>	vector<Vector3d> orientations = nanoParticle.getOrientations();
130	>
131	>
132	>	std::vector<int> vacancyTargets;
133	>	vector<bool> isVacancy;
134	>
135	>	Vector3d myLoc;
136	>	RealType myR;
137	>
138	>	for (int i = 0; i < sites.size(); i++)
139	>	isVacancy.push_back(false);
140	>
141	>	if (args_info.vacancyPercent_given) {
142	>	if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
143	>	sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
144	>	painCave.isFatal = 1;
145	>	simError();
146	>	} else {
147	>	RealType vF = args_info.vacancyPercent_arg / 100.0;
148	>	RealType vIR;
149	>	RealType vOR;
150	>	if (args_info.vacancyInnerRadius_given) {
151	>	vIR = args_info.vacancyInnerRadius_arg;
152	>	} else {
153	>	vIR = 0.0;
154	>	}
155	>	if (args_info.vacancyOuterRadius_given) {
156	>	vOR = args_info.vacancyOuterRadius_arg;
157	>	} else {
158	>	vOR = particleRadius;
159	>	}
160	>	if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
161	>
162	>	for (int i = 0; i < sites.size(); i++) {
163	>	myLoc = sites[i];
164	>	myR = myLoc.length();
165	>	if (myR >= vIR && myR <= vOR) {
166	>	vacancyTargets.push_back(i);
167	>	}
168	>	}
169	>	std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
170	>
171	>	int nTargets = vacancyTargets.size();
172	>	vacancyTargets.resize((int)(vF * nTargets));
173	>
174	>
175	>	sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
176	>	"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
177	>	vIR, vOR);
178	>	painCave.isFatal = 0;
179	>	simError();
180	>
181	>	isVacancy.clear();
182	>	for (int i = 0; i < sites.size(); i++) {
183	>	bool vac = false;
184	>	for (int j = 0; j < vacancyTargets.size(); j++) {
185	>	if (i == vacancyTargets[j]) vac = true;
186	>	}
187	>	isVacancy.push_back(vac);
188	>	}
189	>
190	>	} else {
191	>	sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
192	>	"\tinner or outer radii.  Check their values.");
193	>	painCave.isFatal = 1;
194	>	simError();
195	>	}
196		}
197		}
198	<
199	<
200	<	//creat lattice
201	<	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
202	<
203	<	if (simpleLat == NULL) {
204	<	std::cerr << "Error in creating lattice" << std::endl;
205	<	exit(1);
198	>
199	>	/* Get number of lattice sites */
200	>	int nSites = sites.size() - vacancyTargets.size();
201	>
202	>	std::vector<Component*> components = simParams->getComponents();
203	>	std::vector<RealType> molFractions;
204	>	std::vector<RealType> shellRadii;
205	>	std::vector<RealType> molecularMasses;
206	>	std::vector<int> nMol;
207	>	std::map<int, int> componentFromSite;
208	>	nComponents = components.size();
209	>
210	>	if (args_info.molFraction_given && args_info.shellRadius_given) {
211	>	sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
212	>	"arguments, but not both!");
213	>	painCave.isFatal = 1;
214	>	simError();
215		}
216
217	<	numMolPerCell = simpleLat->getNumSitesPerCell();
218	<
219	<	/*calculate lattice constant (in Angstrom)
220	<	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
221	<	1.0 / 3.0);*/
222	<
223	<	latticeConstant = args_info.latticeCnst_arg;
224	<	particleRadius = args_info.radius_arg;
225	<	particleDiameter = 2.0 * particleRadius;
226	<
227	<	/* set lattice constant */
228	<	lc.push_back(latticeConstant);
229	<	simpleLat->setLatticeConstant(lc);
230	<
231	<
232	<	/*determine the output file names*/
233	<	if (args_info.output_given)
234	<	outInitFileName = args_info.output_arg;
235	<	else
236	<	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
175	<
176	<
177	<
178	<
179	<
180	<
181	<	/* create Molocators */
182	<	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
183	<
184	<	/* create a new spherical nanoparticle */
185	<	nanoparticle = new sphericalNanoparticle(particleRadius,latticeConstant);
186	<	/* Build a nanoparticle to see how many sites are there */
