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

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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
74	–	//register force fields
75	–	registerForceFields();
75		registerLattice();
76
77		gengetopt_args_info args_info;
78		std::string latticeType;
79		std::string inputFileName;
80	<	std::string outPrefix;
81	<	std::string outMdFileName;
82	<	std::string outInitFileName;
84	<
85	<
86	<
87	<	Lattice *simpleLat;
88	<	int numMol;
80	>	std::string outputFileName;
81	>	MoLocator* locator;
82	>	int nComponents;
83		double latticeConstant;
84	<	std::vector<double> lc;
91	<	double mass;
92	<	const double rhoConvertConst = 1.661;
93	<	double density;
94	<
95	<
96	<
84	>	RealType particleRadius;
85		Mat3x3d hmat;
98	–	MoLocator *locator;
99	–	sphericalNanoparticle *nanoparticle;
100	–	std::vector<Vector3d> latticePos;
101	–	std::vector<Vector3d> latticeOrt;
102	–	int numMolPerCell;
103	–	int nShells; /* Number of shells in nanoparticle*/
104	–	int numSites;
105	–
86		DumpWriter *writer;
87
88	<	// parse command line arguments
88	>	// Parse Command Line Arguments
89		if (cmdline_parser(argc, argv, &args_info) != 0)
90		exit(1);
91	<
112	<
113	<
91	>
92		/* get lattice type */
93	<	latticeType = UpperCase(args_info.latticetype_arg);
94	<
93	>	latticeType = "FCC";
94	>
95		/* get input file name */
96		if (args_info.inputs_num)
97		inputFileName = args_info.inputs[0];
98		else {
99	<	std::cerr << "You must specify a input file name.\n" << std::endl;
99	>	sprintf(painCave.errMsg, "No input .md file name was specified "
100	>	"on the command line");
101	>	painCave.isFatal = 1;
102		cmdline_parser_print_help();
103	<	exit(1);
103	>	simError();
104		}
105
106		/* parse md file and set up the system */
107		SimCreator oldCreator;
108		SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
109
110	<	nShells = 0;
111	<	if (args_info.coreShellRadius_given){
112	<	nShells = args_info.coreShellRadius_given;
133	<	}
110	>	latticeConstant = args_info.latticeConstant_arg;
111	>	particleRadius = args_info.radius_arg;
112	>	Globals* simParams = oldInfo->getSimParams();
113
114	<	nComponents = oldInfo->getNMoleculeStamp();
114	>	/* Create nanoparticle */
115	>	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
116	>	particleRadius);
117
118	<	/* Check to see if we have enough components to build that many shells. */
119	<	if (nShells){
120	<	if (oldInfo->getNMoleculeStamp() != nShells) {
121	<	std::cerr << "Not enough components present in MD file to build specified number of shells"
122	<	<< std::endl;
123	<	exit(1);
118	>	/* Build a lattice and get lattice points for this lattice constant */
119	>	vector<Vector3d> sites = nanoParticle.getSites();
120	>	vector<Vector3d> orientations = nanoParticle.getOrientations();
121	>
122	>
123	>	std::vector<int> vacancyTargets;
124	>	vector<bool> isVacancy;
125	>
126	>	Vector3d myLoc;
127	>	RealType myR;
128	>
129	>	for (unsigned int i = 0; i < sites.size(); i++)
130	>	isVacancy.push_back(false);
131	>
132	>	if (args_info.vacancyPercent_given) {
133	>	if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
134	>	sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
135	>	painCave.isFatal = 1;
136	>	simError();
137	>	} else {
138	>	RealType vF = args_info.vacancyPercent_arg / 100.0;
139	>	RealType vIR;
140	>	RealType vOR;
141	>	if (args_info.vacancyInnerRadius_given) {
142	>	vIR = args_info.vacancyInnerRadius_arg;
143	>	} else {
144	>	vIR = 0.0;
145	>	}
146	>	if (args_info.vacancyOuterRadius_given) {
147	>	vOR = args_info.vacancyOuterRadius_arg;
148	>	} else {
149	>	vOR = particleRadius;
150	>	}
151	>	if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
152	>
153	>	for (unsigned int i = 0; i < sites.size(); i++) {
154	>	myLoc = sites[i];
155	>	myR = myLoc.length();
156	>	if (myR >= vIR && myR <= vOR) {
157	>	vacancyTargets.push_back(i);
158	>	}
159	>	}
160	>	std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
161	>
162	>	int nTargets = vacancyTargets.size();
163	>	vacancyTargets.resize((int)(vF * nTargets));
