# | 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> | |
# | Line 28 | Line 30 | InitializeFromFile::InitializeFromFile( char *in_name | |
30 | ||
31 | InitializeFromFile::InitializeFromFile( char *in_name ){ | |
32 | ||
31 | – | std::cerr << "Hello from Initialize from file.\n"; |
32 | – | |
33 | #ifdef IS_MPI | |
34 | if (worldRank == 0) { | |
35 | #endif | |
# | Line 41 | Line 41 | InitializeFromFile::InitializeFromFile( char *in_name | |
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( ){ | |
# | Line 74 | Line 78 | void InitializeFromFile :: readInit( SimInfo* the_simn | |
78 | ||
79 | void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ | |
80 | ||
81 | < | int i, j, done, which_node, which_atom; // loop counter |
81 | > | int i, j; |
82 | ||
79 | – | const int BUFFERSIZE = 2000; // size of the read buffer |
80 | – | int n_atoms; // the number of atoms |
81 | – | 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; | |
88 | – | int procIndex; |
89 | – | double currTime; |
90 | – | double boxMat[9]; |
91 | – | double theBoxMat3[3][3]; |
93 | ||
94 | + | vector<StuntDouble*> integrableObjects; |
95 | + | vector<StuntDouble*>::iterator iter; |
96 | + | |
97 | simnfo = the_simnfo; | |
98 | ||
99 | ||
# | Line 103 | Line 107 | void InitializeFromFile :: readInit( SimInfo* the_simn | |
107 | simError(); | |
108 | } | |
109 | ||
110 | < | n_atoms = atoi( read_buffer ); |
110 | > | nTotObjs = atoi( read_buffer ); |
111 | ||
112 | < | Atom **atoms = simnfo->atoms; |
109 | < | DirectionalAtom* dAtom; |
110 | < | |
111 | < | if( n_atoms != simnfo->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, simnfo->n_atoms ); |
116 | > | c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
117 | painCave.isFatal = 1; | |
118 | simError(); | |
119 | } | |
120 | < | |
121 | < | //read the box mat from 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 127 | Line 128 | void InitializeFromFile :: readInit( SimInfo* the_simn | |
128 | simError(); | |
129 | } | |
130 | ||
131 | < | parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
131 | > | parseErr = parseCommentLine( read_buffer, simnfo); |
132 | if( parseErr != NULL ){ | |
133 | strcpy( painCave.errMsg, parseErr ); | |
134 | painCave.isFatal = 1; | |
135 | simError(); | |
136 | } | |
137 | ||
138 | < | for(i=0;i<3;i++) |
138 | < | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
138 | > | //parse dump lines |
139 | ||
140 | < | simnfo->setBoxM( theBoxMat3 ); |
141 | < | simnfo->setTime( currTime ); |
140 | > | for( i=0; i < simnfo->n_mol; i++){ |
141 | ||
142 | + | integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
143 | ||
144 | < | for( i=0; i < n_atoms; i++){ |
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, n_atoms, i ); |
153 | < | painCave.isFatal = 1; |
154 | < | simError(); |
155 | < | } |
144 | > | for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++) |
145 | ||
146 | < | |
147 | < | parseErr = parseDumpLine( read_buffer, i ); |
148 | < | if( parseErr != NULL ){ |
149 | < | strcpy( painCave.errMsg, parseErr ); |
150 | < | painCave.isFatal = 1; |
151 | < | simError(); |
152 | < | } |
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 | ||
# | Line 172 | Line 171 | void InitializeFromFile :: readInit( SimInfo* the_simn | |
171 | ||
172 | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone | |
173 | int haveError; | |
174 | < | |
174 | > | |
175 | MPI_Status istatus; | |
176 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
176 | > | int *MolToProcMap = mpiSim->getMolToProcMap(); |
177 | > | int localIndex; |
178 | > | int nCurObj; |
179 | ||
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); |
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 = simnfo->atoms; |
194 | < | DirectionalAtom* dAtom; |
195 | < | |
196 | < | // 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, simnfo->n_atoms ); |
200 | > | c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
201 | haveError= 1; | |
202 | simError(); | |
203 | } | |
204 | < | |
