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

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 949 by chuckv, Tue Apr 25 22:54:55 2006 UTC vs.
Revision 1977 by gezelter, Wed Mar 12 21:35:23 2014 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 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 components,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;
82	<	std::string outMdFileName;
83	<	std::string outInitFileName;
84	<
85	<
86	<
87	<	Lattice *simpleLat;
80	>	std::string outputFileName;
81		MoLocator* locator;
89	–	int* numMol;
82		int nComponents;
83		double latticeConstant;
84	<	std::vector<double> lc;
93	<	double mass;
94	<	const double rhoConvertConst = 1.661;
95	<	double density;
96	<	double particleRadius;
97	<
98	<
99	<
84	>	RealType particleRadius;
85		Mat3x3d hmat;
101	–	std::vector<Vector3d> latticePos;
102	–	std::vector<Vector3d> latticeOrt;
103	–	int numMolPerCell;
104	–	int nShells; /* Number of shells in nanoparticle*/
105	–	int numSites;
106	–
86		DumpWriter *writer;
87
88		// Parse Command Line Arguments
89		if (cmdline_parser(argc, argv, &args_info) != 0)
90		exit(1);
91	<
113	<
114	<
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	<
132	<	/*calculate lattice constant (in Angstrom)
133	<	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
134	<	1.0 / 3.0);*/
135	<
136	<	latticeConstant = args_info.latticeCnst_arg;
110	>	latticeConstant = args_info.latticeConstant_arg;
111		particleRadius = args_info.radius_arg;
112		Globals* simParams = oldInfo->getSimParams();
113
140	–	/* Find out how many different components in this simualtion */
141	–	nComponents =simParams->getNComponents();
142	–
143	–	/*determine the output file names*/
144	–	if (args_info.output_given){
145	–	outInitFileName = args_info.output_arg;
146	–	}else{
147	–	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
148	–	}
149	–
150	–	std::cout <<"Before build shaped lattice. "<<std::endl;
151	–
152	–	/* create Molocators */
153	–	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
154	–
114		/* Create nanoparticle */
115	<	shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
115	>	shapedLatticeSpherical nanoParticle(latticeConstant, latticeType,
116	>	particleRadius);
117
158	–	std::cout <<"Before build getPoints. "<<std::endl;
118		/* Build a lattice and get lattice points for this lattice constant */
119	<	vector<Vector3d> nanoParticleSites = nanoParticle.getPoints();
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	<	/* Get number of lattice sites */
127	<	numSites = nanoParticleSites.size();
126	>	Vector3d myLoc;
127	>	RealType myR;
128
129	<	//std::cout <<"numSites are %d "<<numSites<<std::endl;
130	<	// std::cout <<"nComponents are %d "<<nComponents<<std::endl;
131	<	numMol = new int[nComponents];
132	<
133	<
134	<	/* Random particle is the default case*/
135	<	if (!args_info.ShellRadius_given){
136	<	std::cout << "Creating a random nanoparticle" << std::endl;
137	<	/* Check to see if we have enough components */
138	<	if (nComponents != args_info.molFraction_given && nComponents != 1){
139	<	std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
140	<	exit(1);
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	>	painCave.severity = OPENMD_INFO;
171	>	simError();
172	>
173	>	isVacancy.clear();
174	>	for (unsigned int i = 0; i < sites.size(); i++) {
175	>	bool vac = false;
176	>	for (unsigned int j = 0; j < vacancyTargets.size(); j++) {
177	>	if (i == vacancyTargets[j]) vac = true;
178	>	}
179	>	isVacancy.push_back(vac);
180	>	}
181	>
182	>	} else {
