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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 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, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42
43	<	#include <string.h>
5	<	#include <iostream>
6	<	#include <fstream>
7	<	#include <algorithm>
8	<	#include <utility>
43	>	#include "config.h"
44
45		#ifdef IS_MPI
46		#include <mpi.h>
47	<	#include "brains/mpiSimulation.hpp"
47	>	#endif
48	>
49	>	#include "io/DumpWriter.hpp"
50	>	#include "primitives/Molecule.hpp"
51	>	#include "utils/simError.h"
52	>	#include "io/basic_teebuf.hpp"
53	>	#ifdef HAVE_ZLIB
54	>	#include "io/gzstream.hpp"
55	>	#endif
56	>	#include "io/Globals.hpp"
57
58	<	namespace dWrite{
59	<	void DieDieDie( void );
60	<	}
58	>	#ifdef _MSC_VER
59	>	#define isnan(x) _isnan((x))
60	>	#define isinf(x) (!_finite(x) && !_isnan(x))
61	>	#endif
62
63	<	using namespace dWrite;
64	<	#endif //is_mpi
63	>	using namespace std;
64	>	namespace OpenMD {
65
66	<	#include "io/ReadWrite.hpp"
67	<	#include "utils/simError.h"
66	>	DumpWriter::DumpWriter(SimInfo* info)
67	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68
69	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
69	>	Globals* simParams = info->getSimParams();
70	>	needCompression_   = simParams->getCompressDumpFile();
71	>	needForceVector_   = simParams->getOutputForceVector();
72	>	needParticlePot_   = simParams->getOutputParticlePotential();
73	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
74	>	needElectricField_ = simParams->getOutputElectricField();
75
76	<	entry_plug = the_entry_plug;
76	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77	>	doSiteData_ = true;
78	>	} else {
79	>	doSiteData_ = false;
80	>	}
81
82	+	createDumpFile_ = true;
83	+	#ifdef HAVE_LIBZ
84	+	if (needCompression_) {
85	+	filename_ += ".gz";
86	+	eorFilename_ += ".gz";
87	+	}
88	+	#endif
89	+
90		#ifdef IS_MPI
91	<	if(worldRank == 0 ){
91	>
92	>	if (worldRank == 0) {
93		#endif // is_mpi
94	+
95	+	dumpFile_ = createOStream(filename_);
96
97	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
97	>	if (!dumpFile_) {
98	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99	>	filename_.c_str());
100	>	painCave.isFatal = 1;
101	>	simError();
102	>	}
103
104	<	if( !dumpFile ){
104	>	#ifdef IS_MPI
105
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();
106		}
107
108	<	#ifdef IS_MPI
108	>	#endif // is_mpi
109	>
110		}
111
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	–	}
112
113	<	DumpWriter::~DumpWriter( ){
113	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
114	>	: info_(info), filename_(filename){
115
116	<	#ifdef IS_MPI
117	<	if(worldRank == 0 ){
59	<	#endif // is_mpi
116	>	Globals* simParams = info->getSimParams();
117	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118
119	<	dumpFile.close();
119	>	needCompression_   = simParams->getCompressDumpFile();
120	>	needForceVector_   = simParams->getOutputForceVector();
121	>	needParticlePot_   = simParams->getOutputParticlePotential();
122	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
123	>	needElectricField_ = simParams->getOutputElectricField();
124
125	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126	+	doSiteData_ = true;
127	+	} else {
128	+	doSiteData_ = false;
129	+	}
130	+
131	+	createDumpFile_ = true;
132	+	#ifdef HAVE_LIBZ
133	+	if (needCompression_) {
134	+	filename_ += ".gz";
135	+	eorFilename_ += ".gz";
136	+	}
137	+	#endif
138	+
139		#ifdef IS_MPI
140	<	}
140	>
141	>	if (worldRank == 0) {
142		#endif // is_mpi
66	–	}
143
144	+
145	+	dumpFile_ = createOStream(filename_);
146	+
147	+	if (!dumpFile_) {
148	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149	+	filename_.c_str());
150	+	painCave.isFatal = 1;
151	+	simError();
152	+	}
153	+
154		#ifdef IS_MPI
155
156	<	/**
71	<	* A hook function to load balancing
72	<	*/
156	>	}
157
158	<	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	<	}
