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root/OpenMD/trunk/src/brains/SimCreator.cpp

Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 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		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+
50	+	#ifdef IS_MPI
51	+	#include "mpi.h"
52	+	#include "math/ParallelRandNumGen.hpp"
53	+	#endif
54	+
55		#include <exception>
56		#include <iostream>
57		#include <sstream>
#	Line 55 | Line 61
61		#include "brains/SimCreator.hpp"
62		#include "brains/SimSnapshotManager.hpp"
63		#include "io/DumpReader.hpp"
64	<	#include "UseTheForce/ForceFieldFactory.hpp"
64	>	#include "brains/ForceField.hpp"
65		#include "utils/simError.h"
66		#include "utils/StringUtils.hpp"
67		#include "math/SeqRandNumGen.hpp"
#	Line 75 | Line 81
81		#include "antlr/NoViableAltForCharException.hpp"
82		#include "antlr/NoViableAltException.hpp"
83
84	<	#ifdef IS_MPI
85	<	#include "math/ParallelRandNumGen.hpp"
86	<	#endif
84	>	#include "types/DirectionalAdapter.hpp"
85	>	#include "types/MultipoleAdapter.hpp"
86	>	#include "types/EAMAdapter.hpp"
87	>	#include "types/SuttonChenAdapter.hpp"
88	>	#include "types/PolarizableAdapter.hpp"
89	>	#include "types/FixedChargeAdapter.hpp"
90	>	#include "types/FluctuatingChargeAdapter.hpp"
91
92	<	namespace oopse {
92	>
93	>	namespace OpenMD {
94
95	<	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
95	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
96		Globals* simParams = NULL;
97		try {
98
#	Line 90 | Line 101 | namespace oopse {
101		#ifdef IS_MPI
102		int streamSize;
103		const int masterNode = 0;
104	<	int commStatus;
104	>
105		if (worldRank == masterNode) {
106	<	#endif
107	<
106	>	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
107	>	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
108	>	#endif
109		SimplePreprocessor preprocessor;
110	<	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
110	>	preprocessor.preprocess(rawMetaDataStream, filename,
111	>	startOfMetaDataBlock, ppStream);
112
113		#ifdef IS_MPI
114	<	//brocasting the stream size
114	>	//broadcasting the stream size
115		streamSize = ppStream.str().size() +1;
116	<	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
116	>	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117	>	MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118	>	streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119
120	<	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
121	<
122	<
120	>	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121	>	// MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
122	>	//                       streamSize, MPI::CHAR, masterNode);
123	>
124		} else {
109	–	//get stream size
110	–	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
125
126	+	MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
127	+	// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
128	+
129	+	//get stream size
130	+	MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
131	+	// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
132		char* buf = new char[streamSize];
133		assert(buf);
134
135		//receive file content
136	<	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137	<
136	>	MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137	>	// MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
138	>
139		ppStream.str(buf);
140		delete [] buf;
120	–
141		}
142		#endif
143		// Create a scanner that reads from the input stream
#	Line 139 | Line 159 | namespace oopse {
159		parser.initializeASTFactory(factory);
160		parser.setASTFactory(&factory);
161		parser.mdfile();
142	–
162		// Create a tree parser that reads information into Globals
163		MDTreeParser treeParser;
164		treeParser.initializeASTFactory(factory);
#	Line 214 | Line 233 | namespace oopse {
233		painCave.isFatal = 1;
234		simError();
235		}
236	<	catch (OOPSEException& e) {
236	>	catch (OpenMDException& e) {
237		sprintf(painCave.errMsg,
238		"%s\n",
239		e.getMessage().c_str());
#	Line 229 | Line 248 | namespace oopse {
248		simError();
249		}
250
251	+	simParams->setMDfileVersion(mdFileVersion);
252		return simParams;
253		}
254
255		SimInfo*  SimCreator::createSim(const std::string & mdFileName,
256		bool loadInitCoords) {
257	<
257	>
258		const int bufferSize = 65535;
259		char buffer[bufferSize];
260		int lineNo = 0;
261		std::string mdRawData;
262		int metaDataBlockStart = -1;
263		int metaDataBlockEnd = -1;
264	<	int i;
265	<	int mdOffset;
264	>	int i, j;
265	>	streamoff mdOffset;
266	>	int mdFileVersion;
267
268	+	// Create a string for embedding the version information in the MetaData
269	+	std::string version;
270	+	version.assign("## Last run using OpenMD Version: ");
271	+	version.append(OPENMD_VERSION_MAJOR);
272	+	version.append(".");
273	+	version.append(OPENMD_VERSION_MINOR);
274	+
275	+	std::string svnrev;
276	+	//convert a macro from compiler to a string in c++
277	+	STR_DEFINE(svnrev, SVN_REV );
278	+	version.append(" Revision: ");
279	+	// If there's no SVN revision, just call this the RELEASE revision.
