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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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|
|
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#include <stdlib.h> |
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#include <string.h> |
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|
|
55 |
< |
|
56 |
< |
#include "io/ReadWrite.hpp" |
55 |
> |
#include "io/DumpReader.hpp" |
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> |
#include "primitives/Molecule.hpp" |
57 |
|
#include "utils/simError.h" |
58 |
+ |
#include "utils/MemoryUtils.hpp" |
59 |
+ |
#include "utils/StringTokenizer.hpp" |
60 |
|
|
61 |
|
#ifdef IS_MPI |
62 |
+ |
|
63 |
|
#include <mpi.h> |
20 |
– |
#include "brains/mpiSimulation.hpp" |
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|
#define TAKE_THIS_TAG_CHAR 0 |
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|
#define TAKE_THIS_TAG_INT 1 |
66 |
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|
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|
#endif // is_mpi |
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|
|
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|
|
70 |
< |
DumpReader :: DumpReader(const char *in_name ){ |
27 |
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|
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isScanned = false; |
29 |
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|
30 |
< |
#ifdef IS_MPI |
31 |
< |
if (worldRank == 0) { |
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< |
#endif |
33 |
< |
|
34 |
< |
inFile = fopen(in_name, "r"); |
35 |
< |
if(inFile == NULL){ |
36 |
< |
sprintf(painCave.errMsg, |
37 |
< |
"Cannot open file: %s\n", in_name); |
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< |
painCave.isFatal = 1; |
39 |
< |
simError(); |
40 |
< |
} |
70 |
> |
namespace oopse { |
71 |
|
|
72 |
< |
inFileName = in_name; |
72 |
> |
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
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> |
: info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
74 |
> |
|
75 |
|
#ifdef IS_MPI |
76 |
< |
} |
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< |
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
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< |
MPIcheckPoint(); |
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|
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> |
if (worldRank == 0) { |
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|
#endif |
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return; |
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} |
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|
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< |
DumpReader :: ~DumpReader( ){ |
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|
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> |
inFile_ = fopen(filename_.c_str(), "r"); |
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|
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> |
if (inFile_ == NULL) { |
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> |
sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
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> |
painCave.isFatal = 1; |
85 |
> |
simError(); |
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> |
} |
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> |
|
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|
#ifdef IS_MPI |
89 |
< |
if (worldRank == 0) { |
89 |
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|
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} |
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|
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strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
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MPIcheckPoint(); |
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|
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#endif |
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vector<fpos_t*>::iterator i; |
97 |
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|
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< |
int error; |
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error = fclose( inFile ); |
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< |
if( error ){ |
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sprintf( painCave.errMsg, |
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"Error closing %s\n", inFileName.c_str()); |
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simError(); |
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} |
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|
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for(i = framePos.begin(); i != framePos.end(); ++i) |
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delete *i; |
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framePos.clear(); |
96 |
> |
|
97 |
> |
return; |
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> |
} |
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|
|
100 |
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DumpReader::~DumpReader() { |
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|
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|
#ifdef IS_MPI |
70 |
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} |
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strcpy( checkPointMsg, "Dump file closed successfully." ); |
72 |
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MPIcheckPoint(); |
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#endif |
