# | Line 1 | Line 1 | |
---|---|---|
1 | + | #define _FILE_OFFSET_BITS 64 |
2 | #include <iostream> | |
3 | < | #include <cmath> |
3 | > | #include <math.h> |
4 | ||
5 | #include <stdio.h> | |
6 | #include <stdlib.h> | |
# | Line 10 | Line 11 | |
11 | ||
12 | #include "ReadWrite.hpp" | |
13 | #include "simError.h" | |
14 | + | #include "GenericData.hpp" |
15 | ||
16 | #ifdef IS_MPI | |
17 | #include <mpi.h> | |
16 | – | #include <mpi++.h> |
18 | #include "mpiSimulation.hpp" | |
19 | < | #define TAKE_THIS_TAG 0 |
19 | > | #define TAKE_THIS_TAG_CHAR 0 |
20 | > | #define TAKE_THIS_TAG_INT 1 |
21 | > | |
22 | > | namespace initFile{ |
23 | > | void nodeZeroError( void ); |
24 | > | void anonymousNodeDie( void ); |
25 | > | } |
26 | > | |
27 | > | using namespace initFile; |
28 | > | |
29 | #endif // is_mpi | |
30 | ||
31 | < | InitializeFromFile :: InitializeFromFile( char *in_name ){ |
31 | > | InitializeFromFile::InitializeFromFile( char *in_name ){ |
32 | > | |
33 | #ifdef IS_MPI | |
34 | if (worldRank == 0) { | |
35 | #endif | |
# | Line 30 | Line 41 | InitializeFromFile :: InitializeFromFile( char *in_nam | |
41 | painCave.isFatal = 1; | |
42 | simError(); | |
43 | } | |
44 | < | |
44 | > | |
45 | strcpy( c_in_name, in_name); | |
46 | #ifdef IS_MPI | |
47 | } | |
48 | < | strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
48 | > | else{ |
49 | > | sprintf( c_in_name, "mpiNodeParser_%d", worldRank ); |
50 | > | } |
51 | > | |
52 | > | strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
53 | MPIcheckPoint(); | |
54 | #endif | |
55 | < | return; |
55 | > | return; |
56 | } | |
57 | ||
58 | < | InitializeFromFile :: ~InitializeFromFile( ){ |
58 | > | InitializeFromFile::~InitializeFromFile( ){ |
59 | #ifdef IS_MPI | |
60 | if (worldRank == 0) { | |
61 | #endif | |
# | Line 61 | Line 76 | InitializeFromFile :: ~InitializeFromFile( ){ | |
76 | } | |
77 | ||
78 | ||
79 | < | void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
79 | > | void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
80 | ||
81 | < | int i, j, done, which_node, which_atom; // loop counter |
81 | > | int i, j; |
82 | ||
68 | – | const int BUFFERSIZE = 2000; // size of the read buffer |
69 | – | int n_atoms; // the number of atoms |
70 | – | char read_buffer[BUFFERSIZE]; //the line buffer for reading |
83 | #ifdef IS_MPI | |
84 | < | char send_buffer[BUFFERSIZE]; |
85 | < | #endif |
84 | > | int done, which_node, which_atom; // loop counter |
85 | > | #endif //is_mpi |
86 | ||
87 | < | char *eof_test; // ptr to see when we reach the end of the file |
87 | > | const int BUFFERSIZE = 2000; // size of the read buffer |
88 | > | int nTotObjs; // the number of atoms |
89 | > | char read_buffer[BUFFERSIZE]; //the line buffer for reading |
90 | > | |
91 | > | char *eof_test; // ptr to see when we reach the end of the file |
92 | char *parseErr; | |
77 | – | int procIndex; |
93 | ||
94 | < | entry_plug = the_entry_plug; |
94 | > | vector<StuntDouble*> integrableObjects; |
95 | > | vector<StuntDouble*>::iterator iter; |
96 | ||
97 | + | simnfo = the_simnfo; |
98 | ||
99 | + | |
100 | #ifndef IS_MPI | |
101 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
102 | if( eof_test == NULL ){ | |
# | Line 89 | Line 107 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
107 | simError(); | |
108 | } | |
109 | ||
110 | < | n_atoms = atoi( read_buffer ); |
110 | > | nTotObjs = atoi( read_buffer ); |
111 | ||
112 | < | Atom **atoms = entry_plug->atoms; |
95 | < | DirectionalAtom* dAtom; |
96 | < | |
97 | < | if( n_atoms != entry_plug->n_atoms ){ |
112 | > | if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
113 | sprintf( painCave.errMsg, | |
114 | "Initialize from File error. %s n_atoms, %d, " | |
115 | "does not match the BASS file's n_atoms, %d.\n", | |
116 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
116 | > | c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
117 | painCave.isFatal = 1; | |
118 | simError(); | |
119 | } | |
120 | < | |
121 | < | //read and toss the comment line |
122 | < | |
120 | > | |
121 | > | //read the box mat from the comment line |
122 | > | |
123 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
124 | if(eof_test == NULL){ | |
125 | sprintf( painCave.errMsg, | |
# | Line 113 | Line 128 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
128 | simError(); | |
129 | } | |
130 | ||
131 | < | for( i=0; i < n_atoms; i++){ |
132 | < | |
133 | < | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
134 | < | if(eof_test == NULL){ |
135 | < | sprintf(painCave.errMsg, |
136 | < | "error in reading file %s\n" |
122 | < | "natoms = %d; index = %d\n" |
123 | < | "error reading the line from the file.\n", |
124 | < | c_in_name, n_atoms, i ); |
125 | < | painCave.isFatal = 1; |
126 | < | simError(); |
127 | < | } |
131 | > | parseErr = parseCommentLine( read_buffer, simnfo); |
132 | > | if( parseErr != NULL ){ |
133 | > | strcpy( painCave.errMsg, parseErr ); |
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 | < | } |
138 | > | //parse dump lines |
139 | > | |
140 | > | for( i=0; i < simnfo->n_mol; i++){ |
141 | > | |
142 | > | integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
143 | > | |
144 | > | for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++) |
145 | > | |
146 | > | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
147 | > | if(eof_test == NULL){ |
148 | > | sprintf(painCave.errMsg, |
149 | > | "error in reading file %s\n" |
150 | > | "natoms = %d; index = %d\n" |
151 | > | "error reading the line from the file.\n", |
152 | > | c_in_name, nTotObjs, i ); |
153 | > | painCave.isFatal = 1; |
154 | > | simError(); |
155 | > | } |
156 | > | |
157 | > | parseErr = parseDumpLine( read_buffer, *iter); |
158 | > | if( parseErr != NULL ){ |
159 | > | strcpy( painCave.errMsg, parseErr ); |
160 | > | painCave.isFatal = 1; |
161 | > | simError(); |
162 | > | } |
163 | } | |
164 | ||
165 | ||
166 | // MPI Section of code.......... | |
167 | #else //IS_MPI | |
168 | ||
169 | < | MPI::Status istatus; |
170 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
169 | > | // first thing first, suspend fatalities. |
170 | > | painCave.isEventLoop = 1; |
171 | ||
172 | + | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
173 | + | int haveError; |
174 | + | |
175 | + | MPI_Status istatus; |
176 | + | int *MolToProcMap = mpiSim->getMolToProcMap(); |
177 | + | int localIndex; |
178 | + | int nCurObj; |
179 | + | |
180 | + | haveError = 0; |
181 | if (worldRank == 0) { | |
182 | + | |
183 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
184 | if( eof_test == NULL ){ | |
185 | sprintf( painCave.errMsg, | |
186 | < | "Error reading 1st line of %d \n ",c_in_name); |
187 | < | painCave.isFatal = 1; |
186 | > | "Error reading 1st line of %s \n ",c_in_name); |
187 | > | haveError = 1; |
188 | simError(); | |
189 | } | |
190 | < | |
191 | < | n_atoms = atoi( read_buffer ); |
192 | < | |
193 | < | Atom **atoms = entry_plug->atoms; |
157 | < | DirectionalAtom* dAtom; |
158 | < | |
159 | < | // Check to see that the number of atoms in the intial configuration file is the |
190 | > | |
191 | > | nTotObjs = atoi( read_buffer ); |
192 | > | |
193 | > | // Check to see that the number of integrable objects in the intial configuration file is the |
194 | // same as declared in simBass. | |
195 | < | |
196 | < | if( n_atoms != mpiSim->getTotAtoms() ){ |
195 | > | |
196 | > | if( nTotObjs != simnfo->getTotIntegrableObjects()){ |
197 | sprintf( painCave.errMsg, | |
198 | "Initialize from File error. %s n_atoms, %d, " | |
199 | "does not match the BASS file's n_atoms, %d.\n", | |
200 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
201 | < | painCave.isFatal = 1; |
200 | > | c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
201 | > | haveError= 1; |
202 | simError(); | |
203 | } | |
204 | < | |
205 | < | //read and toss the comment line |
206 | < | |
204 | > | |
205 | > | //read the boxMat from the comment line |
206 | > | |
207 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
208 | if(eof_test == NULL){ | |
209 | sprintf( painCave.errMsg, | |
210 | "error in reading commment in %s\n", c_in_name); | |
211 | < | painCave.isFatal = 1; |
211 | > | haveError = 1; |
212 | simError(); | |
213 | } | |
180 | – | |
214 | ||
215 | < | for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
215 | > | //Every single processor will parse the comment line by itself |
216 | > | //By using this way, we might lose some efficiency, but if we want to add |
217 | > | //more parameters into comment line, we only need to modify function |
218 | > | //parseCommentLine |
219 | > | |
220 | > | MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
221 | > | |
222 | > | parseErr = parseCommentLine( read_buffer, simnfo); |
223 | > | |
224 | > | if( parseErr != NULL ){ |
225 | > | strcpy( painCave.errMsg, parseErr ); |
226 | > | haveError = 1; |
227 | > | simError(); |
228 | > | } |
229 | > | |
230 | > | for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
231 | > | which_node = MolToProcMap[i]; |
232 | > | if(which_node == 0){ |
233 | > | //molecules belong to master node |
234 | > | |
235 | > | localIndex = mpiSim->getGlobalToLocalMol(i); |
236 | > | |
237 | > | if(localIndex == -1) { |
238 | > | strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
239 | > | haveError = 1; |
240 | > | simError(); |
241 | > | } |
242 | > | |
243 | > | integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
244 | > | for(j=0; j < integrableObjects.size(); j++){ |
245 | > | |
246 | > | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
247 | > | if(eof_test == NULL){ |
248 | > | sprintf(painCave.errMsg, |
249 | > | "error in reading file %s\n" |
250 | > | "natoms = %d; index = %d\n" |
251 | > | "error reading the line from the file.\n", |
252 | > | c_in_name, nTotObjs, i ); |
253 | > | haveError= 1; |
254 | > | simError(); |
255 | > | } |
256 | > | |
257 | > | if(haveError) nodeZeroError(); |
258 | > | |
259 | > | parseDumpLine(read_buffer, integrableObjects[i]); |
260 | > | |
261 | > | } |
262 | > | |
263 | > | |
264 | > | } |
265 | > | else{ |
266 | > | //molecule belongs to slave nodes |
267 | > | |
268 | > | MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
269 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
270 | ||
271 | < | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
272 | < | if(eof_test == NULL){ |
273 | < | sprintf(painCave.errMsg, |
274 | < | "error in reading file %s\n" |
275 | < | "natoms = %d; index = %d\n" |
276 | < | "error reading the line from the file.\n", |
277 | < | c_in_name, n_atoms, i ); |
278 | < | painCave.isFatal = 1; |
279 | < | simError(); |
271 | > | for(j=0; j < integrableObjects.size(); j++){ |
272 | > | |
273 | > | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
274 | > | if(eof_test == NULL){ |
275 | > | sprintf(painCave.errMsg, |
276 | > | "error in reading file %s\n" |
277 | > | "natoms = %d; index = %d\n" |
278 | > | "error reading the line from the file.\n", |
279 | > | c_in_name, nTotObjs, i ); |
280 | > | haveError= 1; |
281 | > | simError(); |
282 | > | } |
283 | > | |
284 | > | if(haveError) nodeZeroError(); |
285 | > | |
286 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
287 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
288 | > | |
289 | > | } |
290 | > | |
291 | } | |
292 | + | |
293 | + | } |
294 | ||
295 | < | // Get the Node number which wants this atom: |
296 | < | which_node = AtomToProcMap[i]; |
297 | < | if (which_node == mpiSim->getMyNode()) { |
298 | < | parseErr = parseDumpLine( read_buffer, i ); |
299 | < | if( parseErr != NULL ){ |
300 | < | strcpy( painCave.errMsg, parseErr ); |
301 | < | painCave.isFatal = 1; |
295 | > | } |
296 | > | else{ |
297 | > | //actions taken at slave nodes |
298 | > | for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
299 | > | which_node = MolToProcMap[i]; |
300 | > | |
301 | > | if(which_node == worldRank){ |
302 | > | //molecule with global index i belongs to this processor |
303 | > | |
304 | > | localIndex = mpiSim->getGlobalToLocalMol(i); |
305 | > | |
306 | > | if(localIndex == -1) { |
307 | > | sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
308 | > | haveError = 1; |
309 | simError(); | |
310 | < | } |
204 | < | } else { |
205 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
206 | < | TAKE_THIS_TAG); |
207 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
208 | < | } |
209 | < | } |
210 | < | sprintf(read_buffer, "GAMEOVER"); |
211 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
212 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
213 | < | TAKE_THIS_TAG); |
214 | < | } |
310 | > | } |
311 | ||
312 | < | } else { |
312 | > | integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
313 | ||
314 | < | done = 0; |
315 | < | while (!done) { |
316 | < | MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
317 | < | TAKE_THIS_TAG, istatus); |
318 | < | if (strcmp(read_buffer, "GAMEOVER")) { |
319 | < | done = 1; |
320 | < | continue; |
321 | < | } else { |
322 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
323 | < | TAKE_THIS_TAG, istatus); |
324 | < | parseErr = parseDumpLine( read_buffer, which_atom ); |
325 | < | if( parseErr != NULL ){ |
326 | < | strcpy( painCave.errMsg, parseErr ); |
327 | < | painCave.isFatal = 1; |
328 | < | simError(); |
329 | < | } |
314 | > | nCurObj = integrableObjects.size(); |
315 | > | |
316 | > | MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
317 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
318 | > | |
319 | > | for(j = 0; j < integrableObjects.size(); j++){ |
320 | > | |
321 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
322 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
323 | > | |
324 | > | parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
325 | > | |
326 | > | if( parseErr != NULL ){ |
327 | > | strcpy( painCave.errMsg, parseErr ); |
328 | > | simError(); |
329 | > | } |
330 | > | |
331 | > | } |
332 | > | |
333 | } | |
334 | + | |
335 | } | |
336 | + | |
337 | } | |
237 | – | |
338 | #endif | |
339 | } | |
340 | ||
341 | < | char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
341 | > | char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){ |
342 | ||
343 | < | char *foo; // the pointer to the current string token |
344 | < | |
345 | < | double rx, ry, rz; // position place holders |
346 | < | double vx, vy, vz; // velocity placeholders |
347 | < | double q[4]; // the quaternions |
348 | < | double jx, jy, jz; // angular velocity placeholders; |
343 | > | char *foo; // the pointer to the current string token |
344 | > | |
345 | > | double pos[3]; // position place holders |
346 | > | double vel[3]; // velocity placeholders |
347 | > | double q[4]; // the quaternions |
348 | > | double ji[3]; // angular velocity placeholders; |
349 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
250 | – | |
251 | – | Atom **atoms = entry_plug->atoms; |
252 | – | DirectionalAtom* dAtom; |
253 | – | |
254 | – | int n_atoms; |
350 | ||
256 | – | #ifdef IS_MPI |
257 | – | n_atoms = mpiSim->getTotAtoms(); |
258 | – | #else |
259 | – | n_atoms = entry_plug->n_atoms; |
260 | – | #endif // is_mpi |
351 | ||
262 | – | |
352 | // set the string tokenizer | |
353 | < | |
353 | > | |
354 | foo = strtok(readLine, " ,;\t"); | |
355 | < | |
355 | > | |
356 | // check the atom name to the current atom | |
357 | < | |
358 | < | if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
357 | > | |
358 | > | if( strcmp( foo, sd->getType() ) ){ |
359 | sprintf( painCave.errMsg, | |
360 | < | "Initialize from file error. Atom %s at index %d " |
272 | < | "in file %s does not" |
360 | > | "Initialize from file error. Does not" |
361 | " match the BASS atom %s.\n", | |
362 | < | foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
362 | > | sd->getType() ); |
363 | return strdup( painCave.errMsg ); | |
364 | } | |
365 | < | |
365 | > | |
366 | // get the positions | |
367 | ||
368 | foo = strtok(NULL, " ,;\t"); | |
369 | if(foo == NULL){ | |
370 | sprintf( painCave.errMsg, | |
371 | < | "error in reading postition x from %s\n" |
372 | < | "natoms = %d, index = %d\n", |
285 | < | c_in_name, n_atoms, atomIndex ); |
371 | > | "error in reading postition x from %s\n", |
372 | > | c_in_name); |
373 | return strdup( painCave.errMsg ); | |
374 | } | |
375 | < | rx = atof( foo ); |
376 | < | |
375 | > | pos[0] = atof( foo ); |
376 | > | |
377 | foo = strtok(NULL, " ,;\t"); | |
378 | if(foo == NULL){ | |
379 | sprintf( painCave.errMsg, | |
380 | < | "error in reading postition y from %s\n" |
381 | < | "natoms = %d, index = %d\n", |
295 | < | c_in_name, n_atoms, atomIndex ); |
380 | > | "error in reading postition y from %s\n", |
381 | > | c_in_name); |
382 | return strdup( painCave.errMsg ); | |
383 | } | |
384 | < | ry = atof( foo ); |
385 | < | |
384 | > | pos[1] = atof( foo ); |
385 | > | |
386 | foo = strtok(NULL, " ,;\t"); | |
387 | if(foo == NULL){ | |
388 | sprintf( painCave.errMsg, | |
389 | < | "error in reading postition z from %s\n" |
390 | < | "natoms = %d, index = %d\n", |
305 | < | c_in_name, n_atoms, atomIndex ); |
389 | > | "error in reading postition z from %s\n", |
390 | > | c_in_name); |
391 | return strdup( painCave.errMsg ); | |
392 | } | |
393 | < | rz = atof( foo ); |
393 | > | pos[2] = atof( foo ); |
394 | ||
395 | ||
396 | // get the velocities | |
# | Line 313 | Line 398 | char* InitializeFromFile::parseDumpLine(char* readLine | |
398 | foo = strtok(NULL, " ,;\t"); | |
399 | if(foo == NULL){ | |
400 | sprintf( painCave.errMsg, | |
401 | < | "error in reading velocity x from %s\n" |
402 | < | "natoms = %d, index = %d\n", |
318 | < | c_in_name, n_atoms, atomIndex ); |
401 | > | "error in reading velocity x from %s\n", |
402 | > | c_in_name ); |
403 | return strdup( painCave.errMsg ); | |
404 | } | |
405 | < | vx = atof( foo ); |
406 | < | |
405 | > | vel[0] = atof( foo ); |
406 | > | |
407 | foo = strtok(NULL, " ,;\t"); | |
408 | if(foo == NULL){ | |
409 | sprintf( painCave.errMsg, | |
410 | < | "error in reading velocity y from %s\n" |
411 | < | "natoms = %d, index = %d\n", |
328 | < | c_in_name, n_atoms, atomIndex ); |
410 | > | "error in reading velocity x from %s\n", |
411 | > | c_in_name ); |
412 | return strdup( painCave.errMsg ); | |
413 | } | |
414 | < | vy = atof( foo ); |
415 | < | |
414 | > | vel[1] = atof( foo ); |
415 | > | |
416 | foo = strtok(NULL, " ,;\t"); | |
417 | if(foo == NULL){ | |
418 | sprintf( painCave.errMsg, | |
419 | < | "error in reading velocity z from %s\n" |
420 | < | "natoms = %d, index = %d\n", |
338 | < | c_in_name, n_atoms, atomIndex ); |
419 | > | "error in reading velocity x from %s\n", |
420 | > | c_in_name ); |
421 | return strdup( painCave.errMsg ); | |
422 | } | |
423 | < | vz = atof( foo ); |
424 | < | |
425 | < | |
423 | > | vel[2] = atof( foo ); |
424 | > | |
425 | > | |
426 | > | // add the positions and velocities to the atom |
427 | > | |
428 | > | sd->setPos( pos ); |
429 | > | sd->setVel( vel ); |
430 | > | |
431 | > | if (!sd->isDirectional()) |
432 | > | return NULL; |
433 | > | |
434 | // get the quaternions | |
435 | < | |
436 | < | if( atoms[atomIndex]->isDirectional() ){ |
437 | < | |
435 | > | |
436 | > | if( sd->isDirectional() ){ |
437 | > | |
438 | foo = strtok(NULL, " ,;\t"); | |
439 | if(foo == NULL){ | |
440 | < | sprintf(painCave.errMsg, |
441 | < | "error in reading quaternion 0 from %s\n" |
442 | < | "natoms = %d, index = %d\n", |
353 | < | c_in_name, n_atoms, atomIndex ); |
440 | > | sprintf( painCave.errMsg, |
441 | > | "error in reading velocity x from %s\n", |
442 | > | c_in_name ); |
443 | return strdup( painCave.errMsg ); | |
444 | } | |
445 | q[0] = atof( foo ); | |
446 | < | |
446 | > | |
447 | foo = strtok(NULL, " ,;\t"); | |
448 | if(foo == NULL){ | |
449 | sprintf( painCave.errMsg, | |
450 | < | "error in reading quaternion 1 from %s\n" |
451 | < | "natoms = %d, index = %d\n", |
363 | < | c_in_name, n_atoms, atomIndex ); |
450 | > | "error in reading velocity x from %s\n", |
451 | > | c_in_name ); |
452 | return strdup( painCave.errMsg ); | |
453 | } | |
454 | q[1] = atof( foo ); | |
455 | < | |
455 | > | |
456 | foo = strtok(NULL, " ,;\t"); | |
457 | if(foo == NULL){ | |
458 | sprintf( painCave.errMsg, | |
459 | < | "error in reading quaternion 2 from %s\n" |
460 | < | "natoms = %d, index = %d\n", |
373 | < | c_in_name, n_atoms, atomIndex ); |
459 | > | "error in reading velocity x from %s\n", |
460 | > | c_in_name ); |
461 | return strdup( painCave.errMsg ); | |
462 | } | |
463 | q[2] = atof( foo ); | |
464 | < | |
464 | > | |
465 | foo = strtok(NULL, " ,;\t"); | |
466 | if(foo == NULL){ | |
467 | sprintf( painCave.errMsg, | |
468 | < | "error in reading quaternion 3 from %s\n" |
469 | < | "natoms = %d, index = %d\n", |
383 | < | c_in_name, n_atoms, atomIndex ); |
468 | > | "error in reading velocity x from %s\n", |
469 | > | c_in_name ); |
