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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 1993 by gezelter, Tue Apr 29 17:32:31 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()),
68	>	eorFilename_(info->getFinalConfigFileName()){
69
70	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
70	>	Globals* simParams = info->getSimParams();
71	>	needCompression_   = simParams->getCompressDumpFile();
72	>	needForceVector_   = simParams->getOutputForceVector();
73	>	needParticlePot_   = simParams->getOutputParticlePotential();
74	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
75	>	needElectricField_ = simParams->getOutputElectricField();
76	>	needSitePotential_ = simParams->getOutputSitePotential();
77
78	<	entry_plug = the_entry_plug;
78	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
79	>	needSitePotential_) {
80	>	doSiteData_ = true;
81	>	} else {
82	>	doSiteData_ = false;
83	>	}
84
85	+	createDumpFile_ = true;
86	+	#ifdef HAVE_LIBZ
87	+	if (needCompression_) {
88	+	filename_ += ".gz";
89	+	eorFilename_ += ".gz";
90	+	}
91	+	#endif
92	+
93		#ifdef IS_MPI
94	<	if(worldRank == 0 ){
94	>
95	>	if (worldRank == 0) {
96		#endif // is_mpi
97	+
98	+	dumpFile_ = createOStream(filename_);
99
100	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
100	>	if (!dumpFile_) {
101	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
102	>	filename_.c_str());
103	>	painCave.isFatal = 1;
104	>	simError();
105	>	}
106
107	<	if( !dumpFile ){
107	>	#ifdef IS_MPI
108
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();
109		}
110
111	<	#ifdef IS_MPI
111	>	#endif // is_mpi
112	>
113		}
114
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	–	}
115
116	<	DumpWriter::~DumpWriter( ){
116	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
117	>	: info_(info), filename_(filename){
118
119	<	#ifdef IS_MPI
120	<	if(worldRank == 0 ){
59	<	#endif // is_mpi
119	>	Globals* simParams = info->getSimParams();
120	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
121
122	<	dumpFile.close();
122	>	needCompression_   = simParams->getCompressDumpFile();
123	>	needForceVector_   = simParams->getOutputForceVector();
124	>	needParticlePot_   = simParams->getOutputParticlePotential();
125	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
126	>	needElectricField_ = simParams->getOutputElectricField();
127	>	needSitePotential_ = simParams->getOutputSitePotential();
128
129	+	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
130	+	needSitePotential_) {
131	+	doSiteData_ = true;
132	+	} else {
133	+	doSiteData_ = false;
134	+	}
135	+
136	+	createDumpFile_ = true;
137	+	#ifdef HAVE_LIBZ
138	+	if (needCompression_) {
139	+	filename_ += ".gz";
140	+	eorFilename_ += ".gz";
141	+	}
142	+	#endif
143	+
144		#ifdef IS_MPI
145	<	}
145	>
146	>	if (worldRank == 0) {
147		#endif // is_mpi
66	–	}
148
149	+
150	+	dumpFile_ = createOStream(filename_);
151	+
152	+	if (!dumpFile_) {
153	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
154	+	filename_.c_str());
155	+	painCave.isFatal = 1;
156	+	simError();
157	+	}
158	+
159		#ifdef IS_MPI
160
161	<	/**
71	<	* A hook function to load balancing
72	<	*/
161	>	}
162
163	<	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	<	}
163	>	#endif // is_mpi
164
165	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
165	>	}
166
167	<	for(int i = 0; i < entry_plug->n_mol;i++)
168	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
169	<
170	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
171	<	}
167	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
168	>	: info_(info), filename_(filename){
169	>
170	>	Globals* simParams = info->getSimParams();
171	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
172	>
173	>	needCompression_   = simParams->getCompressDumpFile();
174	>	needForceVector_   = simParams->getOutputForceVector();
175	>	needParticlePot_   = simParams->getOutputParticlePotential();
176	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
177	>	needElectricField_ = simParams->getOutputElectricField();