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|
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return; |
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} |
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|
78 |
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int DumpReader::getNframes( void ){ |
79 |
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|
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if( !isScanned ) |
81 |
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scanFile(); |
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return framePos.size(); |
83 |
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} |
84 |
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|
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void DumpReader::scanFile( void ){ |
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|
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int i, j; |
88 |
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int lineNum = 0; |
89 |
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char readBuffer[2000]; |
90 |
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fpos_t *currPos; |
91 |
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|
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#ifdef IS_MPI |
93 |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
103 |
|
|
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rewind( inFile ); |
105 |
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|
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currPos = new fpos_t; |
99 |
< |
fgetpos( inFile, currPos ); |
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< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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< |
lineNum++; |
102 |
< |
if( feof( inFile ) ){ |
103 |
< |
sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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< |
inFileName.c_str(), |
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< |
lineNum ); |
107 |
< |
painCave.isFatal = 1; |
108 |
< |
simError(); |
109 |
< |
} |
110 |
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|
111 |
< |
while( !feof( inFile ) ){ |
104 |
> |
if (worldRank == 0) { |
105 |
> |
#endif |
106 |
|
|
107 |
< |
framePos.push_back(currPos); |
108 |
< |
|
115 |
< |
i = atoi(readBuffer); |
107 |
> |
int error; |
108 |
> |
error = fclose(inFile_); |
109 |
|
|
110 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
111 |
< |
lineNum++; |
112 |
< |
if( feof( inFile ) ){ |
113 |
< |
sprintf( painCave.errMsg, |
121 |
< |
"File \"%s\" ended unexpectedly at line %d\n", |
122 |
< |
inFileName.c_str(), |
123 |
< |
lineNum ); |
124 |
< |
painCave.isFatal = 1; |
125 |
< |
simError(); |
110 |
> |
if (error) { |
111 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str()); |
112 |
> |
painCave.isFatal = 1; |
113 |
> |
simError(); |
114 |
|
} |
127 |
– |
|
128 |
– |
for(j=0; j<i; j++){ |
129 |
– |
|
130 |
– |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
131 |
– |
lineNum++; |
132 |
– |
if( feof( inFile ) ){ |
133 |
– |
sprintf( painCave.errMsg, |
134 |
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"File \"%s\" ended unexpectedly at line %d," |
135 |
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" with atom %d\n", |
136 |
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inFileName.c_str(), |
137 |
– |
lineNum, |
138 |
– |
j ); |
139 |
– |
painCave.isFatal = 1; |
140 |
– |
simError(); |
141 |
– |
} |
142 |
– |
|
143 |
– |
} |
115 |
|
|
116 |
< |
currPos = new fpos_t; |
117 |
< |
fgetpos( inFile, currPos ); |
118 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
119 |
< |
lineNum++; |
116 |
> |
MemoryUtils::deletePointers(framePos_); |
117 |
> |
|
118 |
> |
#ifdef IS_MPI |
119 |
> |
|
120 |
|
} |
121 |
|
|
122 |
< |
delete currPos; |
123 |
< |
rewind( inFile ); |
124 |
< |
|
125 |
< |
isScanned = true; |
126 |
< |
|
127 |
< |
#ifdef IS_MPI |
122 |
> |
strcpy(checkPointMsg, "Dump file closed successfully."); |
123 |
> |
MPIcheckPoint(); |
124 |
> |
|
125 |
> |
#endif |
126 |
> |
|
127 |
> |
return; |
128 |
|
} |
129 |
< |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
130 |
< |
MPIcheckPoint(); |
131 |
< |
#endif // is_mpi |
132 |
< |
} |
133 |
< |
|
134 |
< |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
135 |
< |
|
165 |
< |
simnfo = the_simnfo; |
166 |
< |
|
167 |
< |
this->readSet( whichFrame ); |
168 |
< |
} |
169 |
< |
|
170 |
< |
|
171 |
< |
|
172 |
< |
void DumpReader :: readSet( int whichFrame ){ |
173 |
< |
|
174 |
< |
int i; |
175 |
< |
unsigned int j; |
176 |
< |
|
177 |
< |
#ifdef IS_MPI |
178 |
< |
int done, which_node, which_atom; // loop counter |
179 |
< |
#endif //is_mpi |
180 |
< |
|
181 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
182 |
< |
int nTotObjs; // the number of atoms |
183 |
< |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
184 |
< |
|
185 |
< |
char *eof_test; // ptr to see when we reach the end of the file |
186 |
< |
char *parseErr; |
187 |
< |
|
188 |
< |
vector<StuntDouble*> integrableObjects; |
189 |
< |
|
190 |
< |
|
191 |
< |
#ifndef IS_MPI |
192 |
< |
|
193 |
< |
fsetpos(inFile, framePos[whichFrame]); |
194 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
195 |
< |
if( eof_test == NULL ){ |
196 |
< |
sprintf( painCave.errMsg, |
197 |
< |
"DumpReader error: error reading 1st line of \"%s\"\n", |
198 |
< |
inFileName.c_str() ); |
199 |
< |
painCave.isFatal = 1; |
200 |
< |
simError(); |
129 |
> |
|
130 |
> |
int DumpReader::getNFrames(void) { |
131 |
> |
|
132 |
> |
if (!isScanned_) |
133 |
> |
scanFile(); |
134 |
> |
|
135 |
> |
return nframes_; |
