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Merge pull request #1110 from sirocco-rt/main
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Merge some changes that had been made in main only
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@jhmatthews
jhmatthews authored Oct 21, 2024
2 parents 8469061 + 614dbae commit b626ee7
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -11,7 +11,7 @@ Documentation is hosted on [ReadTheDocs](http://sirocco-rt.readthedocs.io/en/dev

[![C/C++ CI](https://github.com/sirocco-rt/sirocco/actions/workflows/build.yml/badge.svg)](https://github.com/sirocco-rt/sirocco/actions/workflows/build.yml)

[![Documentation Status](https://readthedocs.org/projects/agnwinds/badge/?version=latest)](https://agnwinds.readthedocs.io/en/latest/?badge=latest)
[![Documentation Status](https://readthedocs.org/projects/sirocco-rt/badge/?version=latest)](https://sirocco-rt.readthedocs.io/en/latest/?badge=latest)

## Installation

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2 changes: 2 additions & 0 deletions docs/pydocs/README.md
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Expand Up @@ -2,3 +2,5 @@ This directory contains help files created from doc strings from
python scripts in the py_progs directory.

To create the documentation yourself, simply run `write_docs.py`.

This procedure should be largely superseded by https://agnwinds.readthedocs.io/en/dev/py_progs.html but that page is not currently complete.
2 changes: 1 addition & 1 deletion docs/sphinx/requirements.txt
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Expand Up @@ -9,7 +9,7 @@ numpy
matplotlib
scipy
sqlalchemy
jinja2==3.0.3
jinja2==3.1.4
sphinx_gallery
pyhdf
sphinx-autoapi==3.1.1
55 changes: 28 additions & 27 deletions examples/basic/tde_standard.pf
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@@ -1,16 +1,16 @@
System_type(star,cv,bh,agn,previous) agn

### Parameters for the Central Object
Central_object.mass(msol) 3e7
Central_object.radius(cm) 2.65e13
Central_object.mass(msol) 3e6
Central_object.radius(cm) 2.65e12

### Parameters for the Disk (if there is one)
Disk.type(none,flat,vertically.extended) flat
Disk.type(none,flat,vertically.extended,rmin>central.obj.rad) flat
Disk.radiation(yes,no) yes
Disk.rad_type_to_make_wind(bb,models) bb
Disk.rad_type_to_make_wind(bb,models,mod_bb) bb
Disk.temperature.profile(standard,readin) standard
Disk.mdot(msol/yr) 0.01
Disk.radmax(cm) 1e15
Disk.mdot(msol/yr) 9.98e-03
Disk.radmax(cm) 1.00885e+14

### Parameters for Boundary Layer or the compact object in an X-ray Binary or AGN
Central_object.radiation(yes,no) no
Expand All @@ -24,52 +24,53 @@ Wind.dim.in.z_or_theta.direction 100

### Parameters associated with photon number, cycles,ionization and radiative transfer options
Photons_per_cycle 5e7
Ionization_cycles 15
Ionization_cycles 25
Spectrum_cycles 5
Wind.ionization(on.the.spot,ML93,LTE_tr,LTE_te,fixed,matrix_bb,matrix_pow,matrix_est) matrix_pow
Line_transfer(pure_abs,pure_scat,sing_scat,escape_prob,thermal_trapping,macro_atoms_escape_prob,macro_atoms_thermal_trapping) macro_atoms_thermal_trapping
Atomic_data data/h20_hetop_standard80.dat
Matom_transition_mode(mc_jumps,matrix) matrix
Surface.reflection.or.absorption(reflect,absorb,thermalized.rerad) reflect
Wind_heating.extra_processes(none,adiabatic,nonthermal,both) adiabatic
Atomic_data data/h20_hetop_standard80.dat

### Parameters for Domain 0
Wind.mdot(msol/yr) 0.01
Wind.mdot(msol/yr) 9.98e-03
SV.diskmin(units_of_rstar) 1
SV.diskmax(units_of_rstar) 30
SV.diskmax(units_of_rstar) 3.80699e+01
SV.thetamin(deg) 20
SV.thetamax(deg) 65
SV.mdot_r_exponent 0
SV.v_infinity(in_units_of_vescape 1
SV.acceleration_length(cm) 5e16
SV.acceleration_exponent 1.5
SV.mdot_r_exponent 2.0
SV.v_infinity(in_units_of_vescape 0.3
SV.acceleration_length(cm) 8.856670e+14
SV.acceleration_exponent 4.000000
SV.gamma(streamline_skew;1=usually) 1.0
SV.v_zero_mode(fixed,sound_speed) sound_speed
SV.v_zero(multiple_of_sound_speed) 1
Wind.radmax(cm) 5e17
Wind.t.init 40000
Wind.t.init 35000
Wind.filling_factor(1=smooth,<1=clumped) 0.1

### Parameters defining the spectra seen by observers

Disk.rad_type_in_final_spectrum(bb,models,uniform) bb
Disk.rad_type_in_final_spectrum(bb,models,uniform,mono,mod_bb) bb

### The minimum and maximum wavelengths in the final spectra
Spectrum.nwave 10000
Spectrum.wavemin(Angstroms) 100
Spectrum.wavemax(Angstroms) 10000
### The minimum and maximum wavelengths in the final spectra and the number of wavelength bins
Spectrum.nwave 10000
Spectrum.wavemin(Angstroms) 100
Spectrum.wavemax(Angstroms) 10000

### The observers and their location relative to the system
Spectrum.no_observers 5
Spectrum.angle(0=pole) 10
Spectrum.angle(0=pole) 35
Spectrum.angle(0=pole) 60
Spectrum.angle(0=pole) 75
Spectrum.angle(0=pole) 85
Spectrum.no_observers 5
Spectrum.angle(0=pole) 10
Spectrum.angle(0=pole) 35
Spectrum.angle(0=pole) 60
Spectrum.angle(0=pole) 75
Spectrum.angle(0=pole) 85
Spectrum.live_or_die(live.or.die,extract) extract
Spectrum.type(flambda,fnu,basic) flambda

### Parameters for Reverberation Modeling (if needed)
Reverb.type(none,photon,wind,matom) none

### Other parameters
Photon_sampling.approach(T_star,cv,yso,AGN,tde_bb,min_max_freq,user_bands,cloudy_test,wide,logarithmic) agn
Photon_sampling.approach(T_star,cv,yso,AGN,tde_bb,min_max_freq,user_bands,cloudy_test,wide,logarithmic) tde_bb
34 changes: 25 additions & 9 deletions source/rad_hydro_files.c
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Expand Up @@ -42,6 +42,8 @@
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <gsl/gsl_errno.h>


#include "atomic.h"
#include "sirocco.h"
Expand Down Expand Up @@ -143,7 +145,7 @@ main (argc, argv)

struct photon ptest; //We need a test photon structure in order to compute t

FILE *fptr_hc, *fptr_drive, *fptr_ion, *fptr_spec, *fptr_pcon, *fptr_debug, *fptr_flux, *fptr_flux_theta, *fptr_flux_phi, *fptr_flux_r, *fopen (); /*This is the file to communicate with zeus */
FILE *fptr_hc, *fptr_drive, *fptr_ion, *fptr_spec, *fptr_pcon, *fptr_debug, *fptr_flux, *fptr_flux_theta, *fptr_flux_phi, *fptr_flux_r, *fopen (); /*This is the file to communicate with zeus */
domain = geo.hydro_domain_number;

/* Initialize MPI, which is needed because some of the routines are MPI enabled */
Expand All @@ -166,7 +168,8 @@ main (argc, argv)

/* MPI intialiazation is complete */


/* Disable GSL error handling, so we can handle errors ourselves */
gsl_set_error_handler_off ();

strcpy (parameter_file, "NONE");

Expand All @@ -181,9 +184,13 @@ main (argc, argv)
strcat (windsavefile, ".wind_save");
strcat (outputfile, ".txt");


/* Read in the wind file */

/* Allocate memory required for domain, and read in the wind file */
zdom = calloc (MAX_DOM, sizeof (domain_dummy));
if (zdom == NULL)
{
Error ("Failed to allocate memory for domain\n");
return (EXIT_FAILURE);
}
if (wind_read (windsavefile) < 0)
{
Error ("swind: Could not open %s", windsavefile);
Expand Down Expand Up @@ -269,7 +276,7 @@ main (argc, argv)
}
else if (zdom[domain].coord_type == RTHETA)
{
fprintf (fptr_drive, "i j rcen thetacen vol rho ne F_vis_x F_vis_y F_vis_z F_vis_mod F_UV_theta F_UV_phi F_UV_r F_UV_mod F_Xray_x F_Xray_y F_Xray_z F_Xray_mod es_f_x es_f_y es_f_z es_f_mod bf_f_x bf_f_y bf_f_z bf_f_mod\n"); //directional flux by band
fprintf (fptr_drive, "i j rcen thetacen vol rho ne F_vis_x F_vis_y F_vis_z F_vis_mod F_UV_theta F_UV_phi F_UV_r F_UV_mod F_Xray_x F_Xray_y F_Xray_z F_Xray_mod es_f_x es_f_y es_f_z es_f_mod bf_f_x bf_f_y bf_f_z bf_f_mod\n"); //directional flux by band
fprintf (fptr_flux, "i j rcen thetacen F_vis_x F_vis_y F_vis_z F_vis_mod F_UV_x F_UV_y F_UV_z F_UV_mod F_Xray_x F_Xray_y F_Xray_z F_Xray_mod\n"); //directional flux by band
}

Expand Down Expand Up @@ -305,9 +312,18 @@ main (argc, argv)
nplasma = wmain[nwind].nplasma;
wind_n_to_ij (domain, plasmamain[nplasma].nwind, &i, &j);

fprintf (fptr_flux_theta, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
fprintf (fptr_flux_phi, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
fprintf (fptr_flux_r, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
if (zdom[domain].coord_type == SPHERICAL || zdom[domain].coord_type == RTHETA)
{
fprintf (fptr_flux_theta, "%3d %3d %3d %10.8e %10.8e ", i, j, wmain[nwind].inwind, wmain[nwind].rcen, wmain[nwind].thetacen / RADIAN); //output geometric things
fprintf (fptr_flux_phi, "%3d %3d %3d %10.8e %10.8e ", i, j, wmain[nwind].inwind, wmain[nwind].rcen, wmain[nwind].thetacen / RADIAN); //output geometric things
fprintf (fptr_flux_r, "%3d %3d %3d %10.8e %10.8e ", i, j, wmain[nwind].inwind, wmain[nwind].rcen, wmain[nwind].thetacen / RADIAN); //output geometric things
}
else if (zdom[domain].coord_type == CYLIND)
{
fprintf (fptr_flux_theta, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
fprintf (fptr_flux_phi, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
fprintf (fptr_flux_r, "%3d %3d %3d %10.3e %10.3e ", i, j, wmain[nwind].inwind, wmain[nwind].xcen[0], wmain[nwind].xcen[2]); //output geometric things
}
for (ii = 0; ii < NFLUX_ANGLES; ii++)
{
fprintf (fptr_flux_theta, "%10.3e ", plasmamain[nplasma].F_UV_ang_theta_persist[ii]);
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