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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 1712 by gezelter, Sat May 19 13:30:21 2012 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	>	cerr << "DW npp = " << needParticlePot_ << "\n";
66	>	createDumpFile_ = true;
67	>	#ifdef HAVE_LIBZ
68	>	if (needCompression_) {
69	>	filename_ += ".gz";
70	>	eorFilename_ += ".gz";
71	>	}
72	>	#endif
73	>
74		#ifdef IS_MPI
75	<	if(worldRank == 0 ){
75	>
76	>	if (worldRank == 0) {
77		#endif // is_mpi
78	+
79	+	dumpFile_ = createOStream(filename_);
80
81	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
81	>	if (!dumpFile_) {
82	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
83	>	filename_.c_str());
84	>	painCave.isFatal = 1;
85	>	simError();
86	>	}
87
88	<	if( !dumpFile ){
88	>	#ifdef IS_MPI
89
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();
90		}
91
92	<	#ifdef IS_MPI
92	>	#endif // is_mpi
93	>
94		}
95
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	–	}
96
97	<	DumpWriter::~DumpWriter( ){
97	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
98	>	: info_(info), filename_(filename){
99
100	+	Globals* simParams = info->getSimParams();
101	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
102	+
103	+	needCompression_ = simParams->getCompressDumpFile();
104	+	needForceVector_ = simParams->getOutputForceVector();
105	+	needParticlePot_ = simParams->getOutputParticlePotential();
106	+	createDumpFile_ = true;
107	+	#ifdef HAVE_LIBZ
108	+	if (needCompression_) {
109	+	filename_ += ".gz";
110	+	eorFilename_ += ".gz";
111	+	}
112	+	#endif
113	+
114		#ifdef IS_MPI
115	<	if(worldRank == 0 ){
115	>
116	>	if (worldRank == 0) {
117		#endif // is_mpi
118
119	<	dumpFile.close();
119	>
120	>	dumpFile_ = createOStream(filename_);
121
122	<	#ifdef IS_MPI
123	<	}
124	<	#endif // is_mpi
125	<	}
122	>	if (!dumpFile_) {
123	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
124	>	filename_.c_str());
125	>	painCave.isFatal = 1;
126	>	simError();
127	>	}
128
129		#ifdef IS_MPI
130
131	<	/**
71	<	* A hook function to load balancing
72	<	*/
131	>	}
132
133	<	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	<	}
133	>	#endif // is_mpi
134
135	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
135	>	}
136
137	<	for(int i = 0; i < entry_plug->n_mol;i++)
138	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
139	<
140	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
141	<	}
142	<
137	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
138	>	: info_(info), filename_(filename){
139	>
140	>	Globals* simParams = info->getSimParams();
141	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
142	>
143	>	needCompression_ = simParams->getCompressDumpFile();
144	>	needForceVector_ = simParams->getOutputForceVector();
145	>	needParticlePot_ = simParams->getOutputParticlePotential();
146	>
147	>	#ifdef HAVE_LIBZ
148	>	if (needCompression_) {
149	>	filename_ += ".gz";
150	>	eorFilename_ += ".gz";
151	>	}
152		#endif
153	+
154	+	#ifdef IS_MPI
155	+
156	+	if (worldRank == 0) {
157	+	#endif // is_mpi
158	+
159	+	createDumpFile_ = writeDumpFile;
160	+	if (createDumpFile_) {
161	+	dumpFile_ = createOStream(filename_);
162	+
163	+	if (!dumpFile_) {
164	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
165	+	filename_.c_str());
166	+	painCave.isFatal = 1;
167	+	simError();
168	+	}
169	+	}
170	+	#ifdef IS_MPI
171	+
172	+	}
173
174	<	void DumpWriter::writeDump(double currentTime){
174	>
175	>	#endif // is_mpi
176	>
177	>	}
178
179	<	ofstream finalOut;
105	<	vector<ofstream*> fileStreams;
179	>	DumpWriter::~DumpWriter() {
180
181		#ifdef IS_MPI
182	<	if(worldRank == 0 ){
183	<	#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	<	}
182	>
183	>	if (worldRank == 0) {
184		#endif // is_mpi
185	+	if (createDumpFile_){
186	+	writeClosing(*dumpFile_);
187	+	delete dumpFile_;
188	+	}
189	+	#ifdef IS_MPI
190
191	<	fileStreams.push_back(&finalOut);
123	<	fileStreams.push_back(&dumpFile);
191	>	}
192
193	<	writeFrame(fileStreams, currentTime);
193	>	#endif // is_mpi
194
195	<	#ifdef IS_MPI
128	<	finalOut.close();
129	<	#endif
130	<
131	<	}
195	>	}
196
197	<	void DumpWriter::writeFinal(double currentTime){
197	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
198
199	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
199	>	char buffer[1024];
200
201	<	#ifdef IS_MPI
139	<	if(worldRank == 0 ){
140	<	#endif // is_mpi
201	>	os << "    <FrameData>\n";
202
203	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
203	>	RealType currentTime = s->getTime();
204
205	<	if( !finalOut ){
205	>	if (isinf(currentTime) || isnan(currentTime)) {
206		sprintf( painCave.errMsg,
207	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
207	>	"DumpWriter detected a numerical error writing the time");
208		painCave.isFatal = 1;
209		simError();
210		}
211	+
212	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
213	+	os << buffer;
214
215	<	#ifdef IS_MPI
216	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
215	>	Mat3x3d hmat;
216	>	hmat = s->getHmat();
217
218	<	#ifdef IS_MPI
219	<	finalOut.close();
220	<	#endif
221	<
222	<	}
223	<
224	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
225	<
226	<	const int BUFFERSIZE = 2000;
227	<	const int MINIBUFFERSIZE = 100;
228	<
229	<	char tempBuffer[BUFFERSIZE];
230	<	char writeLine[BUFFERSIZE];
231	<
232	<	int i;
233	<	unsigned int k;
218	>	for (unsigned int i = 0; i < 3; i++) {
219	>	for (unsigned int j = 0; j < 3; j++) {
220	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
221	>	sprintf( painCave.errMsg,
222	>	"DumpWriter detected a numerical error writing the box");
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	}
227	>	}
228	>
229	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
230	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
231	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
232	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
233	>	os << buffer;
234
235	<	#ifdef IS_MPI
236	<
237	<	/*********************************************************************
238	<	* Documentation?  You want DOCUMENTATION?
239	<	*
240	<	* Why all the potatoes below?
241	<	*
242	<	* To make a long story short, the original version of DumpWriter
243	<	* worked in the most inefficient way possible.  Node 0 would
244	<	* poke each of the node for an individual atom's formatted data
245	<	* 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	<	*********************************************************************/
235	>	RealType chi = s->getChi();
236	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
237	>	if (isinf(chi) || isnan(chi) ||
238	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
239	>	sprintf( painCave.errMsg,
240	>	"DumpWriter detected a numerical error writing the thermostat");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
245	>	os << buffer;
246
247	<	int *potatoes;
248	<	int myPotato;
247	>	Mat3x3d eta;
248	>	eta = s->getEta();
249
250	<	int nProc;
251	<	int j, which_node, done, which_atom, local_index, currentIndex;
252	<	double atomData[13];
253	<	int isDirectional;
254	<	char* atomTypeString;
255	<	char MPIatomTypeString[MINIBUFFERSIZE];
256	<	int nObjects;
257	<	int msgLen; // the length of message actually recieved at master nodes
258	<	#endif //is_mpi
250	>	for (unsigned int i = 0; i < 3; i++) {
251	>	for (unsigned int j = 0; j < 3; j++) {
252	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
253	>	sprintf( painCave.errMsg,
254	>	"DumpWriter detected a numerical error writing the barostat");
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>	}
259	>	}
260
261	<	double q[4], ji[3];
262	<	DirectionalAtom* dAtom;
263	<	double pos[3], vel[3];
264	<	int nTotObjects;
265	<	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";
261	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
262	>	eta(0, 0), eta(1, 0), eta(2, 0),
263	>	eta(0, 1), eta(1, 1), eta(2, 1),
264	>	eta(0, 2), eta(1, 2), eta(2, 2));
265	>	os << buffer;
266
267	<	*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;
267	>	os << "    </FrameData>\n";
268		}
258	–
259	–	for( i=0; i< entry_plug->n_mol; i++ ){
269
270	<	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);
270	>	void DumpWriter::writeFrame(std::ostream& os) {
271
272	<	sprintf( tempBuffer,
273	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
274	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
272	>	#ifdef IS_MPI
273	>	MPI_Status istatus;
274	>	#endif
275
276	<	if( sd->isDirectional() ){
276	>	Molecule* mol;
277	>	StuntDouble* integrableObject;
278	>	SimInfo::MoleculeIterator mi;
279	>	Molecule::IntegrableObjectIterator ii;
280
281	<	sd->getQ( q );
282	<	sd->getJ( ji );
281	>	#ifndef IS_MPI
282	>	os << "  <Snapshot>\n";
283	>
284	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
285
286	<	sprintf( tempBuffer,
287	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
288	<	q[0],
289	<	q[1],
290	<	q[2],
291	<	q[3],
292	<	ji[0],
293	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
286	>	os << "    <StuntDoubles>\n";
287	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
288	>
289	>
290	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(ii)) {
292	>	os << prepareDumpLine(integrableObject);
293	>
294		}
295	<	else
296	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295	>	}
296	>	os << "    </StuntDoubles>\n";
297
298	<	for(k = 0; k < outFile.size(); k++)
299	<	*outFile[k] << writeLine;
298	>	os << "  </Snapshot>\n";
299	>
300	>	os.flush();
301	>	#else
302	>	//every node prepares the dump lines for integrable objects belong to itself
303	>	std::string buffer;
304	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
305	>
306	>
307	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(ii)) {
309	>	buffer += prepareDumpLine(integrableObject);
310	>	}
311		}
312
313	<	}
313	>	const int masterNode = 0;
314	>	int nProc;
315	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
316	>	if (worldRank == masterNode) {
317	>	os << "  <Snapshot>\n";
318	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319	>	os << "    <StuntDoubles>\n";
320	>
321	>	os << buffer;
322
323	<	#else // is_mpi
323	>	for (int i = 1; i < nProc; ++i) {
324
325	<	/* code to find maximum tag value */
326	<
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	<	}
325	>	// receive the length of the string buffer that was
326	>	// prepared by processor i
327
328	<	int haveError;
328	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
329	>	int recvLength;
330	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
331	>	char* recvBuffer = new char[recvLength];
332	>	if (recvBuffer == NULL) {
333	>	} else {
334	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
335	>	os << recvBuffer;
336	>	delete [] recvBuffer;
337	>	}
338	>	}
339	>	os << "    </StuntDoubles>\n";
340	>
341	>	os << "  </Snapshot>\n";
342	>	os.flush();
343	>	} else {
344	>	int sendBufferLength = buffer.size() + 1;
345	>	int myturn = 0;
346	>	for (int i = 1; i < nProc; ++i){
347	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
348	>	if (myturn == worldRank){
349	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
350	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
351	>	}
352	>	}
353	>	}
354
355	<	MPI_Status istatus;
320	<	int nCurObj;
321	<	int *MolToProcMap = mpiSim->getMolToProcMap();
355	>	#endif // is_mpi
356
357	<	// write out header and node 0's coordinates
357	>	}
358
359	<	if( worldRank == 0 ){
359	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
360	>
361	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
362	>	std::string type("pv");
363	>	std::string line;
364	>	char tempBuffer[4096];
365
366	<	// Node 0 needs a list of the magic potatoes for each processor;
366	>	Vector3d pos;
367	>	Vector3d vel;
368	>	pos = integrableObject->getPos();
369
370	<	nProc = mpiSim->getNProcessors();
371	<	potatoes = new int[nProc];
372	<
373	<	//write out the comment lines
374	<	for (i = 0; i < nProc; i++)
375	<	potatoes[i] = 0;
376	<
377	<	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;
370	>	if (isinf(pos[0]) || isnan(pos[0]) ||
371	>	isinf(pos[1]) || isnan(pos[1]) ||
372	>	isinf(pos[2]) || isnan(pos[2]) ) {
373	>	sprintf( painCave.errMsg,
374	>	"DumpWriter detected a numerical error writing the position"
375	>	" for object %d", index);
376	>	painCave.isFatal = 1;
377	>	simError();
378		}
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:
379
380	<	potatoes[which_node] = 0;
371	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
372	<	MPI_COMM_WORLD);
373	<
374	<	}
380	>	vel = integrableObject->getVel();
381
382	<	myPotato = potatoes[which_node];
382	>	if (isinf(vel[0]) || isnan(vel[0]) ||
383	>	isinf(vel[1]) || isnan(vel[1]) ||
384	>	isinf(vel[2]) || isnan(vel[2]) ) {
385	>	sprintf( painCave.errMsg,
386	>	"DumpWriter detected a numerical error writing the velocity"
387	>	" for object %d", index);
