1 |
gezelter |
830 |
#define _FILE_OFFSET_BITS 64 |
2 |
mmeineke |
377 |
#include <iostream> |
3 |
gezelter |
829 |
#include <math.h> |
4 |
mmeineke |
377 |
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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> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
14 |
tim |
837 |
#include "GenericData.hpp" |
15 |
mmeineke |
377 |
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16 |
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#ifdef IS_MPI |
17 |
gezelter |
417 |
#include <mpi.h> |
18 |
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 |
21 |
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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 |
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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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37 |
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c_in_file = fopen(in_name, "r"); |
38 |
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if(c_in_file == NULL){ |
39 |
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sprintf(painCave.errMsg, |
40 |
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"Cannot open file: %s\n", in_name); |
41 |
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painCave.isFatal = 1; |
42 |
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simError(); |
43 |
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} |
44 |
tim |
837 |
|
45 |
mmeineke |
377 |
strcpy( c_in_name, in_name); |
46 |
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#ifdef IS_MPI |
47 |
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} |
48 |
mmeineke |
874 |
else{ |
49 |
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sprintf( c_in_name, "mpiNodeParser_%d", worldRank ); |
50 |
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} |
51 |
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52 |
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
53 |
mmeineke |
377 |
MPIcheckPoint(); |
54 |
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#endif |
55 |
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) { |
61 |
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#endif |
62 |
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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 |
70 |
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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; |
82 |
tim |
837 |
|
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mmeineke |
787 |
#ifdef IS_MPI |
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int done, which_node, which_atom; // loop counter |
85 |
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#endif //is_mpi |
86 |
mmeineke |
377 |
|
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const int BUFFERSIZE = 2000; // size of the read buffer |
88 |
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int n_atoms; // the number of atoms |
89 |
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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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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n_atoms = atoi( read_buffer ); |
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mmeineke |
586 |
if( n_atoms != simnfo->n_atoms ){ |
110 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
111 |
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"Initialize from File error. %s n_atoms, %d, " |
112 |
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"does not match the BASS file's n_atoms, %d.\n", |
113 |
mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
114 |
mmeineke |
377 |
painCave.isFatal = 1; |
115 |
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simError(); |
116 |
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} |
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tim |
837 |
|
118 |
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//read the box mat from the comment line |
119 |
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mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
121 |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
123 |
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"error in reading commment in %s\n", c_in_name); |
