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 |
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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> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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tim |
837 |
#include "GenericData.hpp" |
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mmeineke |
377 |
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#ifdef IS_MPI |
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gezelter |
417 |
#include <mpi.h> |
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mmeineke |
377 |
#include "mpiSimulation.hpp" |
19 |
chuckv |
436 |
#define TAKE_THIS_TAG_CHAR 0 |
20 |
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#define TAKE_THIS_TAG_INT 1 |
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22 |
mmeineke |
440 |
namespace initFile{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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} |
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chuckv |
436 |
|
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mmeineke |
440 |
using namespace initFile; |
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29 |
mmeineke |
377 |
#endif // is_mpi |
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tim |
689 |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
32 |
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mmeineke |
377 |
#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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c_in_file = fopen(in_name, "r"); |
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if(c_in_file == NULL){ |
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sprintf(painCave.errMsg, |
40 |
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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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} |
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tim |
837 |
|
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mmeineke |
377 |
strcpy( c_in_name, in_name); |
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#ifdef IS_MPI |
47 |
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} |
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mmeineke |
874 |
else{ |
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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; |
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mmeineke |
377 |
} |
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58 |
tim |
689 |
InitializeFromFile::~InitializeFromFile( ){ |
59 |
mmeineke |
377 |
#ifdef IS_MPI |
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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 ){ |
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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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vector<StuntDouble*>::iterator iter; |
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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 ); |
111 |
mmeineke |
377 |
|
112 |
tim |
1108 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
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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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} |
120 |
tim |
837 |
|
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//read the box mat from the comment line |
122 |
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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; |
128 |
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simError(); |
129 |
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} |
130 |
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tim |
837 |
parseErr = parseCommentLine( read_buffer, simnfo); |
132 |
mmeineke |
586 |
if( parseErr != NULL ){ |
133 |
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strcpy( painCave.errMsg, parseErr ); |
134 |
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painCave.isFatal = 1; |
135 |
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simError(); |
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} |
137 |
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tim |
837 |
//parse dump lines |
139 |
mmeineke |
586 |
|
140 |
tim |
1108 |
for( i=0; i < simnfo->n_mol; i++){ |
141 |
mmeineke |
586 |
|
142 |
tim |
1108 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
143 |
mmeineke |
377 |
|
144 |
tim |
1108 |
for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++) |
145 |
tim |
837 |
|
146 |
tim |
1108 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
147 |
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if(eof_test == NULL){ |
148 |
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sprintf(painCave.errMsg, |
149 |
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"error in reading file %s\n" |
150 |
