fargopy 0.2.1__py3-none-any.whl → 0.3.0__py3-none-any.whl

fargopy/conf.py

@@ -1,20 +0,0 @@
-###############################################################
-# FARGOpy interdependencies
-###############################################################
-import fargopy
-
-###############################################################
-# Required packages
-###############################################################
-
-###############################################################
-# Classes
-###############################################################
-
-#/////////////////////////////////////
-# CONFIGURATION CLASS
-#/////////////////////////////////////
-class Conf(object):
-    """Configuration class.
-    """
-    

fargopy/fargo3d.py

@@ -1,561 +0,0 @@
-###############################################################
-# FARGOpy interdependencies
-###############################################################
-import fargopy
-
-###############################################################
-# Required packages
-###############################################################
-import os
-import numpy as np
-import re
-
-###############################################################
-# Constants
-###############################################################
-KB = 1.380650424e-16  # Boltzmann constant: erg/K, erg = g cm^2 / s^2
-MP = 1.672623099e-24 # Mass of the proton, g
-GCONST = 6.67259e-8 # Gravitational constant, cm^3/g/s^2 
-RGAS = 8.314472e7 # Gas constant, erg /K/mol
-MSUN = 1.9891e33 # g
-AU = 1.49598e13 # cm
-YEAR = 31557600.0 # s
-
-# Map of coordinates into FARGO3D coordinates
-COORDS_MAP = dict(
-    cartesian = dict(x='x',y='y',z='z'),
-    cylindrical = dict(phi='x',r='y',z='z'),
-    spherical = dict(phi='x',r='y',theta='z'),
-)
-
-###############################################################
-# Classes
-###############################################################
-class Fargobj(object):
-    def __init__(self):
-        self.fobject = True
-
-    def has(self,key):
-        if key in self.__dict__.keys():
-            return True
-        else:
-            return False
-
-class Fargo3d(Fargobj):
-
-    def __init__(self):
-        super().__init__()
-   
-    def compile_fargo3d(self,clean=True):
-        if Conf._check_fargo(Conf.FARGO3D_FULLDIR):    
-            if clean:
-                Util.sysrun(f'make -C {Conf.FARGO3D_FULLDIR} clean mrproper',verbose=False)
-            
-            error,out = Util.sysrun(f'make -C {Conf.FARGO3D_FULLDIR} PARALLEL={self.parallel} GPU={self.gpu}',verbose=False)
-            if error:
-                if not Conf._check_fargo_binary(Conf.FARGO3D_FULLDIR,quiet=True):
-                    print("An error compiling the code arose. Check dependencies.")
-                    print(Util.STDERR)
-                return False
-            
-            return True
-
-class Field(Fargobj):
-    """Fields:
-
-    Attributes:
-        coordinates: type of coordinates (cartesian, cylindrical, spherical)
-        data: numpy arrays with data of the field
-
-    Methods:
-        slice: get an slice of a field along a given spatial direction.
-            Examples: 
-                density.slice(r=0.5) # Take the closest slice to r = 0.5
-                density.slice(ir=20) # Take the slice through the 20 shell
-                density.slice(phi=30*RAD,interp='nearest') # Take a slice interpolating to the nearest
-    """
-
-    def __init__(self,data=None,coordinates='cartesian',domains=None,type='scalar'):
-        self.data = data
-        self.coordinates = coordinates
-        self.domains = domains
-        self.type = type
-
-    def meshslice(self,slice=None,component=0):
-        """Perform a slice on a field and produce as an output the 
-        corresponding field slice and the associated matrices of
-        coordinates for plotting.
-        """
-        # Analysis of the slice 
-        if slice is None:
-            raise ValueError("You must provide a slice option.")
-
-        # Perform the slice
-        slice_cmd = f"self.slice({slice},pattern=True)"
-        slice,pattern = eval(slice_cmd)
-        
-        # Create the mesh
-        if self.coordinates == 'cartesian':
-            z,y,x = np.meshgrid(self.domains.z,self.domains.y,self.domains.x,indexing='ij')
-            x = eval(f"x[{pattern}]")
-            y = eval(f"y[{pattern}]")
-            z = eval(f"z[{pattern}]")
-            
-            mesh = fargopy.Dictobj(dict=dict(x=x,y=y,z=z))
-
-        if self.coordinates == 'cylindrical':
-            z,r,phi = np.meshgrid(self.domains.z,self.domains.r,self.domains.phi,indexing='ij')
-            x,y,z = r*np.cos(phi),r*np.sin(phi),z
-
-            x = eval(f"x[{pattern}]")
-            y = eval(f"y[{pattern}]")
-            z = eval(f"z[{pattern}]")
-            r = eval(f"r[{pattern}]")
-            phi = eval(f"phi[{pattern}]")
-
-            mesh = fargopy.Dictobj(dict=dict(r=r,phi=phi,x=x,y=y,z=z))
-
