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,
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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
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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
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[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 )
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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
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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
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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
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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
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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.
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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.
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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.
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- 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!
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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
jonorbe
bb700ebd7c
Added output_art.cc file.
2012-07-19 18:31:29 +02:00
Oliver Hahn
f10f8f9a6c
version freeze for Santa Cruz Code Comparison Project
2012-07-11 17:15:45 -07:00
Oliver Hahn
3c12876d5e
Added a temporary workaround for the 'music' transfer function plugin that
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catches cases where the transfer functions become negative at very large k.
2011-09-07 22:28:39 -07:00