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painCave.isFatal = 1; |
125 |
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simError(); |
126 |
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} |
127 |
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128 |
tim |
837 |
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129 |
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130 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
131 |
mmeineke |
586 |
if( parseErr != NULL ){ |
132 |
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strcpy( painCave.errMsg, parseErr ); |
133 |
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painCave.isFatal = 1; |
134 |
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simError(); |
135 |
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} |
136 |
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137 |
tim |
837 |
//parse dump lines |
138 |
mmeineke |
586 |
|
139 |
tim |
837 |
for( i=0; i < n_atoms; i++){ |
140 |
mmeineke |
586 |
|
141 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
142 |
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if(eof_test == NULL){ |
143 |
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sprintf(painCave.errMsg, |
144 |
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"error in reading file %s\n" |
145 |
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"natoms = %d; index = %d\n" |
146 |
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"error reading the line from the file.\n", |
147 |
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c_in_name, n_atoms, i ); |
148 |
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painCave.isFatal = 1; |
149 |
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simError(); |
150 |
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} |
151 |
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152 |
tim |
837 |
|
153 |
mmeineke |
377 |
parseErr = parseDumpLine( read_buffer, i ); |
154 |
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if( parseErr != NULL ){ |
155 |
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strcpy( painCave.errMsg, parseErr ); |
156 |
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painCave.isFatal = 1; |
157 |
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simError(); |
158 |
mmeineke |
586 |
} |
159 |
mmeineke |
377 |
} |
160 |
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161 |
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162 |
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// MPI Section of code.......... |
163 |
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#else //IS_MPI |
164 |
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165 |
chuckv |
436 |
// first thing first, suspend fatalities. |
166 |
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painCave.isEventLoop = 1; |
167 |
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168 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
169 |
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int haveError; |
170 |
tim |
837 |
|
171 |
mmeineke |
447 |
MPI_Status istatus; |
172 |
gezelter |
417 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
173 |
mmeineke |
377 |
|
174 |
tim |
837 |
|
175 |
chuckv |
436 |
haveError = 0; |
176 |
mmeineke |
377 |
if (worldRank == 0) { |
177 |
chuckv |
436 |
|
178 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
179 |
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if( eof_test == NULL ){ |
180 |
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sprintf( painCave.errMsg, |
181 |
mmeineke |
787 |
"Error reading 1st line of %s \n ",c_in_name); |
182 |
chuckv |
436 |
haveError = 1; |
183 |
mmeineke |
377 |
simError(); |
184 |
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} |
185 |
tim |
837 |
|
186 |
mmeineke |
377 |
n_atoms = atoi( read_buffer ); |
187 |
tim |
837 |
|
188 |
mmeineke |
377 |
// Check to see that the number of atoms in the intial configuration file is the |
189 |
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// same as declared in simBass. |
190 |
tim |
837 |
|
191 |
mmeineke |
377 |
if( n_atoms != mpiSim->getTotAtoms() ){ |
192 |
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sprintf( painCave.errMsg, |