178	>	needSitePotential_ = simParams->getOutputSitePotential();
179
180	<	#endif
180	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181	>	needSitePotential_) {
182	>	doSiteData_ = true;
183	>	} else {
184	>	doSiteData_ = false;
185	>	}
186
187	<	void DumpWriter::writeDump(double currentTime){
188	<
189	<	ofstream finalOut;
190	<	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();
187	>	#ifdef HAVE_LIBZ
188	>	if (needCompression_) {
189	>	filename_ += ".gz";
190	>	eorFilename_ += ".gz";
191		}
192	+	#endif
193	+
194		#ifdef IS_MPI
195	<	}
195	>
196	>	if (worldRank == 0) {
197		#endif // is_mpi
198	+
199	+	createDumpFile_ = writeDumpFile;
200	+	if (createDumpFile_) {
201	+	dumpFile_ = createOStream(filename_);
202	+
203	+	if (!dumpFile_) {
204	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
205	+	filename_.c_str());
206	+	painCave.isFatal = 1;
207	+	simError();
208	+	}
209	+	}
210	+	#ifdef IS_MPI
211	+
212	+	}
213
214	<	fileStreams.push_back(&finalOut);
215	<	fileStreams.push_back(&dumpFile);
214	>
215	>	#endif // is_mpi
216	>
217	>	}
218
219	<	writeFrame(fileStreams, currentTime);
219	>	DumpWriter::~DumpWriter() {
220
221		#ifdef IS_MPI
128	–	finalOut.close();
129	–	#endif
130	–
131	–	}
222
223	<	void DumpWriter::writeFinal(double currentTime){
223	>	if (worldRank == 0) {
224	>	#endif // is_mpi
225	>	if (createDumpFile_){
226	>	writeClosing(*dumpFile_);
227	>	delete dumpFile_;
228	>	}
229	>	#ifdef IS_MPI
230
231	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
231	>	}
232
138	–	#ifdef IS_MPI
139	–	if(worldRank == 0 ){
233		#endif // is_mpi
234
235	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
235	>	}
236
237	<	if( !finalOut ){
237	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
238	>
239	>	char buffer[1024];
240	>
241	>	os << "    <FrameData>\n";
242	>
243	>	RealType currentTime = s->getTime();
244	>
245	>	if (isinf(currentTime) || isnan(currentTime)) {
246		sprintf( painCave.errMsg,
247	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
247	>	"DumpWriter detected a numerical error writing the time");
248		painCave.isFatal = 1;
249		simError();
250		}
251	+
252	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
253	+	os << buffer;
254
255	<	#ifdef IS_MPI
256	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
255	>	Mat3x3d hmat;
256	>	hmat = s->getHmat();
257
258	<	#ifdef IS_MPI
259	<	finalOut.close();
260	<	#endif
261	<
262	<	}
258	>	for (unsigned int i = 0; i < 3; i++) {
259	>	for (unsigned int j = 0; j < 3; j++) {
260	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
261	>	sprintf( painCave.errMsg,
262	>	"DumpWriter detected a numerical error writing the box");
263	>	painCave.isFatal = 1;
264	>	simError();
265	>	}
266	>	}
267	>	}
268	>
269	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
270	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
271	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
272	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
273	>	os << buffer;
274
275	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276
277	<	const int BUFFERSIZE = 2000;
278	<	const int MINIBUFFERSIZE = 100;
277	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
278	>	isinf(thermostat.second) || isnan(thermostat.second)) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the thermostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
285	>	thermostat.second);
286	>	os << buffer;
287
288	<	char tempBuffer[BUFFERSIZE];
289	<	char writeLine[BUFFERSIZE];
288	>	Mat3x3d eta;
289	>	eta = s->getBarostat();
290
291	<	int i;
292	<	unsigned int k;
291	>	for (unsigned int i = 0; i < 3; i++) {
292	>	for (unsigned int j = 0; j < 3; j++) {
293	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
294	>	sprintf( painCave.errMsg,
295	>	"DumpWriter detected a numerical error writing the barostat");
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300	>	}
301
302	<	#ifdef IS_MPI
303	<
304	<	/*********************************************************************
305	<	* Documentation?  You want DOCUMENTATION?
306	<	*
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	<	*********************************************************************/
302	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
303	>	eta(0, 0), eta(1, 0), eta(2, 0),
304	>	eta(0, 1), eta(1, 1), eta(2, 1),
305	>	eta(0, 2), eta(1, 2), eta(2, 2));
306	>	os << buffer;
307
308	<	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;
308	>	os << "    </FrameData>\n";
309		}
258	–
259	–	for( i=0; i< entry_plug->n_mol; i++ ){
310
311	<	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);
311	>	void DumpWriter::writeFrame(std::ostream& os) {
312
313	<	sprintf( tempBuffer,
314	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
315	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
313	>	#ifdef IS_MPI
314	>	MPI_Status istatus;
315	>	#endif
316
317	<	if( sd->isDirectional() ){
317	>	Molecule* mol;
318	>	StuntDouble* sd;
319	>	SimInfo::MoleculeIterator mi;
320	>	Molecule::IntegrableObjectIterator ii;
321	>	RigidBody::AtomIterator ai;
322
323	<	sd->getQ( q );
324	<	sd->getJ( ji );
323	>	#ifndef IS_MPI
324	>	os << "  <Snapshot>\n";
325	>
326	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328	<	sprintf( tempBuffer,
329	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
330	<	q[0],
331	<	q[1],
332	<	q[2],
333	<	q[3],
334	<	ji[0],
335	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
328	>	os << "    <StuntDoubles>\n";
329	>	for (mol = info_->beginMolecule(mi); mol != NULL;
330	>	mol = info_->nextMolecule(mi)) {
331	>
332	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
333	>	sd = mol->nextIntegrableObject(ii)) {
334	>	os << prepareDumpLine(sd);
335	>
336		}
337	<	else
338	<	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	<	}
337	>	}
338	>	os << "    </StuntDoubles>\n";
339
340	<	#else // is_mpi
340	>	if (doSiteData_) {
341	>	os << "    <SiteData>\n";
342	>	for (mol = info_->beginMolecule(mi); mol != NULL;
343	>	mol = info_->nextMolecule(mi)) {
344	>
345	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
346	>	sd = mol->nextIntegrableObject(ii)) {
347
348	<	/* code to find maximum tag value */
349	<
350	<	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	<	}
348	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
349	>	// do one for the IO itself
350	>	os << prepareSiteLine(sd, ioIndex, 0);
351
352	<	int haveError;
352	>	if (sd->isRigidBody()) {
353	>
354	>	RigidBody* rb = static_cast<RigidBody*>(sd);
355	>	int siteIndex = 0;
356	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
357	>	atom = rb->nextAtom(ai)) {
358	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
359	>	siteIndex++;
360	>	}
361	>	}
362	>	}
363	>	}
364	>	os << "    </SiteData>\n";
365	>	}
366	>	os << "  </Snapshot>\n";
367
368	<	MPI_Status istatus;
369	<	int nCurObj;
321	<	int *MolToProcMap = mpiSim->getMolToProcMap();
368	>	os.flush();
369	>	#else
370
371	<	// write out header and node 0's coordinates
371	>	const int masterNode = 0;
372	>	int worldRank;
373	>	int nProc;
374
375	<	if( worldRank == 0 ){
375	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377
327	–	// Node 0 needs a list of the magic potatoes for each processor;
378
379	<	nProc = mpiSim->getNProcessors();
380	<	potatoes = new int[nProc];
379	>	if (worldRank == masterNode) {
380	>	os << "  <Snapshot>\n";
381	>	writeFrameProperties(os,
382	>	info_->getSnapshotManager()->getCurrentSnapshot());
383	>	os << "    <StuntDoubles>\n";
384	>	}
385
386	<	//write out the comment lines
387	<	for (i = 0; i < nProc; i++)
388	<	potatoes[i] = 0;
389	<
390	<	for(k = 0; k < outFile.size(); k++){
391	<	*outFile[k] << nTotObjects << "\n";
392	<
393	<	*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;
386	>	//every node prepares the dump lines for integrable objects belong to itself
387	>	std::string buffer;
388	>	for (mol = info_->beginMolecule(mi); mol != NULL;
389	>	mol = info_->nextMolecule(mi)) {
390	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
391	>	sd = mol->nextIntegrableObject(ii)) {
392	>	buffer += prepareDumpLine(sd);
393	>	}
394		}
395
396	<	currentIndex = 0;
397	<
358	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
396	>	if (worldRank == masterNode) {
397	>	os << buffer;
398
399	<	// Get the Node number which has this atom;
400	<
401	<	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:
399	>	for (int i = 1; i < nProc; ++i) {
400	>	// tell processor i to start sending us data:
401	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
402
403	<	potatoes[which_node] = 0;
404	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
405	<	MPI_COMM_WORLD);
406	<
403	>	// receive the length of the string buffer that was
404	>	// prepared by processor i:
405	>	int recvLength;
406	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
407	>	&istatus);
408	>
409	>	// create a buffer to receive the data
410	>	char* recvBuffer = new char[recvLength];
411	>	if (recvBuffer == NULL) {
412	>	} else {
413	>	// receive the data:
414	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
415	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
416	>	// send it to the file:
417	>	os << recvBuffer;
418	>	// get rid of the receive buffer:
419	>	delete [] recvBuffer;
420		}
421	+	}
422	+	} else {
423	+	int sendBufferLength = buffer.size() + 1;
424	+	int myturn = 0;
425	+	for (int i = 1; i < nProc; ++i){
426	+	// wait for the master node to call our number:
427	+	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
428	+	if (myturn == worldRank){
429	+	// send the length of our buffer:
430	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
431
432	<	myPotato = potatoes[which_node];
432	>	// send our buffer:
433	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
434	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435
436	<	//recieve the number of integrableObject in current molecule
437	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
438	<	myPotato, MPI_COMM_WORLD, &istatus);
439	<	myPotato++;
440	<
441	<	for(int l = 0; l < nCurObj; l++){
442	<
385	<	if (potatoes[which_node] + 2 >= MAXTAG) {
386	<	// The potato was going to exceed the maximum value,
387	<	// so wrap this processor potato back to 0:
388	<
389	<	potatoes[which_node] = 0;
390	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
391	<
392	<	}
393	<
394	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395	<	myPotato, MPI_COMM_WORLD, &istatus);
396	<
397	<	atomTypeString = MPIatomTypeString;
398	<
399	<	myPotato++;
400	<
401	<	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;
436	>	}
437	>	}
438	>	}
439	>
440	>	if (worldRank == masterNode) {
441	>	os << "    </StuntDoubles>\n";
442	>	}
443
444	<	}// end for(int l =0)
445	<	potatoes[which_node] = myPotato;
446	<
444	>	if (doSiteData_) {
445	>	if (worldRank == masterNode) {
446	>	os << "    <SiteData>\n";
447		}
448	<	else {
449	<
450	<	haveError = 0;
451	<
452	<	local_index = indexArray[currentIndex].first;
453	<
454	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
448	>	buffer.clear();
449	>	for (mol = info_->beginMolecule(mi); mol != NULL;
450	>	mol = info_->nextMolecule(mi)) {
451	>
452	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
453	>	sd = mol->nextIntegrableObject(ii)) {
454	>
455	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
456	>	// do one for the IO itself
457	>	buffer += prepareSiteLine(sd, ioIndex, 0);
458
459	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
465	<	sd = *iter;
466	<	atomTypeString = sd->getType();
