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

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 1075 by gezelter, Tue Oct 17 17:51:52 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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 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		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;
#	Line 85 | Line 84 | int main(int argc, char *argv []) {
84		double latticeConstant;
85		std::vector<double> lc;
86
87	<	double particleRadius;
87	>	RealType particleRadius;
88
89		Mat3x3d hmat;
90		std::vector<Vector3d> latticePos;
#	Line 104 | Line 103 | int main(int argc, char *argv []) {
103		if (args_info.inputs_num)
104		inputFileName = args_info.inputs[0];
105		else {
106	<	sprintf(painCave.errMsg, "No input .md file name was specified"
106	>	sprintf(painCave.errMsg, "No input .md file name was specified "
107		"on the command line");
108		painCave.isFatal = 1;
109		cmdline_parser_print_help();
#	Line 115 | Line 114 | int main(int argc, char *argv []) {
114		SimCreator oldCreator;
115		SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
116
117	<	latticeConstant = args_info.latticeCnst_arg;
117	>	latticeConstant = args_info.latticeConstant_arg;
118		particleRadius = args_info.radius_arg;
119		Globals* simParams = oldInfo->getSimParams();
120
#	Line 127 | Line 126 | int main(int argc, char *argv []) {
126		vector<Vector3d> sites = nanoParticle.getSites();
127		vector<Vector3d> orientations = nanoParticle.getOrientations();
128
130	–	std::cout <<"nSites: " << sites.size() << std::endl;
129
130	+	std::vector<int> vacancyTargets;
131	+	vector<bool> isVacancy;
132	+
133	+	Vector3d myLoc;
134	+	RealType myR;
135	+
136	+	for (int i = 0; i < sites.size(); i++)
137	+	isVacancy.push_back(false);
138	+
139	+	if (args_info.vacancyPercent_given) {
140	+	if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
141	+	sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value.");
142	+	painCave.isFatal = 1;
143	+	simError();
144	+	} else {
145	+	RealType vF = args_info.vacancyPercent_arg / 100.0;
146	+	RealType vIR;
147	+	RealType vOR;
148	+	if (args_info.vacancyInnerRadius_given) {
149	+	vIR = args_info.vacancyInnerRadius_arg;
150	+	} else {
151	+	vIR = 0.0;
152	+	}
153	+	if (args_info.vacancyOuterRadius_given) {
154	+	vOR = args_info.vacancyOuterRadius_arg;
155	+	} else {
156	+	vOR = particleRadius;
157	+	}
158	+	if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) {
159	+
160	+	for (int i = 0; i < sites.size(); i++) {
161	+	myLoc = sites[i];
162	+	myR = myLoc.length();
163	+	if (myR >= vIR && myR <= vOR) {
164	+	vacancyTargets.push_back(i);
165	+	}
166	+	}
167	+	std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
168	+
169	+	int nTargets = vacancyTargets.size();
170	+	vacancyTargets.resize((int)(vF * nTargets));
171	+
172	+
173	+	sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
174	+	"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
175	+	vIR, vOR);
176	+	painCave.isFatal = 0;
177	+	simError();
178	+
179	+	isVacancy.clear();
180	+	for (int i = 0; i < sites.size(); i++) {
181	+	bool vac = false;
182	+	for (int j = 0; j < vacancyTargets.size(); j++) {
183	+	if (i == vacancyTargets[j]) vac = true;
184	+	}
185	+	isVacancy.push_back(vac);
186	+	}
187	+
188	+	} else {
189	+	sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
190	+	"\tinner or outer radii.  Check their values.");
191	+	painCave.isFatal = 1;
192	+	simError();
193	+	}
194	+	}
195	+	}
196	+
197		/* Get number of lattice sites */
198	<	int nSites = sites.size();
198	>	int nSites = sites.size() - vacancyTargets.size();
199
200		std::vector<Component*> components = simParams->getComponents();
201		std::vector<RealType> molFractions;
#	Line 140 | Line 205 | int main(int argc, char *argv []) {
205		std::map<int, int> componentFromSite;
206		nComponents = components.size();
207
208	<	if (args_info.molFraction_given && args_info.ShellRadius_given) {
209	<	sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius "
208	>	if (args_info.molFraction_given && args_info.shellRadius_given) {
209	>	sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
210		"arguments, but not both!");
211		painCave.isFatal = 1;
212		simError();
#	Line 168 | Line 233 | int main(int argc, char *argv []) {
233		painCave.isFatal = 1;
234		simError();
235		}
236	<	} else if ((int)args_info.ShellRadius_given) {
237	<	if ((int)args_info.ShellRadius_given == nComponents) {
236	>	} else if ((int)args_info.shellRadius_given) {
237	>	if ((int)args_info.shellRadius_given == nComponents) {
238		for (int i = 0; i < nComponents; i++) {
239	<	shellRadii.push_back(args_info.ShellRadius_arg[i]);
239	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
240		}
241	<	} else if ((int)args_info.ShellRadius_given == nComponents-1) {
241	>	} else if ((int)args_info.shellRadius_given == nComponents-1) {
242		for (int i = 0; i < nComponents-1; i++) {
243	<	shellRadii.push_back(args_info.ShellRadius_arg[i]);
243	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
244		}
245		shellRadii.push_back(particleRadius);
246		} else {
247	<	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the shell radii "
248	<	"for all of the components in the <MetaData> block.");
247	>	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n"
248	>	"\tshell radii for all of the components in the <MetaData> block.");
249		painCave.isFatal = 1;
250		simError();
251		}
252		} else {
253	<	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not "
254	<	"specified either molFraction or ShellRadius arguments.");
253	>	sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
254	>	"\tbut have not specified either molFraction or shellRadius arguments.");
255		painCave.isFatal = 1;
256		simError();
257		}
#	Line 253 | Line 318 | int main(int argc, char *argv []) {
318		}
319		}
320		}
321	<
322	<	vector<int> ids;
258	<	for (int i = 0; i < sites.size(); i++) ids.push_back(i);
259	<	/* Random particle is the default case*/
321	>
322	>	vector<int> ids;
323		if ((int)args_info.molFraction_given){
324		sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle.");
325		painCave.isFatal = 0;
326		simError();
327	+	/* Random particle is the default case*/
328	+
329	+	for (int i = 0; i < sites.size(); i++)
330	+	if (!isVacancy[i]) ids.push_back(i);
331	+
332		std::random_shuffle(ids.begin(), ids.end());
333	+
334		} else{
335		sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle.");
336		painCave.isFatal = 0;
337		simError();
338
270	–	Vector3d myLoc;
271	–	RealType myR;
339		RealType smallestSoFar;
340		int myComponent = -1;
341		nMol.clear();
#	Line 277 | Line 344 | int main(int argc, char *argv []) {
344		for (int i = 0; i < sites.size(); i++) {
345		myLoc = sites[i];
346		myR = myLoc.length();
347	<	smallestSoFar = particleRadius;
348	<
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;
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	<	componentFromSite[i] = myComponent;
361	<	nMol[myComponent]++;
292	<	}
293	<	}
360	>	}
361	>	}
362
363		outputFileName = args_info.output_arg;
364	<
297	<
364	>
365		//creat new .md file on fly which corrects the number of molecule
366		createMdFile(inputFileName, outputFileName, nMol);
367
#	Line 308 | Line 375 | int main(int argc, char *argv []) {
375		Molecule* mol;
376		SimInfo::MoleculeIterator mi;
377		mol = NewInfo->beginMolecule(mi);
378	+
379		int l = 0;
380	+	int whichSite = 0;
381
382		for (int i = 0; i < nComponents; i++){
383		locator = new MoLocator(NewInfo->getMoleculeStamp(i),
384		NewInfo->getForceField());
385	<
386	<	if (args_info.ShellRadius_given) {
385	>
386	>	if (!args_info.molFraction_given) {
387		for (int n = 0; n < sites.size(); n++) {
388	<	if (componentFromSite[n] == i) {
389	<	mol = NewInfo->getMoleculeByGlobalIndex(l);
390	<	locator->placeMol(sites[n], orientations[n], mol);
391	<	l++;
388	>	if (!isVacancy[n]) {
389	>	if (componentFromSite[n] == i) {
390	>	mol = NewInfo->getMoleculeByGlobalIndex(l);
391	>	locator->placeMol(sites[n], orientations[n], mol);
392	>	l++;
393	>	}
394		}
395		}
396		} else {
#	Line 329 | Line 400 | int main(int argc, char *argv []) {
400		l++;
401		}
402		}
403	<	}
403	>	}
404
405		//fill Hmat
406		hmat(0, 0)=  10.0*particleRadius;
#	Line 352 | Line 423 | int main(int argc, char *argv []) {
423		writer = new DumpWriter(NewInfo, outputFileName);
424
425		if (writer == NULL) {
426	<	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
426	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
427		painCave.isFatal = 1;
428		simError();
429		}
#	Line 364 | Line 435 | int main(int argc, char *argv []) {
435		delete writer;
436
437		// cleanup a by calling sim error.....
438	<	sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
438	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
439		"generated.\n", outputFileName.c_str());
440		painCave.isFatal = 0;
441		simError();
#	Line 382 | Line 453 | void createMdFile(const std::string&oldMdFileName,
453		//create new .md file based on old .md file
454		oldMdFile.open(oldMdFileName.c_str());
455		newMdFile.open(newMdFileName.c_str());
385	–
456		oldMdFile.getline(buffer, MAXLEN);
457	<
457	>
458		int i = 0;
459		while (!oldMdFile.eof()) {
460	<
460	>
461		//correct molecule number
462		if (strstr(buffer, "nMol") != NULL) {
463		if(i<nMol.size()){
464	<	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
464	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
465		newMdFile << buffer << std::endl;
466		i++;
467		}
#	Line 403 | Line 473 | void createMdFile(const std::string&oldMdFileName,
473
474		oldMdFile.close();
475		newMdFile.close();
476	+
477	+	if (i != nMol.size()) {
478	+	sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n"
479	+	"\tstatements in component blocks.  Make sure that all\n"
480	+	"\tcomponents in the template file have nMol=1");
481	+	painCave.isFatal = 1;
482	+	simError();
483	+	}
484	+
485		}
486

Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (property svn:keywords):
Revision 1075 by gezelter, Tue Oct 17 17:51:52 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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