further documentation updates to catch renames

docs/sphinx/source/atomic/bound_bound.rst

@@ -24,7 +24,7 @@ We have also used a line list from Verner in the past
 
 Translation to SIROCCO format
 ============================
-There are several steps to creating the data used in SIROCCO from that in gfall.dat, that are carried out by py_read_kurucz and py_link. The first routine reads the gfall.dat file and creates two output files, a file containing the lines and the associated such as the effective oscillatory strength and a file which contains information about the ion levels.  py_read_kurucz chooses only a portion of the Kurucz lines, namely those associated with ions with ionization potentials in a certain range and lines with gf factors exceeding a certain value. The second program py_link attempts to create a model ion with links between the levels and the ions.  Both of these routines are driven by .pf files, similar to what are used in python.  Examples of the .pf files are in the directory py_kurucz
+There are several steps to creating the data used in SIROCCO from that in gfall.dat, that are carried out by py_read_kurucz and py_link. The first routine reads the gfall.dat file and creates two output files, a file containing the lines and the associated such as the effective oscillatory strength and a file which contains information about the ion levels.  py_read_kurucz chooses only a portion of the Kurucz lines, namely those associated with ions with ionization potentials in a certain range and lines with gf factors exceeding a certain value. The second program py_link attempts to create a model ion with links between the levels and the ions.  Both of these routines are driven by .pf files, similar to what are used in SIROCCO.  Examples of the .pf files are in the directory py_kurucz
 
 In practice we have not used these data for any SIROCCO publications. At some point early in the AGN project, NSH increased the number of lines, and generated lines\_linked\_ver\_2.dat and levels\_ver\_2.dat. I think this was because there was a small bug which meant the oscillator strength cut that was stated was not that which was applied.
 
@@ -75,6 +75,6 @@ Line data is stored in the data structure **lines**
 
 Comments
 ========
-The version of gfall.dat that is used in SIROCCO is out of date, though whether this affects any of the lines actually used in python is unclear.  The website listed above has a link to newer versions of gfall.dat.
+The version of gfall.dat that is used in SIROCCO is out of date, though whether this affects any of the lines actually used in SIROCCO is unclear.  The website listed above has a link to newer versions of gfall.dat.
 
 

docs/sphinx/source/atomic/bound_free_topbase.rst

@@ -119,6 +119,6 @@ This is the shape of a hydrogenic cross-section and whilst it is not accurate
 for non-hydrogenic ions, it is more realistic (and conservative) than some of 
 the unphysically shallow gradients that were being found.
 This is also briefly described in section~3.7.2 of Matthews PhD thesis.
-The python scripts can be found in the `data-gen <https://github.com/agnwinds/data-gen>`_ repository progs/extrapolate\_xs/ 
+The python scripts can be found in the `data-gen <https://github.com/sirocco-rt/data-gen>`_ repository progs/extrapolate\_xs/ 
 with docstrings describing their use.
 

docs/sphinx/source/atomic/electron_yields.rst

@@ -38,7 +38,7 @@ The data is linked to the correct inner shell photoionization cross section (and
 SIROCCO structure
 ================
 
-The data is stored in python in the inner_elec_yield structure which contains
+The data is stored in SIROCCO in the inner_elec_yield structure which contains
 
 - int nion - Index to the ion which was the parent of the inner shell ionization
 - int z, istate - element and ionization state of parent ion

docs/sphinx/source/atomic/elem_ions.rst

@@ -10,7 +10,7 @@ This data comes from `Verner, Barthel & Tytler, 1994, ApJ 108, 287. <http://arti
 
 
 
-Translation to python:
+Translation to SIROCCO:
 ======================
 
 The original data and the translation can be found in py\_verner.  A simple awkscript converts the downloaded data to SIROCCO format.

docs/sphinx/source/atomic/free-free.rst

@@ -14,13 +14,13 @@ The free-free Gaunt factors are taken from  `Sutherland 1998, MNRAS, 300, 321. <
 
 The last file is the one we use to calculate free-free emission, since this in integrated gaunt factor over a population of electrons  with a Boltzmann distribution of velocities.  The other two files could be of use in the future should we wish to have gaunt factor corrections for the heating rates,in which case we should use the gffgu.dat data file. However generally speaking free-free heating is never important and there would be significant overhead in calculating a gaunt factor for each photon.
 
-Translation to python
+Translation to SIROCCO
 =====================
 The file is simply modified by hand to put a label "FF\_GAUNT" at the start of each data line and a hash at the start of each comment line.
 
 Datafile - gffint.dat:
 ======================
-The format of the data file to be read into python is as follows:
+The format of the data file to be read into SIROCCO is as follows:
 
 +----------+------------------------+---------------------------+-----------+-----------+-----------+
 |Label     | :math:`\log(\gamma^2)` |:math:`<g_{ff}(\gamma^2)>` |:math:`s_1`|:math:`s_2`|:math:`s_3`|

docs/sphinx/source/atomic/levels.rst

@@ -13,7 +13,7 @@ Level information can be derived from a variety of sources, by:
    * more commonly, for data abstracted from TopBase or Chianti
 
 
-Translation to python:
+Translation to SIROCCO:
 ======================
 
 
@@ -83,7 +83,7 @@ between ions, and so it includes the ionization energy of the lower level ioniza
 Note that the radiative rates are not used. The original intention was to use this to define the 
 difference between metastable and normal levels, with the expectation that if the level was metastable it 
 would be put in Boltzmann equilibrium with the ground state. 
-Right now python uses :math:`10^{15}` seconds, essentially a Hubble time to do this, but this portion of the 
+Right now SIROCCO uses :math:`10^{15}` seconds, essentially a Hubble time to do this, but this portion of the 
 code is not, according to ss, tested. 
 
 The primary source for this is usually the NIST database, although similar information is usually available in Chianti. 

docs/sphinx/source/atomic/photon_yields.rst

@@ -37,7 +37,7 @@ The data is linked to the correct inner shell photoionization cross section (and
 SIROCCO structure
 ================
 
-The data is stored in python in the inner_fluor_yield structure which contains
+The data is stored in SIROCCO in the inner_fluor_yield structure which contains
 
 
 - int nion - Index to the ion which was the parent of the inner shell ionization

docs/sphinx/source/developer/cuda.rst

@@ -241,7 +241,7 @@ The following code exert is an example of using the wrapper function to solve a
 .. code:: c
     :caption: The API to solve a linear system hasn't changed
 
-    #include "python.h"
+    #include "sirocco.h"
 
     double *populations = malloc(nions * sizeof(*populations));
     double *ion_density = malloc(nions * sizeof(*populations));
@@ -269,7 +269,7 @@ Here is an example of using a similar wrapper function to calculate the inverse
 .. code:: c
     :caption: The API has changed slightly for calculating the inverse, now that it has a wrapper function
 
-    #include "python.h"
+    #include "sirocco.h"
 
     double Q_matrix = malloc(matrix_size * matrix_size * sizeof(double));
     double Q_inverse = malloc(matrix_size * matrix_size * sizeof(double));
@@ -383,7 +383,7 @@ The steps for compiling and link GPU and CPU code are outlined below in pseudo-M
     $(CC) $(C_FLAGS) $(C_SOURCE) -c -o $(C_OBJECTS)
 
     # Link the CUDA and C object code and libraries together using the C compiler
-    $(CC) $(CUDA_OBJECTS) $(C_OBJECTS) -o python $(CUDA_LIBS) $(C_LIBS)
+    $(CC) $(CUDA_OBJECTS) $(C_OBJECTS) -o sirocco $(CUDA_LIBS) $(C_LIBS)
 