136 |
|
} |
137 |
< |
|
138 |
< |
nTotObjs = atoi( read_buffer ); |
139 |
< |
|
140 |
< |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
141 |
< |
sprintf( painCave.errMsg, |
142 |
< |
"DumpReader error. %s nIntegrable, %d, " |
143 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
144 |
< |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
145 |
< |
painCave.isFatal = 1; |
146 |
< |
simError(); |
147 |
< |
} |
148 |
< |
|
149 |
< |
//read the box mat from the comment line |
150 |
< |
|
151 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
152 |
< |
if(eof_test == NULL){ |
153 |
< |
sprintf( painCave.errMsg, |
154 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
155 |
< |
painCave.isFatal = 1; |
156 |
< |
simError(); |
222 |
< |
} |
223 |
< |
|
224 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
225 |
< |
if( parseErr != NULL ){ |
226 |
< |
strcpy( painCave.errMsg, parseErr ); |
227 |
< |
painCave.isFatal = 1; |
228 |
< |
simError(); |
229 |
< |
} |
230 |
< |
|
231 |
< |
//parse dump lines |
232 |
< |
|
233 |
< |
for( i=0; i < simnfo->n_mol; i++){ |
234 |
< |
|
235 |
< |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
236 |
< |
|
237 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
238 |
< |
|
239 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
240 |
< |
if(eof_test == NULL){ |
137 |
> |
|
138 |
> |
void DumpReader::scanFile(void) { |
139 |
> |
int i, j; |
140 |
> |
int lineNum = 0; |
141 |
> |
char readBuffer[maxBufferSize]; |
142 |
> |
fpos_t * currPos; |
143 |
> |
|
144 |
> |
#ifdef IS_MPI |
145 |
> |
|
146 |
> |
if (worldRank == 0) { |
147 |
> |
#endif // is_mpi |
148 |
> |
|
149 |
> |
rewind(inFile_); |
150 |
> |
|
151 |
> |
currPos = new fpos_t; |
152 |
> |
fgetpos(inFile_, currPos); |
153 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
154 |
> |
lineNum++; |
155 |
> |
|
156 |
> |
if (feof(inFile_)) { |
157 |
|
sprintf(painCave.errMsg, |
158 |
< |
"error in reading file %s\n" |
159 |
< |
"natoms = %d; index = %d\n" |
160 |
< |
"error reading the line from the file.\n", |
245 |
< |
inFileName.c_str(), nTotObjs, i ); |
158 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
159 |
> |
filename_.c_str(), |
160 |
> |
lineNum); |
161 |
|
painCave.isFatal = 1; |
162 |
|
simError(); |
163 |
|
} |
164 |
|
|
165 |
< |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
166 |
< |
if( parseErr != NULL ){ |
167 |
< |
strcpy( painCave.errMsg, parseErr ); |
168 |
< |
painCave.isFatal = 1; |
169 |
< |
simError(); |
165 |
> |
while (!feof(inFile_)) { |
166 |
> |
framePos_.push_back(currPos); |
167 |
> |
|
168 |
> |
i = atoi(readBuffer); |
169 |
> |
|
170 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
171 |
> |
lineNum++; |
172 |
> |
|
173 |
> |
if (feof(inFile_)) { |
174 |
> |
sprintf(painCave.errMsg, |
175 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
176 |
> |
filename_.c_str(), |
177 |
> |
lineNum); |
178 |
> |
painCave.isFatal = 1; |
179 |
> |
simError(); |
180 |
> |
} |
181 |
> |
|
182 |
> |
for(j = 0; j < i; j++) { |
183 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
184 |
> |
lineNum++; |
185 |
> |
|
186 |
> |
if (feof(inFile_)) { |
187 |
> |
sprintf(painCave.errMsg, |
188 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
189 |
> |
" with atom %d\n", filename_.c_str(), |
190 |
> |
lineNum, |
191 |
> |
j); |
192 |
> |
|
193 |
> |
painCave.isFatal = 1; |
194 |
> |
simError(); |
195 |
> |
} |
196 |
> |
} |
197 |
> |
|
198 |
> |
currPos = new fpos_t; |
199 |
> |
fgetpos(inFile_, currPos); |
200 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
201 |
> |
lineNum++; |
202 |
|
} |
203 |
+ |
|
204 |
+ |
delete currPos; |
205 |
+ |
rewind(inFile_); |
206 |
+ |
|
207 |
+ |
nframes_ = framePos_.size(); |
208 |
+ |
#ifdef IS_MPI |
209 |
|
} |
210 |
+ |
|
211 |
+ |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
212 |
+ |
|
213 |
+ |
strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
214 |
+ |
MPIcheckPoint(); |
215 |
+ |
|
216 |
+ |
#endif // is_mpi |
217 |
+ |
|
218 |
+ |
isScanned_ = true; |
219 |
|
} |
220 |
< |
|
221 |
< |
// MPI Section of code.......... |
222 |
< |
#else //IS_MPI |
223 |
< |
|
224 |
< |
// first thing first, suspend fatalities. |
225 |
< |
painCave.isEventLoop = 1; |
226 |
< |
|
227 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
228 |
< |
int haveError; |
229 |
< |
|
230 |
< |
MPI_Status istatus; |
269 |
< |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
270 |
< |
int localIndex; |
271 |
< |
int nCurObj; |
272 |
< |
int nitems; |
273 |
< |
|
274 |
< |
nTotObjs = simnfo->getTotIntegrableObjects(); |
275 |
< |
haveError = 0; |
276 |
< |
if (worldRank == 0) { |
277 |
< |
fsetpos(inFile, framePos[whichFrame]); |
278 |
< |
|
279 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
280 |
< |
if( eof_test == NULL ){ |
281 |
< |
sprintf( painCave.errMsg, |
282 |
< |
"Error reading 1st line of %s \n ",inFileName.c_str()); |
283 |
< |
haveError = 1; |
284 |
< |
simError(); |
220 |
> |
|
221 |
> |
void DumpReader::readFrame(int whichFrame) { |
222 |
> |
if (!isScanned_) |
223 |
> |
scanFile(); |
224 |
> |
|
225 |
> |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
226 |
> |
|
227 |
> |
if (storageLayout & DataStorage::dslPosition) { |
228 |
> |
needPos_ = true; |
229 |
> |
} else { |
230 |
> |
needPos_ = false; |
231 |
|
} |
232 |
< |
|
233 |
< |
nitems = atoi( read_buffer ); |
234 |
< |
|
235 |
< |
// Check to see that the number of integrable objects in the |
236 |
< |
// intial configuration file is the same as derived from the |
237 |
< |
// meta-data file. |
238 |
< |
|
239 |
< |
if( nTotObjs != nitems){ |
240 |
< |
sprintf( painCave.errMsg, |
241 |
