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#include <iostream> |
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< |
#include <cmath> |
2 |
> |
#include <math.h> |
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4 |
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#include <stdio.h> |
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#include <stdlib.h> |
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#ifdef IS_MPI |
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#include <mpi.h> |
16 |
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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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|
20 |
< |
void nodeZeroError( void ); |
21 |
< |
void anonymousNodeDie( void ); |
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> |
namespace initFile{ |
21 |
> |
void nodeZeroError( void ); |
22 |
> |
void anonymousNodeDie( void ); |
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> |
} |
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|
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using namespace initFile; |
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|
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#endif // is_mpi |
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|
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< |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
29 |
> |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
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> |
|
31 |
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#ifdef IS_MPI |
32 |
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if (worldRank == 0) { |
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#endif |
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return; |
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} |
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|
52 |
< |
InitializeFromFile :: ~InitializeFromFile( ){ |
52 |
> |
InitializeFromFile::~InitializeFromFile( ){ |
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#ifdef IS_MPI |
54 |
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if (worldRank == 0) { |
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#endif |
70 |
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} |
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< |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
73 |
> |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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|
75 |
< |
int i, j, done, which_node, which_atom; // loop counter |
75 |
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int i, j; |
76 |
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|
77 |
> |
#ifdef IS_MPI |
78 |
> |
int done, which_node, which_atom; // loop counter |
79 |
> |
#endif //is_mpi |
80 |
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|
81 |
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const int BUFFERSIZE = 2000; // size of the read buffer |
82 |
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int n_atoms; // the number of atoms |
83 |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
76 |
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#ifdef IS_MPI |
77 |
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char send_buffer[BUFFERSIZE]; |
78 |
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#endif |
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|
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char *eof_test; // ptr to see when we reach the end of the file |
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char *parseErr; |
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int procIndex; |
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|
88 |
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entry_plug = the_entry_plug; |
88 |
> |
double currTime; |
89 |
> |
double boxMat[9]; |
90 |
> |
double theBoxMat3[3][3]; |
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|
92 |
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simnfo = the_simnfo; |
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|
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|
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#ifndef IS_MPI |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
97 |
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if( eof_test == NULL ){ |
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|
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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
100 |
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DirectionalAtom* dAtom; |
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|
102 |
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if( n_atoms != entry_plug->n_atoms ){ |
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if( n_atoms != simnfo->n_atoms ){ |
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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", |
111 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
111 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//read and toss the comment line |
116 |
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//read the box mat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
