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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1711 by gezelter, Sat May 19 02:58:35 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	+	createDumpFile_ = true;
106	+	#ifdef HAVE_LIBZ
107	+	if (needCompression_) {
108	+	filename_ += ".gz";
109	+	eorFilename_ += ".gz";
110	+	}
111	+	#endif
112	+
113		#ifdef IS_MPI
114	<	if(worldRank == 0 ){
114	>
115	>	if (worldRank == 0) {
116		#endif // is_mpi
117
118	<	dumpFile.close();
118	>
119	>	dumpFile_ = createOStream(filename_);
120
121	<	#ifdef IS_MPI
122	<	}
123	<	#endif // is_mpi
124	<	}
121	>	if (!dumpFile_) {
122	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
123	>	filename_.c_str());
124	>	painCave.isFatal = 1;
125	>	simError();
126	>	}
127
128		#ifdef IS_MPI
129
130	<	/**
71	<	* A hook function to load balancing
72	<	*/
130	>	}
131
132	<	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	<	}
132	>	#endif // is_mpi
133
134	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
134	>	}
135
136	<	for(int i = 0; i < entry_plug->n_mol;i++)
137	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
138	<
139	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
140	<	}
141	<
136	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
137	>	: info_(info), filename_(filename){
138	>
139	>	Globals* simParams = info->getSimParams();
140	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
141	>
142	>	needCompression_ = simParams->getCompressDumpFile();
143	>	needForceVector_ = simParams->getOutputForceVector();
144	>	needParticlePot_ = simParams->getOutputParticlePotential();
145	>
146	>	#ifdef HAVE_LIBZ
147	>	if (needCompression_) {
148	>	filename_ += ".gz";
149	>	eorFilename_ += ".gz";
150	>	}
151		#endif
152	+
153	+	#ifdef IS_MPI
154	+
155	+	if (worldRank == 0) {
156	+	#endif // is_mpi
157	+
158	+	createDumpFile_ = writeDumpFile;
159	+	if (createDumpFile_) {
160	+	dumpFile_ = createOStream(filename_);
161	+
162	+	if (!dumpFile_) {
163	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
164	+	filename_.c_str());
165	+	painCave.isFatal = 1;
166	+	simError();
167	+	}
168	+	}
169	+	#ifdef IS_MPI
170	+
171	+	}
172
173	<	void DumpWriter::writeDump(double currentTime){
173	>
174	>	#endif // is_mpi
175	>
176	>	}
177
178	<	ofstream finalOut;
105	<	vector<ofstream*> fileStreams;
178	>	DumpWriter::~DumpWriter() {
179
180		#ifdef IS_MPI
181	<	if(worldRank == 0 ){
182	<	#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	<	}
181	>
182	>	if (worldRank == 0) {
183		#endif // is_mpi
184	+	if (createDumpFile_){
185	+	writeClosing(*dumpFile_);
186	+	delete dumpFile_;
187	+	}
188	+	#ifdef IS_MPI
189
190	<	fileStreams.push_back(&finalOut);
123	<	fileStreams.push_back(&dumpFile);
190	>	}
191
192	<	writeFrame(fileStreams, currentTime);
192	>	#endif // is_mpi
193
194	<	#ifdef IS_MPI
128	<	finalOut.close();
129	<	#endif
130	<
131	<	}
194	>	}
195
196	<	void DumpWriter::writeFinal(double currentTime){
196	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
197
198	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
198	>	char buffer[1024];
199
200	<	#ifdef IS_MPI
139	<	if(worldRank == 0 ){
140	<	#endif // is_mpi
200	>	os << "    <FrameData>\n";
201
202	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
202	>	RealType currentTime = s->getTime();
203
204	<	if( !finalOut ){
204	>	if (isinf(currentTime) || isnan(currentTime)) {
205		sprintf( painCave.errMsg,
206	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
206	>	"DumpWriter detected a numerical error writing the time");
207		painCave.isFatal = 1;
208		simError();
209		}
210	+
211	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
212	+	os << buffer;
213
214	<	#ifdef IS_MPI
215	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
214	>	Mat3x3d hmat;
215	>	hmat = s->getHmat();
216
217	<	#ifdef IS_MPI
218	<	finalOut.close();
219	<	#endif
220	<
221	<	}
222	<
223	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
224	<
225	<	const int BUFFERSIZE = 2000;
226	<	const int MINIBUFFERSIZE = 100;
169	<
170	<	char tempBuffer[BUFFERSIZE];
171	<	char writeLine[BUFFERSIZE];
172	<
173	<	int i;
174	<	unsigned int k;
175	<
176	<	#ifdef IS_MPI
177	<
178	<	/*********************************************************************
179	<	* Documentation?  You want DOCUMENTATION?