158	>	#endif // is_mpi
159
160	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
160	>	}
161
162	<	for(int i = 0; i < entry_plug->n_mol;i++)
163	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
164	<
165	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
166	<	}
162	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
163	>	: info_(info), filename_(filename){
164	>
165	>	Globals* simParams = info->getSimParams();
166	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
167	>
168	>	needCompression_   = simParams->getCompressDumpFile();
169	>	needForceVector_   = simParams->getOutputForceVector();
170	>	needParticlePot_   = simParams->getOutputParticlePotential();
171	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
172	>	needElectricField_ = simParams->getOutputElectricField();
173
174	<	#endif
174	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175	>	doSiteData_ = true;
176	>	} else {
177	>	doSiteData_ = false;
178	>	}
179
180	<	void DumpWriter::writeDump(double currentTime){
181	<
182	<	ofstream finalOut;
183	<	vector<ofstream*> fileStreams;
106	<
107	<	#ifdef IS_MPI
108	<	if(worldRank == 0 ){
109	<	#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();
180	>	#ifdef HAVE_LIBZ
181	>	if (needCompression_) {
182	>	filename_ += ".gz";
183	>	eorFilename_ += ".gz";
184		}
185	+	#endif
186	+
187		#ifdef IS_MPI
188	<	}
188	>
189	>	if (worldRank == 0) {
190		#endif // is_mpi
191	+
192	+	createDumpFile_ = writeDumpFile;
193	+	if (createDumpFile_) {
194	+	dumpFile_ = createOStream(filename_);
195	+
196	+	if (!dumpFile_) {
197	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
198	+	filename_.c_str());
199	+	painCave.isFatal = 1;
200	+	simError();
201	+	}
202	+	}
203	+	#ifdef IS_MPI
204	+
205	+	}
206
207	<	fileStreams.push_back(&finalOut);
208	<	fileStreams.push_back(&dumpFile);
207	>
208	>	#endif // is_mpi
209	>
210	>	}
211
212	<	writeFrame(fileStreams, currentTime);
212	>	DumpWriter::~DumpWriter() {
213
214		#ifdef IS_MPI
128	–	finalOut.close();
129	–	#endif
130	–
131	–	}
215
216	<	void DumpWriter::writeFinal(double currentTime){
216	>	if (worldRank == 0) {
217	>	#endif // is_mpi
218	>	if (createDumpFile_){
219	>	writeClosing(*dumpFile_);
220	>	delete dumpFile_;
221	>	}
222	>	#ifdef IS_MPI
223
224	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
224	>	}
225
138	–	#ifdef IS_MPI
139	–	if(worldRank == 0 ){
226		#endif // is_mpi
227
228	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
228	>	}
229
230	<	if( !finalOut ){
230	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
231	>
232	>	char buffer[1024];
233	>
234	>	os << "    <FrameData>\n";
235	>
236	>	RealType currentTime = s->getTime();
237	>
238	>	if (isinf(currentTime) || isnan(currentTime)) {
239		sprintf( painCave.errMsg,
240	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
240	>	"DumpWriter detected a numerical error writing the time");
241		painCave.isFatal = 1;
242		simError();
243		}
244	+
245	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
246	+	os << buffer;
247
248	<	#ifdef IS_MPI
249	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
248	>	Mat3x3d hmat;
249	>	hmat = s->getHmat();
250
251	<	#ifdef IS_MPI
252	<	finalOut.close();
253	<	#endif
254	<
255	<	}
251	>	for (unsigned int i = 0; i < 3; i++) {
252	>	for (unsigned int j = 0; j < 3; j++) {
253	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
254	>	sprintf( painCave.errMsg,
255	>	"DumpWriter detected a numerical error writing the box");
256	>	painCave.isFatal = 1;
257	>	simError();
258	>	}
259	>	}
260	>	}
261	>
262	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
264	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
265	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
266	>	os << buffer;
267
268	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
268	>	pair<RealType, RealType> thermostat = s->getThermostat();
269
270	<	const int BUFFERSIZE = 2000;
271	<	const int MINIBUFFERSIZE = 100;