183	>	sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
184	>	"\tinner or outer radii.  Check their values.");
185	>	painCave.isFatal = 1;
186	>	simError();
187	>	}
188		}
178	–	/* Build the mole fractions and number of molecules of each type */
179	–	int totComponents = 0;
180	–	for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */
181	–	numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
182	–	std::cout<<numMol[i]<<std::endl;
183	–	totComponents += numMol[i];
184	–	}
185	–	numMol[nComponents-1] = numSites - totComponents;
186	–
187	–	/* do the iPod thing, Shuffle da vector */
188	–	std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end());
189	–	} else{ /*Handle core-shell with multiple components.*/
190	–	std::cout << "Creating a core-shell nanoparticle." << std::endl;
191	–	if (nComponents != args_info.ShellRadius_given + 1){
192	–	std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
193	–	exit(1);
194	–	}
195	–
189		}
190
191	+	/* Get number of lattice sites */
192	+	int nSites = sites.size() - vacancyTargets.size();
193	+
194	+	std::vector<Component*> components = simParams->getComponents();
195	+	std::vector<RealType> molFractions;
196	+	std::vector<RealType> shellRadii;
197	+	std::vector<int> nMol;
198	+	std::map<int, int> componentFromSite;
199	+	nComponents = components.size();
200	+
201	+	if (args_info.molFraction_given && args_info.shellRadius_given) {
202	+	sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
203	+	"arguments, but not both!");
204	+	painCave.isFatal = 1;
205	+	simError();
206	+	}
207
208	<	//get the orientation of the cell sites
209	<	//for the same type of molecule in same lattice, it will not change
210	<	latticeOrt = nanoParticle.getPointsOrt();
211	<	std::cout<<"Orientational vector Size: "<< std::endl;
212	<	std::cout<<latticeOrt.size()<< std::endl;
208	>	if (nComponents == 1) {
209	>	molFractions.push_back(1.0);
210	>	shellRadii.push_back(particleRadius);
211	>	} else if (args_info.molFraction_given) {
212	>	if ((int)args_info.molFraction_given == nComponents) {
213	>	for (int i = 0; i < nComponents; i++) {
214	>	molFractions.push_back(args_info.molFraction_arg[i]);
215	>	}
216	>	} else if ((int)args_info.molFraction_given == nComponents-1) {
217	>	RealType remainingFraction = 1.0;
218	>	for (int i = 0; i < nComponents-1; i++) {
219	>	molFractions.push_back(args_info.molFraction_arg[i]);
220	>	remainingFraction -= molFractions[i];
221	>	}
222	>	molFractions.push_back(remainingFraction);
223	>	} else {
224	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
225	>	"for all of the components in the <MetaData> block.");
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	} else if ((int)args_info.shellRadius_given) {
230	>	if ((int)args_info.shellRadius_given == nComponents) {
231	>	for (int i = 0; i < nComponents; i++) {
232	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
233	>	}
234	>	} else if ((int)args_info.shellRadius_given == nComponents-1) {
235	>	for (int i = 0; i < nComponents-1; i++) {
236	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
237	>	}
238	>	shellRadii.push_back(particleRadius);
239	>	} else {
240	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
241	>	"\tshell radii for all of the components in the <MetaData> block.");
242	>	painCave.isFatal = 1;
243	>	simError();
244	>	}
245	>	} else {
246	>	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
247	>	"\tbut have not specified either molFraction or shellRadius arguments.");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>
