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405 commits 1 branch 1 tag 2.4 MiB
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192 commits

Author SHA1 Message Date
Oliver Hahn
c74e6dbd55 added missing random number plugin 2013-10-24 11:27:09 +02:00
Raul Angulo
14c92dd4ff adding missing headers 2013-10-24 11:20:01 +02:00
Oliver Hahn
ccaf6762bd merging upstream changes 2013-10-24 10:53:40 +02:00
Oliver Hahn
82beef69a6 fixed a bug when expanding convex hulls 2013-10-23 23:16:47 +02:00
Oliver Hahn
f920a3377e merge 2013-10-23 23:03:59 +02:00
Oliver Hahn
507b6daa41 added output plugin with refined tetrahedral mesh connectivity structure 2013-10-23 22:56:35 +02:00
Dylan Nelson
3c67f672d3 fix potential segfault related to STL in convex_hull.hh 2013-10-22 18:30:10 +00:00
Dylan Nelson
60d2aede0f generalize output_arepo for non-box regions 2013-10-22 18:28:48 +00:00
Oliver Hahn
a1cf2812fe fixed a bug when expanding convex hulls 2013-10-17 17:27:56 +02:00
Oliver Hahn
09c8251d06 merge 2013-10-13 00:14:26 +02:00
Oliver Hahn
7177cfe2bf initial local commit of MUSIC 2.0 2013-10-10 23:24:21 +02:00
Oliver Hahn
ef46d58653 added new parameter file options to specify the bounding ellipsoid directly, 
the new options are region_ellipsoid_matrix[0-2] for the matrix and
region_ellipsoid_center for the ellipsoid center.

fixed a bug that caused velocity data to be used from region_point file
(need to check the units in all tools, so better to disable it atm)
 2013-09-25 21:02:12 +02:00
Oliver Hahn
814247421b added parameters to specify the ellipsoid explicitly 2013-09-25 06:05:17 +02:00
Oliver Hahn
7db63aba4a fixes the missing 'exit' in arepo plugin. now plugin (as ENZO and generic) is simply unavailable 
when HDF5 is not present
 2013-08-23 08:11:41 -07:00
Oliver Hahn
6e785f642d minor fixes of compilation/makefile issues 2013-08-15 16:32:37 -07:00
Oliver Hahn
a17f70e119 fixed a compile error in arepo plugin when HAVEHDF5=no 2013-08-08 15:23:12 +02:00
Dylan Nelson
69236a2032 Initial addition of output plugin for Arepo (HDF5). 2013-08-07 16:45:11 -04:00
Oliver Hahn
6d29773b3a fixed a compilation error in convex_hull.hh 2013-08-07 14:11:28 +02:00
Oliver Hahn
a0f6dc2ba2 added proper expanding of convex hull, some optimisations 2013-08-07 12:29:23 +02:00
Oliver Hahn
d3e48b3ec9 added support for convex hull based high-res regions 2013-08-05 00:40:34 +02:00
Oliver Hahn
0c5cb001e9 moved point file reader to its own class 2013-08-04 23:58:56 +02:00
Oliver Hahn
3343fd7cdd added a new transfer function 'eisenstein_suppress' with an additional parameter 
[cosmology]/ktrunc to suppress large-scale power
 2013-07-05 18:43:40 +02:00
Oliver Hahn
eb86e9c56b Merged in jfe/music/nyx (pull request #6) 
merge des nyx plugins
 2013-06-04 09:56:37 +02:00
JFEngels
efba81d2a8 some more cleanup 2013-05-30 13:41:00 +02:00
JFEngels
6575a9f836 some cleanup 2013-05-30 12:06:11 +02:00
JFEngels
cd33d50702 improve last commit 2013-05-13 17:19:37 +02:00
JFEngels
44854adb14 make inputs file contain the correct blocking factor 2013-05-13 17:02:50 +02:00
JFEngels
48e4f7004d we now enforce the blocking factor...this time for real 2013-05-10 12:24:50 +02:00
