1 |
tim |
1078 |
#define _LARGEFILE_SOURCE64 |
2 |
mmeineke |
643 |
#define _FILE_OFFSET_BITS 64 |
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4 |
mmeineke |
804 |
#include <sys/types.h> |
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#include <sys/stat.h> |
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gezelter |
637 |
#include <iostream> |
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gezelter |
829 |
#include <math.h> |
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gezelter |
637 |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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mmeineke |
804 |
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gezelter |
637 |
#include "ReadWrite.hpp" |
16 |
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#include "simError.h" |
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18 |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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mmeineke |
647 |
#endif // is_mpi |
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gezelter |
637 |
|
25 |
mmeineke |
647 |
|
26 |
tim |
1074 |
DumpReader :: DumpReader(const char *in_name ){ |
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mmeineke |
647 |
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isScanned = false; |
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gezelter |
637 |
#ifdef IS_MPI |
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if (worldRank == 0) { |
32 |
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#endif |
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mmeineke |
647 |
inFile = fopen(in_name, "r"); |
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if(inFile == NULL){ |
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gezelter |
637 |
sprintf(painCave.errMsg, |
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"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
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simError(); |
40 |
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} |
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42 |
tim |
1118 |
inFileName = in_name; |
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gezelter |
637 |
#ifdef IS_MPI |
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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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#endif |
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return; |
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} |
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DumpReader :: ~DumpReader( ){ |
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#ifdef IS_MPI |
53 |
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if (worldRank == 0) { |
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#endif |
55 |
tim |
1118 |
vector<fpos_t*>::iterator i; |
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gezelter |
637 |
int error; |
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mmeineke |
647 |
error = fclose( inFile ); |
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gezelter |
637 |
if( error ){ |
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sprintf( painCave.errMsg, |
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tim |
1118 |
"Error closing %s\n", inFileName.c_str()); |
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gezelter |
637 |
simError(); |
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} |
64 |
tim |
1118 |
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for(i = framePos.begin(); i != framePos.end(); ++i) |
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delete *i; |
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framePos.clear(); |
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gezelter |
637 |
#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Dump file closed successfully." ); |
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MPIcheckPoint(); |
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#endif |
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return; |
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} |
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mmeineke |
647 |
int DumpReader::getNframes( void ){ |
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gezelter |
637 |
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tim |
1118 |
if( !isScanned ) |
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scanFile(); |
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return framePos.size(); |
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mmeineke |
