ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1921 by gezelter, Thu Aug 1 18:23:07 2013 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 "io/DumpWriter.hpp"
44	>	#include "primitives/Molecule.hpp"
45	>	#include "utils/simError.h"
46	>	#include "io/basic_teebuf.hpp"
47	>	#ifdef HAVE_ZLIB
48	>	#include "io/gzstream.hpp"
49	>	#endif
50	>	#include "io/Globals.hpp"
51
52	<	#include <string.h>
53	<	#include <iostream>
54	<	#include <fstream>
55	<	#include <algorithm>
8	<	#include <utility>
52	>	#ifdef _MSC_VER
53	>	#define isnan(x) _isnan((x))
54	>	#define isinf(x) (!_finite(x) && !_isnan(x))
55	>	#endif
56
57		#ifdef IS_MPI
58		#include <mpi.h>
59	<	#include "brains/mpiSimulation.hpp"
59	>	#endif
60
61	<	namespace dWrite{
62	<	void DieDieDie( void );
16	<	}
61	>	using namespace std;
62	>	namespace OpenMD {
63
64	<	using namespace dWrite;
65	<	#endif //is_mpi
64	>	DumpWriter::DumpWriter(SimInfo* info)
65	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66
67	<	#include "io/ReadWrite.hpp"
68	<	#include "utils/simError.h"
67	>	Globals* simParams = info->getSimParams();
68	>	needCompression_   = simParams->getCompressDumpFile();
69	>	needForceVector_   = simParams->getOutputForceVector();
70	>	needParticlePot_   = simParams->getOutputParticlePotential();
71	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
72	>	needElectricField_ = simParams->getOutputElectricField();
73
74	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
74	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75	>	doSiteData_ = true;
76	>	} else {
77	>	doSiteData_ = false;
78	>	}
79
80	<	entry_plug = the_entry_plug;
81	<
80	>	createDumpFile_ = true;
81	>	#ifdef HAVE_LIBZ
82	>	if (needCompression_) {
83	>	filename_ += ".gz";
84	>	eorFilename_ += ".gz";
85	>	}
86	>	#endif
87	>
88		#ifdef IS_MPI
89	<	if(worldRank == 0 ){
89	>
90	>	if (worldRank == 0) {
91		#endif // is_mpi
92	+
93	+	dumpFile_ = createOStream(filename_);
94
95	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
95	>	if (!dumpFile_) {
96	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	>	filename_.c_str());
98	>	painCave.isFatal = 1;
99	>	simError();
100	>	}
101
102	<	if( !dumpFile ){
102	>	#ifdef IS_MPI
103
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();
104		}
105
106	<	#ifdef IS_MPI
106	>	#endif // is_mpi
107	>
108		}
109
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	–	}
110
111	<	DumpWriter::~DumpWriter( ){
111	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112	>	: info_(info), filename_(filename){
113
114	<	#ifdef IS_MPI
115	<	if(worldRank == 0 ){
59	<	#endif // is_mpi
114	>	Globals* simParams = info->getSimParams();
115	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116
117	<	dumpFile.close();
117	>	needCompression_   = simParams->getCompressDumpFile();
118	>	needForceVector_   = simParams->getOutputForceVector();
119	>	needParticlePot_   = simParams->getOutputParticlePotential();
120	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
121	>	needElectricField_ = simParams->getOutputElectricField();
122
123	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124	+	doSiteData_ = true;
125	+	} else {
126	+	doSiteData_ = false;
127	+	}
128	+
129	+	createDumpFile_ = true;
130	+	#ifdef HAVE_LIBZ
131	+	if (needCompression_) {
132	+	filename_ += ".gz";
133	+	eorFilename_ += ".gz";
134	+	}
135	+	#endif
136	+
137		#ifdef IS_MPI
138	<	}
138	>
139	>	if (worldRank == 0) {
140		#endif // is_mpi
66	–	}
141
142	+
143	+	dumpFile_ = createOStream(filename_);
144	+
145	+	if (!dumpFile_) {
146	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	+	filename_.c_str());
148	+	painCave.isFatal = 1;
149	+	simError();
150	+	}
151	+
152		#ifdef IS_MPI
153
154	<	/**
71	<	* A hook function to load balancing
72	<	*/
154	>	}
155
156	<	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	<	}
156	>	#endif // is_mpi
157
158	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
158	>	}
159
160	<	for(int i = 0; i < entry_plug->n_mol;i++)
161	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
162	<
163	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
