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root/OpenMD/branches/development/src/io/DumpWriter.cpp

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trunk/src/io/DumpWriter.cpp (file contents), Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	#define _LARGEFILE_SOURCE64
2	<	#define _FILE_OFFSET_BITS 64
1	>	/*
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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	>	#include "io/gzstream.hpp"
48	>	#include "io/Globals.hpp"
49
4	–	#include <string.h>
5	–	#include <iostream>
6	–	#include <fstream>
7	–	#include <algorithm>
8	–	#include <utility>
50
51		#ifdef IS_MPI
52		#include <mpi.h>
12	–	#include "brains/mpiSimulation.hpp"
13	–
14	–	namespace dWrite{
15	–	void DieDieDie( void );
16	–	}
17	–
18	–	using namespace dWrite;
53		#endif //is_mpi
54
55	<	#include "io/ReadWrite.hpp"
56	<	#include "utils/simError.h"
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60
61	<	entry_plug = the_entry_plug;
62	<
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_ = simParams->getCompressDumpFile();
63	>	needForceVector_ = simParams->getOutputForceVector();
64	>	needParticlePot_ = simParams->getOutputParticlePotential();
65	>	createDumpFile_ = true;
66	>	#ifdef HAVE_LIBZ
67	>	if (needCompression_) {
68	>	filename_ += ".gz";
69	>	eorFilename_ += ".gz";
70	>	}
71	>	#endif
72	>
73		#ifdef IS_MPI
74	<	if(worldRank == 0 ){
74	>
75	>	if (worldRank == 0) {
76		#endif // is_mpi
77	+
78	+	dumpFile_ = createOStream(filename_);
79
80	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
80	>	if (!dumpFile_) {
81	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
82	>	filename_.c_str());
83	>	painCave.isFatal = 1;
84	>	simError();
85	>	}
86
87	<	if( !dumpFile ){
87	>	#ifdef IS_MPI
88
36	–	sprintf( painCave.errMsg,
37	–	"Could not open \"%s\" for dump output.\n",
38	–	entry_plug->sampleName.c_str());
39	–	painCave.isFatal = 1;
40	–	simError();
89		}
90
91	<	#ifdef IS_MPI
91	>	#endif // is_mpi
92	>
93		}
94
46	–	//sort the local atoms by global index
47	–	sortByGlobalIndex();
48	–
49	–	sprintf( checkPointMsg,
50	–	"Sucessfully opened output file for dumping.\n");
51	–	MPIcheckPoint();
52	–	#endif // is_mpi
53	–	}
95
96	<	DumpWriter::~DumpWriter( ){
96	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
97	>	: info_(info), filename_(filename){
98
99	+	Globals* simParams = info->getSimParams();
100	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
101	+
102	+	needCompression_ = simParams->getCompressDumpFile();
103	+	needForceVector_ = simParams->getOutputForceVector();
104	+	createDumpFile_ = true;
105	+	#ifdef HAVE_LIBZ
106	+	if (needCompression_) {
107	+	filename_ += ".gz";
108	+	eorFilename_ += ".gz";
109	+	}
110	+	#endif
111	+
112		#ifdef IS_MPI
113	<	if(worldRank == 0 ){
113	>
114	>	if (worldRank == 0) {
115		#endif // is_mpi
116
117	<	dumpFile.close();
117	>
118	>	dumpFile_ = createOStream(filename_);
119
120	<	#ifdef IS_MPI
121	<	}
122	<	#endif // is_mpi
123	<	}
120	>	if (!dumpFile_) {
121	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122	>	filename_.c_str());
123	>	painCave.isFatal = 1;
124	>	simError();
125	>	}
126
127		#ifdef IS_MPI
128
129	<	/**
71	<	* A hook function to load balancing
72	<	*/
129	>	}
130
131	<	void DumpWriter::update(){
75	<	sortByGlobalIndex();
76	<	}
77	<
78	<	/**
79	<	* Auxiliary sorting function
80	<	*/
81	<
82	<	bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83	<	return p1.second < p2.second;
84	<	}
131	>	#endif // is_mpi
132
133	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
133	>	}
134
135	<	for(int i = 0; i < entry_plug->n_mol;i++)
136	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
137	<
138	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
139	<	}
140	<
135	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