470 | return strdup( painCave.errMsg ); | |
471 | } | |
472 | q[3] = atof( foo ); | |
473 | < | |
473 | > | |
474 | // get the angular velocities | |
475 | < | |
475 | > | |
476 | foo = strtok(NULL, " ,;\t"); | |
477 | if(foo == NULL){ | |
478 | sprintf( painCave.errMsg, | |
479 | < | "error in reading angular momentum jx from %s\n" |
480 | < | "natoms = %d, index = %d\n", |
395 | < | c_in_name, n_atoms, atomIndex ); |
479 | > | "error in reading velocity x from %s\n", |
480 | > | c_in_name ); |
481 | return strdup( painCave.errMsg ); | |
482 | } | |
483 | < | jx = atof( foo ); |
484 | < | |
483 | > | ji[0] = atof( foo ); |
484 | > | |
485 | foo = strtok(NULL, " ,;\t"); | |
486 | if(foo == NULL){ | |
487 | sprintf( painCave.errMsg, | |
488 | < | "error in reading angular momentum jy from %s\n" |
489 | < | "natoms = %d, index = %d\n", |
405 | < | c_in_name, n_atoms, atomIndex ); |
488 | > | "error in reading velocity x from %s\n", |
489 | > | c_in_name ); |
490 | return strdup( painCave.errMsg ); | |
491 | } | |
492 | < | jy = atof(foo ); |
493 | < | |
492 | > | ji[1] = atof(foo ); |
493 | > | |
494 | foo = strtok(NULL, " ,;\t"); | |
495 | if(foo == NULL){ | |
496 | sprintf( painCave.errMsg, | |
497 | < | "error in reading angular momentum jz from %s\n" |
498 | < | "natoms = %d, index = %d\n", |
415 | < | c_in_name, n_atoms, atomIndex ); |
497 | > | "error in reading velocity x from %s\n", |
498 | > | c_in_name ); |
499 | return strdup( painCave.errMsg ); | |
500 | } | |
501 | < | jz = atof( foo ); |
419 | < | |
420 | < | dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
501 | > | ji[2] = atof( foo ); |
502 | ||
503 | + | |
504 | // check that the quaternion vector is normalized | |
505 | ||
506 | qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); | |
507 | < | |
507 | > | |
508 | qLength = sqrt( qSqr ); | |
509 | q[0] = q[0] / qLength; | |
510 | q[1] = q[1] / qLength; | |
511 | q[2] = q[2] / qLength; | |
512 | q[3] = q[3] / qLength; | |
431 | – | |
432 | – | dAtom->setQ( q ); |
433 | – | |
434 | – | // add the angular velocities |
513 | ||
514 | < | dAtom->setJx( jx ); |
515 | < | dAtom->setJy( jy ); |
516 | < | dAtom->setJz( jz ); |
514 | > | // add quaternion and angular velocities |
515 | > | |
516 | > | sd->setQ( q ); |
517 | > | sd->setJ( ji ); |
518 | } | |
519 | + | |
520 | + | |
521 | + | |
522 | + | return NULL; |
523 | + | } |
524 | + | |
525 | + | |
526 | + | char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
527 | + | |
528 | + | double currTime; |
529 | + | double boxMat[9]; |
530 | + | double theBoxMat3[3][3]; |
531 | + | double chi; |
532 | + | double integralOfChidt; |
533 | + | double eta[9]; |
534 | + | |
535 | + | char *foo; // the pointer to the current string token |
536 | + | |
537 | + | // set the string tokenizer |
538 | + | |
539 | + | foo = strtok(readLine, " ,;\t"); |
540 | + | // set the timeToken. |
541 | + | |
542 | + | if(foo == NULL){ |
543 | + | sprintf( painCave.errMsg, |
544 | + | "error in reading Time from %s\n", |
545 | + | c_in_name ); |
546 | + | return strdup( painCave.errMsg ); |
547 | + | } |
548 | + | |
549 | + | currTime = atof( foo ); |
550 | + | entry_plug->setTime( currTime ); |
551 | + | |
552 | + | //get H-Matrix |
553 | + | |
554 | + | for(int i = 0 ; i < 9; i++){ |
555 | + | foo = strtok(NULL, " ,;\t"); |
556 | + | if(foo == NULL){ |
557 | + | sprintf( painCave.errMsg, |
558 | + | "error in reading H[%d] from %s\n", i, c_in_name ); |