187	<	numSites = new int[nComponents]
188	<	nanoparticle.getNMol(numSites);
189	<
190	<	numMol = new int[nComponents];
191	<	/* Random particle is the default case*/
192	<	if (!args_info.ShellRadius_given){
193	<	std::cout << "Creating a random nanoparticle" << std::endl;
194	<	/* Check to see if we have enough components */
195	<	if (nComponents != args_info.molFraction_given + 1){
196	<	std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
197	<	exit 1;
217	>	if (nComponents == 1) {
218	>	molFractions.push_back(1.0);
219	>	shellRadii.push_back(particleRadius);
220	>	} else if (args_info.molFraction_given) {
221	>	if ((int)args_info.molFraction_given == nComponents) {
222	>	for (int i = 0; i < nComponents; i++) {
223	>	molFractions.push_back(args_info.molFraction_arg[i]);
224	>	}
225	>	} else if ((int)args_info.molFraction_given == nComponents-1) {
226	>	RealType remainingFraction = 1.0;
227	>	for (int i = 0; i < nComponents-1; i++) {
228	>	molFractions.push_back(args_info.molFraction_arg[i]);
229	>	remainingFraction -= molFractions[i];
230	>	}
231	>	molFractions.push_back(remainingFraction);
232	>	} else {
233	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
234	>	"for all of the components in the <MetaData> block.");
235	>	painCave.isFatal = 1;
236	>	simError();
237		}
238	<	int totComponents = 0;
239	<	for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
240	<	numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
241	<	totComponents += numMol[i];
242	<	}
243	<	numMol[nComponents-1] = numSites - totComponents;
244	<
245	<	} else{ /*Handle core-shell with multiple components.*/
246	<	std::cout << "Creating a core-shell nanoparticle." << std::endl;
247	<	if (nComponents != args_info.ShellRadius_given + 1){
248	<	std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
249	<	exit 1;
238	>	} else if ((int)args_info.shellRadius_given) {
239	>	if ((int)args_info.shellRadius_given == nComponents) {
240	>	for (int i = 0; i < nComponents; i++) {
241	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
242	>	}
243	>	} else if ((int)args_info.shellRadius_given == nComponents-1) {
244	>	for (int i = 0; i < nComponents-1; i++) {
245	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
246	>	}
247	>	shellRadii.push_back(particleRadius);
248	>	} else {
249	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
250	>	"\tshell radii for all of the components in the <MetaData> block.");
251	>	painCave.isFatal = 1;
252	>	simError();
253		}
254	+	} else {
255	+	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
256	+	"\tbut have not specified either molFraction or shellRadius arguments.");
257	+	painCave.isFatal = 1;
258	+	simError();
259	+	}
260
261	+	if (args_info.molFraction_given) {
262	+	RealType totalFraction = 0.0;
263
264	+	/* Do some simple sanity checking*/
265
266	+	for (int i = 0; i < nComponents; i++) {
267	+	if (molFractions.at(i) < 0.0) {
268	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
269	+	" less than zero!");
270	+	painCave.isFatal = 1;
271	+	simError();
272	+	}
273	+	if (molFractions.at(i) > 1.0) {
274	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
275	+	" greater than one!");
276	+	painCave.isFatal = 1;
277	+	simError();
278	+	}
279	+	totalFraction += molFractions.at(i);
280	+	}
281	+	if (abs(totalFraction - 1.0) > 1e-6) {
282	+	sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
283	+	painCave.isFatal = 1;
284	+	simError();
285	+	}
286	+
287	+	int remaining = nSites;
288	+	for (int i=0; i < nComponents-1; i++) {
289	+	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
290	+	remaining -= nMol.at(i);
291	+	}
292	+	nMol.push_back(remaining);
293	+
294	+	// recompute actual mol fractions and perform final sanity check:
295	+
296	+	int totalMolecules = 0;
297	+	for (int i=0; i < nComponents; i++) {
