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#define _FILE_OFFSET_BITS 64 |
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#include <iostream> |
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#include <cmath> |
3 |
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#include <math.h> |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
18 |
< |
#define TAKE_THIS_TAG 0 |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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|
21 |
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namespace initFile{ |
22 |
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void nodeZeroError( void ); |
23 |
> |
void anonymousNodeDie( void ); |
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} |
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|
26 |
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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 ){ |
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InitializeFromFile::InitializeFromFile( char *in_name ){ |
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|
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#ifdef IS_MPI |
33 |
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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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|
53 |
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InitializeFromFile :: ~InitializeFromFile( ){ |
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InitializeFromFile::~InitializeFromFile( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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} |
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|
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|
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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|
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int i, j, done, which_node, which_atom; // loop counter |
76 |
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int i, j; |
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|
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#ifdef IS_MPI |
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int done, which_node, which_atom; // loop counter |
80 |
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#endif //is_mpi |
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|
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const int BUFFERSIZE = 2000; // size of the read buffer |
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int n_atoms; // the number of atoms |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
71 |
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#ifdef IS_MPI |
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char send_buffer[BUFFERSIZE]; |
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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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|
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entry_plug = the_entry_plug; |
89 |
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double currTime; |
90 |
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double boxMat[9]; |
91 |
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double theBoxMat3[3][3]; |
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|
93 |
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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); |
98 |
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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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|
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Atom **atoms = entry_plug->atoms; |
95 |
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DirectionalAtom* dAtom; |
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|
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if( n_atoms != entry_plug->n_atoms ){ |
108 |
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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", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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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 |
117 |
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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); |
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if(eof_test == NULL){ |
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simError(); |
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} |
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|
127 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
128 |
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if( parseErr != NULL ){ |
129 |
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strcpy( painCave.errMsg, parseErr ); |
130 |
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painCave.isFatal = 1; |
131 |
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simError(); |
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} |
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|
134 |
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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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|