180	<	*
181	<	* Why all the potatoes below?
182	<	*
183	<	* To make a long story short, the original version of DumpWriter
184	<	* worked in the most inefficient way possible.  Node 0 would
185	<	* poke each of the node for an individual atom's formatted data
186	<	* 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	<	*********************************************************************/
214	<
215	<	int *potatoes;
216	<	int myPotato;
217	<
218	<	int nProc;
219	<	int j, which_node, done, which_atom, local_index, currentIndex;
220	<	double atomData[13];
221	<	int isDirectional;
222	<	char* atomTypeString;
223	<	char MPIatomTypeString[MINIBUFFERSIZE];
224	<	int nObjects;
225	<	int msgLen; // the length of message actually recieved at master nodes
226	<	#endif //is_mpi
227	<
228	<	double q[4], ji[3];
229	<	DirectionalAtom* dAtom;
230	<	double pos[3], vel[3];
231	<	int nTotObjects;
232	<	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";
241	<
242	<	*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;
257	<	}
258	<
259	<	for( i=0; i< entry_plug->n_mol; i++ ){
260	<
261	<	integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262	<	molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
217	>	for (unsigned int i = 0; i < 3; i++) {
218	>	for (unsigned int j = 0; j < 3; j++) {
219	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
220	>	sprintf( painCave.errMsg,
221	>	"DumpWriter detected a numerical error writing the box");
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	}
226	>	}
227
228	<	for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
229	<	sd = *iter;
230	<	sd->getPos(pos);
231	<	sd->getVel(vel);
228	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
229	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
230	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
231	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
232	>	os << buffer;
233
234	<	sprintf( tempBuffer,
235	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
236	<	sd->getType(),
237	<	pos[0],
238	<	pos[1],
239	<	pos[2],
240	<	vel[0],
241	<	vel[1],
242	<	vel[2]);
243	<	strcpy( writeLine, tempBuffer );
234	>	RealType chi = s->getChi();
235	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
236	>	if (isinf(chi) || isnan(chi) ||
237	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
238	>	sprintf( painCave.errMsg,
239	>	"DumpWriter detected a numerical error writing the thermostat");
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
244	>	os << buffer;
245
246	<	if( sd->isDirectional() ){
246	>	Mat3x3d eta;
247	>	eta = s->getEta();
248
249	<	sd->getQ( q );
250	<	sd->getJ( ji );
251	<
252	<	sprintf( tempBuffer,
253	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
254	<	q[0],
255	<	q[1],
256	<	q[2],
290	<	q[3],
291	<	ji[0],
292	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the barostat");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257		}
296	–	else
297	–	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298	–
299	–	for(k = 0; k < outFile.size(); k++)
300	–	*outFile[k] << writeLine;
258		}
259
260	<	}
260	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	eta(0, 0), eta(1, 0), eta(2, 0),
262	>	eta(0, 1), eta(1, 1), eta(2, 1),
263	>	eta(0, 2), eta(1, 2), eta(2, 2));
264	>	os << buffer;
265
266	<	#else // is_mpi
266	>	os << "    </FrameData>\n";
267	>	}
268
269	<	/* code to find maximum tag value */