193 |
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"Initialize from File error. %s n_atoms, %d, " |
194 |
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"does not match the BASS file's n_atoms, %d.\n", |
195 |
mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
196 |
chuckv |
436 |
haveError= 1; |
197 |
mmeineke |
377 |
simError(); |
198 |
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} |
199 |
tim |
837 |
|
200 |
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//read the boxMat from the comment line |
201 |
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202 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
203 |
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if(eof_test == NULL){ |
204 |
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sprintf( painCave.errMsg, |
205 |
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"error in reading commment in %s\n", c_in_name); |
206 |
mmeineke |
586 |
haveError = 1; |
207 |
mmeineke |
377 |
simError(); |
208 |
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} |
209 |
tim |
837 |
|
210 |
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//Every single processor will parse the comment line by itself |
211 |
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//By using this way, we might lose some efficiency, but if we want to add |
212 |
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//more parameters into comment line, we only need to modify function |
213 |
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//parseCommentLine |
214 |
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215 |
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MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
216 |
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217 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
218 |
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219 |
mmeineke |
586 |
if( parseErr != NULL ){ |
220 |
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strcpy( painCave.errMsg, parseErr ); |
221 |
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haveError = 1; |
222 |
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simError(); |
223 |
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} |
224 |
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225 |
tim |
837 |
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
226 |
gezelter |
417 |
|
227 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
228 |
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if(eof_test == NULL){ |
229 |
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sprintf(painCave.errMsg, |
230 |
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"error in reading file %s\n" |
231 |
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"natoms = %d; index = %d\n" |
232 |
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"error reading the line from the file.\n", |
233 |
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c_in_name, n_atoms, i ); |
234 |
chuckv |
436 |
haveError= 1; |
235 |
mmeineke |
377 |
simError(); |
236 |
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} |
237 |
tim |
837 |
|
238 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
239 |
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|
240 |
gezelter |
417 |
// Get the Node number which wants this atom: |
241 |
tim |
837 |
which_node = AtomToProcMap[i]; |
242 |
chuckv |
436 |
if (which_node == 0) { |
243 |
gezelter |
417 |
parseErr = parseDumpLine( read_buffer, i ); |
244 |
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if( parseErr != NULL ){ |
245 |
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strcpy( painCave.errMsg, parseErr ); |
246 |
chuckv |
436 |
haveError = 1; |
247 |
gezelter |
417 |
simError(); |
248 |
tim |
837 |
} |
249 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
250 |
tim |
837 |
} |
251 |
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|
252 |
chuckv |
436 |
else { |
253 |
tim |
837 |
|
254 |
chuckv |
436 |
myStatus = 1; |
255 |
tim |
837 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
256 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
257 |
tim |
837 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
258 |
mmeineke |
