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

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 875 by chuckv, Thu Jan 19 22:54:23 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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
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;
131	<	if (args_info.coreShellRadius_given){
132	<	nShells = args_info.coreShellRadius_given;
133	<	}
134	<
135	<	nComponents = oldInfo->getNMoleculeStamp();
136	<
137	<	/* Check to see if we have enough components to build that many shells. */
138	<	if (nShells){
139	<	if (oldInfo->getNMoleculeStamp() != nShells) {
140	<	std::cerr << "Not enough components present in MD file to build specified number of shells"
141	<	<< std::endl;
142	<	exit(1);
143	<	}
144	<	}
145	<
146	<
147	<	//creat lattice
148	<	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
149	<
150	<	if (simpleLat == NULL) {
151	<	std::cerr << "Error in creating lattice" << std::endl;
152	<	exit(1);
153	<	}
154	<
155	<	numMolPerCell = simpleLat->getNumSitesPerCell();
156	<
157	<	/*calculate lattice constant (in Angstrom)
158	<	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
159	<	1.0 / 3.0);*/
160	<
161	<	latticeConstant = args_info.latticeCnst_arg;
110	>	latticeConstant = args_info.latticeConstant_arg;
111		particleRadius = args_info.radius_arg;
112	<	particleDiameter = 2.0 * particleRadius;
112	>	Globals* simParams = oldInfo->getSimParams();
113
114	<	/* set lattice constant */
115	<	lc.push_back(latticeConstant);
116	<	simpleLat->setLatticeConstant(lc);
114	>	/* Create nanoparticle */
115	>	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
116	>	particleRadius);
117
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<std::size_t> vacancyTargets;
124	+	vector<bool> isVacancy;
125
126	<	/*determine the output file names*/
127	<	if (args_info.output_given){
128	<	outInitFileName = args_info.output_arg;
129	<	}else{
130	<	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	<	int numSites = nanoparticle.getNMol(simpleLat);
189	<
126	>	Vector3d myLoc;
127	>	RealType myR;
128	>
129	>	for (unsigned int i = 0; i < sites.size(); i++)
130	>	isVacancy.push_back(false);
131
132	<	/* Random particle is the default case*/
133	<	if (!args_info.ShellRadius_given){
134	<	std::cout << "Creating a random nanoparticle" << std::endl;
135	<	/* Check to see if we have enough components */
136	<	if (nComponents != args_info.molFraction_given + 1){
137	<	std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
138	<	exit 1;
132	>	if (args_info.vacancyPercent_given) {
133	>	if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
134	>	sprintf(painCave.errMsg,
135	>	"vacancyPercent was set to a non-sensical value.");
136	>	painCave.isFatal = 1;
137	>	simError();
138	>	} else {
139	>	RealType vF = args_info.vacancyPercent_arg / 100.0;
140	>	RealType vIR;
141	>	RealType vOR;
142	>	if (args_info.vacancyInnerRadius_given) {
143	>	vIR = args_info.vacancyInnerRadius_arg;
144	>	} else {
145	>	vIR = 0.0;
146	>	}
147	>	if (args_info.vacancyOuterRadius_given) {
148	>	vOR = args_info.vacancyOuterRadius_arg;
149	>	} else {
150	>	vOR = particleRadius;
151	>	}
152	>	if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
153	>
154	>	for (std::size_t i = 0; i < sites.size(); i++) {
155	>	myLoc = sites[i];
156	>	myR = myLoc.length();
157	>	if (myR >= vIR && myR <= vOR) {
158	>	vacancyTargets.push_back(i);
159	>	}
160	>	}
161	>	std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
162	>
163	>	int nTargets = vacancyTargets.size();
164	>	vacancyTargets.resize((int)(vF * nTargets));