270	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271	>	isinf(thermostat.second) || isnan(thermostat.second)) {
272	>	sprintf( painCave.errMsg,
273	>	"DumpWriter detected a numerical error writing the thermostat");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278	>	thermostat.second);
279	>	os << buffer;
280
281	<	char tempBuffer[BUFFERSIZE];
282	<	char writeLine[BUFFERSIZE];
281	>	Mat3x3d eta;
282	>	eta = s->getBarostat();
283
284	<	int i;
285	<	unsigned int k;
284	>	for (unsigned int i = 0; i < 3; i++) {
285	>	for (unsigned int j = 0; j < 3; j++) {
286	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
287	>	sprintf( painCave.errMsg,
288	>	"DumpWriter detected a numerical error writing the barostat");
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	}
293	>	}
294	>
295	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296	>	eta(0, 0), eta(1, 0), eta(2, 0),
297	>	eta(0, 1), eta(1, 1), eta(2, 1),
298	>	eta(0, 2), eta(1, 2), eta(2, 2));
299	>	os << buffer;
300
301	<	#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;
301	>	os << "    </FrameData>\n";
302		}
258	–
259	–	for( i=0; i< entry_plug->n_mol; i++ ){
303
304	<	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);
304	>	void DumpWriter::writeFrame(std::ostream& os) {
305
306	<	sprintf( tempBuffer,
307	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
308	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
306	>	#ifdef IS_MPI
307	>	MPI_Status istatus;
308	>	#endif
309
310	<	if( sd->isDirectional() ){
310	>	Molecule* mol;
311	>	StuntDouble* sd;
312	>	SimInfo::MoleculeIterator mi;
313	>	Molecule::IntegrableObjectIterator ii;
314	>	RigidBody::AtomIterator ai;
315
316	<	sd->getQ( q );
317	<	sd->getJ( ji );
316	>	#ifndef IS_MPI
317	>	os << "  <Snapshot>\n";
318	>
319	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321	<	sprintf( tempBuffer,
322	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
323	<	q[0],
324	<	q[1],
325	<	q[2],
326	<	q[3],
327	<	ji[0],
328	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
321	>	os << "    <StuntDoubles>\n";
322	>	for (mol = info_->beginMolecule(mi); mol != NULL;
323	>	mol = info_->nextMolecule(mi)) {
324	>
325	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
326	>	sd = mol->nextIntegrableObject(ii)) {
327	>	os << prepareDumpLine(sd);
328	>
329		}
330	<	else
331	<	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;
301	<	}
302	<
303	<	}
330	>	}
331	>	os << "    </StuntDoubles>\n";
332
333	<	#else // is_mpi
333	>	if (doSiteData_) {
334	>	os << "    <SiteData>\n";
335	>	for (mol = info_->beginMolecule(mi); mol != NULL;
336	>	mol = info_->nextMolecule(mi)) {
337	>
338	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
339	>	sd = mol->nextIntegrableObject(ii)) {
340
341	<	/* code to find maximum tag value */
342	<
343	<	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	<	}
341	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
342	>	// do one for the IO itself
343	>	os << prepareSiteLine(sd, ioIndex, 0);
344
345	<	int haveError;
345	>	if (sd->isRigidBody()) {
346	>
347	>	RigidBody* rb = static_cast<RigidBody*>(sd);
348	>	int siteIndex = 0;
349	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
350	>	atom = rb->nextAtom(ai)) {
351	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
352	>	siteIndex++;
353	>	}
354	>	}
355	>	}
356	>	}
357	>	os << "    </SiteData>\n";
358	>	}
359	>	os << "  </Snapshot>\n";
360
361	<	MPI_Status istatus;
362	<	int nCurObj;
321	<	int *MolToProcMap = mpiSim->getMolToProcMap();
361	>	os.flush();
362	>	#else
363
364	<	// write out header and node 0's coordinates
364	>	const int masterNode = 0;
365	>	int worldRank;
366	>	int nProc;
367
368	<	if( worldRank == 0 ){
368	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
369	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
370
327	–	// Node 0 needs a list of the magic potatoes for each processor;
371