447 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
259 |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
260 |
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MPI_COMM_WORLD); |
261 |
tim |
837 |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
262 |
mmeineke |
447 |
MPI_COMM_WORLD, &istatus); |
263 |
tim |
837 |
|
264 |
chuckv |
436 |
if(!myStatus) nodeZeroError(); |
265 |
mmeineke |
377 |
} |
266 |
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} |
267 |
chuckv |
436 |
myStatus = -1; |
268 |
tim |
905 |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
269 |
tim |
837 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
270 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
271 |
gezelter |
417 |
} |
272 |
tim |
837 |
|
273 |
gezelter |
417 |
} else { |
274 |
mmeineke |
586 |
|
275 |
tim |
837 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
276 |
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277 |
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parseErr = parseCommentLine( read_buffer, simnfo); |
278 |
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279 |
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if( parseErr != NULL ){ |
280 |
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strcpy( painCave.errMsg, parseErr ); |
281 |
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haveError = 1; |
282 |
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simError(); |
283 |
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} |
284 |
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285 |
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286 |
gezelter |
417 |
done = 0; |
287 |
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while (!done) { |
288 |
chuckv |
436 |
|
289 |
tim |
837 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
290 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 |
tim |
837 |
|
292 |
chuckv |
436 |
if(!myStatus) anonymousNodeDie(); |
293 |
tim |
837 |
|
294 |
chuckv |
436 |
if(myStatus < 0) break; |
295 |
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|
296 |
tim |
837 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
297 |
mmeineke |
447 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
298 |
tim |
837 |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
299 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
300 |
tim |
837 |
|
301 |
chuckv |
436 |
myStatus = 1; |
302 |
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parseErr = parseDumpLine( read_buffer, which_atom ); |
303 |
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if( parseErr != NULL ){ |
304 |
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strcpy( painCave.errMsg, parseErr ); |
305 |
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myStatus = 0;; |
306 |
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simError(); |
307 |
mmeineke |
377 |
} |
308 |
tim |
837 |
|
309 |
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MPI_Send( &myStatus, 1, MPI_INT, 0, |
310 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
311 |
tim |
837 |
|
312 |
mmeineke |
377 |
} |
313 |
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} |
314 |
tim |
837 |
|
315 |
chuckv |
436 |
// last thing last, enable fatalities. |
316 |
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painCave.isEventLoop = 0; |
317 |
mmeineke |
586 |
|
318 |
mmeineke |
590 |
|
319 |
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|
320 |
mmeineke |
377 |
#endif |
321 |
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} |
322 |
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|
323 |
gezelter |
419 |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
324 |
mmeineke |
377 |
|
325 |
tim |
837 |
char *foo; // the pointer to the current string token |
326 |
|
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|
327 |
mmeineke |
670 |
double pos[3]; // position place holders |
328 |
|
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double vel[3]; // velocity placeholders |
329 |
mmeineke |
377 |
double q[4]; // the quaternions |
330 |
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double jx, jy, jz; // angular velocity placeholders; |
331 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
332 |
tim |
837 |
|
333 |
mmeineke |
586 |
Atom **atoms = simnfo->atoms; |
334 |
mmeineke |
377 |
DirectionalAtom* dAtom; |
335 |
tim |
837 |
|
336 |
mmeineke |
787 |
int n_atoms, atomIndex; |
337 |
mmeineke |
377 |
|
338 |
|
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#ifdef IS_MPI |
339 |
mmeineke |
787 |
int j; |
340 |
|
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|
341 |
mmeineke |
377 |
n_atoms = mpiSim->getTotAtoms(); |
342 |
tim |
837 |
atomIndex=-1; |
343 |
gezelter |
419 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
344 |
|
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if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
345 |
|
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} |
346 |
|
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if (atomIndex == -1) { |
347 |
|
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sprintf( painCave.errMsg, |
348 |
|
|
"Initialize from file error. Atom at index %d " |
349 |
|
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"in file %s does not exist on processor %d .\n", |
350 |
|
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globalIndex, c_in_name, mpiSim->getMyNode() ); |
351 |
|
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return strdup( painCave.errMsg ); |
352 |
tim |
837 |
} |
353 |
mmeineke |
377 |
#else |
354 |
mmeineke |
586 |
n_atoms = simnfo->n_atoms; |
355 |
gezelter |
419 |
atomIndex = globalIndex; |
356 |
mmeineke |
377 |
#endif // is_mpi |
357 |
|
|
|
358 |
|
|
// set the string tokenizer |
359 |
tim |
837 |
|
360 |
mmeineke |
377 |
foo = strtok(readLine, " ,;\t"); |
361 |
tim |
837 |
|
362 |
mmeineke |
377 |
// check the atom name to the current atom |
363 |
tim |
837 |
|
364 |
mmeineke |
377 |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
365 |
|
|
sprintf( painCave.errMsg, |
366 |
|
|
"Initialize from file error. Atom %s at index %d " |
367 |
|
|
"in file %s does not" |
368 |
|
|
" match the BASS atom %s.\n", |
369 |
|
|
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
370 |
|
|
return strdup( painCave.errMsg ); |
371 |
|
|
} |
372 |
tim |
837 |
|
373 |
mmeineke |
377 |
// get the positions |
374 |
|
|
|
375 |
|
|
foo = strtok(NULL, " ,;\t"); |
376 |
|
|
if(foo == NULL){ |
377 |
|
|
sprintf( painCave.errMsg, |
378 |
|
|
"error in reading postition x from %s\n" |
379 |
|
|
"natoms = %d, index = %d\n", |
380 |
|
|
c_in_name, n_atoms, atomIndex ); |
381 |
|
|
return strdup( painCave.errMsg ); |
382 |
|
|
} |
383 |
mmeineke |
670 |
pos[0] = atof( foo ); |
384 |
tim |
837 |
|
385 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
386 |
|
|
if(foo == NULL){ |
387 |
|
|
sprintf( painCave.errMsg, |
388 |
|
|
"error in reading postition y from %s\n" |
389 |
|
|
"natoms = %d, index = %d\n", |
390 |
|
|
c_in_name, n_atoms, atomIndex ); |
391 |
|
|
return strdup( painCave.errMsg ); |
392 |
|
|
} |
393 |
mmeineke |
670 |
pos[1] = atof( foo ); |
394 |
tim |
837 |
|
395 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
396 |
|
|
if(foo == NULL){ |
397 |
|
|
sprintf( painCave.errMsg, |
398 |
|
|
"error in reading postition z from %s\n" |
399 |
|
|
"natoms = %d, index = %d\n", |
400 |
|
|
c_in_name, n_atoms, atomIndex ); |
401 |
|
|
return strdup( painCave.errMsg ); |
402 |
|
|
} |
403 |
tim |
837 |
pos[2] = atof( foo ); |
404 |
mmeineke |
377 |
|
405 |
|
|
|
406 |
|
|
// get the velocities |
407 |
|
|
|
408 |
|
|
foo = strtok(NULL, " ,;\t"); |
409 |
|
|
if(foo == NULL){ |
410 |
|
|
sprintf( painCave.errMsg, |
411 |
|
|
"error in reading velocity x from %s\n" |
412 |
|
|
"natoms = %d, index = %d\n", |
413 |
|
|
c_in_name, n_atoms, atomIndex ); |
414 |
|
|
return strdup( painCave.errMsg ); |
415 |
|
|
} |
416 |
mmeineke |
670 |
vel[0] = atof( foo ); |
417 |
tim |
837 |
|
418 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
419 |
|
|
if(foo == NULL){ |
420 |
|
|
sprintf( painCave.errMsg, |
421 |
|
|
"error in reading velocity y from %s\n" |
422 |
|
|
"natoms = %d, index = %d\n", |
423 |
|
|
c_in_name, n_atoms, atomIndex ); |
424 |
|
|
return strdup( painCave.errMsg ); |
425 |
|
|
} |
426 |
mmeineke |
670 |
vel[1] = atof( foo ); |
427 |
tim |
837 |
|
428 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
429 |
|
|
if(foo == NULL){ |
430 |
|
|
sprintf( painCave.errMsg, |
431 |
|
|
