### Install ExoPlaSim via pip

Source: https://exoplasim.readthedocs.io/en/latest/_sources/index.rst.txt

Standard installation command for the ExoPlaSim package.

```bash
pip install exoplasim
```

--------------------------------

### Install ExoPlaSim in a Conda environment

Source: https://exoplasim.readthedocs.io/en/latest/_sources/index.rst.txt

Recommended installation workflow using conda-forge for compiler dependencies and OpenMPI.

```bash
conda install -c conda-forge gcc gxx gfortran "openmpi<5.0.1" python
pip install exoplasim
python -c "import exoplasim; exoplasim.sysconfigure()"
```

--------------------------------

### Install ExoPlaSim with netCDF and HDF5 support

Source: https://exoplasim.readthedocs.io/en/latest/postprocessor.html

Use this command to ensure the necessary dependencies for netCDF and HDF5 output formats are installed.

```bash
pip install exoplasim[netCDF4,HDF5]
```

--------------------------------

### Configure and Initialize ExoPlaSim Environment

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

Handles system-level configuration, including Python version-specific setup and marking the first run of the application.

```python
sysconfigure()
#compile_pyfft() #This will be called from sysconfigure()
os.system(f"touch {sourcedir}/firstrun")
```

--------------------------------

### Instantiate an ExoPlaSim Model

Source: https://exoplasim.readthedocs.io/en/latest/_sources/tutorial.rst.txt

Initialize the model instance with a working directory, resolution, and output format. Ensure the specified output format dependencies like netCDF4 or h5py are installed if using formats other than .npz.

```python
import exoplasim as exo
toi700d = exo.Model(workdir="toi700d_run",modelname="TOI-700d",
                    ncpus=4,resolution="T21",outputtype=".npz")
```

--------------------------------

### exoplasim.printsysconfig

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Prints the system configuration file generated on the first installation of ExoPlaSim.

```APIDOC
## exoplasim.printsysconfig(ncpus=4)

### Description
Print the system configuration file ExoPlaSim generated on its first installation.

### Parameters
- **ncpus** (int, optional) - Number of cores you want to use. The configuration differs for single-core vs parallel execution.

### Returns
- **dict** - The contents of the configuration file as a dictionary.
```

--------------------------------

### Test NetCDF library installation

Source: https://exoplasim.readthedocs.io/en/latest/_sources/index.rst.txt

Run this command in the run folder to check for missing linked objects related to NetCDF.

```bash
./burn7.x -n<example.nl>burnout MOST.00000 MOST.00000.nc
```

--------------------------------

### Print System Configuration

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

Retrieves and displays the system configuration file generated during installation. Requires specifying the number of CPUs to select between single-core and parallel configurations.

```python
def printsysconfig(ncpus=4):
    '''Print the system configuration file ExoPlaSim generated on its first installation.
    
    Parameters
    ----------
    ncpus : int, optional
        Number of cores you want to use. The configuration differs for single-core vs 
        parallel execution, so make sure you are checking the correct configuration.
        
    Returns
    -------
    dict
        The contents of the configuration file as a dictionary
    '''
    
    sourcedir = "/".join(__file__.split("/")[:-1]) #Get the absolute path for the module
    if ncpus==1:
        if not os.path.exists(sourcedir+"/most_compiler"):
            raise Exception("""ExoPlaSim has not yet been configured. Please configure it by
instantiating a Model or running exoplasim.sysconfigure().""")
        with open(sourcedir+"/most_compiler") as f:
            result = f.read()
    else:
        if not os.path.exists(sourcedir+"/most_compiler_mpi"):
            raise Exception("""ExoPlaSim has not yet been configured. Please configure it by
instantiating a Model or running exoplasim.sysconfigure().""")
        with open(sourcedir+"/most_compiler_mpi") as f:
            result = f.read()
            
    print(result)
    config = {}
    result = result.split('\n')
    for line in result:
        if '=' in line:
            setting = line.split('=')
            config[setting[0]] = setting[1]
    return config
```

--------------------------------

### Initialize and run an ExoPlaSim model

Source: https://exoplasim.readthedocs.io/en/latest/_sources/index.rst.txt

Demonstrates the standard workflow of creating a model instance, configuring it, exporting settings, running the simulation, and finalizing output.

```python
import exoplasim as exo
mymodel = exo.Model(workdir="mymodel_testrun",modelname="mymodel",resolution="T21",layers=10,ncpus=8)
mymodel.configure()
mymodel.exportcfg()
mymodel.run(years=100,crashifbroken=True)
mymodel.finalize("mymodel_output")
```

--------------------------------

### Configure physics filters

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Examples of specifying physics filters using the physicsfilter parameter.

```python
physicsfilter="gp|exp|sp"
```

```python
physicsfilter="gp|cesaro"
```

--------------------------------

### Define Other Arguments

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Example format for passing custom namelist parameters via the otherargs dictionary.

```python
otherargs={"N_RUN_MONTHS@plasim_namelist":'4',"NGUI@plasim_namelist:'1'}
```

