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Author SHA1 Message Date
Grzegorz Kowal
c66bfc1b0a IO: Format change for storing data blocks in restart files. 
This format change is required to remove unnecessary allocation of large
arrays in order to store primitive and conservative variables in the
restart files. With this format change the memory limit of the half of
the available total memory is removed. However, in the case of use of
the data compression the sizes of restart files are typically large. The
compression ratio, however, can be improved by repacking the files using
the tools provided by the HDF5 libraries.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-10-22 08:51:12 -02:00
Grzegorz Kowal
eea602a673 MPITOOLS: Don't use timers if MPI=N. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-10-11 22:06:21 -03:00
Grzegorz Kowal
6c223c2e3b MESH: Increase exponent digit number in mesh statistics. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-27 14:07:12 -03:00
Grzegorz Kowal
402357eff1 INTEGRALS: Make sure tiny numbers represented in the integral files. 
With the standard formatting, there are only two digits for the
exponent, however, the double precision numbers can have exponents down
to -308 and up to 308. That means that three digit exponents are
required to the number representation in the integral files.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-27 14:02:27 -03:00
Grzegorz Kowal
5997d7310d REFINEMENT: Return current density not its square. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-23 14:17:38 -03:00
Grzegorz Kowal
736912f791 REFINEMENT: Add refinement criterion based on current density magnitude. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-23 11:24:52 -03:00
Grzegorz Kowal
a2cfc96f10 PROBLEMS: Update problem parameter files. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-19 08:23:49 -03:00
Grzegorz Kowal
310961ca7e SOURCES: Implement GLM-MHD source terms (EGLM and HEGLM). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-19 08:04:48 -03:00
Grzegorz Kowal
f9d3ed87df OPERATORS: Add support for module profiling. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-19 07:34:04 -03:00
Grzegorz Kowal
e00dd584e4 OPERATORS: Add gradient operator. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-19 07:17:28 -03:00
Grzegorz Kowal
7c3a621096 MESH: Redistribute all variable arrays in redistribute_blocks(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-17 08:34:47 -03:00
Grzegorz Kowal
f89d213386 EVOLUTION: Add support for profiling. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-14 20:38:53 -03:00
Grzegorz Kowal
d1e78eb0b7 MESH: Replace pblock with pmeta in some subroutines. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 10:19:25 -03:00
Grzegorz Kowal
2960aea9c4 EVOLUTION: Update some comments. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 10:17:02 -03:00
Grzegorz Kowal
8f86be865f EVOLUTION: Slightly rewrite update_fluxes(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 10:15:34 -03:00
Grzegorz Kowal
f11cdf7097 EVOLUTION: Slightly rewrite evolve_rk3(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 10:10:54 -03:00
Grzegorz Kowal
984fec49ed EVOLUTION: Slightly rewrite evolve_rk2(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 10:00:16 -03:00
Grzegorz Kowal
2c359fd5f2 EVOLUTION: Slightly rewrite evolve_euler(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 09:53:40 -03:00
Grzegorz Kowal
b5d1896d30 EVOLUTION: Slightly rewrite new_time_step(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-13 09:47:07 -03:00
Grzegorz Kowal
557abc5b82 MESH: Make MPI tag in redistribute_blocks() consistent. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-11 20:00:06 -03:00
Grzegorz Kowal
5eecf860ef BOUNDARIES: Make sure MPI tags are unique and valid. 
The tag for boundary flux update was overfloating producing invalid tag
for MPI Send, while using high number of processes. Make sure that all
tags in module BOUNDARIES are generated without overflow.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-09-11 19:48:46 -03:00
Grzegorz Kowal
39483913e9 COORDINATES: Add domain boundary areas. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-29 09:08:13 -03:00
Grzegorz Kowal
809426e6c9 MPITOOLS: Add profiling to module subroutines. 