"error in reading velocity z from %s\n" |
432 |
|
|
"natoms = %d, index = %d\n", |
433 |
|
|
c_in_name, n_atoms, atomIndex ); |
434 |
|
|
return strdup( painCave.errMsg ); |
435 |
|
|
} |
436 |
mmeineke |
670 |
vel[2] = atof( foo ); |
437 |
tim |
837 |
|
438 |
|
|
|
439 |
mmeineke |
377 |
// get the quaternions |
440 |
tim |
837 |
|
441 |
mmeineke |
377 |
if( atoms[atomIndex]->isDirectional() ){ |
442 |
tim |
837 |
|
443 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
444 |
|
|
if(foo == NULL){ |
445 |
|
|
sprintf(painCave.errMsg, |
446 |
|
|
"error in reading quaternion 0 from %s\n" |
447 |
|
|
"natoms = %d, index = %d\n", |
448 |
|
|
c_in_name, n_atoms, atomIndex ); |
449 |
|
|
return strdup( painCave.errMsg ); |
450 |
|
|
} |
451 |
|
|
q[0] = atof( foo ); |
452 |
tim |
837 |
|
453 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
454 |
|
|
if(foo == NULL){ |
455 |
|
|
sprintf( painCave.errMsg, |
456 |
|
|
"error in reading quaternion 1 from %s\n" |
457 |
|
|
"natoms = %d, index = %d\n", |
458 |
|
|
c_in_name, n_atoms, atomIndex ); |
459 |
|
|
return strdup( painCave.errMsg ); |
460 |
|
|
} |
461 |
|
|
q[1] = atof( foo ); |
462 |
tim |
837 |
|
463 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
464 |
|
|
if(foo == NULL){ |
465 |
|
|
sprintf( painCave.errMsg, |
466 |
|
|
"error in reading quaternion 2 from %s\n" |
467 |
|
|
"natoms = %d, index = %d\n", |
468 |
|
|
c_in_name, n_atoms, atomIndex ); |
469 |
|
|
return strdup( painCave.errMsg ); |
470 |
|
|
} |
471 |
|
|
q[2] = atof( foo ); |
472 |
tim |
837 |
|
473 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
474 |
|
|
if(foo == NULL){ |
475 |
|
|
sprintf( painCave.errMsg, |
476 |
|
|
"error in reading quaternion 3 from %s\n" |
477 |
|
|
"natoms = %d, index = %d\n", |
478 |
|
|
c_in_name, n_atoms, atomIndex ); |
479 |
|
|
return strdup( painCave.errMsg ); |
480 |
|
|
} |
481 |
|
|
q[3] = atof( foo ); |
482 |
tim |
837 |
|
483 |
mmeineke |
377 |
// get the angular velocities |
484 |
tim |
837 |
|
485 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
486 |
|
|
if(foo == NULL){ |
487 |
|
|
sprintf( painCave.errMsg, |
488 |
|
|
"error in reading angular momentum jx from %s\n" |
489 |
|
|
"natoms = %d, index = %d\n", |
490 |
|
|
c_in_name, n_atoms, atomIndex ); |
491 |
|
|
return strdup( painCave.errMsg ); |
492 |
|
|
} |
493 |
|
|
jx = atof( foo ); |
494 |
tim |
837 |
|
495 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
496 |
|
|
if(foo == NULL){ |
497 |
|
|
sprintf( painCave.errMsg, |
498 |
|
|
"error in reading angular momentum jy from %s\n" |
499 |
|
|
"natoms = %d, index = %d\n", |
500 |
|
|
c_in_name, n_atoms, atomIndex ); |
501 |
|
|
return strdup( painCave.errMsg ); |
502 |
|
|
} |
503 |
|
|
jy = atof(foo ); |
504 |
tim |
837 |
|
505 |
mmeineke |
377 |
foo = strtok(NULL, " ,;\t"); |
506 |
|
|
if(foo == NULL){ |
507 |
|
|
sprintf( painCave.errMsg, |
508 |
|
|
"error in reading angular momentum jz from %s\n" |
509 |
|
|
"natoms = %d, index = %d\n", |
510 |
|
|
c_in_name, n_atoms, atomIndex ); |
511 |
|
|
return strdup( painCave.errMsg ); |
512 |
|
|
} |
513 |
|
|
jz = atof( foo ); |
514 |
tim |
837 |
|
515 |
mmeineke |
377 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
516 |
|
|
|
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 |
mmeineke |
377 |
dAtom->setQ( q ); |
528 |
tim |
837 |
|
529 |
mmeineke |
377 |
// add the angular velocities |
530 |
|
|
|
531 |
|
|
dAtom->setJx( jx ); |
532 |
|
|
dAtom->setJy( jy ); |
533 |
|
|
dAtom->setJz( jz ); |
534 |
|
|
} |
535 |
tim |
837 |
|
536 |
mmeineke |
377 |
// add the positions and velocities to the atom |
537 |
tim |
837 |
|
538 |
mmeineke |
670 |
atoms[atomIndex]->setPos( pos ); |
539 |
|
|
atoms[atomIndex]->setVel( vel ); |
540 |
mmeineke |
377 |
|
541 |
|
|
return NULL; |
542 |
|
|
} |
543 |
chuckv |
436 |
|
544 |
|
|
|
545 |
tim |
837 |
char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
546 |
mmeineke |
586 |
|
547 |
tim |
837 |
double currTime; |
548 |
|
|
double boxMat[9]; |
549 |
|
|
double theBoxMat3[3][3]; |
550 |
|
|
double chi; |
551 |
|
|
double integralOfChidt; |
552 |
|
|
double eta[9]; |
553 |
mmeineke |
586 |
|
554 |
tim |
837 |
char *foo; // the pointer to the current string token |
555 |
|
|
|
556 |
mmeineke |
586 |
// set the string tokenizer |