JFEngels
6c2a606108 we now write multiple boxes instead of one large 2013-05-07 15:28:24 +02:00
Oliver Hahn
1579ffc95a some convenience adjustments to output better ramses namelist files 2013-05-03 16:23:52 +02:00
JFEngels
024e81dc8d some merge... 2013-04-23 18:02:16 +02:00
Oliver Hahn
ad67f23f30 reduced the padding around ellipsoids when not using RAMSES output 2013-04-21 11:55:36 +02:00
Oliver Hahn
72ea09abcb fixed a numerical accuracy issue with the ellipsoid regions 2013-04-21 11:43:11 +02:00
Oliver Hahn
9ace4d1dd3 merge 2013-04-19 16:45:56 +02:00
Oliver Hahn
ead40fd5b6 added support for ellipsoid region files that include velocity information 
to correctly deal with the initial displacement of the particles from their
Lagrangian coordinates
 2013-04-19 16:45:48 +02:00
galtay
60aa00bb83 Added #include <unistd.h> to output plugins so they can see unlink in gnu >= 4.7.0 2013-04-16 14:28:52 -05:00
Oliver Hahn
7d156c8958 fixes to CAMB transfer function plugin. now supports extrapolation out of tabulated region 2013-04-07 21:59:43 +02:00
Oliver Hahn
b09262124f fixed a bug that WDM transfer functions did not work properly with some compilers 2013-04-04 23:37:10 +02:00
Oliver Hahn
7e69a43036 added new option "gadget_cell_centered=yes/no" to enable half-cell shift for gadget particle positions 2013-03-21 22:09:59 +01:00
Oliver Hahn
edb2dce773 gadget2: added option to write out long ids, even if not needed for ICs themselves 2013-03-15 16:15:36 -07:00
Oliver Hahn
b0ffdc5d62 Merged in ohahn/music-iodevel (pull request #4) 2013-03-08 11:39:47 -08:00
Oliver Hahn
c08d523265 Added enzo_refine_region_fraction parameter. 
It sets the erfine region output in the parameter file to this
fraction times the finest grid size.

Also made the align_top field not required to be true as this
is only needed for old enzo versions.
 2013-03-07 17:39:57 -08:00
Oliver Hahn
9c89e837b5 added notification mechanism so that region generator plugins can be updated about the grid hierarchy that was actually created. this fixes also the problem with high res regions not being necessarily equal to the grid size available when using the is_refined member function 2013-02-22 00:01:37 +01:00
JFEngels
14675047ef some corrections to the grid layout... 2013-02-19 14:52:53 +01:00
Oliver Hahn
77183c6e20 improvements to WDM transfer function parameterisations, now support for Bode et al. 2001 and Viel et al. 2005 parameterisations, fixed missing factor of h in old Bode+2001 parameterisation 2013-02-18 16:17:13 +01:00
ch b
048bd978f5 removed fortran warning flag in inputs file generation. 2013-02-18 14:49:50 +01:00
JFEngels
06bbc50da4 i dont know...maybe merge 2013-02-13 18:02:06 +01:00
JFEngels
ebf6fa6167 some units fixed 2013-02-13 17:55:01 +01:00
ch b
eea7b8a8ca removed a line from inputs file that isnt neccessay 2013-02-13 16:48:41 +01:00
JFEngels
ae521fc683 this one fixes a "bug" for nyx and regridding...we also go for multithreaded... 2013-02-13 14:59:47 +01:00
JFEngels
6ad387c0ce some improvements to makefiles... 2013-02-07 16:34:34 +01:00
JFEngels
2c8023c1f2 Most of the stuff needed to produce initial conditions for Nyx. 
Still a little fragile...
 2013-02-07 15:02:07 +01:00
Sam Leitner
d0b3896c47 if mkdir fails because directory already exists plugin should continue 2013-02-05 12:55:57 -06:00
Sam Leitner
ee563ab1f7 new cart plugin 2013-02-05 12:48:30 -06:00
Oliver Hahn
41aca84102 ramses output: fixed support for refinement masks, added passive scalar masks 2013-01-23 21:52:08 +01:00
Oliver Hahn
eb30a6014f fixed an arithmetic precision issue when computing the ellipsoid region 2013-01-23 00:05:05 +01:00
Oliver Hahn
65ed455e36 gadget2 plugin: empty part of header is now initialized to zero, this makes it compatible with non-public gadget-2 and 3 2013-01-22 22:10:02 +01:00
Oliver Hahn
2705f78e69 fixed correction for previous grid shift when centering velocities via explicit shift 2013-01-08 17:14:02 +01:00
Oliver Hahn
2f4794e408 initial support for explicit shift compensation with center_vel, center_vel_posfinal... 2013-01-08 17:11:32 +01:00
Oliver Hahn
83e381f5cb some code cleanup 2012-12-17 10:33:18 +01:00
Oliver Hahn
f36f73fba4 added back support for regions of fixed dimension 2012-12-17 10:01:28 +01:00
Oliver Hahn
1f6059943e changed region code to have 1 cell additional bounding around ellipsoid 
ramses output working with masks, needs more testing
 2012-12-15 00:53:01 +01:00
Oliver Hahn
3b89c9b5cc grafic output plugin now writes out RAMSES nmls with mask support 
the old nmls can be written by setting output/ramses_old_nml=yes
instead of output/ramses_nml=yes
 2012-12-14 15:26:20 +01:00
Oliver Hahn
ce5a0253d5 fixed correct mask restriction for RAMSES/grafic 2012-12-14 15:00:25 +01:00
Oliver Hahn
3d548c3083 fixed a bug when using boxy high-res regions 
fixed a bug when particles for ellipsoid generations have shift
 2012-12-12 22:40:12 +01:00
Oliver Hahn
2e0fad972b fixed correct name for RAMSES refinement maps 2012-12-11 03:26:17 +01:00
Oliver Hahn
0db06e159c fixed a bug in the ellipsoid bounding box calculation 2012-12-11 03:14:36 +01:00
Oliver Hahn
77a6920ed1 added support to account for shifting of region defining particles when initializing from zoomed sim 2012-12-11 02:48:52 +01:00
Oliver Hahn
d1022359e9 added untested support for output of refinement mask with RAMSES 2012-12-11 02:40:40 +01:00
Oliver Hahn
ce3b5d3029 accuracy fixes to ellipsoid determination 2012-12-11 02:31:06 +01:00
Oliver Hahn
7cbfb01605 updates and fixes to refinement region infrastructure 
support for gadget preliminary tests ok
 2012-12-11 02:11:04 +01:00
Oliver Hahn
1df02fcbf6 started infrastructure for more advanced high-res regions (not cuboid) 
added implementation for minimal enclosing ellipsoid
 2012-12-09 16:42:47 +01:00
Oliver Hahn
025c9fbad0 bit of cleanup in the ART plugin, avoid a few compiler warnings 2012-12-09 16:42:00 +01:00
Oliver Hahn
f4556c30b3 merge 2012-11-20 16:06:49 +01:00
Oliver Hahn
fd9759e866 ENZO-plugin: added higher precision of refinement region position output to ENZO parameter file 2012-11-20 16:06:24 +01:00
Jose Onorbe
c85b99f9cd - Some corrections to avoid warnings during compilation. 
- Added information about initial temperature for the baryons in the log.
- Modified output file names when doing a baryon run.
- Corrected bug of hubble constant units in header. Did not affect dark matter only results.
 2012-11-14 14:28:04 -08:00
Michael Kuhlen
f98688bd23 Added the option to write out tipsy files in native binary format, which is much faster to read in than the XDR encoded default. Choose this option by setting 'tipsy_native = yes' under [output]. 2012-11-14 13:01:58 -08:00
Michael Kuhlen
94f863917c Unified tabbing (whitespace) in plugins/output_tipsy.cc (BSD-style with 4-space indentation). 2012-11-14 10:59:22 -08:00
Jose Onorbe
c1bb82e30b - Some corrections to avoid warnings during compilation. 
- Added information about initial temperature for the baryons in the log.
- Modified output file names when doing a baryon run.
- Corrected bug of hubble constant units in header. Did not affect dark matter only results.