298	+	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
299	+	totalMolecules += nMol.at(i);
300	+	}
301	+
302	+	if (totalMolecules != nSites) {
303	+	sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
304	+	"to the number of lattice sites!");
305	+	painCave.isFatal = 1;
306	+	simError();
307	+	}
308	+	} else {
309	+
310	+	for (int i = 0; i < shellRadii.size(); i++) {
311	+	if (shellRadii.at(i) > particleRadius + 1e-6 ) {
312	+	sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
313	+	painCave.isFatal = 1;
314	+	simError();
315	+	}
316	+	if (shellRadii.at(i) <= 0.0 ) {
317	+	sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
318	+	painCave.isFatal = 1;
319	+	simError();
320	+	}
321	+	}
322		}
323
324	<	//get the orientation of the cell sites
325	<	//for the same type of molecule in same lattice, it will not change
326	<	latticeOrt = simpleLat->getLatticePointsOrt();
324	>	vector<int> ids;
325	>	if ((int)args_info.molFraction_given){
326	>	sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
327	>	painCave.isFatal = 0;
328	>	simError();
329	>	/* Random particle is the default case*/
330	>
331	>	for (int i = 0; i < sites.size(); i++)
332	>	if (!isVacancy[i]) ids.push_back(i);
333	>
334	>	std::random_shuffle(ids.begin(), ids.end());
335	>
336	>	} else{
337	>	sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
338	>	painCave.isFatal = 0;
339	>	simError();
340	>
341	>	RealType smallestSoFar;
342	>	int myComponent = -1;
343	>	nMol.clear();
344	>	nMol.resize(nComponents);
345	>
346	>	for (int i = 0; i < sites.size(); i++) {
347	>	myLoc = sites[i];
348	>	myR = myLoc.length();
349	>	smallestSoFar = particleRadius;
350	>	if (!isVacancy[i]) {
351	>	for (int j = 0; j < nComponents; j++) {
352	>	if (myR <= shellRadii[j]) {
353	>	if (shellRadii[j] <= smallestSoFar) {
354	>	smallestSoFar = shellRadii[j];
355	>	myComponent = j;
356	>	}
357	>	}
358	>	}
359	>	componentFromSite[i] = myComponent;
360	>	nMol[myComponent]++;
361	>	}
362	>	}
363	>	}
364
365	+	outputFileName = args_info.output_arg;
366	+
367	+	//creat new .md file on fly which corrects the number of molecule
368	+	createMdFile(inputFileName, outputFileName, nMol);
369
222	–
223	–	// needed for writing out new md file.
224	–
225	–	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
226	–	outMdFileName = outPrefix + ".md";
227	–
228	–	//creat new .md file on fly which corrects the number of molecule
229	–	createMdFile(inputFileName, outMdFileName, numcomponents,numMol);
230	–
370		if (oldInfo != NULL)
371		delete oldInfo;
372
373	<
374	<	// We need to read in new siminfo object.
375	<	//parse md file and set up the system
376	<	//SimCreator NewCreator;
238	<
239	<	SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
240	<
241	<	// This was so much fun the first time, lets do it again.
242	<
373	>	SimCreator newCreator;
374	>	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
375	>
376	>	// Place molecules
377		Molecule* mol;
378		SimInfo::MoleculeIterator mi;
379		mol = NewInfo->beginMolecule(mi);
380
381	+	int l = 0;
382	+	int whichSite = 0;
383
384	<	for(int i = -nx; i < nx; i++) {
385	<	for(int j = -ny; j < ny; j++) {
386	<	for(int k = -nz; k < nz; k++) {
387	<
388	<	//get the position of the cell sites
389	<	simpleLat->getLatticePointsPos(latticePos, i, j, k);
390	<
391	<	for(int l = 0; l < numMolPerCell; l++) {
392	<	#ifdef HAVE_CGAL
393	<	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
394	<	#endif
395	<	if (mol != NULL) {
260	<	locator->placeMol(latticePos[l], latticeOrt[l], mol);
261	<	} else {
262	<	std::cerr<<"Error in placing molecule " << std::endl;
263	<	}
264	<	mol = NewInfo->nextMolecule(mi);
265	<	#ifdef HAVE_CGAL
266	<	}
267	<	#endif
268	<	}
384	>	for (int i = 0; i < nComponents; i++){
385	>	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
386	>	NewInfo->getForceField());
387	>
