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hdf5_plasma.c
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1
9#include <stdio.h>
10#include <stdlib.h>
11#include <hdf5.h>
12#include <hdf5_hl.h>
13#include "../ascot5.h"
14#include "../plasma.h"
15#include "../plasma/plasma_1D.h"
16#include "../plasma/plasma_1Dt.h"
17#include "../plasma/plasma_1DS.h"
18#include "../consts.h"
19#include "hdf5_helpers.h"
20#include "hdf5_plasma.h"
21
22#define PLSPATH
23
24int hdf5_plasma_read_1D(hid_t f, plasma_1D_data* data, char* qid);
25int hdf5_plasma_read_1Dt(hid_t f, plasma_1Dt_data* data, char* qid);
26int hdf5_plasma_read_1DS(hid_t f, plasma_1DS_data* data, char* qid);
36int hdf5_plasma_init(hid_t f, plasma_data* data, char* qid) {
37
38 char path[256];
39 int err = 1;
40
41 /* Read data the QID corresponds to */
42 hdf5_gen_path("/plasma/plasma_1D_XXXXXXXXXX", qid, path);
43 if(hdf5_find_group(f, path) == 0) {
44 data->type = plasma_type_1D;
45 err = hdf5_plasma_read_1D(f, &data->plasma_1D, qid);
46 }
47 hdf5_gen_path("/plasma/plasma_1Dt_XXXXXXXXXX", qid, path);
48 if(hdf5_find_group(f, path) == 0) {
49 data->type = plasma_type_1Dt;
50 err = hdf5_plasma_read_1Dt(f, &data->plasma_1Dt, qid);
51 }
52 hdf5_gen_path("/plasma/plasma_1DS_XXXXXXXXXX", qid, path);
53 if(hdf5_find_group(f, path) == 0) {
54 data->type = plasma_type_1DS;
55 err = hdf5_plasma_read_1DS(f, &data->plasma_1DS, qid);
56 }
57 return err;
58}
59
69int hdf5_plasma_read_1D(hid_t f, plasma_1D_data* data, char* qid) {
70 #undef PLSPATH
71 #define PLSPATH "/plasma/plasma_1D_XXXXXXXXXX/"
72
73 int n_rho, n_ions;
74 if( hdf5_read_int(PLSPATH "nion", &n_ions,
75 f, qid, __FILE__, __LINE__) ) {return 1;}
76 if( hdf5_read_int(PLSPATH "nrho", &n_rho,
77 f, qid, __FILE__, __LINE__) ) {return 1;}
78
79 int* q = (int*) malloc( n_ions * sizeof(int) );
80 int* znum = (int*) malloc( n_ions * sizeof(int) );
81 int* anum = (int*) malloc( n_ions * sizeof(int) );
82 real* mass = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
83 real* charge = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
84 if( hdf5_read_int(PLSPATH "znum", znum,
85 f, qid, __FILE__, __LINE__) ) {return 1;}
86 if( hdf5_read_int(PLSPATH "anum", anum,
87 f, qid, __FILE__, __LINE__) ) {return 1;}
88 if( hdf5_read_int(PLSPATH "charge", q,
89 f, qid, __FILE__, __LINE__) ) {return 1;}
90 if( hdf5_read_double(PLSPATH "mass", &mass[1],
91 f, qid, __FILE__, __LINE__) ) {return 1;}
92 charge[0] = -1 * CONST_E;
93 for(int i = 0; i < n_ions; i++) {
94 charge[i+1] = q[i] * CONST_E;
95 }
96 mass[0] = CONST_M_E;
97 for(int i = 0; i < n_ions; i++) {
98 mass[i+1] *= CONST_U;
99 }
100 free(q);
101
102 real* Te = (real*) malloc( n_rho*sizeof(real) );
103 real* Ti = (real*) malloc( n_rho*sizeof(real) );
104 real* ne = (real*) malloc( n_rho*sizeof(real) );
105 real* ni = (real*) malloc( n_rho*n_ions*sizeof(real) );
106 real* rho = (real*) malloc( n_rho*sizeof(real) );
107 real* vtor = (real*) malloc( n_rho*sizeof(real) );
108 if( hdf5_read_double(PLSPATH "rho", rho,
109 f, qid, __FILE__, __LINE__) ) {return 1;}
110 if( hdf5_read_double(PLSPATH "vtor", vtor,
111 f, qid, __FILE__, __LINE__) ) {return 1;}
112 if( hdf5_read_double(PLSPATH "etemperature", Te,
113 f, qid, __FILE__, __LINE__) ) {return 1;}