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"natoms = %d; index = %d\n" |
151 |
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"error reading the line from the file.\n", |
152 |
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c_in_name, nTotObjs, i ); |
153 |
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painCave.isFatal = 1; |
154 |
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simError(); |
155 |
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} |
156 |
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157 |
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parseErr = parseDumpLine( read_buffer, *iter); |
158 |
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if( parseErr != NULL ){ |
159 |
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strcpy( painCave.errMsg, parseErr ); |
160 |
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painCave.isFatal = 1; |
161 |
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simError(); |
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} |
163 |
mmeineke |
377 |
} |
164 |
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165 |
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166 |
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// MPI Section of code.......... |
167 |
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#else //IS_MPI |
168 |
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169 |
chuckv |
436 |
// first thing first, suspend fatalities. |
170 |
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painCave.isEventLoop = 1; |
171 |
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172 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
173 |
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int haveError; |
174 |
tim |
837 |
|
175 |
mmeineke |
447 |
MPI_Status istatus; |
176 |
tim |
1108 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
177 |
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int localIndex; |
178 |
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int nCurObj; |
179 |
mmeineke |
377 |
|
180 |
chuckv |
436 |
haveError = 0; |
181 |
mmeineke |
377 |
if (worldRank == 0) { |
182 |
chuckv |
436 |
|
183 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
184 |
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if( eof_test == NULL ){ |
185 |
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sprintf( painCave.errMsg, |
186 |
mmeineke |
787 |
"Error reading 1st line of %s \n ",c_in_name); |
187 |
chuckv |
436 |
haveError = 1; |
188 |
mmeineke |
377 |
simError(); |
189 |
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} |
190 |
tim |
837 |
|
191 |
tim |
1108 |
nTotObjs = atoi( read_buffer ); |
192 |
tim |
837 |
|
193 |
tim |
1108 |
// Check to see that the number of integrable objects in the intial configuration file is the |
194 |
mmeineke |
377 |
// same as declared in simBass. |
195 |
tim |
837 |
|
196 |
tim |
1108 |
if( nTotObjs != simnfo->getTotIntegrableObjects()){ |
197 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
198 |
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"Initialize from File error. %s n_atoms, %d, " |
199 |
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"does not match the BASS file's n_atoms, %d.\n", |
200 |
tim |
1108 |
c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
201 |
chuckv |
436 |
haveError= 1; |
202 |
mmeineke |
377 |
simError(); |
203 |
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} |
204 |
tim |
837 |
|
205 |
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//read the boxMat from the comment line |
206 |
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207 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
208 |
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if(eof_test == NULL){ |
209 |
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sprintf( painCave.errMsg, |
210 |
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"error in reading commment in %s\n", c_in_name); |
211 |
mmeineke |
586 |
haveError = 1; |
212 |
mmeineke |
377 |
simError(); |
213 |
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} |
214 |
tim |
837 |
|
215 |
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//Every single processor will parse the comment line by itself |
216 |
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//By using this way, we might lose some efficiency, but if we want to add |
217 |
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//more parameters into comment line, we only need to modify function |
218 |
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//parseCommentLine |
219 |
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220 |
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MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
221 |
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222 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