388	>	if (!args_info.molFraction_given) {
389	>	for (int n = 0; n < sites.size(); n++) {
390	>	if (!isVacancy[n]) {
391	>	if (componentFromSite[n] == i) {
392	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
393	>	locator->placeMol(sites[n], orientations[n], mol);
394	>	l++;
395	>	}
396		}
397	<	}
397	>	}
398	>	} else {
399	>	for (int n = 0; n < nMol.at(i); n++) {
400	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
401	>	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
402	>	l++;
403	>	}
404	>	}
405		}
406
273	–
274	–
407		//fill Hmat
408	<	hmat(0, 0)= nx * latticeConstant;
408	>	hmat(0, 0)=  10.0*particleRadius;
409		hmat(0, 1) = 0.0;
410		hmat(0, 2) = 0.0;
411
412		hmat(1, 0) = 0.0;
413	<	hmat(1, 1) = ny * latticeConstant;
413	>	hmat(1, 1) =  10.0*particleRadius;
414		hmat(1, 2) = 0.0;
415
416		hmat(2, 0) = 0.0;
417		hmat(2, 1) = 0.0;
418	<	hmat(2, 2) = nz * latticeConstant;
418	>	hmat(2, 2) =  10.0*particleRadius;
419
420		//set Hmat
421		NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
422
423
424		//create dumpwriter and write out the coordinates
425	<	NewInfo->setFinalConfigFileName(outInitFileName);
294	<	writer = new DumpWriter(NewInfo);
425	>	writer = new DumpWriter(NewInfo, outputFileName);
426
427		if (writer == NULL) {
428	<	std::cerr << "error in creating DumpWriter" << std::endl;
429	<	exit(1);
428	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
429	>	painCave.isFatal = 1;
430	>	simError();
431		}
432
433		writer->writeDump();
434	<	std::cout << "new initial configuration file: " << outInitFileName
435	<	<< " is generated." << std::endl;
436	<
437	<	//delete objects
438	<
439	<	//delete oldInfo and oldSimSetup
440	<
441	<	if (NewInfo != NULL)
442	<	delete NewInfo;
443	<
312	<	if (writer != NULL)
313	<	delete writer;
314	<	delete simpleLat;
315	<	cmdline_parser_free(&args_info);
434	>
435	>	// deleting the writer will put the closing at the end of the dump file
436	>
437	>	delete writer;
438	>
439	>	// cleanup a by calling sim error.....
440	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
441	>	"generated.\n", outputFileName.c_str());
442	>	painCave.isFatal = 0;
443	>	simError();
444		return 0;
445		}
446
447	<	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
448	<	int components,int &nummol) {
447	>	void createMdFile(const std::string&oldMdFileName,
448	>	const std::string&newMdFileName,
449	>	std::vector<int> nMol) {
450		ifstream oldMdFile;
451		ofstream newMdFile;
452		const int MAXLEN = 65535;
#	Line 326 | Line 455 | void createMdFile(const std::string&oldMdFileName, con
455		//create new .md file based on old .md file
456		oldMdFile.open(oldMdFileName.c_str());
457		newMdFile.open(newMdFileName.c_str());
329	–
458		oldMdFile.getline(buffer, MAXLEN);
459	<
459	>
460	>	int i = 0;
461		while (!oldMdFile.eof()) {
462	<
462	>
463		//correct molecule number
464		if (strstr(buffer, "nMol") != NULL) {
465	<	sprintf(buffer, "\tnMol = %i;", numMol);
466	<	newMdFile << buffer << std::endl;
465	>	if(i<nMol.size()){
466	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
467	>	newMdFile << buffer << std::endl;
468	>	i++;
469	>	}
470		} else
471		newMdFile << buffer << std::endl;
472
#	Line 343 | Line 475 | void createMdFile(const std::string&oldMdFileName, con
475
476		oldMdFile.close();
477		newMdFile.close();
478	+
479	+	if (i != nMol.size()) {
480	+	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
481	+	"\tstatements in component blocks.  Make sure that all\n"
482	+	"\tcomponents in the template file have nMol=1");
483	+	painCave.isFatal = 1;
484	+	simError();
485	+	}
486	+
487		}
488

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords), Revision 1704 by gezelter, Tue Apr 24 20:40:04 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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