 These steps are effectively replicated in the Makefile :code:`$SIROCCO/source/Makefile`, where a deconstructed example is
 shown below.
@@ -409,8 +409,8 @@ shown below.
     endif
 
     # So to compile SIROCCO, we have something which looks vaguely like this. Note that
-    # we use the CUDA_OBJECTS recipe as a requirement for the python recipe. This CUSOLVER_STATUS_SUCCESS
+    # we use the CUDA_OBJECTS recipe as a requirement for the sirocco recipe. This CUSOLVER_STATUS_SUCCESS
     # the CUDA source to be compiled to object code *if* NVCC is defined
-    python: startup python.o $(python_objects) $(CUDA_OBJECTS)
-        $(CC) $(CFLAGS) python.o $(python_objects) $(CUDA_OBJECTS) $(kpar_objects) $(LDFLAGS) -o python
+   sirocco: startup sirocco.o $(sirocco_objects) $(CUDA_OBJECTS)
+        $(CC) $(CFLAGS) sirocco.o $(sirocco_objects) $(CUDA_OBJECTS) $(kpar_objects) $(LDFLAGS) -o sirocco
 

docs/sphinx/source/developer/programmer_notes.rst

@@ -30,7 +30,7 @@ The main header files  are:
   strengths, photoionization cross-sections, elemental abundances, etc.  These data are
   read in at the beginning of the program (see atomicdata.c and other similarly named
   routines)
-* python.h - This contains the structures and other data that comprise the wind as well
+* sirocco.h - This contains the structures and other data that comprise the wind as well
   as the parameters of the model.  (This is fairly well-documented, or should be)
 
 
@@ -94,7 +94,7 @@ The portions of the routine that are parallelize are:
   the radiative transfer step in the detailed spectrum phase.
 
 
-MPI requires intialization. For python this is carried out in python.c.  Various subroutines make
+MPI requires intialization. For SIROCCO this is carried out in sirocco.c.  Various subroutines make
 use of MPI, and as a result, programmers need to be aware of this fact when they write auxiliary
 routines that use the various subroutines called by SIROCCO.
 
@@ -128,13 +128,13 @@ In the latest generations of gcc,  the standards for extenral variiables have be
 If one wishes to define an external variable, one must first declare it as eternal, and then one
 must initialize it outside a specific routine exactly in one place.
 
-The standard convention is that the variables are declared as external in a header file, e.g python.h,
-and then intialized in a separate .c file, e.g python_extern_init.c.   Unless, a variable is actually
+The standard convention is that the variables are declared as external in a header file, e.g sirocco.h,
+and then intialized in a separate .c file, e.g sirocco_extern_init.c.   Unless, a variable is actually
 initialized, no space will be allocated for the variable.
 
 So if variables are added (or subtracted), one must make a change both in the relavant .h file.
 
-Currently has three.c files atomic_extern_init.c, models_extern_init.c, python_extern_init.c
-corresponding to the three main .h files, atommic.h, models.h and python.h
+Currently has three.c files atomic_extern_init.c, models_extern_init.c, sirocco_extern_init.c
+corresponding to the three main .h files, atommic.h, models.h and sirocco.h
 
 

docs/sphinx/source/developer/tests.rst

@@ -151,16 +151,16 @@ implementation. If you need to create your own assertion, these should be kept i
     }
 
 
-.. admonition:: Including :code:`python.h` in your tests
+.. admonition:: Including :code:`sirocco.h` in your tests
 
-    If you need to access various structures or other things defined in :code:`python.h`, it is possible to include
+    If you need to access various structures or other things defined in :code:`sirocco.h`, it is possible to include
     the header file in your test source code as in the example below (there are some data structures which depend
     on values defined in :code:`atomic.h`),
 
     .. code:: c
 
         #include "../../atomic.h"
-        #include "../../python.h"
+        #include "../../sirocco.h"
 
     In some situations this might complicate compilation of the unit test. In those cases, it could be better to
     re-define anything you need in the source file for the unit test.

docs/sphinx/source/input.rst

@@ -3,7 +3,7 @@ Inputs
 
 A comprehensive section and lists of all possible parameter inputs for various models.
 
-**Overview** describes how python uses keywords for a .pf parameter file and how a user can create their own parameter files.
+**Overview** describes how SIROCCO uses keywords for a .pf parameter file and how a user can create their own parameter files.
 
 **System Description** describes the initial system parameters for a model with an example to indicate what .pf output looks like. 
 

docs/sphinx/source/input/parameters/Disk/Disk.T_profile_file.rst

@@ -8,7 +8,7 @@ Type
   String
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.colour_correction.rst

@@ -11,7 +11,7 @@ Values
 
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.mdot.rst

@@ -9,7 +9,7 @@ Unit
   :math:`M_{\odot}/yr`
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.rad_type_in_final_spectrum.rst

@@ -17,7 +17,7 @@ Values
 
 
 File
-  `python.c <https://github.com/agnwinds/python/blob/master/source/python.c>`_
+  `sirocco.c <https://github.com/sirocco-rt/sirocco/blob/master/source/sirocco.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.rad_type_to_make_wind.rst

@@ -17,7 +17,7 @@ Values
 
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.radiation.rst

@@ -6,7 +6,7 @@ Type
   Boolean(yes/no)
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.radmax.rst

@@ -14,7 +14,7 @@ Values
   Greater than 0
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.radmin.rst

@@ -13,7 +13,7 @@ Values
   Equal to or greater than :ref:`Central_object.radius`.
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 Parent(s)
   * :ref:`Disk.type`: :code:`rmin>central.obj.rad`

docs/sphinx/source/input/parameters/Disk/Disk.temperature.profile.rst

@@ -14,7 +14,7 @@ Values
 
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.type.rst

@@ -17,7 +17,7 @@ Values
 
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Child(ren)

docs/sphinx/source/input/parameters/Disk/Disk.z0.rst

@@ -10,7 +10,7 @@ Values
   Greater than 0
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Disk/Disk.z1.rst

@@ -11,7 +11,7 @@ Values
   Greater than 0
 
 File
-  `setup_disk.c <https://github.com/agnwinds/python/blob/master/source/setup_disk.c>`_
+  `setup_disk.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup_disk.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Input_spectra.model_file.rst

@@ -12,7 +12,7 @@ Type
   String
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.angle.rst

@@ -14,7 +14,7 @@ Values
   0 to 90 degrees, where 0 is normal to the disk and 90 is on the disk plane
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.live_or_die.rst

@@ -24,7 +24,7 @@ Values
 
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.no_observers.rst

@@ -10,7 +10,7 @@ Values
   Greater than 0
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.nwave.rst

@@ -10,7 +10,7 @@ Values
   Greater than 100
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 Parent(s)
   * :ref:`Spectrum_cycles`: Greater than or equal to 0

docs/sphinx/source/input/parameters/Spectrum/Spectrum.orbit_phase.rst

@@ -14,7 +14,7 @@ Values
   Between 0 and 1
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.select_azimuth.rst

@@ -16,7 +16,7 @@ Values
   Between 0, and 360 or -180 to 180
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.select_location.rst

@@ -23,7 +23,7 @@ Values
 
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.select_photons_by_position.rst

@@ -19,7 +19,7 @@ Type
   Boolean (yes/no)
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.select_r.rst

@@ -13,7 +13,7 @@ Values
   Greater than 0
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)

docs/sphinx/source/input/parameters/Spectrum/Spectrum.select_rho.rst

@@ -16,7 +16,7 @@ Values
   Condition e.g. greater than 0 or list e.g. [1, 2, 5]
 
 File
-  `setup.c <https://github.com/agnwinds/python/blob/master/source/setup.c>`_
+  `setup.c <https://github.com/sirocco-rt/sirocco/blob/master/source/setup.c>`_
 
 
 Parent(s)