647 |
} |
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mmeineke |
643 |
|
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mmeineke |
647 |
void DumpReader::scanFile( void ){ |
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int vectorSize; |
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int i, j, k; |
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int lineNum = 0; |
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char readBuffer[2000]; |
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char* foo; |
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fpos_t *currPos; |
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mmeineke |
804 |
double time; |
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mmeineke |
647 |
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mmeineke |
804 |
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mmeineke |
647 |
#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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rewind( inFile ); |
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currPos = new fpos_t; |
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fgetpos( inFile, currPos ); |
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mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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mmeineke |
647 |
lineNum++; |
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mmeineke |
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if( feof( inFile ) ){ |
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mmeineke |
647 |
sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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tim |
1118 |
inFileName.c_str(), |
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mmeineke |
647 |
lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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tim |
1118 |
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mmeineke |
804 |
while( !feof( inFile ) ){ |
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tim |
1119 |
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framePos.push_back(currPos); |
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mmeineke |
804 |
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mmeineke |
647 |
i = atoi(readBuffer); |
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mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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mmeineke |
647 |
lineNum++; |
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mmeineke |
804 |
if( feof( inFile ) ){ |
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mmeineke |
647 |
sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
127 |
tim |
1118 |
inFileName.c_str(), |
128 |
mmeineke |
647 |
lineNum ); |
129 |
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painCave.isFatal = 1; |
130 |
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simError(); |
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} |
132 |
tim |
1118 |
|
133 |
mmeineke |
647 |
for(j=0; j<i; j++){ |
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mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
136 |
mmeineke |
647 |
lineNum++; |
137 |
mmeineke |
804 |
if( feof( inFile ) ){ |
138 |
mmeineke |
647 |
sprintf( painCave.errMsg, |
139 |
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"File \"%s\" ended unexpectedly at line %d," |
140 |
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" with atom %d\n", |
141 |
tim |
1118 |
inFileName.c_str(), |
142 |
mmeineke |
647 |
lineNum, |
143 |
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j ); |
144 |
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painCave.isFatal = 1; |
145 |
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simError(); |
146 |
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} |
147 |
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148 |
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} |
149 |
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currPos = new fpos_t; |
151 |
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fgetpos( inFile, currPos ); |
152 |
mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
153 |
mmeineke |
647 |
lineNum++; |
154 |
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} |
155 |
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156 |
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delete currPos; |
157 |
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rewind( inFile ); |
158 |
tim |
1118 |
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159 |