119 |
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if(eof_test == NULL){ |
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simError(); |
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} |
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|
126 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
127 |
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if( parseErr != NULL ){ |
128 |
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strcpy( painCave.errMsg, parseErr ); |
129 |
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painCave.isFatal = 1; |
130 |
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simError(); |
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} |
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|
133 |
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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simnfo->setTime( currTime ); |
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|
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|
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for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
159 |
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} |
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} |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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|
172 |
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MPI::Status istatus; |
172 |
> |
MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
180 |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
182 |
< |
"Error reading 1st line of %d \n ",c_in_name); |
182 |
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"Error reading 1st line of %s \n ",c_in_name); |
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haveError = 1; |
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simError(); |
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} |
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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
171 |
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DirectionalAtom* dAtom; |
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|
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// Check to see that the number of atoms in the intial configuration file is the |
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// same as declared in simBass. |
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|
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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", |
196 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
196 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
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haveError= 1; |
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simError(); |
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} |
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|
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//read and toss the comment line |
201 |
> |
//read the boxMat from the comment line |
202 |
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|
203 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
204 |
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if(eof_test == NULL){ |
205 |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
207 |
< |
haveError= 1; |
207 |
> |
haveError = 1; |
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simError(); |
209 |
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} |
210 |
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|
211 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
212 |
+ |
if( parseErr != NULL ){ |
213 |
+ |
strcpy( painCave.errMsg, parseErr ); |
214 |
+ |
haveError = 1; |
215 |
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simError(); |
216 |
+ |
} |
217 |
+ |
|
218 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
219 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
220 |
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|
221 |
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if(haveError) nodeZeroError(); |
222 |
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|
250 |
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else { |
251 |
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|
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myStatus = 1; |
253 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
254 |
< |
TAKE_THIS_TAG_INT); |
255 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
256 |
< |
TAKE_THIS_TAG_CHAR); |
257 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
258 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
253 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
254 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
255 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
256 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
257 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
258 |
> |
MPI_COMM_WORLD); |
259 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
260 |
> |
MPI_COMM_WORLD, &istatus); |
261 |
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|
262 |
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if(!myStatus) nodeZeroError(); |
263 |
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} |
264 |
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} |
265 |
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myStatus = -1; |
266 |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
267 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
268 |
< |
TAKE_THIS_TAG_INT); |
267 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
268 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
269 |
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} |
270 |
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|
271 |
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} else { |
272 |
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|
273 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
274 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
275 |
+ |
|
276 |
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done = 0; |
277 |
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while (!done) { |
278 |
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|
279 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
280 |
< |
TAKE_THIS_TAG_INT, istatus); |
279 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
280 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
281 |
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|
282 |
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if(!myStatus) anonymousNodeDie(); |
283 |
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|
284 |
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if(myStatus < 0) break; |
285 |
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|
286 |
< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
287 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
288 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
289 |
< |
TAKE_THIS_TAG_INT, istatus); |
286 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
287 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
288 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
289 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
290 |
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|
291 |
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myStatus = 1; |
292 |
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parseErr = parseDumpLine( read_buffer, which_atom ); |
296 |
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simError(); |
297 |
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} |
298 |
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|
299 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
300 |
< |
TAKE_THIS_TAG_INT); |
299 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
300 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
301 |
|
|
302 |
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} |
303 |
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} |
304 |
|
|
305 |
|
// last thing last, enable fatalities. |
306 |
|
painCave.isEventLoop = 0; |
307 |
+ |
|
308 |
+ |
for(i=0;i<3;i++) |
309 |
+ |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
310 |
+ |
|
311 |
+ |
simnfo->setBoxM( theBoxMat3 ); |
312 |
+ |
simnfo->setTime( currTime ); |
313 |
+ |
|
314 |
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|
315 |
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#endif |
316 |
|
} |
319 |
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|
320 |
|
char *foo; // the pointer to the current string token |
321 |
|
|
322 |
< |
double rx, ry, rz; // position place holders |
323 |
< |
double vx, vy, vz; // velocity placeholders |
322 |
> |
double pos[3]; // position place holders |
323 |
> |
double vel[3]; // velocity placeholders |
324 |
|
double q[4]; // the quaternions |
325 |
|
double jx, jy, jz; // angular velocity placeholders; |
326 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
327 |
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|
328 |
< |
Atom **atoms = entry_plug->atoms; |
328 |
> |
Atom **atoms = simnfo->atoms; |
329 |
|
DirectionalAtom* dAtom; |
330 |
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|
331 |
< |
int j, n_atoms, atomIndex; |
331 |
> |
int n_atoms, atomIndex; |
332 |
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|
333 |
|
#ifdef IS_MPI |
334 |
+ |
int j; |
335 |
+ |
|
336 |
|
n_atoms = mpiSim->getTotAtoms(); |
337 |
|
atomIndex=-1; |
338 |
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
346 |
|
return strdup( painCave.errMsg ); |
347 |
|
} |
348 |
|
#else |
349 |
< |
n_atoms = entry_plug->n_atoms; |
349 |
> |
n_atoms = simnfo->n_atoms; |
350 |
|
atomIndex = globalIndex; |
351 |
|
#endif // is_mpi |
352 |
|
|
375 |
|
c_in_name, n_atoms, atomIndex ); |
376 |
|
return strdup( painCave.errMsg ); |
377 |
|
} |
378 |
< |
rx = atof( foo ); |
378 |
> |
pos[0] = atof( foo ); |
379 |
|
|
380 |
|
foo = strtok(NULL, " ,;\t"); |
381 |
|
if(foo == NULL){ |
385 |
|
c_in_name, n_atoms, atomIndex ); |
386 |
|
return strdup( painCave.errMsg ); |
387 |
|
} |
388 |
< |
ry = atof( foo ); |
388 |
> |
pos[1] = atof( foo ); |
389 |
|
|
390 |
|
foo = strtok(NULL, " ,;\t"); |
391 |
|
if(foo == NULL){ |
395 |
|
c_in_name, n_atoms, atomIndex ); |
396 |
|
return strdup( painCave.errMsg ); |
397 |
|
} |
398 |
< |
rz = atof( foo ); |
398 |
> |
pos[2] = atof( foo ); |
399 |
|
|
400 |
|
|
401 |
|
// get the velocities |
408 |
|