 2012-10-31 00:54:31 -07:00
Oliver Hahn
b6e86bb6fb Merged in ohahn/music-iodevel (pull request #2) 2012-10-25 14:14:16 +02:00
Oliver Hahn
e505f97b9a fixed compatibility with gcc 4.7, unistd.h needs to be explicitly included 2012-10-16 10:13:14 +02:00
Oliver Hahn
d9fbe83bbc added new parameter [setup]/ref_dims=NX,NY,NZ to explicitly specify the resoluti 
on of the high resolution region.
added output of comoving size of high-res region to screen
added output of densest point also when using the generic output plugin
 2012-09-28 15:17:25 +02:00
Jose Onorbe
8ccd7c7dfe Implemented baryon output for ART module. Still under testing. 
Done some cleaning and commenting in all the ART module code.
 2012-09-11 16:30:20 -07:00
jonorbeb
f45bed11a9 Dark matter only art module tested and working ok. Units checked and ok. 
All previous questions solved.
Still waiting for one last zoom test (moderate resolution 512^3) to compare it with
gadget results but full box and low res zoom look ok.

We should start thinking in the baryon format output.
 2012-09-04 20:28:22 -07:00
Oliver Hahn
9275aa4529 added output of density extrema to ENZO plugin 2012-08-24 12:11:17 -07:00
jonorbe
bf38faaf23 Swap endianness option fully enabled for ART module: header, particle data and pt files. 2012-08-19 16:43:31 -07:00
Oliver Hahn
8040f40104 Gadget-2 plugin: added new parameters for length and mass units, allowed gadget coarse particle type to be specified in parameter file. Fixed bug that H0 instead of h was written to Gadget header. 2012-08-19 13:38:49 -07:00
Oliver Hahn
9b34875aa5 added change of endianness to data arrays in ART plugin, header etc. still need to be adjusted 2012-08-17 17:38:35 -07:00
jonorbe
ab24981135 - Fixed velocity units conversion. Still final test needed. 
- Header ascii variable can be set in the config file.
- astep variable for ART has to be given in the config file.
 2012-07-31 01:36:58 -07:00
jonorbe
c7e6cd5825 ART module for dm-only operative. Right now the module generates all the files necessary with the correct format and (re-check mandatory) units. Therefore, ICs generated should run! 
Here I write a list of to-do things:

- Find a clever way to set the char array in header. Should be set in the config file and then probably use some getValue?
- Re-check velocity units
- How important is the EKIN parameter of the header to start ART. We are not calculating it. It could be done when writing the files but seems to much work taking into account that it is probably calculated at each timestep.
- astep parameter: clarification on how is set/chosen for the initial conditions. It is important for subsequent steps or ART auto-regulates the next steps?
- Need some clarifications for zoom-in simulations:
	+ which NROWC and NGRIDC is used (now using levelmin, but levelmax?)
        + Number of files. Not clear if all together in one or one for each level (in the last case we will need to do some important changes in the module)
- Confirm our current format is standard for all ART versions.
 2012-07-27 20:17:12 -07:00
Oliver Hahn
3806e940c6 added code outline to read DM temporary particle files and assemble them 2012-07-27 12:27:27 -07:00
jonorbe
39025f7173 Assigning correct values to the parameters in header file. 2012-07-27 11:43:58 -07:00
Oliver Hahn
bc7d5de346 added baryon support to tipsy output plugin 2012-07-23 12:17:24 -07:00
Oliver Hahn
2ed1414fba added correct averaging of SPH+DM particles in coarse region 2012-07-23 12:16:05 -07:00
Oliver Hahn
448796873d added temp file output for DM data in ART plugin 2012-07-20 19:36:59 -07:00
Oliver Hahn
c3f5a14438 made art plugin compilable 2012-07-20 19:27:33 -07:00
Oliver Hahn
b7dd1cd8e3 added baryons to tipsy file output plugin 2012-07-20 19:17:18 -07:00
jonorbe
6d43639fc6 changes output_art.cc 2012-07-19 20:26:19 +02:00
jonorbe
aa80db066a Changes is output_art.cc 2012-07-19 19:41:57 +02:00
jonorbe
e121d9547c Some changes in output_art.cc 2012-07-19 19:14:34 +02:00