467	<
468	<	sd->getPos(pos);
469	<	sd->getVel(vel);
470	<
471	<	atomData[0] = pos[0];
472	<	atomData[1] = pos[1];
473	<	atomData[2] = pos[2];
474	<
475	<	atomData[3] = vel[0];
476	<	atomData[4] = vel[1];
477	<	atomData[5] = vel[2];
478	<
479	<	isDirectional = 0;
480	<
481	<	if( sd->isDirectional() ){
482	<
483	<	isDirectional = 1;
484	<
485	<	sd->getQ( q );
486	<	sd->getJ( ji );
487	<
488	<	for (int j = 0; j < 6 ; j++)
489	<	atomData[j] = atomData[j];
490	<
491	<	atomData[6] = q[0];
492	<	atomData[7] = q[1];
493	<	atomData[8] = q[2];
494	<	atomData[9] = q[3];
495	<
496	<	atomData[10] = ji[0];
497	<	atomData[11] = ji[1];
498	<	atomData[12] = ji[2];
499	<	}
459	>	if (sd->isRigidBody()) {
460
461	<	// If we've survived to here, format the line:
462	<
463	<	if (!isDirectional) {
464	<
465	<	sprintf( writeLine,
466	<	"%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	<
461	>	RigidBody* rb = static_cast<RigidBody*>(sd);
462	>	int siteIndex = 0;
463	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
464	>	atom = rb->nextAtom(ai)) {
465	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
466	>	siteIndex++;
467		}
468	<
469	<	for(k = 0; k < outFile.size(); k++)
540	<	*outFile[k] << writeLine;
541	<
542	<
543	<	}//end for(iter = integrableObject.begin())
544	<
545	<	currentIndex++;
468	>	}
469	>	}
470		}
471
472	<	}//end for(i = 0; i < mpiSim->getNmol())
472	>	if (worldRank == masterNode) {
473	>	os << buffer;
474	>
475	>	for (int i = 1; i < nProc; ++i) {
476	>
477	>	// tell processor i to start sending us data:
478	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
479	>
480	>	// receive the length of the string buffer that was
481	>	// prepared by processor i:
482	>	int recvLength;
483	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
484	>	&istatus);
485	>
486	>	// create a buffer to receive the data
487	>	char* recvBuffer = new char[recvLength];
488	>	if (recvBuffer == NULL) {
489	>	} else {
490	>	// receive the data:
491	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
492	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
493	>	// send it to the file:
494	>	os << recvBuffer;
495	>	// get rid of the receive buffer:
496	>	delete [] recvBuffer;
497	>	}
498	>	}
499	>	} else {
500	>	int sendBufferLength = buffer.size() + 1;
501	>	int myturn = 0;
502	>	for (int i = 1; i < nProc; ++i){
503	>	// wait for the master node to call our number:
504	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
505	>	if (myturn == worldRank){
506	>	// send the length of our buffer:
507	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
508	>	// send our buffer:
509	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
510	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
511	>	}
512	>	}
513	>	}
514	>
515	>	if (worldRank == masterNode) {
516	>	os << "    </SiteData>\n";
517	>	}
518	>	}
519
520	<	for(k = 0; k < outFile.size(); k++)
521	<	outFile[k]->flush();
520	>	if (worldRank == masterNode) {
521	>	os << "  </Snapshot>\n";
522	>	os.flush();
523	>	}
524
525	<	sprintf( checkPointMsg,
554	<	"Sucessfully took a dump.\n");
525	>	#endif // is_mpi
526
527	<	MPIcheckPoint();
557	<
558	<	delete[] potatoes;
559	<
560	<	} else {
527	>	}
528
529	<	// worldRank != 0, so I'm a remote node.
529	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
530	>
531	>	int index = sd->getGlobalIntegrableObjectIndex();
532	>	std::string type("pv");
533	>	std::string line;
534	>	char tempBuffer[4096];
535
536	<	// Set my magic potato to 0:
536	>	Vector3d pos;
537	>	Vector3d vel;
538	>	pos = sd->getPos();
539
540	<	myPotato = 0;
541	<	currentIndex = 0;
542	<
543	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
544	<
545	<	// Am I the node which has this integrableObject?
546	<
547	<	if (MolToProcMap[i] == worldRank) {
540	>	if (isinf(pos[0]) || isnan(pos[0]) ||
541	>	isinf(pos[1]) || isnan(pos[1]) ||
542	>	isinf(pos[2]) || isnan(pos[2]) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the position"
545	>	" for object %d", index);
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549
550	+	vel = sd->getVel();
551
552	<	if (myPotato + 1 >= MAXTAG) {
553	<
554	<	// The potato was going to exceed the maximum value,
555	<	// so wrap this processor potato back to 0 (and block until
556	<	// node 0 says we can go:
557	<
558	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
559	<
560	<	}
552	>	if (isinf(vel[0]) || isnan(vel[0]) ||
553	>	isinf(vel[1]) || isnan(vel[1]) ||
554	>	isinf(vel[2]) || isnan(vel[2]) ) {
555	>	sprintf( painCave.errMsg,
556	>	"DumpWriter detected a numerical error writing the velocity"
557	>	" for object %d", index);
558	>	painCave.isFatal = 1;
559	>	simError();
560	>	}
561
562	<	local_index = indexArray[currentIndex].first;
563	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
564	<
565	<	nCurObj = integrableObjects.size();
590	<
591	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
592	<	myPotato, MPI_COMM_WORLD);
593	<	myPotato++;
562	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
563	>	pos[0], pos[1], pos[2],
564	>	vel[0], vel[1], vel[2]);
565	>	line += tempBuffer;
566
567	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
567	>	if (sd->isDirectional()) {
568	>	type += "qj";
569	>	Quat4d q;
570	>	Vector3d ji;
571	>	q = sd->getQ();
572
573	<	if (myPotato + 2 >= MAXTAG) {
574	<
575	<	// The potato was going to exceed the maximum value,
576	<	// so wrap this processor potato back to 0 (and block until
577	<	// node 0 says we can go:
578	<
579	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
580	<
581	<	}
582	<
607	<	sd = *iter;
608	<
609	<	atomTypeString = sd->getType();
573	>	if (isinf(q[0]) || isnan(q[0]) ||
574	>	isinf(q[1]) || isnan(q[1]) ||
575	>	isinf(q[2]) || isnan(q[2]) ||
576	>	isinf(q[3]) || isnan(q[3]) ) {
577	>	sprintf( painCave.errMsg,
578	>	"DumpWriter detected a numerical error writing the quaternion"
579	>	" for object %d", index);
580	>	painCave.isFatal = 1;
581	>	simError();
582	>	}
583
584	<	sd->getPos(pos);
612	<	sd->getVel(vel);
584	>	ji = sd->getJ();
585
586	<	atomData[0] = pos[0];
587	<	atomData[1] = pos[1];
588	<	atomData[2] = pos[2];
589	<
590	<	atomData[3] = vel[0];
591	<	atomData[4] = vel[1];
592	<	atomData[5] = vel[2];
593	<
594	<	isDirectional = 0;
586	>	if (isinf(ji[0]) || isnan(ji[0]) ||
587	>	isinf(ji[1]) || isnan(ji[1]) ||
588	>	isinf(ji[2]) || isnan(ji[2]) ) {
589	>	sprintf( painCave.errMsg,
590	>	"DumpWriter detected a numerical error writing the angular"
591	>	" momentum for object %d", index);
592	>	painCave.isFatal = 1;
593	>	simError();
594	>	}
595
596	<	if( sd->isDirectional() ){
596	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
597	>	q[0], q[1], q[2], q[3],
598	>	ji[0], ji[1], ji[2]);
599	>	line += tempBuffer;
600	>	}
601
602	<	isDirectional = 1;
603	<
604	<	sd->getQ( q );
605	<	sd->getJ( ji );
606	<
607	<
608	<	atomData[6] = q[0];
609	<	atomData[7] = q[1];
610	<	atomData[8] = q[2];
611	<	atomData[9] = q[3];
602	>	if (needForceVector_) {
603	>	type += "f";
604	>	Vector3d frc = sd->getFrc();
605	>	if (isinf(frc[0]) || isnan(frc[0]) ||
606	>	isinf(frc[1]) || isnan(frc[1]) ||
607	>	isinf(frc[2]) || isnan(frc[2]) ) {
608	>	sprintf( painCave.errMsg,
609	>	"DumpWriter detected a numerical error writing the force"
610	>	" for object %d", index);
611	>	painCave.isFatal = 1;
612	>	simError();
613	>	}
614	>	sprintf(tempBuffer, " %13e %13e %13e",
615	>	frc[0], frc[1], frc[2]);
616	>	line += tempBuffer;