165	>
166	>
167	>	sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
168	>	"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
169	>	vIR, vOR);
170	>	painCave.isFatal = 0;
171	>	painCave.severity = OPENMD_INFO;
172	>	simError();
173	>
174	>	isVacancy.clear();
175	>	for (std::size_t i = 0; i < sites.size(); i++) {
176	>	bool vac = false;
177	>	for (std::size_t j = 0; j < vacancyTargets.size(); j++) {
178	>	if (i == vacancyTargets[j]) vac = true;
179	>	}
180	>	isVacancy.push_back(vac);
181	>	}
182	>
183	>	} else {
184	>	sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
185	>	"\tinner or outer radii.  Check their values.");
186	>	painCave.isFatal = 1;
187	>	simError();
188	>	}
189		}
190	<	int totComponents = 0;
200	<	for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
201	<	numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
202	<	totComponents += numMol[i];
203	<	}
204	<	numMol[nComponents-1] = numSites - totComponents;
190	>	}
191
192	<	} else{ /*Handle core-shell with multiple components.*/
193	<	std::cout << "Creating a core-shell nanoparticle." << std::endl;
194	<	if (nComponents != args_info.ShellRadius_given + 1){
195	<	std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
196	<	exit 1;
192	>	/* Get number of lattice sites */
193	>	std::size_t nSites = sites.size() - vacancyTargets.size();
194	>
195	>	std::vector<Component*> components = simParams->getComponents();
196	>	std::vector<RealType> molFractions;
197	>	std::vector<RealType> shellRadii;
198	>	std::vector<int> nMol;
199	>	std::map<int, int> componentFromSite;
200	>	nComponents = components.size();
201	>
202	>	if (args_info.molFraction_given && args_info.shellRadius_given) {
203	>	sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
204	>	"arguments, but not both!");
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>
209	>	if (nComponents == 1) {
210	>	molFractions.push_back(1.0);
211	>	shellRadii.push_back(particleRadius);
212	>	} else if (args_info.molFraction_given) {
213	>	if ((int)args_info.molFraction_given == nComponents) {
214	>	for (int i = 0; i < nComponents; i++) {
215	>	molFractions.push_back(args_info.molFraction_arg[i]);
216	>	}
217	>	} else if ((int)args_info.molFraction_given == nComponents-1) {
218	>	RealType remainingFraction = 1.0;
219	>	for (int i = 0; i < nComponents-1; i++) {
220	>	molFractions.push_back(args_info.molFraction_arg[i]);
221	>	remainingFraction -= molFractions[i];
222	>	}
223	>	molFractions.push_back(remainingFraction);
224	>	} else {
225	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
226	>	"for all of the components in the <MetaData> block.");
227	>	painCave.isFatal = 1;
228	>	simError();
229	>	}
230	>	} else if ((int)args_info.shellRadius_given) {
231	>	if ((int)args_info.shellRadius_given == nComponents) {
232	>	for (int i = 0; i < nComponents; i++) {
233	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
234	>	}
235	>	} else if ((int)args_info.shellRadius_given == nComponents-1) {
236	>	for (int i = 0; i < nComponents-1; i++) {
237	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
238	>	}
239	>	shellRadii.push_back(particleRadius);
240	>	} else {
241	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
242	>	"\tshell radii for all of the components in the <MetaData> block.");
243	>	painCave.isFatal = 1;
244	>	simError();
245		}
246	+	} else {
247	+	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
248	+	"\tbut have not specified either molFraction or shellRadius arguments.");
249	+	painCave.isFatal = 1;
250	+	simError();
251	+	}
252
253	+	if (args_info.molFraction_given) {
