1 |
gezelter |
830 |
#define _FILE_OFFSET_BITS 64 |
2 |
mmeineke |
377 |
#include <iostream> |
3 |
gezelter |
829 |
#include <math.h> |
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mmeineke |
377 |
|
5 |
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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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#include <unistd.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
11 |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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tim |
837 |
#include "GenericData.hpp" |
15 |
mmeineke |
377 |
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16 |
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#ifdef IS_MPI |
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gezelter |
417 |
#include <mpi.h> |
18 |
mmeineke |
377 |
#include "mpiSimulation.hpp" |
19 |
tim |
1130 |
#define TAKE_THIS_TAG_CHAR 3134 |
20 |
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#define TAKE_THIS_TAG_INT 3135 |
21 |
chuckv |
436 |
|
22 |
mmeineke |
440 |
namespace initFile{ |
23 |
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void nodeZeroError( void ); |
24 |
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void anonymousNodeDie( void ); |
25 |
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} |
26 |
chuckv |
436 |
|
27 |
mmeineke |
440 |
using namespace initFile; |
28 |
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29 |
mmeineke |
377 |
#endif // is_mpi |
30 |
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31 |
tim |
689 |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
32 |
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33 |
mmeineke |
377 |
#ifdef IS_MPI |
34 |
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if (worldRank == 0) { |
35 |
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#endif |
36 |
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c_in_file = fopen(in_name, "r"); |
38 |
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if(c_in_file == NULL){ |
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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(); |
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} |
44 |
tim |
837 |
|
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mmeineke |
377 |
strcpy( c_in_name, in_name); |
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#ifdef IS_MPI |
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} |
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mmeineke |
874 |
else{ |
49 |
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sprintf( c_in_name, "mpiNodeParser_%d", worldRank ); |
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} |
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
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mmeineke |
377 |
MPIcheckPoint(); |
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#endif |
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tim |
837 |
return; |
56 |
mmeineke |
377 |
} |
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58 |
tim |
689 |
InitializeFromFile::~InitializeFromFile( ){ |
59 |
mmeineke |
377 |
#ifdef IS_MPI |
60 |
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if (worldRank == 0) { |
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#endif |
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int error; |
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error = fclose( c_in_file ); |
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if( error ){ |
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sprintf( painCave.errMsg, |
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"Error closing %s\n", c_in_name ); |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Infile 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 |
641 |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
80 |
mmeineke |
377 |
|
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mmeineke |
787 |
int i, j; |
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tim |
837 |
|
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mmeineke |
787 |
#ifdef IS_MPI |
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int done, which_node, which_atom; // loop counter |
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#endif //is_mpi |
86 |
mmeineke |
377 |
|
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const int BUFFERSIZE = 2000; // size of the read buffer |
88 |
tim |
1108 |
int nTotObjs; // the number of atoms |
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tim |