mmeineke |
804 |
isScanned = true; |
160 |
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161 |
mmeineke |
647 |
#ifdef IS_MPI |
162 |
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} |
163 |
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strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
164 |
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MPIcheckPoint(); |
165 |
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#endif // is_mpi |
166 |
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} |
167 |
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168 |
mmeineke |
656 |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
169 |
mmeineke |
647 |
|
170 |
mmeineke |
656 |
simnfo = the_simnfo; |
171 |
mmeineke |
647 |
|
172 |
mmeineke |
656 |
this->readSet( whichFrame ); |
173 |
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} |
174 |
gezelter |
637 |
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175 |
mmeineke |
656 |
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176 |
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177 |
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void DumpReader :: readSet( int whichFrame ){ |
178 |
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179 |
tim |
1118 |
int i, j; |
180 |
gezelter |
637 |
|
181 |
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#ifdef IS_MPI |
182 |
tim |
1118 |
int done, which_node, which_atom; // loop counter |
183 |
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#endif //is_mpi |
184 |
gezelter |
637 |
|
185 |
tim |
1118 |
const int BUFFERSIZE = 2000; // size of the read buffer |
186 |
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int nTotObjs; // the number of atoms |
187 |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
188 |
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189 |
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char *eof_test; // ptr to see when we reach the end of the file |
190 |
gezelter |
637 |
char *parseErr; |
191 |
mmeineke |
804 |
|
192 |
tim |
1118 |
vector<StuntDouble*> integrableObjects; |
193 |
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194 |
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195 |
mmeineke |
656 |
#ifndef IS_MPI |
196 |
gezelter |
637 |
|
197 |
tim |
1118 |
fsetpos(inFile, framePos[whichFrame]); |
198 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
199 |
gezelter |
637 |
if( eof_test == NULL ){ |
200 |
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sprintf( painCave.errMsg, |
201 |
tim |
1119 |
"DumpReader error: error reading 1st line of \"%s\"\n", |
202 |
tim |
1118 |
inFileName.c_str() ); |
203 |
gezelter |
637 |
painCave.isFatal = 1; |
204 |
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simError(); |
205 |
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} |
206 |
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207 |
tim |
1118 |
nTotObjs = atoi( read_buffer ); |
208 |
gezelter |
637 |
|
209 |
tim |
1118 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
210 |
gezelter |
637 |
sprintf( painCave.errMsg, |
211 |
tim |
1119 |
"DumpReader error. %s n_atoms, %d, " |
212 |
gezelter |
637 |
"does not match the BASS file's n_atoms, %d.\n", |
213 |
tim |
1118 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
214 |
gezelter |
637 |
painCave.isFatal = 1; |
215 |
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simError(); |
216 |
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} |
217 |
tim |
1118 |
|
218 |
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//read the box mat from the comment line |
219 |
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220 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
221 |
gezelter |
637 |
if(eof_test == NULL){ |
222 |
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sprintf( painCave.errMsg, |
223 |
tim |
1118 |
"error in reading commment in %s\n", inFileName.c_str()); |
224 |
gezelter |
637 |
painCave.isFatal = 1; |
225 |
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simError(); |
226 |
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} |
227 |
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228 |
tim |
1118 |
parseErr = parseCommentLine( read_buffer, simnfo); |
229 |
gezelter |
637 |
if( parseErr != NULL ){ |
230 |
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strcpy( painCave.errMsg, parseErr ); |
231 |
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painCave.isFatal = 1; |
232 |
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simError(); |
233 |
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} |
234 |