136	>	: info_(info), filename_(filename){
137	>
138	>	Globals* simParams = info->getSimParams();
139	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
140	>
141	>	needCompression_ = simParams->getCompressDumpFile();
142	>	needForceVector_ = simParams->getOutputForceVector();
143	>	needParticlePot_ = simParams->getOutputParticlePotential();
144	>
145	>	#ifdef HAVE_LIBZ
146	>	if (needCompression_) {
147	>	filename_ += ".gz";
148	>	eorFilename_ += ".gz";
149	>	}
150		#endif
151	+
152	+	#ifdef IS_MPI
153	+
154	+	if (worldRank == 0) {
155	+	#endif // is_mpi
156	+
157	+	createDumpFile_ = writeDumpFile;
158	+	if (createDumpFile_) {
159	+	dumpFile_ = createOStream(filename_);
160	+
161	+	if (!dumpFile_) {
162	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
163	+	filename_.c_str());
164	+	painCave.isFatal = 1;
165	+	simError();
166	+	}
167	+	}
168	+	#ifdef IS_MPI
169	+
170	+	}
171
172	<	void DumpWriter::writeDump(double currentTime){
172	>
173	>	#endif // is_mpi
174	>
175	>	}
176
177	<	ofstream finalOut;
105	<	vector<ofstream*> fileStreams;
177	>	DumpWriter::~DumpWriter() {
178
179		#ifdef IS_MPI
180	<	if(worldRank == 0 ){
181	<	#endif
110	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
111	<	if( !finalOut ){
112	<	sprintf( painCave.errMsg,
113	<	"Could not open \"%s\" for final dump output.\n",
114	<	entry_plug->finalName.c_str() );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
118	<	#ifdef IS_MPI
119	<	}
180	>
181	>	if (worldRank == 0) {
182		#endif // is_mpi
183	+	if (createDumpFile_){
184	+	writeClosing(*dumpFile_);
185	+	delete dumpFile_;
186	+	}
187	+	#ifdef IS_MPI
188
189	<	fileStreams.push_back(&finalOut);
123	<	fileStreams.push_back(&dumpFile);
189	>	}
190
191	<	writeFrame(fileStreams, currentTime);
191	>	#endif // is_mpi
192
193	<	#ifdef IS_MPI
128	<	finalOut.close();
129	<	#endif
130	<
131	<	}
193	>	}
194
195	<	void DumpWriter::writeFinal(double currentTime){
195	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
196
197	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
197	>	char buffer[1024];
198
199	<	#ifdef IS_MPI
139	<	if(worldRank == 0 ){
140	<	#endif // is_mpi
199	>	os << "    <FrameData>\n";
200
201	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
201	>	RealType currentTime = s->getTime();
202
203	<	if( !finalOut ){
203	>	if (isinf(currentTime) || isnan(currentTime)) {
204		sprintf( painCave.errMsg,
205	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
205	>	"DumpWriter detected a numerical error writing the time");
206		painCave.isFatal = 1;
207		simError();
208		}
209	+
210	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
211	+	os << buffer;
212
213	<	#ifdef IS_MPI
214	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
213	>	Mat3x3d hmat;
214	>	hmat = s->getHmat();
215
216	<	#ifdef IS_MPI
217	<	finalOut.close();
218	<	#endif
219	<
220	<	}
221	<
222	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
223	<
224	<	const int BUFFERSIZE = 2000;
225	<	const int MINIBUFFERSIZE = 100;
226	<
227	<	char tempBuffer[BUFFERSIZE];
228	<	char writeLine[BUFFERSIZE];
229	<
230	<	int i;
231	<	unsigned int k;
216	>	for (unsigned int i = 0; i < 3; i++) {
217	>	for (unsigned int j = 0; j < 3; j++) {
218	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
219	>	sprintf( painCave.errMsg,
220	>	"DumpWriter detected a numerical error writing the box");
221	>	painCave.isFatal = 1;
222	>	simError();
223	>	}
224	>	}
225	>	}
226	>
227	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
228	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
229	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
230	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
231	>	os << buffer;
232
233	<	#ifdef IS_MPI
234	<
235	<	/*********************************************************************
236	<	* Documentation?  You want DOCUMENTATION?