114 if( hdf5_read_double(PLSPATH "edensity", ne,
115 f, qid, __FILE__, __LINE__) ) {return 1;}
116 if( hdf5_read_double(PLSPATH "itemperature", Ti,
117 f, qid, __FILE__, __LINE__) ) {return 1;}
118 if( hdf5_read_double(PLSPATH "idensity", ni,
119 f, qid, __FILE__, __LINE__) ) {return 1;}
120
121 for(int i = 0; i < n_rho; i++) {
122 Te[i] = Te[i] * CONST_E;
123 Ti[i] = Ti[i] * CONST_E;
124 }
125
126 int err = plasma_1D_init(data, n_rho, n_ions, rho, anum, znum, mass, charge,
127 Te, Ti, ne, ni, vtor);
128 free(Te);
129 free(Ti);
130 free(ne);
131 free(ni);
132 free(rho);
133 free(znum);
134 free(anum);
135 free(mass);
136 free(charge);
137 return err;
138}
139
149int hdf5_plasma_read_1Dt(hid_t f, plasma_1Dt_data* data, char* qid) {
150 #undef PLSPATH
151 #define PLSPATH "/plasma/plasma_1Dt_XXXXXXXXXX/"
152
153 /* Read rhogrid size and number of species */
154 int n_rho, n_time, n_ions;
155 if( hdf5_read_int(PLSPATH "nion", &n_ions,
156 f, qid, __FILE__, __LINE__) ) {return 1;}
157 if( hdf5_read_int(PLSPATH "nrho", &n_rho,
158 f, qid, __FILE__, __LINE__) ) {return 1;}
159 if( hdf5_read_int(PLSPATH "ntime", &n_time,
160 f, qid, __FILE__, __LINE__) ) {return 1;}
161
162 int* q = (int*) malloc( n_ions * sizeof(int) );
163 int* znum = (int*) malloc( n_ions * sizeof(int) );
164 int* anum = (int*) malloc( n_ions * sizeof(int) );
165 real* mass = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
166 real* charge = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
167 if( hdf5_read_int(PLSPATH "znum", znum,
168 f, qid, __FILE__, __LINE__) ) {return 1;}
169 if( hdf5_read_int(PLSPATH "anum", anum,
170 f, qid, __FILE__, __LINE__) ) {return 1;}
171 if( hdf5_read_int(PLSPATH "charge", q,
172 f, qid, __FILE__, __LINE__) ) {return 1;}
173 if( hdf5_read_double(PLSPATH "mass", &mass[1],
174 f, qid, __FILE__, __LINE__) ) {return 1;}
175 charge[0] = -1 * CONST_E;
176 for(int i = 0; i < n_ions; i++) {
177 charge[i+1] = q[i] * CONST_E;
178 }
179 mass[0] = CONST_M_E;
180 for(int i = 0; i < n_ions; i++) {
181 mass[i+1] *= CONST_U;
182 }
183 free(q);
184
185 real* rho = (real*) malloc( n_rho * sizeof(real) );
186 real* time = (real*) malloc( n_time * sizeof(real) );
187 if( hdf5_read_double(PLSPATH "rho", rho,
188 f, qid, __FILE__, __LINE__) ) {return 1;}
189 if( hdf5_read_double(PLSPATH "time", time,
190 f, qid, __FILE__, __LINE__) ) {return 1;}
191
192 real* vtor = (real*) malloc( n_time*n_rho*sizeof(real) );
193 real* Te = (real*) malloc( n_time*n_rho*sizeof(real) );
194 real* Ti = (real*) malloc( n_time*n_rho*sizeof(real) );
195 real* ne = (real*) malloc( n_time*n_rho*sizeof(real) );
196 real* ni = (real*) malloc( n_time*n_ions*n_rho*sizeof(real) );
197 if( hdf5_read_double(PLSPATH "etemperature", Te,
198 f, qid, __FILE__, __LINE__) ) {return 1;}
199 if( hdf5_read_double(PLSPATH "itemperature", Ti,
200 f, qid, __FILE__, __LINE__) ) {return 1;}
201 if( hdf5_read_double(PLSPATH "vtor", vtor,
202 f, qid, __FILE__, __LINE__) ) {return 1;}
203
204 for(int i_time = 0; i_time < n_time; i_time++) {
205 for(int i_rho = 0; i_rho < n_rho; i_rho++) {
206 Te[i_time*n_rho+i_rho] *= CONST_E;
207 Ti[i_time*n_rho+i_rho] *= CONST_E;
208 }
209 }
210
211 if( hdf5_read_double(PLSPATH "edensity", ne,