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235 |
tim |
1118 |
//parse dump lines |
236 |
gezelter |
637 |
|
237 |
tim |
1118 |
for( i=0; i < simnfo->n_mol; i++){ |
238 |
gezelter |
637 |
|
239 |
tim |
1118 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
240 |
gezelter |
637 |
|
241 |
tim |
1118 |
for(j = 0; j < integrableObjects.size(); j++){ |
242 |
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243 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
244 |
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if(eof_test == NULL){ |
245 |
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sprintf(painCave.errMsg, |
246 |
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"error in reading file %s\n" |
247 |
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"natoms = %d; index = %d\n" |
248 |
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"error reading the line from the file.\n", |
249 |
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inFileName.c_str(), nTotObjs, i ); |
250 |
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painCave.isFatal = 1; |
251 |
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simError(); |
252 |
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} |
253 |
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254 |
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parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
255 |
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if( parseErr != NULL ){ |
256 |
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strcpy( painCave.errMsg, parseErr ); |
257 |
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painCave.isFatal = 1; |
258 |
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simError(); |
259 |
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} |
260 |
gezelter |
637 |
} |
261 |
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} |
262 |
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263 |
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// MPI Section of code.......... |
264 |
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#else //IS_MPI |
265 |
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266 |
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// first thing first, suspend fatalities. |
267 |
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painCave.isEventLoop = 1; |
268 |
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269 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
270 |
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int haveError; |
271 |
tim |
1118 |
|
272 |
gezelter |
637 |
MPI_Status istatus; |
273 |
tim |
1118 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
274 |
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int localIndex; |
275 |
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int nCurObj; |
276 |
gezelter |
637 |
|
277 |
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haveError = 0; |
278 |
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if (worldRank == 0) { |
279 |
tim |
1118 |
fsetpos(inFile, framePos[whichFrame]); |
280 |
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281 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
282 |
gezelter |
637 |
if( eof_test == NULL ){ |
283 |
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sprintf( painCave.errMsg, |
284 |
tim |
1118 |
"Error reading 1st line of %s \n ",inFileName.c_str()); |
285 |
gezelter |
637 |
haveError = 1; |
286 |
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simError(); |
287 |
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} |
288 |
tim |
1118 |
|
289 |
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nTotObjs = atoi( read_buffer ); |
290 |
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291 |
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// Check to see that the number of integrable objects in the intial configuration file is the |
292 |
gezelter |
637 |
// same as declared in simBass. |
293 |
tim |
1118 |
|
294 |
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if( nTotObjs != simnfo->getTotIntegrableObjects()){ |
295 |
gezelter |
637 |
sprintf( painCave.errMsg, |
296 |
tim |
1119 |
"DumpReadererror. %s n_atoms, %d, " |
297 |
gezelter |
637 |
"does not match the BASS file's n_atoms, %d.\n", |
298 |
tim |
1118 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
299 |
gezelter |
637 |
haveError= 1; |
300 |
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simError(); |
301 |
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} |
302 |
tim |
1118 |
|
303 |
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//read the boxMat from the comment line |