837 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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mmeineke |
377 |
|
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tim |
837 |
char *eof_test; // ptr to see when we reach the end of the file |
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mmeineke |
377 |
char *parseErr; |
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mmeineke |
787 |
|
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tim |
1108 |
vector<StuntDouble*> integrableObjects; |
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mmeineke |
586 |
simnfo = the_simnfo; |
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mmeineke |
377 |
|
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#ifndef IS_MPI |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
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c_in_name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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tim |
1108 |
nTotObjs = atoi( read_buffer ); |
110 |
mmeineke |
377 |
|
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tim |
1108 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
112 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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tim |
1108 |
c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
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mmeineke |
377 |
painCave.isFatal = 1; |
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simError(); |
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} |
119 |
tim |
837 |
|
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//read the box mat from the comment line |
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mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
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painCave.isFatal = 1; |
127 |
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simError(); |
128 |
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} |
129 |
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tim |
837 |
parseErr = parseCommentLine( read_buffer, simnfo); |
131 |
mmeineke |
586 |
if( parseErr != NULL ){ |
132 |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
136 |
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tim |
837 |
//parse dump lines |
138 |
mmeineke |
586 |
|
139 |
tim |
1108 |
for( i=0; i < simnfo->n_mol; i++){ |
140 |
mmeineke |
586 |
|
141 |
tim |
1108 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
142 |
mmeineke |
377 |
|
143 |
tim |
1113 |
for(j = 0; j < integrableObjects.size(); j++){ |
144 |
tim |
837 |
|
145 |
tim |
1108 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
146 |
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if(eof_test == NULL){ |
147 |
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sprintf(painCave.errMsg, |
148 |
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"error in reading file %s\n" |
149 |
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"natoms = %d; index = %d\n" |
150 |
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"error reading the line from the file.\n", |
151 |
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c_in_name, nTotObjs, i ); |
152 |
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painCave.isFatal = 1; |
153 |
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simError(); |
154 |
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} |
155 |
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156 |
tim |
1113 |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
157 |
tim |
1108 |
if( parseErr != NULL ){ |
158 |
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strcpy( painCave.errMsg, parseErr ); |
159 |
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painCave.isFatal = 1; |
160 |
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simError(); |
161 |
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} |
162 |
tim |
1113 |
} |
163 |
mmeineke |
377 |
} |
164 |
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165 |
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// MPI Section of code.......... |
166 |
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#else //IS_MPI |
167 |
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168 |
chuckv |
436 |
// first thing first, suspend fatalities. |
169 |
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painCave.isEventLoop = 1; |
170 |
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171 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
172 |
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int haveError; |
173 |