164	>
165	>
166	>	sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
167	>	"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
168	>	vIR, vOR);
169	>	painCave.isFatal = 0;
170	>	simError();
171	>
172	>	isVacancy.clear();
173	>	for (unsigned int i = 0; i < sites.size(); i++) {
174	>	bool vac = false;
175	>	for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
176	>	if (i == vacancyTargets[j]) vac = true;
177	>	}
178	>	isVacancy.push_back(vac);
179	>	}
180	>
181	>	} else {
182	>	sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
183	>	"\tinner or outer radii.  Check their values.");
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187		}
188		}
189	<
190	<
191	<	//creat lattice
192	<	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
193	<
194	<	if (simpleLat == NULL) {
195	<	std::cerr << "Error in creating lattice" << std::endl;
196	<	exit(1);
189	>
190	>	/* Get number of lattice sites */
191	>	int nSites = sites.size() - vacancyTargets.size();
192	>
193	>	std::vector<Component*> components = simParams->getComponents();
194	>	std::vector<RealType> molFractions;
195	>	std::vector<RealType> shellRadii;
196	>	std::vector<int> nMol;
197	>	std::map<int, int> componentFromSite;
198	>	nComponents = components.size();
199	>
200	>	if (args_info.molFraction_given && args_info.shellRadius_given) {
201	>	sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
202	>	"arguments, but not both!");
203	>	painCave.isFatal = 1;
204	>	simError();
205		}
206
207	<	numMolPerCell = simpleLat->getNumSitesPerCell();
208	<
209	<	/*calculate lattice constant (in Angstrom)
210	<	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
211	<	1.0 / 3.0);*/
212	<
213	<	latticeConstant = args_info.latticeCnst_arg;
214	<	particleRadius = args_info.radius_arg;
215	<	particleDiameter = 2.0 * particleRadius;
216	<
217	<	/* set lattice constant */
218	<	lc.push_back(latticeConstant);
219	<	simpleLat->setLatticeConstant(lc);
220	<
221	<
222	<	/*determine the output file names*/
223	<	if (args_info.output_given)
224	<	outInitFileName = args_info.output_arg;
225	<	else
226	<	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;
207	>	if (nComponents == 1) {
208	>	molFractions.push_back(1.0);
209	>	shellRadii.push_back(particleRadius);
210	>	} else if (args_info.molFraction_given) {
211	>	if ((int)args_info.molFraction_given == nComponents) {
212	>	for (int i = 0; i < nComponents; i++) {
213	>	molFractions.push_back(args_info.molFraction_arg[i]);
214	>	}
215	>	} else if ((int)args_info.molFraction_given == nComponents-1) {
216	>	RealType remainingFraction = 1.0;
217	>	for (int i = 0; i < nComponents-1; i++) {
218	>	molFractions.push_back(args_info.molFraction_arg[i]);
219	>	remainingFraction -= molFractions[i];
220	>	}
221	>	molFractions.push_back(remainingFraction);
222	>	} else {
223	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
224	>	"for all of the components in the <MetaData> block.");
225	>	painCave.isFatal = 1;
226	>	simError();
227		}
228	<	int totComponents = 0;
229	<	for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
230	<	numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
231	<	totComponents += numMol[i];
232	<	}
233	<	numMol[nComponents-1] = numSites - totComponents;
234	<
235	<	} else{ /*Handle core-shell with multiple components.*/
236	<	std::cout << "Creating a core-shell nanoparticle." << std::endl;
237	<	if (nComponents != args_info.ShellRadius_given + 1){
238	<	std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
239	<	exit 1;
228	>	} else if ((int)args_info.shellRadius_given) {
229	>	if ((int)args_info.shellRadius_given == nComponents) {
230	>	for (int i = 0; i < nComponents; i++) {
231	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
232	>	}
233	>	} else if ((int)args_info.shellRadius_given == nComponents-1) {
234	>	for (int i = 0; i < nComponents-1; i++) {
235	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
236	>	}
237	>	shellRadii.push_back(particleRadius);
238	>	} else {
239	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