--------------------------------

### get(year, snapshot=False, highcadence=False)

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Retrieves an open NetCDF data object for a specific year.

```APIDOC
## get(year, snapshot=False, highcadence=False)

### Description
Return an open NetCDF data object for the given year. Defaults to returning time-averaged output.

### Parameters
- **year** (int) - Required - Integer year of output to return.
- **snapshot** (bool) - Optional - If True, return the snapshot version.
- **highcadence** (bool) - Optional - If True, return the high-cadence version.

### Returns
- **netCDF4.Dataset** - An open netCDF4 data object.
```

--------------------------------

### Initialize pRT Atmosphere and Configure Simulation

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/pRT.html

Sets up the Radtrans object with species, opacities, and scattering parameters, and performs initial physical constant and stellar spectrum calculations.

```python
_log(logfile,"===================================")
_log(logfile,"| ExoPlaSim->petitRADTRANS Engine |")
_log(logfile,"|   v1.0, Adiv Paradise (c) 2021  |")
_log(logfile,"===================================")
_log(logfile,"
")
_log(logfile,"-------------Direct Imager----------")
_log(logfile,"
")

#Compute zenith angle from czen
#Figure out how to output spectra
#Get surface type from model output
#Turn off reflection for night-time grid cells

gravity *= 100.0 #SI->CGS

atmosphere = Radtrans(line_species = ['H2O_'+h2o_lines,
                                      'CO2',
                                      'O3'],
                      rayleigh_species = ['N2', 'O2', 'CO2', 'H2', 'He'],
                      continuum_opacities = ['N2-N2', 'N2-O2','O2-O2',
                                             'CO2-CO2','H2-H2','H2-He'],
                      wlen_bords_micron = [0.3, 20],
                      do_scat_emis = True,
                      cloud_species = ['H2O(c)_cd'],)

if cloudfunc is None:
    cloudfunc = basicclouds

planckh =  6.62607015e-34
boltzk = 1.380649e-23
cc = 2.99792458e8

if stellarspec is None:
    SIwvl = spec.wvl*1.0e-6 #um->m
    stellarspec = 1.0e-6 * 2*planckh*cc**2/SIwvl**5    \
                  /(np.exp(planckh*cc/(SIwvl*boltzk*Tstar))-1)
    # W sr-1 m-2 um-1
```

--------------------------------

### Verify system configuration

Source: https://exoplasim.readthedocs.io/en/latest/_sources/index.rst.txt

Use these commands to print and return the execution configuration files for single-core and parallel runs.

```python
exoplasim.printsysconfig(ncpus=1)
exoplasim.printsysconfig(ncpus=2)
```

--------------------------------

### exoplasim.compile_pyfft()

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Compiles or recompiles the pyfft libraries required for ExoPlaSim. This operation requires meson, ninja, gfortran, and gcc to be installed on the system.

```APIDOC
## exoplasim.compile_pyfft()

### Description
Compile or recompile the pyfft libraries. Requires meson, ninja, gfortran, and gcc.
```

--------------------------------

### Initialize ExoPlaSim Model

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

The __init__ method configures the model environment, including resolution, hardware settings, and compilation flags.

```python
"""
def __init__(self,resolution="T21",layers=10,ncpus=4,precision=8,debug=False,inityear=0,
            recompile=False,optimization=None,mars=False,workdir="most",source=None,force991=False,
            modelname="MOST_EXP",outputtype=".npz",crashtolerant=False,outputfaulttolerant=False,
            hyperthreading=True,mpi_opts=None):
    
    global sourcedir
    
    #self.burn7 = burn7
    self.mars = mars
    
    self.extension = outputtype
    self.extensions = {"regular"     : self.extension,
                       "snapshot"    : self.extension,
                       "highcadence" : self.extension}
    self._configuredpostprocessor = {"regular":False,"snapshot":False,"highcadence":False}
    
    self.postprocessordefaults = {"regular"     : {},
                                  "snapshot"    : {"times":None,"timeaverage":False,"stdev":False},
                                  "highcadence" : {"times":None,"timeaverage":False,"stdev":False}}
    self.postprocessorcfgs = {"regular":{},"snapshot":{},"highcadence":{}}
    self.pRTopts = {}
    for ftype in ['regular','snapshot','highcadence']:
        self.pRTopts[ftype] = {"transit":False,
                               "image":False,
                               "h2o_linelist" : 'Exomol',
                               "cloudfunc":None,
                               "smooth":False,
                               "smoothweight": 0.95}
                    
    self.crashtolerant = crashtolerant
    self.outputfaulttolerant = outputfaulttolerant
    
    if self.extension not in pyburn.SUPPORTED:
        raise Exception("Unsupported output format detected. Supported formats are:\n\t\n\t%s"%("\n\t".join(pyburn.SUPPORTED)))
    
    sourcedir = "/".join(__file__.split("/")[:-1]) #Get the absolute path for the module
    
    if not os.path.isfile(sourcedir+"/firstrun") or not os.path.isfile(sourcedir+"/most_compiler")\
        or not os.path.isfile(sourcedir+"/most_compiler_mpi"): #This means we haven't run yet, and have some post-install work to do
        recompile=True
        #os.system('spth=$(python%s -c "import exoplasim as exo; print(exo.__path__)") && echo $spth>sourcepath'%sys.version[0])
        #with open("sourcepath","r") as spf:
            #sourcedir = spf.read().strip()
            #if sourcedir[0]=="[":
                #sourcedir=sourcedir[1:]
            #if sourcedir[-1]=="]":
                #sourcedir=sourcedir[:-1]
            #if sourcedir[0]=="'":
                #sourcedir=sourcedir[1:]
            #if sourcedir[-1]=="'":
                #sourcedir=sourcedir[:-1]
        #os.system("rm sourcepath")
        #with open("%s/__init__.py"%sourcedir,"r") as sourcef:
            #sourcecode = sourcef.read().split('\n')
        #sourcecode[2] = 'sourcedir = "%s"'%sourcedir
        #sourcecode = '\n'.join(sourcecode)
        #os.system("cp %s/__init__.py %s/preinit.py"%(sourcedir,sourcedir))
        #try:
            ##with open("%s/__init__.py"%sourcedir,"w") as sourcef:
                ##sourcef.write(sourcecode)
            #cwd = os.getcwd()
            #os.chdir(sourcedir)
            #pyversion = ".".join(sys.version.split(".")[:2])
            #for pyfftfile in glob.glob(os.path.join(sourcedir,"pyfft*.so")):
                #os.remove(pyfftfile)
```

--------------------------------

### exoplasim.Earthlike.__init__

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Initializes a new Earth-like model instance with specified resolution, layers, and performance settings.

```APIDOC
## class exoplasim.Earthlike

### Description
Creates an Earth-like model instance. This class inherits from Model and provides default configurations suitable for Earth-like simulations.

### Parameters
- **resolution** (str) - Optional - Model resolution (default 'T21').
- **layers** (int) - Optional - Number of vertical layers (default 10).
- **ncpus** (int) - Optional - Number of CPUs to use (default 4).
- **precision** (int) - Optional - Precision setting (default 8).
- **debug** (bool) - Optional - Enable debug mode (default False).
- **inityear** (int) - Optional - Initial year (default 0).
- **recompile** (bool) - Optional - Force recompile (default False).
- **optimization** (str) - Optional - Optimization level.
- **mars** (bool) - Optional - Enable Mars-like configuration (default False).
- **workdir** (str) - Optional - Working directory (default 'most').
- **source** (str) - Optional - Source path.
- **force991** (bool) - Optional - Force 991 compatibility (default False).
- **modelname** (str) - Optional - Name of the model (default 'MOST_EXP').
- **outputtype** (str) - Optional - Output file format (default '.npz').
- **crashtolerant** (bool) - Optional - Enable crash tolerance (default False).
- **outputfaulttolerant** (bool) - Optional - Enable output fault tolerance (default False).
- **hyperthreading** (bool) - Optional - Enable hyperthreading (default True).
- **mpi_opts** (str) - Optional - MPI options.
```

--------------------------------

### Parse Configuration and Initialize Dataset

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/pyburn.html

Parses input arguments to configure physical parameters like radius, gravity, and gas constants before initializing the dataset object.

```python
                    elif int(arg)==2:
                        stdev = True
                    elif int(arg)==3:
                        timeaverage=True
                        stdev = True
                elif key=="radius" or key=="RADIUS":
                    radius = float(arg)/6371220.0      #Radii in the namelist are given in metres
                elif key=="gravity" or key=="GRAVITY":
                    gravity = float(arg)
                elif (key=="mars" or key=="MARS") and int(arg)==1:
                    gravity = MARS_GRAV
                    radius  = MARS_RADIUS/6371220.0    #We want to start off with radii in Earth radii
                    gascon  = MARS_RD      #This is called RD in burn7, not gascon
        data = dataset(rawfile, variables, mode=mode,radius=radius,gravity=gravity,gascon=gascon, 
                       zonal=zonal, substellarlon=substellarlon, physfilter=physfilter,logfile=logfile)
```

--------------------------------

### Rerun ExoPlaSim system configuration

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

Use this function to re-run the configuration script if compilers or libraries have changed, or if the initial setup failed.

```python
def sysconfigure():
    '''Rerun the ExoPlaSim system configuration script.
    
    If compilers/libraries have changed since you first configured ExoPlaSim,
    or the initial configuration failed, you should call this function.
    '''
    
    sourcedir = "/".join(__file__.split("/")[:-1]) #Get the absolute path for the module
     
    try:
        cwd = os.getcwd()
        os.chdir(sourcedir)
        pyversion = ".".join(sys.version.split(".")[:2])
        #for pyfftfile in glob.glob(os.path.join(sourcedir,"pyfft*.so")):
            #os.remove(pyfftfile)
        if float(pyversion)>=3.5 and float(pyversion)<3.7:
            print("./configure -v %s"%(pyversion))
            result = subprocess.run(["./configure.sh -v %s"%(pyversion)],shell=True,check=True,
                                    stdout=subprocess.PIPE,stderr=subprocess.PIPE,
                                    universal_newlines=True)
            print(result.stdout)
            print(result.stderr)
        elif float(pyversion)>=3.7:
            print("./configure -v %s"%(pyversion))
            result = subprocess.run(["./configure.sh -v %s"%(pyversion)],shell=True,check=True,
                            capture_output=True,universal_newlines=True)
            print(result.stdout)
            print(result.stderr)
        elif float(pyversion)<3.5 and float(pyversion)>=3.0:
            print("./configure -v %s"%(pyversion))
            os.system("./configure.sh -v %s"%(pyversion))
            result=""
        else:
            print("./configure -v 3")
            os.system("./configure.sh -v 3")
            result=""
            
        if not os.path.isfile(sourcedir+"/firstrun") :
            os.system(f"touch {sourcedir}/firstrun")
            compile_pyfft()
            
        #import numpy.f2py
        #with open("pyfft.f90","r") as pyfft_file:
            #pyfft_source = pyfft_file.read()
        #failed = pyburn.f2py_compile(pyfft_source,modulename='pyfft',
                                    #extra_args='--f90exec=gfortran --f77exec=gfortran --f90flags="-O3"',
                                    #extension='.f90')
        #if failed!=0:
            #print(failed)
            ##raise Exception("Encountered an error in pyfft compilation with f2py.... please ensure gfortran is installed and configured correctly.")
        
        #with open("pyfft991.f90","r") as pyfft991_file:
            #pyfft991_source = pyfft991_file.read()
        #failed = pyburn.f2py_compile(pyfft991_source,modulename='pyfft991',
                                    #extra_args='--f90exec=gfortran --f77exec=gfortran --f90flags="-O3"',
                                    #extension='.f90')
        #if failed!=0:
            #print(failed)
            #raise Exception("Encountered an error in pyfft991 compilation with f2py.... please ensure gfortran is installed and configured correctly.")
            
        #if self.burn7:
            #os.system("nc-config --version > ncversion.tmp")
            #with open("ncversion.tmp","r") as ncftmpf:
                #version = float('.'.join(ncftmpf.read().split()[1].split('.')[:2]))
            #if version>4.2:
                #os.system("cd postprocessor && ./build_init.sh || ./build_init_compatibility.sh")
            #else:
                #os.system("cd postprocessor && rm burn7.x && make")
            #os.chdir(cwd)
            #os.system("touch %s/postprocessor/netcdfbuilt"%sourcedir)
        os.chdir(cwd)
    except PermissionError:
        raise PermissionError("\nHi! Welcome to ExoPlaSim. It looks like this is the first "+
                            "time you're using this program since installing, and you "+
                            "may have installed it to a location that needs root "+
                            "privileges to modify. This is not ideal! If you want to "+
                            "use the program this way, you will need to run python code"+
                            " that uses ExoPlaSim with sudo privileges; i.e. sudo "+
                            "python3 myscript.py. If you did this because pip install "+
                            "breaks without sudo privileges, then try using \n\n\tpip "+ "install --user exoplasim \n\ninstead. It is generally a "+
                                "very bad idea to install things with sudo pip install.")
    except Exception as e:
        print(result.stderr)
        raise e
```

--------------------------------

### Configure Atmospheric and Simulation Parameters

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

This block manages the initialization of atmospheric gas pressures, calculates the mean molecular weight, and updates the corresponding Fortran namelists for the simulation.

```python
            self._edit_namelist("aero_namelist","l_aerorad",str(self.aerorad*1))
            self._edit_namelist("aero_namelist","aerofile","'%s.dat'"%aerofile)
            aerofile+=".dat"
        self.aerofile = aerofile
        
        if pH2:
            self.pgases["pH2"]=pH2
        if pHe:
            self.pgases["pHe"]=pHe
        if pN2:
            self.pgases["pN2"]=pN2
        if pO2:
            self.pgases["pO2"]=pO2
        if pCO2:
            self.pgases["pCO2"]=pCO2
        if pAr:
            self.pgases["pAr"]=pAr
        if pNe:
            self.pgases["pNe"]=pNe
        if pKr:
            self.pgases["pKr"]=pKr
        if pH2O:
            self.pgases["pH2O"]=pH2O
        if pCH4:
            self.pgases["pCH4"]=pCH4
        
        if len(self.pgases)==0:
            if not pressure:
                #self.pgases=gases_default
                #self.pressure=0.0
                #for gas in self.pgases:
                    #self.pressure+=self.pgases[gas] #in bars
                if self.mars:
                    self.pressure = 6.36e-3
                else:
                    self.pressure = 1.011
            else:
                self.pressure = pressure
        
        else:
            self.pressure=0.0
            for gas in self.pgases:
                self.pressure+=self.pgases[gas]
        
        gasesvx = {}
        for gas in self.pgases:
            gasesvx[gas[1:]] = self.pgases[gas]/self.pressure
        self.mmw = 0
        for gas in gasesvx:
            self.mmw += gasesvx[gas]*smws['m'+gas]
        if self.mmw==0:
            if self.mars:
                self.mmw = MARS_MMW #43.991866
            else:
                self.mmw = 28.970253
        self.gascon = 8314.46261815324 / self.mmw
        
        if gascon:
            self.gascon=gascon
            self.mmw = 8314.46261815324/self.gascon
        
        print('Mean Molecular Weight set to %1.4f g/mol'%self.mmw)
        
        if pressure:
            if pressure != self.pressure:  #User has specified a different pressure than sum of gas pressures
                self.pressure = pressure
        
        self.CO2ppmv = 300.0
        if 'pCO2' in self.pgases:
            self.CO2ppmv = self.pgases['pCO2']/self.pressure * 1.0e6 #ppmv
        
        self._edit_namelist("radmod_namelist","CO2",str(self.CO2ppmv))
        self._edit_namelist("plasim_namelist","PSURF",str(self.pressure*1.0e5)) #Pa
        self._edit_namelist("planet_namelist","GASCON",str(self.gascon))
        self._edit_namelist("radmod_namelist","NPBROADEN",str(pressurebroaden*1))
        self.pressurebroaden=pressurebroaden
        self._edit_namelist("plasim_namelist","NEQSIG",str(vtype))
        self.vtype=vtype
        
        self._edit_namelist("plasim_namelist","MPSTEP",str(timestep))
        self._edit_namelist("plasim_namelist","NSTPW",str(int(7200//int(timestep))))
        self.timestep=timestep
        
        if year:
            self._edit_namelist("plasim_namelist","N_DAYS_PER_YEAR",str(int(year)))
            self._edit_namelist("planet_namelist","SIDEREAL_YEAR",str(year*86400.0))
            self.stepsperyear=float(year)*1440.0/self.timestep
        else:
            self.stepsperyear=360.*1440.0/self.timestep
        self.sidyear=year
        if rotationperiod!=1.0:
            self._edit_namelist("planet_namelist","ROTSPD",str(1.0/float(rotationperiod)))
            self._edit_namelist("plasim_namelist","N_DAYS_PER_YEAR",
                                str(max(int(360.0/float(rotationperiod)/12+0.5),1)*12))
            #if rotationperiod>80.0 and type(top_restoretime)==type(None):
                #top_restoretime = 1.0 #If we have a long rotation period, apply top-layer forcing
            nsteps = max(1,int(round(360.0*1440.0/self.timestep+0.49999)))
            self._edit_namelist("plasim_namelist","N_RUN_STEPS",str(nsteps))
        if runsteps is not None:
            self._edit_namelist("plasim_namelist","N_RUN_STEPS",str(runsteps))
        self.runsteps = runsteps
        self.rotationperiod=rotationperiod
        if synchronous:
            self._edit_namelist("radmod_namelist","NFIXED","1")
            self._edit_namelist("plasim_namelist","FIXEDLON",str(substellarlon))
        self.synchronous=synchronous
        self.substellarlon=substellarlon
        self._edit_namelist("radmod_namelist","DESYNC",str(desync))
        self.desync=desync
        self._edit_namelist("plasim_namelist","DTTL",str(tlcontrast))
        self.tlcontrast=tlcontrast
        if top_restoretime:
            #self._edit_namelist("plasim_namelist","RESTIM","%f,%d*0.0"%(top_restoretime,self.layers-1))
            self._edit_namelist("plasim_namelist","NSPONGE","1")
            self._edit_namelist("plasim_namelist","DAMPSP","%f"%top_restoretime)
        self.top_restoretime = top_restoretime
        
        if restartfile:
            os.system("cp %s %s/plasim_restart"%(restartfile,self.workdir))
```

--------------------------------

### Compute transit spectrum for a single column

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/pRT.html

Calculates the transmission radius for a single atmospheric column, including vertical profile setup and ozone parameterization.

```python
def _transitcolumn(atmosphere, pressures, psurf, temperature, humidity, clouds, 
                   gases_vmr, gascon, gravity, rplanet,
                   h2o_lines,cloudfunc,smooth,smoothweight,ozone,ozoneheight,ozonespread,num):
    '''Compute the transit spectrum through a single column.
    
    Parameters
    ----------
    atmosphere : Radtrans.Atmosphere
        Initialized Atmosphere object
    pressures : numpy.ndarray
        Pressure array in hPa, with the surface at the end of the array
    psurf : float
        Surface pressure in hPa
    temperature : numpy.ndarray
        Array of air temperatures, with the surface at the end of the array
    humidity : numpy.ndarray
        Specific humidity in the column [kg/kg]
    clouds : numpy.ndarray
        Cloud water mass fraction in each cell [kg/kg]
    gases_vmr : dict
        Dictionary of component gases and their volume mixing ratios
    gascon : float
        Specific gas constant
    gravity : float
        Surface gravity in SI units
    rplanet : float
        Planet radius in kilometers
    h2o_lines : {'HITEMP', 'EXOMOL'}
        Line list to use for H2O absorption. Options are 'HITEMP' or 'EXOMOL'.
    cloudfunc : function
        A routine which takes pressure, temperature, and cloud water content
        as arguments, and returns keyword arguments to be unpacked into calc_flux_transm.
    smooth : bool
        Whether or not to smooth humidity and cloud columns. As of Nov 12, 2021, it 
        is recommended that you use smooth=True for well-behaved spectra. This is a
        conservative smoothing operation, meaning the water and cloud column mass should
        be conserved--what this does is move some water from the water-rich layers into
        the layers directly above and below.
    smoothweight : float
        The fraction of the water in a layer that should be retained during smoothing.
        A higher value means the smoothing is less severe. 0.95 is probably the upper
        limit for well-behaved spectra.
    ozone : float
        Ozone column amount [cm-STP]
    ozoneheight : float
        Altitude of maximum ozone concentration [m]
    ozonespread : float
        Width of the ozone gaussian distribution [m]
    num : int, float
        Which number column this is (used for reporting)
        
        
    Returns
    -------
    numpy.ndarray
        Transmission radius in kilometers
    '''
    
    print("Doing column %d"%num)
    
    
    temperature = temperature[0]
    pressures = pressures[0]
    humidity = humidity[0]
    clouds = clouds[0]
    
    
    #Define vertical profiles with ghost stratosphere
    extp = np.append(np.geomspace(1.0e-6,0.5*pressures[0],num=20),pressures)
    try:
        extta = np.append(np.ones(20)*temperature[0],temperature)
    except:
        print(temperature.shape)
        raise
    exthus = np.append(np.zeros(20),humidity)
    extcl = np.append(np.zeros(20),clouds)
    
    if smooth:
        exthus = _smooth(exthus,xcoords=extp,xN=psurf,centerweight=smoothweight)
        extcl = _smooth(extcl,xcoords=extp,xN=psurf,centerweight=smoothweight)
    
    #Set up atmosphere
    atmosphere.setup_opa_structure(extp*1.0e-3)
    MMW = 8.31446261815324/gascon*1.0e3*np.ones_like(extp) #grams per mole
    
    #Set absorber fractions
    mass_fractions = {}
    for gas in gases_vmr:
        mmass = smws['m'+gas]
        mass_fractions[gas] = gases_vmr[gas] * mmass/MMW * (1-exthus-extcl)
        
    mass_fractions['H2O_'+h2o_lines] = exthus*(1-extcl)
    mass_fractions['H2O(c)'] = extcl
    kwargs = cloudfunc(extp,extta,extcl)
    
    #Compute ozone from parameterization
    mass_fractions['O3'] = np.zeros_like(extp)
    zfo3 = 100./2.14
    zo3t = ozone
    bo3 = ozoneheight
    co3 = ozonespread
    zh = 0.0
    zconst  = np.exp(-bo3/co3)
    ga = gravity*0.01 #SI units
    extdp = np.gradient(extp)*1e2
    for k in range(len(extp)-1,0,-1):
        zh -= extta[k]*gascon/ga*np.log(extp[k-1]/extp[k])
        zo3 = -(ozone + ozone*zconst)/(1.+np.exp((zh-bo3)/co3))+zo3t
        mass_fractions['O3'][k]=zo3*ga/(zfo3*extdp[k])
        zo3t -= zo3
    mass_fractions['O3'][0] = zo3t * ga / (zfo3 * extdp[0])
    
    if smooth:
        mass_fractions['O3'] = _smooth(mass_fractions['O3'],xcoords=extp,xN=psurf,centerweight=smoothweight)
    
    
    
    #Compute flux
    atmosphere.calc_transm(extta, mass_fractions, gravity, MMW, \
                           P0_bar=psurf*1.0e-3, R_pl=rplanet*1e5,**kwargs)
    
    return atmosphere.transm_rad*1e-5 #kilometers
```

--------------------------------

### exoplasim.sysconfigure

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Reruns the ExoPlaSim system configuration script.

```APIDOC
## exoplasim.sysconfigure()

### Description
Rerun the ExoPlaSim system configuration script. Call this if compilers/libraries have changed or the initial configuration failed.
```

--------------------------------

### Initialize Dataset Processing

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/pyburn.html

Sets up the dataset object based on provided variables or namelist configuration.

```python
if namelist is None:
        if variables is None:
            variables = list(ilibrary.keys())
        if mars:
            radius = MARS_RADIUS/6371220.0
            gascon = MARS_RD
            gravity = MARS_GRAV
        if type(variables)==tuple or type(variables)==list:
            data = dataset(rawfile, variables, mode=mode,radius=radius,gravity=gravity,gascon=gascon, 
                           zonal=zonal, substellarlon=substellarlon, 
                           physfilter=physfilter,logfile=logfile)
        elif type(variables)==dict: #for advancedDataset
            data = advancedDataset(rawfile, variables, mode=mode,radius=radius,gravity=gravity,
                                   gascon=gascon, zonal=zonal, substellarlon=substellarlon, 
                                   physfilter=physfilter, logfile=logfile)
```

--------------------------------

### Importing exoplasim.gcmt dependencies

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/gcmt.html

Initializes the module by importing necessary libraries and file support utilities.

```python
import numpy as np
import exoplasim.filesupport
from exoplasim.filesupport import SUPPORTED
import os, glob
```

--------------------------------

### Configure ExoPlaSim simulation parameters

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim.html

Logic for updating namelist files and managing simulation resources based on input keys.

```python
                str(self.highcadence["start"]))
                self._edit_namelist("plasim_namelist","HCENDSTEP",
                                    str(self.highcadence["end"]))
                self._edit_namelist("plasim_namelist","HCINTERVAL",
                                    str(self.highcadence["interval"]))
                
            if key=="snapshots":
                self.snapshots=value
                if self.snapshots:
                    self._edit_namelist("plasim_namelist","NSNAPSHOT","1")
                    self._edit_namelist("plasim_namelist","NSTPS",str(self.snapshots))
                else:
                    self._rm_namelist_param("plasim_namelist","NSTPS")
                    self._edit_namelist("plasim_namelist","NSNAPSHOT","0")
                    
            if key=="resources":
                self.resources=value
                if len(self.resources)>0:
                    for res in self.resources:
                        os.system("cp %s %s/"%(res,self.workdir))
                
            if key=="landmap":
                self.landmap=value
                changeland=True
            if key=="topomap":
                self.topomap=value
                changeland=True
                
            if key=="stormclim":
                self.stormclim=value
                if self.stormclim:
                    self._edit_namelist("hurricane_namelist","NSTORMDIAG","1")
                    self._add_postcodes("example.nl",[322,323,324,325,326,327,328,329])
                    self._add_postcodes("snapshot.nl",[322,323,324,325,326,327,328,329])
                else:
                    self._edit_namelist("hurricane_namelist","NSTORMDIAG","0")
                    self._rm_postcodes("example.nl",[322,323,324,325,326,327,328,329])
                    self._rm_postcodes("snapshot.nl",[322,323,324,325,326,327,328,329])
            if key=="nstorms":
                self.nstorms=value
                self._edit_namelist("hurricane_namelist","NSTORMS",str(self.int(nstorms)))
            if key=="stormcapture":
                self.stormcapture=value
                if self.stormcapture["toggle"]:
                    self._edit_namelist("hurricane_namelist","HC_CAPTURE","1")
                    for param in self.stormcapture:
                        if param!="toggle":
                            self._edit_namelist("hurricane_namelist",param,
                                                str(self.stormcapture[param]))
                else:
                    self._edit_namelist("hurricane_namelist","HC_CAPTURE","0")
            
            if key=="threshold":
                self.threshold = value
                
            if key=="aerosol":
                self.aerosol = value
                self._edit_namelist("plasim_namelist","L_AERO",str(self.aerosol*1))
                
            if key=="asource":
                self.asource = value
                self._edit_namelist("aero_namelist","l_source",str(self.asource))
                
            if key=="apart":
                self.apart = value
                self._edit_namelist("aero_namelist","apart",str(self.apart))
                
            if key=="rhop":
                self.rhop = value
                self._edit_namelist("aero_namelist","rhop",str(self.rhop))
                
            if key=="fcoeff":
                self.fcoeff = value
                self._edit_namelist("aero_namelist","fcoeff",str(self.fcoeff))
            
            if key=="aerobulk":
                self.aerobulk = value
                self._edit_namelist("aero_namelist","l_source",str(self.aerobulk))
                
            if key=="aerorad":
                self.aerorad = value
                if "aerofile" not in kwargs and self.aerorad:
                    self.aerofile = "gj667_constants_500.dat"
                elif "aerofile" in kwargs and self.aerorad:
                    self.aerofile = kwargs["aerofile"]
                    if self.aerofile is None:
                        self.aerofile = "gj667_constants_500.dat"
                if self.aerorad:
                    if f"{sourcedir}/hazeconstants/{self.aerofile}" in glob.glob(f"{sourcedir}/hazeconstants/*.dat"):
                        os.system(f"cp {sourcedir}/hazeconstants/{self.aerofile} {self.workdir}/")
                    elif f"{sourcedir}/hazeconstants/{self.aerofile}.dat" in glob.glob(f"{sourcedir}/hazeconstants/*.dat"):
                        os.system(f"cp {sourcedir}/hazeconstants/{self.aerofile}.dat {self.workdir}/")
                    if self.aerofile[-4:]==".dat":
                        self.aerofile=aerofile[:-4]
                    self.aerorad=True
                    self._edit_namelist("aero_namelist","l_aerorad",str(self.aerorad*1))
                    self._edit_namelist("aero_namelist","aerofile","'%s.dat'"%self.aerofile)
                    self.aerofile+=".dat"
```

--------------------------------

### Configure Ozone and Surface Albedo

Source: https://exoplasim.readthedocs.io/en/latest/_modules/exoplasim/pRT.html

Sets ozone parameters and calculates surface albedo based on ice, snow, and vegetation coverage.

```python
    try:
        starseparation = orbdistances[idx]
    except:
        starseparation = orbdistances
    
    if ozone is False:
        a0o3 = 0.
        a1o3 = 0.
        aco3 = 0.
        bo3 = 20000.
        co3 = 5000.
        toffo3 = 0.0
    elif ozone is True:
        a0o3 = 0.25
        a1o3 = 0.11
        aco3 = 0.08
        bo3 = 20000.
        co3 = 5000.
        toffo3 = 0.25
    else:
        a0o3 = ozone["amount"]
        a1o3 = ozone["varlat"]
        aco3 = ozone["varseason"]
        toffo3 = ozone["seasonoffset"]
        bo3 = ozone["height"]
        co3 = ozone["spread"]
        
    dt = output.variables['time'][0] / stepsperyear
    rlats = ilats*np.pi/180.
    o3 = a0o3+a1o3*abs(np.sin(rlats))+aco3*np.sin(rlats)*np.cos(2*np.pi*(dt-toffo3))
    
    albedo = output.variables['alb'][0,...].flatten()
    ice = output.variables['sit'][0,...]+output.variables['snd'][0,...]
    ice = ice.flatten()
    #icemap = 2.0*(ice>0.001) #1 mm probably not enough to make everything white
    ice = np.minimum(ice/0.02,1.0) #0-1 with a cap at 2 cm of snow
    snow = 1.0*(output.variables['snd'][0,...].flatten()>0.02) #absorbed by vegetation
    forest = np.zeros_like(ice)
    desertf = np.zeros_like(ice)
    mntf = np.zeros_like(ice)
    
    ice[forest>0] *= 1 - 0.82*forest[forest>0] 
    forest[ice>0] *= 0.82*forest[ice>0]
    bare = 1-(ice+forest)
    #sfctype = np.maximum(sea,icemap).astype(int)
       # Sea with no ice:  1
       # Sea with ice:     2
       # Land with no ice: 0   (since both are 0)
       # Land with ice:    2
    #surfaces = []
    #for n in range(len(sfctype)):
    #    surfaces.append({'type':sfctype[n],'albedo':albedo[n]})
        
    surfspecs = (sfcalbedo*(1-output.variables['sic'][0,...].flatten())[:,np.newaxis]+
                 surfaces[2][np.newaxis,:]*(output.variables['sic'][0,...].flatten())[:,np.newaxis])
    surfspecs = (surfspecs*bare[:,np.newaxis] + surfaces[2][np.newaxis,:]*ice[:,np.newaxis]+
                 surfaces[3][np.newaxis,:]*forest[:,np.newaxis])
    
    clt = output.variables['clt'][0,...].flatten()
    for n in range(len(albedo)):
        bol_alb = np.trapz(stellarspec*surfspecs[n,:],x=spec.wvl)/ \
```

--------------------------------

### exoplasim.Model

Source: https://exoplasim.readthedocs.io/en/latest/source/exoplasim.html

Initializes an ExoPlaSim model in a specified directory, compiling the executable if it does not exist.

```APIDOC
## class exoplasim.Model

### Description
Create and initialize an ExoPlaSim model in a particular directory. If the necessary executable does not yet exist, it will be compiled.

### Parameters
- **resolution** (str) - Optional - Model resolution (default 'T21')
- **layers** (int) - Optional - Number of vertical layers (default 10)
- **ncpus** (int) - Optional - Number of CPUs to use (default 4)
- **precision** (int) - Optional - Precision (default 8)
- **debug** (bool) - Optional - Enable debug mode (default False)
- **inityear** (int) - Optional - Initial year (default 0)
- **recompile** (bool) - Optional - Force recompile (default False)
- **optimization** (str) - Optional - Optimization level
- **mars** (bool) - Optional - Enable Mars mode (default False)
- **workdir** (str) - Optional - Working directory (default 'most')
- **source** (str) - Optional - Source path
- **force991** (bool) - Optional - Force 991 (default False)
- **modelname** (str) - Optional - Model name (default 'MOST_EXP')
- **outputtype** (str) - Optional - Output file type (default '.npz')
- **crashtolerant** (bool) - Optional - Enable crash tolerance (default False)
- **outputfaulttolerant** (bool) - Optional - Enable output fault tolerance (default False)
- **hyperthreading** (bool) - Optional - Enable hyperthreading (default True)
- **mpi_opts** (str) - Optional - MPI options
```