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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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} |
160 |
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} |
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} |
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// MPI Section of code.......... |
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#else //IS_MPI |
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|
167 |
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MPI::Status istatus; |
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// first thing first, suspend fatalities. |
168 |
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painCave.isEventLoop = 1; |
169 |
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|
170 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
171 |
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int haveError; |
172 |
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|
173 |
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MPI_Status istatus; |
174 |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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|
177 |
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haveError = 0; |
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if (worldRank == 0) { |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
181 |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error reading 1st line of %d \n ",c_in_name); |
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painCave.isFatal = 1; |
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"Error reading 1st line of %s \n ",c_in_name); |
184 |
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haveError = 1; |
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simError(); |
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} |
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|
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n_atoms = atoi( read_buffer ); |
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|
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Atom **atoms = entry_plug->atoms; |
157 |
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DirectionalAtom* dAtom; |
158 |
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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", |
197 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
198 |
< |
painCave.isFatal = 1; |
197 |
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c_in_name, n_atoms, simnfo->n_atoms ); |
198 |
> |
haveError= 1; |
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simError(); |
200 |
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} |
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|
202 |
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//read and toss the comment line |
202 |
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//read the boxMat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
205 |
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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); |
208 |
< |
painCave.isFatal = 1; |
208 |
> |
haveError = 1; |
209 |
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simError(); |
210 |
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} |
211 |
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|
212 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
213 |
+ |
if( parseErr != NULL ){ |
214 |
+ |
strcpy( painCave.errMsg, parseErr ); |
215 |
+ |
haveError = 1; |
216 |
+ |
simError(); |
217 |
+ |
} |
218 |
+ |
|
219 |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
220 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
221 |
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|
222 |
+ |
if(haveError) nodeZeroError(); |
223 |
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|
224 |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
225 |
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|
230 |
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"natoms = %d; index = %d\n" |
231 |
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"error reading the line from the file.\n", |
232 |
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c_in_name, n_atoms, i ); |
233 |
< |
painCave.isFatal = 1; |
233 |
> |
haveError= 1; |
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simError(); |
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} |
236 |
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|
237 |
+ |
if(haveError) nodeZeroError(); |
238 |
+ |
|
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// Get the Node number which wants this atom: |
240 |
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which_node = AtomToProcMap[i]; |
241 |
< |
if (which_node == mpiSim->getMyNode()) { |
241 |
> |
if (which_node == 0) { |
242 |
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parseErr = parseDumpLine( read_buffer, i ); |
243 |
|
if( parseErr != NULL ){ |
244 |
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strcpy( painCave.errMsg, parseErr ); |
245 |
< |
painCave.isFatal = 1; |
245 |
> |