c_in_name, n_atoms, atomIndex ); |
409 |
|
return strdup( painCave.errMsg ); |
410 |
|
} |
411 |
< |
vx = atof( foo ); |
411 |
> |
vel[0] = atof( foo ); |
412 |
|
|
413 |
|
foo = strtok(NULL, " ,;\t"); |
414 |
|
if(foo == NULL){ |
418 |
|
c_in_name, n_atoms, atomIndex ); |
419 |
|
return strdup( painCave.errMsg ); |
420 |
|
} |
421 |
< |
vy = atof( foo ); |
421 |
> |
vel[1] = atof( foo ); |
422 |
|
|
423 |
|
foo = strtok(NULL, " ,;\t"); |
424 |
|
if(foo == NULL){ |
428 |
|
c_in_name, n_atoms, atomIndex ); |
429 |
|
return strdup( painCave.errMsg ); |
430 |
|
} |
431 |
< |
vz = atof( foo ); |
431 |
> |
vel[2] = atof( foo ); |
432 |
|
|
433 |
|
|
434 |
|
// get the quaternions |
530 |
|
|
531 |
|
// add the positions and velocities to the atom |
532 |
|
|
533 |
< |
atoms[atomIndex]->setX( rx ); |
534 |
< |
atoms[atomIndex]->setY( ry ); |
495 |
< |
atoms[atomIndex]->setZ( rz ); |
496 |
< |
|
497 |
< |
atoms[atomIndex]->set_vx( vx ); |
498 |
< |
atoms[atomIndex]->set_vy( vy ); |
499 |
< |
atoms[atomIndex]->set_vz( vz ); |
533 |
> |
atoms[atomIndex]->setPos( pos ); |
534 |
> |
atoms[atomIndex]->setVel( vel ); |
535 |
|
|
536 |
|
return NULL; |
537 |
|
} |
538 |
|
|
539 |
|
|
540 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
541 |
+ |
double &time ){ |
542 |
+ |
|
543 |
+ |
char *foo; // the pointer to the current string token |
544 |
+ |
|
545 |
+ |
// set the string tokenizer |
546 |
+ |
|
547 |
+ |
foo = strtok(readLine, " ,;\t"); |
548 |
+ |
// set the timeToken. |
549 |
+ |
|
550 |
+ |
if(foo == NULL){ |
551 |
+ |
sprintf( painCave.errMsg, |
552 |
+ |
"error in reading Time from %s\n", |
553 |
+ |
c_in_name ); |
554 |
+ |
return strdup( painCave.errMsg ); |
555 |
+ |
} |
556 |
+ |
time = atof( foo ); |
557 |
+ |
|
558 |
+ |
// get the Hx vector |
559 |
+ |
|
560 |
+ |
foo = strtok(NULL, " ,;\t"); |
561 |
+ |
if(foo == NULL){ |
562 |
+ |
sprintf( painCave.errMsg, |
563 |
+ |
"error in reading Hx[0] from %s\n", |
564 |
+ |
c_in_name ); |
565 |
+ |
return strdup( painCave.errMsg ); |
566 |
+ |
} |
567 |
+ |
boxMat[0] = atof( foo ); |
568 |
+ |
|
569 |
+ |
foo = strtok(NULL, " ,;\t"); |
570 |
+ |
if(foo == NULL){ |
571 |
+ |
sprintf( painCave.errMsg, |
572 |
+ |
"error in reading Hx[1] from %s\n", |
573 |
+ |
c_in_name ); |
574 |
+ |
return strdup( painCave.errMsg ); |
575 |
+ |
} |
576 |
+ |
boxMat[1] = atof( foo ); |
577 |
+ |
|
578 |
+ |
foo = strtok(NULL, " ,;\t"); |
579 |
+ |
if(foo == NULL){ |
580 |
+ |
sprintf( painCave.errMsg, |
581 |
+ |
"error in reading Hx[2] from %s\n", |
582 |
+ |
c_in_name ); |
583 |
+ |
return strdup( painCave.errMsg ); |
584 |
+ |
} |
585 |
+ |
boxMat[2] = atof( foo ); |
586 |
+ |
|
587 |
+ |
// get the Hy vector |
588 |
+ |
|
589 |
+ |
foo = strtok(NULL, " ,;\t"); |
590 |
+ |
if(foo == NULL){ |
591 |
+ |
sprintf( painCave.errMsg, |
592 |
+ |
"error in reading Hy[0] from %s\n", |
593 |
+ |
c_in_name ); |
594 |
+ |
return strdup( painCave.errMsg ); |
595 |
+ |
} |
596 |
+ |
boxMat[3] = atof( foo ); |
597 |
+ |
|
598 |
+ |
foo = strtok(NULL, " ,;\t"); |
599 |
+ |
if(foo == NULL){ |
600 |
+ |
sprintf( painCave.errMsg, |
601 |
+ |
"error in reading Hy[1] from %s\n", |
602 |
+ |
c_in_name ); |
603 |
+ |
return strdup( painCave.errMsg ); |
604 |
+ |
} |
605 |
+ |
boxMat[4] = atof( foo ); |
606 |
+ |
|
607 |
+ |
foo = strtok(NULL, " ,;\t"); |
608 |
+ |
if(foo == NULL){ |
609 |
+ |
sprintf( painCave.errMsg, |
610 |
+ |
"error in reading Hy[2] from %s\n", |
611 |
+ |
c_in_name ); |
612 |
+ |
return strdup( painCave.errMsg ); |
613 |
+ |
} |
614 |
+ |
boxMat[5] = atof( foo ); |
615 |
+ |
|
616 |
+ |
// get the Hz vector |
617 |
+ |
|
618 |
+ |
foo = strtok(NULL, " ,;\t"); |
619 |
+ |
if(foo == NULL){ |
620 |
+ |
sprintf( painCave.errMsg, |
621 |
+ |
"error in reading Hz[0] from %s\n", |
622 |
+ |
c_in_name ); |
623 |
+ |
return strdup( painCave.errMsg ); |
624 |
+ |
} |
625 |
+ |
boxMat[6] = atof( foo ); |
626 |
+ |
|
627 |
+ |
foo = strtok(NULL, " ,;\t"); |
628 |
+ |
if(foo == NULL){ |
629 |
+ |
sprintf( painCave.errMsg, |
630 |
+ |
"error in reading Hz[1] from %s\n", |
631 |
+ |
c_in_name ); |
632 |
+ |
return strdup( painCave.errMsg ); |
633 |
+ |
} |
634 |
+ |
boxMat[7] = atof( foo ); |
635 |
+ |
|
636 |
+ |
foo = strtok(NULL, " ,;\t"); |
637 |
+ |
if(foo == NULL){ |
638 |
+ |
sprintf( painCave.errMsg, |
639 |
+ |
"error in reading Hz[2] from %s\n", |
640 |
+ |
c_in_name ); |
641 |
+ |
return strdup( painCave.errMsg ); |
642 |
+ |
} |
643 |
+ |
boxMat[8] = atof( foo ); |
644 |
+ |
|
645 |
+ |
return NULL; |
646 |
+ |
} |
647 |
+ |
|
648 |
+ |
|
649 |
|
#ifdef IS_MPI |
650 |
|
|
651 |
|
// a couple of functions to let us escape the read loop |
652 |
|
|
653 |
< |
void nodeZeroError( void ){ |
653 |
> |
void initFile::nodeZeroError( void ){ |
654 |
|
int j, myStatus; |
655 |
|
|
656 |
|
myStatus = 0; |
657 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
658 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
659 |
< |
TAKE_THIS_TAG_INT); |
658 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
659 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
660 |
|
} |
661 |
|
|
662 |
|
|
665 |
|
|
666 |
|
} |
667 |
|
|
668 |
< |
void anonymousNodeDie( void ){ |
668 |
> |
void initFile::anonymousNodeDie( void ){ |
669 |
|
|
670 |
|
MPI_Finalize(); |
671 |
|
exit (0); |