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root/OpenMD/trunk/src/io/DumpWriter.cpp

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
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 "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#ifdef HAVE_ZLIB
48		#include "io/gzstream.hpp"
49	+	#endif
50		#include "io/Globals.hpp"
51
52	+	#ifdef _MSC_VER
53	+	#define isnan(x) _isnan((x))
54	+	#define isinf(x) (!_finite(x) && !_isnan(x))
55	+	#endif
56	+
57		#ifdef IS_MPI
58		#include <mpi.h>
59	<	#endif //is_mpi
59	>	#endif
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64		DumpWriter::DumpWriter(SimInfo* info)
65		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66
67		Globals* simParams = info->getSimParams();
68	<	needCompression_ = simParams->getCompressDumpFile();
69	<	needForceVector_ = simParams->getOutputForceVector();
68	>	needCompression_   = simParams->getCompressDumpFile();
69	>	needForceVector_   = simParams->getOutputForceVector();
70	>	needParticlePot_   = simParams->getOutputParticlePotential();
71	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
72	>	needElectricField_ = simParams->getOutputElectricField();
73	>
74	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75	>	doSiteData_ = true;
76	>	} else {
77	>	doSiteData_ = false;
78	>	}
79	>
80		createDumpFile_ = true;
81		#ifdef HAVE_LIBZ
82		if (needCompression_) {
#	Line 95 | Line 114 | namespace oopse {
114		Globals* simParams = info->getSimParams();
115		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116
117	<	needCompression_ = simParams->getCompressDumpFile();
118	<	needForceVector_ = simParams->getOutputForceVector();
117	>	needCompression_   = simParams->getCompressDumpFile();
118	>	needForceVector_   = simParams->getOutputForceVector();
119	>	needParticlePot_   = simParams->getOutputParticlePotential();
120	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
121	>	needElectricField_ = simParams->getOutputElectricField();
122	>
123	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124	>	doSiteData_ = true;
125	>	} else {
126	>	doSiteData_ = false;
127	>	}
128	>
129		createDumpFile_ = true;
130		#ifdef HAVE_LIBZ
131		if (needCompression_) {
#	Line 134 | Line 163 | namespace oopse {
163		Globals* simParams = info->getSimParams();
164		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165
166	<	needCompression_ = simParams->getCompressDumpFile();
167	<	needForceVector_ = simParams->getOutputForceVector();
168	<
166	>	needCompression_   = simParams->getCompressDumpFile();
167	>	needForceVector_   = simParams->getOutputForceVector();
168	>	needParticlePot_   = simParams->getOutputParticlePotential();
169	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	>	needElectricField_ = simParams->getOutputElectricField();
171	>
172	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	>	doSiteData_ = true;
174	>	} else {
175	>	doSiteData_ = false;
176	>	}
177	>
178		#ifdef HAVE_LIBZ
179		if (needCompression_) {
180		filename_ += ".gz";
#	Line 194 | Line 232 | namespace oopse {
232		os << "    <FrameData>\n";
233
234		RealType currentTime = s->getTime();
235	+
236	+	if (isinf(currentTime) || isnan(currentTime)) {
237	+	sprintf( painCave.errMsg,
238	+	"DumpWriter detected a numerical error writing the time");
239	+	painCave.isFatal = 1;
240	+	simError();
241	+	}
242	+
243		sprintf(buffer, "        Time: %.10g\n", currentTime);
244		os << buffer;
245
246		Mat3x3d hmat;
247		hmat = s->getHmat();
248	+
249	+	for (unsigned int i = 0; i < 3; i++) {
250	+	for (unsigned int j = 0; j < 3; j++) {
251	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	+	sprintf( painCave.errMsg,
253	+	"DumpWriter detected a numerical error writing the box");
254	+	painCave.isFatal = 1;
255	+	simError();
256	+	}
257	+	}
258	+	}
259	+
260		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261		hmat(0, 0), hmat(1, 0), hmat(2, 0),
262		hmat(0, 1), hmat(1, 1), hmat(2, 1),
263		hmat(0, 2), hmat(1, 2), hmat(2, 2));
264		os << buffer;
265
266	<	RealType chi = s->getChi();
267	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
268	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267	>
268	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269	>	isinf(thermostat.second) || isnan(thermostat.second)) {
270	>	sprintf( painCave.errMsg,
271	>	"DumpWriter detected a numerical error writing the thermostat");
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276	>	thermostat.second);
277		os << buffer;
278
279		Mat3x3d eta;
280	<	eta = s->getEta();
280	>	eta = s->getBarostat();
281	>
282	>	for (unsigned int i = 0; i < 3; i++) {
283	>	for (unsigned int j = 0; j < 3; j++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292	>
293		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294		eta(0, 0), eta(1, 0), eta(2, 0),
295		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 228 | Line 306 | namespace oopse {
306		#endif
307
308		Molecule* mol;
309	<	StuntDouble* integrableObject;
309	>	StuntDouble* sd;
310		SimInfo::MoleculeIterator mi;
311		Molecule::IntegrableObjectIterator ii;
312	+	RigidBody::AtomIterator ai;
313	+	Atom* atom;
314
315		#ifndef IS_MPI
316		os << "  <Snapshot>\n";
#	Line 241 | Line 321 | namespace oopse {
321		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323
324	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
325	<	integrableObject = mol->nextIntegrableObject(ii)) {
326	<	os << prepareDumpLine(integrableObject);
324	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
325	>	sd = mol->nextIntegrableObject(ii)) {
326	>	os << prepareDumpLine(sd);
327
328		}
329		}
330		os << "    </StuntDoubles>\n";
331	<
331	>
332	>	if (doSiteData_) {
333	>	os << "    <SiteData>\n";
334	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338	>
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342	>
343	>	if (sd->isRigidBody()) {
344	>
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346	>	int siteIndex = 0;
347	>	for (atom = rb->beginAtom(ai); atom != NULL;
348	>	atom = rb->nextAtom(ai)) {
349	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
350	>	siteIndex++;
351	>	}
352	>	}
353	>	}
354	>	}
355	>	os << "    </SiteData>\n";
356	>	}
357		os << "  </Snapshot>\n";
358
359		os.flush();
#	Line 258 | Line 363 | namespace oopse {
363		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
364
365
366	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
367	<	integrableObject = mol->nextIntegrableObject(ii)) {
368	<	buffer += prepareDumpLine(integrableObject);
366	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
367	>	sd = mol->nextIntegrableObject(ii)) {
368	>	buffer += prepareDumpLine(sd);
369		}
370		}
371
372		const int masterNode = 0;
373	<
373	>	int nProc;
374	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
375		if (worldRank == masterNode) {
376		os << "  <Snapshot>\n";
377		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 273 | Line 379 | namespace oopse {
379
380		os << buffer;
381
276	–	int nProc;
277	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
382		for (int i = 1; i < nProc; ++i) {
383
384		// receive the length of the string buffer that was
385		// prepared by processor i
386
387	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
388		int recvLength;
389		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
390		char* recvBuffer = new char[recvLength];
#	Line 296 | Line 401 | namespace oopse {
401		os.flush();
402		} else {
403		int sendBufferLength = buffer.size() + 1;
404	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
405	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
404	>	int myturn = 0;
405	>	for (int i = 1; i < nProc; ++i){
406	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
407	>	if (myturn == worldRank){
408	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
409	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
410	>	}
411	>	}
412		}
413
414		#endif // is_mpi
415
416		}
417
418	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
418	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
419
420	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
420	>	int index = sd->getGlobalIntegrableObjectIndex();
421		std::string type("pv");
422		std::string line;
423		char tempBuffer[4096];
424
425		Vector3d pos;
426		Vector3d vel;
427	<	pos = integrableObject->getPos();
428	<	vel = integrableObject->getVel();
427	>	pos = sd->getPos();
428	>
429	>	if (isinf(pos[0]) || isnan(pos[0]) ||
430	>	isinf(pos[1]) || isnan(pos[1]) ||
431	>	isinf(pos[2]) || isnan(pos[2]) ) {
432	>	sprintf( painCave.errMsg,
433	>	"DumpWriter detected a numerical error writing the position"
434	>	" for object %d", index);
435	>	painCave.isFatal = 1;
436	>	simError();
437	>	}
438	>
439	>	vel = sd->getVel();
440	>
441	>	if (isinf(vel[0]) || isnan(vel[0]) ||
442	>	isinf(vel[1]) || isnan(vel[1]) ||
443	>	isinf(vel[2]) || isnan(vel[2]) ) {
444	>	sprintf( painCave.errMsg,
445	>	"DumpWriter detected a numerical error writing the velocity"
446	>	" for object %d", index);
447	>	painCave.isFatal = 1;
448	>	simError();
449	>	}
450	>
451		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
452		pos[0], pos[1], pos[2],
453		vel[0], vel[1], vel[2]);
454		line += tempBuffer;
455
456	<	if (integrableObject->isDirectional()) {
456	>	if (sd->isDirectional()) {
457		type += "qj";
458		Quat4d q;
459		Vector3d ji;
460	<	q = integrableObject->getQ();
461	<	ji = integrableObject->getJ();
460	>	q = sd->getQ();
461	>
462	>	if (isinf(q[0]) || isnan(q[0]) ||
463	>	isinf(q[1]) || isnan(q[1]) ||
464	>	isinf(q[2]) || isnan(q[2]) ||
465	>	isinf(q[3]) || isnan(q[3]) ) {
466	>	sprintf( painCave.errMsg,
467	>	"DumpWriter detected a numerical error writing the quaternion"
468	>	" for object %d", index);
469	>	painCave.isFatal = 1;
470	>	simError();
471	>	}
472	>
473	>	ji = sd->getJ();
474	>
475	>	if (isinf(ji[0]) || isnan(ji[0]) ||
476	>	isinf(ji[1]) || isnan(ji[1]) ||
477	>	isinf(ji[2]) || isnan(ji[2]) ) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the angular"
480	>	" momentum for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484	>
485		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
486		q[0], q[1], q[2], q[3],
487		ji[0], ji[1], ji[2]);
#	Line 333 | Line 489 | namespace oopse {
489		}
490
491		if (needForceVector_) {
492	<	type += "ft";
493	<	Vector3d frc;
494	<	Vector3d trq;
495	<	frc = integrableObject->getFrc();
496	<	trq = integrableObject->getTrq();
497	<
498	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
499	<	frc[0], frc[1], frc[2],
500	<	trq[0], trq[1], trq[2]);
492	>	type += "f";
493	>	Vector3d frc = sd->getFrc();
494	>	if (isinf(frc[0]) || isnan(frc[0]) ||
495	>	isinf(frc[1]) || isnan(frc[1]) ||
496	>	isinf(frc[2]) || isnan(frc[2]) ) {
497	>	sprintf( painCave.errMsg,
498	>	"DumpWriter detected a numerical error writing the force"
499	>	" for object %d", index);
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	sprintf(tempBuffer, " %13e %13e %13e",
504	>	frc[0], frc[1], frc[2]);
505		line += tempBuffer;
506	+
507	+	if (sd->isDirectional()) {
508	+	type += "t";
509	+	Vector3d trq = sd->getTrq();
510	+	if (isinf(trq[0]) || isnan(trq[0]) ||
511	+	isinf(trq[1]) || isnan(trq[1]) ||
512	+	isinf(trq[2]) || isnan(trq[2]) ) {
513	+	sprintf( painCave.errMsg,
514	+	"DumpWriter detected a numerical error writing the torque"
515	+	" for object %d", index);
516	+	painCave.isFatal = 1;
517	+	simError();
518	+	}
519	+	sprintf(tempBuffer, " %13e %13e %13e",
520	+	trq[0], trq[1], trq[2]);
521	+	line += tempBuffer;
522	+	}
523		}
524	<
524	>
525		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
526		return std::string(tempBuffer);
527		}
528
529	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
530	+
531	+
532	+	std::string id;
533	+	std::string type;
534	+	std::string line;
535	+	char tempBuffer[4096];
536	+
537	+	if (sd->isRigidBody()) {
538	+	sprintf(tempBuffer, "%10d           ", ioIndex);
539	+	id = std::string(tempBuffer);
540	+	} else {
541	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
542	+	id = std::string(tempBuffer);
543	+	}
544	+
545	+	if (needFlucQ_) {
546	+	type += "cw";
547	+	RealType fqPos = sd->getFlucQPos();
548	+	if (isinf(fqPos) || isnan(fqPos) ) {
549	+	sprintf( painCave.errMsg,
550	+	"DumpWriter detected a numerical error writing the"
551	+	" fluctuating charge for object %s", id.c_str());
552	+	painCave.isFatal = 1;
553	+	simError();
554	+	}
555	+	sprintf(tempBuffer, " %13e ", fqPos);
556	+	line += tempBuffer;
557	+
558	+	RealType fqVel = sd->getFlucQVel();
559	+	if (isinf(fqVel) || isnan(fqVel) ) {
560	+	sprintf( painCave.errMsg,
561	+	"DumpWriter detected a numerical error writing the"
562	+	" fluctuating charge velocity for object %s", id.c_str());
563	+	painCave.isFatal = 1;
564	+	simError();
565	+	}
566	+	sprintf(tempBuffer, " %13e ", fqVel);
567	+	line += tempBuffer;
568	+
569	+	if (needForceVector_) {
570	+	type += "g";
571	+	RealType fqFrc = sd->getFlucQFrc();
572	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
573	+	sprintf( painCave.errMsg,
574	+	"DumpWriter detected a numerical error writing the"
575	+	" fluctuating charge force for object %s", id.c_str());
576	+	painCave.isFatal = 1;
577	+	simError();
578	+	}
579	+	sprintf(tempBuffer, " %13e ", fqFrc);
580	+	line += tempBuffer;
581	+	}
582	+	}
583	+
584	+	if (needElectricField_) {
585	+	type += "e";
586	+	Vector3d eField= sd->getElectricField();
587	+	if (isinf(eField[0]) || isnan(eField[0]) ||
588	+	isinf(eField[1]) || isnan(eField[1]) ||
589	+	isinf(eField[2]) || isnan(eField[2]) ) {
590	+	sprintf( painCave.errMsg,
591	+	"DumpWriter detected a numerical error writing the electric"
592	+	" field for object %s", id.c_str());
593	+	painCave.isFatal = 1;
594	+	simError();
595	+	}
596	+	sprintf(tempBuffer, " %13e %13e %13e",
597	+	eField[0], eField[1], eField[2]);
598	+	line += tempBuffer;
599	+	}
600	+
601	+
602	+	if (needParticlePot_) {
603	+	type += "u";
604	+	RealType particlePot = sd->getParticlePot();
605	+	if (isinf(particlePot) || isnan(particlePot)) {
606	+	sprintf( painCave.errMsg,
607	+	"DumpWriter detected a numerical error writing the particle "
608	+	" potential for object %s", id.c_str());
609	+	painCave.isFatal = 1;
610	+	simError();
611	+	}
612	+	sprintf(tempBuffer, " %13e", particlePot);
613	+	line += tempBuffer;
614	+	}
615	+
616	+
617	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
618	+	return std::string(tempBuffer);
619	+	}
620	+
621		void DumpWriter::writeDump() {
622		writeFrame(*dumpFile_);
623		}
#	Line 416 | Line 685 | namespace oopse {
685		std::ostream* DumpWriter::createOStream(const std::string& filename) {
686
687		std::ostream* newOStream;
688	<	#ifdef HAVE_LIBZ
688	>	#ifdef HAVE_ZLIB
689		if (needCompression_) {
690		newOStream = new ogzstream(filename.c_str());
691		} else {
#	Line 426 | Line 695 | namespace oopse {
695		newOStream = new std::ofstream(filename.c_str());
696		#endif
697		//write out MetaData first
698	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
698	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
699		(*newOStream) << "  <MetaData>" << std::endl;
700		(*newOStream) << info_->getRawMetaData();
701		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 435 | Line 704 | namespace oopse {
704
705		void DumpWriter::writeClosing(std::ostream& os) {
706
707	<	os << "</OOPSE>\n";
707	>	os << "</OpenMD>\n";
708		os.flush();
709		}
710
711	<	}//end namespace oopse
711	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

#	Line 0 | Line 1
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