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Python code for stellar spectral analysis

License: MIT License

Python 84.87% Shell 0.89% TeX 14.25%

fasma-synthesis's Introduction

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fasma-synthesis's Issues

No such file or directory: 'summary.out'

Hi guys,

When I run "fasma", It doesn't produce a file called summary.out.

When I install the fasma using install_fasma.sh, it stops when it compiles the install_fasma.sh, the error is:

Moogsilent.f:21:72:

21 | moogpath =
| 1
Error: Invalid character in name at (1)
make: *** [Moogsilent.o] Error 1
MOOGSILENT is not installed properly!

But when I pick out the sentence "make -C FASMA/MOOG/ -f Makefile.maclapsilent clean ; make -C FASMA/MOOG/ -f Makefile.maclapsilent" and run it, there is no error.

I do not know whether the lack of summary.out is caused by the installation.

Troubles in setting up the configuration file

Hi Maria,
Nice work, congratulation for the paper!
I have troubles in setting up the configuration file when I want to add the additional options, e.g. the 'model' keyword is not read and I cannot switch to the 'marcs' model - I have to modify synthDriver.py to make FASMA work. Could you provide some examples in the repository?
Cheers
Luca

long paths for moog problem??

Hi,

When trying to install to give it a try I still find some problems when with long paths for the moog install.
I was trying in this folder:
"/home/sousasag/Programas/GIT_Projects/FASMA-synthesis/"
Then it worked out of the box when using a shorter path:
"/home/sousasag/Programas/FASMA-synthesis/"

I think it may be related with this line in your install script:

printf $MOOGDATAPATH | awk 'BEGIN{RS="/";c=""} {if($RN>1) {printf (" . %s\"/%s\"\n",c,$1);c="//"}}' >> FASMA/MOOG/Moogsilent.f

install FASMA with mac

Hi,
There is this problem when runing install_fasma.sh for mac. Any ideas?

 Press the type of system you have: 'rh64', 'rh', 'maclap', 'macdesk' maclap

/Users/benamis/tools/FASMA-synthesis/FASMA/MOOG/data/

awk: illegal field $(), name "RN"

 input record number 1, file 

 source line number 1

rm -f *.o MOOGSILENT libMOOGSILENT.a

gfortran -std=legacy  -w   -c -o Abfind.o Abfind.f
gfortran -std=legacy  -w   -c -o Abpop.o Abpop.f
gfortran -std=legacy  -w   -c -o Batom.o Batom.f
gfortran -std=legacy  -w   -c -o Begin.o Begin.f
gfortran -std=legacy  -w   -c -o Binary.o Binary.f
gfortran -std=legacy  -w   -c -o Binplotprep.o Binplotprep.f
gfortran -std=legacy  -w   -c -o Blankstring.o Blankstring.f
gfortran -std=legacy  -w   -c -o Blends.o Blends.f
gfortran -std=legacy  -w   -c -o Bmolec.o Bmolec.f
gfortran -std=legacy  -w   -c -o Boxit.o Boxit.f
gfortran -std=legacy  -w   -c -o Calmod.o Calmod.f
gfortran -std=legacy  -w   -c -o Cdcalc.o Cdcalc.f
gfortran -std=legacy  -w   -c -o Chabund.o Chabund.f
gfortran -std=legacy  -w   -c -o Cog.o Cog.f
gfortran -std=legacy  -w   -c -o Cogsyn.o Cogsyn.f
gfortran -std=legacy  -w   -c -o Correl.o Correl.f
gfortran -std=legacy  -w   -c -o Crosscorr.o Crosscorr.f
gfortran -std=legacy  -w   -c -o Curve.o Curve.f
gfortran -std=legacy  -w   -c -o Damping.o Damping.f
gfortran -std=legacy  -w   -c -o Discov.o Discov.f
gfortran -std=legacy  -w   -c -o Doflux.o Doflux.f
gfortran -std=legacy  -w   -c -o Eqlib.o Eqlib.f
gfortran -std=legacy  -w   -c -o Ewfind.o Ewfind.f
gfortran -std=legacy  -w   -c -o Ewweighted.o Ewweighted.f
gfortran -std=legacy  -w   -c -o Fakeline.o Fakeline.f
gfortran -std=legacy  -w   -c -o Findtic.o Findtic.f
gfortran -std=legacy  -w   -c -o Finish.o Finish.f
gfortran -std=legacy  -w   -c -o Gammabark.o Gammabark.f
gfortran -std=legacy  -w   -c -o Getasci.o Getasci.f
gfortran -std=legacy  -w   -c -o Getcount.o Getcount.f
gfortran -std=legacy  -w   -c -o Getnum.o Getnum.f
gfortran -std=legacy  -w   -c -o Getsyns.o Getsyns.f
gfortran -std=legacy  -w   -c -o Gridplo.o Gridplo.f
gfortran -std=legacy  -w   -c -o Gridsyn.o Gridsyn.f
gfortran -std=legacy  -w   -c -o Infile.o Infile.f
gfortran -std=legacy  -w   -c -o Inlines.o Inlines.f
gfortran -std=legacy  -w   -c -o Inmodel.o Inmodel.f
gfortran -std=legacy  -w   -c -o Invert.o Invert.f
gfortran -std=legacy  -w   -c -o Jexpint.o Jexpint.f
gfortran -std=legacy  -w   -c -o Lineinfo.o Lineinfo.f
gfortran -std=legacy  -w   -c -o Lineabund.o Lineabund.f
gfortran -std=legacy  -w   -c -o Linlimit.o Linlimit.f
gfortran -std=legacy  -w   -c -o Molquery.o Molquery.f
gfortran -std=legacy  -w   -c -o Moogsilent.o Moogsilent.f

Moogsilent.f:21:72:


   21 |       moogpath =

      |                                                                        1

Error: Invalid character in name at (1)

make: *** [Moogsilent.o] Error 1

MOOGSILENT is not installed properly!