308	<
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	<	}
269	>	void DumpWriter::writeFrame(std::ostream& os) {
270
271	<	int haveError;
271	>	#ifdef IS_MPI
272	>	MPI_Status istatus;
273	>	#endif
274
275	<	MPI_Status istatus;
276	<	int nCurObj;
277	<	int *MolToProcMap = mpiSim->getMolToProcMap();
275	>	Molecule* mol;
276	>	StuntDouble* integrableObject;
277	>	SimInfo::MoleculeIterator mi;
278	>	Molecule::IntegrableObjectIterator ii;
279
280	<	// write out header and node 0's coordinates
280	>	#ifndef IS_MPI
281	>	os << "  <Snapshot>\n";
282	>
283	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
284
285	<	if( worldRank == 0 ){
285	>	os << "    <StuntDoubles>\n";
286	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
287
288	<	// Node 0 needs a list of the magic potatoes for each processor;
289	<
290	<	nProc = mpiSim->getNProcessors();
291	<	potatoes = new int[nProc];
292	<
293	<	//write out the comment lines
294	<	for (i = 0; i < nProc; i++)
295	<	potatoes[i] = 0;
288	>
289	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(ii)) {
291	>	os << prepareDumpLine(integrableObject);
292	>
293	>	}
294	>	}
295	>	os << "    </StuntDoubles>\n";
296
297	<	for(k = 0; k < outFile.size(); k++){
337	<	*outFile[k] << nTotObjects << "\n";
297	>	os << "  </Snapshot>\n";
298
299	<	*outFile[k] << currentTime << ";\t"
300	<	<< entry_plug->Hmat[0][0] << "\t"
301	<	<< entry_plug->Hmat[1][0] << "\t"
302	<	<< entry_plug->Hmat[2][0] << ";\t"
299	>	os.flush();
300	>	#else
301	>	//every node prepares the dump lines for integrable objects belong to itself
302	>	std::string buffer;
303	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
304
344	–	<< entry_plug->Hmat[0][1] << "\t"
345	–	<< entry_plug->Hmat[1][1] << "\t"
346	–	<< entry_plug->Hmat[2][1] << ";\t"
305
306	<	<< entry_plug->Hmat[0][2] << "\t"
307	<	<< entry_plug->Hmat[1][2] << "\t"
308	<	<< entry_plug->Hmat[2][2] << ";";
309	<
352	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
306	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
307	>	integrableObject = mol->nextIntegrableObject(ii)) {
308	>	buffer += prepareDumpLine(integrableObject);
309	>	}
310		}
311	+
312	+	const int masterNode = 0;
313	+	int nProc;
314	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
315	+	if (worldRank == masterNode) {
316	+	os << "  <Snapshot>\n";
317	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318	+	os << "    <StuntDoubles>\n";
319	+
320	+	os << buffer;
321
322	<	currentIndex = 0;
322	>	for (int i = 1; i < nProc; ++i) {
323
324	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
324	>	// receive the length of the string buffer that was
325	>	// prepared by processor i
326	>
327	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
328	>	int recvLength;
329	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
330	>	char* recvBuffer = new char[recvLength];
331	>	if (recvBuffer == NULL) {
332	>	} else {
333	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
334	>	os << recvBuffer;
335	>	delete [] recvBuffer;
336	>	}
337	>	}
338	>	os << "    </StuntDoubles>\n";
339
340	<	// Get the Node number which has this atom;
341	<
342	<	which_node = MolToProcMap[i];
343	<
344	<	if (which_node != 0) {
345	<
346	<	if (potatoes[which_node] + 1 >= MAXTAG) {
347	<	// The potato was going to exceed the maximum value,
348	<	// so wrap this processor potato back to 0:
