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

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 1032 by gezelter, Fri Sep 1 19:16:02 2006 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 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	>	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		}
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	–
188		}
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	<	//get the orientation of the cell sites
208	<	//for the same type of molecule in same lattice, it will not change
209	<	latticeOrt = nanoParticle.getPointsOrt();
210	<	std::cout<<"Orientational vector Size: "<< std::endl;
211	<	std::cout<<latticeOrt.size()<< std::endl;
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	>	} 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	>	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	<
356	<
207	<	// needed for writing out new md file.
208	<
209	<	outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
210	<	outMdFileName = outPrefix + ".md";
211	<
355	>	outputFileName = args_info.output_arg;
356	>
357		//creat new .md file on fly which corrects the number of molecule
358	<	createMdFile(inputFileName, outMdFileName, nComponents,numMol);
358	>	createMdFile(inputFileName, outputFileName, nMol);
359
360	<	if (oldInfo != NULL)
216	<	delete oldInfo;
360	>	delete oldInfo;
361
218	–
219	–	// We need to read in new siminfo object.
220	–	//parse md file and set up the system
221	–	//SimCreator NewCreator;
362		SimCreator newCreator;
363	<	SimInfo* NewInfo = newCreator.createSim(outMdFileName, false);
364	<
225	<
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	<	for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
372	<	locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol);
373	<	l++;
371	>
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	>	}
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		}
235	–
394
395		//fill Hmat
396	<	hmat(0, 0)=  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) =  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) =  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);
256	<	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	<
274	<	if (writer != NULL)
275	<	delete writer;
276	<	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 287 | 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());
290	–
446		oldMdFile.getline(buffer, MAXLEN);
447	<
448	<	int i = 0;
447	>
448	>	unsigned int i = 0;
449		while (!oldMdFile.eof()) {
450	<
450	>
451		//correct molecule number
452		if (strstr(buffer, "nMol") != NULL) {
453	<	if(i<components){
454	<	sprintf(buffer, "\tnMol = %i;", numMol[i]);
453	>	if(i<nMol.size()){
454	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
455		newMdFile << buffer << std::endl;
456		i++;
457		}
#	Line 308 | 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 1032 by gezelter, Fri Sep 1 19:16:02 2006 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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