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