tim |
837 |
|
174 |
mmeineke |
447 |
MPI_Status istatus; |
175 |
tim |
1108 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
176 |
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int localIndex; |
177 |
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int nCurObj; |
178 |
tim |
1129 |
int nItems; |
179 |
mmeineke |
377 |
|
180 |
tim |
1129 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
181 |
chuckv |
436 |
haveError = 0; |
182 |
mmeineke |
377 |
if (worldRank == 0) { |
183 |
chuckv |
436 |
|
184 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
185 |
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if( eof_test == NULL ){ |
186 |
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sprintf( painCave.errMsg, |
187 |
mmeineke |
787 |
"Error reading 1st line of %s \n ",c_in_name); |
188 |
chuckv |
436 |
haveError = 1; |
189 |
mmeineke |
377 |
simError(); |
190 |
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} |
191 |
tim |
837 |
|
192 |
tim |
1129 |
nItems = atoi( read_buffer ); |
193 |
tim |
837 |
|
194 |
tim |
1108 |
// Check to see that the number of integrable objects in the intial configuration file is the |
195 |
mmeineke |
377 |
// same as declared in simBass. |
196 |
tim |
837 |
|
197 |
tim |
1129 |
if( nTotObjs != nItems){ |
198 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
199 |
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"Initialize from File error. %s n_atoms, %d, " |
200 |
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"does not match the BASS file's n_atoms, %d.\n", |
201 |
tim |
1108 |
c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
202 |
chuckv |
436 |
haveError= 1; |
203 |
mmeineke |
377 |
simError(); |
204 |
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} |
205 |
tim |
837 |
|
206 |
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//read the boxMat from the comment line |
207 |
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208 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
209 |
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if(eof_test == NULL){ |
210 |
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sprintf( painCave.errMsg, |
211 |
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"error in reading commment in %s\n", c_in_name); |
212 |
mmeineke |
586 |
haveError = 1; |
213 |
mmeineke |
377 |
simError(); |
214 |
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} |
215 |
tim |
837 |
|
216 |
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//Every single processor will parse the comment line by itself |
217 |
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//By using this way, we might lose some efficiency, but if we want to add |
218 |
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//more parameters into comment line, we only need to modify function |
219 |
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//parseCommentLine |
220 |
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221 |
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MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
222 |
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223 |
tim |
1130 |
|
224 |
tim |
837 |
parseErr = parseCommentLine( read_buffer, simnfo); |
225 |
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226 |
mmeineke |
586 |
if( parseErr != NULL ){ |
227 |
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strcpy( painCave.errMsg, parseErr ); |
228 |
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haveError = 1; |
229 |
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simError(); |
230 |
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} |
231 |
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232 |
tim |
1108 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
233 |
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which_node = MolToProcMap[i]; |
234 |
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if(which_node == 0){ |
235 |
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//molecules belong to master node |
236 |
gezelter |
417 |
|
237 |
tim |
1108 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
238 |
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239 |
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if(localIndex == -1) { |
240 |
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strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
241 |
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haveError = 1; |
242 |
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simError(); |
243 |
mmeineke |
377 |
} |
244 |