164	<	}
160	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161	>	: info_(info), filename_(filename){
162	>
163	>	Globals* simParams = info->getSimParams();
164	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165	>
166	>	needCompression_   = simParams->getCompressDumpFile();
167	>	needForceVector_   = simParams->getOutputForceVector();
168	>	needParticlePot_   = simParams->getOutputParticlePotential();
169	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	>	needElectricField_ = simParams->getOutputElectricField();
171
172	<	#endif
172	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	>	doSiteData_ = true;
174	>	} else {
175	>	doSiteData_ = false;
176	>	}
177
178	<	void DumpWriter::writeDump(double currentTime){
179	<
180	<	ofstream finalOut;
181	<	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();
178	>	#ifdef HAVE_LIBZ
179	>	if (needCompression_) {
180	>	filename_ += ".gz";
181	>	eorFilename_ += ".gz";
182		}
183	+	#endif
184	+
185		#ifdef IS_MPI
186	<	}
186	>
187	>	if (worldRank == 0) {
188		#endif // is_mpi
189	+
190	+	createDumpFile_ = writeDumpFile;
191	+	if (createDumpFile_) {
192	+	dumpFile_ = createOStream(filename_);
193	+
194	+	if (!dumpFile_) {
195	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
196	+	filename_.c_str());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+	}
201	+	#ifdef IS_MPI
202	+
203	+	}
204
205	<	fileStreams.push_back(&finalOut);
206	<	fileStreams.push_back(&dumpFile);
205	>
206	>	#endif // is_mpi
207	>
208	>	}
209
210	<	writeFrame(fileStreams, currentTime);
210	>	DumpWriter::~DumpWriter() {
211
212		#ifdef IS_MPI
128	–	finalOut.close();
129	–	#endif
130	–
131	–	}
213
214	<	void DumpWriter::writeFinal(double currentTime){
214	>	if (worldRank == 0) {
215	>	#endif // is_mpi
216	>	if (createDumpFile_){
217	>	writeClosing(*dumpFile_);
218	>	delete dumpFile_;
219	>	}
220	>	#ifdef IS_MPI
221
222	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
222	>	}
223
138	–	#ifdef IS_MPI
139	–	if(worldRank == 0 ){
224		#endif // is_mpi
225
226	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
226	>	}
227
228	<	if( !finalOut ){
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229	>
230	>	char buffer[1024];
231	>
232	>	os << "    <FrameData>\n";
233	>
234	>	RealType currentTime = s->getTime();
235	>
236	>	if (isinf(currentTime) || isnan(currentTime)) {
237		sprintf( painCave.errMsg,
238	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
238	>	"DumpWriter detected a numerical error writing the time");
239		painCave.isFatal = 1;
240		simError();
241		}
242	+
243	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	+	os << buffer;
245
246	<	#ifdef IS_MPI
247	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
246	>	Mat3x3d hmat;
247	>	hmat = s->getHmat();
248
249	<	#ifdef IS_MPI
250	<	finalOut.close();
251	<	#endif
252	<
253	<	}
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the box");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259	>
260	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
262	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
263	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
264	>	os << buffer;
265
266	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	const int BUFFERSIZE = 2000;
269	<	const int MINIBUFFERSIZE = 100;
268	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269	>	isinf(thermostat.second) || isnan(thermostat.second)) {
270	>	sprintf( painCave.errMsg,
271	>	"DumpWriter detected a numerical error writing the thermostat");
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276	>	thermostat.second);
277	>	os << buffer;
278
279	<	char tempBuffer[BUFFERSIZE];
280	<	char writeLine[BUFFERSIZE];
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281
282	<	int i;
283	<	unsigned int k;
282	>	for (unsigned int i = 0; i < 3; i++) {
283	>	for (unsigned int j = 0; j < 3; j++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292
293	<	#ifdef IS_MPI
294	<
295	<	/*********************************************************************
296	<	* Documentation?  You want DOCUMENTATION?