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391
392	<	//recieve the number of integrableObject in current molecule
393	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
394	<	myPotato, MPI_COMM_WORLD, &istatus);
395	<	myPotato++;
382	<
383	<	for(int l = 0; l < nCurObj; l++){
392	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
393	>	pos[0], pos[1], pos[2],
394	>	vel[0], vel[1], vel[2]);
395	>	line += tempBuffer;
396
397	<	if (potatoes[which_node] + 2 >= MAXTAG) {
398	<	// The potato was going to exceed the maximum value,
399	<	// so wrap this processor potato back to 0:
397	>	if (integrableObject->isDirectional()) {
398	>	type += "qj";
399	>	Quat4d q;
400	>	Vector3d ji;
401	>	q = integrableObject->getQ();
402
403	<	potatoes[which_node] = 0;
404	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
405	<
406	<	}
403	>	if (isinf(q[0]) || isnan(q[0]) ||
404	>	isinf(q[1]) || isnan(q[1]) ||
405	>	isinf(q[2]) || isnan(q[2]) ||
406	>	isinf(q[3]) || isnan(q[3]) ) {
407	>	sprintf( painCave.errMsg,
408	>	"DumpWriter detected a numerical error writing the quaternion"
409	>	" for object %d", index);
410	>	painCave.isFatal = 1;
411	>	simError();
412	>	}
413
414	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395	<	myPotato, MPI_COMM_WORLD, &istatus);
414	>	ji = integrableObject->getJ();
415
416	<	atomTypeString = MPIatomTypeString;
416	>	if (isinf(ji[0]) || isnan(ji[0]) ||
417	>	isinf(ji[1]) || isnan(ji[1]) ||
418	>	isinf(ji[2]) || isnan(ji[2]) ) {
419	>	sprintf( painCave.errMsg,
420	>	"DumpWriter detected a numerical error writing the angular"
421	>	" momentum for object %d", index);
422	>	painCave.isFatal = 1;
423	>	simError();
424	>	}
425
426	<	myPotato++;
426	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
427	>	q[0], q[1], q[2], q[3],
428	>	ji[0], ji[1], ji[2]);
429	>	line += tempBuffer;
430	>	}
431
432	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
433	<	myPotato++;
432	>	if (needForceVector_) {
433	>	type += "f";
434	>	Vector3d frc;
435
436	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
436	>	frc = integrableObject->getFrc();
437
438	<	if(msgLen  == 13)
439	<	isDirectional = 1;
440	<	else
441	<	isDirectional = 0;
442	<
443	<	// If we've survived to here, format the line:
444	<
445	<	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	<
438	>	if (isinf(frc[0]) || isnan(frc[0]) ||
439	>	isinf(frc[1]) || isnan(frc[1]) ||
440	>	isinf(frc[2]) || isnan(frc[2]) ) {
441	>	sprintf( painCave.errMsg,
442	>	"DumpWriter detected a numerical error writing the force"
443	>	" for object %d", index);
444	>	painCave.isFatal = 1;
445	>	simError();
446		}
447	<	else {
448	<
449	<	haveError = 0;
447	>	sprintf(tempBuffer, " %13e %13e %13e",
448	>	frc[0], frc[1], frc[2]);
449	>	line += tempBuffer;
450	>
451	>	if (integrableObject->isDirectional()) {
452	>	type += "t";
453	>	Vector3d trq;
454
455	<	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())
455	>	trq = integrableObject->getTrq();
456
457	<	currentIndex++;
458	<	}
457	>	if (isinf(trq[0]) || isnan(trq[0]) ||
458	>	isinf(trq[1]) || isnan(trq[1]) ||
459	>	isinf(trq[2]) || isnan(trq[2]) ) {
460	>	sprintf( painCave.errMsg,
461	>	"DumpWriter detected a numerical error writing the torque"
462	>	" for object %d", index);
463	>	painCave.isFatal = 1;
464	>	simError();
465	>	}
466	>
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472	>	if (needParticlePot_) {
473	>	type += "u";
474	>	RealType particlePot;
475
476	<	}//end for(i = 0; i < mpiSim->getNmol())
476	>	particlePot = integrableObject->getParticlePot();
477	>
478	>	if (isinf(particlePot) || isnan(particlePot)) {
479	>	sprintf( painCave.errMsg,
480	>	"DumpWriter detected a numerical error writing the particle "
481	>	" potential for object %d", index);
482	>	painCave.isFatal = 1;
483	>	simError();
484	>	}
485	>	sprintf(tempBuffer, " %13e", particlePot);
486	>	line += tempBuffer;
487	>	}
488
489	<	for(k = 0; k < outFile.size(); k++)
490	<	outFile[k]->flush();
491	<
553	<	sprintf( checkPointMsg,
554	<	"Sucessfully took a dump.\n");
555	<
556	<	MPIcheckPoint();
557	<
558	<	delete[] potatoes;
559	<
560	<	} else {
489	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
490	>	return std::string(tempBuffer);
491	>	}
492
493	<	// worldRank != 0, so I'm a remote node.
493	>	void DumpWriter::writeDump() {
494	>	writeFrame(*dumpFile_);
495	>	}
496
497	<	// Set my magic potato to 0:
498	<
566	<	myPotato = 0;
567	<	currentIndex = 0;
497	>	void DumpWriter::writeEor() {
498	>	std::ostream* eorStream;
499
500	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
501	<
502	<	// Am I the node which has this integrableObject?
572	<
573	<	if (MolToProcMap[i] == worldRank) {
500	>	#ifdef IS_MPI
501	>	if (worldRank == 0) {
502	>	#endif // is_mpi
503
504	+	eorStream = createOStream(eorFilename_);
505
506	<	if (myPotato + 1 >= MAXTAG) {
507	<
508	<	// 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	<	}
506	>	#ifdef IS_MPI
507	>	}
508	>	#endif // is_mpi
509
510	<	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++;
510	>	writeFrame(*eorStream);
511
512	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
512	>	#ifdef IS_MPI
513	>	if (worldRank == 0) {
514	>	#endif // is_mpi
515	>	writeClosing(*eorStream);
516	>	delete eorStream;
517	>	#ifdef IS_MPI
518	>	}
519	>	#endif // is_mpi
520
521	<	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();
521	>	}
522
611	–	sd->getPos(pos);
612	–	sd->getVel(vel);
523
524	<	atomData[0] = pos[0];
525	<	atomData[1] = pos[1];
526	<	atomData[2] = pos[2];
524	>	void DumpWriter::writeDumpAndEor() {
525	>	std::vector<std::streambuf*> buffers;
526	>	std::ostream* eorStream;
527	>	#ifdef IS_MPI
528	>	if (worldRank == 0) {
529	>	#endif // is_mpi
530
531	<	atomData[3] = vel[0];
619	<	atomData[4] = vel[1];
620	<	atomData[5] = vel[2];
621	<
622	<	isDirectional = 0;
531	>	buffers.push_back(dumpFile_->rdbuf());
532
533	<	if( sd->isDirectional() ){
533	>	eorStream = createOStream(eorFilename_);
534
535	<	isDirectional = 1;
536	<
537	<	sd->getQ( q );
538	<	sd->getJ( ji );
539	<
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	<	}
535	>	buffers.push_back(eorStream->rdbuf());
536	>
537	>	#ifdef IS_MPI
538	>	}
539	>	#endif // is_mpi
540
541	<
542	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
541	>	TeeBuf tbuf(buffers.begin(), buffers.end());
542	>	std::ostream os(&tbuf);
543
544	<	// null terminate the string before sending (just in case):
646	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
544	>	writeFrame(os);
545
546	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
547	<	myPotato, MPI_COMM_WORLD);
548	<
549	<	myPotato++;
550	<
551	<	if (isDirectional) {
552	<
553	<	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();
546	>	#ifdef IS_MPI
547	>	if (worldRank == 0) {
548	>	#endif // is_mpi
549	>	writeClosing(*eorStream);
550	>	delete eorStream;
551	>	#ifdef IS_MPI
552	>	}
553	>	#endif // is_mpi
554
555		}
679	–
680	–	#endif // is_mpi
681	–	}
556
557	<	#ifdef IS_MPI
557	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
558
559	<	// a couple of functions to let us escape the write loop
559	>	std::ostream* newOStream;
560	>	#ifdef HAVE_LIBZ
561	>	if (needCompression_) {
562	>	newOStream = new ogzstream(filename.c_str());
563	>	} else {
564	>	newOStream = new std::ofstream(filename.c_str());
565	>	}
566	>	#else
567	>	newOStream = new std::ofstream(filename.c_str());
568	>	#endif
569	>	//write out MetaData first
570	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
571	>	(*newOStream) << "  <MetaData>" << std::endl;
572	>	(*newOStream) << info_->getRawMetaData();
573	>	(*newOStream) << "  </MetaData>" << std::endl;
574	>	return newOStream;
575	>	}
576
577	<	void dWrite::DieDieDie( void ){
577	>	void DumpWriter::writeClosing(std::ostream& os) {
578
579	<	MPI_Finalize();
580	<	exit (0);
581	<	}
579	>	os << "</OpenMD>\n";
580	>	os.flush();
581	>	}
582
583	<	#endif //is_mpi
583	>	}//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 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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