252	>	if (args_info.molFraction_given) {
253	>	RealType totalFraction = 0.0;
254	>
255	>	/* Do some simple sanity checking*/
256	>
257	>	for (int i = 0; i < nComponents; i++) {
258	>	if (molFractions.at(i) < 0.0) {
259	>	sprintf(painCave.errMsg, "One of the requested molFractions was"
260	>	" less than zero!");
261	>	painCave.isFatal = 1;
262	>	simError();
263	>	}
264	>	if (molFractions.at(i) > 1.0) {
265	>	sprintf(painCave.errMsg, "One of the requested molFractions was"
266	>	" greater than one!");
267	>	painCave.isFatal = 1;
268	>	simError();
269	>	}
270	>	totalFraction += molFractions.at(i);
271	>	}
272	>	if (abs(totalFraction - 1.0) > 1e-6) {
273	>	sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>
278	>	int remaining = nSites;
279	>	for (int i=0; i < nComponents-1; i++) {
280	>	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
281	>	remaining -= nMol.at(i);
282	>	}
283	>	nMol.push_back(remaining);
284	>
285	>	// recompute actual mol fractions and perform final sanity check:
286	>
287	>	int totalMolecules = 0;
288	>	for (int i=0; i < nComponents; i++) {
289	>	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
290	>	totalMolecules += nMol.at(i);
291	>	}
292	>
293	>	if (totalMolecules != nSites) {
294	>	sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
295	>	"to the number of lattice sites!");
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	} else {
300	>
301	>	for (unsigned int i = 0; i < shellRadii.size(); i++) {
302	>	if (shellRadii.at(i) > particleRadius + 1e-6 ) {
303	>	sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius.");
304	>	painCave.isFatal = 1;
305	>	simError();
306	>	}
307	>	if (shellRadii.at(i) <= 0.0 ) {
308	>	sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!");
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	}
314	>
315	>	vector<int> ids;
316	>	if ((int)args_info.molFraction_given){
317	>	sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
318	>	painCave.isFatal = 0;
319	>	painCave.severity = OPENMD_INFO;
320	>	simError();
321	>	/* Random particle is the default case*/
322	>
323	>	for (unsigned int i = 0; i < sites.size(); i++)
324	>	if (!isVacancy[i]) ids.push_back(i);
325	>
326	>	std::random_shuffle(ids.begin(), ids.end());
327	>
328	>	} else{
329	>	sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
330	>	painCave.isFatal = 0;
331	>	painCave.severity = OPENMD_INFO;
332	>	simError();
333	>
334	>	RealType smallestSoFar;
335	>	int myComponent = -1;
336	>	nMol.clear();
337	>	nMol.resize(nComponents);
338	>
339	>	for (unsigned int i = 0; i < sites.size(); i++) {
340	>	myLoc = sites[i];
341	>	myR = myLoc.length();
342	>	smallestSoFar = particleRadius;
343	>	if (!isVacancy[i]) {
344	>	for (int j = 0; j < nComponents; j++) {
345	>	if (myR <= shellRadii[j]) {
346	>	if (shellRadii[j] <= smallestSoFar) {
347	>	smallestSoFar = shellRadii[j];
348	>	myComponent = j;
349	>	}
350	>	}
351	>	}
352	>	componentFromSite[i] = myComponent;
353	>	nMol[myComponent]++;
354	>	}
355	>	}
356	>	}
357
358	<
359	<
207	<	// needed for writing out new md file.
208	<
209	<	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
210	<	outMdFileName = outPrefix + ".md";
211	<
358	>	outputFileName = args_info.output_arg;
359	>
360		//creat new .md file on fly which corrects the number of molecule
361	<	createMdFile(inputFileName, outMdFileName, nComponents,numMol);
361	>	createMdFile(inputFileName, outputFileName, nMol);
362
363	<	if (oldInfo != NULL)
216	<	delete oldInfo;
363	>	delete oldInfo;
364
218	–
219	–	// We need to read in new siminfo object.