254	+	RealType totalFraction = 0.0;
255
256	+	/* Do some simple sanity checking*/
257
258	+	for (int i = 0; i < nComponents; i++) {
259	+	if (molFractions.at(i) < 0.0) {
260	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
261	+	" less than zero!");
262	+	painCave.isFatal = 1;
263	+	simError();
264	+	}
265	+	if (molFractions.at(i) > 1.0) {
266	+	sprintf(painCave.errMsg, "One of the requested molFractions was"
267	+	" greater than one!");
268	+	painCave.isFatal = 1;
269	+	simError();
270	+	}
271	+	totalFraction += molFractions.at(i);
272	+	}
273	+	if (abs(totalFraction - 1.0) > 1e-6) {
274	+	sprintf(painCave.errMsg,
275	+	"The sum of molFractions was not close enough to 1.0");
276	+	painCave.isFatal = 1;
277	+	simError();
278	+	}
279	+
280	+	int remaining = nSites;
281	+	for (int i=0; i < nComponents-1; i++) {
282	+	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
283	+	remaining -= nMol.at(i);
284	+	}
285	+	nMol.push_back(remaining);
286	+
287	+	// recompute actual mol fractions and perform final sanity check:
288	+
289	+	std::size_t totalMolecules = 0;
290	+	for (int i=0; i < nComponents; i++) {
291	+	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
292	+	totalMolecules += nMol.at(i);
293	+	}
294	+
295	+	if (totalMolecules != nSites) {
296	+	sprintf(painCave.errMsg,
297	+	"Computed total number of molecules is not equal "
298	+	"to the number of lattice sites!");
299	+	painCave.isFatal = 1;
300	+	simError();
301	+	}
302	+	} else {
303	+
304	+	for (unsigned int i = 0; i < shellRadii.size(); i++) {
305	+	if (shellRadii.at(i) > particleRadius + 1e-6 ) {
306	+	sprintf(painCave.errMsg,
307	+	"One of the shellRadius values exceeds the particle Radius.");
308	+	painCave.isFatal = 1;
309	+	simError();
310	+	}
311	+	if (shellRadii.at(i) <= 0.0 ) {
312	+	sprintf(painCave.errMsg,
313	+	"One of the shellRadius values is smaller than zero!");
314	+	painCave.isFatal = 1;
315	+	simError();
316	+	}
317	+	}
318		}
319
320	<	//get the orientation of the cell sites
321	<	//for the same type of molecule in same lattice, it will not change
322	<	latticeOrt = simpleLat->getLatticePointsOrt();
320	>	vector<int> ids;
321	>	if ((int)args_info.molFraction_given){
322	>	sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
323	>	painCave.isFatal = 0;
324	>	painCave.severity = OPENMD_INFO;
325	>	simError();
326	>	/* Random particle is the default case*/
327	>
328	>	for (unsigned int i = 0; i < sites.size(); i++)
329	>	if (!isVacancy[i]) ids.push_back(i);
330	>
331	>	std::random_shuffle(ids.begin(), ids.end());
332	>
333	>	} else{
334	>	sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
335	>	painCave.isFatal = 0;
336	>	painCave.severity = OPENMD_INFO;
337	>	simError();
338	>
339	>	RealType smallestSoFar;
340	>	int myComponent = -1;
341	>	nMol.clear();
342	>	nMol.resize(nComponents);
343	>
344	>	for (unsigned int i = 0; i < sites.size(); i++) {
345	>	myLoc = sites[i];
346	>	myR = myLoc.length();
347	>	smallestSoFar = particleRadius;
348	>	if (!isVacancy[i]) {
349	>	for (int j = 0; j < nComponents; j++) {
350	>	if (myR <= shellRadii[j]) {
351	>	if (shellRadii[j] <= smallestSoFar) {
352	>	smallestSoFar = shellRadii[j];
353	>	myComponent = j;
354	>	}
355	>	}
356	>	}
357	>	componentFromSite[i] = myComponent;
358	>	nMol[myComponent]++;
359	>	}
360	>	}
361	>	}
362
363	+	outputFileName = args_info.output_arg;
364	+
365	+	//creat new .md file on fly which corrects the number of molecule
366	+	createMdFile(inputFileName, outputFileName, nMol);
367
368	+	delete oldInfo;
369
370	<	// needed for writing out new md file.