372	<	nProc = mpiSim->getNProcessors();
373	<	potatoes = new int[nProc];
372	>	if (worldRank == masterNode) {
373	>	os << "  <Snapshot>\n";
374	>	writeFrameProperties(os,
375	>	info_->getSnapshotManager()->getCurrentSnapshot());
376	>	os << "    <StuntDoubles>\n";
377	>	}
378
379	<	//write out the comment lines
380	<	for (i = 0; i < nProc; i++)
381	<	potatoes[i] = 0;
382	<
383	<	for(k = 0; k < outFile.size(); k++){
384	<	*outFile[k] << nTotObjects << "\n";
385	<
386	<	*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;
379	>	//every node prepares the dump lines for integrable objects belong to itself
380	>	std::string buffer;
381	>	for (mol = info_->beginMolecule(mi); mol != NULL;
382	>	mol = info_->nextMolecule(mi)) {
383	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
384	>	sd = mol->nextIntegrableObject(ii)) {
385	>	buffer += prepareDumpLine(sd);
386	>	}
387		}
388
389	<	currentIndex = 0;
390	<
358	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
389	>	if (worldRank == masterNode) {
390	>	os << buffer;
391
392	<	// Get the Node number which has this atom;
393	<
394	<	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:
392	>	for (int i = 1; i < nProc; ++i) {
393	>	// tell processor i to start sending us data:
394	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
395
396	<	potatoes[which_node] = 0;
397	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
398	<	MPI_COMM_WORLD);
399	<
400	<	}
396	>	// receive the length of the string buffer that was
397	>	// prepared by processor i:
398	>	int recvLength;
399	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
400	>	&istatus);
401
402	<	myPotato = potatoes[which_node];
403	<
404	<	//recieve the number of integrableObject in current molecule
405	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
406	<	myPotato, MPI_COMM_WORLD, &istatus);
407	<	myPotato++;
408	<
409	<	for(int l = 0; l < nCurObj; l++){
410	<
411	<	if (potatoes[which_node] + 2 >= MAXTAG) {
412	<	// The potato was going to exceed the maximum value,
413	<	// so wrap this processor potato back to 0:
414	<
415	<	potatoes[which_node] = 0;
416	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
417	<
418	<	}
419	<
420	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
421	<	myPotato, MPI_COMM_WORLD, &istatus);
422	<
423	<	atomTypeString = MPIatomTypeString;
424	<
425	<	myPotato++;
426	<
427	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
402	<	myPotato++;
403	<
404	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
405	<
406	<	if(msgLen  == 13)
407	<	isDirectional = 1;
408	<	else
409	<	isDirectional = 0;
410	<
411	<	// If we've survived to here, format the line:
412	<
413	<	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;
402	>	// create a buffer to receive the data
403	>	char* recvBuffer = new char[recvLength];
404	>	if (recvBuffer == NULL) {
405	>	} else {
406	>	// receive the data:
407	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
408	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
409	>	// send it to the file:
410	>	os << recvBuffer;
411	>	// get rid of the receive buffer:
412	>	delete [] recvBuffer;
413	>	}
414	>	}
415	>	} else {
416	>	int sendBufferLength = buffer.size() + 1;
417	>	int myturn = 0;
418	>	for (int i = 1; i < nProc; ++i){
419	>	// wait for the master node to call our number:
420	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
421	>	if (myturn == worldRank){
422	>	// send the length of our buffer:
423	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
424	>
425	>	// send our buffer:
426	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
427	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
428
429	<	}// end for(int l =0)
453	<	potatoes[which_node] = myPotato;
454	<
429	>	}
430		}
431	<	else {
432	<
433	<	haveError = 0;
434	<
435	<	local_index = indexArray[currentIndex].first;
461	<
462	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
431	>	}
432	>
433	>	if (worldRank == masterNode) {
434	>	os << "    </StuntDoubles>\n";
435	>	}
436
437	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
438	<	sd = *iter;
439	<	atomTypeString = sd->getType();
440	<
441	<	sd->getPos(pos);
442	<	sd->getVel(vel);
443	<
444	<	atomData[0] = pos[0];
445	<	atomData[1] = pos[1];
446	<	atomData[2] = pos[2];
437	>	if (doSiteData_) {
438	>	if (worldRank == masterNode) {
439	>	os << "    <SiteData>\n";
440	>	}
441	>	buffer.clear();
442	>	for (mol = info_->beginMolecule(mi); mol != NULL;
443	>	mol = info_->nextMolecule(mi)) {
444	>
445	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
446	>	sd = mol->nextIntegrableObject(ii)) {
447	>
448	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
449	>	// do one for the IO itself
450	>	buffer += prepareSiteLine(sd, ioIndex, 0);
451
452	<	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	<	}
452	>	if (sd->isRigidBody()) {
453
454	<	// If we've survived to here, format the line:
455	<
456	<	if (!isDirectional) {
457	<
458	<	sprintf( writeLine,
459	<	"%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	<
454	>	RigidBody* rb = static_cast<RigidBody*>(sd);
455	>	int siteIndex = 0;
456	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
457	>	atom = rb->nextAtom(ai)) {
458	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
459	>	siteIndex++;
460		}
461	<
462	<	for(k = 0; k < outFile.size(); k++)
540	<	*outFile[k] << writeLine;
541	<
542	<
543	<	}//end for(iter = integrableObject.begin())
544	<
545	<	currentIndex++;
461	>	}
462	>	}
463		}
464
465	<	}//end for(i = 0; i < mpiSim->getNmol())
465	>	if (worldRank == masterNode) {
466	>	os << buffer;
467	>
468	>	for (int i = 1; i < nProc; ++i) {
469	>
470	>	// tell processor i to start sending us data:
471	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
472	>
473	>	// receive the length of the string buffer that was
474	>	// prepared by processor i:
475	>	int recvLength;
476	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
477	>	&istatus);
478	>
479	>	// create a buffer to receive the data
480	>	char* recvBuffer = new char[recvLength];
481	>	if (recvBuffer == NULL) {
482	>	} else {
483	>	// receive the data:
484	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
485	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
486	>	// send it to the file:
487	>	os << recvBuffer;
488	>	// get rid of the receive buffer:
489	>	delete [] recvBuffer;
490	>	}
491	>	}
492	>	} else {
493	>	int sendBufferLength = buffer.size() + 1;
494	>	int myturn = 0;
495	>	for (int i = 1; i < nProc; ++i){
496	>	// wait for the master node to call our number:
497	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
498	>	if (myturn == worldRank){
499	>	// send the length of our buffer:
500	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
501	>	// send our buffer:
502	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
503	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
504	>	}
505	>	}
506	>	}
507	>
508	>	if (worldRank == masterNode) {
509	>	os << "    </SiteData>\n";
510	>	}
511	>	}
512
513	<	for(k = 0; k < outFile.size(); k++)
514	<	outFile[k]->flush();
513	>	if (worldRank == masterNode) {
514	>	os << "  </Snapshot>\n";
515	>	os.flush();
516	>	}
517
518	<	sprintf( checkPointMsg,
554	<	"Sucessfully took a dump.\n");
518	>	#endif // is_mpi
519
520	<	MPIcheckPoint();
557	<
558	<	delete[] potatoes;
559	<
560	<	} else {
520	>	}
521
522	<	// worldRank != 0, so I'm a remote node.
522	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
523	>
524	>	int index = sd->getGlobalIntegrableObjectIndex();
525	>	std::string type("pv");
526	>	std::string line;
527	>	char tempBuffer[4096];
528
529	<	// Set my magic potato to 0:
529	>	Vector3d pos;
530	>	Vector3d vel;
531	>	pos = sd->getPos();
532
533	<	myPotato = 0;
534	<	currentIndex = 0;
535	<
536	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
537	<
538	<	// Am I the node which has this integrableObject?
539	<
540	<	if (MolToProcMap[i] == worldRank) {
533	>	if (isinf(pos[0]) || isnan(pos[0]) ||
534	>	isinf(pos[1]) || isnan(pos[1]) ||
535	>	isinf(pos[2]) || isnan(pos[2]) ) {
536	>	sprintf( painCave.errMsg,
537	>	"DumpWriter detected a numerical error writing the position"
538	>	" for object %d", index);
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542
543	+	vel = sd->getVel();
544
545	<	if (myPotato + 1 >= MAXTAG) {
546	<
547	<	// The potato was going to exceed the maximum value,
548	<	// so wrap this processor potato back to 0 (and block until
549	<	// node 0 says we can go:
550	<
551	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
552	<
553	<	}
545	>	if (isinf(vel[0]) || isnan(vel[0]) ||
546	>	isinf(vel[1]) || isnan(vel[1]) ||
547	>	isinf(vel[2]) || isnan(vel[2]) ) {
548	>	sprintf( painCave.errMsg,
549	>	"DumpWriter detected a numerical error writing the velocity"
550	>	" for object %d", index);
551	>	painCave.isFatal = 1;
552	>	simError();
553	>	}
554
555	<	local_index = indexArray[currentIndex].first;
556	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
557	<
558	<	nCurObj = integrableObjects.size();
590	<
591	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
592	<	myPotato, MPI_COMM_WORLD);
593	<	myPotato++;
555	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
556	>	pos[0], pos[1], pos[2],
557	>	vel[0], vel[1], vel[2]);
558	>	line += tempBuffer;
559
560	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
560	>	if (sd->isDirectional()) {
561	>	type += "qj";
562	>	Quat4d q;
563	>	Vector3d ji;
564	>	q = sd->getQ();
565
566	<	if (myPotato + 2 >= MAXTAG) {
567	<
568	<	// The potato was going to exceed the maximum value,
569	<	// so wrap this processor potato back to 0 (and block until
570	<	// node 0 says we can go:
571	<
572	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
573	<
574	<	}
575	<
607	<	sd = *iter;
608	<
609	<	atomTypeString = sd->getType();
566	>	if (isinf(q[0]) || isnan(q[0]) ||
567	>	isinf(q[1]) || isnan(q[1]) ||
568	>	isinf(q[2]) || isnan(q[2]) ||
569	>	isinf(q[3]) || isnan(q[3]) ) {
570	>	sprintf( painCave.errMsg,
571	>	"DumpWriter detected a numerical error writing the quaternion"
572	>	" for object %d", index);
573	>	painCave.isFatal = 1;
574	>	simError();
575	>	}
576
577	<	sd->getPos(pos);
578	<	sd->getVel(vel);
577	>	ji = sd->getJ();
578	>
579	>	if (isinf(ji[0]) || isnan(ji[0]) ||
580	>	isinf(ji[1]) || isnan(ji[1]) ||
581	>	isinf(ji[2]) || isnan(ji[2]) ) {
582	>	sprintf( painCave.errMsg,
583	>	"DumpWriter detected a numerical error writing the angular"
584	>	" momentum for object %d", index);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588
589	<	atomData[0] = pos[0];
590	<	atomData[1] = pos[1];
591	<	atomData[2] = pos[2];
589	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
590	>	q[0], q[1], q[2], q[3],
591	>	ji[0], ji[1], ji[2]);
592	>	line += tempBuffer;
593	>	}
594
595	<	atomData[3] = vel[0];
596	<	atomData[4] = vel[1];
597	<	atomData[5] = vel[2];
598	<
599	<	isDirectional = 0;
600	<
601	<	if( sd->isDirectional() ){
602	<
603	<	isDirectional = 1;
604	<
605	<	sd->getQ( q );
606	<	sd->getJ( ji );
607	<
608	<
609	<	atomData[6] = q[0];
633	<	atomData[7] = q[1];
634	<	atomData[8] = q[2];
635	<	atomData[9] = q[3];
595	>	if (needForceVector_) {
596	>	type += "f";
597	>	Vector3d frc = sd->getFrc();
598	>	if (isinf(frc[0]) || isnan(frc[0]) ||
599	>	isinf(frc[1]) || isnan(frc[1]) ||
600	>	isinf(frc[2]) || isnan(frc[2]) ) {
601	>	sprintf( painCave.errMsg,
602	>	"DumpWriter detected a numerical error writing the force"
603	>	" for object %d", index);
604	>	painCave.isFatal = 1;
605	>	simError();
606	>	}
607	>	sprintf(tempBuffer, " %13e %13e %13e",
608	>	frc[0], frc[1], frc[2]);
609	>	line += tempBuffer;
610
611	<	atomData[10] = ji[0];
612	<	atomData[11] = ji[1];
613	<	atomData[12] = ji[2];
614	<	}
611	>	if (sd->isDirectional()) {
612	>	type += "t";
613	>	Vector3d trq = sd->getTrq();
614	>	if (isinf(trq[0]) || isnan(trq[0]) ||
615	>	isinf(trq[1]) || isnan(trq[1]) ||
616	>	isinf(trq[2]) || isnan(trq[2]) ) {
617	>	sprintf( painCave.errMsg,
618	>	"DumpWriter detected a numerical error writing the torque"
619	>	" for object %d", index);
620	>	painCave.isFatal = 1;
621	>	simError();
622	>	}
623	>	sprintf(tempBuffer, " %13e %13e %13e",
624	>	trq[0], trq[1], trq[2]);
625	>	line += tempBuffer;
626	>	}
627	>	}
628
629	<
630	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
629	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
630	>	return std::string(tempBuffer);
631	>	}
632
633	<	// null terminate the string before sending (just in case):
634	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
633	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
634	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
635
636	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
637	<	myPotato, MPI_COMM_WORLD);
638	<
639	<	myPotato++;
652	<
653	<	if (isDirectional) {
636	>	std::string id;
637	>	std::string type;
638	>	std::string line;
639	>	char tempBuffer[4096];
640
641	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
642	<	myPotato, MPI_COMM_WORLD);
641	>	if (sd->isRigidBody()) {
642	>	sprintf(tempBuffer, "%10d           ", ioIndex);
643	>	id = std::string(tempBuffer);
644	>	} else {
645	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
646	>	id = std::string(tempBuffer);
647	>	}
648
649	<	} else {
649	>	if (needFlucQ_) {
650	>	if (storageLayout & DataStorage::dslFlucQPosition) {
651	>	type += "c";
652	>	RealType fqPos = sd->getFlucQPos();
653	>	if (isinf(fqPos) || isnan(fqPos) ) {
654	>	sprintf( painCave.errMsg,
655	>	"DumpWriter detected a numerical error writing the"
656	>	" fluctuating charge for object %s", id.c_str());
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>	sprintf(tempBuffer, " %13e ", fqPos);
661	>	line += tempBuffer;
662	>	}
663
664	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
665	<	myPotato, MPI_COMM_WORLD);
666	<	}
664	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
665	>	type += "w";
666	>	RealType fqVel = sd->getFlucQVel();
667	>	if (isinf(fqVel) || isnan(fqVel) ) {
668	>	sprintf( painCave.errMsg,
669	>	"DumpWriter detected a numerical error writing the"
670	>	" fluctuating charge velocity for object %s", id.c_str());
671	>	painCave.isFatal = 1;
672	>	simError();
673	>	}
674	>	sprintf(tempBuffer, " %13e ", fqVel);
675	>	line += tempBuffer;
676	>	}
677
678	<	myPotato++;
679	<
678	>	if (needForceVector_) {
679	>	if (storageLayout & DataStorage::dslFlucQForce) {
680	>	type += "g";
681	>	RealType fqFrc = sd->getFlucQFrc();
682	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
683	>	sprintf( painCave.errMsg,
684	>	"DumpWriter detected a numerical error writing the"
685	>	" fluctuating charge force for object %s", id.c_str());
686	>	painCave.isFatal = 1;
687	>	simError();
688		}
689	+	sprintf(tempBuffer, " %13e ", fqFrc);
690	+	line += tempBuffer;
691	+	}
692	+	}
693	+	}
694	+
695	+	if (needElectricField_) {
696	+	if (storageLayout & DataStorage::dslElectricField) {
697	+	type += "e";
698	+	Vector3d eField= sd->getElectricField();
699	+	if (isinf(eField[0]) || isnan(eField[0]) ||