304 |
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|
305 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
306 |
gezelter |
637 |
if(eof_test == NULL){ |
307 |
|
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sprintf( painCave.errMsg, |
308 |
tim |
1118 |
"error in reading commment in %s\n", inFileName.c_str()); |
309 |
gezelter |
637 |
haveError = 1; |
310 |
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simError(); |
311 |
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} |
312 |
tim |
1118 |
|
313 |
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//Every single processor will parse the comment line by itself |
314 |
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//By using this way, we might lose some efficiency, but if we want to add |
315 |
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//more parameters into comment line, we only need to modify function |
316 |
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//parseCommentLine |
317 |
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318 |
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MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
319 |
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|
320 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
321 |
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|
322 |
gezelter |
637 |
if( parseErr != NULL ){ |
323 |
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strcpy( painCave.errMsg, parseErr ); |
324 |
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haveError = 1; |
325 |
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simError(); |
326 |
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} |
327 |
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|
328 |
tim |
1118 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
329 |
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which_node = MolToProcMap[i]; |
330 |
|
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if(which_node == 0){ |
331 |
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//molecules belong to master node |
332 |
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|
333 |
|
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localIndex = mpiSim->getGlobalToLocalMol(i); |
334 |
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|
335 |
|
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if(localIndex == -1) { |
336 |
|
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strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
337 |
|
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haveError = 1; |
338 |
|
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simError(); |
339 |
gezelter |
637 |
} |
340 |
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|
341 |
tim |
1118 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
342 |
|
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for(j=0; j < integrableObjects.size(); j++){ |
343 |
|
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|
344 |
|
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
345 |
|
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if(eof_test == NULL){ |
346 |
|
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sprintf(painCave.errMsg, |
347 |
|
|
"error in reading file %s\n" |
348 |
|
|
"natoms = %d; index = %d\n" |
349 |
|
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"error reading the line from the file.\n", |
350 |
|
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inFileName.c_str(), nTotObjs, i ); |
351 |
|
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haveError= 1; |
352 |
|
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simError(); |
353 |
|
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} |
354 |
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|
355 |
|
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if(haveError) nodeZeroError(); |
356 |
|
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|
357 |
|
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parseDumpLine(read_buffer, integrableObjects[i]); |
358 |
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|
359 |
|
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} |
360 |
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|
361 |
|
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|
362 |
gezelter |
637 |
} |
363 |
tim |
1118 |
else{ |
364 |
|
|
//molecule belongs to slave nodes |
365 |
gezelter |
637 |
|
366 |
tim |
1118 |
MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
367 |
gezelter |
637 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
368 |
|
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|
369 |
tim |
1118 |
for(j=0; j < integrableObjects.size(); j++){ |
370 |
|
|
|
371 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
372 |
|
|
if(eof_test == NULL){ |
373 |
|
|
sprintf(painCave.errMsg, |
374 |
|
|
"error in reading file %s\n" |
375 |
|
|
"natoms = %d; index = %d\n" |
376 |
|
|
"error reading the line from the file.\n", |
377 |
|
|
inFileName.c_str(), nTotObjs, i ); |
378 |
|
|
haveError= 1; |
379 |
|
|
simError(); |
380 |
|
|
} |
381 |
|
|
|
382 |
|
|
if(haveError) nodeZeroError(); |
383 |
gezelter |
637 |
|
384 |
tim |
1118 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
385 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
386 |
|
|
|
387 |
|
|
} |
388 |
|
|
|
389 |
gezelter |
637 |
} |
390 |
|
|
|
391 |
|
|
} |
392 |
tim |
1118 |
|
393 |
gezelter |
637 |
} |
394 |
tim |
1118 |
else{ |
395 |
|
|
//actions taken at slave nodes |
396 |
|
|
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
397 |
|
|
which_node = MolToProcMap[i]; |
398 |
|
|
|
399 |
|
|
if(which_node == worldRank){ |
400 |
|
|
//molecule with global index i belongs to this processor |
401 |
|
|
|
402 |
|
|
localIndex = mpiSim->getGlobalToLocalMol(i); |
403 |
gezelter |
637 |
|
404 |
tim |
1118 |
if(localIndex == -1) { |
405 |
|
|
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
406 |
|
|
haveError = 1; |
407 |
|
|
simError(); |
408 |
|
|
} |
409 |
gezelter |
637 |
|
410 |
tim |
1118 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
411 |
gezelter |
637 |
|
412 |
tim |
1118 |
nCurObj = integrableObjects.size(); |
413 |
|
|
|
414 |
|
|
MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
415 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
416 |
gezelter |
637 |
|
417 |
tim |
1118 |
for(j = 0; j < integrableObjects.size(); j++){ |
418 |
|
|
|
419 |
|
|
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
420 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
421 |
|
|
|
422 |
|
|
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
423 |
|
|
|
424 |
|
|
if( parseErr != NULL ){ |
425 |
|
|
strcpy( painCave.errMsg, parseErr ); |
426 |
|
|
simError(); |
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
} |
430 |
|
|
|
431 |
|
|
} |
432 |
|
|
|
433 |
|
|
} |
434 |
|
|
|
435 |
|
|
} |
436 |
|
|
|
437 |
gezelter |
637 |
#endif |
438 |
|
|
} |
439 |
|
|
|
440 |
tim |
1118 |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
441 |
gezelter |
637 |
|
442 |
tim |
1118 |
char *foo; // the pointer to the current string token |
443 |
|
|
|
444 |
|
|
double pos[3]; // position place holders |
445 |
|
|
double vel[3]; // velocity placeholders |
446 |
|
|
double q[4]; // the quaternions |
447 |
|
|
double ji[3]; // angular velocity placeholders; |
448 |
gezelter |
637 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
449 |
|
|
|
450 |
|
|
|
451 |
|
|
// set the string tokenizer |
452 |
tim |
1118 |
|
453 |
gezelter |
637 |
foo = strtok(readLine, " ,;\t"); |
454 |
tim |
1118 |
|
455 |
gezelter |
637 |
// check the atom name to the current atom |
456 |
tim |
1118 |
|
457 |
|
|
if( strcmp( foo, sd->getType() ) ){ |
458 |
|
|
sprintf( painCave.errMsg, |
459 |
tim |
1119 |
"DumpReader error. Does not" |
460 |
tim |
1118 |
" match the BASS atom %s.\n", |
461 |
|
|
sd->getType() ); |
462 |
|
|
return strdup( painCave.errMsg ); |
463 |
|
|
} |
464 |
|
|
|
465 |
gezelter |
637 |
// get the positions |
466 |
|
|
|
467 |
|
|
foo = strtok(NULL, " ,;\t"); |
468 |
|
|
if(foo == NULL){ |
469 |
|
|
sprintf( painCave.errMsg, |
470 |
tim |
1118 |
"error in reading postition x from %s\n", |
471 |
|
|
inFileName.c_str()); |
472 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
473 |
|
|
} |
474 |
mmeineke |
804 |
pos[0] = atof( foo ); |
475 |
tim |
1118 |
|
476 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
477 |
|
|
if(foo == NULL){ |
478 |
|
|
sprintf( painCave.errMsg, |
479 |
tim |
1118 |
"error in reading postition y from %s\n", |
480 |
|
|
inFileName.c_str()); |
481 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
482 |
|
|
} |
483 |
mmeineke |
804 |
pos[1] = atof( foo ); |
484 |
tim |
1118 |
|
485 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
486 |
|
|
if(foo == NULL){ |
487 |
|
|
sprintf( painCave.errMsg, |
488 |
tim |
1118 |
"error in reading postition z from %s\n", |
489 |
|
|
inFileName.c_str()); |
490 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
491 |
|
|
} |
492 |
tim |
1118 |
pos[2] = atof( foo ); |
493 |
gezelter |
637 |
|
494 |
|
|
|
495 |
|
|
// get the velocities |
496 |
|
|
|
497 |
|
|
foo = strtok(NULL, " ,;\t"); |
498 |
|
|
if(foo == NULL){ |
499 |
|
|
sprintf( painCave.errMsg, |
500 |
tim |
1118 |
"error in reading velocity x from %s\n", |
501 |
|
|
inFileName.c_str() ); |
502 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
503 |
|
|
} |
504 |
mmeineke |
804 |
vel[0] = atof( foo ); |
505 |
tim |
1118 |
|
506 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
507 |
|
|
if(foo == NULL){ |
508 |
|
|
sprintf( painCave.errMsg, |
509 |
tim |
1118 |
"error in reading velocity x from %s\n", |
510 |
|
|
inFileName.c_str() ); |
511 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
512 |
|
|
} |
513 |
mmeineke |
804 |
vel[1] = atof( foo ); |
514 |
tim |
1118 |
|
515 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
516 |
|
|
if(foo == NULL){ |
517 |
|
|
sprintf( painCave.errMsg, |
518 |
tim |
1118 |
"error in reading velocity x from %s\n", |
519 |
|
|
inFileName.c_str() ); |
520 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
521 |
|
|
} |
522 |
mmeineke |
804 |
vel[2] = atof( foo ); |
523 |
tim |
1118 |
|
524 |
|
|
|
525 |
|
|
// add the positions and velocities to the atom |
526 |
|
|
|
527 |
|
|
sd->setPos( pos ); |
528 |
|
|
sd->setVel( vel ); |
529 |
|
|
|
530 |
|
|
if (!sd->isDirectional()) |
531 |
|
|
return NULL; |
532 |
|
|
|
533 |
gezelter |
637 |
// get the quaternions |
534 |
tim |
1118 |
|
535 |
|
|
if( sd->isDirectional() ){ |
536 |
|
|
|
537 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
538 |
|
|
if(foo == NULL){ |
539 |
tim |
1118 |
sprintf( painCave.errMsg, |
540 |
|
|
"error in reading velocity x from %s\n", |
541 |
|
|
inFileName.c_str() ); |
542 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
543 |
|
|
} |
544 |
|
|
q[0] = atof( foo ); |
545 |
tim |
1118 |
|
546 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
547 |
|
|
if(foo == NULL){ |
548 |
|
|
sprintf( painCave.errMsg, |
549 |
tim |
1118 |
"error in reading velocity x from %s\n", |
550 |
|
|
inFileName.c_str() ); |
551 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
552 |
|
|
} |
553 |
|
|
q[1] = atof( foo ); |
554 |
tim |
1118 |
|
555 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
556 |
|
|
if(foo == NULL){ |
557 |
|
|
sprintf( painCave.errMsg, |
558 |
tim |
1118 |
"error in reading velocity x from %s\n", |
559 |
|
|
inFileName.c_str() ); |
560 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
561 |
|
|
} |
562 |
|
|
q[2] = atof( foo ); |
563 |
tim |
1118 |
|
564 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
565 |
|
|
if(foo == NULL){ |
566 |
|
|
sprintf( painCave.errMsg, |
567 |
tim |
1118 |
"error in reading velocity x from %s\n", |
568 |
|
|
inFileName.c_str() ); |
569 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
570 |
|
|
} |
571 |
|
|
q[3] = atof( foo ); |
572 |
tim |
1118 |
|
573 |
gezelter |
637 |
// get the angular velocities |
574 |
tim |
1118 |
|
575 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
576 |
|
|
if(foo == NULL){ |
577 |
|
|
sprintf( painCave.errMsg, |
578 |
tim |
1118 |
"error in reading velocity x from %s\n", |
579 |
|
|
inFileName.c_str() ); |
580 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
581 |
|
|
} |
582 |
gezelter |
1097 |
ji[0] = atof( foo ); |
583 |
tim |
1118 |
|
584 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
585 |
|
|
if(foo == NULL){ |
586 |
|
|
sprintf( painCave.errMsg, |
587 |
tim |
1118 |
"error in reading velocity x from %s\n", |
588 |
|
|
inFileName.c_str() ); |
589 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
590 |
|
|
} |
591 |
gezelter |
1097 |
ji[1] = atof(foo ); |
592 |
tim |
1118 |
|
593 |
gezelter |
637 |
foo = strtok(NULL, " ,;\t"); |
594 |
|
|
if(foo == NULL){ |
595 |
|
|
sprintf( painCave.errMsg, |
596 |
tim |
1118 |
"error in reading velocity x from %s\n", |
597 |
|
|
inFileName.c_str() ); |
598 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
599 |
|
|
} |
600 |
gezelter |
1097 |
ji[2] = atof( foo ); |
601 |
gezelter |
637 |
|
602 |
tim |
1118 |
|
603 |
gezelter |
637 |
// check that the quaternion vector is normalized |
604 |
|
|
|
605 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
606 |
tim |
1118 |
|
607 |
gezelter |
637 |
qLength = sqrt( qSqr ); |
608 |
|
|
q[0] = q[0] / qLength; |
609 |
|
|
q[1] = q[1] / qLength; |
610 |
|
|
q[2] = q[2] / qLength; |
611 |
|
|
q[3] = q[3] / qLength; |
612 |
|
|
|
613 |
tim |
1118 |
// add quaternion and angular velocities |
614 |
|
|
|
615 |
|
|
sd->setQ( q ); |
616 |
|
|
sd->setJ( ji ); |
617 |
gezelter |
637 |
} |
618 |
|
|
|
619 |
mmeineke |
804 |
|
620 |
tim |
1118 |
|
621 |
gezelter |
637 |
return NULL; |
622 |
|
|
} |
623 |
|
|
|
624 |
|
|
|
625 |
tim |
1118 |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
626 |
gezelter |
637 |
|
627 |
tim |
1118 |
double currTime; |
628 |
|
|
double boxMat[9]; |
629 |
|
|
double theBoxMat3[3][3]; |
630 |
|
|
double chi; |
631 |
|
|
double integralOfChidt; |
632 |
mmeineke |
847 |
double eta[9]; |
633 |
gezelter |
637 |
|
634 |
tim |
1118 |
char *foo; // the pointer to the current string token |
635 |
|
|
|
636 |
gezelter |
637 |
// set the string tokenizer |
637 |
tim |
1118 |
|
638 |
gezelter |
637 |
foo = strtok(readLine, " ,;\t"); |
639 |
tim |
1118 |
// set the timeToken. |
640 |
|
|
|
641 |
gezelter |
637 |
if(foo == NULL){ |
642 |
|
|
sprintf( painCave.errMsg, |
643 |
tim |
1118 |
"error in reading Time from %s\n", |
644 |
|
|
inFileName.c_str() ); |
645 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
646 |
|
|
} |
647 |
|
|
|
648 |
tim |
1118 |
currTime = atof( foo ); |
649 |
|
|
entry_plug->setTime( currTime ); |
650 |
gezelter |
637 |
|
651 |
tim |
1118 |
//get H-Matrix |
652 |
gezelter |
637 |
|
653 |
tim |
1118 |
for(int i = 0 ; i < 9; i++){ |
654 |
|
|
foo = strtok(NULL, " ,;\t"); |
655 |
|
|
if(foo == NULL){ |
656 |
|
|
sprintf( painCave.errMsg, |
657 |
|
|
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
658 |
|
|
return strdup( painCave.errMsg ); |
659 |
|
|
} |
660 |
|
|
boxMat[i] = atof( foo ); |
661 |
gezelter |
637 |
} |
662 |
|
|
|
663 |
tim |
1118 |
for(int i=0;i<3;i++) |
664 |
|
|
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
665 |
gezelter |
637 |
|
666 |
tim |
1118 |
//set H-Matrix |
667 |
|
|
entry_plug->setBoxM( theBoxMat3 ); |
668 |
gezelter |
637 |
|
669 |
tim |
1118 |
//get chi and integralOfChidt, they should appear by pair |
670 |
mmeineke |
847 |
|
671 |
tim |
1118 |
if( entry_plug->useInitXSstate ){ |
672 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
673 |
|
|
if(foo != NULL){ |
674 |
|
|
chi = atof(foo); |
675 |
|
|
|
676 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
677 |
|
|
if(foo == NULL){ |
678 |
|
|
sprintf( painCave.errMsg, |
679 |
|
|
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
680 |
|
|
return strdup( painCave.errMsg ); |
681 |
|
|
} |
682 |
|
|
integralOfChidt = atof( foo ); |
683 |
|
|
|
684 |
|
|
//push chi and integralOfChidt into SimInfo::properties which can be |
685 |
|
|
//retrieved by integrator later |
686 |
|
|
DoubleData* chiValue = new DoubleData(); |
687 |
|
|
chiValue->setID(CHIVALUE_ID); |
688 |
|
|
chiValue->setData(chi); |
689 |
|
|
entry_plug->addProperty(chiValue); |
690 |
|
|
|
691 |
|
|
DoubleData* integralOfChidtValue = new DoubleData(); |
692 |
|
|
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
693 |
|
|
integralOfChidtValue->setData(integralOfChidt); |
694 |
|
|
entry_plug->addProperty(integralOfChidtValue); |
695 |
|
|
|
696 |
|
|
} |
697 |
|
|
else |
698 |
|
|
return NULL; |
699 |
mmeineke |
847 |
|
700 |
tim |
1118 |
//get eta |
701 |
mmeineke |
847 |
foo = strtok(NULL, " ,;\t\n"); |
702 |
tim |
1118 |
if(foo != NULL ){ |
703 |
|
|
|
704 |
|
|
for(int i = 0 ; i < 9; i++){ |
705 |
|
|
|
706 |
|
|
if(foo == NULL){ |
707 |
|
|
sprintf( painCave.errMsg, |
708 |
|
|
"error in reading eta[%d] from %s\n", i, inFileName.c_str() ); |
709 |
|
|
return strdup( painCave.errMsg ); |
710 |
|
|
} |
711 |
|
|
eta[i] = atof( foo ); |
712 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
713 |
|
|
} |
714 |
mmeineke |
847 |
} |
715 |
tim |
1118 |
else |
716 |
|
|
return NULL; |
717 |
mmeineke |
847 |
|
718 |
tim |
1118 |
//push eta into SimInfo::properties which can be |
719 |
mmeineke |
847 |
//retrieved by integrator later |
720 |
tim |
1118 |
//entry_plug->setBoxM( theBoxMat3 ); |
721 |
|
|
DoubleArrayData* etaValue = new DoubleArrayData(); |
722 |
|
|
etaValue->setID(ETAVALUE_ID); |
723 |
|
|
etaValue->setData(eta, 9); |
724 |
|
|
entry_plug->addProperty(etaValue); |
725 |
mmeineke |
847 |
} |
726 |
tim |
1118 |
|
727 |
mmeineke |
847 |
return NULL; |
728 |
gezelter |
637 |
} |
729 |
|
|
|
730 |
|
|
#ifdef IS_MPI |
731 |
tim |
1118 |
void DumpReader::nodeZeroError( void ){ |
732 |
|
|
int j, myStatus; |
733 |
gezelter |
637 |
|
734 |
|
|
myStatus = 0; |
735 |
tim |
1118 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
736 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
737 |
gezelter |
637 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
738 |
tim |
1118 |
} |
739 |
gezelter |
637 |
|
740 |
tim |
1118 |
|
741 |
gezelter |
637 |
MPI_Finalize(); |
742 |
|
|
exit (0); |
743 |
tim |
1118 |
|
744 |
gezelter |
637 |
} |
745 |
|
|
|
746 |
tim |
1118 |
void DumpReader::anonymousNodeDie( void ){ |
747 |
gezelter |
637 |
|
748 |
|
|
MPI_Finalize(); |
749 |
|
|
exit (0); |
750 |
|
|
} |
751 |
tim |
1118 |
#endif |