297	<	*
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	<	*********************************************************************/
293	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294	>	eta(0, 0), eta(1, 0), eta(2, 0),
295	>	eta(0, 1), eta(1, 1), eta(2, 1),
296	>	eta(0, 2), eta(1, 2), eta(2, 2));
297	>	os << buffer;
298
299	<	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;
299	>	os << "    </FrameData>\n";
300		}
258	–
259	–	for( i=0; i< entry_plug->n_mol; i++ ){
301
302	<	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);
302	>	void DumpWriter::writeFrame(std::ostream& os) {
303
304	<	sprintf( tempBuffer,
305	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
306	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
304	>	#ifdef IS_MPI
305	>	MPI::Status istatus;
306	>	#endif
307
308	<	if( sd->isDirectional() ){
308	>	Molecule* mol;
309	>	StuntDouble* sd;
310	>	SimInfo::MoleculeIterator mi;
311	>	Molecule::IntegrableObjectIterator ii;
312	>	RigidBody::AtomIterator ai;
313
314	<	sd->getQ( q );
315	<	sd->getJ( ji );
314	>	#ifndef IS_MPI
315	>	os << "  <Snapshot>\n";
316	>
317	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318
319	<	sprintf( tempBuffer,
320	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
321	<	q[0],
288	<	q[1],
289	<	q[2],
290	<	q[3],
291	<	ji[0],
292	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
295	<	}
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;
301	<	}
302	<
303	<	}
304	<
305	<	#else // is_mpi
306	<
307	<	/* 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	<	}
316	<
317	<	int haveError;
318	<
319	<	MPI_Status istatus;
320	<	int nCurObj;
321	<	int *MolToProcMap = mpiSim->getMolToProcMap();
322	<
323	<	// write out header and node 0's coordinates
324	<
325	<	if( worldRank == 0 ){
326	<
327	<	// Node 0 needs a list of the magic potatoes for each processor;
328	<
329	<	nProc = mpiSim->getNProcessors();
330	<	potatoes = new int[nProc];
331	<
332	<	//write out the comment lines
333	<	for (i = 0; i < nProc; i++)
334	<	potatoes[i] = 0;
335	<
336	<	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() << endl;
353	<	}
354	<
355	<	currentIndex = 0;
356	<
357	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
319	>	os << "    <StuntDoubles>\n";
320	>	for (mol = info_->beginMolecule(mi); mol != NULL;
321	>	mol = info_->nextMolecule(mi)) {
322
323	<	// Get the Node number which has this atom;
324	<
325	<	which_node = MolToProcMap[i];
362	<
363	<	if (which_node != 0) {
364	<
365	<	if (potatoes[which_node] + 1 >= MAXTAG) {
366	<	// The potato was going to exceed the maximum value,
367	<	// so wrap this processor potato back to 0:
368	<
369	<	potatoes[which_node] = 0;
370	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
323	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
324	>	sd = mol->nextIntegrableObject(ii)) {
325	>	os << prepareDumpLine(sd);
326
327	<	}
327	>	}
328	>	}
329	>	os << "    </StuntDoubles>\n";
330
331	<	myPotato = potatoes[which_node];
331	>	if (doSiteData_) {
332	>	os << "    <SiteData>\n";
333	>	for (mol = info_->beginMolecule(mi); mol != NULL;
334	>	mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	<	//recieve the number of integrableObject in current molecule
340	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
341	<	myPotato, MPI_COMM_WORLD, &istatus);
379	<	myPotato++;
380	<
381	<	for(int l = 0; l < nCurObj; l++){
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	if (potatoes[which_node] + 2 >= MAXTAG) {
384	<	// The potato was going to exceed the maximum value,
385	<	// so wrap this processor potato back to 0:
386	<
387	<	potatoes[which_node] = 0;
388	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
343	>	if (sd->isRigidBody()) {
344
345	+	RigidBody* rb = static_cast<RigidBody*>(sd);
346	+	int siteIndex = 0;
347	+	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
348	+	atom = rb->nextAtom(ai)) {
349	+	os << prepareSiteLine(atom, ioIndex, siteIndex);
350	+	siteIndex++;
351	+	}
352		}
353	+	}
354	+	}
355	+	os << "    </SiteData>\n";
356	+	}
357	+	os << "  </Snapshot>\n";
358
359	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
360	<	myPotato, MPI_COMM_WORLD, &istatus);
359	>	os.flush();
360	>	#else
361
362	<	atomTypeString = MPIatomTypeString;
362	>	const int masterNode = 0;
363	>	int worldRank = MPI::COMM_WORLD.Get_rank();
364	>	int nProc = MPI::COMM_WORLD.Get_size();
365
366	<	myPotato++;
366	>	if (worldRank == masterNode) {
367	>	os << "  <Snapshot>\n";
368	>	writeFrameProperties(os,
369	>	info_->getSnapshotManager()->getCurrentSnapshot());
370	>	os << "    <StuntDoubles>\n";
371	>	}
372
373	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
374	<	myPotato++;
373	>	//every node prepares the dump lines for integrable objects belong to itself
374	>	std::string buffer;
375	>	for (mol = info_->beginMolecule(mi); mol != NULL;
376	>	mol = info_->nextMolecule(mi)) {
377	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378	>	sd = mol->nextIntegrableObject(ii)) {
379	>	buffer += prepareDumpLine(sd);
380	>	}
381	>	}
382	>
383	>	if (worldRank == masterNode) {
384	>	os << buffer;
385	>
386	>	for (int i = 1; i < nProc; ++i) {
387	>	// tell processor i to start sending us data:
388	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389
390	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
390	>	// receive the length of the string buffer that was
391	>	// prepared by processor i:
392	>	int recvLength;
393	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394	>	istatus);
395
396	<	if(msgLen  == 13)
397	<	isDirectional = 1;
398	<	else
399	<	isDirectional = 0;
396	>	// create a buffer to receive the data
397	>	char* recvBuffer = new char[recvLength];
398	>	if (recvBuffer == NULL) {
399	>	} else {
400	>	// receive the data:
401	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
402	>	MPI::ANY_TAG, istatus);
403	>	// send it to the file:
404	>	os << recvBuffer;
405	>	// get rid of the receive buffer:
406	>	delete [] recvBuffer;
407	>	}
408	>	}
409	>	} else {
410	>	int sendBufferLength = buffer.size() + 1;
411	>	int myturn = 0;
412	>	for (int i = 1; i < nProc; ++i){
413	>	// wait for the master node to call our number:
414	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415	>	if (myturn == worldRank){
416	>	// send the length of our buffer:
417	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418	>
419	>	// send our buffer:
420	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421	>	MPI::CHAR, masterNode, 0);
422	>
423	>	}
424	>	}
425	>	}
426	>
427	>	if (worldRank == masterNode) {
428	>	os << "    </StuntDoubles>\n";
429	>	}
430	>
431	>	if (doSiteData_) {
432	>	if (worldRank == masterNode) {
433	>	os << "    <SiteData>\n";
434	>	}
435	>	buffer.clear();
436	>	for (mol = info_->beginMolecule(mi); mol != NULL;
437	>	mol = info_->nextMolecule(mi)) {
438	>
439	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
440	>	sd = mol->nextIntegrableObject(ii)) {
441
442	<	// If we've survived to here, format the line:
442	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
443	>	// do one for the IO itself
444	>	buffer += prepareSiteLine(sd, ioIndex, 0);
445	>
446	>	if (sd->isRigidBody()) {
447
448	<	if (!isDirectional) {
449	<
450	<	sprintf( writeLine,
451	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
452	<	atomTypeString,
453	<	atomData[0],
454	<	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	<
448	>	RigidBody* rb = static_cast<RigidBody*>(sd);
449	>	int siteIndex = 0;
450	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
451	>	atom = rb->nextAtom(ai)) {
452	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
453	>	siteIndex++;
454	>	}
455		}
456	+	}
457	+	}
458	+
459	+	if (worldRank == masterNode) {
460	+	os << buffer;
461	+
462	+	for (int i = 1; i < nProc; ++i) {
463
464	<	for(k = 0; k < outFile.size(); k++)
465	<	*outFile[k] << writeLine;
464	>	// tell processor i to start sending us data:
465	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
466	>
467	>	// receive the length of the string buffer that was
468	>	// prepared by processor i:
469	>	int recvLength;
470	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
471	>	istatus);
472	>
473	>	// create a buffer to receive the data
474	>	char* recvBuffer = new char[recvLength];
475	>	if (recvBuffer == NULL) {
476	>	} else {
477	>	// receive the data:
478	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
479	>	MPI::ANY_TAG, istatus);
480	>	// send it to the file:
481	>	os << recvBuffer;
482	>	// get rid of the receive buffer:
483	>	delete [] recvBuffer;
484	>	}
485	>	}
486	>	} else {
487	>	int sendBufferLength = buffer.size() + 1;
488	>	int myturn = 0;
489	>	for (int i = 1; i < nProc; ++i){
490	>	// wait for the master node to call our number:
491	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
492	>	if (myturn == worldRank){
493	>	// send the length of our buffer:
494	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
495	>	// send our buffer:
496	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
497	>	MPI::CHAR, masterNode, 0);
498	>	}
499	>	}
500	>	}
501	>
502	>	if (worldRank == masterNode) {
503	>	os << "    </SiteData>\n";
504	>	}
505	>	}
506	>
507	>	if (worldRank == masterNode) {
508	>	os << "  </Snapshot>\n";
509	>	os.flush();
510	>	}
511	>
512	>	#endif // is_mpi
513	>
514	>	}
515
516	<	}// end for(int l =0)
517	<	potatoes[which_node] = myPotato;
516	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
517	>
518	>	int index = sd->getGlobalIntegrableObjectIndex();
519	>	std::string type("pv");
520	>	std::string line;
521	>	char tempBuffer[4096];
522
523	<	}
524	<	else {
525	<
456	<	haveError = 0;
457	<
458	<	local_index = indexArray[currentIndex].first;
523	>	Vector3d pos;
524	>	Vector3d vel;
525	>	pos = sd->getPos();
526
527	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
527	>	if (isinf(pos[0]) || isnan(pos[0]) ||
528	>	isinf(pos[1]) || isnan(pos[1]) ||
529	>	isinf(pos[2]) || isnan(pos[2]) ) {
530	>	sprintf( painCave.errMsg,
531	>	"DumpWriter detected a numerical error writing the position"
532	>	" for object %d", index);
533	>	painCave.isFatal = 1;
534	>	simError();
535	>	}
536
537	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
463	<	sd = *iter;
464	<	atomTypeString = sd->getType();
465	<
466	<	sd->getPos(pos);
467	<	sd->getVel(vel);
468	<
469	<	atomData[0] = pos[0];
470	<	atomData[1] = pos[1];
471	<	atomData[2] = pos[2];
537	>	vel = sd->getVel();
538
539	<	atomData[3] = vel[0];
540	<	atomData[4] = vel[1];
541	<	atomData[5] = vel[2];
542	<
543	<	isDirectional = 0;
539	>	if (isinf(vel[0]) || isnan(vel[0]) ||
540	>	isinf(vel[1]) || isnan(vel[1]) ||
541	>	isinf(vel[2]) || isnan(vel[2]) ) {
542	>	sprintf( painCave.errMsg,
543	>	"DumpWriter detected a numerical error writing the velocity"
544	>	" for object %d", index);
545	>	painCave.isFatal = 1;
546	>	simError();
547	>	}
548
549	<	if( sd->isDirectional() ){
549	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
550	>	pos[0], pos[1], pos[2],
551	>	vel[0], vel[1], vel[2]);
552	>	line += tempBuffer;
553
554	<	isDirectional = 1;
555	<
556	<	sd->getQ( q );
557	<	sd->getJ( ji );
554	>	if (sd->isDirectional()) {
555	>	type += "qj";
556	>	Quat4d q;
557	>	Vector3d ji;
558	>	q = sd->getQ();
559
560	<	for (int j = 0; j < 6 ; j++)
561	<	atomData[j] = atomData[j];
562	<
563	<	atomData[6] = q[0];
564	<	atomData[7] = q[1];
565	<	atomData[8] = q[2];
566	<	atomData[9] = q[3];
567	<
568	<	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++;
560	>	if (isinf(q[0]) || isnan(q[0]) ||
561	>	isinf(q[1]) || isnan(q[1]) ||
562	>	isinf(q[2]) || isnan(q[2]) ||
563	>	isinf(q[3]) || isnan(q[3]) ) {
564	>	sprintf( painCave.errMsg,
565	>	"DumpWriter detected a numerical error writing the quaternion"
566	>	" for object %d", index);
567	>	painCave.isFatal = 1;
568	>	simError();
569		}
570
571	<	}//end for(i = 0; i < mpiSim->getNmol())
547	<
548	<	for(k = 0; k < outFile.size(); k++)
549	<	outFile[k]->flush();
550	<
551	<	sprintf( checkPointMsg,
552	<	"Sucessfully took a dump.\n");
553	<
554	<	MPIcheckPoint();
555	<
556	<	delete[] potatoes;
557	<
558	<	} else {
571	>	ji = sd->getJ();
572
573	<	// worldRank != 0, so I'm a remote node.
573	>	if (isinf(ji[0]) || isnan(ji[0]) ||
574	>	isinf(ji[1]) || isnan(ji[1]) ||
575	>	isinf(ji[2]) || isnan(ji[2]) ) {
576	>	sprintf( painCave.errMsg,
577	>	"DumpWriter detected a numerical error writing the angular"
578	>	" momentum for object %d", index);
579	>	painCave.isFatal = 1;
580	>	simError();
581	>	}
582
583	<	// Set my magic potato to 0:
583	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
584	>	q[0], q[1], q[2], q[3],
585	>	ji[0], ji[1], ji[2]);
586	>	line += tempBuffer;
587	>	}
588
589	<	myPotato = 0;
590	<	currentIndex = 0;
591	<
592	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
589	>	if (needForceVector_) {
590	>	type += "f";
591	>	Vector3d frc = sd->getFrc();
592	>	if (isinf(frc[0]) || isnan(frc[0]) ||
593	>	isinf(frc[1]) || isnan(frc[1]) ||
594	>	isinf(frc[2]) || isnan(frc[2]) ) {
595	>	sprintf( painCave.errMsg,
596	>	"DumpWriter detected a numerical error writing the force"
597	>	" for object %d", index);
598	>	painCave.isFatal = 1;
599	>	simError();
600	>	}
601	>	sprintf(tempBuffer, " %13e %13e %13e",
602	>	frc[0], frc[1], frc[2]);
603	>	line += tempBuffer;
604
605	<	// Am I the node which has this integrableObject?
606	<
607	<	if (MolToProcMap[i] == worldRank) {
605	>	if (sd->isDirectional()) {
606	>	type += "t";
607	>	Vector3d trq = sd->getTrq();
608	>	if (isinf(trq[0]) || isnan(trq[0]) ||
609	>	isinf(trq[1]) || isnan(trq[1]) ||
610	>	isinf(trq[2]) || isnan(trq[2]) ) {
611	>	sprintf( painCave.errMsg,
612	>	"DumpWriter detected a numerical error writing the torque"
613	>	" for object %d", index);
614	>	painCave.isFatal = 1;
615	>	simError();
616	>	}
617	>	sprintf(tempBuffer, " %13e %13e %13e",
618	>	trq[0], trq[1], trq[2]);
619	>	line += tempBuffer;
620	>	}
621	>	}
622
623	+	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
624	+	return std::string(tempBuffer);
625	+	}
626
627	<	if (myPotato + 1 >= MAXTAG) {
628	<
576	<	// The potato was going to exceed the maximum value,
577	<	// so wrap this processor potato back to 0 (and block until
578	<	// node 0 says we can go:
579	<
580	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581	<
582	<	}
627	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
629
630	<	local_index = indexArray[currentIndex].first;
631	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
632	<
633	<	nCurObj = integrableObjects.size();
588	<
589	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
590	<	myPotato, MPI_COMM_WORLD);
591	<	myPotato++;
630	>	std::string id;
631	>	std::string type;
632	>	std::string line;
633	>	char tempBuffer[4096];
634
635	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
636	<
637	<	if (myPotato + 2 >= MAXTAG) {
638	<
639	<	// The potato was going to exceed the maximum value,
640	<	// so wrap this processor potato back to 0 (and block until
641	<	// node 0 says we can go:
600	<
601	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
635	>	if (sd->isRigidBody()) {
636	>	sprintf(tempBuffer, "%10d           ", ioIndex);
637	>	id = std::string(tempBuffer);
638	>	} else {
639	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
640	>	id = std::string(tempBuffer);
641	>	}
642
643	<	}
644	<
645	<	sd = *iter;
646	<
647	<	atomTypeString = sd->getType();
643	>	if (needFlucQ_) {
644	>	if (storageLayout & DataStorage::dslFlucQPosition) {
645	>	type += "c";
646	>	RealType fqPos = sd->getFlucQPos();
647	>	if (isinf(fqPos) || isnan(fqPos) ) {
648	>	sprintf( painCave.errMsg,
649	>	"DumpWriter detected a numerical error writing the"
650	>	" fluctuating charge for object %s", id.c_str());
651	>	painCave.isFatal = 1;
652	>	simError();
653	>	}
654	>	sprintf(tempBuffer, " %13e ", fqPos);
655	>	line += tempBuffer;
656	>	}
657
658	<	sd->getPos(pos);
659	<	sd->getVel(vel);
658	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
659	>	type += "w";
660	>	RealType fqVel = sd->getFlucQVel();
661	>	if (isinf(fqVel) || isnan(fqVel) ) {
662	>	sprintf( painCave.errMsg,
663	>	"DumpWriter detected a numerical error writing the"
664	>	" fluctuating charge velocity for object %s", id.c_str());
665	>	painCave.isFatal = 1;
666	>	simError();
667	>	}
668	>	sprintf(tempBuffer, " %13e ", fqVel);
669	>	line += tempBuffer;
670	>	}
671
672	<	atomData[0] = pos[0];
673	<	atomData[1] = pos[1];
674	<	atomData[2] = pos[2];
672	>	if (needForceVector_) {
673	>	if (storageLayout & DataStorage::dslFlucQForce) {
674	>	type += "g";
675	>	RealType fqFrc = sd->getFlucQFrc();
676	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
677	>	sprintf( painCave.errMsg,
678	>	"DumpWriter detected a numerical error writing the"
679	>	" fluctuating charge force for object %s", id.c_str());
680	>	painCave.isFatal = 1;
681	>	simError();
682	>	}
683	>	sprintf(tempBuffer, " %13e ", fqFrc);
684	>	line += tempBuffer;
685	>	}
686	>	}
687	>	}
688	>
689	>	if (needElectricField_) {
690	>	if (storageLayout & DataStorage::dslElectricField) {
691	>	type += "e";
692	>	Vector3d eField= sd->getElectricField();
693	>	if (isinf(eField[0]) || isnan(eField[0]) ||
694	>	isinf(eField[1]) || isnan(eField[1]) ||
695	>	isinf(eField[2]) || isnan(eField[2]) ) {
696	>	sprintf( painCave.errMsg,
697	>	"DumpWriter detected a numerical error writing the electric"
698	>	" field for object %s", id.c_str());
699	>	painCave.isFatal = 1;
700	>	simError();
701	>	}
702	>	sprintf(tempBuffer, " %13e %13e %13e",
703	>	eField[0], eField[1], eField[2]);
704	>	line += tempBuffer;
705	>	}
706	>	}
707
616	–	atomData[3] = vel[0];
617	–	atomData[4] = vel[1];
618	–	atomData[5] = vel[2];
619	–
620	–	isDirectional = 0;
708
709	<	if( sd->isDirectional() ){
709	>	if (needParticlePot_) {
710	>	if (storageLayout & DataStorage::dslParticlePot) {
711	>	type += "u";
712	>	RealType particlePot = sd->getParticlePot();
713	>	if (isinf(particlePot) || isnan(particlePot)) {
714	>	sprintf( painCave.errMsg,
715	>	"DumpWriter detected a numerical error writing the particle "
716	>	" potential for object %s", id.c_str());
717	>	painCave.isFatal = 1;
718	>	simError();
719	>	}
720	>	sprintf(tempBuffer, " %13e", particlePot);
721	>	line += tempBuffer;
722	>	}
723	>	}
724	>
725	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
726	>	return std::string(tempBuffer);
727	>	}
728
729	<	isDirectional = 1;
730	<
731	<	sd->getQ( q );
732	<	sd->getJ( ji );
733	<
734	<
735	<	atomData[6] = q[0];
736	<	atomData[7] = q[1];
737	<	atomData[8] = q[2];
738	<	atomData[9] = q[3];
729	>	void DumpWriter::writeDump() {
730	>	writeFrame(*dumpFile_);
731	>	}
732	>
733	>	void DumpWriter::writeEor() {
734	>	std::ostream* eorStream;
735	>
736	>	#ifdef IS_MPI
737	>	if (worldRank == 0) {
738	>	#endif // is_mpi
739
740	<	atomData[10] = ji[0];
636	<	atomData[11] = ji[1];
637	<	atomData[12] = ji[2];
638	<	}
740	>	eorStream = createOStream(eorFilename_);
741
742	<
743	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
742	>	#ifdef IS_MPI
743	>	}
744	>	#endif
745	>
746	>	writeFrame(*eorStream);
747	>
748	>	#ifdef IS_MPI
749	>	if (worldRank == 0) {
750	>	#endif
751	>
752	>	writeClosing(*eorStream);
753	>	delete eorStream;
754	>
755	>	#ifdef IS_MPI
756	>	}
757	>	#endif // is_mpi
758
759	<	// null terminate the string before sending (just in case):
644	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
759	>	}
760
646	–	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647	–	myPotato, MPI_COMM_WORLD);
648	–
649	–	myPotato++;
650	–
651	–	if (isDirectional) {
761
762	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
763	<	myPotato, MPI_COMM_WORLD);
764	<
765	<	} else {
762	>	void DumpWriter::writeDumpAndEor() {
763	>	std::vector<std::streambuf*> buffers;
764	>	std::ostream* eorStream;
765	>	#ifdef IS_MPI
766	>	if (worldRank == 0) {
767	>	#endif // is_mpi
768
769	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659	<	myPotato, MPI_COMM_WORLD);
660	<	}
769	>	buffers.push_back(dumpFile_->rdbuf());
770
771	<	myPotato++;
771	>	eorStream = createOStream(eorFilename_);
772
773	<	}
774	<
775	<	currentIndex++;
667	<
668	<	}
669	<
670	<	}
671	<
672	<	sprintf( checkPointMsg,
673	<	"Sucessfully took a dump.\n");
674	<	MPIcheckPoint();
675	<
773	>	buffers.push_back(eorStream->rdbuf());
774	>
775	>	#ifdef IS_MPI
776		}
777	+	#endif // is_mpi
778
779	+	TeeBuf tbuf(buffers.begin(), buffers.end());
780	+	std::ostream os(&tbuf);
781
782	<
680	<	#endif // is_mpi
681	<	}
782	>	writeFrame(os);
783
784		#ifdef IS_MPI
785	+	if (worldRank == 0) {
786	+	#endif // is_mpi
787	+	writeClosing(*eorStream);
788	+	delete eorStream;
789	+	#ifdef IS_MPI
790	+	}
791	+	#endif // is_mpi
792	+
793	+	}
794
795	<	// a couple of functions to let us escape the write loop
795	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
796
797	<	void dWrite::DieDieDie( void ){
797	>	std::ostream* newOStream;
798	>	#ifdef HAVE_ZLIB
799	>	if (needCompression_) {
800	>	newOStream = new ogzstream(filename.c_str());
801	>	} else {
802	>	newOStream = new std::ofstream(filename.c_str());
803	>	}
804	>	#else
805	>	newOStream = new std::ofstream(filename.c_str());
806	>	#endif
807	>	//write out MetaData first
808	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
809	>	(*newOStream) << "  <MetaData>" << std::endl;
810	>	(*newOStream) << info_->getRawMetaData();
811	>	(*newOStream) << "  </MetaData>" << std::endl;
812	>	return newOStream;
813	>	}
814
815	<	MPI_Finalize();
690	<	exit (0);
691	<	}
815	>	void DumpWriter::writeClosing(std::ostream& os) {
816
817	<	#endif //is_mpi
817	>	os << "</OpenMD>\n";
818	>	os.flush();
819	>	}
820	>
821	>	}//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.
Revision 1921 by gezelter, Thu Aug 1 18:23:07 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines