[arts-users] PSA: pyarts-2.6.4 compatibility with numpy 2.0
Dear all, pyarts 2.6.4 has a compatibility issue with the newly released numpy 2.0. If you update your conda environment, you'll receive an error about `np.infty` when importing pyarts. As a workaround, you can downgrade the numpy package for now: mamba install "numpy<2" This problem will be fixed in the next point release of pyarts. Cheers, Oliver smime.p7s Description: S/MIME cryptographic signature
[arts-users] ARTS 2.6.4 released
Dear all, Today we released ARTS 2.6.4, squashing a few bugs and and tweaking the online documentation. A detailed list of changes since 2.6.2 can be found on the GitHub release page: https://github.com/atmtools/arts/releases/tag/v2.6.4 Updated conda packages are also available. We recommend to install ARTS in Miniforge3[1] with `mamba install -c rttools pyarts`. Existing environments can be updated with `mamba update -c rttools pyarts`. Best wishes, The ARTS Developers [1] https://github.com/conda-forge/miniforge ARTS homepage: https://www.radiativetransfer.org/
Re: [arts-users] Is there a readable file for the surface_type_mask.xml.bin file
Hi Li,
You can load the files with pyarts and then save them in pure ascii xml format
or any other format you prefer:
import pyarts
x = pyarts.xml.load("./surface_type_mask.xml")
x.savexml("surface_type_mask_ascii.xml", type="ascii")
Cheers,
Oliver
> On 12. May 2024, at 17:14, li zhuoyang via arts_users.mi
> wrote:
>
> Dear all：
> I hope to write the surface temperature data, surface wind speed data, and
> surface type data from ERA5 into surface_t_field.xml, surface_w_field.xml,
> and surface_type_mask.xml, similar to the
> controlfiles/surfacetypes/TestSurfaceTypes.arts. However, since the files
> surface_t_field.xml.bin, surface_w_field.xml.bin, and
> surface_type_mask.xml.bin are binary files, it is inconvenient for me to
> directly read the data and content within, especially
> surface_type_mask.xml.bin. Could you provide these three files in a more
> readable format, such as surface_t_field.xml, surface_w_field.xml, and
> surface_type_mask.xml? This would make it easier for me to understand and
> learn the content of surface_type_mask.
> Thank you for reading my letter. Looking forward to your reply!
> Yours,
> Li Zhuoyang
>
Re: [arts-users] Question about ARTS set up
Hi Sebastian, pyarts provides a function to automatically download the catalog data. Put the following code at the beginning of your script: import pyarts pyarts.cat.download.retrieve() Here is an example that also shows it: https://atmtools.github.io/arts-docs-2.6/examples.arts-catalogue-data.lines.html This will download the catalogs and automatically set the search path. By default the catalogs are downloaded to ~/.cache/arts/ . It skips the download if the catalogs are already present in that location. Have a look at the documentation of that function for additional options such as specifying a custom path for the downloads. Hope this helps. Cheers, Oliver > On 1. May 2024, at 05:54, s.hermosilla via arts_users.mi > wrote: > > Heelo, my name is Sebastián Hermosilla. > > I'm currently diving into ARTS and have successfully installed it on my > system. However, I'm encountering problems with the files that need to be > uploaded. Specifically, I'm unsure about the placement of files such as > "lines/O2-66.xml" and "lines/O3-666.xml". > > Could you kindly guide me on where these files should be uploaded? Do they > require a specific directory or folder? > > I'm attempting to execute the codes from the examples folder in the GitHub > repository. (https://github.com/atmtools/arts/tree/v2.6.0) > > Thank you in advance for your assistance. > Best regards, > Sebastián smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Does ARTS 2.6.2 support OpenMPI
Hi Li, We currently do not support MPI. The flag you found was used in the past for a specific case in the OEM code, but the corresponding code is currently disabled. Cheers, Oliver > On 28. Apr 2024, at 17:11, li zhuoyang via arts_users.mi > wrote: > > Dear all > During the installation and compilation of ARTS 2.6.2, I noticed a line in > the cmakelists.txt file: option (ENABLE_MPI "Turn on MPI" OFF). I would like > to confirm whether ARTS 2.6.2 supports multi-node operation on > supercomputers. After changing the 'OFF' in option (ENABLE_MPI "Turn on MPI" > OFF) to 'ON', I always encounter the following compilation error, despite > trying many different MPI compilers, the same error persists. > Are there any more compilation guidelines regarding MPI? > In file included from > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.cc:10: > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h: In function > 'void WriteXML(const String&, const T&, const String&, const Index&, const > String&, const String&, const String&, const Verbosity&)': > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h:118:3: error: > there are no arguments to 'MPI_Initialized' that depend on a template > parameter, so a declaration of 'MPI_Initialized' must be available > [-fpermissive] 118 | MPI_Initialized(); | ^~~ > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h:118:3: note: > (if you use '-fpermissive', G++ will accept your code, but allowing the use > of an undeclared name is deprecated) > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h:120:5: error: > there are no arguments to 'MPI_Init' that depend on a template parameter, so > a declaration of 'MPI_Init' must be available [-fpermissive] 120 | > MPI_Init(nullptr, nullptr); | ^~~~ > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h:123:17: error: > 'MPI_COMM_WORLD' was not declared in this scope 123 | > MPI_Comm_rank(MPI_COMM_WORLD, ); | ^~ > /public/home/elzd_2024_000173/lzy/arts/arts-2.6.2/src/m_xml.h:123:3: error: > there are no arguments to 'MPI_Comm_rank' that depend on a template > parameter, so a declaration of 'MPI_Comm_rank' must be available > [-fpermissive] 123 | MPI_Comm_rank(MPI_COMM_WORLD, ); | ^ > gmake[2]: *** [src/CMakeFiles/artscore.dir/m_xml.cc.o] Error 1 gmake[1]: *** > [src/CMakeFiles/artscore.dir/all] Error 2 gmake: *** [all] Error 2 > Thank you for reading my letter. Looking forward to your reply! > Yours, > Li Zhuoyang >
Re: [arts-users] Question about pyarts
Hi Wang, ArrayOfAgendaAppend is a relict from the old controlfiles and not available in pyarts. Something we need to fix in our docs. You can use the Append method instead: ws.Append(ws.pnd_agenda_array, pnd_agenda1) ws.Append(ws.pnd_agenda_array, pnd_agenda2) or set the names manually and then initialize from a list: pnd_agenda1.name = "pnd_agenda_array" pnd_agenda2.name = "pnd_agenda_array" ws.pnd_agenda_array = [pnd_agenda1, pnd_agenda2] The error "The agenda pnd_agenda_array must use the input WSV agenda_array_index, but it does not." means that the pnd_agenda1 you defined does not use the all the variables defined by the pnd_agenda_array interface. Your agenda needs to use all [IN] variables and generate all [OUT] variables defined in the interface: https://atmtools.github.io/arts-docs-2.6/stubs/pyarts.workspace.Workspace.pnd_agenda_array.html If needed, interface variables you don't want to use can be ignored with ws.Ignore(ws.agenda_array_index) inside the agenda. Cheers, Oliver > On 26. Mar 2024, at 02:45, bing wang wrote: > > Dear all, > > I'm using pyarts 2.6 for scattering calculations, but I don't know how to > assign an Agenda to pnd_agenda_array after creating arts.Agenda like > "TestScatSolvers.arts", there doesn't seem to be an ArrayOfAgendaAppend() > method in pyarts, and using a List, e.g., the ws.pnd_agenda_ > array=[pnd_agenda1, pnd_agenda2] will prompt "An ArrayOfAgenda must only > consist of agendas with the same name", directly assign ws. > agenda_array=[pnd_agenda1] will prompt "The agenda pnd_agenda_array must use > the input WSV agenda_array_index, but it does not. " Does anyone know how to > create an ArrayOfAgenda? > > Many thanks. > > Wang
[arts-users] ARTS 2.6.2 released
Dear all, Today we released ARTS 2.6.2, squashing a bug and providing additional xml data files. For details, see the GitHub release page: https://github.com/atmtools/arts/releases/tag/v2.6.2 Updated conda package are also available. Existing environments can be updated with: `conda update -c rttools pyarts` Best wishes, The ARTS Developers
[arts-users] GitHub ARTS master branch renamed
Hi all, Read this if you have checked out a local copy of the ARTS source code directly from `atmtools/arts`, basically if you have done this: git clone https://github.com/atmtools/arts The `master` branch which contains ARTS 2.6 is now named `v2.6.x`. Also, the current development version is now in the new default `main` branch. To get the correct updates for ARTS 2.6 when you `pull` in your local copy, you have to point your local copy to the new branch name by running these commands: git branch -m master v2.6.x git fetch origin git branch -u origin/v2.6.x v2.6.x git remote set-head origin -a Alternatively if you have no local changes, you can also delete your local copy and do a fresh checkout for ARTS 2.6: git clone -b v2.6.x https://github.com/atmtools/arts And please don't try to use the current `main` branch if you're not an ARTS developer. It is in heavy development and not usable for users yet. Cheers, Oliver smime.p7s Description: S/MIME cryptographic signature
[arts-users] ARTS 2.6.0 released
Dear all, We're happy to announce a new release of ARTS[1]. Many changes have gone into ARTS since the 2.4.0 release. Below you find some key features and improvements in ARTS 2.6.0: - extension to shortwave radiation - support of measured cross-section data (e.g. HITRAN absorption cross sections) - new clear-sky solver with support for shortwave radiation (iyClearsky) - molecular scattering (clear-sky Rayleigh scattering) - improved DISORT interface - much improved Python integration We recommend to install ARTS in Miniforge3[2] with `conda install -c rttools pyarts`. Further details can be found on the documentation page[3]. Enjoy, The ARTS Developers [1] https://www.radiativetransfer.org/getarts/ [2] https://github.com/conda-forge/miniforge [3] https://atmtools.github.io/arts-docs-2.6/installation.html
Re: [arts-users] Kristineberg ARTS workshop 2024, register now
Hi all, Unfortunately, due to technical issues with our university's web service, the registration form is currently unavailable. We are working with our IT department to resolve this issue and get the registration form back online as quickly as possible. Sorry for the inconvenience. Cheers, Oliver > On 30. Jan 2024, at 10:11, Stefan Buehler > wrote: > > Dear all, > > summer 2024 is drawing closer, and so is the highlight of this summer, the > ARTS radiative transfer workshop at Kristineberg research station, on the > Swedish west coast. > > The workshop will be on June 4-7, 2024 (from noon to noon). The target > audience are users and developers of the atmospheric radiative transfer > simulator ARTS, and also anyone interested in spectroscopy or radiation that > can give us new impulses. > > Anticipated topics are: > Gas absorption > Scattering > Surface interaction > The shortwave side of things (since this is new in ARTS) > ARTS applications > New sensors > > We anticipate that there will be dedicated talks sessions on these topics, > plus posters, and also space for informal discussion and practical help with > ARTS. Please indicate your contribution(s) with the registration, we will > then compile an explicit agenda. > > Some practicalities: > > There will be a free bus transfer from Göteborg on June 4 at 10:00, and back > to Göteborg on June 7, arriving approximately at 15:00. The workshop fee is > around 460€ all inclusive if you stay at the research station, and > approximately 280€ (including lunch and dinner) if you stay at one of the > nearby hotels (plus the cost of the hotel). You pay the fee directly to the > research station's staff (only card payment). The number of participants is > limited to 50, due to the size of the bus, and the number of beds at the > research station itself is limited to 45, so register soon if you want to > take part! > > Note also that there are only a few single rooms at the research station, so > most people staying on-site will have to share a double room. The > registration form allows you to indicate if room sharing is ok for you or not. > > Registration: https://www.mi.uni-hamburg.de/arts2024 > > Registration deadline: February 29 > > Some useful links: > > Kristineberg marine research station: > https://www.gu.se/en/kristineberg > > Hotels within walking distance (Gullmarsstrand, Slipens): > https://gullmarsstrand.se/en/hotel/ > https://www.slipenshotell.se/ (link seems not to work for some people, > alternative: https://www.booking.com/Share-8DAo0f ) > > Hoping to meet you in June! > > Patrick and Stefan
Re: [arts-users] line-by-line
Hi Yiwen, You almost got it right, just need to add the ".par line" as well. Here's a screenshot of the correct settings: https://attachment.rrz.uni-hamburg.de/97c802f4/Screenshot-2023-12-04-at-14.04.57.png Make sure the order of the fields exactly matches the screenshot. Cheers, Oliver > On 28. Dec 2023, at 08:11, 王毅文 wrote: > > Dear ARTS team > I'm calculating Jacobian of temperature of 1D atomsphere in the clearsky > condition using pyarts version 2.5.13.The abs_species are H2O, CO2 and O2,the > pressure levels is 101,the f_grid is from 52GHz to 57GHz step by 0.2GHz,the > sensor_pos is 35786e3 and the sensor_los is 180.I want to use explicit > line-by-line gas absorption model.How can I get the abs_lines from HITRAN > data,what output format of HITRAN online data I shoud specified.Could you > give me a simple demo. > Best wishes > yiwen wang smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Another newbie build question
Hi Geoff, In the past, "Native" didn't work on ARM Macs, only on x86 machines. Out of curiosity, since you mentioned it, I just tried to compile with Native again and it seems to be fixed now (tested with gcc-13, clang 17 from homebrew and clang 16 from conda on M1). In theory, "Native" should give at least a slight speed boost, but we haven't done any specific benchmarks comparing Release vs Native. Cheers, Oliver > On 14. Dec 2023, at 14:15, Smith, Geoffrey CIV USN NRL (7233) Washington DC > (USA) wrote: > > All — > > Since I am starting with a fresh build and am moving to the dev version, I am > curious about another possibility. Is there any experience with the native > build option for Apple ARM64 M2 Max architecture? Certainly at first I will > not be desperate to eke out every last drop of performance, but since I am > starting fresh I would not mind exploring the available options. > > Any advice, positive or negative, is appreciated. > > -geoff > > — > Dr. Geoffrey B. Smith > Head, Ocean Applications Section > Remote Sensing Division > Naval Research Laboratory > > geoffrey.sm...@nrl.navy.mil > 202.404.6324 smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] New ARTS 2.4 build Mac OS 14.1.2
Hi Geoff,
I strongly recommend to not use the Apple Clang compiler because it does not
support OpenMP. This will prevent your ARTS calculations from running on more
than a single core.
You can pass the compiler when running cmake in the build directory (start with
an empty build directory before switching compilers):
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=gcc-13
-DCMAKE_CXX_COMPILER=g++-13 ..
Cheers,
Oliver
> On 13. Dec 2023, at 18:27, Smith, Geoffrey CIV USN NRL (7233) Washington DC
> (USA) wrote:
>
> Oliver - Thanks for the help! My next question was going to be ‘please
> refresh my memory on how to use the home-brew gcc instead of the apple
> default’, but now I can re-clone the repo and test that instead?
>
> -Geoff
>
>> On Dec 13, 2023, at 4:36 AM, Lemke, Oliver
>> wrote:
>>
>> Hi again,
>>
>> I've committed a fix to the ARTS 2.4.x branch which should resolve the
>> problem.
>>
>> Cheers,
>> Oliver
>>
>>
>>> On 13. Dec 2023, at 08:04, Lemke, Oliver
>>> wrote:
>>>
>>> Hi Geoff,
>>>
>>> Unfortunately, the binary_function has been removed in recent versions of
>>> the Clang compiler. As a workaround, you can change `binary_function` in
>>> line 48 of src/sorting.h to `std::__binary_function`. That fixes the
>>> compilation with Clang.
>>>
>>> Alternatively, you can use gcc-13 from homebrew as a compiler which still
>>> works without modifying the code.
>>>
>>> Cheers,
>>> Oliver
>>>
>>>
>>>> On 12. Dec 2023, at 20:27, Smith, Geoffrey CIV USN NRL (7233) Washington
>>>> DC (USA) wrote:
>>>>
>>>> Hi —
>>>>
>>>> Sorry if this question is too basic; I did some searching of the mail
>>>> archive and did not see a solution, but I certainly could have missed it.
>>>>
>>>> I am trying to build a fresh clone of ARTS 2.4 on a clean, updated,
>>>> MacBook Pro M2 running 14.1.2. I am getting an error during make…. I am
>>>> attempting to include the relevant parts here:
>>>>
>>>> [ 12%] Building CXX object src/CMakeFiles/matpack.dir/lin_alg.cc.o
>>>> [ 13%] Building CXX object src/CMakeFiles/matpack.dir/logic.cc.o
>>>> In file included from /Users/gbsmith/local/arts/src/logic.cc:38:
>>>> /Users/gbsmith/local/arts/src/sorting.h:48:26: error: no template named
>>>> 'binary_function'; did you mean '__binary_function'?
>>>> class IndexComp : public binary_function {
>>>> ^~~
>>>> __binary_function
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include/c++/v1/__functional/binary_function.h:49:1:
>>>> note: '__binary_function' declared here
>>>> using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2,
>>>> _Result>;
>>>> ^
>>>> 1 error generated.
>>>> make[2]: *** [src/CMakeFiles/matpack.dir/logic.cc.o] Error 1
>>>> make[1]: *** [src/CMakeFiles/matpack.dir/all] Error 2
>>>>
>>>> I am not sure what to try next except move to the development version.
>>>> Any advice appreciated; any additional information that might help please
>>>> just let me know.
>>>>
>>>> Thanks much,
>>>>
>>>> Geoff Smith
>>>> Remote Sensing Division
>>>> Naval Research Laboratory
>>>> geoffrey.sm...@nrl.navy.mil
smime.p7s
Description: S/MIME cryptographic signature
Re: [arts-users] New ARTS user/Tests question
Hi Geoff, Those tests fail because they need additional input files from the arts-xml-data package. For arts 2.4 you can find the download links here: https://www.radiativetransfer.org/tools/ Unpack the arts-xml-data-2.4.0.tar.gz in the same folder where your arts folder is located, rename it from arts-xml-data-2.4.0 to arts-xml-data and cmake will detect the location automatically. Since you wrote that you're just starting with ARTS and RT, I have another recommendation for you. Instead of using ARTS 2.4, consider to use the current development version of ARTS instead. We're working on a 2.6 release which will happen soon(ish). Since there are quite a few changes, especially a stronger move towards Python integration, I think it would be easier for you to start with that. We also made improvements to the documentation especially on how to get started with ARTS. Also, once 2.6 is released you then don't have to adapt your scripts or relearn things for the new version. You can install the latest pre-release (2.5.12) directly in a Miniforge3[1] Python environment and don't need to compile it yourself. You can find the current documentation here: https://atmtools.github.io/arts-docs-2.6/installation.html Cheers, Oliver [1] https://github.com/conda-forge/miniforge > On 13. Dec 2023, at 19:13, Smith, Geoffrey CIV USN NRL (7233) Washington DC > (USA) wrote: > > Hello All — > > I am working with a fresh install of 2.4.x on a MacBook Pro M2 running macOS > 14.1.2. > > Thanks to a tweak by Oliver Lemke I successfully (I believe) built ARTS and > am testing. > > I installed (I believe successfully) PyARTS as well. > > I ran ‘make check’ and 100% of all tests passed successfully. > > I then ran ‘make check-all’ and 96% of tests passed. I have zero experience > with radiative transfer or ARTS, but am getting started. > > Can anyone offer any insight regarding the 6 tests that failed? Should I be > concerned and try and fix? Are they known/common failures? OS specific? > > Here is the relevant part of the report: > > 96% tests passed, 6 tests failed out of 160 > > Total Test time (real) = 546.90 sec > > The following tests FAILED: > 27 - arts.ctlfile.slow.artscomponents.absorption.TestIsoRatios (Failed) > 28 - python.arts.ctlfile.slow.artscomponents.absorption.TestIsoRatios (Failed) > 41 - arts.ctlfile.slow.artscomponents.clearsky.TestBatch (Failed) > 42 - python.arts.ctlfile.slow.artscomponents.clearsky.TestBatch (Failed) > 69 - arts.ctlfile.slow.artscomponents.nlte.testRotationalConvergence (Failed) > 70 - python.arts.ctlfile.slow.artscomponents.nlte.testRotationalConvergence > (Failed) > Errors while running CTest > make[3]: *** [CMakeFiles/check-all] Error 8 > make[2]: *** [CMakeFiles/check-all.dir/all] Error 2 > make[1]: *** [CMakeFiles/check-all.dir/rule] Error 2 > make: *** [check-all] Error 2 > > > Thanks much for any info and/or reassurances — > > Geoff smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] New ARTS 2.4 build Mac OS 14.1.2
Hi again,
I've committed a fix to the ARTS 2.4.x branch which should resolve the problem.
Cheers,
Oliver
> On 13. Dec 2023, at 08:04, Lemke, Oliver wrote:
>
> Hi Geoff,
>
> Unfortunately, the binary_function has been removed in recent versions of the
> Clang compiler. As a workaround, you can change `binary_function` in line 48
> of src/sorting.h to `std::__binary_function`. That fixes the compilation with
> Clang.
>
> Alternatively, you can use gcc-13 from homebrew as a compiler which still
> works without modifying the code.
>
> Cheers,
> Oliver
>
>
>> On 12. Dec 2023, at 20:27, Smith, Geoffrey CIV USN NRL (7233) Washington DC
>> (USA) wrote:
>>
>> Hi —
>>
>> Sorry if this question is too basic; I did some searching of the mail
>> archive and did not see a solution, but I certainly could have missed it.
>>
>> I am trying to build a fresh clone of ARTS 2.4 on a clean, updated, MacBook
>> Pro M2 running 14.1.2. I am getting an error during make…. I am attempting
>> to include the relevant parts here:
>>
>> [ 12%] Building CXX object src/CMakeFiles/matpack.dir/lin_alg.cc.o
>> [ 13%] Building CXX object src/CMakeFiles/matpack.dir/logic.cc.o
>> In file included from /Users/gbsmith/local/arts/src/logic.cc:38:
>> /Users/gbsmith/local/arts/src/sorting.h:48:26: error: no template named
>> 'binary_function'; did you mean '__binary_function'?
>> class IndexComp : public binary_function {
>> ^~~
>> __binary_function
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include/c++/v1/__functional/binary_function.h:49:1:
>> note: '__binary_function' declared here
>> using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2,
>> _Result>;
>> ^
>> 1 error generated.
>> make[2]: *** [src/CMakeFiles/matpack.dir/logic.cc.o] Error 1
>> make[1]: *** [src/CMakeFiles/matpack.dir/all] Error 2
>>
>> I am not sure what to try next except move to the development version. Any
>> advice appreciated; any additional information that might help please just
>> let me know.
>>
>> Thanks much,
>>
>> Geoff Smith
>> Remote Sensing Division
>> Naval Research Laboratory
>> geoffrey.sm...@nrl.navy.mil
smime.p7s
Description: S/MIME cryptographic signature
Re: [arts-users] New ARTS 2.4 build Mac OS 14.1.2
Hi Geoff,
Unfortunately, the binary_function has been removed in recent versions of the
Clang compiler. As a workaround, you can change `binary_function` in line 48 of
src/sorting.h to `std::__binary_function`. That fixes the compilation with
Clang.
Alternatively, you can use gcc-13 from homebrew as a compiler which still works
without modifying the code.
Cheers,
Oliver
> On 12. Dec 2023, at 20:27, Smith, Geoffrey CIV USN NRL (7233) Washington DC
> (USA) wrote:
>
> Hi —
>
> Sorry if this question is too basic; I did some searching of the mail archive
> and did not see a solution, but I certainly could have missed it.
>
> I am trying to build a fresh clone of ARTS 2.4 on a clean, updated, MacBook
> Pro M2 running 14.1.2. I am getting an error during make…. I am attempting
> to include the relevant parts here:
>
> [ 12%] Building CXX object src/CMakeFiles/matpack.dir/lin_alg.cc.o
> [ 13%] Building CXX object src/CMakeFiles/matpack.dir/logic.cc.o
> In file included from /Users/gbsmith/local/arts/src/logic.cc:38:
> /Users/gbsmith/local/arts/src/sorting.h:48:26: error: no template named
> 'binary_function'; did you mean '__binary_function'?
> class IndexComp : public binary_function {
>^~~
>__binary_function
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include/c++/v1/__functional/binary_function.h:49:1:
> note: '__binary_function' declared here
> using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2,
> _Result>;
> ^
> 1 error generated.
> make[2]: *** [src/CMakeFiles/matpack.dir/logic.cc.o] Error 1
> make[1]: *** [src/CMakeFiles/matpack.dir/all] Error 2
>
> I am not sure what to try next except move to the development version. Any
> advice appreciated; any additional information that might help please just
> let me know.
>
> Thanks much,
>
> Geoff Smith
> Remote Sensing Division
> Naval Research Laboratory
> geoffrey.sm...@nrl.navy.mil
>
>
smime.p7s
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Re: [arts-users] ReadHITRAN problem
Hi Jiaan, All parameters ARTS can us are included in the .par line (including broadening). ARTS will not utilize any other parameters besides what's contained in the .par line, qns' and qns''. Adding other parameters will also most likely break our reading routine. Cheers, Oliver > On 5. Dec 2023, at 02:30, suifengbenpao2023 wrote: > > > Hi Oliver， > > Thank you for your help! Thank you for providing the online screenshot. May I > ask if you need to add any other parameters that can be obtained to define > the new output format according to your screenshot? For example, self > widening, external widening, etc. > > Looking forward to your reply！Thank you! > Best wishes, > Jiaan He > > At 2023-12-04 21:26:59, "Lemke, Oliver" wrote: > >Hi Jiaan, > > > >"Online" is the recommended way. You also need to define a custom output > >format to include the .par line and the quantum numbers qns' and qns''. Here > >is a screenshot with the configuration from the HITRAN online page: > > > >https://attachment.rrz.uni-hamburg.de/97c802f4/Screenshot-2023-12-04-at-14.04.57.png > > > >Cheers, > >Oliver > > > > > >> On 4. Dec 2023, at 13:33, suifengbenpao2023 > >> wrote: > >> > >> Dear ARTS community, > >> > >> When I directly use the data downloaded from hitranonline (without > >> changing the data format), I can run the ReadHITRAN method to extract > >> lines data. I used the "Post2004" and "Online" methods, and the results > >> are the same. Is this correct? > >> > >> Looking forward to your reply！Thank you! > >> Best wishes, > >> Jiaan He > > smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] catch exception in ARTS
Hi Shaofei, You can pass the robust=1 option to ybatchCalc to avoid termination on failed batch cases. Cheers, Oliver > On 20. Nov 2023, at 11:20, Shaofei Wang wrote: > > Hi, all > > When i use ybatchCalc to simulate bt, some errors are triggered and then ARTS > terminates. > > I would like to ask if there is a way to skip the wrong simulation and move > on to the next simulation. > > I've tried converting .arts to.py and adding "try" and "except" in the .py > file. > > However, it seems that try and except must be placed in the > ybatch_calc_agenda. > Therefore, i set allow_callbacks=True and ws.Touch(y, y_aux, jacobian). But > it still can't work correctly. > > Best regards, > Shaofei Wang smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] pyARTS OEM Error?
Hi Mathias, A couple of ideas: 1. Since the frequency value in the error output has only 5 digits after the decimal[1], it might well be that your extension by 700 kHz is not sufficient and still leads to the same error message due to rounding. I'd propose to extend f_grid by 2 MHz and see if that fixes the problem. 2. You probably did this but to be sure I'll ask anyway: Did you recalculate the lookup table after extending the f_grid? Cheers, Oliver [1] we'll apply a fix to improve that output > On 30. Jun 2023, at 09:00, Mathias Milz wrote: > > Dear all, > Maybe someone here can help me: > > I set up a new retrieval for high resolving spectrometer using pyARTS with > OEM. Since it covers a wider range of the spectrum with higher resolution, > I've expanded the f_grid accordingly (with relatively high resolution, lower > than the spectrum). > pyARTS calculates the LookUp Table as it should. > If the run then goes into ws.OEM, then it stops with the error message > below. > I extended the spectrum by 700kHz and the error occurs again. > According to the error message, it happens in yCalc. > What makes me suspisious: The pure forward calculation withy Calc (i.e. > without OEM call) with the LUT read in runs perfectly. > Does anyone here have an idea what the problem could be? > Thanks in advance > Mathias > And here the error message: > Run-time error in method: yCalc > User Error: failed > Error is found at: > > /usr/local/miniconda/envs/pyarts-build/conda-bld/pyarts_1675241025317/work/src/m_rte.cc:2774 > Please follow these instructions to correct your error: > User Error: failed > Error is found at: > > /usr/local/miniconda/envs/pyarts-build/conda-bld/pyarts_1675241025317/work/src/rte.cc:1750 > Please follow these instructions to correct your error: > Run-time error in function: iyb_calc > Run-time error in agenda: iy_main_agenda > Run-time error in method: iyClearsky > User Error: do_abort > Error is found at: > > /usr/local/miniconda/envs/pyarts-build/conda-bld/pyarts_1675241025317/work/src/m_rte.cc:656 > Please follow these instructions to correct your error: > Error messages from failed cases: > Runtime-error in source calculation at index 122: > Run-time error in agenda: propmat_clearsky_agenda > Run-time error in method: propmat_clearskyAddFromLookup > Problem with gas absorption lookup table. > At least one frequency is outside the range covered by the lookup table. > Your new frequency value is 2.32501e+11 Hz. > The allowed range is 2.295e+11 to 2.32501e+11 Hz. Runtime-error in source > calculation at index 162: > Run-time error in agenda: propmat_clearsky_agenda > Run-time error in method: propmat_clearskyAddFromLookup > Problem with gas absorption lookup table. smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Nashmil Ahmadiani a Ph.D candidate (from Iran at university of Hormozgan)
Hi Nashmil, You need to install the openblas and zlib packages (as listed in the README.md file under `Build prerequisites`). Please understand that there are many different Linux distributions and package managers out there. All we can provide is a list of required dependencies for ARTS. How to install packages for your specific distribution is something you have to figure out yourself. Distributions usually offer documentation or forums where you can learn how things work. That being said, here are some hints to get you started: I'm not familiar with Rocky Linux but understand that it is a derivative of RHEL. You should be able to install the required libraries with sudo dnf install openblas-devel zlib-devel The openblas-devel package is provided in the RHEL PowerTools repository (RHEL 8/Rocky Linux 8). You might have to manually enable the repository if above command can't find the package: sudo dnf config-manager --set-enabled powertools Note that you need the -devel packages because they include the header files of the libraries. Just installing the library itself is not sufficient. If you decide to switch to Ubuntu Linux, the required packages can be installed as follows: sudo apt install zlib1g-dev libopenblas-dev Hope this helps. Cheers, Oliver > On 26. Jan 2023, at 10:00, Nashmil Ahmadiani wrote: > > Dear Sir > > I am writing to seek your help in regards to difficulty installing ARTS > software. I am Mrs. Nashmil Ahmadiani a Ph.D candidate (from Iran) and I need > this software for my Ph.D thesis. > I have faced a difficulty installing this software , during installation , > after few steps(according to Github.com/atmtools –Building ARTS) it > encounters to an error due to inability to find one of the libraries it halts > the installation. I have attached the black page down below for your review. > Please do have a look at it and see if you can give me any solution for that. > The error says “ please specify library location “ Would you please informing > me how I can do that? > I should say I am using Rocky Linux but when I searched the net , Ubuntu was > suggested to be used , would you mind telling me if that is the issue. > Also I would like to request you indicating how I can install optional > softwares too since I get the error “ not found”. > > I appreciate your help > I am looking forward to hear from you soon > > Faithfully yours > Nashmil Ahmadiani Ph.D candidate > 02.29.22.jpeg>
Re: [arts-users] Consultant about the softwear "arts" and "qpack2"
Hi Jiawei Zhu, > On 19. Dec 2022, at 21:42, Patrick Eriksson > wrote: > > That said, there is no automatic way to select the line data to use for a > simulation, neither in qpack2 nor ARTS. The safest option is to load HITRAN > or arts-cat_data for a broad frequency range surrounding your frequency of > interest. But you could still need to complement this with some "continua". Note that if you're using ARTS 2.4, you find the catalogs in the arts-xml-data package [1] in the subfolders spectroscopy/cat and spectroscopy/Hitran. arts-cat-data [2] is only compatible with the current development version 2.5.x. Cheers, Oliver [1] https://radiativetransfer.org/misc/download/stable/2.4/ [2] https://radiativetransfer.org/misc/download/unstable/ smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] scat_meta_single to scat_meta
Hi Patrick, hi Vito, > On 14. Dec 2022, at 20:04, Patrick Eriksson > wrote: > >> pndFromPsdBasic >> } >> Append( scat_species, species_id_string ) >> Append( pnd_agenda_array_input_names, pnd_agenda_input_names ) >> But the error message is that: >> The method requires that length of *psd_size_grid* is >= 2. > > I must ask what ARTS version you are using? In the version I have on my > computer it looks OK. At least, I can not find this error message. Tbe check does exist in ARTS master as well as 2.4. It's the first check in pndFromPsdBasic in m_microphysics.cc. Cheers, Oliver smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Inquiry about arts-lectures on github
Hi Ryosuke, Unfortunately, there is currently no arts-lectures package available for ARTS 2.4. The master branch is not compatible with any released ARTS version. We are in the process of updating the lecture package to be compatible with the latest pre-release version (2.5.6) of ARTS. But note that this is a work in progress and currently only exercises 1, 2, 4 and 7 have been updated to work with that version. The develop branch of the arts-lectures package can be found here: https://github.com/atmtools/arts-lectures/tree/develop The README contains links to matching catalog versions. While the source code for ARTS 2.5.6 is available on Github[1], the easiest way to get up and running is to create an environment with conda, preferably from mambaforge/miniforge[2]. This will install a precompiled version of PyARTS and thus eliminating the need to compile ARTS yourself: conda create -n pyarts -c rttools -c conda-forge python=3.10 pyarts ipympl jupyterlab typhon conda activate pyarts export ARTS_DATA_PATH=/home/username/arts-cat-data-snapshot-arts-2.5.6:/home/username/arts-xml-data-snapshot-arts-2.5.6 jupyter-lab arts-lectures/exercises/01-molecule_spectra/absorption.ipynb Adapt the ARTS_DATA_PATH according to the locations on your system. Cheers, Oliver [1] https://github.com/atmtools/arts/releases/tag/v2.5.6 [2] https://github.com/conda-forge/miniforge > On 9 Nov 2022, at 03:38, 田村 亮祐 wrote: > > Dear ARTS members > Nice to meet you. > I’m Ryosuke Tamura working at Japanese Space Agency. > Dr Y. Kasai invited me to arts mailing list. > Now, I want to use arts-lecture on github. > https://github.com/atmtools/arts-lectures/blob/master/exercises/01-rotational_spectra/absorption.ipynb > To calculate absorption cross section, I have downloaded XML data style > catalog from > https://radiativetransfer.org/misc/download/stable/2.4/. > Absorption_module.py program inside arts-lecture defines the data catalog > path as follows. > ws.abs_lines_per_speciesReadSpeciesSplitCatalog( >basename="spectroscopy/Artscat/" > ) > However, the downloaded XLM data (version2.4) doesn’t have the name of > directory “Artscat”. > To use the arts-lecture program, how to set basename=”” ? > If latest XML data catalog doesn’t have Artscat, > I’d appreciate it if you tell me the version and its URL of the catalog which > has Artscat. > Best regards > > RYOSUKE Tamura > Sensor System Research Group > Japan Aerospace Exploration Agency (JAXA) > 2-1-1, Sengen, Tsukuba, Ibaraki, 305-8505, Japan > tamura.ryohs...@jaxa.jp > smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] How to set up the ARTS program to run batch scattering calculations more efficiently by using a multicore processor
Hi Song shuhua, The ybatchCalc workspace method is the best way to make a calculation for multiple profiles. ARTS will then parallelize over the batch cases which is most efficient. This of course assumes that you have more batch cases than you have cores, otherwise some of the cores cannot be utilized. Here is a controlfile example for ARTS 2.4 which demonstrates the use of ybatchCalc: https://github.com/atmtools/arts/blob/v2.4.x/controlfiles/artscomponents/clearsky/TestBatch.arts Hope this helps. Cheers, Oliver > On 4 Nov 2022, at 10:16, 宋淑华 wrote: > > Dear all, Hello, I am running a batch scattering radiation simulation program > on a multi-core processor. It involves the simulation of multiple profiles on > multiple frequency grids. And the scattering data I use is the ARTS single > scattering database. However, it is found that the role of multi-core > processors cannot be fully realized. Even though I choose multiple cores by > running the command "-n", the actual operation only use a few cores. I'm > sure that the ARTS I compiled supported OpenMP. I guess maybe my program is > not efficient enough. I would like to ask how to make calculations more > efficient through reasonable settings when writing programs. For example, > loop multiple profiles for a single frequency point, or calculate multiple > frequency grids for a single profile, or other more reasonable ways. Looking > forward to your replies and suggestions. > > Best Regards, Song shuhua smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] [EXTERNAL] Custom antenna response
Hi Frank,
I'm sorry, after reading Michael's mail, I jumped to the conclusion that you're
also using the latest version of ARTS. In version 2.4 things are of course very
different. :-)
Due to some limitations in that version, you need to save the created antenna
response to a file and then read it back into the antenna_response workspace
variable.
Here is the code for 2.4:
---
import numpy as np
import pyarts
ant = pyarts.classes.GriddedField4()
ant.gridnames = ["Polarisation", "Frequency", "Zenith angle", "Azimuth angle"]
ant.grids = [
pyarts.classes.ArrayOfString(["NaN"]), # Polarisation grid
pyarts.classes.Vector([-999.]), # Frequency grid
pyarts.classes.Vector(np.linspace(-1.91097, 1.91097, 61)), # Zenith angle
grid
pyarts.classes.Vector([0.]) # Azimuth angle grid
]
ant.data = np.array(
0.00260905], [0.00350429], [0.00465987], [0.00613486], [0.00799636],
[0.010319], [0.01318377], [0.01667627], [0.02088407], [0.02589336],
[0.03178475], [0.03862836], [0.04647835], [0.05536716], [0.06529965],
[0.07624766], [0.08814531], [0.10088555], [0.1143183], [0.12825067],
[0.14244938], [0.15664572], [0.17054287], [0.18382546], [0.19617099],
[0.20726262], [0.21680248], [0.22452492], [0.23020879], [0.23368795],
[0.23485932], [0.23368795], [0.23020879], [0.22452492], [0.21680248],
[0.20726262], [0.19617099], [0.18382546], [0.17054287], [0.15664572],
[0.14244938], [0.12825067], [0.1143183], [0.10088555], [0.08814531],
[0.07624766], [0.06529965], [0.05536716], [0.04647835], [0.03862836],
[0.03178475], [0.02589336], [0.02088407], [0.01667627], [0.01318377],
[0.010319], [0.00799636], [0.00613486], [0.00465987], [0.00350429],
[0.00260905)
ant.savexml("antenna_response.xml")
ws = pyarts.workspace.Workspace()
ws.ReadXML(ws.antenna_response, "antenna_response.xml")
print(ws.antenna_response.value)
---
Cheers,
Oliver
> On 19 Oct 2022, at 00:31, Werner, Frank (329D)
> wrote:
>
> Hi Oliver,
>
> Thanks for your quick response! For now I simply tried to run your code
> examples to see whether they work. Unfortunately, I couldn’t get either of
> your suggestions to run.
>
> The first one, where I change an already existing antenna response, give me
> the following error:
> >>>
> ws.antenna_response.value.set_grid(ws.antenna_response.value.gridnames.index("Zenith
> angle"), np.linspace(-2, 2, 61))
> - WriteXML
> Traceback (most recent call last):
> File "", line 1, in
> AttributeError: 'GriddedField4' object has no attribute
> 'set_grid'
>
> The second example, where I set up a Gridded field myself, doesn’t run
> because the compiler complains that:
> "AttributeError: module 'pyarts' has no attribute 'arts' "
>
> Indeed, if I go to this directory:
> '~/.conda/envs/fwerner-env/lib/python3.9/site-packages/pyarts/'
> And check it's content, there is no 'arts.py' script in there. There is one
> in the 'utilities' subdirectory, but this one doesn't work either. There is a
> 'griddedfield.py' script, but this one does not get included in
> '__init__.py'...
>
> FYI, I've been using the stable 2.4 version and pyarts has worked great for
> me. This is the first time I am running into trouble.
>
> Any advice? Thanks again for your help and best wishes,
> Frank
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Re: [arts-users] failure to build arts v2.5.7
Hi Michael, > On 18 Oct 2022, at 00:04, Schwartz, Michael J (US 329D) > wrote: > > Hello > I am trying to build the development version of arts and pyarts on a linux > system with gcc version 11.2.1 20220127 (Red Hat 11.2.1-9.1.0.2) (GCC). I > also tried on a macbook, but will focus on the linux attempt. > > I downloaded the source and the arts-cat-data and arts-xml-data. > When I try to make arts, it goes well until nearly the end: > > (mjschwar-env) dweezil:build$ make > -- ARTS version: 2.5.7 (git: 007883e7) > [ 0%] Built target auto_version.txt > … > [ 90%] Built target arts_developer-stamp > [ 90%] Built target arts_user-stamp > doc/uguide/CMakeFiles/arts_developer-stage1.dir/build.make:169: *** target > pattern contains no '%'. Stop. > make[1]: *** [CMakeFiles/Makefile2:2971: > doc/uguide/CMakeFiles/arts_developer-stage1.dir/all] Error 2 > make: *** [Makefile:160: all] Error 2 > > So this seems to be failing somewhere in the building or checking of > documentation. I'm not sure what the issue here is. Please send me line 169 of build/doc/uguide/CMakeFiles/arts_developer-stage1.dir/build.make to further look into this. > I can (seemingly successfully) specifically make only the targets arts and > pyarts: > > make arts > make pyarts > cd python > python3 -m pip install --user -e . > > > > I then did > conda install docutils matplotlib netCDF4 numpy pytest scipy setuptools xarray > pip install lark-parser This seems a bit suspicious to me. Did you really install these packages AFTER compiling ARTS? Since cmake does check for these packages during configuration, you should not have been able to compile ARTS if these were not installed. Which makes me wonder if you have two different Python versions installed, which might also lead to the error you're seeing below. > but when I try to import pyarts, > > $ python > Python 3.9.13 (main, Oct 13 2022, 21:15:33) > [GCC 11.2.0] :: Anaconda, Inc. on linux > Type "help", "copyright", "credits" or "license" for more information. > >>> import pyarts > Traceback (most recent call last): > File "", line 1, in > File "/users/michael/ARTS/arts-2.5/build/python/pyarts/__init__.py", line > 8, in > from pyarts import arts # noqa > ImportError: cannot import name 'arts' from partially initialized module > 'pyarts' (most likely due to a circular import) > (/users/michael/ARTS/arts-2.5/build/python/pyarts/__init__.py) > >>> > > > It seems that it is trying, during the initialization of pyarts, to import > arts from pyarts. > This is the same error message that I get to with the install on my macbook. > > Do you have any suggestions? The import error indicates that Python cannot find the arts cpython library. Please double check that this file exists: /users/michael/ARTS/arts-2.5/build/python/pyarts/arts.cpython-39-x86_64-linux-gnu.so If the filename does not contain "-39-" but "-38-" or "-310-", that would indicate that during cmake configuration the wrong Python version was used. Double-check the output of cmake during configuration to make sure that it finds the same Python version which you are using later to import pyarts into. The output during configuration looks like this: -- Found Python3: YOURPYTHONPATH/bin/python3.X (found version "3.X.X") found components: Interpreter Development.Module Cheers, Oliver smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Custom antenna response
Hi Frank, I'm not familiar with how the antenna works exactly, but I'll try to get you started on how to modify or create a GriddedField. A GriddedField consists of the data and the corresponding grids. In the case of the antenna_response these are: print(ws.antenna_response.value.gridnames) [Polarisation, Frequency, Zenith angle, Azimuth angle] Since you already use AntennaConstantGaussian1D, the easiest way to inject your own data is probably to modify the existing antenna_response: ws.AntennaConstantGaussian1D(n_za_grid=1, fwhm=1.5) ws.antenna_response.value.data = np.array( 0.00260905], [0.00350429], [0.00465987], [0.00613486], [0.00799636], [0.010319], [0.01318377], [0.01667627], [0.02088407], [0.02589336], [0.03178475], [0.03862836], [0.04647835], [0.05536716], [0.06529965], [0.07624766], [0.08814531], [0.10088555], [0.1143183], [0.12825067], [0.14244938], [0.15664572], [0.17054287], [0.18382546], [0.19617099], [0.20726262], [0.21680248], [0.22452492], [0.23020879], [0.23368795], [0.23485932], [0.23368795], [0.23020879], [0.22452492], [0.21680248], [0.20726262], [0.19617099], [0.18382546], [0.17054287], [0.15664572], [0.14244938], [0.12825067], [0.1143183], [0.10088555], [0.08814531], [0.07624766], [0.06529965], [0.05536716], [0.04647835], [0.03862836], [0.03178475], [0.02589336], [0.02088407], [0.01667627], [0.01318377], [0.010319], [0.00799636], [0.00613486], [0.00465987], [0.00350429], [0.00260905) Grids can be modified like this: ws.antenna_response.value.set_grid(ws.antenna_response.value.gridnames.index( "Zenith angle"), np.linspace(-2, 2, 61)) After changing the grids or the data, make sure to run a consistency check between data and grids: ws.antenna_response.value.checksize_strict() To create your own GriddedField4 from scratch, this is what the constructor call would look like: ws.antenna_response = pyarts.arts.GriddedField4( gridnames=["Polarisation", "Frequency", "Zenith angle", "Azimuth angle"], grids=[ ["NaN"], # Polarisation grid [-999.], # Frequency grid np.linspace(-1.91097, 1.91097, 61), # Zenith angle grid [0.] # Azimuth angle grid ], data=np.array( 0.00260905], [0.00350429], [0.00465987], [0.00613486], [0.00799636], [0.010319], [0.01318377], [0.01667627], [0.02088407], [0.02589336], [0.03178475], [0.03862836], [0.04647835], [0.05536716], [0.06529965], [0.07624766], [0.08814531], [0.10088555], [0.1143183], [0.12825067], [0.14244938], [0.15664572], [0.17054287], [0.18382546], [0.19617099], [0.20726262], [0.21680248], [0.22452492], [0.23020879], [0.23368795], [0.23485932], [0.23368795], [0.23020879], [0.22452492], [0.21680248], [0.20726262], [0.19617099], [0.18382546], [0.17054287], [0.15664572], [0.14244938], [0.12825067], [0.1143183], [0.10088555], [0.08814531], [0.07624766], [0.06529965], [0.05536716], [0.04647835], [0.03862836], [0.03178475], [0.02589336], [0.02088407], [0.01667627], [0.01318377], [0.010319], [0.00799636], [0.00613486], [0.00465987], [0.00350429], [0.00260905) ) ws.antenna_response.value.checksize_strict() Hope this helps. Cheers, Oliver > On 17 Oct 2022, at 19:06, Werner, Frank (329D) > wrote: > > … just as an update: > > I also tried manually creating a simple 1d pattern with the > ‘sensor_responseAntenna’ workspace method: > > ws.sensor_responseAntenna(ws.sensor_response, > ws.sensor_response_f, > ws.sensor_response_pol, > ws.sensor_response_dlos, > ws.sensor_response_dlos_grid, > [11875000], > [1], > 3, > 1, > [[0.]], > > np.array(0.00260905],[0.00350429],[0.00465987],[0.00613486],[0.00799636], > [0.010319 > ],[0.01318377],[0.01667627],[0.02088407],[0.02589336], > > [0.03178475],[0.03862836],[0.04647835],[0.05536716],[0.06529965], > > [0.07624766],[0.08814531],[0.10088555],[0.1143183 ],[0.12825067], > > [0.14244938],[0.15664572],[0.17054287],[0.18382546],[0.19617099], > > [0.20726262],[0.21680248],[0.22452492],[0.23020879],[0.23368795], > > [0.23485932],[0.23368795],[0.23020879],[0.22452492],[0.21680248], > >
[arts-users] Fwd: Direct radiation is subtracted when it should not
Forwarding Freddy's answer to the list. :-) > Begin forwarded message: > > From: Manfred Brath > Subject: Re: Fwd: [arts-users] Direct radiation is subtracted when it should > not > Date: 17 October 2022 at 14:38:24 CEST > To: > Cc: Oliver Lemke > > Hello Xia, > > since the star related methods are still under development, some > documentation is still missing. Therefore, you chose unfortunately the wrong > surface agenda. The iySurfaceRtpropAgenda calculates only the surface > reflection/scattering from the diffusive radiation field. No direct radiation > is intended to be considered by this method. > > If stars are present you should use following surface methods: > > for a Lambertian surface with predefined reflectivity > > iySurfaceLambertian > iySurfaceLambertianDirect > for a flat surface with predefined reflectivity > iySurfaceFlatReflectivity > iySurfaceFlatReflectivityDirect > for a flat surface (Fresnel reflection) with defined refractive index > iySurfaceFlatRefractiveIndex > iySurfaceFlatRefractiveIndexDirect > > > Here is a example for a surface agenda with a Lambertian surface > > @arts_agenda > def iy_surface_agenda(ws): > ws.iySurfaceInit() > ws.Ignore(ws.dsurface_rmatrix_dx) > ws.Ignore(ws.dsurface_emission_dx) > ws.iySurfaceLambertian() > ws.iySurfaceLambertianDirect() > > > > and for a flat surface with Fresnel reflection > > @arts_agenda > def iy_surface_agenda(ws): > ws.iySurfaceInit() > ws.iySurfaceFlatRefractiveIndex() > ws.iySurfaceFlatRefractiveIndexDirect() > > > > I hope this could help you. > > Cheers, > > Freddy > > Am 17.10.22 um 13:06 schrieb Lemke, Oliver: >> >> >>> Begin forwarded message: >>> >>> From: Xia Mengqi mailto:mengqi@epfl.ch>> >>> Subject: [arts-users] Direct radiation is subtracted when it should not >>> Date: 16 October 2022 at 14:05:16 CEST >>> To: "arts_users.mi@lists.uni-hamburg.de >>> <mailto:arts_users.mi@lists.uni-hamburg.de>" >>> >> <mailto:arts_users.mi@lists.uni-hamburg.de>> >>> >>> Hi, >>> >>> I'm new to ARTS and I set up a simple 1D test where there is sun, >>> absorption only gas and a specular surface with reflectivity 1. The sun and >>> sensor is both at 0 latitude and 0 longitude, with the sensor looking down >>> (los=180). For simplicity I force it to be just 1 layer by providing the >>> pressures on the top of the atmosphere and at 0km. I noticed that the >>> radiance output is almost zero, which is unexpected. However, if I comment >>> out the operation that subtracts the direct radiation (iy-=iy_aux[0]) in >>> iySurfaceRtpropAgenda the result looks correct (and validated against >>> libRadtran). I'm puzzled why in this case the subtraction is needed; or >>> maybe I made simple mistakes in the set up. It would be great if you could >>> help me with this problem. Thank you! >>> >>> >>> The main part of the code is copied here: >>> >>> ws = Workspace(verbosity=2) >>> ws.ReadHITRAN(filename='/home/mandy/Github/MiAtmosphere/HITRAN/ALL.par', >>> hitran_type="Online", abs_lines=ws.abs_lines) >>> >>> ws.LegacyContinuaInit() >>> ws.water_p_eq_agendaSet() >>> ws.gas_scattering_agendaSet() >>> ws.PlanetSet(option="Earth") >>> ws.iy_main_agendaSet( option="Clearsky" ) >>> ws.iy_space_agendaSet( option="CosmicBackground" ) >>> ws.iy_surface_agendaSet() >>> >>> ws.ArrayOfStringSet( ws.iy_aux_vars, [ "Optical depth", "Radiative >>> background"] ) >>> >>> ws.propmat_clearsky_agenda=propmat_clearsky_agenda >>> >>> ws.NumericSet( ws.ppath_lmax, 1e10) >>> ws.ppath_step_agendaSet( option="GeometricPath" ) >>> ws.ppath_agendaSet( option="FollowSensorLosPath" ) >>> >>> # define environment >>> # >>> = >>> # Number of Stokes components to be computed >>> ws.IndexSet(ws.stokes_dim, 1) >>> >>> # Read the spectroscopic line data from the ARTS catalogue and >>> # create the workspace variable `lines'. >>> ws.ReadHITRAN(filename='/home/mandy/Github/MiAtmosphere/HITRAN/ALL.par', >>> hitran_type="Online", abs_lines=ws.abs_lines) >>> ws.abs_linesNormalization(ws.abs_lines, &
Re: [arts-users] Temperature Retrievals of Oxygen emission lines with Zeeman effect and line mixing
Hi Witali, Great that it worked with GCC. The problem with Clang is a known issue on operating systems that link by default against the GNU libstdc++. In the case of Ubuntu, compiling with clang requires explicit linking against LLVM's libc++ by setting `export CXXFLAGS=-stdlib=libc++` before calling cmake. I'm working on a pull request[1] that updates our cmake configuration to output proper errors if the available compiler is too old and will also add the automatic switch to libc++ if clang is used. Thanks for your feedback and good luck with the line mixing! Cheers, Oliver [1] https://github.com/atmtools/arts/pull/526 > On 14 Sep 2022, at 17:48, witali.kroc...@unibe.ch wrote: > > I was running Ubuntu 20.04LTS which only offers gcc 9 and clang 10. Upgrading > gcc and clang on 20.04 was not possible (at least not easily). After > upgrading to 22.10 which does provide gcc 11 and clang 14 I managed to > install ARTS, but only using gcc. When trying to use clang as directed in > "LLVM/Clang compiler" section on the gitpage there was an error: > "fatal error: instantiating fold expression with 2003 arguments exceeded > expression nesting limit of 256" > > Will try to run the line mixing module know. > > Best regards > Witali smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Temperature Retrievals of Oxygen emission lines with Zeeman effect and line mixing
Hi Witali, That is indeed strange. Which compiler are you using? You need at least GCC 11 or LLVM/Clang 13. Cheers, Oliver > On 14 Sep 2022, at 14:22, > wrote: > > Thank you very much for the support. > > After installing the master branch and running the 'make check' command, I > got a weird error message that read: > > [ 10%] Building CXX object > src/CMakeFiles/make_workspace_memory_handler_cc.dir/make_workspace_memory_handler_cc.cc.o > In file included from /opt/arts-master/src/matpackI.h:102, > from /opt/arts-master/src/methods.h:32, > from /opt/arts-master/src/global_data.h:31, > from > opt/arts-master/src/make_workspace_memory_handler_cc.cc:24: > /opt/arts-master/src/matpack_concepts.h:4:10: fatal error: concepts: No such > file or directory > 4 | #include > | ^~ > compilation terminated. > > I'm sure this file exists and my machine should meet the requirements as well. > Reinstalling ARTS 2.4 worked fine before. > > > Is this a known issue? > > Best regards > Witali smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Temperature Retrievals of Oxygen emission lines with Zeeman effect and line mixing
Hi Witali, The error you're seeing indicates that you're using an older ARTS version. To read the newest version of the arts-cat-data, you also need to compile the latest ARTS development version from the master branch at https://github.com/atmtools/arts . Cheers, Oliver > On 13 Sep 2022, at 17:18, witali.kroc...@unibe.ch wrote: > > Thank you for the quick reply and comments on the updated papers. > > > We will definitely add Mr. Larsson to the list of co-authors when the > research using this dataset is published. > > > Unfortunately, I am already having problems reading the dataset. > I have downloaded the file "O2-66.xml" from > https://arts.mi.uni-hamburg.de/svn/rt/arts-cat-data/trunk/lines/, > but I cannot read the file with any reading function that are known to me. > > > For example, the following line: > "ReadXML(abs_lines, "O2-66.xml")" > > > Generates the following error message: > "Species "" is not a valid species." > > I've tried several other read functions, but I have a feeling I'm missing > something. > > Best regards > Witali
Re: [arts-users] ART question- sim 1D cloud
Hi Caroline, The error message you're seeing suggests that your cmake version (check with `cmake --version`) is not recent enough. You need to have at least cmake 3.18 installed. If your operating system does not provide a newer version and you're using anaconda or miniforge as your python environment, you can install a newer version that way (with `conda install cmake`). If you're not using an anaconda flavor, it is also possible to install cmake via pip with `pip install --user cmake`. You then just have to make sure that you call the right cmake binary when configuring ARTS. You might have to provide the full path to the pip cmake version, e.g. `$HOME/.local/bin/cmake ..` Cheers, Oliver > On 23 Aug 2022, at 16:17, Caroline Cox - STFC UKRI > wrote: > > Thanks, Patrick for your reply. > > I am using ARTS 2.2 as I am having problems getting the latest version to > run. This is not ideal, I'd rather run the most recent version, but I am > finding an error message "[module] requires the language dialect "cxx17" , > but cmake does not know the compile flags to use to enable it.". I've > updated all my compilers, but does not seem to fix this issue. If anyone has > any experience with this then do let me know. > > Anyway, version 2.2 runs for clear-sky, so until I get the later version > going this is fine. I have compiled with fortran options to enable the > Tmatrix code, and I can use it to produce single scattering xml files. These > however, do not appear to be the format needed by the test file TestDOIT, and > I am getting xml syntax errors reported. > > If there are any other sources of information out there with a few more > detailed examples on how to use this for clouds, I would really interested to > see them. > > Thanks > > Caroline smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] generating scattering data
Hi Will, ARTS is using the Tmatrix code by the late M. I. Mishchenko. While generally working very well, it is known to have certain limitations depending on the chosen combination of parameters. We ran into similar issues before and sometimes could regain convergence by tweaking the aspect ratio. But I'm afraid I cannot give you a good hint on how to circumvent these issues. You might want to have a look at the Tmatrix publications that describe the method in detail listed in the documentation here: https://github.com/atmtools/arts/blob/master/3rdparty/tmatrix/License.txt Cheers, Oliver > On 27 Apr 2022, at 22:33, Krolick, William C. (MSFC-ER42)[ESSCA] > wrote: > > Hello, > > I have been attempting to generate some scattering data files with the > command “scat_data_singleTmatrix(…”, and am running into some issues. I get > the following error after running for a while: “CONVERGENCE IS NOT OBTAINED > FOR NPN1=300. EXECUTION TERMINATED“. I am running with a wavelength range of > 3.5e-7-6.8e-7 meters and between 50-500 grid points. Increasing the > wavelength does make the code with the given run file converge, but I would > of course like to have it converge for my desired range. Any obvious things > to look at to debug this issue? > > Thank you, > Will Krolick > > Senior Project Engineer, CFD Analyst > NASA Marshall Space Flight Center, ER 42 > Jacobs Space Exploration Group, ESSCA > CFD Research Corporation smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] Compiling with T-matrix support
Hi Will, From your other mail I assume you managed to solve this problem by passing the -DENABLE_FORTRAN=1 option to cmake to enable the Tmatrix module. Cheers, Oliver > On 27 Apr 2022, at 17:33, Krolick, William C. (MSFC-ER42)[ESSCA] > wrote: > > Hello, > > My name is Will Krolick, and I have been using your solver for some work I am > doing with passive sensors in the fluid dynamics branch (ER 42) at NASA. I > have been attempting to generate some scattering data files, and am running > into a problem with the T-matrix capability in arts. I have compiled ARTS > successfully following all the standard steps from the documentation, but > when the code comes to the command “scat_data_singleTmatrix(…” it outputs the > following error: > > “terminate called after throwing an instance of 'std::runtime_error' > what(): This version of ARTS was compiled without T-Matrix support.” > > I cannot seem to find the error in my compilation and am wondering if you can > provide some assistance on this. Is there some flag I am missing that needs > to be set? Any information would be appreciated. > > Thank you, > Will Krolick > > Senior Project Engineer, CFD Analyst > NASA Marshall Space Flight Center, ER 42 > Jacobs Space Exploration Group, ESSCA > CFD Research Corporation smime.p7s Description: S/MIME cryptographic signature
Re: [arts-users] sensitivity of SAPHIR frequencies (183.31GHZ)
Hi Sisma, The example comes with a pre-calculated lookup table in the exact frequency range of the example. If you change the f_grid, you need to re-calculate the lookup table. You can do this by putting the following snippet of code in doit_setup.arts. VectorSet( f_grid, [183.31e9,183.32e9] ) doit_setup.arts, lines 65ff: abs_lines_per_speciesSetEmpty atmfields_checkedCalc lbl_checkedCalc abs_lines_per_speciesSetEmpty abs_xsec_agenda_checkedCalc abs_lookupSetup abs_lookupCalc Also make sure to comment out the line where the example lookup table is read: # ReadXML( abs_lookup, "testdata/testdoit_gas_abs_lookup.xml" ) Most of this is already present in doit_setup.arts at lines 65ff. Just note that I also added abs_lines_per_speciesSetEmpty and lbl_checkedCalc which are missing in the example. Also note that for simplicity, the example only uses full absorption models. It might be desirable to read absorption lines from an ARTS line catalog depending on the purpose of your calculations. And finally, you also need to provide scattering particles that cover the selected frequency range. The example reads two files that are only defined for the frequencies used in the example code. I've replaced these with two Mie particles from arts-xml-data. I'm not experienced with the physics of scattering particles and these particles might not make sense to use here. doit_setup.arts, line ~149ff: ScatElementsPndAndScatAdd( scat_data_files=["/Users/olemke/Hacking/uhh/arts-xml-data-2.4/scattering/H2O_ice/MieSphere_R1.0e+00um.xml", "/Users/olemke/Hacking/uhh/arts-xml-data-2.4/scattering/H2O_ice/MieSphere_R1.25000e+01um.xml"], pnd_field_files=["testdata/testdoit_pnd_field_1D.xml", "testdata/testdoit_pnd_field_1D.xml"] ) You need to adjust the paths above to the location of your arts-xml-data directory. Hope this helps, Oliver > On 15 Mar 2022, at 10:12, Sisma Samuel wrote: > > Hi, > I was trying to simulate the sensitivity of SAPHIR frequencies (183.31GHZ). > I tried to run > /home/nizy/arts-2.4.0/controlfiles/artscomponents/doit/TestDOIT.arts > > To simulate for SAPHR frequencies by modifying doit_setup.arts > Frequency grid > # -- > # Note: The frequencies must be contained in the gas absorption lookup table. > VectorSet( f_grid,183.31e9,1836.32e9] ) > > > but my output was > This run took 0.06s (1.32s CPU time) > Run-time error in controlfile: doit_setup_saphir.arts > Run-time error in method: abs_lookupAdapt > Cannot find new frequency 0 (1.8331e+11Hz) in the lookup table frequency grid. > Stopping ARTS execution. > > > Regards > Sisma > ___ > arts_users.mi mailing list > arts_users.mi@lists.uni-hamburg.de > https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi ___ arts_users.mi mailing list arts_users.mi@lists.uni-hamburg.de https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
Re: [arts-users] AgendaSet in pyarts
Hi Frank,
There is a decorator provided by Python you can use to create an agenda from a
function:
import pyarts
ws = pyarts.workspace.Workspace()
@pyarts.workspace.arts_agenda
def my_iy_main_agenda(ws):
ws.ppathCalc()
ws.iyEmissionStandard()
ws.iy_main_agenda = my_iy_main_agenda
Cheers,
Oliver
> On 21 Feb 2022, at 21:28, Werner, Frank (329D)
> wrote:
>
> Dear ARTS developers,
>
> I am trying to use ‘AgendaSet’ in the pyarts environment.
>
> Naturally, the common way (used in an ‘.arts’ control file) results in a
> syntax error:
> ‘ws.AgendaSet(ws.iy_main_agenda){ws.ppathCalc, ws.iyEmissionStandard}’.
>
> I tried playing around with different commands, as well as ‘AgendaAppend’,
> but nothing seems to work. Is ‘AgendaSet’ even possible in pyarts? If so,
> what is the correct syntax for calling it?
>
> Thanks for your help and best wishes,
> Frank
>
> --
> Frank Werner
> Mail Stop 183-701, Jet Propulsion Laboratory
> 4800 Oak Grove Drive, Pasadena, California 91109, United States
> Phone: +1 818 354-1918
> Fax: +1 818 393 5065
>
> ___
> arts_users.mi mailing list
> arts_users.mi@lists.uni-hamburg.de
> https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
___
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Re: [arts-users] Cannot create abs_lookup with arts 2.5
Hi Mattia,
For ARTS 2.5, the line catalog has been updated and moved from arts-xml-data
into its own package arts-cat-data. It's best to use this updated version with
the development version of ARTS. You can obtain it from SVN:
svn co https://arts.mi.uni-hamburg.de/svn/rt/arts-cat-data/trunk/ arts-cat-data
You find the catalog in the "lines" subdirectory.
Cheers,
Oliver
> On 14 Feb 2022, at 12:23, Mattia Sabatini
> wrote:
>
> Hi Jana,
>
> thanks a lot. By changing the spectroscopic line data from the default
> lines.xml to the cat folder in arts-xml-data/spectroscopy/, I correctly
> obtain the cross section values for all the abs species now. Thank you again.
>
> Mattia
>
>
> Da: Jana Mendrok
> Inviato: lunedì 14 febbraio 2022 12:10
> A: Mattia Sabatini
> Cc: Pengwang Zhai; Lemke, Oliver; ARTS Users List
> Oggetto: Re: [arts-users] R: Cannot create abs_lookup with arts 2.5
>
> Hi Mattia, Pengwang,
>
> are you using an appropriate line catalog file (H2O-PWR98 is a so-called
> "full absorption model" with its parameters implemented within ARTS, while
> "H2O" triggers a line-by-line calculation that needs the line parameters as
> input). I am not sure whether that specific test case comes with (or applies)
> a suitable line file...
>
> Best,
> Jana
>
> On Mon, Feb 14, 2022 at 11:00 AM Mattia Sabatini
> wrote:
> Hello again Pengwang,
>
> I tested controlfile TestAbs.arts with your edit:
>
> AgendaSet( abs_xsec_agenda ){
>abs_xsec_per_speciesInit
>abs_xsec_per_speciesAddConts
>lbl_checkedCalc
>abs_xsec_per_speciesAddLines
> }
>
> And with the following abs species:
>
> abs_speciesSet( species=[ "H2O", "H2O-PWR98", "O2-PWR93",
> "N2-SelfContStandardType" ] ).
>
> I thought that by adding abs_xsec_per_speciesAddLines in abs_xsec_agenda,
> just like Richard suggested me to do in my post
> (https://www.mail-archive.com/arts_users.mi@lists.uni-hamburg.de/msg00471.html),
> would solve the problem you were experiencing of having a lookup table
> filled with zeros. Unfortunately this is still an issue for me, even with the
> above settings: the H2O cross section values are all zeros, while values for
> "H2O-PWR98", "O2-PWR93", "N2-SelfContStandardType” are not. Also, during the
> execution I had this “Deprecated function warning”:
>
> abs_xsec_per_speciesAddLines is deprecated since 2021-07-13
>
> This function is no longer up to date. It only exists to satisfy lookup
> table calculations before these are updated.
> Once the lookup table calculations are up-to-date, this function is fully
> replaced with propmat_clearskyAddLines, with better functionality
>
> Apparently, abs_xsec_per_speciesAddConts is doing its job but
> abs_xsec_per_speciesAddLines does not. Did you had the chance to test it too?
>
> Mattia
>
>
>
>
>
>
> Thanks, Oliver and Mattia, for you help.
>
> After studying Mattia and Richard's posts, I figured out the following:
>
> Comment out line 15 of TestAbs.arts:
>
> #Copy(abs_xsec_agenda, abs_xsec_agenda__noCIA)
>
> And insert the following to line 16:
>
> AgendaSet( abs_xsec_agenda ){
>abs_xsec_per_speciesInit
>abs_xsec_per_speciesAddConts
>lbl_checkedCalc
>abs_xsec_per_speciesAddLines
> }
>
> Now it seems working, though I have not yet got the chance to check the
> outputs as it is still running.
>
> Yours
>
> Pengwang
>
>
>
>
>
>
>
> > On Feb 11, 2022, at 2:06 AM, Lemke, Oliver
> > wrote:
> >
> > Hi Mattia, hi Pengwang,
> >
> > Thanks Mattia for helping out. :-)
> >
> > Since you were referring to Richard's earlier post, I'll take this
> > opportunity to point out the searchable archive of this list, which might
> > come in handy at times:
> >
> > https://www.mail-archive.com/arts_users.mi@lists.uni-hamburg.de/
> >
> > Here is the post Mattia was referring to:
> >
> > https://www.mail-archive.com/arts_users.mi@lists.uni-hamburg.de/msg00471.html
> >
> > Cheers,
> > Oliver
> >
> >
> >> On 10 Feb 2022, at 17:38, mattia.sabat...@artov.ismar.cnr.it wrote:
> >>
> >> Pengwang,
> >>
> >> sorry for my partial answer. Recently I compiled ARTS 2.5 and I had a
> >> similar issue concerning the absorption lookup table. Richard Larsson,
> >> helped me replying to my mail sent in this mailing list, suggesting to add
> >> abs_xsec_per_speciesAddLines into m
Re: [arts-users] Cannot create abs_lookup with arts 2.5
Hi Mattia, hi Pengwang,
Thanks Mattia for helping out. :-)
Since you were referring to Richard's earlier post, I'll take this opportunity
to point out the searchable archive of this list, which might come in handy at
times:
https://www.mail-archive.com/arts_users.mi@lists.uni-hamburg.de/
Here is the post Mattia was referring to:
https://www.mail-archive.com/arts_users.mi@lists.uni-hamburg.de/msg00471.html
Cheers,
Oliver
> On 10 Feb 2022, at 17:38, mattia.sabat...@artov.ismar.cnr.it wrote:
>
> Pengwang,
>
> sorry for my partial answer. Recently I compiled ARTS 2.5 and I had a similar
> issue concerning the absorption lookup table. Richard Larsson, helped me
> replying to my mail sent in this mailing list, suggesting to add
> abs_xsec_per_speciesAddLines into my cross-section agenda.
>
> He also added:
>
> "We are currently in a transition in the 2.5-branch of moving away from
> abs_xsec_agenda entirely. There are some lingering problems when using
> lookup table calculations at this time. Mainly, since the line calculations
> should happen in propmat_clearsky_agenda now, they are not part of any of the
> default cross-section agendas as in the past. The lookup generation
> interface is currently under active development, so this interface might
> change in the near future."
>
> Best regards,
> Mattia
>
>
>
>
>
> Pengwang Zhai ha scritto:
>
>> Thanks, Mattia. Would you advise how TestAbs.arts can be revised to include
>> line-by-line calculation?
>>
>> Note that the behavior of TestAbs.arts is different in arts2.3, which does
>> calculate line-by-line absorption coefficients.
>>
>> I do not want continua, as I am mainly interested in the visible spectra,
>> which is out of most of those continuum models. Based on my experience with
>> previous arts version, arts does not check the spectrum limits for the
>> continuum models. I am not sure whether arts 2.5 has been improved on this.
>>
>> Pengwang
>>
>>
>>
>>
>>
>>
>>> On Feb 10, 2022, at 9:46 AM, mattia.sabat...@artov.ismar.cnr.it wrote:
>>>
>>> Hi Pengwang,
>>>
>>> the controlfile TestAbs.arts, in line 15, has the following:
>>> Copy(abs_xsec_agenda, abs_xsec_agenda__noCIA)
>>>
>>> I checked in controlfiles/general/agendas.arts for what
>>> abs_xsec_agenda__noCIA does:
>>> AgendaCreate( abs_xsec_agenda__noCIA )
>>> AgendaSet( abs_xsec_agenda__noCIA ){
>>> abs_xsec_per_speciesInit
>>> abs_xsec_per_speciesAddConts
>>> }
>>>
>>> Therefore the agenda calculates absorption for continua tag only (see
>>> https://atmtools.github.io/arts-docs-master/docserver/methods/abs_xsec_per_speciesAddConts.html).
>>> You selected H2O, and by doing this my guess is that you are not
>>> considering continuum, as it is written in lines 36-37 of TestAbs.arts.
>>>
>>> I hope that this will help you,
>>>
>>> Mattia
>>>
>>>
>>> Pengwang Zhai ha scritto:
>>>
Hello, ARTS community,
I downloaded and compiled the latest version of arts. Now I tested the the
creation of abs_lookup with the example control file located in:
arts/controlfiles/artscomponents/absorption/TestAbs.arts
I only modified two occurrences of:
abs_speciesSet( species=[ "H2O-PWR98",
"O2-PWR93",
"N2-SelfContStandardType" ] )
to:
abs_speciesSet( species=[ "H2O" ] )
and run
arts TestAbs.arts
The resultant abs_lookup are all ZEROs.
Any help?
More background information: I used arts 2.3 to create abs_lookup for H2O,
CO2, etc. in the visible by reading from HITRAN 2012. The baseline example
was TestAbs.arts provided by the arts installation. Now I need to revisit
the calculation based on HITRAN 2020, and the lookup table calculation
seems not working with arts 2.5. I greatly appreciate it if you could
provide a working example on how to create a abs_lookup with arts 2.5.
Pengwang
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Re: [arts-users] cannot compile the latest version of ARTS
Hi Pengwang, Thanks for reporting this bug. I'll merge a PR with a fix soon. See https://github.com/atmtools/arts/pull/394 However, if you don't plan to use or modify the lookup tables outside of ARTS, I recommend that you save them as binary XML instead for best efficiency: WriteXML( "binary", abs_lookup, "lookup.xml" ) Cheers, Oliver > On 8 Feb 2022, at 20:02, Pengwang Zhai wrote: > > Hello, > > I had some issue with arts 2.4 in reading HITRAN par file. I was advised to > use the latest version of arts. I did the following: > > git clone https://github.com/atmtools/arts.git > cd arts > mkdir build > cd build > cmake -DENABLE_NETCDF=1 .. > make > > The compilation stoped at 25%, with the following error message: > > /arts/src/nc_io.h:37:10: fatal error: 'abs_species_tags.h' file not found > #include "abs_species_tags.h" > ^~~~ > 1 error generated. > make[2]: *** [src/CMakeFiles/artscore.dir/auto_md.cc.o] Error 1 > make[1]: *** [src/CMakeFiles/artscore.dir/all] Error 2 > make: *** [all] Error 2 > > Any suggestion here on how to fix this? > > Note that my purpose is to create an absorption lookup table from HITRAN > 2020. I need the NetCDF support to make the resultant absorption lookup table > manageable. > > Appreciate it very much, > > Yours, > > Pengwang > > > > > > > ___ > arts_users.mi mailing list > arts_users.mi@lists.uni-hamburg.de > https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi ___ arts_users.mi mailing list arts_users.mi@lists.uni-hamburg.de https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
Re: [arts-users] TMatrix in ARTS-2.4.0
Hi, Did you run `make` after enabling Fortran to recompile ARTS with the newly enabled features? You can call arts with the `-v` option to double-check which features are enabled in your current arts executable. Cheers, Oliver > On 17 Nov 2021, at 08:13, 王韶飞 wrote: > > Hi, everyone > Recently, I try to generate Single Scattering Data with Tmatrix (WSM > scat_data_singleTmatrix). However, the execution was aborted with the reason > "This version of ARTS was compiled without T-Matrix support". > Then, i use the code "cmake -DENABLE_FORTRAN=1 > -DCMAKE_Fortran_COMPILER=gfortran .." to include features that rely on > Fortran code located in the 3rdparty subdirectory. The output display TMatrix > enabled (Please see the attachment). But I still can't execute TMatrix > correctly, and the reason is still "This version of ARTS was compiled without > T-Matrix support". > So, what do I need to do to solve this problem？ > > Best Regards, > Shaofei Wang > > > > ___ > arts_users.mi mailing list > arts_users.mi@lists.uni-hamburg.de > https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi ___ arts_users.mi mailing list arts_users.mi@lists.uni-hamburg.de https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
Re: [arts-users] importing data in format of NetCDF
Hi Bi YM, ARTS does not support reading re-analysis or model data directly from NetCDF files. The common workflow is to use a Python script to extract the necessary variables from NetCDF and convert them into the ARTS batch_atm_fields_compact format using PyARTS. @all: Maybe someone on this list has already done this and happens to have an example script at hand to share? Cheers, Oliver > On 29 Oct 2021, at 10:14, b...@cma.cn wrote: > > Hi, everyone > > I try to use ARTS in the simulation of satellite ovservation. For > importing data of background profiles in format of NetCDF, for example, > ERA-5 or NCEP files that include many variables， how to read these data into > ARTS WSV? > > Regards, > Bi YM ___ arts_users.mi mailing list arts_users.mi@lists.uni-hamburg.de https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