700	+	isinf(eField[1]) || isnan(eField[1]) ||
701	+	isinf(eField[2]) || isnan(eField[2]) ) {
702	+	sprintf( painCave.errMsg,
703	+	"DumpWriter detected a numerical error writing the electric"
704	+	" field for object %s", id.c_str());
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708	+	sprintf(tempBuffer, " %13e %13e %13e",
709	+	eField[0], eField[1], eField[2]);
710	+	line += tempBuffer;
711	+	}
712	+	}
713
714	<	currentIndex++;
715	<
714	>
715	>	if (needParticlePot_) {
716	>	if (storageLayout & DataStorage::dslParticlePot) {
717	>	type += "u";
718	>	RealType particlePot = sd->getParticlePot();
719	>	if (isinf(particlePot) || isnan(particlePot)) {
720	>	sprintf( painCave.errMsg,
721	>	"DumpWriter detected a numerical error writing the particle "
722	>	" potential for object %s", id.c_str());
723	>	painCave.isFatal = 1;
724	>	simError();
725		}
726	<
726	>	sprintf(tempBuffer, " %13e", particlePot);
727	>	line += tempBuffer;
728		}
729	+	}
730	+
731	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
732	+	return std::string(tempBuffer);
733	+	}
734
735	<	sprintf( checkPointMsg,
736	<	"Successfully took a dump.\n");
737	<	MPIcheckPoint();
735	>	void DumpWriter::writeDump() {
736	>	writeFrame(*dumpFile_);
737	>	}
738	>
739	>	void DumpWriter::writeEor() {
740	>
741	>	std::ostream* eorStream = NULL;
742	>
743	>	#ifdef IS_MPI
744	>	if (worldRank == 0) {
745	>	#endif // is_mpi
746	>
747	>	eorStream = createOStream(eorFilename_);
748	>
749	>	#ifdef IS_MPI
750	>	}
751	>	#endif
752
753	+	writeFrame(*eorStream);
754	+
755	+	#ifdef IS_MPI
756	+	if (worldRank == 0) {
757	+	#endif
758	+
759	+	writeClosing(*eorStream);
760	+	delete eorStream;
761	+
762	+	#ifdef IS_MPI
763	+	}
764	+	#endif // is_mpi
765	+
766		}
767	<
767	>
768	>
769	>	void DumpWriter::writeDumpAndEor() {
770	>	std::vector<std::streambuf*> buffers;
771	>	std::ostream* eorStream;
772	>	#ifdef IS_MPI
773	>	if (worldRank == 0) {
774		#endif // is_mpi
775	<	}
775	>	buffers.push_back(dumpFile_->rdbuf());
776	>	eorStream = createOStream(eorFilename_);
777	>	buffers.push_back(eorStream->rdbuf());
778	>	#ifdef IS_MPI
779	>	}
780	>	#endif // is_mpi
781
782	+	TeeBuf tbuf(buffers.begin(), buffers.end());
783	+	std::ostream os(&tbuf);
784	+	writeFrame(os);
785	+
786		#ifdef IS_MPI
787	+	if (worldRank == 0) {
788	+	#endif // is_mpi
789	+	writeClosing(*eorStream);
790	+	delete eorStream;
791	+	#ifdef IS_MPI
792	+	}
793	+	#endif // is_mpi
794	+	}
795
796	<	// a couple of functions to let us escape the write loop
796	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
797
798	<	void dWrite::DieDieDie( void ){
798	>	std::ostream* newOStream;
799	>	#ifdef HAVE_ZLIB
800	>	if (needCompression_) {
801	>	newOStream = new ogzstream(filename.c_str());
802	>	} else {
803	>	newOStream = new std::ofstream(filename.c_str());
804	>	}
805	>	#else
806	>	newOStream = new std::ofstream(filename.c_str());
807	>	#endif
808	>	//write out MetaData first
809	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
810	>	(*newOStream) << "  <MetaData>" << std::endl;
811	>	(*newOStream) << info_->getRawMetaData();
812	>	(*newOStream) << "  </MetaData>" << std::endl;
813	>	return newOStream;
814	>	}
815
816	<	MPI_Finalize();
690	<	exit (0);
691	<	}
816	>	void DumpWriter::writeClosing(std::ostream& os) {
817
818	<	#endif //is_mpi
818	>	os << "</OpenMD>\n";
819	>	os.flush();
820	>	}
821	>
822	>	}//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.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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