haveError = 1; |
246 |
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simError(); |
247 |
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} |
248 |
< |
} else { |
249 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
250 |
< |
TAKE_THIS_TAG); |
251 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
248 |
> |
if(haveError) nodeZeroError(); |
249 |
> |
} |
250 |
> |
|
251 |
> |
else { |
252 |
> |
|
253 |
> |
myStatus = 1; |
254 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
255 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
256 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
258 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
259 |
> |
MPI_COMM_WORLD); |
260 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
261 |
> |
MPI_COMM_WORLD, &istatus); |
262 |
> |
|
263 |
> |
if(!myStatus) nodeZeroError(); |
264 |
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} |
265 |
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} |
266 |
< |
sprintf(read_buffer, "GAMEOVER"); |
266 |
> |
myStatus = -1; |
267 |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
268 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
269 |
< |
TAKE_THIS_TAG); |
268 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
269 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
270 |
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} |
271 |
|
|
272 |
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} else { |
273 |
|
|
274 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
275 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
276 |
+ |
|
277 |
|
done = 0; |
278 |
|
while (!done) { |
279 |
< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
280 |
< |
TAKE_THIS_TAG, istatus); |
281 |
< |
if (strcmp(read_buffer, "GAMEOVER")) { |
282 |
< |
done = 1; |
283 |
< |
continue; |
284 |
< |
} else { |
285 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
286 |
< |
TAKE_THIS_TAG, istatus); |
287 |
< |
|
288 |
< |
parseErr = parseDumpLine( read_buffer, which_atom ); |
289 |
< |
if( parseErr != NULL ){ |
290 |
< |
strcpy( painCave.errMsg, parseErr ); |
291 |
< |
painCave.isFatal = 1; |
292 |
< |
simError(); |
293 |
< |
} |
279 |
> |
|
280 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
281 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
282 |
> |
|
283 |
> |
if(!myStatus) anonymousNodeDie(); |
284 |
> |
|
285 |
> |
if(myStatus < 0) break; |
286 |
> |
|
287 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
288 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
289 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
290 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 |
> |
|
292 |
> |
myStatus = 1; |
293 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
294 |
> |
if( parseErr != NULL ){ |
295 |
> |
strcpy( painCave.errMsg, parseErr ); |
296 |
> |
myStatus = 0;; |
297 |
> |
simError(); |
298 |
|
} |
299 |
+ |
|
300 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
301 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
302 |
+ |
|
303 |
|
} |
304 |
|
} |
305 |
< |
|
305 |
> |
|
306 |
> |
// last thing last, enable fatalities. |
307 |
> |
painCave.isEventLoop = 0; |
308 |
> |
|
309 |
> |
for(i=0;i<3;i++) |
310 |
> |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
311 |
> |
|
312 |
> |
simnfo->setBoxM( theBoxMat3 ); |
313 |
> |
simnfo->setTime( currTime ); |
314 |
> |
|
315 |
> |
|
316 |
|
#endif |
317 |
|
} |
318 |
|
|
320 |
|
|
321 |
|
char *foo; // the pointer to the current string token |
322 |
|
|
323 |
< |
double rx, ry, rz; // position place holders |
324 |
< |
double vx, vy, vz; // velocity placeholders |
323 |
> |
double pos[3]; // position place holders |
324 |
> |
double vel[3]; // velocity placeholders |
325 |
|
double q[4]; // the quaternions |
326 |
|
double jx, jy, jz; // angular velocity placeholders; |
327 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
328 |
|
|
329 |
< |
Atom **atoms = entry_plug->atoms; |
329 |
> |
Atom **atoms = simnfo->atoms; |
330 |
|
DirectionalAtom* dAtom; |
331 |
|
|
332 |
< |
int j, n_atoms, atomIndex; |
332 |
> |
int n_atoms, atomIndex; |
333 |
|
|
334 |
|
#ifdef IS_MPI |
335 |
+ |
int j; |
336 |
+ |
|
337 |
|
n_atoms = mpiSim->getTotAtoms(); |
338 |
|
atomIndex=-1; |
339 |
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
347 |
|
return strdup( painCave.errMsg ); |
348 |
|
} |
349 |
|
#else |
350 |
< |
n_atoms = entry_plug->n_atoms; |
350 |
> |
n_atoms = simnfo->n_atoms; |
351 |
|
atomIndex = globalIndex; |
352 |
|
#endif // is_mpi |
353 |
|
|
376 |
|
c_in_name, n_atoms, atomIndex ); |
377 |
|
return strdup( painCave.errMsg ); |
378 |
|
} |
379 |
< |
rx = atof( foo ); |
379 |
> |
pos[0] = atof( foo ); |
380 |
|
|
381 |
|
foo = strtok(NULL, " ,;\t"); |
382 |
|
if(foo == NULL){ |
386 |
|
c_in_name, n_atoms, atomIndex ); |
387 |
|
return strdup( painCave.errMsg ); |
388 |
|
} |
389 |
< |
ry = atof( foo ); |
389 |
> |
pos[1] = atof( foo ); |
390 |
|
|
391 |
|
foo = strtok(NULL, " ,;\t"); |
392 |
|
if(foo == NULL){ |
396 |
|
c_in_name, n_atoms, atomIndex ); |
397 |
|
return strdup( painCave.errMsg ); |
398 |
|
} |
399 |
< |
rz = atof( foo ); |
399 |
> |
pos[2] = atof( foo ); |
400 |
|
|
401 |
|
|
402 |
|
// get the velocities |
409 |
|
c_in_name, n_atoms, atomIndex ); |
410 |
|
return strdup( painCave.errMsg ); |
411 |
|
} |
412 |
< |
vx = atof( foo ); |
412 |
> |
vel[0] = atof( foo ); |
413 |
|
|
414 |
|
foo = strtok(NULL, " ,;\t"); |
415 |
|
if(foo == NULL){ |
419 |
|
c_in_name, n_atoms, atomIndex ); |
420 |
|
return strdup( painCave.errMsg ); |
421 |
|
} |
422 |
< |
vy = atof( foo ); |
422 |
> |
vel[1] = atof( foo ); |
423 |
|
|
424 |
|
foo = strtok(NULL, " ,;\t"); |
425 |
|
if(foo == NULL){ |
429 |
|
c_in_name, n_atoms, atomIndex ); |
430 |
|
return strdup( painCave.errMsg ); |
431 |
|
} |
432 |
< |
vz = atof( foo ); |
432 |
> |
vel[2] = atof( foo ); |
433 |
|
|
434 |
|
|
435 |
|
// get the quaternions |
531 |
|
|
532 |
|
// add the positions and velocities to the atom |
533 |
|
|
534 |
< |
atoms[atomIndex]->setX( rx ); |
535 |
< |
atoms[atomIndex]->setY( ry ); |
457 |
< |
atoms[atomIndex]->setZ( rz ); |
458 |
< |
|
459 |
< |
atoms[atomIndex]->set_vx( vx ); |
460 |
< |
atoms[atomIndex]->set_vy( vy ); |
461 |
< |
atoms[atomIndex]->set_vz( vz ); |
534 |
> |
atoms[atomIndex]->setPos( pos ); |
535 |
> |
atoms[atomIndex]->setVel( vel ); |
536 |
|
|
537 |
|
return NULL; |
538 |
|
} |
539 |
+ |
|
540 |
+ |
|
541 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
542 |
+ |
double &time ){ |
543 |
+ |
|
544 |
+ |
char *foo; // the pointer to the current string token |
545 |
+ |
|
546 |
+ |
// set the string tokenizer |
547 |
+ |
|
548 |
+ |
foo = strtok(readLine, " ,;\t"); |
549 |
+ |
// set the timeToken. |
550 |
+ |
|
551 |
+ |
if(foo == NULL){ |
552 |
+ |
sprintf( painCave.errMsg, |
553 |
+ |
"error in reading Time from %s\n", |
554 |
+ |
c_in_name ); |
555 |
+ |
return strdup( painCave.errMsg ); |
556 |
+ |
} |
557 |
+ |
time = atof( foo ); |
558 |
+ |
|
559 |
+ |
// get the Hx vector |
560 |
+ |
|
561 |
+ |
foo = strtok(NULL, " ,;\t"); |
562 |
+ |
if(foo == NULL){ |
563 |
+ |
sprintf( painCave.errMsg, |
564 |
+ |
"error in reading Hx[0] from %s\n", |
565 |
+ |
c_in_name ); |
566 |
+ |
return strdup( painCave.errMsg ); |
567 |
+ |
} |
568 |
+ |
boxMat[0] = atof( foo ); |
569 |
+ |
|
570 |
+ |
foo = strtok(NULL, " ,;\t"); |
571 |
+ |
if(foo == NULL){ |
572 |
+ |
sprintf( painCave.errMsg, |
573 |
+ |
"error in reading Hx[1] from %s\n", |
574 |
+ |
c_in_name ); |
575 |
+ |
return strdup( painCave.errMsg ); |
576 |
+ |
} |
577 |
+ |
boxMat[1] = atof( foo ); |
578 |
+ |
|
579 |
+ |
foo = strtok(NULL, " ,;\t"); |
580 |
+ |
if(foo == NULL){ |
581 |
+ |
sprintf( painCave.errMsg, |
582 |
+ |
"error in reading Hx[2] from %s\n", |
583 |
+ |
c_in_name ); |
584 |
+ |
return strdup( painCave.errMsg ); |
585 |
+ |
} |
586 |
+ |
boxMat[2] = atof( foo ); |
587 |
+ |
|
588 |
+ |
// get the Hy vector |
589 |
+ |
|
590 |
+ |
foo = strtok(NULL, " ,;\t"); |
591 |
+ |
if(foo == NULL){ |
592 |
+ |
sprintf( painCave.errMsg, |
593 |
+ |
"error in reading Hy[0] from %s\n", |
594 |
+ |
c_in_name ); |
595 |
+ |
return strdup( painCave.errMsg ); |
596 |
+ |
} |
597 |
+ |
boxMat[3] = atof( foo ); |
598 |
+ |
|
599 |
+ |
foo = strtok(NULL, " ,;\t"); |
600 |
+ |
if(foo == NULL){ |
601 |
+ |
sprintf( painCave.errMsg, |
602 |
+ |
"error in reading Hy[1] from %s\n", |
603 |
+ |
c_in_name ); |
604 |
+ |
return strdup( painCave.errMsg ); |
605 |
+ |
} |
606 |
+ |
boxMat[4] = atof( foo ); |
607 |
+ |
|
608 |
+ |
foo = strtok(NULL, " ,;\t"); |
609 |
+ |
if(foo == NULL){ |
610 |
+ |
sprintf( painCave.errMsg, |
611 |
+ |
"error in reading Hy[2] from %s\n", |
612 |
+ |
c_in_name ); |
613 |
+ |
return strdup( painCave.errMsg ); |
614 |
+ |
} |
615 |
+ |
boxMat[5] = atof( foo ); |
616 |
+ |
|
617 |
+ |
// get the Hz vector |
618 |
+ |
|
619 |
+ |
foo = strtok(NULL, " ,;\t"); |
620 |
+ |
if(foo == NULL){ |
621 |
+ |
sprintf( painCave.errMsg, |
622 |
+ |
"error in reading Hz[0] from %s\n", |
623 |
+ |
c_in_name ); |
624 |
+ |
return strdup( painCave.errMsg ); |
625 |
+ |
} |
626 |
+ |
boxMat[6] = atof( foo ); |
627 |
+ |
|
628 |
+ |
foo = strtok(NULL, " ,;\t"); |
629 |
+ |
if(foo == NULL){ |
630 |
+ |
sprintf( painCave.errMsg, |
631 |
+ |
"error in reading Hz[1] from %s\n", |
632 |
+ |
c_in_name ); |
633 |
+ |
return strdup( painCave.errMsg ); |
634 |
+ |
} |
635 |
+ |
boxMat[7] = atof( foo ); |
636 |
+ |
|
637 |
+ |
foo = strtok(NULL, " ,;\t"); |
638 |
+ |
if(foo == NULL){ |
639 |
+ |
sprintf( painCave.errMsg, |
640 |
+ |
"error in reading Hz[2] from %s\n", |
641 |
+ |
c_in_name ); |
642 |
+ |
return strdup( painCave.errMsg ); |
643 |
+ |
} |
644 |
+ |
boxMat[8] = atof( foo ); |
645 |
+ |
|
646 |
+ |
return NULL; |
647 |
+ |
} |
648 |
+ |
|
649 |
+ |
|
650 |
+ |
#ifdef IS_MPI |
651 |
+ |
|
652 |
+ |
// a couple of functions to let us escape the read loop |
653 |
+ |
|
654 |
+ |
void initFile::nodeZeroError( void ){ |
655 |
+ |
int j, myStatus; |
656 |
+ |
|
657 |
+ |
myStatus = 0; |
658 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, j, |
660 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 |
+ |
} |
662 |
+ |
|
663 |
+ |
|
664 |
+ |
MPI_Finalize(); |
665 |
+ |
exit (0); |
666 |
+ |
|
667 |
+ |
} |
668 |
+ |
|
669 |
+ |
void initFile::anonymousNodeDie( void ){ |
670 |
+ |
|
671 |
+ |
MPI_Finalize(); |
672 |
+ |
exit (0); |
673 |
+ |
} |
674 |
+ |
|
675 |
+ |
#endif //is_mpi |