< |
"DumpReader Error. %s nIntegrable, %d, " |
242 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
243 |
< |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
244 |
< |
haveError= 1; |
232 |
> |
|
233 |
> |
if (storageLayout & DataStorage::dslVelocity) { |
234 |
> |
needVel_ = true; |
235 |
> |
} else { |
236 |
> |
needVel_ = false; |
237 |
> |
} |
238 |
> |
|
239 |
> |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
240 |
> |
needQuaternion_ = true; |
241 |
> |
} else { |
242 |
> |
needQuaternion_ = false; |
243 |
> |
} |
244 |
> |
|
245 |
> |
if (storageLayout & DataStorage::dslAngularMomentum) { |
246 |
> |
needAngMom_ = true; |
247 |
> |
} else { |
248 |
> |
needAngMom_ = false; |
249 |
> |
} |
250 |
> |
|
251 |
> |
readSet(whichFrame); |
252 |
> |
} |
253 |
> |
|
254 |
> |
void DumpReader::readSet(int whichFrame) { |
255 |
> |
int i; |
256 |
> |
int nTotObjs; // the number of atoms |
257 |
> |
char read_buffer[maxBufferSize]; //the line buffer for reading |
258 |
> |
char * eof_test; // ptr to see when we reach the end of the file |
259 |
> |
|
260 |
> |
Molecule* mol; |
261 |
> |
StuntDouble* integrableObject; |
262 |
> |
SimInfo::MoleculeIterator mi; |
263 |
> |
Molecule::IntegrableObjectIterator ii; |
264 |
> |
|
265 |
> |
#ifndef IS_MPI |
266 |
> |
|
267 |
> |
fsetpos(inFile_, framePos_[whichFrame]); |
268 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
269 |
> |
|
270 |
> |
if (eof_test == NULL) { |
271 |
> |
sprintf(painCave.errMsg, |
272 |
> |
"DumpReader error: error reading 1st line of \"%s\"\n", |
273 |
> |
filename_.c_str()); |
274 |
> |
painCave.isFatal = 1; |
275 |
|
simError(); |
276 |
|
} |
277 |
< |
|
278 |
< |
//read the boxMat from the comment line |
279 |
< |
|
280 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
281 |
< |
if(eof_test == NULL){ |
282 |
< |
sprintf( painCave.errMsg, |
283 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
284 |
< |
haveError = 1; |
277 |
> |
|
278 |
> |
nTotObjs = atoi(read_buffer); |
279 |
> |
|
280 |
> |
if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
281 |
> |
sprintf(painCave.errMsg, |
282 |
> |
"DumpReader error. %s nIntegrable, %d, " |
283 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
284 |
> |
filename_.c_str(), |
285 |
> |
nTotObjs, |
286 |
> |
info_->getNGlobalIntegrableObjects()); |
287 |
> |
|
288 |
> |
painCave.isFatal = 1; |
289 |
|
simError(); |
290 |
|
} |
291 |
< |
|
292 |
< |
//Every single processor will parse the comment line by itself |
293 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
294 |
< |
//more parameters into comment line, we only need to modify function |
295 |
< |
//parseCommentLine |
296 |
< |
|
297 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
298 |
< |
|
299 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
320 |
< |
|
321 |
< |
if( parseErr != NULL ){ |
322 |
< |
strcpy( painCave.errMsg, parseErr ); |
323 |
< |
haveError = 1; |
291 |
> |
|
292 |
> |
//read the box mat from the comment line |
293 |
> |
|
294 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
295 |
> |
|
296 |
> |
if (eof_test == NULL) { |
297 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
298 |
> |
filename_.c_str()); |
299 |
> |
painCave.isFatal = 1; |
300 |
|
simError(); |
301 |
|
} |
302 |
< |
|
303 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
304 |
< |
which_node = MolToProcMap[i]; |
305 |
< |
if(which_node == 0){ |
306 |
< |
//molecules belong to master node |
307 |
< |
|
308 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
309 |
< |
|
310 |
< |
if(localIndex == -1) { |
311 |
< |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
312 |
< |
haveError = 1; |
302 |
> |
|
303 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
304 |
> |
|
305 |
> |
//parse dump lines |
306 |
> |
|
307 |
> |
i = 0; |
308 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
309 |
> |
|
310 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
311 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
312 |
> |
|
313 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
314 |
> |
|
315 |
> |
if (eof_test == NULL) { |
316 |
> |
sprintf(painCave.errMsg, |
317 |
> |
"DumpReader Error: error in reading file %s\n" |
318 |
> |
"natoms = %d; index = %d\n" |
319 |
> |
"error reading the line from the file.\n", |
320 |
> |
filename_.c_str(), |
321 |
> |
nTotObjs, |
322 |
> |
i); |
323 |
> |
|
324 |
> |
painCave.isFatal = 1; |
325 |
> |
simError(); |
326 |
> |
} |
327 |
> |
|
328 |
> |
parseDumpLine(read_buffer, integrableObject); |
329 |
> |
i++; |
330 |
> |
} |
331 |
> |
} |
332 |
> |
|
333 |
> |
// MPI Section of code.......... |
334 |
> |
|
335 |
> |
#else //IS_MPI |
336 |
> |
|
337 |
> |
// first thing first, suspend fatalities. |
338 |
> |
int masterNode = 0; |
339 |
> |
int nCurObj; |
340 |
> |
painCave.isEventLoop = 1; |
341 |
> |
|
342 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
343 |
> |
int haveError; |
344 |
> |
|
345 |
> |
MPI_Status istatus; |
346 |
> |
int nitems; |
347 |
> |
|
348 |
> |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
349 |
> |
haveError = 0; |
350 |
> |
|
351 |
> |
if (worldRank == masterNode) { |
352 |
> |
fsetpos(inFile_, framePos_[whichFrame]); |
353 |
> |
|
354 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
355 |
> |
|
356 |
> |
if (eof_test == NULL) { |
357 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
358 |
> |
filename_.c_str()); |
359 |
> |
painCave.isFatal = 1; |
360 |
|
simError(); |
361 |
|
} |
362 |
< |
|
363 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
364 |
< |
for(j=0; j < integrableObjects.size(); j++){ |
362 |
> |
|
363 |
> |
nitems = atoi(read_buffer); |
364 |