237	<	*
238	<	* Why all the potatoes below?
239	<	*
240	<	* To make a long story short, the original version of DumpWriter
241	<	* worked in the most inefficient way possible.  Node 0 would
242	<	* poke each of the node for an individual atom's formatted data
243	<	* as node 0 worked its way down the global index. This was particularly
187	<	* inefficient since the method blocked all processors at every atom
188	<	* (and did it twice!).
189	<	*
190	<	* An intermediate version of DumpWriter could be described from Node
191	<	* zero's perspective as follows:
192	<	*
193	<	*  1) Have 100 of your friends stand in a circle.
194	<	*  2) When you say go, have all of them start tossing potatoes at
195	<	*     you (one at a time).
196	<	*  3) Catch the potatoes.
197	<	*
198	<	* It was an improvement, but MPI has buffers and caches that could
199	<	* best be described in this analogy as "potato nets", so there's no
200	<	* need to block the processors atom-by-atom.
201	<	*
202	<	* This new and improved DumpWriter works in an even more efficient
203	<	* way:
204	<	*
205	<	*  1) Have 100 of your friend stand in a circle.
206	<	*  2) When you say go, have them start tossing 5-pound bags of
207	<	*     potatoes at you.
208	<	*  3) Once you've caught a friend's bag of potatoes,
209	<	*     toss them a spud to let them know they can toss another bag.
210	<	*
211	<	* How's THAT for documentation?
212	<	*
213	<	*********************************************************************/
233	>	RealType chi = s->getChi();
234	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
235	>	if (isinf(chi) || isnan(chi) ||
236	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the thermostat");
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
243	>	os << buffer;
244
245	<	int *potatoes;
246	<	int myPotato;
245	>	Mat3x3d eta;
246	>	eta = s->getEta();
247
248	<	int nProc;
249	<	int j, which_node, done, which_atom, local_index, currentIndex;
250	<	double atomData[13];
251	<	int isDirectional;
252	<	char* atomTypeString;
253	<	char MPIatomTypeString[MINIBUFFERSIZE];
254	<	int nObjects;
255	<	int msgLen; // the length of message actually recieved at master nodes
256	<	#endif //is_mpi
248	>	for (unsigned int i = 0; i < 3; i++) {
249	>	for (unsigned int j = 0; j < 3; j++) {
250	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
251	>	sprintf( painCave.errMsg,
252	>	"DumpWriter detected a numerical error writing the barostat");
253	>	painCave.isFatal = 1;
254	>	simError();
255	>	}
256	>	}
257	>	}
258
259	<	double q[4], ji[3];
260	<	DirectionalAtom* dAtom;
261	<	double pos[3], vel[3];
262	<	int nTotObjects;
263	<	StuntDouble* sd;
233	<	char* molName;
234	<	vector<StuntDouble*> integrableObjects;
235	<	vector<StuntDouble*>::iterator iter;
236	<	nTotObjects = entry_plug->getTotIntegrableObjects();
237	<	#ifndef IS_MPI
238	<
239	<	for(k = 0; k < outFile.size(); k++){
240	<	*outFile[k] << nTotObjects << "\n";
259	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
260	>	eta(0, 0), eta(1, 0), eta(2, 0),
261	>	eta(0, 1), eta(1, 1), eta(2, 1),
262	>	eta(0, 2), eta(1, 2), eta(2, 2));
263	>	os << buffer;
264
265	<	*outFile[k] << currentTime << ";\t"
243	<	<< entry_plug->Hmat[0][0] << "\t"
244	<	<< entry_plug->Hmat[1][0] << "\t"
245	<	<< entry_plug->Hmat[2][0] << ";\t"
246	<
247	<	<< entry_plug->Hmat[0][1] << "\t"
248	<	<< entry_plug->Hmat[1][1] << "\t"