617
618	<	atomData[10] = ji[0];
619	<	atomData[11] = ji[1];
620	<	atomData[12] = ji[2];
621	<	}
618	>	if (sd->isDirectional()) {
619	>	type += "t";
620	>	Vector3d trq = sd->getTrq();
621	>	if (isinf(trq[0]) || isnan(trq[0]) ||
622	>	isinf(trq[1]) || isnan(trq[1]) ||
623	>	isinf(trq[2]) || isnan(trq[2]) ) {
624	>	sprintf( painCave.errMsg,
625	>	"DumpWriter detected a numerical error writing the torque"
626	>	" for object %d", index);
627	>	painCave.isFatal = 1;
628	>	simError();
629	>	}
630	>	sprintf(tempBuffer, " %13e %13e %13e",
631	>	trq[0], trq[1], trq[2]);
632	>	line += tempBuffer;
633	>	}
634	>	}
635
636	<
637	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
636	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
637	>	return std::string(tempBuffer);
638	>	}
639
640	<	// null terminate the string before sending (just in case):
641	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
640	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642
643	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
644	<	myPotato, MPI_COMM_WORLD);
645	<
646	<	myPotato++;
652	<
653	<	if (isDirectional) {
643	>	std::string id;
644	>	std::string type;
645	>	std::string line;
646	>	char tempBuffer[4096];
647
648	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
649	<	myPotato, MPI_COMM_WORLD);
648	>	if (sd->isRigidBody()) {
649	>	sprintf(tempBuffer, "%10d           ", ioIndex);
650	>	id = std::string(tempBuffer);
651	>	} else {
652	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
653	>	id = std::string(tempBuffer);
654	>	}
655
656	<	} else {
656	>	if (needFlucQ_) {
657	>	if (storageLayout & DataStorage::dslFlucQPosition) {
658	>	type += "c";
659	>	RealType fqPos = sd->getFlucQPos();
660	>	if (isinf(fqPos) || isnan(fqPos) ) {
661	>	sprintf( painCave.errMsg,
662	>	"DumpWriter detected a numerical error writing the"
663	>	" fluctuating charge for object %s", id.c_str());
664	>	painCave.isFatal = 1;
665	>	simError();
666	>	}
667	>	sprintf(tempBuffer, " %13e ", fqPos);
668	>	line += tempBuffer;
669	>	}
670
671	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
672	<	myPotato, MPI_COMM_WORLD);
673	<	}
671	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
672	>	type += "w";
673	>	RealType fqVel = sd->getFlucQVel();
674	>	if (isinf(fqVel) || isnan(fqVel) ) {
675	>	sprintf( painCave.errMsg,
676	>	"DumpWriter detected a numerical error writing the"
677	>	" fluctuating charge velocity for object %s", id.c_str());
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681	>	sprintf(tempBuffer, " %13e ", fqVel);
682	>	line += tempBuffer;
683	>	}
684
685	<	myPotato++;
686	<
685	>	if (needForceVector_) {
686	>	if (storageLayout & DataStorage::dslFlucQForce) {
687	>	type += "g";
688	>	RealType fqFrc = sd->getFlucQFrc();
689	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
690	>	sprintf( painCave.errMsg,
691	>	"DumpWriter detected a numerical error writing the"
692	>	" fluctuating charge force for object %s", id.c_str());
693	>	painCave.isFatal = 1;
694	>	simError();
695		}
696	+	sprintf(tempBuffer, " %13e ", fqFrc);
697	+	line += tempBuffer;
698	+	}
699	+	}
700	+	}
701	+
702	+	if (needElectricField_) {
703	+	if (storageLayout & DataStorage::dslElectricField) {
704	+	type += "e";
705	+	Vector3d eField= sd->getElectricField();
706	+	if (isinf(eField[0]) || isnan(eField[0]) ||
707	+	isinf(eField[1]) || isnan(eField[1]) ||
708	+	isinf(eField[2]) || isnan(eField[2]) ) {
709	+	sprintf( painCave.errMsg,
710	+	"DumpWriter detected a numerical error writing the electric"
711	+	" field for object %s", id.c_str());
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	sprintf(tempBuffer, " %13e %13e %13e",
