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root/OpenMD/branches/development/src/visitors/OtherVisitor.cpp

Comparing:
trunk/src/visitors/OtherVisitor.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41		#include "selection/SelectionManager.hpp"
42		#include "visitors/OtherVisitor.hpp"
#	Line 44 | Line 44
44		#include "primitives/RigidBody.hpp"
45		#include "primitives/Molecule.hpp"
46		#include "brains/SimInfo.hpp"
47	<	namespace oopse {
47	>	namespace OpenMD {
48
49		void WrappingVisitor::visit(Atom *atom) {
50		internalVisit(atom);
#	Line 77 | Line 77 | namespace oopse {
77		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78
79		for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80	<	currSnapshot->wrapVector(atomInfo->pos);
80	>	Vector3d newPos = atomInfo->pos - origin_;
81	>	currSnapshot->wrapVector(newPos);
82	>	atomInfo->pos = newPos;
83		}
84		}
85
86	+	void WrappingVisitor::update() {
87	+	if (useCom_){
88	+	origin_ = info->getCom();
89	+	}
90	+	}
91	+
92		const std::string WrappingVisitor::toString() {
93		char        buffer[65535];
94		std::string result;
#	Line 215 | Line 223 | namespace oopse {
223		return result;
224		}
225
226	<	//----------------------------------------------------------------------------//
226	>	//------------------------------------------------------------------------//
227
228	<	XYZVisitor::XYZVisitor(SimInfo *info) :
229	<	BaseVisitor(), seleMan(info), evaluator(info){
230	<	this->info = info;
231	<	visitorName = "XYZVisitor";
232	<
233	<	evaluator.loadScriptString("select all");
234	<
235	<	if (!evaluator.isDynamic()) {
236	<	seleMan.setSelectionSet(evaluator.evaluate());
237	<	}
238	<
239	<	}
240	<
228	>	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
229	>	evaluator(info), doPositions_(true),
230	>	doVelocities_(false),
231	>	doForces_(false), doVectors_(false),
232	>	doCharges_(false) {
233	>	this->info = info;
234	>	visitorName = "XYZVisitor";
235	>
236	>	evaluator.loadScriptString("select all");
237	>
238	>	if (!evaluator.isDynamic()) {
239	>	seleMan.setSelectionSet(evaluator.evaluate());
240	>	}
241	>	}
242	>
243		XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
244	<	BaseVisitor(), seleMan(info), evaluator(info) {
245	<	this->info = info;
246	<	visitorName = "XYZVisitor";
247	<
248	<	evaluator.loadScriptString(script);
249	<
250	<	if (!evaluator.isDynamic()) {
251	<	seleMan.setSelectionSet(evaluator.evaluate());
252	<	}
253	<
244	>	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
245	>	doVelocities_(false), doForces_(false), doVectors_(false),
246	>	doCharges_(false) {
247	>
248	>	this->info = info;
249	>	visitorName = "XYZVisitor";
250	>
251	>	evaluator.loadScriptString(script);
252	>
253	>	if (!evaluator.isDynamic()) {
254	>	seleMan.setSelectionSet(evaluator.evaluate());
255		}
256	+	}
257
258		void XYZVisitor::visit(Atom *atom) {
259		if (isSelected(atom))
#	Line 252 | Line 264 | namespace oopse {
264		if (isSelected(datom))
265		internalVisit(datom);
266		}
267	<
267	>
268		void XYZVisitor::visit(RigidBody *rb) {
269		if (isSelected(rb))
270		internalVisit(rb);
271		}
272	<
272	>
273		void XYZVisitor::update() {
274		//if dynamic, we need to re-evaluate the selection
275		if (evaluator.isDynamic()) {
276		seleMan.setSelectionSet(evaluator.evaluate());
277		}
278		}
279	<
279	>
280		void XYZVisitor::internalVisit(StuntDouble *sd) {
281		GenericData *                     data;
282		AtomData *                        atomData;
283		AtomInfo *                        atomInfo;
284		std::vector<AtomInfo *>::iterator i;
285		char                              buffer[1024];
286	<
286	>
287		//if there is not atom data, just skip it
288		data = sd->getPropertyByName("ATOMDATA");
289	<
289	>
290		if (data != NULL) {
291		atomData = dynamic_cast<AtomData *>(data);
292	<
292	>
293		if (atomData == NULL)
294		return;
295		} else
296		return;
297
298		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
299	<	atomInfo = atomData->nextAtomInfo(i) ) {
300	<	sprintf(buffer,
301	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
302	<	atomInfo->atomTypeName.c_str(),
303	<	atomInfo->pos[0],
304	<	atomInfo->pos[1],
305	<	atomInfo->pos[2],
306	<	atomInfo->dipole[0],
307	<	atomInfo->dipole[1],
308	<	atomInfo->dipole[2]);
309	<	frame.push_back(buffer);
310	<	}
299	>	atomInfo = atomData->nextAtomInfo(i) ) {
300	>
301	>	std::string line;
302	>	sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