> |
|
365 |
> |
// Check to see that the number of integrable objects in the |
366 |
> |
// intial configuration file is the same as derived from the |
367 |
> |
// meta-data file. |
368 |
> |
|
369 |
> |
if (nTotObjs != nitems) { |
370 |
> |
sprintf(painCave.errMsg, |
371 |
> |
"DumpReader Error. %s nIntegrable, %d, " |
372 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
373 |
> |
filename_.c_str(), |
374 |
> |
nTotObjs, |
375 |
> |
info_->getNGlobalIntegrableObjects()); |
376 |
|
|
377 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
378 |
< |
if(eof_test == NULL){ |
345 |
< |
sprintf(painCave.errMsg, |
346 |
< |
"error in reading file %s\n" |
347 |
< |
"natoms = %d; index = %d\n" |
348 |
< |
"error reading the line from the file.\n", |
349 |
< |
inFileName.c_str(), nTotObjs, i ); |
350 |
< |
haveError= 1; |
351 |
< |
simError(); |
352 |
< |
} |
353 |
< |
|
354 |
< |
if(haveError) nodeZeroError(); |
355 |
< |
|
356 |
< |
parseDumpLine(read_buffer, integrableObjects[j]); |
357 |
< |
|
358 |
< |
} |
359 |
< |
|
360 |
< |
|
377 |
> |
painCave.isFatal = 1; |
378 |
> |
simError(); |
379 |
|
} |
362 |
– |
else{ |
363 |
– |
//molecule belongs to slave nodes |
364 |
– |
|
365 |
– |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
366 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
380 |
|
|
381 |
< |
for(j=0; j < nCurObj; j++){ |
381 |
> |
//read the boxMat from the comment line |
382 |
> |
|
383 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
384 |
> |
|
385 |
> |
if (eof_test == NULL) { |
386 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
387 |
> |
filename_.c_str()); |
388 |
> |
painCave.isFatal = 1; |
389 |
> |
simError(); |
390 |
> |
} |
391 |
> |
|
392 |
> |
//Every single processor will parse the comment line by itself |
393 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
394 |
> |
//more parameters into comment line, we only need to modify function |
395 |
> |
//parseCommentLine |
396 |
> |
|
397 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
398 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
399 |
> |
|
400 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
401 |
> |
int which_node = info_->getMolToProc(i); |
402 |
|
|
403 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
404 |
< |
if(eof_test == NULL){ |
405 |
< |
sprintf(painCave.errMsg, |
406 |
< |
"error in reading file %s\n" |
407 |
< |
"natoms = %d; index = %d\n" |
408 |
< |
"error reading the line from the file.\n", |
409 |
< |
inFileName.c_str(), nTotObjs, i ); |
410 |
< |
haveError= 1; |
411 |
< |
simError(); |
403 |
> |
if (which_node == masterNode) { |
404 |
> |
//molecules belong to master node |
405 |
> |
|
406 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
407 |
> |
|
408 |
> |
if (mol == NULL) { |
409 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
410 |
> |
painCave.isFatal = 1; |
411 |
> |
simError(); |
412 |
|
} |
413 |
|
|
414 |
< |
if(haveError) nodeZeroError(); |
415 |
< |
|
416 |
< |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
417 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
418 |
< |
|
419 |
< |
} |
420 |
< |
|
414 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
415 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
416 |
> |
|
417 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
418 |
> |
|
419 |
> |
if (eof_test == NULL) { |
420 |
> |
sprintf(painCave.errMsg, |
421 |
> |
"DumpReader Error: error in reading file %s\n" |
422 |
> |
"natoms = %d; index = %d\n" |
423 |
> |
"error reading the line from the file.\n", |
424 |
> |
filename_.c_str(), |
425 |
> |
nTotObjs, |
426 |
> |
i); |
427 |
> |
|
428 |
> |
painCave.isFatal = 1; |
429 |
> |
simError(); |
430 |
> |
} |
431 |
> |
|
432 |
> |
parseDumpLine(read_buffer, integrableObject); |
433 |
> |
} |
434 |
> |
} else { |
435 |
> |
//molecule belongs to slave nodes |
436 |
> |
|
437 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
438 |
> |
MPI_COMM_WORLD, &istatus); |
439 |
> |
|
440 |
> |
for(int j = 0; j < nCurObj; j++) { |
441 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
442 |
> |
|
443 |
> |
if (eof_test == NULL) { |
444 |
> |
sprintf(painCave.errMsg, |
445 |
> |
"DumpReader Error: error in reading file %s\n" |
446 |
> |
"natoms = %d; index = %d\n" |
447 |
> |
"error reading the line from the file.\n", |
448 |
> |
filename_.c_str(), |
449 |
> |
nTotObjs, |
450 |
> |
i); |
451 |
> |
|
452 |
> |
painCave.isFatal = 1; |
453 |
> |
simError(); |
454 |
> |
} |
455 |
> |
|
456 |
> |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
457 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
458 |
> |
} |
459 |
> |
} |
460 |
|
} |
461 |
+ |
} else { |
462 |
+ |
//actions taken at slave nodes |
463 |
+ |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
464 |
|
|
465 |
+ |
/**@todo*/ |
466 |
+ |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
467 |
+ |
|
468 |
+ |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
469 |
+ |
int which_node = info_->getMolToProc(i); |
470 |
+ |
|
471 |
+ |
if (which_node == worldRank) { |
472 |
+ |
//molecule with global index i belongs to this processor |
473 |
+ |
|
474 |
+ |
mol = info_->getMoleculeByGlobalIndex(i); |
475 |
+ |
if (mol == NULL) { |
476 |
+ |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
477 |
+ |
painCave.isFatal = 1; |
478 |
+ |
simError(); |
479 |
+ |
} |
480 |
+ |
|
481 |
+ |
nCurObj = mol->getNIntegrableObjects(); |
482 |
+ |
|
483 |
+ |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
484 |
+ |
MPI_COMM_WORLD); |
485 |
+ |
|
486 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
487 |
+ |
integrableObject = mol->nextIntegrableObject(ii)){ |
488 |
+ |
|
489 |
+ |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
490 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
491 |
+ |
|
492 |
+ |
parseDumpLine(read_buffer, integrableObject); |
493 |
+ |
} |
494 |
+ |
|
495 |
+ |
} |
496 |
+ |
|
497 |
+ |
} |
498 |
+ |
|
499 |
|
} |
500 |
|
|
501 |
+ |
#endif |
502 |
+ |
|
503 |
|
} |
504 |
< |
else{ |
505 |
< |
//actions taken at slave nodes |
506 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
507 |
< |
|
508 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
509 |
< |
|
510 |
< |
if( parseErr != NULL ){ |
511 |
< |
strcpy( painCave.errMsg, parseErr ); |
512 |
< |
haveError = 1; |
504 |
> |
|
505 |
> |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
506 |
> |
|
507 |
> |
Vector3d pos; // position place holders |
508 |
> |
Vector3d vel; // velocity placeholders |
509 |
> |
Quat4d q; // the quaternions |
510 |
> |
Vector3d ji; // angular velocity placeholders; |
511 |
> |
StringTokenizer tokenizer(line); |
512 |
> |
int nTokens; |
513 |
> |
|
514 |
> |
nTokens = tokenizer.countTokens(); |
515 |
> |
|
516 |
> |
if (nTokens < 14) { |
517 |
> |
sprintf(painCave.errMsg, |
518 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
519 |
> |
painCave.isFatal = 1; |
520 |
|
simError(); |
521 |
|
} |
522 |
< |
|
523 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
524 |
< |
which_node = MolToProcMap[i]; |
522 |
> |
|
523 |
> |
std::string name = tokenizer.nextToken(); |
524 |
> |
|
525 |
> |
if (name != integrableObject->getType()) { |
526 |
|
|
527 |
< |
if(which_node == worldRank){ |
528 |
< |
//molecule with global index i belongs to this processor |
527 |
> |
sprintf(painCave.errMsg, |
528 |
> |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
529 |
> |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
530 |
> |
painCave.isFatal = 1; |
531 |
> |
simError(); |
532 |
> |
} |
533 |
> |
|
534 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
535 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
536 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
537 |
> |
if (needPos_) { |
538 |
> |
integrableObject->setPos(pos); |
539 |
> |
} |
540 |
> |
|
541 |
> |
vel[0] = tokenizer.nextTokenAsDouble(); |
542 |
> |
vel[1] = tokenizer.nextTokenAsDouble(); |
543 |
> |
vel[2] = tokenizer.nextTokenAsDouble(); |
544 |
> |
if (needVel_) { |
545 |
> |
integrableObject->setVel(vel); |
546 |
> |
} |
547 |
> |
|
548 |
> |
if (integrableObject->isDirectional()) { |
549 |
|
|
550 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
551 |
< |
|
552 |
< |
if(localIndex == -1) { |
553 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
554 |
< |
haveError = 1; |
555 |
< |
simError(); |
556 |
< |
} |
418 |
< |
|
419 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
420 |
< |
|
421 |
< |
nCurObj = integrableObjects.size(); |
550 |
> |
q[0] = tokenizer.nextTokenAsDouble(); |
551 |
> |
q[1] = tokenizer.nextTokenAsDouble(); |
552 |
> |
q[2] = tokenizer.nextTokenAsDouble(); |
553 |
> |
q[3] = tokenizer.nextTokenAsDouble(); |
554 |
> |
|
555 |
> |
double qlen = q.length(); |
556 |
> |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
557 |
|
|
558 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
559 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
560 |
< |
|
561 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
562 |
< |
|
563 |
< |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
564 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
565 |
< |
|
566 |
< |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
567 |
< |
|
433 |
< |
if( parseErr != NULL ){ |
434 |
< |
strcpy( painCave.errMsg, parseErr ); |
435 |
< |
simError(); |
436 |
< |
} |
437 |
< |
|
438 |
< |
} |
439 |
< |
|
558 |
> |
sprintf(painCave.errMsg, |
559 |
> |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
560 |
> |
painCave.isFatal = 1; |
561 |
> |
simError(); |
562 |
> |
|
563 |
> |
} |
564 |
> |
|
565 |
> |
q.normalize(); |
566 |
> |
if (needQuaternion_) { |
567 |
> |
integrableObject->setQ(q); |
568 |
|
} |
569 |
|
|
570 |
+ |
ji[0] = tokenizer.nextTokenAsDouble(); |
571 |
+ |
ji[1] = tokenizer.nextTokenAsDouble(); |
572 |
+ |
ji[2] = tokenizer.nextTokenAsDouble(); |
573 |
+ |
if (needAngMom_) { |
574 |
+ |
integrableObject->setJ(ji); |
575 |
+ |
} |
576 |
|
} |
577 |
< |
|
577 |
> |
|
578 |
|
} |
579 |
< |
|
580 |
< |
#endif |
581 |
< |
} |
582 |
< |
|
583 |
< |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
584 |
< |
|
585 |
< |
char *foo; // the pointer to the current string token |
586 |
< |
|
587 |
< |
double pos[3]; // position place holders |
588 |
< |
double vel[3]; // velocity placeholders |
589 |
< |
double q[4]; // the quaternions |
590 |
< |
double ji[3]; // angular velocity placeholders; |
591 |
< |
double qSqr, qLength; // needed to normalize the quaternion vector. |
592 |
< |
|
593 |
< |
|
594 |
< |
// set the string tokenizer |
461 |
< |
|
462 |
< |
foo = strtok(readLine, " ,;\t"); |
463 |
< |
|
464 |
< |
// check the atom name to the current atom |
465 |
< |
|
466 |
< |
if( strcmp( foo, sd->getType() ) ){ |
467 |
< |
sprintf( painCave.errMsg, |
468 |
< |
"DumpReader error. Does not" |
469 |
< |
" match the meta-data atom %s.\n", |
470 |
< |
sd->getType() ); |
471 |
< |
return strdup( painCave.errMsg ); |
472 |
< |
} |
473 |
< |
|
474 |
< |
// get the positions |
475 |
< |
|
476 |
< |
foo = strtok(NULL, " ,;\t"); |
477 |
< |
if(foo == NULL){ |
478 |
< |
sprintf( painCave.errMsg, |
479 |
< |
"error in reading postition x from %s\n", |
480 |
< |
inFileName.c_str()); |
481 |
< |
return strdup( painCave.errMsg ); |
482 |
< |
} |
483 |
< |
pos[0] = atof( foo ); |
484 |
< |
|
485 |
< |
foo = strtok(NULL, " ,;\t"); |
486 |
< |
if(foo == NULL){ |
487 |
< |
sprintf( painCave.errMsg, |
488 |
< |
"error in reading postition y from %s\n", |
489 |
< |
inFileName.c_str()); |
490 |
< |
return strdup( painCave.errMsg ); |
491 |
< |
} |
492 |
< |
pos[1] = atof( foo ); |
493 |
< |
|
494 |
< |
foo = strtok(NULL, " ,;\t"); |
495 |
< |
if(foo == NULL){ |
496 |
< |
sprintf( painCave.errMsg, |
497 |
< |
"error in reading postition z from %s\n", |
498 |
< |
inFileName.c_str()); |
499 |
< |
return strdup( painCave.errMsg ); |
500 |
< |
} |
501 |
< |
pos[2] = atof( foo ); |
502 |
< |
|
503 |
< |
|
504 |
< |
// get the velocities |
505 |
< |
|
506 |
< |
foo = strtok(NULL, " ,;\t"); |
507 |
< |
if(foo == NULL){ |
508 |
< |
sprintf( painCave.errMsg, |
509 |
< |
"error in reading velocity x from %s\n", |
510 |
< |
inFileName.c_str() ); |
511 |
< |
return strdup( painCave.errMsg ); |
512 |
< |
} |
513 |
< |
vel[0] = atof( foo ); |
514 |
< |
|
515 |
< |
foo = strtok(NULL, " ,;\t"); |
516 |
< |
if(foo == NULL){ |
517 |
< |
sprintf( painCave.errMsg, |
518 |
< |
"error in reading velocity x from %s\n", |
519 |
< |
inFileName.c_str() ); |
520 |
< |
return strdup( painCave.errMsg ); |
521 |
< |
} |
522 |
< |
vel[1] = atof( foo ); |
523 |
< |
|
524 |
< |
foo = strtok(NULL, " ,;\t"); |
525 |
< |
if(foo == NULL){ |
526 |
< |
sprintf( painCave.errMsg, |
527 |
< |
"error in reading velocity x from %s\n", |
528 |
< |
inFileName.c_str() ); |
529 |
< |
return strdup( painCave.errMsg ); |
530 |
< |
} |
531 |
< |
vel[2] = atof( foo ); |
532 |
< |
|
533 |
< |
|
534 |
< |
// add the positions and velocities to the atom |
535 |
< |
|
536 |
< |
sd->setPos( pos ); |
537 |
< |
sd->setVel( vel ); |
538 |
< |
|
539 |
< |
if (!sd->isDirectional()) |
540 |
< |
return NULL; |
541 |
< |
|
542 |
< |
// get the quaternions |
543 |
< |
|
544 |
< |
if( sd->isDirectional() ){ |
545 |
< |
|
546 |
< |
foo = strtok(NULL, " ,;\t"); |
547 |
< |
if(foo == NULL){ |
548 |
< |
sprintf( painCave.errMsg, |
549 |
< |
"error in reading velocity x from %s\n", |
550 |
< |
inFileName.c_str() ); |
551 |
< |
return strdup( painCave.errMsg ); |
552 |
< |
} |
553 |
< |
q[0] = atof( foo ); |
554 |
< |
|
555 |
< |
foo = strtok(NULL, " ,;\t"); |
556 |
< |
if(foo == NULL){ |
557 |
< |
sprintf( painCave.errMsg, |
558 |
< |
"error in reading velocity x from %s\n", |
559 |
< |
inFileName.c_str() ); |
560 |
< |
return strdup( painCave.errMsg ); |
561 |
< |
} |
562 |
< |
q[1] = atof( foo ); |
563 |
< |
|
564 |
< |
foo = strtok(NULL, " ,;\t"); |
565 |
< |
if(foo == NULL){ |
566 |
< |
sprintf( painCave.errMsg, |
567 |
< |
"error in reading velocity x from %s\n", |
568 |
< |
inFileName.c_str() ); |
569 |
< |
return strdup( painCave.errMsg ); |
570 |
< |
} |
571 |
< |
q[2] = atof( foo ); |
572 |
< |
|
573 |
< |
foo = strtok(NULL, " ,;\t"); |
574 |
< |
if(foo == NULL){ |
575 |
< |
sprintf( painCave.errMsg, |
576 |
< |
"error in reading velocity x from %s\n", |
577 |
< |
inFileName.c_str() ); |
578 |
< |
return strdup( painCave.errMsg ); |
579 |
< |
} |
580 |
< |
q[3] = atof( foo ); |
581 |
< |
|
582 |
< |
// get the angular velocities |
583 |
< |
|
584 |
< |
foo = strtok(NULL, " ,;\t"); |
585 |
< |
if(foo == NULL){ |
586 |
< |
sprintf( painCave.errMsg, |
587 |
< |
"error in reading velocity x from %s\n", |
588 |
< |
inFileName.c_str() ); |
589 |
< |
return strdup( painCave.errMsg ); |
590 |
< |
} |
591 |
< |
ji[0] = atof( foo ); |
592 |
< |
|
593 |
< |
foo = strtok(NULL, " ,;\t"); |
594 |
< |
if(foo == NULL){ |
595 |
< |
sprintf( painCave.errMsg, |
596 |
< |
"error in reading velocity x from %s\n", |
597 |
< |
inFileName.c_str() ); |
598 |
< |
return strdup( painCave.errMsg ); |
599 |
< |
} |
600 |
< |
ji[1] = atof(foo ); |
601 |
< |
|
602 |
< |
foo = strtok(NULL, " ,;\t"); |
603 |
< |
if(foo == NULL){ |
604 |
< |
sprintf( painCave.errMsg, |
605 |
< |
"error in reading velocity x from %s\n", |
606 |
< |
inFileName.c_str() ); |
607 |
< |
return strdup( painCave.errMsg ); |
608 |
< |
} |
609 |
< |
ji[2] = atof( foo ); |
610 |
< |
|
611 |
< |
|
612 |
< |
// check that the quaternion vector is normalized |
613 |
< |
|
614 |
< |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
615 |
< |
|
616 |
< |
if (fabs(qSqr) < 1e-6) { |
579 |
> |
|
580 |
> |
|
581 |
> |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
582 |
> |
double currTime; |
583 |
> |
Mat3x3d hmat; |
584 |
> |
double chi; |
585 |
> |
double integralOfChiDt; |
586 |
> |
Mat3x3d eta; |
587 |
> |
|
588 |
> |
StringTokenizer tokenizer(line); |
589 |
> |
int nTokens; |
590 |
> |
|
591 |
> |
nTokens = tokenizer.countTokens(); |
592 |
> |
|
593 |
> |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
594 |
> |
if (nTokens < 10) { |
595 |
|
sprintf(painCave.errMsg, |
596 |
< |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
597 |
< |
return strdup(painCave.errMsg); |
596 |
> |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
597 |
> |
painCave.isFatal = 1; |
598 |
> |
simError(); |
599 |
|
} |
600 |
< |
|
601 |
< |
qLength = sqrt( qSqr ); |
602 |
< |
q[0] = q[0] / qLength; |
603 |
< |
q[1] = q[1] / qLength; |
604 |
< |
q[2] = q[2] / qLength; |
605 |
< |
q[3] = q[3] / qLength; |
606 |
< |
|
607 |
< |
// add quaternion and angular velocities |
608 |
< |
|
609 |
< |
sd->setQ( q ); |
610 |
< |
sd->setJ( ji ); |
611 |
< |
} |
612 |
< |
|
613 |
< |
|
614 |
< |
|
615 |
< |
return NULL; |
616 |
< |
} |
617 |
< |
|
618 |
< |
|
619 |
< |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
620 |
< |
|
642 |
< |
double currTime; |
643 |
< |
double boxMat[9]; |
644 |
< |
double theBoxMat3[3][3]; |
645 |
< |
double chi; |
646 |
< |
double integralOfChidt; |
647 |
< |
double eta[9]; |
648 |
< |
|
649 |
< |
char *foo; // the pointer to the current string token |
650 |
< |
|
651 |
< |
// set the string tokenizer |
652 |
< |
|
653 |
< |
foo = strtok(readLine, " ,;\t"); |
654 |
< |
// set the timeToken. |
655 |
< |
|
656 |
< |
if(foo == NULL){ |
657 |
< |
sprintf( painCave.errMsg, |
658 |
< |
"error in reading Time from %s\n", |
659 |
< |
inFileName.c_str() ); |
660 |
< |
return strdup( painCave.errMsg ); |
661 |
< |
} |
662 |
< |
|
663 |
< |
currTime = atof( foo ); |
664 |
< |
entry_plug->setTime( currTime ); |
665 |
< |
|
666 |
< |
//get H-Matrix |
667 |
< |
|
668 |
< |
for(int i = 0 ; i < 9; i++){ |
669 |
< |
foo = strtok(NULL, " ,;\t"); |
670 |
< |
if(foo == NULL){ |
671 |
< |
sprintf( painCave.errMsg, |
672 |
< |
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
673 |
< |
return strdup( painCave.errMsg ); |
674 |
< |
} |
675 |
< |
boxMat[i] = atof( foo ); |
676 |
< |
} |
677 |
< |
|
678 |
< |
for(int i=0;i<3;i++) |
679 |
< |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
680 |
< |
|
681 |
< |
//set H-Matrix |
682 |
< |
entry_plug->setBoxM( theBoxMat3 ); |
683 |
< |
|
684 |
< |
//get chi and integralOfChidt, they should appear by pair |
685 |
< |
|
686 |
< |
if( entry_plug->useInitXSstate ){ |
687 |
< |
foo = strtok(NULL, " ,;\t\n"); |
688 |
< |
if(foo != NULL){ |
689 |
< |
chi = atof(foo); |
600 |
> |
|
601 |
> |
//read current time |
602 |
> |
currTime = tokenizer.nextTokenAsDouble(); |
603 |
> |
s->setTime(currTime); |
604 |
> |
|
605 |
> |
//read h-matrix |
606 |
> |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
607 |
> |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
608 |
> |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
609 |
> |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
610 |
> |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
611 |
> |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
612 |
> |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
613 |
> |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
614 |
> |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
615 |
> |
s->setHmat(hmat); |
616 |
> |
|
617 |
> |
//read chi and integralOfChidt, they should apprear in pair |
618 |
> |
if (tokenizer.countTokens() >= 2) { |
619 |
> |
chi = tokenizer.nextTokenAsDouble(); |
620 |
> |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
621 |
|
|
622 |
< |
foo = strtok(NULL, " ,;\t\n"); |
623 |
< |
if(foo == NULL){ |
693 |
< |
sprintf( painCave.errMsg, |
694 |
< |
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
695 |
< |
return strdup( painCave.errMsg ); |
696 |
< |
} |
697 |
< |
integralOfChidt = atof( foo ); |
698 |
< |
|
699 |
< |
//push chi and integralOfChidt into SimInfo::properties which can be |
700 |
< |
//retrieved by integrator later |
701 |
< |
DoubleGenericData* chiValue = new DoubleGenericData(); |
702 |
< |
chiValue->setID(CHIVALUE_ID); |
703 |
< |
chiValue->setData(chi); |
704 |
< |
entry_plug->addProperty(chiValue); |
705 |
< |
|
706 |
< |
DoubleGenericData* integralOfChidtValue = new DoubleGenericData(); |
707 |
< |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
708 |
< |
integralOfChidtValue->setData(integralOfChidt); |
709 |
< |
entry_plug->addProperty(integralOfChidtValue); |
710 |
< |
|
622 |
> |
s->setChi(chi); |
623 |
> |
s->setIntegralOfChiDt(integralOfChiDt); |
624 |
|
} |
712 |
– |
else |
713 |
– |
return NULL; |
625 |
|
|
626 |
< |
//get eta |
627 |
< |
foo = strtok(NULL, " ,;\t\n"); |
628 |
< |
if(foo != NULL ){ |
629 |
< |
|
630 |
< |
for(int i = 0 ; i < 9; i++){ |
631 |
< |
|
632 |
< |
if(foo == NULL){ |
633 |
< |
sprintf( painCave.errMsg, |
634 |
< |
"error in reading eta[%d] from %s\n", i, inFileName.c_str() ); |
635 |
< |
return strdup( painCave.errMsg ); |
636 |
< |
} |
637 |
< |
eta[i] = atof( foo ); |
638 |
< |
foo = strtok(NULL, " ,;\t\n"); |
728 |
< |
} |
626 |
> |
//read eta (eta is 3x3 matrix) |
627 |
> |
if (tokenizer.countTokens() >= 9) { |
628 |
> |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
629 |
> |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
630 |
> |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
631 |
> |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
632 |
> |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
633 |
> |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
634 |
> |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
635 |
> |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
636 |
> |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
637 |
> |
|
638 |
> |
s->setEta(eta); |
639 |
|
} |
730 |
– |
else |
731 |
– |
return NULL; |
640 |
|
|
641 |
< |
//push eta into SimInfo::properties which can be |
734 |
< |
//retrieved by integrator later |
735 |
< |
//entry_plug->setBoxM( theBoxMat3 ); |
736 |
< |
DoubleVectorGenericData* etaValue = new DoubleVectorGenericData(ETAVALUE_ID); |
737 |
< |
etaValue->insert(etaValue->end(), eta, eta+9); |
738 |
< |
entry_plug->addProperty(etaValue); |
641 |
> |
|
642 |
|
} |
643 |
< |
|
644 |
< |
return NULL; |
742 |
< |
} |
743 |
< |
|
744 |
< |
#ifdef IS_MPI |
745 |
< |
void DumpReader::nodeZeroError( void ){ |
746 |
< |
int j, myStatus; |
747 |
< |
|
748 |
< |
myStatus = 0; |
749 |
< |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
750 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
751 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
752 |
< |
} |
753 |
< |
|
754 |
< |
|
755 |
< |
MPI_Finalize(); |
756 |
< |
exit (0); |
757 |
< |
|
758 |
< |
} |
759 |
< |
|
760 |
< |
void DumpReader::anonymousNodeDie( void ){ |
761 |
< |
|
762 |
< |
MPI_Finalize(); |
763 |
< |
exit (0); |
764 |
< |
} |
765 |
< |
#endif |
643 |
> |
|
644 |
> |
}//end namespace oopse |