223 |
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224 |
mmeineke |
586 |
if( parseErr != NULL ){ |
225 |
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strcpy( painCave.errMsg, parseErr ); |
226 |
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haveError = 1; |
227 |
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simError(); |
228 |
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} |
229 |
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230 |
tim |
1108 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
231 |
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which_node = MolToProcMap[i]; |
232 |
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if(which_node == 0){ |
233 |
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//molecules belong to master node |
234 |
gezelter |
417 |
|
235 |
tim |
1108 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
236 |
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237 |
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if(localIndex == -1) { |
238 |
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strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
239 |
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haveError = 1; |
240 |
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simError(); |
241 |
mmeineke |
377 |
} |
242 |
tim |
837 |
|
243 |
tim |
1108 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
244 |
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for(j=0; j < integrableObjects.size(); j++){ |
245 |
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246 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
247 |
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if(eof_test == NULL){ |
248 |
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sprintf(painCave.errMsg, |
249 |
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"error in reading file %s\n" |
250 |
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"natoms = %d; index = %d\n" |
251 |
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"error reading the line from the file.\n", |
252 |
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c_in_name, nTotObjs, i ); |
253 |
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haveError= 1; |
254 |
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simError(); |
255 |
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} |
256 |
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257 |
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if(haveError) nodeZeroError(); |
258 |
chuckv |
436 |
|
259 |
tim |
1108 |
parseDumpLine(read_buffer, integrableObjects[i]); |
260 |
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261 |
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} |
262 |
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263 |
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264 |
tim |
837 |
} |
265 |
tim |
1108 |
else{ |
266 |
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//molecule belongs to slave nodes |
267 |
tim |
837 |
|
268 |
tim |
1108 |
MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
269 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
270 |
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271 |
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for(j=0; j < integrableObjects.size(); j++){ |
272 |
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273 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
274 |
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if(eof_test == NULL){ |
275 |
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sprintf(painCave.errMsg, |
276 |
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"error in reading file %s\n" |
277 |
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"natoms = %d; index = %d\n" |
278 |
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"error reading the line from the file.\n", |
279 |
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c_in_name, nTotObjs, i ); |
280 |
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haveError= 1; |
281 |
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simError(); |
282 |
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} |
283 |
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284 |
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if(haveError) nodeZeroError(); |
285 |
tim |
837 |
|
286 |
tim |
1108 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
287 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
288 |
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289 |
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} |
290 |
tim |
837 |
|
291 |
mmeineke |
377 |
} |
292 |
tim |
1108 |
|
293 |
mmeineke |
377 |
} |
294 |
tim |
1108 |
|
295 |
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} |
296 |
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else{ |
297 |
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//actions taken at slave nodes |
298 |
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for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
299 |
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which_node = MolToProcMap[i]; |
300 |
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301 |
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if(which_node == worldRank){ |
302 |
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//molecule with global index i belongs to this processor |
303 |
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304 |
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localIndex = mpiSim->getGlobalToLocalMol(i); |
305 |
tim |
837 |
|
306 |
tim |
1108 |
if(localIndex == -1) { |
307 |
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sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
308 |
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haveError = 1; |
309 |
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simError(); |
310 |
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} |
311 |
mmeineke |
586 |
|
312 |
tim |
1108 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
313 |
tim |
837 |
|
314 |
tim |
1108 |
nCurObj = integrableObjects.size(); |
315 |
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|
316 |
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MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
317 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
318 |
tim |
837 |
|
319 |
tim |
1108 |
for(j = 0; j < integrableObjects.size(); j++){ |
320 |
tim |
837 |
|
321 |
tim |
1108 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
322 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
323 |
tim |
837 |
|
324 |
tim |
1108 |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
325 |
chuckv |
436 |
|
326 |
tim |
1108 |
if( parseErr != NULL ){ |
327 |
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strcpy( painCave.errMsg, parseErr ); |
328 |
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simError(); |
329 |
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} |
330 |
tim |
837 |
|
331 |
tim |
1108 |
} |
332 |
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|
333 |
mmeineke |
377 |
} |
334 |
tim |
1108 |
|
335 |
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} |
336 |
tim |
837 |
|
337 |
mmeineke |
377 |
} |
338 |
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#endif |
339 |
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} |
340 |
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|
341 |
tim |
1108 |
char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){ |
342 |
mmeineke |
377 |
|
343 |
tim |
837 |
char *foo; // the pointer to the current string token |
344 |
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|
345 |
mmeineke |
670 |
double pos[3]; // position place holders |
346 |
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double vel[3]; // velocity placeholders |
347 |
mmeineke |
377 |
double q[4]; // the quaternions |
348 |
gezelter |
1097 |
double ji[3]; // angular velocity placeholders; |
349 |
mmeineke |
377 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
350 |
tim |
837 |
|
351 |
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|
352 |
mmeineke |
377 |
// set the string tokenizer |
353 |
tim |
837 |
|
354 |
mmeineke |
377 |
foo = strtok(readLine, " ,;\t"); |
355 |
tim |
837 |
|
356 |
mmeineke |
377 |
// check the atom name to the current atom |
357 |
tim |
837 |
|
358 |
tim |
1108 |
if( strcmp( foo, sd->getType() ) ){ |
359 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
360 |
tim |
1108 |
"Initialize from file error. Does not" |
361 |
mmeineke |
377 |
" match the BASS atom %s.\n", |
362 |
tim |
1108 |
sd->getType() ); |
363 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
364 |
|
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} |
365 |
tim |
837 |
|
366 |
mmeineke |
377 |
// get the positions |
367 |
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|
368 |
|
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foo = strtok(NULL, " ,;\t"); |
369 |
|
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if(foo == NULL){ |
370 |
|
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sprintf( painCave.errMsg, |
371 |
tim |
1108 |
"error in reading postition x from %s\n", |
372 |
|
|
c_in_name); |
373 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
374 |
|
|
} |
375 |
mmeineke |
670 |
pos[0] = atof( foo ); |
376 |
tim |
837 |
|
377 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
378 |
|
|
if(foo == NULL){ |
379 |
|
|
sprintf( painCave.errMsg, |
380 |
tim |
1108 |
"error in reading postition y from %s\n", |
381 |
|
|
c_in_name); |
382 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
383 |
|
|
} |
384 |
mmeineke |
670 |
pos[1] = atof( foo ); |
385 |
tim |
837 |
|
386 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
387 |
|
|
if(foo == NULL){ |
388 |
|
|
sprintf( painCave.errMsg, |
389 |
tim |
1108 |
"error in reading postition z from %s\n", |
390 |
|
|
c_in_name); |
391 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
392 |
|
|
} |
393 |
tim |
837 |
pos[2] = atof( foo ); |
394 |
mmeineke |
377 |
|
395 |
|
|
|
396 |
|
|
// get the velocities |
397 |
|
|
|
398 |
|
|
foo = strtok(NULL, " ,;\t"); |
399 |
|
|
if(foo == NULL){ |
400 |
|
|
sprintf( painCave.errMsg, |
401 |
tim |
1108 |
"error in reading velocity x from %s\n", |
402 |
|
|
c_in_name ); |
403 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
404 |
|
|
} |
405 |
mmeineke |
670 |
vel[0] = atof( foo ); |
406 |
tim |
837 |
|
407 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
408 |
|
|
if(foo == NULL){ |
409 |
|
|
sprintf( painCave.errMsg, |
410 |
tim |
1108 |
"error in reading velocity x from %s\n", |
411 |
|
|
c_in_name ); |
412 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
413 |
|
|
} |
414 |
mmeineke |
670 |
vel[1] = atof( foo ); |
415 |
tim |
837 |
|
416 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
417 |
|
|
if(foo == NULL){ |
418 |
|
|
sprintf( painCave.errMsg, |
419 |
tim |
1108 |
"error in reading velocity x from %s\n", |
420 |
|
|
c_in_name ); |
421 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
422 |
|
|
} |
423 |
mmeineke |
670 |
vel[2] = atof( foo ); |
424 |
tim |
837 |
|
425 |
|
|
|
426 |
tim |
1108 |
// add the positions and velocities to the atom |
427 |
|
|
|
428 |
|
|
sd->setPos( pos ); |
429 |
|
|
sd->setVel( vel ); |
430 |
|
|
|
431 |
|
|
if (!sd->isDirectional()) |
432 |
|
|
return NULL; |
433 |
|
|
|
434 |
mmeineke |
377 |
// get the quaternions |
435 |
tim |
837 |
|
436 |
tim |
1108 |
if( sd->isDirectional() ){ |
437 |
tim |
837 |
|
438 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
439 |
|
|
if(foo == NULL){ |
440 |
tim |
1108 |
sprintf( painCave.errMsg, |
441 |
|
|
"error in reading velocity x from %s\n", |
442 |
|
|
c_in_name ); |
443 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
444 |
|
|
} |
445 |
|
|
q[0] = atof( foo ); |
446 |
tim |
837 |
|
447 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
448 |
|
|
if(foo == NULL){ |
449 |
|
|
sprintf( painCave.errMsg, |
450 |
tim |
1108 |
"error in reading velocity x from %s\n", |
451 |
|
|
c_in_name ); |
452 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
453 |
|
|
} |
454 |
|
|
q[1] = atof( foo ); |
455 |
tim |
837 |
|
456 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
457 |
|
|
if(foo == NULL){ |
458 |
|
|
sprintf( painCave.errMsg, |
459 |
tim |
1108 |
"error in reading velocity x from %s\n", |
460 |
|
|
c_in_name ); |
461 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
462 |
|
|
} |
463 |
|
|
q[2] = atof( foo ); |
464 |
tim |
837 |
|
465 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
466 |
|
|
if(foo == NULL){ |
467 |
|
|
sprintf( painCave.errMsg, |
468 |
tim |
1108 |
"error in reading velocity x from %s\n", |
469 |
|
|
c_in_name ); |
470 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
471 |
|
|
} |
472 |
|
|
q[3] = atof( foo ); |
473 |
tim |
837 |
|
474 |
mmeineke |
377 |
// get the angular velocities |
475 |
tim |
837 |
|
476 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
477 |
|
|
if(foo == NULL){ |
478 |
|
|
sprintf( painCave.errMsg, |
479 |
tim |
1108 |
"error in reading velocity x from %s\n", |
480 |
|
|
c_in_name ); |
481 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
482 |
|
|
} |
483 |
gezelter |
1097 |
ji[0] = atof( foo ); |
484 |
tim |
837 |
|
485 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
486 |
|
|
if(foo == NULL){ |
487 |
|
|
sprintf( painCave.errMsg, |
488 |
tim |
1108 |
"error in reading velocity x from %s\n", |
489 |
|
|
c_in_name ); |
490 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
491 |
|
|
} |
492 |
gezelter |
1097 |
ji[1] = atof(foo ); |
493 |
tim |
837 |
|
494 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
495 |
|
|
if(foo == NULL){ |
496 |
|
|
sprintf( painCave.errMsg, |
497 |
tim |
1108 |
"error in reading velocity x from %s\n", |
498 |
|
|
c_in_name ); |
499 |
mmeineke |
377 |
return strdup( painCave.errMsg ); |
500 |
|
|
} |
501 |
gezelter |
1097 |
ji[2] = atof( foo ); |
502 |
tim |
837 |
|
503 |
mmeineke |
377 |
|
504 |
|
|
// check that the quaternion vector is normalized |
505 |
|
|
|
506 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
507 |
tim |
837 |
|
508 |
mmeineke |
377 |
qLength = sqrt( qSqr ); |
509 |
|
|
q[0] = q[0] / qLength; |
510 |
|
|
q[1] = q[1] / qLength; |
511 |
|
|
q[2] = q[2] / qLength; |
512 |
|
|
q[3] = q[3] / qLength; |
513 |
tim |
837 |
|
514 |
tim |
1108 |
// add quaternion and angular velocities |
515 |
tim |
837 |
|
516 |
tim |
1108 |
sd->setQ( q ); |
517 |
|
|
sd->setJ( ji ); |
518 |
mmeineke |
377 |
} |
519 |
tim |
837 |
|
520 |
|
|
|
521 |
mmeineke |
377 |
|
522 |
|
|
return NULL; |
523 |
|
|
} |
524 |
chuckv |
436 |
|
525 |
|
|
|
526 |
tim |
837 |
char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
527 |
mmeineke |
586 |
|
528 |
tim |
837 |
double currTime; |
529 |
|
|
double boxMat[9]; |
530 |
|
|
double theBoxMat3[3][3]; |
531 |
|
|
double chi; |
532 |
|
|
double integralOfChidt; |
533 |
|
|
double eta[9]; |
534 |
mmeineke |
586 |
|
535 |
tim |
837 |
char *foo; // the pointer to the current string token |
536 |
|
|
|
537 |
mmeineke |
586 |
// set the string tokenizer |
538 |
tim |
837 |
|
539 |
mmeineke |
586 |
foo = strtok(readLine, " ,;\t"); |
540 |
mmeineke |
641 |
// set the timeToken. |
541 |
mmeineke |
586 |
|
542 |
mmeineke |
641 |
if(foo == NULL){ |
543 |
|
|
sprintf( painCave.errMsg, |
544 |
|
|
"error in reading Time from %s\n", |
545 |
|
|
c_in_name ); |
546 |
|
|
return strdup( painCave.errMsg ); |
547 |
|
|
} |
548 |
mmeineke |
586 |
|
549 |
tim |
837 |
currTime = atof( foo ); |
550 |
|
|
entry_plug->setTime( currTime ); |
551 |
mmeineke |
586 |
|
552 |
tim |
837 |
//get H-Matrix |
553 |
|
|
|
554 |
|
|
for(int i = 0 ; i < 9; i++){ |
555 |
|
|
foo = strtok(NULL, " ,;\t"); |
556 |
|
|
if(foo == NULL){ |
557 |
|
|
sprintf( painCave.errMsg, |
558 |
|
|
"error in reading H[%d] from %s\n", i, c_in_name ); |
559 |
|
|
return strdup( painCave.errMsg ); |
560 |
|
|
} |
561 |
|
|
boxMat[i] = atof( foo ); |
562 |
mmeineke |
586 |
} |
563 |
|
|
|
564 |
tim |
837 |
for(int i=0;i<3;i++) |
565 |
|
|
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
566 |
mmeineke |
586 |
|
567 |
tim |
837 |
//set H-Matrix |
568 |
|
|
entry_plug->setBoxM( theBoxMat3 ); |
569 |
mmeineke |
586 |
|
570 |
tim |
837 |
//get chi and integralOfChidt, they should appear by pair |
571 |
mmeineke |
586 |
|
572 |
mmeineke |
906 |
if( entry_plug->useInitXSstate ){ |
573 |
tim |
837 |
foo = strtok(NULL, " ,;\t\n"); |
574 |
mmeineke |
906 |
if(foo != NULL){ |
575 |
|
|
chi = atof(foo); |
576 |
|
|
|
577 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
578 |
|
|
if(foo == NULL){ |
579 |
|
|
sprintf( painCave.errMsg, |
580 |
|
|
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
581 |
|
|
return strdup( painCave.errMsg ); |
582 |
|
|
} |
583 |
|
|
integralOfChidt = atof( foo ); |
584 |
|
|
|
585 |
|
|
//push chi and integralOfChidt into SimInfo::properties which can be |
586 |
|
|
//retrieved by integrator later |
587 |
|
|
DoubleData* chiValue = new DoubleData(); |
588 |
|
|
chiValue->setID(CHIVALUE_ID); |
589 |
|
|
chiValue->setData(chi); |
590 |
|
|
entry_plug->addProperty(chiValue); |
591 |
|
|
|
592 |
|
|
DoubleData* integralOfChidtValue = new DoubleData(); |
593 |
|
|
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
594 |
|
|
integralOfChidtValue->setData(integralOfChidt); |
595 |
|
|
entry_plug->addProperty(integralOfChidtValue); |
596 |
|
|
|
597 |
tim |
837 |
} |
598 |
mmeineke |
906 |
else |
599 |
|
|
return NULL; |
600 |
|
|
|
601 |
|
|
//get eta |
602 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
603 |
mmeineke |
909 |
if(foo != NULL ){ |
604 |
mmeineke |
911 |
|
605 |
mmeineke |
909 |
for(int i = 0 ; i < 9; i++){ |
606 |
|
|
|
607 |
|
|
if(foo == NULL){ |
608 |
|
|
sprintf( painCave.errMsg, |
609 |
|
|
"error in reading eta[%d] from %s\n", i, c_in_name ); |
610 |
|
|
return strdup( painCave.errMsg ); |
611 |
|
|
} |
612 |
|
|
eta[i] = atof( foo ); |
613 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
614 |
mmeineke |
906 |
} |
615 |
|
|
} |
616 |
mmeineke |
909 |
else |
617 |
|
|
return NULL; |
618 |
mmeineke |
906 |
|
619 |
|
|
//push eta into SimInfo::properties which can be |
620 |
tim |
837 |
//retrieved by integrator later |
621 |
mmeineke |
906 |
//entry_plug->setBoxM( theBoxMat3 ); |
622 |
|
|
DoubleArrayData* etaValue = new DoubleArrayData(); |
623 |
|
|
etaValue->setID(ETAVALUE_ID); |
624 |
|
|
etaValue->setData(eta, 9); |
625 |
|
|
entry_plug->addProperty(etaValue); |
626 |
mmeineke |
586 |
} |
627 |
tim |
837 |
|
628 |
mmeineke |
586 |
return NULL; |
629 |
|
|
} |
630 |
|
|
|
631 |
chuckv |
436 |
#ifdef IS_MPI |
632 |
|
|
|
633 |
|
|
// a couple of functions to let us escape the read loop |
634 |
|
|
|
635 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
636 |
chuckv |
436 |
int j, myStatus; |
637 |
tim |
837 |
|
638 |
chuckv |
436 |
myStatus = 0; |
639 |
tim |
837 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
640 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
641 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
642 |
tim |
837 |
} |
643 |
chuckv |
436 |
|
644 |
tim |
837 |
|
645 |
chuckv |
436 |
MPI_Finalize(); |
646 |
|
|
exit (0); |
647 |
tim |
837 |
|
648 |
chuckv |
436 |
} |
649 |
|
|
|
650 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
651 |
chuckv |
436 |
|
652 |
|
|
MPI_Finalize(); |
653 |
|
|
exit (0); |
654 |
|
|
} |
655 |
|
|
|
656 |
|
|
#endif //is_mpi |