280	+	if (!svnrev.empty()) {
281	+	version.append(svnrev);
282	+	} else {
283	+	version.append("RELEASE");
284	+	}
285	+
286		#ifdef IS_MPI
287		const int masterNode = 0;
288		if (worldRank == masterNode) {
289		#endif
290
291	<	std::ifstream mdFile_(mdFileName.c_str());
291	>	std::ifstream mdFile_;
292	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
293
294		if (mdFile_.fail()) {
295		sprintf(painCave.errMsg,
#	Line 262 | Line 302 | namespace oopse {
302		mdFile_.getline(buffer, bufferSize);
303		++lineNo;
304		std::string line = trimLeftCopy(buffer);
305	<	i = CaseInsensitiveFind(line, "<OOPSE");
305	>	i = CaseInsensitiveFind(line, "<OpenMD");
306		if (static_cast<size_t>(i) == string::npos) {
307	+	// try the older file strings to see if that works:
308	+	i = CaseInsensitiveFind(line, "<OOPSE");
309	+	}
310	+
311	+	if (static_cast<size_t>(i) == string::npos) {
312	+	// still no luck!
313		sprintf(painCave.errMsg,
314	<	"SimCreator: File: %s is not an OOPSE file!\n",
314	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
315		mdFileName.c_str());
316		painCave.isFatal = 1;
317		simError();
318		}
319	+
320	+	// found the correct opening string, now try to get the file
321	+	// format version number.
322
323	+	StringTokenizer tokenizer(line, "=<> \t\n\r");
324	+	std::string fileType = tokenizer.nextToken();
325	+	toUpper(fileType);
326	+
327	+	mdFileVersion = 0;
328	+
329	+	if (fileType == "OPENMD") {
330	+	while (tokenizer.hasMoreTokens()) {
331	+	std::string token(tokenizer.nextToken());
332	+	toUpper(token);
333	+	if (token == "VERSION") {
334	+	mdFileVersion = tokenizer.nextTokenAsInt();
335	+	break;
336	+	}
337	+	}
338	+	}
339	+
340		//scan through the input stream and find MetaData tag
341		while(mdFile_.getline(buffer, bufferSize)) {
342		++lineNo;
#	Line 311 | Line 377 | namespace oopse {
377
378		mdRawData.clear();
379
380	+	bool foundVersion = false;
381	+
382		for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
383		mdFile_.getline(buffer, bufferSize);
384	<	mdRawData += buffer;
384	>	std::string line = trimLeftCopy(buffer);
385	>	j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
386	>	if (static_cast<size_t>(j) != string::npos) {
387	>	foundVersion = true;
388	>	mdRawData += version;
389	>	} else {
390	>	mdRawData += buffer;
391	>	}
392		mdRawData += "\n";
393		}
394	<
394	>
395	>	if (!foundVersion) mdRawData += version + "\n";
396	>
397		mdFile_.close();
398
399		#ifdef IS_MPI
#	Line 326 | Line 403 | namespace oopse {
403		std::stringstream rawMetaDataStream(mdRawData);
404
405		//parse meta-data file
406	<	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
406	>	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
407	>	metaDataBlockStart + 1);
408
409		//create the force field
410	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
410	>	ForceField * ff = new ForceField(simParams->getForceField());
411
412		if (ff == NULL) {
413		sprintf(painCave.errMsg,
#	Line 363 | Line 441 | namespace oopse {
441		}
442
443		ff->parse(forcefieldFileName);
366	–	ff->setFortranForceOptions();
444		//create SimInfo
445		SimInfo * info = new SimInfo(ff, simParams);
446
#	Line 381 | Line 458 | namespace oopse {
458		//create the molecules
459		createMolecules(info);
460
461	<
461	>	//find the storage layout
462	>
463	>	int storageLayout = computeStorageLayout(info);
464	>
465		//allocate memory for DataStorage(circular reference, need to
466		//break it)
467	<	info->setSnapshotManager(new SimSnapshotManager(info));
467	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
468
469		//set the global index of atoms, rigidbodies and cutoffgroups
470		//(only need to be set once, the global index will never change
#	Line 407 | Line 487 | namespace oopse {
487
488		if (loadInitCoords)
489		loadCoordinates(info, mdFileName);
410	–
490		return info;
491		}
492
#	Line 442 | Line 521 | namespace oopse {
521
522		#ifdef IS_MPI
523		void SimCreator::divideMolecules(SimInfo *info) {
445	–	RealType numerator;
446	–	RealType denominator;
447	–	RealType precast;
448	–	RealType x;
449	–	RealType y;
524		RealType a;
451	–	int old_atoms;
452	–	int add_atoms;
453	–	int new_atoms;
454	–	int nTarget;
455	–	int done;
456	–	int i;
457	–	int j;
458	–	int loops;
459	–	int which_proc;
525		int nProcessors;
526		std::vector<int> atomsPerProc;
527		int nGlobalMols = info->getNGlobalMolecules();
528	<	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
528	>	std::vector<int> molToProcMap(nGlobalMols, -1); // default to an
529	>	// error
530	>	// condition:
531
532	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
532	>	MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);
533	>	//nProcessors = MPI::COMM_WORLD.Get_size();
534
535		if (nProcessors > nGlobalMols) {
536		sprintf(painCave.errMsg,
#	Line 471 | Line 539 | namespace oopse {
539		"\tthe number of molecules.  This will not result in a \n"
540		"\tusable division of atoms for force decomposition.\n"
541		"\tEither try a smaller number of processors, or run the\n"
542	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
542	>	"\tsingle-processor version of OpenMD.\n", nProcessors,
543	>	nGlobalMols);
544
545		painCave.isFatal = 1;
546		simError();
547		}
548
480	–	int seedValue;
549		Globals * simParams = info->getSimParams();
550	<	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
550	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel
551	>	//random number generator
552		if (simParams->haveSeed()) {
553	<	seedValue = simParams->getSeed();
553	>	int seedValue = simParams->getSeed();
554		myRandom = new SeqRandNumGen(seedValue);
555		}else {
556		myRandom = new SeqRandNumGen();
#	Line 494 | Line 563 | namespace oopse {
563		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
564
565		if (worldRank == 0) {
566	<	numerator = info->getNGlobalAtoms();
567	<	denominator = nProcessors;
568	<	precast = numerator / denominator;
569	<	nTarget = (int)(precast + 0.5);
566	>	RealType numerator = info->getNGlobalAtoms();
567	>	RealType denominator = nProcessors;
568	>	RealType precast = numerator / denominator;
569	>	int nTarget = (int)(precast + 0.5);
570
571	<	for(i = 0; i < nGlobalMols; i++) {
572	<	done = 0;
573	<	loops = 0;
571	>	for(int i = 0; i < nGlobalMols; i++) {
572	>
573	>	int done = 0;
574	>	int loops = 0;
575
576		while (!done) {
577		loops++;
578
579		// Pick a processor at random
580
581	<	which_proc = (int) (myRandom->rand() * nProcessors);
581	>	int which_proc = (int) (myRandom->rand() * nProcessors);
582
583		//get the molecule stamp first
584		int stampId = info->getMoleculeStampId(i);
585		MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
586
587		// How many atoms does this processor have so far?
588	<	old_atoms = atomsPerProc[which_proc];
589	<	add_atoms = moleculeStamp->getNAtoms();
590	<	new_atoms = old_atoms + add_atoms;
588	>	int old_atoms = atomsPerProc[which_proc];
589	>	int add_atoms = moleculeStamp->getNAtoms();
590	>	int new_atoms = old_atoms + add_atoms;
591
592		// If we've been through this loop too many times, we need
593		// to just give up and assign the molecule to this processor
594		// and be done with it.
595
596		if (loops > 100) {
597	+
598		sprintf(painCave.errMsg,
599	<	"I've tried 100 times to assign molecule %d to a "
600	<	" processor, but can't find a good spot.\n"
601	<	"I'm assigning it at random to processor %d.\n",
599	>	"There have been 100 attempts to assign molecule %d to an\n"
600	>	"\tunderworked processor, but there's no good place to\n"
601	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
602		i, which_proc);
603	<
603	>
604		painCave.isFatal = 0;
605	+	painCave.severity = OPENMD_INFO;
606		simError();
607
608		molToProcMap[i] = which_proc;
#	Line 559 | Line 631 | namespace oopse {
631		//           Pacc(x) = exp(- a * x)
632		// where a = penalty / (average atoms per molecule)
633
634	<	x = (RealType)(new_atoms - nTarget);
635	<	y = myRandom->rand();
634	>	RealType x = (RealType)(new_atoms - nTarget);
635	>	RealType y = myRandom->rand();
636
637		if (y < exp(- a * x)) {
638		molToProcMap[i] = which_proc;
#	Line 575 | Line 647 | namespace oopse {
647		}
648
649		delete myRandom;
650	<
650	>
651		// Spray out this nonsense to all other processors:
580	–
652		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
653	+	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
654		} else {
655
656		// Listen to your marching orders from processor 0:
585	–
657		MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658	+	// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
659	+
660		}
661
662		info->setMolToProcMap(molToProcMap);
#	Line 606 | Line 679 | namespace oopse {
679		#endif
680
681		stampId = info->getMoleculeStampId(i);
682	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
683	<	stampId, i, info->getLocalIndexManager());
682	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
683	>	info->getMoleculeStamp(stampId),
684	>	stampId, i,
685	>	info->getLocalIndexManager());
686
687		info->addMolecule(mol);
688
#	Line 619 | Line 694 | namespace oopse {
694
695		} //end for(int i=0)
696		}
697	+
698	+	int SimCreator::computeStorageLayout(SimInfo* info) {
699	+
700	+	Globals* simParams = info->getSimParams();
701	+	int nRigidBodies = info->getNGlobalRigidBodies();
702	+	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
703	+	set<AtomType*>::iterator i;
704	+	bool hasDirectionalAtoms = false;
705	+	bool hasFixedCharge = false;
706	+	bool hasDipoles = false;
707	+	bool hasQuadrupoles = false;
708	+	bool hasPolarizable = false;
709	+	bool hasFluctuatingCharge = false;
710	+	bool hasMetallic = false;
711	+	int storageLayout = 0;
712	+	storageLayout |= DataStorage::dslPosition;
713	+	storageLayout |= DataStorage::dslVelocity;
714	+	storageLayout |= DataStorage::dslForce;
715	+
716	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717	+
718	+	DirectionalAdapter da = DirectionalAdapter( (*i) );
719	+	MultipoleAdapter ma = MultipoleAdapter( (*i) );
720	+	EAMAdapter ea = EAMAdapter( (*i) );
721	+	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
722	+	PolarizableAdapter pa = PolarizableAdapter( (*i) );
723	+	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
724	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
725	+
726	+	if (da.isDirectional()){
727	+	hasDirectionalAtoms = true;
728	+	}
729	+	if (ma.isDipole()){
730	+	hasDipoles = true;
731	+	}
732	+	if (ma.isQuadrupole()){
733	+	hasQuadrupoles = true;
734	+	}
735	+	if (ea.isEAM() || sca.isSuttonChen()){
736	+	hasMetallic = true;
737	+	}
738	+	if ( fca.isFixedCharge() ){
739	+	hasFixedCharge = true;
740	+	}
741	+	if ( fqa.isFluctuatingCharge() ){
742	+	hasFluctuatingCharge = true;
743	+	}
744	+	if ( pa.isPolarizable() ){
745	+	hasPolarizable = true;
746	+	}
747	+	}
748
749	+	if (nRigidBodies > 0 || hasDirectionalAtoms) {
750	+	storageLayout |= DataStorage::dslAmat;
751	+	if(storageLayout & DataStorage::dslVelocity) {
752	+	storageLayout |= DataStorage::dslAngularMomentum;
753	+	}
754	+	if (storageLayout & DataStorage::dslForce) {
755	+	storageLayout |= DataStorage::dslTorque;
756	+	}
757	+	}
758	+	if (hasDipoles) {
759	+	storageLayout |= DataStorage::dslDipole;
760	+	}
761	+	if (hasQuadrupoles) {
762	+	storageLayout |= DataStorage::dslQuadrupole;
763	+	}
764	+	if (hasFixedCharge || hasFluctuatingCharge) {
765	+	storageLayout |= DataStorage::dslSkippedCharge;
766	+	}
767	+	if (hasMetallic) {
768	+	storageLayout |= DataStorage::dslDensity;
769	+	storageLayout |= DataStorage::dslFunctional;
770	+	storageLayout |= DataStorage::dslFunctionalDerivative;
771	+	}
772	+	if (hasPolarizable) {
773	+	storageLayout |= DataStorage::dslElectricField;
774	+	}
775	+	if (hasFluctuatingCharge){
776	+	storageLayout |= DataStorage::dslFlucQPosition;
777	+	if(storageLayout & DataStorage::dslVelocity) {
778	+	storageLayout |= DataStorage::dslFlucQVelocity;
779	+	}
780	+	if (storageLayout & DataStorage::dslForce) {
781	+	storageLayout |= DataStorage::dslFlucQForce;
782	+	}
783	+	}
784	+
785	+	// if the user has asked for them, make sure we've got the memory for the
786	+	// objects defined.
787	+
788	+	if (simParams->getOutputParticlePotential()) {
789	+	storageLayout |= DataStorage::dslParticlePot;
790	+	}
791	+
792	+	if (simParams->havePrintHeatFlux()) {
793	+	if (simParams->getPrintHeatFlux()) {
794	+	storageLayout |= DataStorage::dslParticlePot;
795	+	}
796	+	}
797	+
798	+	if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
799	+	storageLayout |= DataStorage::dslElectricField;
800	+	}
801	+
802	+	if (simParams->getOutputFluctuatingCharges()) {
803	+	storageLayout |= DataStorage::dslFlucQPosition;
804	+	storageLayout |= DataStorage::dslFlucQVelocity;
805	+	storageLayout |= DataStorage::dslFlucQForce;
806	+	}
807	+
808	+	info->setStorageLayout(storageLayout);
809	+
810	+	return storageLayout;
811	+	}
812	+
813		void SimCreator::setGlobalIndex(SimInfo *info) {
814		SimInfo::MoleculeIterator mi;
815		Molecule::AtomIterator ai;
816		Molecule::RigidBodyIterator ri;
817		Molecule::CutoffGroupIterator ci;
818	+	Molecule::BondIterator boi;
819	+	Molecule::BendIterator bei;
820	+	Molecule::TorsionIterator ti;
821	+	Molecule::InversionIterator ii;
822		Molecule::IntegrableObjectIterator  ioi;
823	<	Molecule * mol;
824	<	Atom * atom;
825	<	RigidBody * rb;
826	<	CutoffGroup * cg;
823	>	Molecule* mol;
824	>	Atom* atom;
825	>	RigidBody* rb;
826	>	CutoffGroup* cg;
827	>	Bond* bond;
828	>	Bend* bend;
829	>	Torsion* torsion;
830	>	Inversion* inversion;
831		int beginAtomIndex;
832		int beginRigidBodyIndex;
833		int beginCutoffGroupIndex;
834	+	int beginBondIndex;
835	+	int beginBendIndex;
836	+	int beginTorsionIndex;
837	+	int beginInversionIndex;
838		int nGlobalAtoms = info->getNGlobalAtoms();
839	<
638	<	/**@todo fixme */
639	<	#ifndef IS_MPI
839	>	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
840
841		beginAtomIndex = 0;
842	<	beginRigidBodyIndex = 0;
842	>	// The rigid body indices begin immediately after the atom indices:
843	>	beginRigidBodyIndex = info->getNGlobalAtoms();
844		beginCutoffGroupIndex = 0;
845	<
846	<	#else
847	<
848	<	int nproc;
849	<	int myNode;
850	<
650	<	myNode = worldRank;
651	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
652	<
653	<	std::vector < int > tmpAtomsInProc(nproc, 0);
654	<	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
655	<	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
656	<	std::vector < int > NumAtomsInProc(nproc, 0);
657	<	std::vector < int > NumRigidBodiesInProc(nproc, 0);
658	<	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
659	<
660	<	tmpAtomsInProc[myNode] = info->getNAtoms();
661	<	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
662	<	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
663	<
664	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
665	<	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
666	<	MPI_SUM, MPI_COMM_WORLD);
667	<	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
668	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
669	<	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
670	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
671	<
672	<	beginAtomIndex = 0;
673	<	beginRigidBodyIndex = 0;
674	<	beginCutoffGroupIndex = 0;
675	<
676	<	for(int i = 0; i < myNode; i++) {
677	<	beginAtomIndex += NumAtomsInProc[i];
678	<	beginRigidBodyIndex += NumRigidBodiesInProc[i];
679	<	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
680	<	}
681	<
682	<	#endif
683	<
684	<	//rigidbody's index begins right after atom's
685	<	beginRigidBodyIndex += info->getNGlobalAtoms();
686	<
687	<	for(mol = info->beginMolecule(mi); mol != NULL;
688	<	mol = info->nextMolecule(mi)) {
845	>	beginBondIndex = 0;
846	>	beginBendIndex = 0;
847	>	beginTorsionIndex = 0;
848	>	beginInversionIndex = 0;
849	>
850	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
851
852	<	//local index(index in DataStorge) of atom is important
853	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
854	<	atom->setGlobalIndex(beginAtomIndex++);
852	>	#ifdef IS_MPI
853	>	if (info->getMolToProc(i) == worldRank) {
854	>	#endif
855	>	// stuff to do if I own this molecule
856	>	mol = info->getMoleculeByGlobalIndex(i);
857	>
858	>	// The local index(index in DataStorge) of the atom is important:
859	>	for(atom = mol->beginAtom(ai); atom != NULL;
860	>	atom = mol->nextAtom(ai)) {
861	>	atom->setGlobalIndex(beginAtomIndex++);
862	>	}
863	>
864	>	for(rb = mol->beginRigidBody(ri); rb != NULL;
865	>	rb = mol->nextRigidBody(ri)) {
866	>	rb->setGlobalIndex(beginRigidBodyIndex++);
867	>	}
868	>
869	>	// The local index of other objects only depends on the order
870	>	// of traversal:
871	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
872	>	cg = mol->nextCutoffGroup(ci)) {
873	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
874	>	}
875	>	for(bond = mol->beginBond(boi); bond != NULL;
876	>	bond = mol->nextBond(boi)) {
877	>	bond->setGlobalIndex(beginBondIndex++);
878	>	}
879	>	for(bend = mol->beginBend(bei); bend != NULL;
880	>	bend = mol->nextBend(bei)) {
881	>	bend->setGlobalIndex(beginBendIndex++);
882	>	}
883	>	for(torsion = mol->beginTorsion(ti); torsion != NULL;
884	>	torsion = mol->nextTorsion(ti)) {
885	>	torsion->setGlobalIndex(beginTorsionIndex++);
886	>	}
887	>	for(inversion = mol->beginInversion(ii); inversion != NULL;
888	>	inversion = mol->nextInversion(ii)) {
889	>	inversion->setGlobalIndex(beginInversionIndex++);
890	>	}
891	>
892	>	#ifdef IS_MPI
893	>	}  else {
894	>
895	>	// stuff to do if I don't own this molecule
896	>
897	>	int stampId = info->getMoleculeStampId(i);
898	>	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
899	>
900	>	beginAtomIndex += stamp->getNAtoms();
901	>	beginRigidBodyIndex += stamp->getNRigidBodies();
902	>	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
903	>	beginBondIndex += stamp->getNBonds();
904	>	beginBendIndex += stamp->getNBends();
905	>	beginTorsionIndex += stamp->getNTorsions();
906	>	beginInversionIndex += stamp->getNInversions();
907		}
908	<
909	<	for(rb = mol->beginRigidBody(ri); rb != NULL;
910	<	rb = mol->nextRigidBody(ri)) {
911	<	rb->setGlobalIndex(beginRigidBodyIndex++);
698	<	}
699	<
700	<	//local index of cutoff group is trivial, it only depends on the order of travesing
701	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
702	<	cg = mol->nextCutoffGroup(ci)) {
703	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
704	<	}
705	<	}
706	<
908	>	#endif
909	>
910	>	} //end for(int i=0)
911	>
912		//fill globalGroupMembership
913		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
914	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
915	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	<
914	>	for(mol = info->beginMolecule(mi); mol != NULL;
915	>	mol = info->nextMolecule(mi)) {
916	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
917	>	cg = mol->nextCutoffGroup(ci)) {
918		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919		globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
920		}
921
922		}
923		}
924	<
924	>
925		#ifdef IS_MPI
926		// Since the globalGroupMembership has been zero filled and we've only
927		// poked values into the atoms we know, we can do an Allreduce
#	Line 723 | Line 929 | namespace oopse {
929		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
930		// docs said we could.
931		std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
932	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
932	>	MPI_Allreduce(&globalGroupMembership[0],
933	>	&tmpGroupMembership[0], nGlobalAtoms,
934		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
935	+	// MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
936	+	//                           &tmpGroupMembership[0], nGlobalAtoms,
937	+	//                           MPI::INT, MPI::SUM);
938		info->setGlobalGroupMembership(tmpGroupMembership);
939		#else
940		info->setGlobalGroupMembership(globalGroupMembership);
941		#endif
942
943		//fill molMembership
944	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
944	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
945	>	info->getNGlobalRigidBodies(), 0);
946
947	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
947	>	for(mol = info->beginMolecule(mi); mol != NULL;
948	>	mol = info->nextMolecule(mi)) {
949		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
950		globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
951		}
952	+	for (rb = mol->beginRigidBody(ri); rb != NULL;
953	+	rb = mol->nextRigidBody(ri)) {
954	+	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
955	+	}
956		}
957
958		#ifdef IS_MPI
959	<	std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
960	<
961	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
959	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
960	>	info->getNGlobalRigidBodies(), 0);
961	>	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
962	>	nGlobalAtoms + nGlobalRigidBodies,
963		MPI_INT, MPI_SUM, MPI_COMM_WORLD);
964	+	// MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
965	+	//                           nGlobalAtoms + nGlobalRigidBodies,
966	+	//                           MPI::INT, MPI::SUM);
967
968		info->setGlobalMolMembership(tmpMolMembership);
969		#else
#	Line 754 | Line 974 | namespace oopse {
974		// here the molecules are listed by their global indices.
975
976		std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
977	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
977	>	for (mol = info->beginMolecule(mi); mol != NULL;
978	>	mol = info->nextMolecule(mi)) {
979		nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
980		}
981
982		#ifdef IS_MPI
983		std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
984		MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
985	<	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
985	>	info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
986	>	// MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
987	>	//                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
988		#else
989		std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
990		#endif
#	Line 775 | Line 998 | namespace oopse {
998		}
999
1000		std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
1001	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
1001	>	for (mol = info->beginMolecule(mi); mol != NULL;
1002	>	mol = info->nextMolecule(mi)) {
1003		int myGlobalIndex = mol->getGlobalIndex();
1004		int globalIO = startingIOIndexForMol[myGlobalIndex];
1005	<	for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
1006	<	integrableObject = mol->nextIntegrableObject(ioi)) {
1007	<	integrableObject->setGlobalIntegrableObjectIndex(globalIO);
1008	<	IOIndexToIntegrableObject[globalIO] = integrableObject;
1005	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
1006	>	sd = mol->nextIntegrableObject(ioi)) {
1007	>	sd->setGlobalIntegrableObjectIndex(globalIO);
1008	>	IOIndexToIntegrableObject[globalIO] = sd;
1009		globalIO++;
1010		}
1011		}
1012	<
1012	>
1013		info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
1014
1015		}
1016
1017		void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
794	–	Globals* simParams;
795	–	simParams = info->getSimParams();
1018
797	–
1019		DumpReader reader(info, mdFileName);
1020		int nframes = reader.getNFrames();
1021
#	Line 808 | Line 1029 | namespace oopse {
1029		painCave.isFatal = 1;
1030		simError();
1031		}
811	–
1032		//copy the current snapshot to previous snapshot
1033		info->getSnapshotManager()->advance();
1034		}
1035
1036	<	} //end namespace oopse
1036	>	} //end namespace OpenMD
1037
1038

Comparing trunk/src/brains/SimCreator.cpp (property svn:keywords):
Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC

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