371	<
372	<	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
373	<	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	<
370	>	SimCreator newCreator;
371	>	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
372	>
373	>	// Place molecules
374		Molecule* mol;
375		SimInfo::MoleculeIterator mi;
376		mol = NewInfo->beginMolecule(mi);
377
378	+	int l = 0;
379
380	<	for(int i = -nx; i < nx; i++) {
381	<	for(int j = -ny; j < ny; j++) {
382	<	for(int k = -nz; k < nz; k++) {
383	<
384	<	//get the position of the cell sites
385	<	simpleLat->getLatticePointsPos(latticePos, i, j, k);
386	<
387	<	for(int l = 0; l < numMolPerCell; l++) {
388	<	#ifdef HAVE_CGAL
389	<	if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){
390	<	#endif
391	<	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	<	}
380	>	for (int i = 0; i < nComponents; i++){
381	>	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
382	>	NewInfo->getForceField());
383	>
384	>	if (!args_info.molFraction_given) {
385	>	for (unsigned int n = 0; n < sites.size(); n++) {
386	>	if (!isVacancy[n]) {
387	>	if (componentFromSite[n] == i) {
388	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
389	>	locator->placeMol(sites[n], orientations[n], mol);
390	>	l++;
391	>	}
392		}
393	<	}
393	>	}
394	>	} else {
395	>	for (int n = 0; n < nMol.at(i); n++) {
396	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
397	>	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
398	>	l++;
399	>	}
400	>	}
401		}
402
273	–
274	–
403		//fill Hmat
404	<	hmat(0, 0)= nx * latticeConstant;
404	>	hmat(0, 0)=  10.0*particleRadius;
405		hmat(0, 1) = 0.0;
406		hmat(0, 2) = 0.0;
407
408		hmat(1, 0) = 0.0;
409	<	hmat(1, 1) = ny * latticeConstant;
409	>	hmat(1, 1) =  10.0*particleRadius;
410		hmat(1, 2) = 0.0;
411
412		hmat(2, 0) = 0.0;
413		hmat(2, 1) = 0.0;
414	<	hmat(2, 2) = nz * latticeConstant;
414	>	hmat(2, 2) =  10.0*particleRadius;
415
416		//set Hmat
417		NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
418
419
420		//create dumpwriter and write out the coordinates
421	<	NewInfo->setFinalConfigFileName(outInitFileName);
294	<	writer = new DumpWriter(NewInfo);
421	>	writer = new DumpWriter(NewInfo, outputFileName);
422
423		if (writer == NULL) {
424	<	std::cerr << "error in creating DumpWriter" << std::endl;
425	<	exit(1);
424	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
425	>	painCave.isFatal = 1;
426	>	simError();
427		}
428
429		writer->writeDump();
430	<	std::cout << "new initial configuration file: " << outInitFileName
431	<	<< " is generated." << std::endl;
432	<
433	<	//delete objects
434	<
435	<	//delete oldInfo and oldSimSetup
436	<
437	<	if (NewInfo != NULL)
438	<	delete NewInfo;
439	<
440	<	if (writer != NULL)
313	<	delete writer;
314	<	delete simpleLat;
315	<	cmdline_parser_free(&args_info);
430	>
431	>	// deleting the writer will put the closing at the end of the dump file
432	>
433	>	delete writer;
434	>
435	>	// cleanup a by calling sim error.....
436	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
437	>	"generated.\n", outputFileName.c_str());
438	>	painCave.isFatal = 0;
439	>	painCave.severity = OPENMD_INFO;
440	>	simError();
441		return 0;
442		}
443
444	<	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
445	<	int components,int &nummol) {
444	>	void createMdFile(const std::string&oldMdFileName,
445	>	const std::string&newMdFileName,
446	>	std::vector<int> nMol) {
447		ifstream oldMdFile;
448		ofstream newMdFile;
449		const int MAXLEN = 65535;
#	Line 326 | Line 452 | void createMdFile(const std::string&oldMdFileName, con
452		//create new .md file based on old .md file
453		oldMdFile.open(oldMdFileName.c_str());
454		newMdFile.open(newMdFileName.c_str());
329	–
455		oldMdFile.getline(buffer, MAXLEN);
456	<
456	>
457	>	unsigned int i = 0;
458		while (!oldMdFile.eof()) {
459	<
459	>
460		//correct molecule number
461		if (strstr(buffer, "nMol") != NULL) {
462	<	sprintf(buffer, "\tnMol = %i;", numMol);
463	<	newMdFile << buffer << std::endl;
462	>	if(i<nMol.size()){
463	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
464	>	newMdFile << buffer << std::endl;
465	>	i++;
466	>	}
467		} else
468		newMdFile << buffer << std::endl;
469
#	Line 343 | Line 472 | void createMdFile(const std::string&oldMdFileName, con
472
473		oldMdFile.close();
474		newMdFile.close();
475	+
476	+	if (i != nMol.size()) {
477	+	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
478	+	"\tstatements in component blocks.  Make sure that all\n"
479	+	"\tcomponents in the template file have nMol=1");
480	+	painCave.isFatal = 1;
481	+	simError();
482	+	}
483	+
484		}
485

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords):
Revision 875 by chuckv, Thu Jan 19 22:54:23 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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

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