716	+	eField[0], eField[1], eField[2]);
717	+	line += tempBuffer;
718	+	}
719	+	}
720
721	<	currentIndex++;
722	<
721	>	if (needSitePotential_) {
722	>	if (storageLayout & DataStorage::dslSitePotential) {
723	>	type += "s";
724	>	RealType sPot = sd->getSitePotential();
725	>	if (isinf(sPot) || isnan(sPot) ) {
726	>	sprintf( painCave.errMsg,
727	>	"DumpWriter detected a numerical error writing the"
728	>	" site potential for object %s", id.c_str());
729	>	painCave.isFatal = 1;
730	>	simError();
731		}
732	<
732	>	sprintf(tempBuffer, " %13e ", sPot);
733	>	line += tempBuffer;
734		}
735	+	}
736	+
737	+	if (needParticlePot_) {
738	+	if (storageLayout & DataStorage::dslParticlePot) {
739	+	type += "u";
740	+	RealType particlePot = sd->getParticlePot();
741	+	if (isinf(particlePot) || isnan(particlePot)) {
742	+	sprintf( painCave.errMsg,
743	+	"DumpWriter detected a numerical error writing the particle "
744	+	" potential for object %s", id.c_str());
745	+	painCave.isFatal = 1;
746	+	simError();
747	+	}
748	+	sprintf(tempBuffer, " %13e", particlePot);
749	+	line += tempBuffer;
750	+	}
751	+	}
752	+
753	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
754	+	return std::string(tempBuffer);
755	+	}
756
757	<	sprintf( checkPointMsg,
758	<	"Successfully took a dump.\n");
759	<	MPIcheckPoint();
757	>	void DumpWriter::writeDump() {
758	>	writeFrame(*dumpFile_);
759	>	}
760	>
761	>	void DumpWriter::writeEor() {
762	>
763	>	std::ostream* eorStream = NULL;
764	>
765	>	#ifdef IS_MPI
766	>	if (worldRank == 0) {
767	>	#endif // is_mpi
768	>
769	>	eorStream = createOStream(eorFilename_);
770	>
771	>	#ifdef IS_MPI
772	>	}
773	>	#endif
774
775	+	writeFrame(*eorStream);
776	+
777	+	#ifdef IS_MPI
778	+	if (worldRank == 0) {
779	+	#endif
780	+
781	+	writeClosing(*eorStream);
782	+	delete eorStream;
783	+
784	+	#ifdef IS_MPI
785	+	}
786	+	#endif // is_mpi
787	+
788		}
789	<
789	>
790	>
791	>	void DumpWriter::writeDumpAndEor() {
792	>	std::vector<std::streambuf*> buffers;
793	>	std::ostream* eorStream;
794	>	#ifdef IS_MPI
795	>	if (worldRank == 0) {
796		#endif // is_mpi
797	<	}
797	>	buffers.push_back(dumpFile_->rdbuf());
798	>	eorStream = createOStream(eorFilename_);
799	>	buffers.push_back(eorStream->rdbuf());
800	>	#ifdef IS_MPI
801	>	}
802	>	#endif // is_mpi
803
804	+	TeeBuf tbuf(buffers.begin(), buffers.end());
805	+	std::ostream os(&tbuf);
806	+	writeFrame(os);
807	+
808		#ifdef IS_MPI
809	+	if (worldRank == 0) {
810	+	#endif // is_mpi
811	+	writeClosing(*eorStream);
812	+	delete eorStream;
813	+	#ifdef IS_MPI
814	+	}
815	+	#endif // is_mpi
816	+	}
817
818	<	// a couple of functions to let us escape the write loop
818	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
819
820	<	void dWrite::DieDieDie( void ){
820	>	std::ostream* newOStream;
821	>	#ifdef HAVE_ZLIB
822	>	if (needCompression_) {
823	>	newOStream = new ogzstream(filename.c_str());
824	>	} else {
825	>	newOStream = new std::ofstream(filename.c_str());
826	>	}
827	>	#else
828	>	newOStream = new std::ofstream(filename.c_str());
829	>	#endif
830	>	//write out MetaData first
831	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
832	>	(*newOStream) << "  <MetaData>" << std::endl;
833	>	(*newOStream) << info_->getRawMetaData();
834	>	(*newOStream) << "  </MetaData>" << std::endl;
835	>	return newOStream;
836	>	}
837
838	<	MPI_Finalize();
690	<	exit (0);
691	<	}
838	>	void DumpWriter::writeClosing(std::ostream& os) {
839
840	<	#endif //is_mpi
840	>	os << "</OpenMD>\n";
841	>	os.flush();
842	>	}
843	>
844	>	}//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 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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