212 f, qid, __FILE__, __LINE__) ) {return 1;}
213 if( hdf5_read_double(PLSPATH "idensity", ni,
214 f, qid, __FILE__, __LINE__) ) {return 1;}
215 int err = plasma_1Dt_init(data, n_rho, n_time, n_ions, rho, time, anum,
216 znum, mass, charge, Te, Ti, ne, ni, vtor);
217 free(Te);
218 free(Ti);
219 free(ne);
220 free(ni);
221 free(vtor);
222 free(znum);
223 free(anum);
224 free(mass);
225 free(charge);
226 return err;
227}
228
238int hdf5_plasma_read_1DS(hid_t f, plasma_1DS_data* data, char* qid) {
239
240 #undef PLSPATH
241 #define PLSPATH "/plasma/plasma_1DS_XXXXXXXXXX/"
242
243 /* Read rhogrid and number of species */
244 int n_rho, n_ions;
245 real rhomin, rhomax;
246 if( hdf5_read_int(PLSPATH "nion", &n_ions,
247 f, qid, __FILE__, __LINE__) ) {return 1;}
248 if( hdf5_read_int(PLSPATH "nrho", &n_rho,
249 f, qid, __FILE__, __LINE__) ) {return 1;}
250 if( hdf5_read_double(PLSPATH "rhomin", &rhomin,
251 f, qid, __FILE__, __LINE__) ) {return 1;}
252 if( hdf5_read_double(PLSPATH "rhomax", &rhomax,
253 f, qid, __FILE__, __LINE__) ) {return 1;}
254
255 int* q = (int*) malloc( n_ions * sizeof(int) );
256 int* znum = (int*) malloc( n_ions * sizeof(int) );
257 int* anum = (int*) malloc( n_ions * sizeof(int) );
258 real* mass = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
259 real* charge = (real*) malloc( ( n_ions + 1 ) * sizeof(real) );
260 if( hdf5_read_int(PLSPATH "znum", znum,
261 f, qid, __FILE__, __LINE__) ) {return 1;}
262 if( hdf5_read_int(PLSPATH "anum", anum,
263 f, qid, __FILE__, __LINE__) ) {return 1;}
264 if( hdf5_read_int(PLSPATH "charge", q,
265 f, qid, __FILE__, __LINE__) ) {return 1;}
266 if( hdf5_read_double(PLSPATH "mass", &mass[1],
267 f, qid, __FILE__, __LINE__) ) {return 1;}
268 charge[0] = -1 * CONST_E;
269 for(int i = 0; i < n_ions; i++) {
270 charge[i+1] = q[i] * CONST_E;
271 }
272 mass[0] = CONST_M_E;
273 for(int i = 0; i < n_ions; i++) {
274 mass[i+1] *= CONST_U;
275 }
276 free(q);
277
278 real* vtor = (real*) malloc( n_rho*sizeof(real) );
279 real* Te = (real*) malloc( n_rho*sizeof(real) );
280 real* Ti = (real*) malloc( n_rho*sizeof(real) );
281 real* ne = (real*) malloc( n_rho*sizeof(real) );
282 real* ni = (real*) malloc( n_rho*n_ions*sizeof(real) );
283 if( hdf5_read_double(PLSPATH "vtor", vtor,
284 f, qid, __FILE__, __LINE__) ) {return 1;}
285 if( hdf5_read_double(PLSPATH "etemperature", Te,
286 f, qid, __FILE__, __LINE__) ) {return 1;}
287 if( hdf5_read_double(PLSPATH "edensity", ne,
288 f, qid, __FILE__, __LINE__) ) {return 1;}
289 if( hdf5_read_double(PLSPATH "itemperature", Ti,
290 f, qid, __FILE__, __LINE__) ) {return 1;}
291 if( hdf5_read_double(PLSPATH "idensity", ni,
292 f, qid, __FILE__, __LINE__) ) {return 1;}
293
294 for(int i = 0; i < n_rho; i++) {
295 Te[i] = Te[i] * CONST_E;
296 Ti[i] = Ti[i] * CONST_E;
297 }
298
299 int err = plasma_1DS_init(data, n_rho, rhomin, rhomax, n_ions, anum, znum,
300 mass, charge, Te, Ti, ne, ni, vtor);
301
302 free(Te);
303 free(Ti);
304 free(ne);
305 free(ni);
306 free(vtor);
307 free(znum);
308 free(anum);
309 free(mass);
310 free(charge);
311 return err;
312}
ascot5.h
Main header file for ASCOT5.
real
double real
Definition ascot5.h:85
consts.h
Header file containing physical and mathematical constants.
