1 |
mmeineke |
377 |
#include <iostream> |
2 |
|
|
#include <cmath> |
3 |
|
|
|
4 |
|
|
#include <stdio.h> |
5 |
|
|
#include <stdlib.h> |
6 |
|
|
#include <string.h> |
7 |
|
|
#include <unistd.h> |
8 |
|
|
#include <sys/types.h> |
9 |
|
|
#include <sys/stat.h> |
10 |
|
|
|
11 |
|
|
#include "ReadWrite.hpp" |
12 |
|
|
#include "simError.h" |
13 |
|
|
|
14 |
|
|
#ifdef IS_MPI |
15 |
gezelter |
417 |
#include <mpi.h> |
16 |
|
|
#include <mpi++.h> |
17 |
mmeineke |
377 |
#include "mpiSimulation.hpp" |
18 |
chuckv |
436 |
#define TAKE_THIS_TAG_CHAR 0 |
19 |
|
|
#define TAKE_THIS_TAG_INT 1 |
20 |
|
|
|
21 |
mmeineke |
440 |
namespace initFile{ |
22 |
|
|
void nodeZeroError( void ); |
23 |
|
|
void anonymousNodeDie( void ); |
24 |
|
|
} |
25 |
chuckv |
436 |
|
26 |
mmeineke |
440 |
using namespace initFile; |
27 |
|
|
|
28 |
mmeineke |
377 |
#endif // is_mpi |
29 |
|
|
|
30 |
|
|
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
31 |
|
|
#ifdef IS_MPI |
32 |
|
|
if (worldRank == 0) { |
33 |
|
|
#endif |
34 |
|
|
|
35 |
|
|
c_in_file = fopen(in_name, "r"); |
36 |
|
|
if(c_in_file == NULL){ |
37 |
|
|
sprintf(painCave.errMsg, |
38 |
|
|
"Cannot open file: %s\n", in_name); |
39 |
|
|
painCave.isFatal = 1; |
40 |
|
|
simError(); |
41 |
|
|
} |
42 |
|
|
|
43 |
|
|
strcpy( c_in_name, in_name); |
44 |
|
|
#ifdef IS_MPI |
45 |
|
|
} |
46 |
|
|
strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
47 |
|
|
MPIcheckPoint(); |
48 |
|
|
#endif |
49 |
|
|
return; |
50 |
|
|
} |
51 |
|
|
|
52 |
|
|
InitializeFromFile :: ~InitializeFromFile( ){ |
53 |
|
|
#ifdef IS_MPI |
54 |
|
|
if (worldRank == 0) { |
55 |
|
|
#endif |
56 |
|
|
int error; |
57 |
|
|
error = fclose( c_in_file ); |
58 |
|
|
if( error ){ |
59 |
|
|
sprintf( painCave.errMsg, |
60 |
|
|
"Error closing %s\n", c_in_name ); |
61 |
|
|
simError(); |
62 |
|
|
} |
63 |
|
|
#ifdef IS_MPI |
64 |
|
|
} |
65 |
|
|
strcpy( checkPointMsg, "Infile closed successfully." ); |
66 |
|
|
MPIcheckPoint(); |
67 |
|
|
#endif |
68 |
|
|
|
69 |
|
|
return; |
70 |
|
|
} |
71 |
|
|
|
72 |
|
|
|
73 |
|
|
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
74 |
|
|
|
75 |
gezelter |
417 |
int i, j, done, which_node, which_atom; // loop counter |
76 |
mmeineke |
377 |
|
77 |
|
|
const int BUFFERSIZE = 2000; // size of the read buffer |
78 |
|
|
int n_atoms; // the number of atoms |
79 |
|
|
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
80 |
|
|
#ifdef IS_MPI |
81 |
|
|
char send_buffer[BUFFERSIZE]; |
82 |
|
|
#endif |
83 |
|
|
|
84 |
|
|
char *eof_test; // ptr to see when we reach the end of the file |
85 |
|
|
char *parseErr; |
86 |
|
|
int procIndex; |
87 |
|
|
|
88 |
|
|
entry_plug = the_entry_plug; |
89 |
|
|
|
90 |
|
|
|
91 |
|
|
#ifndef IS_MPI |
92 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
93 |
|
|
if( eof_test == NULL ){ |
94 |
|
|
sprintf( painCave.errMsg, |
95 |
|
|
"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
96 |
|
|
c_in_name ); |
97 |
|
|
painCave.isFatal = 1; |
98 |
|
|
simError(); |
99 |
|
|
} |
100 |
|
|
|
101 |
|
|
n_atoms = atoi( read_buffer ); |
102 |
|
|
|
103 |
|
|
Atom **atoms = entry_plug->atoms; |
104 |
|
|
DirectionalAtom* dAtom; |
105 |
|
|
|
106 |
|
|
if( n_atoms != entry_plug->n_atoms ){ |
107 |
|
|
sprintf( painCave.errMsg, |
108 |
|
|
"Initialize from File error. %s n_atoms, %d, " |
109 |
|
|
"does not match the BASS file's n_atoms, %d.\n", |
110 |
|
|
c_in_name, n_atoms, entry_plug->n_atoms ); |
111 |
|
|
painCave.isFatal = 1; |
112 |
|
|
simError(); |
113 |
|
|
} |
114 |
|
|
|
115 |
|
|
//read and toss the comment line |
116 |
|
|
|
117 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
118 |
|
|
if(eof_test == NULL){ |
119 |
|
|
sprintf( painCave.errMsg, |
120 |
|
|
"error in reading commment in %s\n", c_in_name); |
121 |
|
|
painCave.isFatal = 1; |
122 |
|
|
simError(); |
123 |
|
|
} |
124 |
|
|
|
125 |
|
|
for( i=0; i < n_atoms; i++){ |
126 |
|
|
|
127 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
128 |
|
|
if(eof_test == NULL){ |
129 |
|
|
sprintf(painCave.errMsg, |
130 |
|
|
"error in reading file %s\n" |
131 |
|
|
"natoms = %d; index = %d\n" |
132 |
|
|
"error reading the line from the file.\n", |
133 |
|
|
c_in_name, n_atoms, i ); |
134 |
|
|
painCave.isFatal = 1; |
135 |
|
|
simError(); |
136 |
|
|
} |
137 |
|
|
|
138 |
|
|
|
139 |
|
|
parseErr = parseDumpLine( read_buffer, i ); |
140 |
|
|
if( parseErr != NULL ){ |
141 |
|
|
strcpy( painCave.errMsg, parseErr ); |
142 |
|
|
painCave.isFatal = 1; |
143 |
|
|
simError(); |
144 |
|
|
} |
145 |
|
|
} |
146 |
|
|
|
147 |
|
|
|
148 |
|
|
// MPI Section of code.......... |
149 |
|
|
#else //IS_MPI |
150 |
|
|
|
151 |
chuckv |
436 |
// first thing first, suspend fatalities. |
152 |
|
|
painCave.isEventLoop = 1; |
153 |
|
|
|
154 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
155 |
|
|
int haveError; |
156 |
|
|
|
157 |
gezelter |
417 |
MPI::Status istatus; |
158 |
|
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
159 |
mmeineke |
377 |
|
160 |
chuckv |
436 |
|
161 |
|
|
haveError = 0; |
162 |
mmeineke |
377 |
if (worldRank == 0) { |
163 |
chuckv |
436 |
|
164 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
165 |
|
|
if( eof_test == NULL ){ |
166 |
|
|
sprintf( painCave.errMsg, |
167 |
|
|
"Error reading 1st line of %d \n ",c_in_name); |
168 |
chuckv |
436 |
haveError = 1; |
169 |
mmeineke |
377 |
simError(); |
170 |
|
|
} |
171 |
|
|
|
172 |
|
|
n_atoms = atoi( read_buffer ); |
173 |
|
|
|
174 |
|
|
Atom **atoms = entry_plug->atoms; |
175 |
|
|
DirectionalAtom* dAtom; |
176 |
|
|
|
177 |
|
|
// Check to see that the number of atoms in the intial configuration file is the |
178 |
|
|
// same as declared in simBass. |
179 |
|
|
|
180 |
|
|
if( n_atoms != mpiSim->getTotAtoms() ){ |
181 |
|
|
sprintf( painCave.errMsg, |
182 |
|
|
"Initialize from File error. %s n_atoms, %d, " |
183 |
|
|
"does not match the BASS file's n_atoms, %d.\n", |
184 |
|
|
c_in_name, n_atoms, entry_plug->n_atoms ); |
185 |
chuckv |
436 |
haveError= 1; |
186 |
mmeineke |
377 |
simError(); |
187 |
|
|
} |
188 |
|
|
|
189 |
|
|
//read and toss the comment line |
190 |
|
|
|
191 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
192 |
|
|
if(eof_test == NULL){ |
193 |
|
|
sprintf( painCave.errMsg, |
194 |
|
|
"error in reading commment in %s\n", c_in_name); |
195 |
chuckv |
436 |
haveError= 1; |
196 |
mmeineke |
377 |
simError(); |
197 |
|
|
} |
198 |
|
|
|
199 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
200 |
gezelter |
417 |
|
201 |
|
|
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
202 |
|
|
|
203 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
204 |
|
|
if(eof_test == NULL){ |
205 |
|
|
sprintf(painCave.errMsg, |
206 |
|
|
"error in reading file %s\n" |
207 |
|
|
"natoms = %d; index = %d\n" |
208 |
|
|
"error reading the line from the file.\n", |
209 |
|
|
c_in_name, n_atoms, i ); |
210 |
chuckv |
436 |
haveError= 1; |
211 |
mmeineke |
377 |
simError(); |
212 |
|
|
} |
213 |
|
|
|
214 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
215 |
|
|
|
216 |
gezelter |
417 |
// Get the Node number which wants this atom: |
217 |
|
|
which_node = AtomToProcMap[i]; |
218 |
chuckv |
436 |
if (which_node == 0) { |
219 |
gezelter |
417 |
parseErr = parseDumpLine( read_buffer, i ); |
220 |
|
|
if( parseErr != NULL ){ |
221 |
|
|
strcpy( painCave.errMsg, parseErr ); |
222 |
chuckv |
436 |
haveError = 1; |
223 |
gezelter |
417 |
simError(); |
224 |
|
|
} |
225 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
226 |
|
|
} |
227 |
|
|
|
228 |
|
|
else { |
229 |
|
|
|
230 |
|
|
myStatus = 1; |
231 |
|
|
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
232 |
|
|
TAKE_THIS_TAG_INT); |
233 |
gezelter |
417 |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
234 |
chuckv |
436 |
TAKE_THIS_TAG_CHAR); |
235 |
|
|
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
236 |
|
|
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
237 |
|
|
|
238 |
|
|
if(!myStatus) nodeZeroError(); |
239 |
mmeineke |
377 |
} |
240 |
|
|
} |
241 |
chuckv |
436 |
myStatus = -1; |
242 |
gezelter |
417 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
243 |
chuckv |
436 |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
244 |
|
|
TAKE_THIS_TAG_INT); |
245 |
gezelter |
417 |
} |
246 |
gezelter |
419 |
|
247 |
gezelter |
417 |
} else { |
248 |
gezelter |
419 |
|
249 |
gezelter |
417 |
done = 0; |
250 |
|
|
while (!done) { |
251 |
chuckv |
436 |
|
252 |
|
|
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
253 |
|
|
TAKE_THIS_TAG_INT, istatus); |
254 |
|
|
|
255 |
|
|
if(!myStatus) anonymousNodeDie(); |
256 |
|
|
|
257 |
|
|
if(myStatus < 0) break; |
258 |
|
|
|
259 |
gezelter |
417 |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
260 |
chuckv |
436 |
TAKE_THIS_TAG_CHAR, istatus); |
261 |
|
|
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
262 |
|
|
TAKE_THIS_TAG_INT, istatus); |
263 |
|
|
|
264 |
|
|
myStatus = 1; |
265 |
|
|
parseErr = parseDumpLine( read_buffer, which_atom ); |
266 |
|
|
if( parseErr != NULL ){ |
267 |
|
|
strcpy( painCave.errMsg, parseErr ); |
268 |
|
|
myStatus = 0;; |
269 |
|
|
simError(); |
270 |
mmeineke |
377 |
} |
271 |
chuckv |
436 |
|
272 |
|
|
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
273 |
|
|
TAKE_THIS_TAG_INT); |
274 |
|
|
|
275 |
mmeineke |
377 |
} |
276 |
|
|
} |
277 |
chuckv |
436 |
|
278 |
|
|
// last thing last, enable fatalities. |
279 |
|
|
painCave.isEventLoop = 0; |
280 |
|
|
|
281 |
mmeineke |
377 |
#endif |
282 |
|
|
} |
283 |
|
|
|
284 |
gezelter |
419 |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
285 |
mmeineke |
377 |
|
286 |
|
|
char *foo; // the pointer to the current string token |
287 |
|
|
|
288 |
|
|
double rx, ry, rz; // position place holders |
289 |
|
|
double vx, vy, vz; // velocity placeholders |
290 |
|
|
double q[4]; // the quaternions |
291 |
|
|
double jx, jy, jz; // angular velocity placeholders; |
292 |
|
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
293 |
|
|
|
294 |
|
|
Atom **atoms = entry_plug->atoms; |
295 |
|
|
DirectionalAtom* dAtom; |
296 |
|
|
|
297 |
gezelter |
419 |
int j, n_atoms, atomIndex; |
298 |
mmeineke |
377 |
|
299 |
|
|
#ifdef IS_MPI |
300 |
|
|
n_atoms = mpiSim->getTotAtoms(); |
301 |
gezelter |
419 |
atomIndex=-1; |
302 |
|
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
303 |
|
|
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
304 |
|
|
} |
305 |
|
|
if (atomIndex == -1) { |
306 |
|
|
sprintf( painCave.errMsg, |
307 |
|
|
"Initialize from file error. Atom at index %d " |
308 |
|
|
"in file %s does not exist on processor %d .\n", |
309 |
|
|
globalIndex, c_in_name, mpiSim->getMyNode() ); |
310 |
|
|
return strdup( painCave.errMsg ); |
311 |
|
|
} |
312 |
mmeineke |
377 |
#else |
313 |
|
|
n_atoms = entry_plug->n_atoms; |
314 |
gezelter |
419 |
atomIndex = globalIndex; |
315 |
mmeineke |
377 |
#endif // is_mpi |
316 |
|
|
|
317 |
|
|
// set the string tokenizer |
318 |
|
|
|
319 |
|
|
foo = strtok(readLine, " ,;\t"); |
320 |
|
|
|
321 |
|
|
// check the atom name to the current atom |
322 |
|
|
|
323 |
|
|
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
324 |
|
|
sprintf( painCave.errMsg, |
325 |
|
|
"Initialize from file error. Atom %s at index %d " |
326 |
|
|
"in file %s does not" |
327 |
|
|
" match the BASS atom %s.\n", |
328 |
|
|
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
329 |
|
|
return strdup( painCave.errMsg ); |
330 |
|
|
} |
331 |
|
|
|
332 |
|
|
// get the positions |
333 |
|
|
|
334 |
|
|
foo = strtok(NULL, " ,;\t"); |
335 |
|
|
if(foo == NULL){ |
336 |
|
|
sprintf( painCave.errMsg, |
337 |
|
|
"error in reading postition x from %s\n" |
338 |
|
|
"natoms = %d, index = %d\n", |
339 |
|
|
c_in_name, n_atoms, atomIndex ); |
340 |
|
|
return strdup( painCave.errMsg ); |
341 |
|
|
} |
342 |
|
|
rx = atof( foo ); |
343 |
|
|
|
344 |
|
|
foo = strtok(NULL, " ,;\t"); |
345 |
|
|
if(foo == NULL){ |
346 |
|
|
sprintf( painCave.errMsg, |
347 |
|
|
"error in reading postition y from %s\n" |
348 |
|
|
"natoms = %d, index = %d\n", |
349 |
|
|
c_in_name, n_atoms, atomIndex ); |
350 |
|
|
return strdup( painCave.errMsg ); |
351 |
|
|
} |
352 |
|
|
ry = atof( foo ); |
353 |
|
|
|
354 |
|
|
foo = strtok(NULL, " ,;\t"); |
355 |
|
|
if(foo == NULL){ |
356 |
|
|
sprintf( painCave.errMsg, |
357 |
|
|
"error in reading postition z from %s\n" |
358 |
|
|
"natoms = %d, index = %d\n", |
359 |
|
|
c_in_name, n_atoms, atomIndex ); |
360 |
|
|
return strdup( painCave.errMsg ); |
361 |
|
|
} |
362 |
|
|
rz = atof( foo ); |
363 |
|
|
|
364 |
|
|
|
365 |
|
|
// get the velocities |
366 |
|
|
|
367 |
|
|
foo = strtok(NULL, " ,;\t"); |
368 |
|
|
if(foo == NULL){ |
369 |
|
|
sprintf( painCave.errMsg, |
370 |
|
|
"error in reading velocity x from %s\n" |
371 |
|
|
"natoms = %d, index = %d\n", |
372 |
|
|
c_in_name, n_atoms, atomIndex ); |
373 |
|
|
return strdup( painCave.errMsg ); |
374 |
|
|
} |
375 |
|
|
vx = atof( foo ); |
376 |
|
|
|
377 |
|
|
foo = strtok(NULL, " ,;\t"); |
378 |
|
|
if(foo == NULL){ |
379 |
|
|
sprintf( painCave.errMsg, |
380 |
|
|
"error in reading velocity y from %s\n" |
381 |
|
|
"natoms = %d, index = %d\n", |
382 |
|
|
c_in_name, n_atoms, atomIndex ); |
383 |
|
|
return strdup( painCave.errMsg ); |
384 |
|
|
} |
385 |
|
|
vy = atof( foo ); |
386 |
|
|
|
387 |
|
|
foo = strtok(NULL, " ,;\t"); |
388 |
|
|
if(foo == NULL){ |
389 |
|
|
sprintf( painCave.errMsg, |
390 |
|
|
"error in reading velocity z from %s\n" |
391 |
|
|
"natoms = %d, index = %d\n", |
392 |
|
|
c_in_name, n_atoms, atomIndex ); |
393 |
|
|
return strdup( painCave.errMsg ); |
394 |
|
|
} |
395 |
|
|
vz = atof( foo ); |
396 |
|
|
|
397 |
|
|
|
398 |
|
|
// get the quaternions |
399 |
|
|
|
400 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
401 |
|
|
|
402 |
|
|
foo = strtok(NULL, " ,;\t"); |
403 |
|
|
if(foo == NULL){ |
404 |
|
|
sprintf(painCave.errMsg, |
405 |
|
|
"error in reading quaternion 0 from %s\n" |
406 |
|
|
"natoms = %d, index = %d\n", |
407 |
|
|
c_in_name, n_atoms, atomIndex ); |
408 |
|
|
return strdup( painCave.errMsg ); |
409 |
|
|
} |
410 |
|
|
q[0] = atof( foo ); |
411 |
|
|
|
412 |
|
|
foo = strtok(NULL, " ,;\t"); |
413 |
|
|
if(foo == NULL){ |
414 |
|
|
sprintf( painCave.errMsg, |
415 |
|
|
"error in reading quaternion 1 from %s\n" |
416 |
|
|
"natoms = %d, index = %d\n", |
417 |
|
|
c_in_name, n_atoms, atomIndex ); |
418 |
|
|
return strdup( painCave.errMsg ); |
419 |
|
|
} |
420 |
|
|
q[1] = atof( foo ); |
421 |
|
|
|
422 |
|
|
foo = strtok(NULL, " ,;\t"); |
423 |
|
|
if(foo == NULL){ |
424 |
|
|
sprintf( painCave.errMsg, |
425 |
|
|
"error in reading quaternion 2 from %s\n" |
426 |
|
|
"natoms = %d, index = %d\n", |
427 |
|
|
c_in_name, n_atoms, atomIndex ); |
428 |
|
|
return strdup( painCave.errMsg ); |
429 |
|
|
} |
430 |
|
|
q[2] = atof( foo ); |
431 |
|
|
|
432 |
|
|
foo = strtok(NULL, " ,;\t"); |
433 |
|
|
if(foo == NULL){ |
434 |
|
|
sprintf( painCave.errMsg, |
435 |
|
|
"error in reading quaternion 3 from %s\n" |
436 |
|
|
"natoms = %d, index = %d\n", |
437 |
|
|
c_in_name, n_atoms, atomIndex ); |
438 |
|
|
return strdup( painCave.errMsg ); |
439 |
|
|
} |
440 |
|
|
q[3] = atof( foo ); |
441 |
|
|
|
442 |
|
|
// get the angular velocities |
443 |
|
|
|
444 |
|
|
foo = strtok(NULL, " ,;\t"); |
445 |
|
|
if(foo == NULL){ |
446 |
|
|
sprintf( painCave.errMsg, |
447 |
|
|
"error in reading angular momentum jx from %s\n" |
448 |
|
|
"natoms = %d, index = %d\n", |
449 |
|
|
c_in_name, n_atoms, atomIndex ); |
450 |
|
|
return strdup( painCave.errMsg ); |
451 |
|
|
} |
452 |
|
|
jx = atof( foo ); |
453 |
|
|
|
454 |
|
|
foo = strtok(NULL, " ,;\t"); |
455 |
|
|
if(foo == NULL){ |
456 |
|
|
sprintf( painCave.errMsg, |
457 |
|
|
"error in reading angular momentum jy from %s\n" |
458 |
|
|
"natoms = %d, index = %d\n", |
459 |
|
|
c_in_name, n_atoms, atomIndex ); |
460 |
|
|
return strdup( painCave.errMsg ); |
461 |
|
|
} |
462 |
|
|
jy = atof(foo ); |
463 |
|
|
|
464 |
|
|
foo = strtok(NULL, " ,;\t"); |
465 |
|
|
if(foo == NULL){ |
466 |
|
|
sprintf( painCave.errMsg, |
467 |
|
|
"error in reading angular momentum jz from %s\n" |
468 |
|
|
"natoms = %d, index = %d\n", |
469 |
|
|
c_in_name, n_atoms, atomIndex ); |
470 |
|
|
return strdup( painCave.errMsg ); |
471 |
|
|
} |
472 |
|
|
jz = atof( foo ); |
473 |
|
|
|
474 |
|
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
475 |
|
|
|
476 |
|
|
// check that the quaternion vector is normalized |
477 |
|
|
|
478 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
479 |
|
|
|
480 |
|
|
qLength = sqrt( qSqr ); |
481 |
|
|
q[0] = q[0] / qLength; |
482 |
|
|
q[1] = q[1] / qLength; |
483 |
|
|
q[2] = q[2] / qLength; |
484 |
|
|
q[3] = q[3] / qLength; |
485 |
|
|
|
486 |
|
|
dAtom->setQ( q ); |
487 |
|
|
|
488 |
|
|
// add the angular velocities |
489 |
|
|
|
490 |
|
|
dAtom->setJx( jx ); |
491 |
|
|
dAtom->setJy( jy ); |
492 |
|
|
dAtom->setJz( jz ); |
493 |
|
|
} |
494 |
|
|
|
495 |
|
|
// add the positions and velocities to the atom |
496 |
|
|
|
497 |
|
|
atoms[atomIndex]->setX( rx ); |
498 |
|
|
atoms[atomIndex]->setY( ry ); |
499 |
|
|
atoms[atomIndex]->setZ( rz ); |
500 |
|
|
|
501 |
|
|
atoms[atomIndex]->set_vx( vx ); |
502 |
|
|
atoms[atomIndex]->set_vy( vy ); |
503 |
|
|
atoms[atomIndex]->set_vz( vz ); |
504 |
|
|
|
505 |
|
|
return NULL; |
506 |
|
|
} |
507 |
chuckv |
436 |
|
508 |
|
|
|
509 |
|
|
#ifdef IS_MPI |
510 |
|
|
|
511 |
|
|
// a couple of functions to let us escape the read loop |
512 |
|
|
|
513 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
514 |
chuckv |
436 |
int j, myStatus; |
515 |
|
|
|
516 |
|
|
myStatus = 0; |
517 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
518 |
|
|
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
519 |
|
|
TAKE_THIS_TAG_INT); |
520 |
|
|
} |
521 |
|
|
|
522 |
|
|
|
523 |
|
|
MPI_Finalize(); |
524 |
|
|
exit (0); |
525 |
|
|
|
526 |
|
|
} |
527 |
|
|
|
528 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
529 |
chuckv |
436 |
|
530 |
|
|
MPI_Finalize(); |
531 |
|
|
exit (0); |
532 |
|
|
} |
533 |
|
|
|
534 |
|
|
#endif //is_mpi |