557 |
tim |
837 |
|
558 |
mmeineke |
586 |
foo = strtok(readLine, " ,;\t"); |
559 |
mmeineke |
641 |
// set the timeToken. |
560 |
mmeineke |
586 |
|
561 |
mmeineke |
641 |
if(foo == NULL){ |
562 |
|
|
sprintf( painCave.errMsg, |
563 |
|
|
"error in reading Time from %s\n", |
564 |
|
|
c_in_name ); |
565 |
|
|
return strdup( painCave.errMsg ); |
566 |
|
|
} |
567 |
mmeineke |
586 |
|
568 |
tim |
837 |
currTime = atof( foo ); |
569 |
|
|
entry_plug->setTime( currTime ); |
570 |
mmeineke |
586 |
|
571 |
tim |
837 |
//get H-Matrix |
572 |
|
|
|
573 |
|
|
for(int i = 0 ; i < 9; i++){ |
574 |
|
|
foo = strtok(NULL, " ,;\t"); |
575 |
|
|
if(foo == NULL){ |
576 |
|
|
sprintf( painCave.errMsg, |
577 |
|
|
"error in reading H[%d] from %s\n", i, c_in_name ); |
578 |
|
|
return strdup( painCave.errMsg ); |
579 |
|
|
} |
580 |
|
|
boxMat[i] = atof( foo ); |
581 |
mmeineke |
586 |
} |
582 |
|
|
|
583 |
tim |
837 |
for(int i=0;i<3;i++) |
584 |
|
|
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
585 |
mmeineke |
586 |
|
586 |
tim |
837 |
//set H-Matrix |
587 |
|
|
entry_plug->setBoxM( theBoxMat3 ); |
588 |
mmeineke |
586 |
|
589 |
tim |
837 |
//get chi and integralOfChidt, they should appear by pair |
590 |
mmeineke |
586 |
|
591 |
mmeineke |
906 |
if( entry_plug->useInitXSstate ){ |
592 |
tim |
837 |
foo = strtok(NULL, " ,;\t\n"); |
593 |
mmeineke |
906 |
if(foo != NULL){ |
594 |
|
|
chi = atof(foo); |
595 |
|
|
|
596 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
597 |
|
|
if(foo == NULL){ |
598 |
|
|
sprintf( painCave.errMsg, |
599 |
|
|
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
600 |
|
|
return strdup( painCave.errMsg ); |
601 |
|
|
} |
602 |
|
|
integralOfChidt = atof( foo ); |
603 |
|
|
|
604 |
|
|
//push chi and integralOfChidt into SimInfo::properties which can be |
605 |
|
|
//retrieved by integrator later |
606 |
|
|
DoubleData* chiValue = new DoubleData(); |
607 |
|
|
chiValue->setID(CHIVALUE_ID); |
608 |
|
|
chiValue->setData(chi); |
609 |
|
|
entry_plug->addProperty(chiValue); |
610 |
|
|
|
611 |
|
|
DoubleData* integralOfChidtValue = new DoubleData(); |
612 |
|
|
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
613 |
|
|
integralOfChidtValue->setData(integralOfChidt); |
614 |
|
|
entry_plug->addProperty(integralOfChidtValue); |
615 |
|
|
|
616 |
tim |
837 |
} |
617 |
mmeineke |
906 |
else |
618 |
|
|
return NULL; |
619 |
|
|
|
620 |
|
|
//get eta |
621 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
622 |
mmeineke |
909 |
if(foo != NULL ){ |
623 |
mmeineke |
911 |
|
624 |
mmeineke |
909 |
for(int i = 0 ; i < 9; i++){ |
625 |
|
|
|
626 |
|
|
if(foo == NULL){ |
627 |
|
|
sprintf( painCave.errMsg, |
628 |
|
|
"error in reading eta[%d] from %s\n", i, c_in_name ); |
629 |
|
|
return strdup( painCave.errMsg ); |
630 |
|
|
} |
631 |
|
|
eta[i] = atof( foo ); |
632 |
mmeineke |
911 |
foo = strtok(NULL, " ,;\t\n"); |
633 |
mmeineke |
906 |
} |
634 |
|
|
} |
635 |
mmeineke |
909 |
else |
636 |
|
|
return NULL; |
637 |
mmeineke |
906 |
|
638 |
|
|
//push eta into SimInfo::properties which can be |
639 |
tim |
837 |
//retrieved by integrator later |
640 |
mmeineke |
906 |
//entry_plug->setBoxM( theBoxMat3 ); |
641 |
|
|
DoubleArrayData* etaValue = new DoubleArrayData(); |
642 |
|
|
etaValue->setID(ETAVALUE_ID); |
643 |
|
|
etaValue->setData(eta, 9); |
644 |
|
|
entry_plug->addProperty(etaValue); |
645 |
mmeineke |
586 |
} |
646 |
tim |
837 |
|
647 |
mmeineke |
586 |
return NULL; |
648 |
|
|
} |
649 |
|
|
|
650 |
chuckv |
436 |
#ifdef IS_MPI |
651 |
|
|
|
652 |
|
|
// a couple of functions to let us escape the read loop |
653 |
|
|
|
654 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
655 |
chuckv |
436 |
int j, myStatus; |
656 |
tim |
837 |
|
657 |
chuckv |
436 |
myStatus = 0; |
658 |
tim |
837 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
660 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 |
tim |
837 |
} |
662 |
chuckv |
436 |
|
663 |
tim |
837 |
|
664 |
chuckv |
436 |
MPI_Finalize(); |
665 |
|
|
exit (0); |
666 |
tim |
837 |
|
667 |
chuckv |
436 |
} |
668 |
|
|
|
669 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
670 |
chuckv |
436 |
|
671 |
|
|
MPI_Finalize(); |
672 |
|
|
exit (0); |
673 |
|
|
} |
674 |
|
|
|
675 |
|
|
#endif //is_mpi |