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Comparing trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp (file contents):
Revision 1075 by gezelter, Tue Oct 17 17:51:52 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		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 outputFileName;
82	–
81		MoLocator* locator;
82		int nComponents;
83		double latticeConstant;
84	<	std::vector<double> lc;
87	<
88	<	double particleRadius;
89	<
84	>	RealType particleRadius;
85		Mat3x3d hmat;
91	–	std::vector<Vector3d> latticePos;
92	–	std::vector<Vector3d> latticeOrt;
93	–
86		DumpWriter *writer;
87
88		// Parse Command Line Arguments
#	Line 104 | Line 96 | int main(int argc, char *argv []) {
96		if (args_info.inputs_num)
97		inputFileName = args_info.inputs[0];
98		else {
99	<	sprintf(painCave.errMsg, "No input .md file name was specified"
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();
#	Line 115 | Line 107 | int main(int argc, char *argv []) {
107		SimCreator oldCreator;
108		SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
109
110	<	latticeConstant = args_info.latticeCnst_arg;
110	>	latticeConstant = args_info.latticeConstant_arg;
111		particleRadius = args_info.radius_arg;
112		Globals* simParams = oldInfo->getSimParams();
113
#	Line 127 | Line 119 | int main(int argc, char *argv []) {
119		vector<Vector3d> sites = nanoParticle.getSites();
120		vector<Vector3d> orientations = nanoParticle.getOrientations();
121
130	–	std::cout <<"nSites: " << sites.size() << std::endl;
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		/* Get number of lattice sites */
191	<	int nSites = sites.size();
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;
138	–	std::vector<RealType> molecularMasses;
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 "
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();
#	Line 168 | Line 225 | int main(int argc, char *argv []) {
225		painCave.isFatal = 1;
226		simError();
227		}
228	<	} else if ((int)args_info.ShellRadius_given) {
229	<	if ((int)args_info.ShellRadius_given == nComponents) {
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]);
231	>	shellRadii.push_back(args_info.shellRadius_arg[i]);
232		}
233	<	} else if ((int)args_info.ShellRadius_given == nComponents-1) {
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]);
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 shell radii "
240	<	"for all of the components in the <MetaData> block.");
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, but have not "
246	<	"specified either molFraction or ShellRadius arguments.");
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		}
#	Line 240 | Line 297 | int main(int argc, char *argv []) {
297		}
298		} else {
299
300	<	for (int i = 0; i < shellRadii.size(); i++) {
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;
#	Line 253 | Line 310 | int main(int argc, char *argv []) {
310		}
311		}
312		}
313	<
314	<	vector<int> ids;
258	<	for (int i = 0; i < sites.size(); i++) ids.push_back(i);
259	<	/* Random particle is the default case*/
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
270	–	Vector3d myLoc;
271	–	RealType myR;
331		RealType smallestSoFar;
332		int myComponent = -1;
333		nMol.clear();
334		nMol.resize(nComponents);
335
336	<	for (int i = 0; i < sites.size(); i++) {
336	>	for (unsigned int i = 0; i < sites.size(); i++) {
337		myLoc = sites[i];
338		myR = myLoc.length();
339	<	smallestSoFar = particleRadius;
340	<
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;
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	<	componentFromSite[i] = myComponent;
353	<	nMol[myComponent]++;
292	<	}
293	<	}
352	>	}
353	>	}
354
355		outputFileName = args_info.output_arg;
356	<
297	<
356	>
357		//creat new .md file on fly which corrects the number of molecule
358		createMdFile(inputFileName, outputFileName, nMol);
359
360	<	if (oldInfo != NULL)
302	<	delete oldInfo;
360	>	delete oldInfo;
361
362		SimCreator newCreator;
363		SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
#	Line 308 | Line 366 | int main(int argc, char *argv []) {
366		Molecule* mol;
367		SimInfo::MoleculeIterator mi;
368		mol = NewInfo->beginMolecule(mi);
369	+
370		int l = 0;
371
372		for (int i = 0; i < nComponents; i++){
373		locator = new MoLocator(NewInfo->getMoleculeStamp(i),
374		NewInfo->getForceField());
375	<
376	<	if (args_info.ShellRadius_given) {
377	<	for (int n = 0; n < sites.size(); n++) {
378	<	if (componentFromSite[n] == i) {
379	<	mol = NewInfo->getMoleculeByGlobalIndex(l);
380	<	locator->placeMol(sites[n], orientations[n], mol);
381	<	l++;
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 {
#	Line 329 | Line 390 | int main(int argc, char *argv []) {
390		l++;
391		}
392		}
393	<	}
393	>	}
394
395		//fill Hmat
396		hmat(0, 0)=  10.0*particleRadius;
#	Line 352 | Line 413 | int main(int argc, char *argv []) {
413		writer = new DumpWriter(NewInfo, outputFileName);
414
415		if (writer == NULL) {
416	<	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
416	>	sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
417		painCave.isFatal = 1;
418		simError();
419		}
#	Line 364 | Line 425 | int main(int argc, char *argv []) {
425		delete writer;
426
427		// cleanup a by calling sim error.....
428	<	sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
428	>	sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
429		"generated.\n", outputFileName.c_str());
430		painCave.isFatal = 0;
431		simError();
#	Line 382 | Line 443 | void createMdFile(const std::string&oldMdFileName,
443		//create new .md file based on old .md file
444		oldMdFile.open(oldMdFileName.c_str());
445		newMdFile.open(newMdFileName.c_str());
385	–
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<nMol.size()){
454	<	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
454	>	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
455		newMdFile << buffer << std::endl;
456		i++;
457		}
#	Line 403 | Line 463 | void createMdFile(const std::string&oldMdFileName,
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 1075 by gezelter, Tue Oct 17 17:51:52 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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