The timing is counted for four separate groups: broadcasting, reducing,
sending and receiving.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-29 08:58:58 -03:00
Grzegorz Kowal
b69fb5f3d4 EVOLUTION: Correct comments in evolve_ssprk2(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 14:53:11 -03:00
Grzegorz Kowal
dd54da1e5c EVOLUTION: Correct comments in evolve_ssprk35(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 14:51:14 -03:00
Grzegorz Kowal
3738e9dbef EVOLUTION: Rewrite 3rd order 4-stage SSPRK integration. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 14:47:16 -03:00
Grzegorz Kowal
2e5e8b6747 EVOLUTION: Implement 3rd order 5-stage SSPRK integration. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 13:51:11 -03:00
Grzegorz Kowal
074fcb3e54 EVOLUTION: Implement 2nd order multi-stage SSPRK integration. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 13:25:31 -03:00
Grzegorz Kowal
86cf4d059d EQUATIONS: Make csnd2 public too. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-26 07:10:48 -03:00
Grzegorz Kowal
b75ad37011 EVOLUTION: Rename RK coefficients in evolve_rk34(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-21 14:01:27 -03:00
Grzegorz Kowal
f4236e791e EVOLUTION: Remove "method" from intergration method descriptions. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-21 12:39:35 -03:00
Grzegorz Kowal
f7469b1d67 INTEGRALS: Store the current time step, not fractional dt. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-20 18:10:30 -03:00
Grzegorz Kowal
c1d7c9a52f EVOLUTION: Implement 3rd order 4-stage Runge-Kutta integraiton. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-19 21:12:20 -03:00
Grzegorz Kowal
d59a5be1fc EVOLUTION: Implement 3rd order Runge-Kutta temporal integraiton. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-19 20:50:49 -03:00
Grzegorz Kowal
fdf1274b28 EVOLUTION: Fix wrong function name iee_is_nan(). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-13 07:43:14 -03:00
Grzegorz Kowal
39b560065d EVOLUTION: Use ieee_is_nan() instead of isnan() in IBM BG/P. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-13 07:31:05 -03:00
Grzegorz Kowal
02a67e86b2 DRIVER: Print information about the number of MPI processes used. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-09 09:31:52 -03:00
Grzegorz Kowal
5927fb6536 INTERPOLATIONS: Correct warning about too few ghost zones. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-08 08:24:54 -03:00
Grzegorz Kowal
87f74a90ba INTERPOLATIONS: Implement Compact WENO5 with NS stencil weights. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-08 08:16:46 -03:00
Grzegorz Kowal
92da0e6698 INTERPOLATIONS: Remove general method CRWENO5. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-07 19:32:39 -03:00
Grzegorz Kowal
48b962cf54 INTERPOLATIONS: Print warning if nghosts too low for a given method. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-07 19:03:58 -03:00
Grzegorz Kowal
59f25755a6 INTERPOLATIONS: Implement Compact Reconstruction WENO-YS. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-07 14:07:22 -03:00
Grzegorz Kowal
21dbbb2bf0 INTERPOLATIONS: Implement Compact Reconstruction WENO-Z. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-07 13:37:21 -03:00
Grzegorz Kowal
bb0a3dce69 INTERPOLATIONS: Remove general WENO5 method. 
This method is replaced by other 5th order WENO method which are already
optimized.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 17:37:27 -03:00
Grzegorz Kowal
49d5495150 INTERPOLATIONS: Implement 5th order WENO method by Borges et al. (2008). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 17:34:23 -03:00
Grzegorz Kowal
f8dfd77412 INTERPOLATIONS: Implement 5th order WENO by Yamaleev & Carpenter (2009). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 17:27:09 -03:00
Grzegorz Kowal
bba6657498 INTERPOLATIONS: Implement 5th order WENO method by He et al. (2013). 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 17:03:53 -03:00
Grzegorz Kowal
aebbbd126a INTERPOLATIONS: Remove description of non-existing arguments. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 13:11:08 -03:00
Grzegorz Kowal
203d4a943f INTERPOLATIONS: Rewrite weno5_explicit() with new weights. 
Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 13:00:12 -03:00
Grzegorz Kowal
671ac7c153 INTERPOLATIONS: Rewrite smoothness indicators. 
Subroutine smoothness_indicators() has been rewritten and renamed to
smoothness_indicators_js() to allow future implementations of other
smoothness indicators.

This subroutine is now called in stencil weight subroutines instead of
reconstruction ones.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
 2014-08-06 12:48:37 -03:00