tim |
837 |
|
245 |
tim |
1108 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
246 |
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for(j=0; j < integrableObjects.size(); j++){ |
247 |
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248 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
249 |
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if(eof_test == NULL){ |
250 |
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sprintf(painCave.errMsg, |
251 |
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"error in reading file %s\n" |
252 |
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"natoms = %d; index = %d\n" |
253 |
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"error reading the line from the file.\n", |
254 |
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c_in_name, nTotObjs, i ); |
255 |
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haveError= 1; |
256 |
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simError(); |
257 |
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} |
258 |
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259 |
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if(haveError) nodeZeroError(); |
260 |
chuckv |
436 |
|
261 |
tim |
1129 |
parseDumpLine(read_buffer, integrableObjects[j]); |
262 |
tim |
1108 |
|
263 |
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} |
264 |
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265 |
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266 |
tim |
837 |
} |
267 |
tim |
1108 |
else{ |
268 |
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//molecule belongs to slave nodes |
269 |
tim |
837 |
|
270 |
tim |
1129 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
271 |
tim |
1108 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
272 |
tim |
1131 |
|
273 |
tim |
1130 |
for(j=0; j < nCurObj; j++){ |
274 |
tim |
1108 |
|
275 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
276 |
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if(eof_test == NULL){ |
277 |
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sprintf(painCave.errMsg, |
278 |
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"error in reading file %s\n" |
279 |
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"natoms = %d; index = %d\n" |
280 |
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"error reading the line from the file.\n", |
281 |
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c_in_name, nTotObjs, i ); |
282 |
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haveError= 1; |
283 |
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simError(); |
284 |
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} |
285 |
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286 |
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if(haveError) nodeZeroError(); |
287 |
tim |
837 |
|
288 |
tim |
1108 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
289 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
290 |
tim |
1131 |
|
291 |
tim |
1108 |
} |
292 |
tim |
837 |
|
293 |
mmeineke |
377 |
} |
294 |
tim |
1108 |
|
295 |
mmeineke |
377 |
} |
296 |
tim |
1108 |
|
297 |
|
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} |
298 |
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else{ |
299 |
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//actions taken at slave nodes |
300 |
tim |
1129 |
|
301 |
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MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
302 |
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303 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
304 |
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305 |
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if( parseErr != NULL ){ |
306 |
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strcpy( painCave.errMsg, parseErr ); |
307 |
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haveError = 1; |
308 |
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simError(); |
309 |
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} |
310 |
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|
311 |
tim |
1108 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
312 |
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which_node = MolToProcMap[i]; |
313 |
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314 |
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if(which_node == worldRank){ |
315 |
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//molecule with global index i belongs to this processor |
316 |
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|
317 |
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localIndex = mpiSim->getGlobalToLocalMol(i); |
318 |
tim |
837 |
|
319 |
tim |
1108 |
if(localIndex == -1) { |
320 |
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sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
321 |
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haveError = 1; |
322 |
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simError(); |
323 |
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} |
324 |
mmeineke |
586 |
|
325 |
tim |
1108 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
326 |
tim |
837 |
|
327 |
tim |
1108 |
nCurObj = integrableObjects.size(); |
328 |
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|
329 |
tim |
1129 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
330 |
|
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
331 |
tim |
837 |
|
332 |
tim |
1108 |
for(j = 0; j < integrableObjects.size(); j++){ |
333 |
tim |
837 |
|
334 |
tim |
1108 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
335 |
|
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
336 |
tim |
837 |
|
337 |
tim |
1108 |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
338 |
chuckv |
436 |
|
339 |
tim |
1108 |
if( parseErr != NULL ){ |
340 |
|
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strcpy( painCave.errMsg, parseErr ); |
341 |
|
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simError(); |
342 |
|
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} |
343 |
tim |
837 |
|
344 |
tim |
1108 |
} |
345 |
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|
346 |
mmeineke |
377 |
} |
347 |
tim |
1108 |
|
348 |
|
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} |
349 |
tim |
837 |
|
350 |
mmeineke |
377 |
} |
351 |
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#endif |
352 |
|
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} |
353 |
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|
354 |
tim |
1108 |
char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){ |
355 |
mmeineke |
377 |
|
356 |
tim |
837 |
char *foo; // the pointer to the current string token |
357 |
|
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|
358 |
mmeineke |
670 |
double pos[3]; // position place holders |
359 |
|
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double vel[3]; // velocity placeholders |
360 |
mmeineke |
377 |
double q[4]; // the quaternions |
361 |
gezelter |
1097 |
double ji[3]; // angular velocity placeholders; |
362 |
mmeineke |
377 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
363 |
tim |
837 |
|
364 |
|
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|
365 |
mmeineke |
377 |
// set the string tokenizer |
366 |
tim |
837 |
|
367 |
mmeineke |
377 |
foo = strtok(readLine, " ,;\t"); |
368 |
tim |
837 |
|
369 |
mmeineke |
377 |
// check the atom name to the current atom |
370 |
tim |
837 |
|
371 |
tim |
1108 |
if( strcmp( foo, sd->getType() ) ){ |
372 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
373 |
tim |
1108 |
"Initialize from file error. Does not" |
374 |
mmeineke |
377 |
" match the BASS atom %s.\n", |
375 |
tim |
1108 |
sd->getType() ); |
376 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
377 |
|
|
} |
378 |
tim |
837 |
|
379 |
mmeineke |
377 |
// get the positions |
380 |
|
|
|
381 |
|
|
foo = strtok(NULL, " ,;\t"); |
382 |
|
|
if(foo == NULL){ |
383 |
|
|
sprintf( painCave.errMsg, |
384 |
tim |
1108 |
"error in reading postition x from %s\n", |
385 |
|
|
c_in_name); |
386 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
387 |
|
|
} |
388 |
mmeineke |
670 |
pos[0] = atof( foo ); |
389 |
tim |
837 |
|
390 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
391 |
|
|
if(foo == NULL){ |
392 |
|
|
sprintf( painCave.errMsg, |
393 |
tim |
1108 |
"error in reading postition y from %s\n", |
394 |
|
|
c_in_name); |
395 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
396 |
|
|
} |
397 |
mmeineke |
670 |
pos[1] = atof( foo ); |
398 |
tim |
837 |
|
399 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
400 |
|
|
if(foo == NULL){ |
401 |
|
|
sprintf( painCave.errMsg, |
402 |
tim |
1108 |
"error in reading postition z from %s\n", |
403 |
|
|
c_in_name); |
404 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
405 |
|
|
} |
406 |
tim |
837 |
pos[2] = atof( foo ); |
407 |
mmeineke |
377 |
|
408 |
|
|
|
409 |
|
|
// get the velocities |
410 |
|
|
|
411 |
|
|
foo = strtok(NULL, " ,;\t"); |
412 |
|
|
if(foo == NULL){ |
413 |
|
|
sprintf( painCave.errMsg, |
414 |
tim |
1108 |
"error in reading velocity x from %s\n", |
415 |
|
|
c_in_name ); |
416 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
417 |
|
|
} |
418 |
mmeineke |
670 |
vel[0] = atof( foo ); |
419 |
tim |
837 |
|
420 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
421 |
|
|
if(foo == NULL){ |
422 |
|
|
sprintf( painCave.errMsg, |
423 |
tim |
1108 |
"error in reading velocity x from %s\n", |
424 |
|
|
c_in_name ); |
425 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
426 |
|
|
} |
427 |
mmeineke |
670 |
vel[1] = atof( foo ); |
428 |
tim |
837 |
|
429 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
430 |
|
|
if(foo == NULL){ |
431 |
|
|
sprintf( painCave.errMsg, |
432 |
tim |
1108 |
"error in reading velocity x from %s\n", |
433 |
|
|
c_in_name ); |
434 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
435 |
|
|
} |
436 |
mmeineke |
670 |
vel[2] = atof( foo ); |
437 |
tim |
837 |
|
438 |
|
|
|
439 |
tim |
1108 |
// add the positions and velocities to the atom |
440 |
|
|
|
441 |
|
|
sd->setPos( pos ); |
442 |
|
|
sd->setVel( vel ); |
443 |
|
|
|
444 |
|
|
if (!sd->isDirectional()) |
445 |
|
|
return NULL; |
446 |
|
|
|
447 |
mmeineke |
377 |
// get the quaternions |
448 |
tim |
837 |
|
449 |
tim |
1108 |
if( sd->isDirectional() ){ |
450 |
tim |
837 |
|
451 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
452 |
|
|
if(foo == NULL){ |
453 |
tim |
1108 |
sprintf( painCave.errMsg, |
454 |
|
|
"error in reading velocity x from %s\n", |
455 |
|
|
c_in_name ); |
456 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
457 |
|
|
} |
458 |
|
|
q[0] = atof( foo ); |
459 |
tim |
837 |
|
460 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
461 |
|
|
if(foo == NULL){ |
462 |
|
|
sprintf( painCave.errMsg, |
463 |
tim |
1108 |
"error in reading velocity x from %s\n", |
464 |
|
|
c_in_name ); |
465 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
466 |
|
|
} |
467 |
|
|
q[1] = atof( foo ); |
468 |
tim |
837 |
|
469 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
470 |
|
|
if(foo == NULL){ |
471 |
|
|
sprintf( painCave.errMsg, |
472 |
tim |
1108 |
"error in reading velocity x from %s\n", |
473 |
|
|
c_in_name ); |
474 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
475 |
|
|
} |
476 |
|
|
q[2] = atof( foo ); |
477 |
tim |
837 |
|
478 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
479 |
|
|
if(foo == NULL){ |
480 |
|
|
sprintf( painCave.errMsg, |
481 |
tim |
1108 |
"error in reading velocity x from %s\n", |
482 |
|
|
c_in_name ); |
483 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
484 |
|
|
} |
485 |
|
|
q[3] = atof( foo ); |
486 |
tim |
837 |
|
487 |
mmeineke |
377 |
// get the angular velocities |
488 |
tim |
837 |
|
489 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
490 |
|
|
if(foo == NULL){ |
491 |
|
|
sprintf( painCave.errMsg, |
492 |
tim |
1108 |
"error in reading velocity x from %s\n", |
493 |
|
|
c_in_name ); |
494 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
495 |
|
|
} |
496 |
gezelter |
1097 |
ji[0] = atof( foo ); |
497 |
tim |
837 |
|
498 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
499 |
|
|
if(foo == NULL){ |
500 |
|
|
sprintf( painCave.errMsg, |
501 |
tim |
1108 |
"error in reading velocity x from %s\n", |
502 |
|
|
c_in_name ); |
503 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
504 |
|
|
} |
505 |
gezelter |
1097 |
ji[1] = atof(foo ); |
506 |
tim |
837 |
|
507 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
508 |
|
|
if(foo == NULL){ |
509 |
|
|
sprintf( painCave.errMsg, |
510 |
tim |
1108 |
"error in reading velocity x from %s\n", |
511 |
|
|
c_in_name ); |
512 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
513 |
|
|
} |
514 |
gezelter |
1097 |
ji[2] = atof( foo ); |
515 |
tim |
837 |
|
516 |
mmeineke |
377 |
|
517 |
|
|
// check that the quaternion vector is normalized |
518 |
|
|
|
519 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
520 |
tim |
837 |
|
521 |
mmeineke |
377 |
qLength = sqrt( qSqr ); |
522 |
|
|
q[0] = q[0] / qLength; |
523 |
|
|
q[1] = q[1] / qLength; |
524 |
|
|
q[2] = q[2] / qLength; |
525 |
|
|
q[3] = q[3] / qLength; |
526 |
tim |
837 |
|
527 |
tim |
1108 |
// add quaternion and angular velocities |
528 |
tim |
837 |
|
529 |
tim |
1108 |
sd->setQ( q ); |
530 |
|
|
sd->setJ( ji ); |
531 |
mmeineke |
377 |
} |
532 |
tim |
837 |
|
533 |
|
|
|
534 |
mmeineke |
377 |
|
535 |
|
|
return NULL; |
536 |
|
|
} |
537 |
chuckv |
436 |
|
538 |
|
|
|
539 |
tim |
837 |
char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
540 |
mmeineke |
586 |
|
541 |
tim |
837 |
double currTime; |
542 |
|
|
double boxMat[9]; |
543 |
|
|
double theBoxMat3[3][3]; |
544 |
|
|
double chi; |
545 |
|
|
double integralOfChidt; |
546 |
|
|
double eta[9]; |
547 |
mmeineke |
586 |
|
548 |
tim |
837 |
char *foo; // the pointer to the current string token |
549 |
|
|
|
550 |
mmeineke |
586 |
// set the string tokenizer |
551 |
tim |
837 |
|
552 |
mmeineke |
586 |
foo = strtok(readLine, " ,;\t"); |
553 |
mmeineke |
641 |
// set the timeToken. |
554 |
mmeineke |
586 |
|
555 |
mmeineke |
641 |
if(foo == NULL){ |
556 |
|
|
sprintf( painCave.errMsg, |
557 |
|
|
"error in reading Time from %s\n", |
558 |
|
|
c_in_name ); |
559 |
|
|
return strdup( painCave.errMsg ); |
560 |
|
|
} |
561 |
mmeineke |
586 |
|
562 |
tim |
837 |
currTime = atof( foo ); |
563 |
|
|
entry_plug->setTime( currTime ); |
564 |
mmeineke |
586 |
|
565 |
tim |
837 |
//get H-Matrix |
566 |
|
|
|
567 |
|
|
for(int i = 0 ; i < 9; i++){ |
568 |
|
|
foo = strtok(NULL, " ,;\t"); |
569 |
|
|
if(foo == NULL){ |
570 |
|
|
sprintf( painCave.errMsg, |
571 |
|
|
"error in reading H[%d] from %s\n", i, c_in_name ); |
572 |
|
|
return strdup( painCave.errMsg ); |
573 |
|
|
} |
574 |
|
|
boxMat[i] = atof( foo ); |
575 |
mmeineke |
586 |
} |
576 |
|
|
|
577 |
tim |
837 |
for(int i=0;i<3;i++) |
578 |
|
|
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
579 |
mmeineke |
586 |
|
580 |
tim |
837 |
//set H-Matrix |
581 |
|
|
entry_plug->setBoxM( theBoxMat3 ); |
582 |
mmeineke |
586 |
|
583 |
tim |
837 |
//get chi and integralOfChidt, they should appear by pair |
584 |
mmeineke |
586 |
|
585 |
mmeineke |
906 |
if( entry_plug->useInitXSstate ){ |
586 |
tim |
837 |
foo = strtok(NULL, " ,;\t\n"); |
587 |
mmeineke |
906 |
if(foo != NULL){ |
588 |
|
|
chi = atof(foo); |
589 |
|
|
|
590 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
591 |
|
|
if(foo == NULL){ |
592 |
|
|
sprintf( painCave.errMsg, |
593 |
|
|
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
594 |
|
|
return strdup( painCave.errMsg ); |
595 |
|
|
} |
596 |
|
|
integralOfChidt = atof( foo ); |
597 |
|
|
|
598 |
|
|
//push chi and integralOfChidt into SimInfo::properties which can be |
599 |
|
|
//retrieved by integrator later |
600 |
|
|
DoubleData* chiValue = new DoubleData(); |
601 |
|
|
chiValue->setID(CHIVALUE_ID); |
602 |
|
|
chiValue->setData(chi); |
603 |
|
|
entry_plug->addProperty(chiValue); |
604 |
|
|
|
605 |
|
|
DoubleData* integralOfChidtValue = new DoubleData(); |
606 |
|
|
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
607 |
|
|
integralOfChidtValue->setData(integralOfChidt); |
608 |
|
|
entry_plug->addProperty(integralOfChidtValue); |
609 |
|
|
|
610 |
tim |
837 |
} |
611 |
mmeineke |
906 |
else |
612 |
|
|
return NULL; |
613 |
|
|
|
614 |
|
|
//get eta |
615 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
616 |
mmeineke |
909 |
if(foo != NULL ){ |
617 |
mmeineke |
911 |
|
618 |
mmeineke |
909 |
for(int i = 0 ; i < 9; i++){ |
619 |
|
|
|
620 |
|
|
if(foo == NULL){ |
621 |
|
|
sprintf( painCave.errMsg, |
622 |
|
|
"error in reading eta[%d] from %s\n", i, c_in_name ); |
623 |
|
|
return strdup( painCave.errMsg ); |
624 |
|
|
} |
625 |
|
|
eta[i] = atof( foo ); |
626 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
627 |
mmeineke |
906 |
} |
628 |
|
|
} |
629 |
mmeineke |
909 |
else |
630 |
|
|
return NULL; |
631 |
mmeineke |
906 |
|
632 |
|
|
//push eta into SimInfo::properties which can be |
633 |
tim |
837 |
//retrieved by integrator later |
634 |
tim |
1129 |
|
635 |
mmeineke |
906 |
DoubleArrayData* etaValue = new DoubleArrayData(); |
636 |
|
|
etaValue->setID(ETAVALUE_ID); |
637 |
|
|
etaValue->setData(eta, 9); |
638 |
|
|
entry_plug->addProperty(etaValue); |
639 |
mmeineke |
586 |
} |
640 |
tim |
837 |
|
641 |
mmeineke |
586 |
return NULL; |
642 |
|
|
} |
643 |
|
|
|
644 |
chuckv |
436 |
#ifdef IS_MPI |
645 |
|
|
|
646 |
|
|
// a couple of functions to let us escape the read loop |
647 |
|
|
|
648 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
649 |
chuckv |
436 |
int j, myStatus; |
650 |
tim |
837 |
|
651 |
chuckv |
436 |
myStatus = 0; |
652 |
tim |
837 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
653 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
654 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
655 |
tim |
837 |
} |
656 |
chuckv |
436 |
|
657 |
tim |
837 |
|
658 |
chuckv |
436 |
MPI_Finalize(); |
659 |
|
|
exit (0); |
660 |
tim |
837 |
|
661 |
chuckv |
436 |
} |
662 |
|
|
|
663 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
664 |
chuckv |
436 |
|
665 |
|
|
MPI_Finalize(); |
666 |
|
|
exit (0); |
667 |
|
|
} |
668 |
|
|
|
669 |
|
|
#endif //is_mpi |