Failure to install MOOG on Fedora 31 following FASMA instructions

This is connected to the review of this repo on JOSS.

I've just tried to install MOOG, following the FASMA instructions, and it can't find some libraries that are probably related to sm (SuperMongo?).

Line 29 of Moogsilent.f is already

      machine = "pcl"

which I assume is correct given that I'm using Fedora 31. I then ran make -f Makefile.rh64silent and eventually got the error:

gfortran -ff2c -Wall Abfind.o Abpop.o Abunplot.o Batom.o Begin.o Binary.o Binplot.o Binplotprep.o Blankstring.o Blends.o Bmolec.o Boxit.o Calmod.o Cdcalc.o Chabund.o Cog.o Cogplot.o Cogsyn.o Correl.o Crosscorr.o Curve.o Damping.o Defcolor.o Discov.o Doflux.o Drawcurs.o Eqlib.o Ewfind.o Ewweighted.o Fakeline.o Findtic.o Finish.o Fluxplot.o Gammabark.o Getasci.o Getcount.o Getnum.o Getsyns.o Gridplo.o Gridsyn.o Infile.o Inlines.o Inmodel.o Invert.o Jexpint.o Lineinfo.o Lineabund.o Linlimit.o Makeplot.o Molquery.o Moogsilent.o Mydriver.o Nansi.o Nearly.o Number.o Obshead.o Oneline.o Opaccouls.o OpacHelium.o OpacHydrogen.o Opacit.o Opacmetals.o Opacscat.o Params.o Partfn.o Partnew.o Plotit.o Plotremember.o Pltabun.o Pltcog.o Pltflux.o Pltspec.o Pointcurs.o Prinfo.o Putasci.o Readobs.o Rinteg.o Setmols.o Smooth.o Specplot.o Stats.o Sunder.o Synpop.o Synspec.o Synth.o Tablepop.o Taukap.o Total.o Trudamp.o Ucalc.o Vargauss.o Vmacro.o Voigt.o Wavecalc.o Weedout.o Writenumber.o -o MOOGSILENT -Lfakelib -lX11 \
        -Lfakelib -lplotsub -ldevices -lutils
/usr/bin/ld: cannot find -lplotsub
/usr/bin/ld: cannot find -ldevices
/usr/bin/ld: cannot find -lutils
collect2: error: ld returned 1 exit status
make: *** [Makefile.rh64silent:47: MOOGSILENT] Error 1

I've played around a little with the Makefile and I'm pretty sure the missing libraries are associated with sm. i.e. if I remove -L$(SMLIB) -lplotsub -ldevices -lutils I get lots of errors of the form

/usr/bin/ld: Cogplot.f:(.text+0x5e3): undefined reference to `sm_ltype__'

I've spent some time trying to remove the files with the sm calls (mostly *plot.f) but I haven't managed to get anything working.

Support wavelength in nm

This should be quite easy to implement (*10 around the code), but very useful.

Error when having a negative flux

Fluxes shouldn't even be negative, but we are dealing with computers. I've got a case where two flux values in the summary.out file reads 0.000-0.000 without a space, and this gives an error.

Turbospectrum

I have never tried Turbospectrum but it is supposed to treat molecules better than MOOG. It would be nice to implement it. I have no idea of the format of the input data required. Any help appreciated.

Regarding Kurucz model support

Hi Maria, Daniel
I think you should bring back the support to Kurucz models (kurucz95 and more importantly kurucz08). Actually, it would be very useful to extend the support to alpha enhanced models. I understand that you are not allowed to post the atmosphere models, but that doesn't mean you are not allowed to support them, as many other programs (starting from MOOG itself) do. It was quite easy for me to download the models from the official website and format them as required by FASMA, so even if you don't provided them most of the users will still be happy of the support (even more if you provide a script to do the conversion).
Cheers

Configuration file

Hi Maria,

We need to write about the configurations available.
Either we just write it in the README.md or we add a small documentation. Better do it a bit fast since people will be looking for this.

Problem with launching FASMA

alex@alex-System-Product-Name:~/Downloads/FASMA-synthesis-master$ fasma
Traceback (most recent call last):
  File "/home/alex/.local/bin/fasma", line 12, in <module>
    driver = FASMA.FASMA(cfgfile=cfgfile, overwrite=None)
  File "/home/alex/.local/lib/python3.8/site-packages/FASMA/synthDriver.py", line 50, in __init__
    self.synthdriver()
  File "/home/alex/.local/lib/python3.8/site-packages/FASMA/synthDriver.py", line 526, in synthdriver
    for (self.initial, self.options) in self._genStar():
  File "/home/alex/.local/lib/python3.8/site-packages/FASMA/synthDriver.py", line 110, in _genStar
    with open(self.cfgfile, 'r') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'config.yml'

gooey

not able to install with debian