303	>	line += buffer;
304	>
305	>	if (doPositions_){
306	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
307	>	atomInfo->pos[1], atomInfo->pos[2]);
308	>	line += buffer;
309	>	}
310	>	if (doCharges_ && atomInfo->hasCharge) {
311	>	sprintf(buffer, "%15.8f", atomInfo->charge);
312	>	line += buffer;
313	>	}
314	>	if (doVectors_ && atomInfo->hasVector) {
315	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
316	>	atomInfo->vec[1], atomInfo->vec[2]);
317	>	line += buffer;
318	>	}
319	>	if (doVelocities_ && atomInfo->hasVelocity) {
320	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
321	>	atomInfo->vel[1], atomInfo->vel[2]);
322	>	line += buffer;
323	>	}
324	>	if (doForces_ && atomInfo->hasForce) {
325	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
326	>	atomInfo->frc[1], atomInfo->frc[2]);
327	>	line += buffer;
328	>	}
329	>	frame.push_back(line);
330	>	}
331		}
332
333		bool XYZVisitor::isSelected(StuntDouble *sd) {
#	Line 305 | Line 337 | namespace oopse {
337		void XYZVisitor::writeFrame(std::ostream &outStream) {
338		std::vector<std::string>::iterator i;
339		char buffer[1024];
340	<
340	>
341		if (frame.size() == 0)
342		std::cerr << "Current Frame does not contain any atoms" << std::endl;
343	<
343	>
344		//total number of atoms
345		outStream << frame.size() << std::endl;
346	<
346	>
347		//write comment line
348		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
349		Mat3x3d box = currSnapshot->getHmat();
#	Line 322 | Line 354 | namespace oopse {
354		box(0, 0), box(0, 1), box(0, 2),
355		box(1, 0), box(1, 1), box(1, 2),
356		box(2, 0), box(2, 1), box(2, 2));
357	<
357	>
358		outStream << buffer << std::endl;
359	<
359	>
360		for( i = frame.begin(); i != frame.end(); ++i )
361		outStream << *i << std::endl;
362		}
363	<
363	>
364	>	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
365	>	return atomTypeName.substr(0, atomTypeName.find('-'));
366	>	}
367	>
368		const std::string XYZVisitor::toString() {
369		char        buffer[65535];
370		std::string result;
371	<
371	>
372		sprintf(buffer,
373		"------------------------------------------------------------------\n");
374		result += buffer;
375	<
375	>
376		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
377		result += buffer;
378	<
378	>
379		sprintf(buffer,
380		"Visitor Description: assemble the atom data and output xyz file\n");
381		result += buffer;
#	Line 347 | Line 383 | namespace oopse {
383		sprintf(buffer,
384		"------------------------------------------------------------------\n");
385		result += buffer;
386	<
386	>
387		return result;
388		}
389	<
389	>
390		//----------------------------------------------------------------------------//
391	<
391	>
392		void PrepareVisitor::internalVisit(Atom *atom) {
393		GenericData *data;
394		AtomData *   atomData;
395	<
395	>
396		//if visited property is  existed, remove it
397		data = atom->getPropertyByName("VISITED");
398	<
398	>
399		if (data != NULL) {
400		atom->removeProperty("VISITED");
401		}
402	<
402	>
403		//remove atomdata
404		data = atom->getPropertyByName("ATOMDATA");
405
#	Line 432 | Line 468 | namespace oopse {
468		visitorName = "WaterTypeVisitor";
469		waterTypeList.insert("TIP3P_RB_0");
470		waterTypeList.insert("TIP4P_RB_0");
471	+	waterTypeList.insert("TIP4P-Ew_RB_0");
472		waterTypeList.insert("TIP5P_RB_0");
473	+	waterTypeList.insert("TIP5P-E_RB_0");
474		waterTypeList.insert("SPCE_RB_0");
475	+	waterTypeList.insert("SPC_RB_0");
476		}
477
478		void WaterTypeVisitor::visit(RigidBody *rb) {
#	Line 446 | Line 485 | namespace oopse {
485		std::vector<AtomInfo *>::iterator i;
486
487		rbName = rb->getType();
488	<
488	>
489		if (waterTypeList.find(rbName) != waterTypeList.end()) {
490		myAtoms = rb->getAtoms();
491
492		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
493		++atomIter ) {
494		data = (*atomIter)->getPropertyByName("ATOMDATA");
495	<
495	>
496		if (data != NULL) {
497		atomData = dynamic_cast<AtomData *>(data);
498	<
498	>
499		if (atomData == NULL)
500		continue;
501		} else
502		continue;
503	<
503	>
504		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
505		atomInfo = atomData->nextAtomInfo(i) ) {
506		atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
#	Line 496 | Line 535 | namespace oopse {
535		return result;
536		}
537
538	<	} //namespace oopse
538	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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