249	<	<< entry_plug->Hmat[2][1] << ";\t"
250	<
251	<	<< entry_plug->Hmat[0][2] << "\t"
252	<	<< entry_plug->Hmat[1][2] << "\t"
253	<	<< entry_plug->Hmat[2][2] << ";";
254	<
255	<	//write out additional parameters, such as chi and eta
256	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
265	>	os << "    </FrameData>\n";
266		}
258	–
259	–	for( i=0; i< entry_plug->n_mol; i++ ){
267
268	<	integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262	<	molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263	<
264	<	for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265	<	sd = *iter;
266	<	sd->getPos(pos);
267	<	sd->getVel(vel);
268	>	void DumpWriter::writeFrame(std::ostream& os) {
269
270	<	sprintf( tempBuffer,
271	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
272	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
270	>	#ifdef IS_MPI
271	>	MPI_Status istatus;
272	>	#endif
273
274	<	if( sd->isDirectional() ){
274	>	Molecule* mol;
275	>	StuntDouble* integrableObject;
276	>	SimInfo::MoleculeIterator mi;
277	>	Molecule::IntegrableObjectIterator ii;
278
279	<	sd->getQ( q );
280	<	sd->getJ( ji );
279	>	#ifndef IS_MPI
280	>	os << "  <Snapshot>\n";
281	>
282	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
283
284	<	sprintf( tempBuffer,
285	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286	<	q[0],
287	<	q[1],
288	<	q[2],
289	<	q[3],
290	<	ji[0],
291	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
284	>	os << "    <StuntDoubles>\n";
285	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
286	>
287	>
288	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(ii)) {
290	>	os << prepareDumpLine(integrableObject);
291	>
292		}
293	<	else
294	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
293	>	}
294	>	os << "    </StuntDoubles>\n";
295
296	<	for(k = 0; k < outFile.size(); k++)
297	<	*outFile[k] << writeLine;
296	>	os << "  </Snapshot>\n";
297	>
298	>	os.flush();
299	>	#else
300	>	//every node prepares the dump lines for integrable objects belong to itself
301	>	std::string buffer;
302	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
303	>
304	>
305	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(ii)) {
307	>	buffer += prepareDumpLine(integrableObject);
308	>	}
309		}
310
311	<	}
311	>	const int masterNode = 0;
312	>	int nProc;
313	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
314	>	if (worldRank == masterNode) {
315	>	os << "  <Snapshot>\n";
316	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
317	>	os << "    <StuntDoubles>\n";
318	>
319	>	os << buffer;
320
321	<	#else // is_mpi
321	>	for (int i = 1; i < nProc; ++i) {
322
323	<	/* code to find maximum tag value */
324	<
309	<	int *tagub, flag, MAXTAG;
310	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311	<	if (flag) {
312	<	MAXTAG = *tagub;
313	<	} else {
314	<	MAXTAG = 32767;
315	<	}
323	>	// receive the length of the string buffer that was
324	>	// prepared by processor i
325
326	<	int haveError;
326	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
327	>	int recvLength;
328	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
329	>	char* recvBuffer = new char[recvLength];
330	>	if (recvBuffer == NULL) {
331	>	} else {
332	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
333	>	os << recvBuffer;
334	>	delete [] recvBuffer;
335	>	}
336	>	}
337	>	os << "    </StuntDoubles>\n";
338	>
339	>	os << "  </Snapshot>\n";
340	>	os.flush();
341	>	} else {
342	>	int sendBufferLength = buffer.size() + 1;
343	>	int myturn = 0;
344	>	for (int i = 1; i < nProc; ++i){
345	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
346	>	if (myturn == worldRank){
347	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
348	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
349	>	}
350	>	}
351	>	}
352
353	<	MPI_Status istatus;
320	<	int nCurObj;
321	<	int *MolToProcMap = mpiSim->getMolToProcMap();
353	>	#endif // is_mpi
354
355	<	// write out header and node 0's coordinates
355	>	}
356
357	<	if( worldRank == 0 ){
357	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
358	>
359	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
360	>	std::string type("pv");
361	>	std::string line;
362	>	char tempBuffer[4096];
363
364	<	// Node 0 needs a list of the magic potatoes for each processor;
364	>	Vector3d pos;
365	>	Vector3d vel;
366	>	pos = integrableObject->getPos();
367
368	<	nProc = mpiSim->getNProcessors();
369	<	potatoes = new int[nProc];
370	<
371	<	//write out the comment lines
372	<	for (i = 0; i < nProc; i++)
373	<	potatoes[i] = 0;
374	<
375	<	for(k = 0; k < outFile.size(); k++){
337	<	*outFile[k] << nTotObjects << "\n";
338	<
339	<	*outFile[k] << currentTime << ";\t"
340	<	<< entry_plug->Hmat[0][0] << "\t"
341	<	<< entry_plug->Hmat[1][0] << "\t"
342	<	<< entry_plug->Hmat[2][0] << ";\t"
343	<
344	<	<< entry_plug->Hmat[0][1] << "\t"
345	<	<< entry_plug->Hmat[1][1] << "\t"
346	<	<< entry_plug->Hmat[2][1] << ";\t"
347	<
348	<	<< entry_plug->Hmat[0][2] << "\t"
349	<	<< entry_plug->Hmat[1][2] << "\t"
350	<	<< entry_plug->Hmat[2][2] << ";";
351	<
352	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters()
353	<	<< endl;
368	>	if (isinf(pos[0]) || isnan(pos[0]) ||
369	>	isinf(pos[1]) || isnan(pos[1]) ||
370	>	isinf(pos[2]) || isnan(pos[2]) ) {
371	>	sprintf( painCave.errMsg,
372	>	"DumpWriter detected a numerical error writing the position"
373	>	" for object %d", index);
374	>	painCave.isFatal = 1;
375	>	simError();
376		}
355	–
356	–	currentIndex = 0;
357	–
358	–	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
359	–
360	–	// Get the Node number which has this atom;
361	–
362	–	which_node = MolToProcMap[i];
363	–
364	–	if (which_node != 0) {
365	–
366	–	if (potatoes[which_node] + 1 >= MAXTAG) {
367	–	// The potato was going to exceed the maximum value,
368	–	// so wrap this processor potato back to 0:
377
378	<	potatoes[which_node] = 0;
371	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
372	<	MPI_COMM_WORLD);
373	<
374	<	}
378	>	vel = integrableObject->getVel();
379
380	<	myPotato = potatoes[which_node];
380	>	if (isinf(vel[0]) || isnan(vel[0]) ||
381	>	isinf(vel[1]) || isnan(vel[1]) ||
382	>	isinf(vel[2]) || isnan(vel[2]) ) {
383	>	sprintf( painCave.errMsg,
384	>	"DumpWriter detected a numerical error writing the velocity"
385	>	" for object %d", index);
386	>	painCave.isFatal = 1;
387	>	simError();
388	>	}
389
390	<	//recieve the number of integrableObject in current molecule
391	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
392	<	myPotato, MPI_COMM_WORLD, &istatus);
393	<	myPotato++;
382	<
383	<	for(int l = 0; l < nCurObj; l++){
390	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
391	>	pos[0], pos[1], pos[2],
392	>	vel[0], vel[1], vel[2]);
393	>	line += tempBuffer;
394
395	<	if (potatoes[which_node] + 2 >= MAXTAG) {
396	<	// The potato was going to exceed the maximum value,
397	<	// so wrap this processor potato back to 0:
395	>	if (integrableObject->isDirectional()) {
396	>	type += "qj";
397	>	Quat4d q;
398	>	Vector3d ji;
399	>	q = integrableObject->getQ();
400
401	<	potatoes[which_node] = 0;
402	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
403	<
404	<	}
401	>	if (isinf(q[0]) || isnan(q[0]) ||
402	>	isinf(q[1]) || isnan(q[1]) ||
403	>	isinf(q[2]) || isnan(q[2]) ||
404	>	isinf(q[3]) || isnan(q[3]) ) {
405	>	sprintf( painCave.errMsg,
406	>	"DumpWriter detected a numerical error writing the quaternion"
407	>	" for object %d", index);
408	>	painCave.isFatal = 1;
409	>	simError();
410	>	}
411
412	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395	<	myPotato, MPI_COMM_WORLD, &istatus);
412	>	ji = integrableObject->getJ();
413
414	<	atomTypeString = MPIatomTypeString;
414	>	if (isinf(ji[0]) || isnan(ji[0]) ||
415	>	isinf(ji[1]) || isnan(ji[1]) ||
416	>	isinf(ji[2]) || isnan(ji[2]) ) {
417	>	sprintf( painCave.errMsg,
418	>	"DumpWriter detected a numerical error writing the angular"
419	>	" momentum for object %d", index);
420	>	painCave.isFatal = 1;
421	>	simError();
422	>	}
423
424	<	myPotato++;
424	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
425	>	q[0], q[1], q[2], q[3],
426	>	ji[0], ji[1], ji[2]);
427	>	line += tempBuffer;
428	>	}
429
430	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
431	<	myPotato++;
430	>	if (needForceVector_) {
431	>	type += "f";
432	>	Vector3d frc;
433
434	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
434	>	frc = integrableObject->getFrc();
435
436	<	if(msgLen  == 13)
437	<	isDirectional = 1;
438	<	else
439	<	isDirectional = 0;
440	<
441	<	// If we've survived to here, format the line:
442	<
443	<	if (!isDirectional) {
414	<
415	<	sprintf( writeLine,
416	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
417	<	atomTypeString,
418	<	atomData[0],
419	<	atomData[1],
420	<	atomData[2],
421	<	atomData[3],
422	<	atomData[4],
423	<	atomData[5]);
424	<
425	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
426	<
427	<	}
428	<	else {
429	<
430	<	sprintf( writeLine,
431	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
432	<	atomTypeString,
433	<	atomData[0],
434	<	atomData[1],
435	<	atomData[2],
436	<	atomData[3],
437	<	atomData[4],
438	<	atomData[5],
439	<	atomData[6],
440	<	atomData[7],
441	<	atomData[8],
442	<	atomData[9],
443	<	atomData[10],
444	<	atomData[11],
445	<	atomData[12]);
446	<
447	<	}
448	<
449	<	for(k = 0; k < outFile.size(); k++)
450	<	*outFile[k] << writeLine;
451	<
452	<	}// end for(int l =0)
453	<	potatoes[which_node] = myPotato;
454	<
436	>	if (isinf(frc[0]) || isnan(frc[0]) ||
437	>	isinf(frc[1]) || isnan(frc[1]) ||
438	>	isinf(frc[2]) || isnan(frc[2]) ) {
439	>	sprintf( painCave.errMsg,
440	>	"DumpWriter detected a numerical error writing the force"
441	>	" for object %d", index);
442	>	painCave.isFatal = 1;
443	>	simError();
444		}
445	<	else {
446	<
447	<	haveError = 0;
445	>	sprintf(tempBuffer, " %13e %13e %13e",
446	>	frc[0], frc[1], frc[2]);
447	>	line += tempBuffer;
448	>
449	>	if (integrableObject->isDirectional()) {
450	>	type += "t";
451	>	Vector3d trq;
452
453	<	local_index = indexArray[currentIndex].first;
461	<
462	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
463	<
464	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
465	<	sd = *iter;
466	<	atomTypeString = sd->getType();
467	<
468	<	sd->getPos(pos);
469	<	sd->getVel(vel);
470	<
471	<	atomData[0] = pos[0];
472	<	atomData[1] = pos[1];
473	<	atomData[2] = pos[2];
474	<
475	<	atomData[3] = vel[0];
476	<	atomData[4] = vel[1];
477	<	atomData[5] = vel[2];
478	<
479	<	isDirectional = 0;
480	<
481	<	if( sd->isDirectional() ){
482	<
483	<	isDirectional = 1;
484	<
485	<	sd->getQ( q );
486	<	sd->getJ( ji );
487	<
488	<	for (int j = 0; j < 6 ; j++)
489	<	atomData[j] = atomData[j];
490	<
491	<	atomData[6] = q[0];
492	<	atomData[7] = q[1];
493	<	atomData[8] = q[2];
494	<	atomData[9] = q[3];
495	<
496	<	atomData[10] = ji[0];
497	<	atomData[11] = ji[1];
498	<	atomData[12] = ji[2];
499	<	}
500	<
501	<	// If we've survived to here, format the line:
502	<
503	<	if (!isDirectional) {
504	<
505	<	sprintf( writeLine,
506	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
507	<	atomTypeString,
508	<	atomData[0],
509	<	atomData[1],
510	<	atomData[2],
511	<	atomData[3],
512	<	atomData[4],
513	<	atomData[5]);
514	<
515	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
516	<
517	<	}
518	<	else {
519	<
520	<	sprintf( writeLine,
521	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
522	<	atomTypeString,
523	<	atomData[0],
524	<	atomData[1],
525	<	atomData[2],
526	<	atomData[3],
527	<	atomData[4],
528	<	atomData[5],
529	<	atomData[6],
530	<	atomData[7],
531	<	atomData[8],
532	<	atomData[9],
533	<	atomData[10],
534	<	atomData[11],
535	<	atomData[12]);
536	<
537	<	}
538	<
539	<	for(k = 0; k < outFile.size(); k++)
540	<	*outFile[k] << writeLine;
541	<
542	<
543	<	}//end for(iter = integrableObject.begin())
453	>	trq = integrableObject->getTrq();
454
455	<	currentIndex++;
456	<	}
455	>	if (isinf(trq[0]) || isnan(trq[0]) ||
456	>	isinf(trq[1]) || isnan(trq[1]) ||
457	>	isinf(trq[2]) || isnan(trq[2]) ) {
458	>	sprintf( painCave.errMsg,
459	>	"DumpWriter detected a numerical error writing the torque"
460	>	" for object %d", index);
461	>	painCave.isFatal = 1;
462	>	simError();
463	>	}
464	>
465	>	sprintf(tempBuffer, " %13e %13e %13e",
466	>	trq[0], trq[1], trq[2]);
467	>	line += tempBuffer;
468	>	}
469	>	}
470	>	if (needParticlePot_) {
471	>	type += "u";
472	>	RealType particlePot;
473
474	<	}//end for(i = 0; i < mpiSim->getNmol())
474	>	particlePot = integrableObject->getParticlePot();
475	>
476	>	if (isinf(particlePot) || isnan(particlePot)) {
477	>	sprintf( painCave.errMsg,
478	>	"DumpWriter detected a numerical error writing the particle "
479	>	" potential for object %d", index);
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	}
483	>	sprintf(tempBuffer, " %13e", particlePot);
484	>	line += tempBuffer;
485	>	}
486
487	<	for(k = 0; k < outFile.size(); k++)
488	<	outFile[k]->flush();
489	<
553	<	sprintf( checkPointMsg,
554	<	"Sucessfully took a dump.\n");
555	<
556	<	MPIcheckPoint();
557	<
558	<	delete[] potatoes;
559	<
560	<	} else {
487	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
488	>	return std::string(tempBuffer);
489	>	}
490
491	<	// worldRank != 0, so I'm a remote node.
491	>	void DumpWriter::writeDump() {
492	>	writeFrame(*dumpFile_);
493	>	}
494
495	<	// Set my magic potato to 0:
496	<
566	<	myPotato = 0;
567	<	currentIndex = 0;
495	>	void DumpWriter::writeEor() {
496	>	std::ostream* eorStream;
497
498	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
499	<
500	<	// Am I the node which has this integrableObject?
572	<
573	<	if (MolToProcMap[i] == worldRank) {
498	>	#ifdef IS_MPI
499	>	if (worldRank == 0) {
500	>	#endif // is_mpi
501
502	+	eorStream = createOStream(eorFilename_);
503
504	<	if (myPotato + 1 >= MAXTAG) {
505	<
506	<	// The potato was going to exceed the maximum value,
579	<	// so wrap this processor potato back to 0 (and block until
580	<	// node 0 says we can go:
581	<
582	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
583	<
584	<	}
504	>	#ifdef IS_MPI
505	>	}
506	>	#endif // is_mpi
507
508	<	local_index = indexArray[currentIndex].first;
587	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
588	<
589	<	nCurObj = integrableObjects.size();
590	<
591	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
592	<	myPotato, MPI_COMM_WORLD);
593	<	myPotato++;
508	>	writeFrame(*eorStream);
509
510	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
510	>	#ifdef IS_MPI
511	>	if (worldRank == 0) {
512	>	#endif // is_mpi
513	>	writeClosing(*eorStream);
514	>	delete eorStream;
515	>	#ifdef IS_MPI
516	>	}
517	>	#endif // is_mpi
518
519	<	if (myPotato + 2 >= MAXTAG) {
598	<
599	<	// The potato was going to exceed the maximum value,
600	<	// so wrap this processor potato back to 0 (and block until
601	<	// node 0 says we can go:
602	<
603	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
604	<
605	<	}
606	<
607	<	sd = *iter;
608	<
609	<	atomTypeString = sd->getType();
519	>	}
520
611	–	sd->getPos(pos);
612	–	sd->getVel(vel);
521
522	<	atomData[0] = pos[0];
523	<	atomData[1] = pos[1];
524	<	atomData[2] = pos[2];
522	>	void DumpWriter::writeDumpAndEor() {
523	>	std::vector<std::streambuf*> buffers;
524	>	std::ostream* eorStream;
525	>	#ifdef IS_MPI
526	>	if (worldRank == 0) {
527	>	#endif // is_mpi
528
529	<	atomData[3] = vel[0];
619	<	atomData[4] = vel[1];
620	<	atomData[5] = vel[2];
621	<
622	<	isDirectional = 0;
529	>	buffers.push_back(dumpFile_->rdbuf());
530
531	<	if( sd->isDirectional() ){
531	>	eorStream = createOStream(eorFilename_);
532
533	<	isDirectional = 1;
534	<
535	<	sd->getQ( q );
536	<	sd->getJ( ji );
537	<
631	<
632	<	atomData[6] = q[0];
633	<	atomData[7] = q[1];
634	<	atomData[8] = q[2];
635	<	atomData[9] = q[3];
636	<
637	<	atomData[10] = ji[0];
638	<	atomData[11] = ji[1];
639	<	atomData[12] = ji[2];
640	<	}
533	>	buffers.push_back(eorStream->rdbuf());
534	>
535	>	#ifdef IS_MPI
536	>	}
537	>	#endif // is_mpi
538
539	<
540	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
539	>	TeeBuf tbuf(buffers.begin(), buffers.end());
540	>	std::ostream os(&tbuf);
541
542	<	// null terminate the string before sending (just in case):
646	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
542	>	writeFrame(os);
543
544	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
545	<	myPotato, MPI_COMM_WORLD);
546	<
547	<	myPotato++;
548	<
549	<	if (isDirectional) {
550	<
551	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
656	<	myPotato, MPI_COMM_WORLD);
657	<
658	<	} else {
659	<
660	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
661	<	myPotato, MPI_COMM_WORLD);
662	<	}
663	<
664	<	myPotato++;
665	<
666	<	}
667	<
668	<	currentIndex++;
669	<
670	<	}
671	<
672	<	}
673	<
674	<	sprintf( checkPointMsg,
675	<	"Successfully took a dump.\n");
676	<	MPIcheckPoint();
544	>	#ifdef IS_MPI
545	>	if (worldRank == 0) {
546	>	#endif // is_mpi
547	>	writeClosing(*eorStream);
548	>	delete eorStream;
549	>	#ifdef IS_MPI
550	>	}
551	>	#endif // is_mpi
552
553		}
679	–
680	–	#endif // is_mpi
681	–	}
554
555	<	#ifdef IS_MPI
555	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
556
557	<	// a couple of functions to let us escape the write loop
557	>	std::ostream* newOStream;
558	>	#ifdef HAVE_LIBZ
559	>	if (needCompression_) {
560	>	newOStream = new ogzstream(filename.c_str());
561	>	} else {
562	>	newOStream = new std::ofstream(filename.c_str());
563	>	}
564	>	#else
565	>	newOStream = new std::ofstream(filename.c_str());
566	>	#endif
567	>	//write out MetaData first
568	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
569	>	(*newOStream) << "  <MetaData>" << std::endl;
570	>	(*newOStream) << info_->getRawMetaData();
571	>	(*newOStream) << "  </MetaData>" << std::endl;
572	>	return newOStream;
573	>	}
574
575	<	void dWrite::DieDieDie( void ){
575	>	void DumpWriter::writeClosing(std::ostream& os) {
576
577	<	MPI_Finalize();
578	<	exit (0);
579	<	}
577	>	os << "</OpenMD>\n";
578	>	os.flush();
579	>	}
580
581	<	#endif //is_mpi
581	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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