205 | < | //read the boxMat from 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, | |
# | Line 214 | Line 211 | void InitializeFromFile :: readInit( SimInfo* the_simn | |
211 | haveError = 1; | |
212 | simError(); | |
213 | } | |
214 | < | |
215 | < | parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
214 | > | |
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 | < | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
231 | < | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
232 | < | |
233 | < | if(haveError) nodeZeroError(); |
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 | < | for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
236 | < | |
237 | < | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
238 | < | if(eof_test == NULL){ |
239 | < | sprintf(painCave.errMsg, |
240 | < | "error in reading file %s\n" |
236 | < | "natoms = %d; index = %d\n" |
237 | < | "error reading the line from the file.\n", |
238 | < | c_in_name, n_atoms, i ); |
239 | < | haveError= 1; |
240 | < | simError(); |
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 | – | if(haveError) nodeZeroError(); |
242 | ||
243 | < | // Get the Node number which wants this atom: |
244 | < | which_node = AtomToProcMap[i]; |
245 | < | if (which_node == 0) { |
246 | < | parseErr = parseDumpLine( read_buffer, i ); |
247 | < | if( parseErr != NULL ){ |
248 | < | strcpy( painCave.errMsg, parseErr ); |
249 | < | haveError = 1; |
250 | < | simError(); |
251 | < | } |
252 | < | if(haveError) nodeZeroError(); |
253 | < | } |
254 | < | |
255 | < | else { |
256 | < | |
257 | < | myStatus = 1; |
260 | < | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
261 | < | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
262 | < | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
263 | < | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
264 | < | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
265 | < | MPI_COMM_WORLD); |
266 | < | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
267 | < | MPI_COMM_WORLD, &istatus); |
268 | < | |
269 | < | if(!myStatus) nodeZeroError(); |
270 | < | } |
271 | < | } |
272 | < | myStatus = -1; |
273 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
274 | < | MPI_Send( &myStatus, 1, MPI_INT, j, |
275 | < | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
276 | < | } |
277 | < | |
278 | < | } else { |
279 | < | |
280 | < | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
281 | < | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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 | < | done = 0; |
260 | < | while (!done) { |
259 | > | parseDumpLine(read_buffer, integrableObjects[i]); |
260 | > | |
261 | > | } |
262 | ||
286 | – | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
287 | – | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
288 | – | |
289 | – | if(!myStatus) anonymousNodeDie(); |
290 | – | |
291 | – | if(myStatus < 0) break; |
263 | ||
264 | < | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
265 | < | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
266 | < | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
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 | < | myStatus = 1; |
272 | < | parseErr = parseDumpLine( read_buffer, which_atom ); |
273 | < | if( parseErr != NULL ){ |
274 | < | strcpy( painCave.errMsg, parseErr ); |
275 | < | myStatus = 0;; |
276 | < | 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 | ||
306 | – | MPI_Send( &myStatus, 1, MPI_INT, 0, |
307 | – | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
308 | – | |
293 | } | |
294 | + | |
295 | } | |
296 | < | |
297 | < | // last thing last, enable fatalities. |
298 | < | painCave.isEventLoop = 0; |
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 | < | for(i=0;i<3;i++) |
307 | < | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
306 | > | if(localIndex == -1) { |
307 | > | sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
308 | > | haveError = 1; |
309 | > | simError(); |
310 | > | } |
311 | ||
312 | < | simnfo->setBoxM( theBoxMat3 ); |
319 | < | simnfo->setTime( currTime ); |
312 | > | integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
313 | ||
314 | < | |
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 | > | } |
338 | #endif | |
339 | } | |
340 | ||
341 | < | char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
341 | > | char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){ |
342 | ||
343 | < | char *foo; // the pointer to the current string token |
344 | < | |
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 jx, jy, jz; // angular velocity placeholders; |
348 | > | double ji[3]; // angular velocity placeholders; |
349 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
334 | – | |
335 | – | Atom **atoms = simnfo->atoms; |
336 | – | DirectionalAtom* dAtom; |
337 | – | |
338 | – | int j, n_atoms, atomIndex; |
350 | ||
340 | – | #ifdef IS_MPI |
341 | – | n_atoms = mpiSim->getTotAtoms(); |
342 | – | atomIndex=-1; |
343 | – | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
344 | – | if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
345 | – | } |
346 | – | if (atomIndex == -1) { |
347 | – | sprintf( painCave.errMsg, |
348 | – | "Initialize from file error. Atom at index %d " |
349 | – | "in file %s does not exist on processor %d .\n", |
350 | – | globalIndex, c_in_name, mpiSim->getMyNode() ); |
351 | – | return strdup( painCave.errMsg ); |
352 | – | } |
353 | – | #else |
354 | – | n_atoms = simnfo->n_atoms; |
355 | – | atomIndex = globalIndex; |
356 | – | #endif // is_mpi |
351 | ||
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 " |
367 | < | "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", |
380 | < | 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 | pos[0] = atof( foo ); | |
376 | < | |
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", |
390 | < | 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 | pos[1] = atof( foo ); | |
385 | < | |
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", |
400 | < | 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 | < | pos[2] = atof( foo ); |
393 | > | pos[2] = atof( foo ); |
394 | ||
395 | ||
396 | // get the velocities | |
# | Line 408 | 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", |
413 | < | 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 | vel[0] = atof( foo ); | |
406 | < | |
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", |
423 | < | 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 | vel[1] = atof( foo ); | |
415 | < | |
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", |
433 | < | 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 | vel[2] = atof( foo ); | |
424 | < | |
425 | < | |
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", |
448 | < | 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", |
458 | < | 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", |
468 | < | 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", |
478 | < | 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", |
490 | < | 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", |
500 | < | 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", |
510 | < | 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 ); |
514 | < | |
515 | < | 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; | |
526 | – | |
527 | – | dAtom->setQ( q ); |
528 | – | |
529 | – | // 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 | } | |
535 | – | |
536 | – | // add the positions and velocities to the atom |
537 | – | |
538 | – | atoms[atomIndex]->setPos( pos ); |
539 | – | atoms[atomIndex]->setVel( vel ); |
519 | ||
520 | + | |
521 | + | |
522 | return NULL; | |
523 | } | |
524 | ||
525 | ||
526 | < | char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
546 | < | double &time ){ |
526 | > | char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
527 | ||
528 | < | char *foo; // the pointer to the current string token |
529 | < | int j; |
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 | < | |
538 | > | |
539 | foo = strtok(readLine, " ,;\t"); | |
540 | // set the timeToken. | |
541 | ||
# | Line 559 | Line 545 | char* InitializeFromFile::parseBoxLine(char* readLine, | |
545 | c_in_name ); | |
546 | return strdup( painCave.errMsg ); | |
547 | } | |
562 | – | time = atof( foo ); |
548 | ||
549 | < | // get the Hx vector |
550 | < | |
566 | < | foo = strtok(NULL, " ,;\t"); |
567 | < | if(foo == NULL){ |
568 | < | sprintf( painCave.errMsg, |
569 | < | "error in reading Hx[0] from %s\n", |
570 | < | c_in_name ); |
571 | < | return strdup( painCave.errMsg ); |
572 | < | } |
573 | < | boxMat[0] = atof( foo ); |
574 | < | |
575 | < | foo = strtok(NULL, " ,;\t"); |
576 | < | if(foo == NULL){ |
577 | < | sprintf( painCave.errMsg, |
578 | < | "error in reading Hx[1] from %s\n", |
579 | < | c_in_name ); |
580 | < | return strdup( painCave.errMsg ); |
581 | < | } |
582 | < | boxMat[1] = atof( foo ); |
583 | < | |
584 | < | foo = strtok(NULL, " ,;\t"); |
585 | < | if(foo == NULL){ |
586 | < | sprintf( painCave.errMsg, |
587 | < | "error in reading Hx[2] from %s\n", |
588 | < | c_in_name ); |
589 | < | return strdup( painCave.errMsg ); |
590 | < | } |
591 | < | boxMat[2] = atof( foo ); |
549 | > | currTime = atof( foo ); |
550 | > | entry_plug->setTime( currTime ); |
551 | ||
552 | < | // get the Hy vector |
552 | > | //get H-Matrix |
553 | ||
554 | < | foo = strtok(NULL, " ,;\t"); |
555 | < | if(foo == NULL){ |
556 | < | sprintf( painCave.errMsg, |
557 | < | "error in reading Hy[0] from %s\n", |
558 | < | c_in_name ); |
559 | < | return strdup( painCave.errMsg ); |
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 | } | |
602 | – | boxMat[3] = atof( foo ); |
603 | – | |
604 | – | foo = strtok(NULL, " ,;\t"); |
605 | – | if(foo == NULL){ |
606 | – | sprintf( painCave.errMsg, |
607 | – | "error in reading Hy[1] from %s\n", |
608 | – | c_in_name ); |
609 | – | return strdup( painCave.errMsg ); |
610 | – | } |
611 | – | boxMat[4] = atof( foo ); |
612 | – | |
613 | – | foo = strtok(NULL, " ,;\t"); |
614 | – | if(foo == NULL){ |
615 | – | sprintf( painCave.errMsg, |
616 | – | "error in reading Hy[2] from %s\n", |
617 | – | c_in_name ); |
618 | – | return strdup( painCave.errMsg ); |
619 | – | } |
620 | – | boxMat[5] = atof( foo ); |
563 | ||
564 | < | // get the Hz vector |
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 | < | foo = strtok(NULL, " ,;\t"); |
568 | < | if(foo == NULL){ |
569 | < | sprintf( painCave.errMsg, |
570 | < | "error in reading Hz[0] from %s\n", |
571 | < | c_in_name ); |
572 | < | return strdup( painCave.errMsg ); |
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 | > | //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 | > | //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 | } | |
631 | – | boxMat[6] = atof( foo ); |
632 | – | |
633 | – | foo = strtok(NULL, " ,;\t"); |
634 | – | if(foo == NULL){ |
635 | – | sprintf( painCave.errMsg, |
636 | – | "error in reading Hz[1] from %s\n", |
637 | – | c_in_name ); |
638 | – | return strdup( painCave.errMsg ); |
639 | – | } |
640 | – | boxMat[7] = atof( foo ); |
641 | – | |
642 | – | foo = strtok(NULL, " ,;\t"); |
643 | – | if(foo == NULL){ |
644 | – | sprintf( painCave.errMsg, |
645 | – | "error in reading Hz[2] from %s\n", |
646 | – | c_in_name ); |
647 | – | return strdup( painCave.errMsg ); |
648 | – | } |
649 | – | boxMat[8] = atof( foo ); |
627 | ||
628 | return NULL; | |
629 | } | |
630 | ||
654 | – | |
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 | < | |
637 | > | |
638 | myStatus = 0; | |
639 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
640 | < | MPI_Send( &myStatus, 1, MPI_INT, j, |
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 | < | } |
667 | < | |
642 | > | } |
643 | ||
644 | + | |
645 | MPI_Finalize(); | |
646 | exit (0); | |
647 | < | |
647 | > | |
648 | } | |
649 | ||
650 | void initFile::anonymousNodeDie( void ){ |
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