349	<
369	<	potatoes[which_node] = 0;
370	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371	<
340	>	os << "  </Snapshot>\n";
341	>	os.flush();
342	>	} else {
343	>	int sendBufferLength = buffer.size() + 1;
344	>	int myturn = 0;
345	>	for (int i = 1; i < nProc; ++i){
346	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
347	>	if (myturn == worldRank){
348	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
349	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
350		}
351	+	}
352	+	}
353
354	<	myPotato = potatoes[which_node];
354	>	#endif // is_mpi
355
356	<	//recieve the number of integrableObject in current molecule
377	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378	<	myPotato, MPI_COMM_WORLD, &istatus);
379	<	myPotato++;
380	<
381	<	for(int l = 0; l < nCurObj; l++){
356	>	}
357
358	<	if (potatoes[which_node] + 2 >= MAXTAG) {
359	<	// The potato was going to exceed the maximum value,
360	<	// so wrap this processor potato back to 0:
358	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359	>
360	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
361	>	std::string type("pv");
362	>	std::string line;
363	>	char tempBuffer[4096];
364
365	<	potatoes[which_node] = 0;
366	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
367	<
390	<	}
365	>	Vector3d pos;
366	>	Vector3d vel;
367	>	pos = integrableObject->getPos();
368
369	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
370	<	myPotato, MPI_COMM_WORLD, &istatus);
369	>	if (isinf(pos[0]) || isnan(pos[0]) ||
370	>	isinf(pos[1]) || isnan(pos[1]) ||
371	>	isinf(pos[2]) || isnan(pos[2]) ) {
372	>	sprintf( painCave.errMsg,
373	>	"DumpWriter detected a numerical error writing the position"
374	>	" for object %d", index);
375	>	painCave.isFatal = 1;
376	>	simError();
377	>	}
378
379	<	atomTypeString = MPIatomTypeString;
379	>	vel = integrableObject->getVel();
380
381	<	myPotato++;
381	>	if (isinf(vel[0]) || isnan(vel[0]) ||
382	>	isinf(vel[1]) || isnan(vel[1]) ||
383	>	isinf(vel[2]) || isnan(vel[2]) ) {
384	>	sprintf( painCave.errMsg,
385	>	"DumpWriter detected a numerical error writing the velocity"
386	>	" for object %d", index);
387	>	painCave.isFatal = 1;
388	>	simError();
389	>	}
390
391	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
392	<	myPotato++;
391	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
392	>	pos[0], pos[1], pos[2],
393	>	vel[0], vel[1], vel[2]);
394	>	line += tempBuffer;
395
396	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
396	>	if (integrableObject->isDirectional()) {
397	>	type += "qj";
398	>	Quat4d q;
399	>	Vector3d ji;
400	>	q = integrableObject->getQ();
401
402	<	if(msgLen  == 13)
403	<	isDirectional = 1;
404	<	else
405	<	isDirectional = 0;
406	<
407	<	// If we've survived to here, format the line:
408	<
409	<	if (!isDirectional) {
410	<
413	<	sprintf( writeLine,
414	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415	<	atomTypeString,
416	<	atomData[0],
417	<	atomData[1],
418	<	atomData[2],
419	<	atomData[3],
420	<	atomData[4],
421	<	atomData[5]);
422	<
423	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424	<
425	<	}
426	<	else {
427	<
428	<	sprintf( writeLine,
429	<	"%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",
430	<	atomTypeString,
431	<	atomData[0],
432	<	atomData[1],
433	<	atomData[2],
434	<	atomData[3],
435	<	atomData[4],
436	<	atomData[5],
437	<	atomData[6],
438	<	atomData[7],
439	<	atomData[8],
440	<	atomData[9],
441	<	atomData[10],
442	<	atomData[11],
443	<	atomData[12]);
444	<
445	<	}
446	<
447	<	for(k = 0; k < outFile.size(); k++)
448	<	*outFile[k] << writeLine;
449	<
450	<	}// end for(int l =0)
451	<	potatoes[which_node] = myPotato;
452	<
402	>	if (isinf(q[0]) || isnan(q[0]) ||
403	>	isinf(q[1]) || isnan(q[1]) ||
404	>	isinf(q[2]) || isnan(q[2]) ||
405	>	isinf(q[3]) || isnan(q[3]) ) {
406	>	sprintf( painCave.errMsg,
407	>	"DumpWriter detected a numerical error writing the quaternion"
408	>	" for object %d", index);
409	>	painCave.isFatal = 1;
410	>	simError();
411		}
454	–	else {
455	–
456	–	haveError = 0;
457	–
458	–	local_index = indexArray[currentIndex].first;
412
413	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
413	>	ji = integrableObject->getJ();
414
415	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
416	<	sd = *iter;
417	<	atomTypeString = sd->getType();
418	<
419	<	sd->getPos(pos);
420	<	sd->getVel(vel);
421	<
422	<	atomData[0] = pos[0];
470	<	atomData[1] = pos[1];
471	<	atomData[2] = pos[2];
472	<
473	<	atomData[3] = vel[0];
474	<	atomData[4] = vel[1];
475	<	atomData[5] = vel[2];
476	<
477	<	isDirectional = 0;
478	<
479	<	if( sd->isDirectional() ){
480	<
481	<	isDirectional = 1;
482	<
483	<	sd->getQ( q );
484	<	sd->getJ( ji );
485	<
486	<	for (int j = 0; j < 6 ; j++)
487	<	atomData[j] = atomData[j];
488	<
489	<	atomData[6] = q[0];
490	<	atomData[7] = q[1];
491	<	atomData[8] = q[2];
492	<	atomData[9] = q[3];
493	<
494	<	atomData[10] = ji[0];
495	<	atomData[11] = ji[1];
496	<	atomData[12] = ji[2];
497	<	}
498	<
499	<	// If we've survived to here, format the line:
500	<
501	<	if (!isDirectional) {
502	<
503	<	sprintf( writeLine,
504	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505	<	atomTypeString,
506	<	atomData[0],
507	<	atomData[1],
508	<	atomData[2],
509	<	atomData[3],
510	<	atomData[4],
511	<	atomData[5]);
512	<
513	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514	<
515	<	}
516	<	else {
517	<
518	<	sprintf( writeLine,
519	<	"%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",
520	<	atomTypeString,
521	<	atomData[0],
522	<	atomData[1],
523	<	atomData[2],
524	<	atomData[3],
525	<	atomData[4],
526	<	atomData[5],
527	<	atomData[6],
528	<	atomData[7],
529	<	atomData[8],
530	<	atomData[9],
531	<	atomData[10],
532	<	atomData[11],
533	<	atomData[12]);
534	<
535	<	}
536	<
537	<	for(k = 0; k < outFile.size(); k++)
538	<	*outFile[k] << writeLine;
539	<
540	<
541	<	}//end for(iter = integrableObject.begin())
542	<
543	<	currentIndex++;
415	>	if (isinf(ji[0]) || isnan(ji[0]) ||
416	>	isinf(ji[1]) || isnan(ji[1]) ||
417	>	isinf(ji[2]) || isnan(ji[2]) ) {
418	>	sprintf( painCave.errMsg,
419	>	"DumpWriter detected a numerical error writing the angular"
420	>	" momentum for object %d", index);
421	>	painCave.isFatal = 1;
422	>	simError();
423		}
424
425	<	}//end for(i = 0; i < mpiSim->getNmol())
426	<
427	<	for(k = 0; k < outFile.size(); k++)
428	<	outFile[k]->flush();
429	<
551	<	sprintf( checkPointMsg,
552	<	"Sucessfully took a dump.\n");
553	<
554	<	MPIcheckPoint();
555	<
556	<	delete[] potatoes;
557	<
558	<	} else {
425	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
426	>	q[0], q[1], q[2], q[3],
427	>	ji[0], ji[1], ji[2]);
428	>	line += tempBuffer;
429	>	}
430
431	<	// worldRank != 0, so I'm a remote node.
432	<
433	<	// Set my magic potato to 0:
563	<
564	<	myPotato = 0;
565	<	currentIndex = 0;
566	<
567	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568	<
569	<	// Am I the node which has this integrableObject?
570	<
571	<	if (MolToProcMap[i] == worldRank) {
431	>	if (needForceVector_) {
432	>	type += "f";
433	>	Vector3d frc;
434
435	+	frc = integrableObject->getFrc();
436
437	<	if (myPotato + 1 >= MAXTAG) {
438	<
439	<	// The potato was going to exceed the maximum value,
440	<	// so wrap this processor potato back to 0 (and block until
441	<	// node 0 says we can go:
442	<
443	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
444	<
437	>	if (isinf(frc[0]) || isnan(frc[0]) ||
438	>	isinf(frc[1]) || isnan(frc[1]) ||
439	>	isinf(frc[2]) || isnan(frc[2]) ) {
440	>	sprintf( painCave.errMsg,
441	>	"DumpWriter detected a numerical error writing the force"
442	>	" for object %d", index);
443	>	painCave.isFatal = 1;
444	>	simError();
445	>	}
446	>	sprintf(tempBuffer, " %13e %13e %13e",
447	>	frc[0], frc[1], frc[2]);
448	>	line += tempBuffer;
449	>
450	>	if (integrableObject->isDirectional()) {
451	>	type += "t";
452	>	Vector3d trq;
453	>
454	>	trq = integrableObject->getTrq();
455	>
456	>	if (isinf(trq[0]) || isnan(trq[0]) ||
457	>	isinf(trq[1]) || isnan(trq[1]) ||
458	>	isinf(trq[2]) || isnan(trq[2]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the torque"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464		}
465	+
466	+	sprintf(tempBuffer, " %13e %13e %13e",
467	+	trq[0], trq[1], trq[2]);
468	+	line += tempBuffer;
469	+	}
470	+	}
471	+	if (needParticlePot_) {
472	+	type += "u";
473	+	RealType particlePot;
474
475	<	local_index = indexArray[currentIndex].first;
585	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586	<
587	<	nCurObj = integrableObjects.size();
588	<
589	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
590	<	myPotato, MPI_COMM_WORLD);
591	<	myPotato++;
475	>	particlePot = integrableObject->getParticlePot();
476
477	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
477	>	if (isinf(particlePot) || isnan(particlePot)) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the particle "
480	>	" potential for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484	>	sprintf(tempBuffer, " %13e", particlePot);
485	>	line += tempBuffer;
486	>	}
487	>
488	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
489	>	return std::string(tempBuffer);
490	>	}
491
492	<	if (myPotato + 2 >= MAXTAG) {
493	<
494	<	// The potato was going to exceed the maximum value,
598	<	// so wrap this processor potato back to 0 (and block until
599	<	// node 0 says we can go:
600	<
601	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602	<
603	<	}
604	<
605	<	sd = *iter;
606	<
607	<	atomTypeString = sd->getType();
492	>	void DumpWriter::writeDump() {
493	>	writeFrame(*dumpFile_);
494	>	}
495
496	<	sd->getPos(pos);
497	<	sd->getVel(vel);
496	>	void DumpWriter::writeEor() {
497	>	std::ostream* eorStream;
498	>
499	>	#ifdef IS_MPI
500	>	if (worldRank == 0) {
501	>	#endif // is_mpi
502
503	<	atomData[0] = pos[0];
613	<	atomData[1] = pos[1];
614	<	atomData[2] = pos[2];
503	>	eorStream = createOStream(eorFilename_);
504
505	<	atomData[3] = vel[0];
506	<	atomData[4] = vel[1];
507	<	atomData[5] = vel[2];
619	<
620	<	isDirectional = 0;
505	>	#ifdef IS_MPI
506	>	}
507	>	#endif // is_mpi
508
509	<	if( sd->isDirectional() ){
509	>	writeFrame(*eorStream);
510
511	<	isDirectional = 1;
512	<
513	<	sd->getQ( q );
514	<	sd->getJ( ji );
515	<
516	<
517	<	atomData[6] = q[0];
518	<	atomData[7] = q[1];
632	<	atomData[8] = q[2];
633	<	atomData[9] = q[3];
634	<
635	<	atomData[10] = ji[0];
636	<	atomData[11] = ji[1];
637	<	atomData[12] = ji[2];
638	<	}
511	>	#ifdef IS_MPI
512	>	if (worldRank == 0) {
513	>	#endif // is_mpi
514	>	writeClosing(*eorStream);
515	>	delete eorStream;
516	>	#ifdef IS_MPI
517	>	}
518	>	#endif // is_mpi
519
520	<
641	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
520	>	}
521
643	–	// null terminate the string before sending (just in case):
644	–	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
522
523	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
524	<	myPotato, MPI_COMM_WORLD);
525	<
526	<	myPotato++;
527	<
528	<	if (isDirectional) {
523	>	void DumpWriter::writeDumpAndEor() {
524	>	std::vector<std::streambuf*> buffers;
525	>	std::ostream* eorStream;
526	>	#ifdef IS_MPI
527	>	if (worldRank == 0) {
528	>	#endif // is_mpi
529
530	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654	<	myPotato, MPI_COMM_WORLD);
655	<
656	<	} else {
530	>	buffers.push_back(dumpFile_->rdbuf());
531
532	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659	<	myPotato, MPI_COMM_WORLD);
660	<	}
532	>	eorStream = createOStream(eorFilename_);
533
534	<	myPotato++;
535	<
536	<	}
665	<
666	<	currentIndex++;
667	<
668	<	}
669	<
670	<	}
671	<
672	<	sprintf( checkPointMsg,
673	<	"Sucessfully took a dump.\n");
674	<	MPIcheckPoint();
675	<
534	>	buffers.push_back(eorStream->rdbuf());
535	>
536	>	#ifdef IS_MPI
537		}
538	+	#endif // is_mpi
539
540	+	TeeBuf tbuf(buffers.begin(), buffers.end());
541	+	std::ostream os(&tbuf);
542
543	<
680	<	#endif // is_mpi
681	<	}
543	>	writeFrame(os);
544
545		#ifdef IS_MPI
546	+	if (worldRank == 0) {
547	+	#endif // is_mpi
548	+	writeClosing(*eorStream);
549	+	delete eorStream;
550	+	#ifdef IS_MPI
551	+	}
552	+	#endif // is_mpi
553	+
554	+	}
555
556	<	// a couple of functions to let us escape the write loop
556	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557
558	<	void dWrite::DieDieDie( void ){
558	>	std::ostream* newOStream;
559	>	#ifdef HAVE_LIBZ
560	>	if (needCompression_) {
561	>	newOStream = new ogzstream(filename.c_str());
562	>	} else {
563	>	newOStream = new std::ofstream(filename.c_str());
564	>	}
565	>	#else
566	>	newOStream = new std::ofstream(filename.c_str());
567	>	#endif
568	>	//write out MetaData first
569	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
570	>	(*newOStream) << "  <MetaData>" << std::endl;
571	>	(*newOStream) << info_->getRawMetaData();
572	>	(*newOStream) << "  </MetaData>" << std::endl;
573	>	return newOStream;
574	>	}
575
576	<	MPI_Finalize();
690	<	exit (0);
691	<	}
576	>	void DumpWriter::writeClosing(std::ostream& os) {
577
578	<	#endif //is_mpi
578	>	os << "</OpenMD>\n";
579	>	os.flush();
580	>	}
581	>
582	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

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