CONST_U
#define CONST_U
Atomic mass unit in kilograms [kg].
Definition consts.h:32
CONST_M_E
#define CONST_M_E
Electron mass [kg].
Definition consts.h:41
CONST_E
#define CONST_E
Elementary charge [C].
Definition consts.h:35
hdf5_find_group
herr_t hdf5_find_group(hid_t loc, const char *path)
Checks if given group exists within given hdf5 file. Negative value is returned if the group doesn't ...
Definition hdf5_helpers.c:100
hdf5_read_double
int hdf5_read_double(const char *var, real *ptr, hid_t file, char *qid, const char *errfile, int errline)
Read double-valued data from ASCOT5 HDF5 file.
Definition hdf5_helpers.c:166
hdf5_gen_path
char * hdf5_gen_path(const char *original, char *qid, char *path)
Generate a valid path from a given template and qid.
Definition hdf5_helpers.c:131
hdf5_read_int
int hdf5_read_int(const char *var, int *ptr, hid_t file, char *qid, const char *errfile, int errline)
Read int-valued data from ASCOT5 HDF5 file.
Definition hdf5_helpers.c:236
hdf5_helpers.h
Header file for hdf5_helpers.h.
hdf5_plasma_read_1Dt
int hdf5_plasma_read_1Dt(hid_t f, plasma_1Dt_data *data, char *qid)
Read 1Dt plasma data from HDF5 file.
Definition hdf5_plasma.c:149
PLSPATH
#define PLSPATH
Definition hdf5_plasma.c:22
hdf5_plasma_read_1D
int hdf5_plasma_read_1D(hid_t f, plasma_1D_data *data, char *qid)
Read 1D plasma data from HDF5 file.
Definition hdf5_plasma.c:69
hdf5_plasma_init
int hdf5_plasma_init(hid_t f, plasma_data *data, char *qid)
Read plasma data from HDF5 file.
Definition hdf5_plasma.c:36
hdf5_plasma_read_1DS
int hdf5_plasma_read_1DS(hid_t f, plasma_1DS_data *data, char *qid)
Load plasma data from HDF5 file and prepare parameters.
Definition hdf5_plasma.c:238
hdf5_plasma.h
Header file for hdf5_plasma.c.
plasma.h
Header file for plasma.c.
plasma_type_1D
@ plasma_type_1D
Definition plasma.h:21
plasma_type_1Dt
@ plasma_type_1Dt
Definition plasma.h:22
plasma_type_1DS
@ plasma_type_1DS
Definition plasma.h:23
plasma_1DS_init
int plasma_1DS_init(plasma_1DS_data *data, int nrho, real rhomin, real rhomax, int nion, int *anum, int *znum, real *mass, real *charge, real *Te, real *Ti, real *ne, real *ni, real *vtor)
Initialize 1DS plasma data and check inputs.
Definition plasma_1DS.c:43
plasma_1DS.h
Header file for plasma_1DS.c.
plasma_1D_init
int plasma_1D_init(plasma_1D_data *data, int nrho, int nion, real *rho, int *anum, int *znum, real *mass, real *charge, real *Te, real *Ti, real *ne, real *ni, real *vtor)
Initialize 1D plasma data and check inputs.
Definition plasma_1D.c:25
plasma_1D.h
Header file for plasma_1D.c.
plasma_1Dt_init
int plasma_1Dt_init(plasma_1Dt_data *data, int nrho, int ntime, int nion, real *rho, real *time, int *anum, int *znum, real *mass, real *charge, real *Te, real *Ti, real *ne, real *ni, real *vtor)
Initialize 1Dt plasma data and check inputs.
Definition plasma_1Dt.c:22
plasma_1Dt.h
Header file for plasma_1Dt.c.
plasma_1DS_data
1D spline plasma parameters on the target
Definition plasma_1DS.h:15
plasma_1D_data
1D plasma parameters on the target
Definition plasma_1D.h:14
plasma_1Dt_data
1D plasma parameters on the target
Definition plasma_1Dt.h:14
plasma_data
Plasma simulation data.
Definition plasma.h:32
plasma_data::plasma_1D
plasma_1D_data plasma_1D
Definition plasma.h:34
plasma_data::plasma_1Dt
plasma_1Dt_data plasma_1Dt
Definition plasma.h:35
plasma_data::plasma_1DS
plasma_1DS_data plasma_1DS
Definition plasma.h:36
plasma_data::type
plasma_type type
Definition plasma.h:33
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