220	–	//parse md file and set up the system
221	–	//SimCreator NewCreator;
365		SimCreator newCreator;
366	<	SimInfo* NewInfo = newCreator.createSim(outMdFileName, false);
367	<
225	<
366	>	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
367	>
368		// Place molecules
369		Molecule* mol;
370		SimInfo::MoleculeIterator mi;
371		mol = NewInfo->beginMolecule(mi);
372	+
373		int l = 0;
231	–	for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
232	–	locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol);
233	–	l++;
234	–	}
235	–
374
375	<
375	>	for (int i = 0; i < nComponents; i++){
376	>	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
377	>	NewInfo->getForceField());
378	>
379	>	if (!args_info.molFraction_given) {
380	>	for (unsigned int n = 0; n < sites.size(); n++) {
381	>	if (!isVacancy[n]) {
382	>	if (componentFromSite[n] == i) {
383	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
384	>	locator->placeMol(sites[n], orientations[n], mol);
385	>	l++;
386	>	}
387	>	}
388	>	}
389	>	} else {
390	>	for (int n = 0; n < nMol.at(i); n++) {
391	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
392	>	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
393	>	l++;
394	>	}
395	>	}
396	>	}
397
398		//fill Hmat
399	<	hmat(0, 0)=  latticeConstant;
399	>	hmat(0, 0)=  10.0*particleRadius;
400		hmat(0, 1) = 0.0;
401		hmat(0, 2) = 0.0;
402
403		hmat(1, 0) = 0.0;
404	<	hmat(1, 1) =  latticeConstant;
404	>	hmat(1, 1) =  10.0*particleRadius;
405		hmat(1, 2) = 0.0;
406
407		hmat(2, 0) = 0.0;
408		hmat(2, 1) = 0.0;
409	<	hmat(2, 2) =  latticeConstant;
409	>	hmat(2, 2) =  10.0*particleRadius;
410
411		//set Hmat
412		NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
413
414
415		//create dumpwriter and write out the coordinates
416	<	NewInfo->setFinalConfigFileName(outInitFileName);
258	<	writer = new DumpWriter(NewInfo);
416	>	writer = new DumpWriter(NewInfo, outputFileName);
417
418		if (writer == NULL) {
419	<	std::cerr << "error in creating DumpWriter" << std::endl;
420	<	exit(1);
419	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
420	>	painCave.isFatal = 1;
421	>	simError();
422		}
423
424		writer->writeDump();
425	<	std::cout << "new initial configuration file: " << outInitFileName
426	<	<< " is generated." << std::endl;
427	<
428	<	//delete objects
429	<
430	<	//delete oldInfo and oldSimSetup
431	<
432	<	if (NewInfo != NULL)
433	<	delete NewInfo;
434	<
435	<	if (writer != NULL)
277	<	delete writer;
278	<	cmdline_parser_free(&args_info);
425	>
426	>	// deleting the writer will put the closing at the end of the dump file
427	>
428	>	delete writer;
429	>
430	>	// cleanup a by calling sim error.....
431	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
432	>	"generated.\n", outputFileName.c_str());
433	>	painCave.isFatal = 0;
434	>	painCave.severity = OPENMD_INFO;
435	>	simError();
436		return 0;
437		}
438
439	<	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
440	<	int components,int* numMol) {
439	>	void createMdFile(const std::string&oldMdFileName,
440	>	const std::string&newMdFileName,
441	>	std::vector<int> nMol) {
442		ifstream oldMdFile;
443		ofstream newMdFile;
444		const int MAXLEN = 65535;
#	Line 289 | Line 447 | void createMdFile(const std::string&oldMdFileName, con
447		//create new .md file based on old .md file
448		oldMdFile.open(oldMdFileName.c_str());
449		newMdFile.open(newMdFileName.c_str());
292	–
450		oldMdFile.getline(buffer, MAXLEN);
451	<
452	<	int i = 0;
451	>
452	>	unsigned int i = 0;
453		while (!oldMdFile.eof()) {
454	<
454	>
455		//correct molecule number
456		if (strstr(buffer, "nMol") != NULL) {
457	<	if(i<components){
458	<	sprintf(buffer, "\tnMol = %i;", numMol[i]);
457	>	if(i<nMol.size()){
458	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
459		newMdFile << buffer << std::endl;
460		i++;
461		}
#	Line 310 | Line 467 | void createMdFile(const std::string&oldMdFileName, con
467
468		oldMdFile.close();
469		newMdFile.close();
470	+
471	+	if (i != nMol.size()) {
472	+	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
473	+	"\tstatements in component blocks.  Make sure that all\n"
474	+	"\tcomponents in the template file have nMol=1");
475	+	painCave.isFatal = 1;
476	+	simError();
477	+	}
478	+
479		}
480

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords):
Revision 949 by chuckv, Tue Apr 25 22:54:55 2006 UTC vs.
Revision 1977 by gezelter, Wed Mar 12 21:35:23 2014 UTC

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

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