559 | + | return strdup( painCave.errMsg ); |
560 | + | } |
561 | + | boxMat[i] = atof( foo ); |
562 | + | } |
563 | + | |
564 | + | for(int i=0;i<3;i++) |
565 | + | for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
566 | + | |
567 | + | //set H-Matrix |
568 | + | entry_plug->setBoxM( theBoxMat3 ); |
569 | + | |
570 | + | //get chi and integralOfChidt, they should appear by pair |
571 | + | |
572 | + | if( entry_plug->useInitXSstate ){ |
573 | + | foo = strtok(NULL, " ,;\t\n"); |
574 | + | if(foo != NULL){ |
575 | + | chi = atof(foo); |
576 | + | |
577 | + | foo = strtok(NULL, " ,;\t\n"); |
578 | + | if(foo == NULL){ |
579 | + | sprintf( painCave.errMsg, |
580 | + | "chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
581 | + | return strdup( painCave.errMsg ); |
582 | + | } |
583 | + | integralOfChidt = atof( foo ); |
584 | + | |
585 | + | //push chi and integralOfChidt into SimInfo::properties which can be |
586 | + | //retrieved by integrator later |
587 | + | DoubleData* chiValue = new DoubleData(); |
588 | + | chiValue->setID(CHIVALUE_ID); |
589 | + | chiValue->setData(chi); |
590 | + | entry_plug->addProperty(chiValue); |
591 | + | |
592 | + | DoubleData* integralOfChidtValue = new DoubleData(); |
593 | + | integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
594 | + | integralOfChidtValue->setData(integralOfChidt); |
595 | + | entry_plug->addProperty(integralOfChidtValue); |
596 | + | |
597 | + | } |
598 | + | else |
599 | + | return NULL; |
600 | ||
601 | < | // add the positions and velocities to the atom |
601 | > | //get eta |
602 | > | foo = strtok(NULL, " ,;\t\n"); |
603 | > | if(foo != NULL ){ |
604 | > | |
605 | > | for(int i = 0 ; i < 9; i++){ |
606 | > | |
607 | > | if(foo == NULL){ |
608 | > | sprintf( painCave.errMsg, |
609 | > | "error in reading eta[%d] from %s\n", i, c_in_name ); |
610 | > | return strdup( painCave.errMsg ); |
611 | > | } |
612 | > | eta[i] = atof( foo ); |
613 | > | foo = strtok(NULL, " ,;\t\n"); |
614 | > | } |
615 | > | } |
616 | > | else |
617 | > | return NULL; |
618 | ||
619 | < | atoms[atomIndex]->setX( rx ); |
620 | < | atoms[atomIndex]->setY( ry ); |
621 | < | atoms[atomIndex]->setZ( rz ); |
622 | < | |
623 | < | atoms[atomIndex]->set_vx( vx ); |
624 | < | atoms[atomIndex]->set_vy( vy ); |
625 | < | atoms[atomIndex]->set_vz( vz ); |
619 | > | //push eta into SimInfo::properties which can be |
620 | > | //retrieved by integrator later |
621 | > | //entry_plug->setBoxM( theBoxMat3 ); |
622 | > | DoubleArrayData* etaValue = new DoubleArrayData(); |
623 | > | etaValue->setID(ETAVALUE_ID); |
624 | > | etaValue->setData(eta, 9); |
625 | > | entry_plug->addProperty(etaValue); |
626 | > | } |
627 | ||
628 | return NULL; | |
629 | } | |
630 | + | |
631 | + | #ifdef IS_MPI |
632 | + | |
633 | + | // a couple of functions to let us escape the read loop |
634 | + | |
635 | + | void initFile::nodeZeroError( void ){ |
636 | + | int j, myStatus; |
637 | + | |
638 | + | myStatus = 0; |
639 | + | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
640 | + | MPI_Send( &myStatus, 1, MPI_INT, j, |
641 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
642 | + | } |
643 | + | |
644 | + | |
645 | + | MPI_Finalize(); |
646 | + | exit (0); |
647 | + | |
648 | + | } |
649 | + | |
650 | + | void initFile::anonymousNodeDie( void ){ |
651 | + | |
652 | + | MPI_Finalize(); |
653 | + | exit (0); |
654 | + | } |
655 | + | |
656 | + | #endif //is_mpi |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |