common_io.c 14.4 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
/*******************************************************************************
 * This file is part of SWIFT.
 * Coypright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
 *                    Matthieu Schaller (matthieu.schaller@durham.ac.uk).
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * 
 ******************************************************************************/

/* Config parameters. */
#include "../config.h"


#if defined(HAVE_HDF5)

/* Some standard headers. */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stddef.h>
#include <hdf5.h>
#include <math.h>

#include "const.h"
#include "cycle.h"
#include "lock.h"
#include "task.h"
#include "part.h"
#include "space.h"
#include "scheduler.h"
#include "engine.h"
#include "error.h"
#include "kernel.h"
#include "common_io.h"



/**
 * @brief Converts a C data type to the HDF5 equivalent. 
 *
 * This function is a trivial wrapper around the HDF5 types but allows
 * to change the exact storage types matching the code types in a transparent way.
 */
hid_t hdf5Type(enum DATA_TYPE type)
{
  switch(type)
    {
    case INT: return H5T_NATIVE_INT;
    case UINT: return H5T_NATIVE_UINT;
    case LONG: return H5T_NATIVE_LONG;
    case ULONG: return H5T_NATIVE_ULONG;
    case LONGLONG: return H5T_NATIVE_LLONG;
    case ULONGLONG: return H5T_NATIVE_ULLONG;
    case FLOAT: return H5T_NATIVE_FLOAT;
    case DOUBLE: return H5T_NATIVE_DOUBLE;
    case CHAR: return H5T_C_S1;
    default: error("Unknown type"); return 0;
    }
}

/**
 * @brief Returns the memory size of the data type
 */
size_t sizeOfType(enum DATA_TYPE type)
{
  switch(type)
    {
    case INT: return sizeof(int);
    case UINT: return sizeof(unsigned int);
    case LONG: return sizeof(long);
    case ULONG: return sizeof(unsigned long);
    case LONGLONG: return sizeof(long long);
    case ULONGLONG: return sizeof(unsigned long long);
    case FLOAT: return sizeof(float);
    case DOUBLE: return sizeof(double);
    case CHAR: return sizeof(char);
    default: error("Unknown type"); return 0;
    }
}



/**
 * @brief Reads an attribute from a given HDF5 group.
 *
 * @param grp The group from which to read.
 * @param name The name of the attribute to read.
 * @param type The #DATA_TYPE of the attribute.
 * @param data (output) The attribute read from the HDF5 group.
 *
 * Calls #error() if an error occurs.
 */
void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data)
{
  hid_t h_attr=0, h_err=0;

  h_attr = H5Aopen(grp, name, H5P_DEFAULT);
  if(h_attr < 0)
    {
      error( "Error while opening attribute '%s'" , name );
    }

  h_err = H5Aread(h_attr, hdf5Type(type), data);
  if(h_err < 0)
    {
      error( "Error while reading attribute '%s'" , name );
    }

  H5Aclose(h_attr);
}

/**
 * @brief Write an attribute to a given HDF5 group.
 *
 * @param grp The group in which to write.
 * @param name The name of the attribute to write.
 * @param type The #DATA_TYPE of the attribute.
 * @param data The attribute to write.
 * @param num The number of elements to write
 *
 * Calls #error() if an error occurs.
 */
void writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data, int num)
{
  hid_t h_space=0, h_attr=0, h_err=0;
  hsize_t dim[1]={num};

  h_space = H5Screate(H5S_SIMPLE);
  if(h_space < 0)
    {
      error( "Error while creating dataspace for attribute '%s'." , name );
    }

  h_err = H5Sset_extent_simple(h_space, 1, dim, NULL);
  if(h_err < 0)
    {
      error( "Error while changing dataspace shape for attribute '%s'." , name );
    }

  h_attr = H5Acreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT);
  if(h_attr < 0)
    {
      error( "Error while creating attribute '%s'.", name );
    }

  h_err = H5Awrite(h_attr, hdf5Type(type), data);
  if(h_err < 0)
    {
      error( "Error while reading attribute '%s'." , name );
    }

  H5Sclose(h_space);
  H5Aclose(h_attr);
}

/**
 * @brief Write a string as an attribute to a given HDF5 group.
 *
 * @param grp The group in which to write.
 * @param name The name of the attribute to write.
 * @param str The string to write.
 * @param length The length of the string
 *
 * Calls #error() if an error occurs.
 */
void writeStringAttribute(hid_t grp, char* name, char* str, int length)
{
  hid_t h_space=0, h_attr=0, h_err=0, h_type=0;

  h_space = H5Screate(H5S_SCALAR);
  if(h_space < 0)
    {
      error( "Error while creating dataspace for attribute '%s'." , name );
    }

  h_type = H5Tcopy(H5T_C_S1);
  if(h_type < 0)
    {
      error( "Error while copying datatype 'H5T_C_S1'." );
    }

  h_err = H5Tset_size(h_type, length);
  if(h_err < 0)
    {
      error( "Error while resizing attribute tyep to '%i'." , length );
    }

  h_attr = H5Acreate1(grp, name, h_type, h_space, H5P_DEFAULT);
  if(h_attr < 0)
    {
      error( "Error while creating attribute '%s'." , name );
    }

  h_err = H5Awrite(h_attr, h_type, str );
  if(h_err < 0)
    {
      error( "Error while reading attribute '%s'." , name );
    }

  H5Tclose(h_type);
  H5Sclose(h_space);
  H5Aclose(h_attr);
}

/**
 * @brief Writes a double value as an attribute
 * @param grp The groupm in which to write
 * @param name The name of the attribute
 * @param data The value to write
 */
void writeAttribute_d(hid_t grp, char* name, double data)
{
  writeAttribute(grp, name, DOUBLE, &data, 1);
}

/**
 * @brief Writes a float value as an attribute
 * @param grp The groupm in which to write
 * @param name The name of the attribute
 * @param data The value to write
 */
void writeAttribute_f(hid_t grp, char* name, float data)
{
  writeAttribute(grp, name, FLOAT, &data, 1);
}

/**
 * @brief Writes an int value as an attribute
 * @param grp The groupm in which to write
 * @param name The name of the attribute
 * @param data The value to write
 */

void writeAttribute_i(hid_t grp, char* name, int data)
{
  writeAttribute(grp, name, INT, &data, 1);
}

/**
 * @brief Writes a long value as an attribute
 * @param grp The groupm in which to write
 * @param name The name of the attribute
 * @param data The value to write
 */
void writeAttribute_l(hid_t grp, char* name, long data)
{
  writeAttribute(grp, name, LONG, &data, 1);
}

/**
 * @brief Writes a string value as an attribute
 * @param grp The groupm in which to write
 * @param name The name of the attribute
 * @param str The string to write
 */
void writeAttribute_s(hid_t grp, char* name, char* str)
{
  writeStringAttribute(grp, name, str, strlen(str));
}


/* ------------------------------------------------------------------------------------------------ 
 * This part writes the XMF file descriptor enabling a visualisation through ParaView
 * ------------------------------------------------------------------------------------------------ */
/**
 * @brief Writes the current model of SPH to the file
 * @param h_file The (opened) HDF5 file in which to write
 */
void writeSPHflavour(hid_t h_file)
{
  hid_t h_grpsph=0;

  h_grpsph = H5Gcreate1(h_file, "/SPH", 0);
  if(h_grpsph < 0)
    error("Error while creating SPH group");

  writeAttribute_f(h_grpsph, "Kernel eta", const_eta_kernel);
  writeAttribute_f(h_grpsph, "Weighted N_ngb", kernel_nwneigh);
  writeAttribute_f(h_grpsph, "Delta N_ngb", const_delta_nwneigh);
  writeAttribute_f(h_grpsph, "Hydro gamma", const_hydro_gamma);

#ifdef LEGACY_GADGET2_SPH
  writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "(No treatment) Legacy Gadget-2 as in Springel (2005)");  
  writeAttribute_s(h_grpsph, "Viscosity Model", "Legacy Gadget-2 as in Springel (2005)");  
  writeAttribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);  
  writeAttribute_f(h_grpsph, "Viscosity beta", 3.f);  
#else
  writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "Price (2008) without switch");  
  writeAttribute_f(h_grpsph, "Thermal Conductivity alpha", const_conductivity_alpha);  
  writeAttribute_s(h_grpsph, "Viscosity Model", "Morris & Monaghan (1997), Rosswog, Davies, Thielemann & Piran (2000) with additional Balsara (1995) switch");  
  writeAttribute_f(h_grpsph, "Viscosity alpha_min", const_viscosity_alpha_min);  
  writeAttribute_f(h_grpsph, "Viscosity alpha_max", const_viscosity_alpha_max);  
  writeAttribute_f(h_grpsph, "Viscosity beta", 2.f);  
  writeAttribute_f(h_grpsph, "Viscosity decay length", const_viscosity_length);  
#endif

  writeAttribute_f(h_grpsph, "CFL parameter", const_cfl);  
  writeAttribute_f(h_grpsph, "Maximal ln(Delta h) change over dt", const_ln_max_h_change);  
  writeAttribute_f(h_grpsph, "Maximal Delta h change over dt", exp(const_ln_max_h_change));  
  writeAttribute_f(h_grpsph, "Maximal Delta u change over dt", const_max_u_change);  
  writeAttribute_s(h_grpsph, "Kernel", kernel_name);

  H5Gclose(h_grpsph);
}

/**
 * @brief Writes the current Unit System
 * @param h_file The (opened) HDF5 file in which to write
320
 * @param us The UnitSystem used in the run
321
322
323
324
325
326
327
328
329
 */
void writeUnitSystem(hid_t h_file, struct UnitSystem* us)
{
  hid_t h_grpunit=0;

  h_grpunit = H5Gcreate1(h_file, "/Units", 0);
  if(h_grpunit < 0)
    error("Error while creating Unit System group");

330
331
332
333
334
  writeAttribute_d(h_grpunit, "Unit mass in cgs (U_M)", getBaseUnit(us, UNIT_MASS));
  writeAttribute_d(h_grpunit, "Unit length in cgs (U_L)", getBaseUnit(us, UNIT_LENGTH));
  writeAttribute_d(h_grpunit, "Unit time in cgs (U_t)", getBaseUnit(us, UNIT_TIME));
  writeAttribute_d(h_grpunit, "Unit current in cgs (U_I)", getBaseUnit(us, UNIT_CURRENT));
  writeAttribute_d(h_grpunit, "Unit temperature in cgs (U_T)", getBaseUnit(us, UNIT_TEMPERATURE));  
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482

  H5Gclose(h_grpunit);
}



/**
 * @brief Prepares the XMF file for the new entry
 *
 * Creates a temporary file on the disk in order to copy the right lines.
 *
 * @todo Use a proper XML library to avoid stupid copies.
 */
FILE* prepareXMFfile()
{
  char buffer[1024];

  FILE* xmfFile = fopen("output.xmf", "r");
  FILE* tempFile = fopen("output_temp.xmf", "w");

  if(xmfFile == NULL)
    error("Unable to open current XMF file.");

  if(tempFile == NULL)
    error("Unable to open temporary file.");


  /* First we make a temporary copy of the XMF file and count the lines */
  int counter = 0;
  while (fgets(buffer, 1024, xmfFile) != NULL)
    {
      counter++;
      fprintf(tempFile, "%s", buffer);
    }
  fclose(tempFile);
  fclose(xmfFile);
  
  /* We then copy the XMF file back up to the closing lines */
  xmfFile = fopen("output.xmf", "w");
  tempFile = fopen("output_temp.xmf", "r");

  if(xmfFile == NULL)
    error("Unable to open current XMF file.");

  if(tempFile == NULL)
    error("Unable to open temporary file.");

  int i = 0;
  while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3)
    {
      i++;
      fprintf(xmfFile, "%s", buffer);
    }
  fprintf(xmfFile, "\n");
  fclose(tempFile);
  remove("output_temp.xmf");
 
  return xmfFile;
}

/**
 * @brief Writes the begin of the XMF file
 *
 * @todo Exploit the XML nature of the XMF format to write a proper XML writer and simplify all the XMF-related stuff.
 */
void createXMFfile()
{
  FILE* xmfFile = fopen("output.xmf", "w");

  fprintf(xmfFile, "<?xml version=\"1.0\" ?> \n");
  fprintf(xmfFile, "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []> \n");
  fprintf(xmfFile, "<Xdmf xmlns:xi=\"http://www.w3.org/2003/XInclude\" Version=\"2.1\">\n");
  fprintf(xmfFile, "<Domain>\n");
  fprintf(xmfFile, "<Grid Name=\"TimeSeries\" GridType=\"Collection\" CollectionType=\"Temporal\">\n\n");

  fprintf(xmfFile, "</Grid>\n");
  fprintf(xmfFile, "</Domain>\n");
  fprintf(xmfFile, "</Xdmf>\n");

  fclose(xmfFile);
}


/**
 * @brief Writes the part of the XMF entry presenting the geometry of the snapshot
 *
 * @param xmfFile The file to write in.
 * @param Nparts The number of particles.
 * @param hdfFileName The name of the HDF5 file corresponding to this output.
 * @param time The current simulation time.
 */
void writeXMFheader(FILE* xmfFile, long long Nparts, char* hdfFileName, float time)
{
  /* Write end of file */
  
  fprintf(xmfFile, "<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
  fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
  fprintf(xmfFile, "<Grid Name=\"Gas\" GridType=\"Uniform\">\n");
  fprintf(xmfFile, "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%lld\"/>\n", Nparts);
  fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
  fprintf(xmfFile, "<DataItem Dimensions=\"%lld 3\" NumberType=\"Double\" Precision=\"8\" Format=\"HDF\">%s:/PartType0/Coordinates</DataItem>\n", Nparts, hdfFileName);
  fprintf(xmfFile, "</Geometry>");
}


/**
 * @brief Writes the end of the XMF file (closes all open markups)
 *
 * @param xmfFile The file to write in.
 */
void writeXMFfooter(FILE* xmfFile)
{
  /* Write end of the section of this time step */
  
  fprintf(xmfFile, "\n</Grid>\n");
  fprintf(xmfFile, "</Grid>\n");
  fprintf(xmfFile, "\n</Grid>\n");
  fprintf(xmfFile, "</Domain>\n");
  fprintf(xmfFile, "</Xdmf>\n");
  
  fclose(xmfFile);
}


/**
 * @brief Writes the lines corresponding to an array of the HDF5 output
 *
 * @param xmfFile The file in which to write
 * @param fileName The name of the HDF5 file associated to this XMF descriptor.
 * @param name The name of the array in the HDF5 file.
 * @param N The number of particles.
 * @param dim The dimension of the quantity (1 for scalars, 3 for vectors).
 * @param type The type of the data to write.
 *
 * @todo Treat the types in a better way.
 */
void writeXMFline(FILE* xmfFile, char* fileName, char* name, long long N, int dim, enum DATA_TYPE type )
{
  fprintf(xmfFile, "<Attribute Name=\"%s\" AttributeType=\"%s\" Center=\"Node\">\n", name, dim == 1 ? "Scalar": "Vector");
  if(dim == 1)
    fprintf(xmfFile, "<DataItem Dimensions=\"%lld\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, type==FLOAT ? 4:8, fileName, name);
  else
    fprintf(xmfFile, "<DataItem Dimensions=\"%lld %d\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, dim, type==FLOAT ? 4:8, fileName, name);
  fprintf(xmfFile, "</Attribute>\n");
}


#endif