240	>	"\tshell radii for all of the components in the <MetaData> block.");
241	>	painCave.isFatal = 1;
242	>	simError();
243		}
244	+	} else {
245	+	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
246	+	"\tbut have not specified either molFraction or shellRadius arguments.");
247	+	painCave.isFatal = 1;
248	+	simError();
249	+	}
250
251	+	if (args_info.molFraction_given) {
252	+	RealType totalFraction = 0.0;
253
254	+	/* Do some simple sanity checking*/
255
256	+	for (int i = 0; i < nComponents; i++) {
257	+	if (molFractions.at(i) < 0.0) {
258	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
259	+	" less than zero!");
260	+	painCave.isFatal = 1;
261	+	simError();
262	+	}
263	+	if (molFractions.at(i) > 1.0) {
264	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
265	+	" greater than one!");
266	+	painCave.isFatal = 1;
267	+	simError();
268	+	}
269	+	totalFraction += molFractions.at(i);
270	+	}
271	+	if (abs(totalFraction - 1.0) > 1e-6) {
272	+	sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
273	+	painCave.isFatal = 1;
274	+	simError();
275	+	}
276	+
277	+	int remaining = nSites;
278	+	for (int i=0; i < nComponents-1; i++) {
279	+	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
280	+	remaining -= nMol.at(i);
281	+	}
282	+	nMol.push_back(remaining);
283	+
284	+	// recompute actual mol fractions and perform final sanity check:
285	+
286	+	int totalMolecules = 0;
287	+	for (int i=0; i < nComponents; i++) {
288	+	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
289	+	totalMolecules += nMol.at(i);
290	+	}
291	+
292	+	if (totalMolecules != nSites) {
293	+	sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
294	+	"to the number of lattice sites!");
295	+	painCave.isFatal = 1;
296	+	simError();
297	+	}
298	+	} else {
299	+
300	+	for (unsigned int i = 0; i < shellRadii.size(); i++) {
301	+	if (shellRadii.at(i) > particleRadius + 1e-6 ) {
302	+	sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
303	+	painCave.isFatal = 1;
304	+	simError();
305	+	}
306	+	if (shellRadii.at(i) <= 0.0 ) {
307	+	sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
308	+	painCave.isFatal = 1;
309	+	simError();
310	+	}
311	+	}
312		}
313
314	<	//get the orientation of the cell sites
315	<	//for the same type of molecule in same lattice, it will not change
316	<	latticeOrt = simpleLat->getLatticePointsOrt();
314	>	vector<int> ids;
315	>	if ((int)args_info.molFraction_given){
316	>	sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
317	>	painCave.isFatal = 0;
318	>	simError();
319	>	/* Random particle is the default case*/
320	>
321	>	for (unsigned int i = 0; i < sites.size(); i++)
322	>	if (!isVacancy[i]) ids.push_back(i);
323	>
324	>	std::random_shuffle(ids.begin(), ids.end());
325	>
326	>	} else{
327	>	sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
328	>	painCave.isFatal = 0;
329	>	simError();
330	>
331	>	RealType smallestSoFar;
332	>	int myComponent = -1;
333	>	nMol.clear();
334	>	nMol.resize(nComponents);
335	>
336	>	for (unsigned int i = 0; i < sites.size(); i++) {
337	>	myLoc = sites[i];
338	>	myR = myLoc.length();
339	>	smallestSoFar = particleRadius;
340	>	if (!isVacancy[i]) {
341	>	for (int j = 0; j < nComponents; j++) {
342	>	if (myR <= shellRadii[j]) {
343	>	if (shellRadii[j] <= smallestSoFar) {
344	>	smallestSoFar = shellRadii[j];
345	>	myComponent = j;
346	>	}
347	>	}
348	>	}
349	>	componentFromSite[i] = myComponent;
350	>	nMol[myComponent]++;
351	>	}
352	>	}
353	>	}
354
355	+	outputFileName = args_info.output_arg;
356	+
357	+	//creat new .md file on fly which corrects the number of molecule
358	+	createMdFile(inputFileName, outputFileName, nMol);
359
360	+	delete oldInfo;
361
362	<	// needed for writing out new md file.
363	<
364	<	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
365	<	outMdFileName = outPrefix + ".md";
227	<
228	<	//creat new .md file on fly which corrects the number of molecule
229	<	createMdFile(inputFileName, outMdFileName, numcomponents,numMol);
230	<
231	<	if (oldInfo != NULL)
232	<	delete oldInfo;
233	<
234	<
235	<	// We need to read in new siminfo object.
236	<	//parse md file and set up the system
237	<	//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	<
362	>	SimCreator newCreator;
363	>	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
364	>
365	>	// Place molecules
366		Molecule* mol;
367		SimInfo::MoleculeIterator mi;
368		mol = NewInfo->beginMolecule(mi);
369
370	+	int l = 0;
371
372	<	for(int i = -nx; i < nx; i++) {
373	<	for(int j = -ny; j < ny; j++) {
374	<	for(int k = -nz; k < nz; k++) {
375	<
376	<	//get the position of the cell sites
377	<	simpleLat->getLatticePointsPos(latticePos, i, j, k);
378	<
379	<	for(int l = 0; l < numMolPerCell; l++) {
380	<	#ifdef HAVE_CGAL
381	<	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
382	<	#endif
383	<	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	<	}
372	>	for (int i = 0; i < nComponents; i++){
373	>	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
374	>	NewInfo->getForceField());
375	>
376	>	if (!args_info.molFraction_given) {
377	>	for (unsigned int n = 0; n < sites.size(); n++) {
378	>	if (!isVacancy[n]) {
379	>	if (componentFromSite[n] == i) {
380	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
381	>	locator->placeMol(sites[n], orientations[n], mol);
382	>	l++;
383	>	}
384		}
385	<	}
385	>	}
386	>	} else {
387	>	for (int n = 0; n < nMol.at(i); n++) {
388	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
389	>	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
390	>	l++;
391	>	}
392	>	}
393		}
394
273	–
274	–
395		//fill Hmat
396	<	hmat(0, 0)= nx * latticeConstant;
396	>	hmat(0, 0)=  10.0*particleRadius;
397		hmat(0, 1) = 0.0;
398		hmat(0, 2) = 0.0;
399
400		hmat(1, 0) = 0.0;
401	<	hmat(1, 1) = ny * latticeConstant;
401	>	hmat(1, 1) =  10.0*particleRadius;
402		hmat(1, 2) = 0.0;
403
404		hmat(2, 0) = 0.0;
405		hmat(2, 1) = 0.0;
406	<	hmat(2, 2) = nz * latticeConstant;
406	>	hmat(2, 2) =  10.0*particleRadius;
407
408		//set Hmat
409		NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
410
411
412		//create dumpwriter and write out the coordinates
413	<	NewInfo->setFinalConfigFileName(outInitFileName);
294	<	writer = new DumpWriter(NewInfo);
413	>	writer = new DumpWriter(NewInfo, outputFileName);
414
415		if (writer == NULL) {
416	<	std::cerr << "error in creating DumpWriter" << std::endl;
417	<	exit(1);
416	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
417	>	painCave.isFatal = 1;
418	>	simError();
419		}
420
421		writer->writeDump();
422	<	std::cout << "new initial configuration file: " << outInitFileName
423	<	<< " is generated." << std::endl;
424	<
425	<	//delete objects
426	<
427	<	//delete oldInfo and oldSimSetup
428	<
429	<	if (NewInfo != NULL)
430	<	delete NewInfo;
431	<
312	<	if (writer != NULL)
313	<	delete writer;
314	<	delete simpleLat;
315	<	cmdline_parser_free(&args_info);
422	>
423	>	// deleting the writer will put the closing at the end of the dump file
424	>
425	>	delete writer;
426	>
427	>	// cleanup a by calling sim error.....
428	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
429	>	"generated.\n", outputFileName.c_str());
430	>	painCave.isFatal = 0;
431	>	simError();
432		return 0;
433		}
434
435	<	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
436	<	int components,int &nummol) {
435	>	void createMdFile(const std::string&oldMdFileName,
436	>	const std::string&newMdFileName,
437	>	std::vector<int> nMol) {
438		ifstream oldMdFile;
439		ofstream newMdFile;
440		const int MAXLEN = 65535;
#	Line 326 | Line 443 | void createMdFile(const std::string&oldMdFileName, con
443		//create new .md file based on old .md file
444		oldMdFile.open(oldMdFileName.c_str());
445		newMdFile.open(newMdFileName.c_str());
329	–
446		oldMdFile.getline(buffer, MAXLEN);
447	<
447	>
448	>	unsigned int i = 0;
449		while (!oldMdFile.eof()) {
450	<
450	>
451		//correct molecule number
452		if (strstr(buffer, "nMol") != NULL) {
453	<	sprintf(buffer, "\tnMol = %i;", numMol);
454	<	newMdFile << buffer << std::endl;
453	>	if(i<nMol.size()){
454	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
455	>	newMdFile << buffer << std::endl;
456	>	i++;
457	>	}
458		} else
459		newMdFile << buffer << std::endl;
460
#	Line 343 | Line 463 | void createMdFile(const std::string&oldMdFileName, con
463
464		oldMdFile.close();
465		newMdFile.close();
466	+
467	+	if (i != nMol.size()) {
468	+	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
469	+	"\tstatements in component blocks.  Make sure that all\n"
470	+	"\tcomponents in the template file have nMol=1");
471	+	painCave.isFatal = 1;
472	+	simError();
473	+	}
474	+
475		}
476

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords):
Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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

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