-        if self.coordinates == 'spherical':
-            theta,r,phi = np.meshgrid(self.domains.theta,self.domains.r,self.domains.phi,indexing='ij')
-            x,y,z = r*np.sin(theta)*np.cos(phi),r*np.sin(theta)*np.sin(phi),r*np.cos(theta)
-
-            x = eval(f"x[{pattern}]")
-            y = eval(f"y[{pattern}]")
-            z = eval(f"z[{pattern}]")
-            r = eval(f"r[{pattern}]")
-            phi = eval(f"phi[{pattern}]")
-            theta = eval(f"theta[{pattern}]")
-
-            mesh = fargopy.Dictobj(dict=dict(r=r,phi=phi,theta=theta,x=x,y=y,z=z))
-
-        return slice,mesh
-
-    def slice(self,quiet=True,pattern=False,**kwargs):
-        """Extract an slice of a 3-dimensional FARGO3D field
-
-        Parameters:
-            quiet: boolean, default = False:
-                If True extract the slice quietly.
-                Else, print some control messages.
-
-            pattern: boolean, default = False:
-                If True return the pattern of the slice, eg. [:,:,:]
-
-            ir, iphi, itheta, ix, iy, iz: string or integer:
-                Index or range of indexes of the corresponding coordinate.
-
-            r, phi, theta, x, y, z: float:
-                Value for slicing. The slicing search for the closest
-                value in the domain.
-
-        Returns:
-            slice: sliced field.
-
-        Examples:
-            # 0D: Get the value of the field in iphi = 0, itheta = -1 and close to r = 0.82
-            gasvz.slice(iphi=0,itheta=-1,r=0.82)
-
-            # 1D: Get all values of the field in radial direction at iphi = 0, itheta = -1
-            gasvz.slice(iphi=0,itheta=-1)
-
-            # 2D: Get all values of the field for values close to phi = 0
-            gasvz.slice(phi=0)
-        """
-        # By default slice
-        ivar = dict(x=':',y=':',z=':')
-
-        if len(kwargs.keys()) == 0:
-            pattern_str = f"{ivar['z']},{ivar['y']},{ivar['x']}"
-            if pattern:
-                return self.data, pattern_str
-            return self.data
-            
-        # Check all conditions
-        for key,item in kwargs.items():
-            match = re.match('^i(.+)',key)
-            if match:
-                index = item
-                coord = match.group(1)
-                if not quiet:
-                    print(f"Index condition {index} for coordinate {coord}")
-                ivar[COORDS_MAP[self.coordinates][coord]] = index
-            else:
-                if not quiet:
-                    print(f"Numeric condition found for coordinate {key}")
-                if key in self.domains.keys():
-                    # Check if value provided is in range
-                    domain = self.domains.item(key)
-                    extrema = self.domains.extrema[key]
-                    min, max = extrema[0][1], extrema[1][1]
-                    if (item<min) or (item>max):
-                        raise ValueError(f"You are attempting to get a slice in {key} = {item}, but the valid range for this variable is [{min},{max}]")
-                    find = abs(self.domains.item(key) - item)
-                    ivar[COORDS_MAP[self.coordinates][key]] = find.argmin()
-                    
-        pattern_str = f"{ivar['z']},{ivar['y']},{ivar['x']}"
-
-        if self.type == 'scalar':
-            slice_cmd = f"self.data[{pattern_str}]"
-            if not quiet:
-                print(f"Slice: {slice_cmd}")
-            slice = eval(slice_cmd)
-
-        elif self.type == 'vector':
-            slice = np.array(
-                [eval(f"self.data[0,{pattern_str}]"),
-                 eval(f"self.data[1,{pattern_str}]"),
-                 eval(f"self.data[2,{pattern_str}]")]
-            )
-
-        if pattern:
-            return slice,pattern_str
-        return slice
-
-    def to_cartesian(self):
-        if self.type == 'scalar':
-            # Scalar fields are invariant under coordinate transformations
-            return self
-        elif self.type == 'vector':
-            # Vector fields must be transformed according to domain
-            if self.coordinates == 'cartesian':
-                return self
-            
-            if self.coordinates == 'cylindrical':
-                z,r,phi = np.meshgrid(self.domains.z,self.domains.r,self.domains.phi,indexing='ij')
-                vphi = self.data[0]
-                vr = self.data[1]
-                vz = self.data[2]
-                vx = vr*np.cos(phi) 
-                vy = vr*np.sin(phi)
-                
-                return (Field(vx,coordinates=self.coordinates,domains=self.domains,type='scalar'),
-                        Field(vy,coordinates=self.coordinates,domains=self.domains,type='scalar'),
-                        Field(vz,coordinates=self.coordinates,domains=self.domains,type='scalar'))
-            
-            if self.coordinates == 'spherical':
-
-                theta,r,phi = np.meshgrid(self.domains.theta,self.domains.r,self.domains.phi,indexing='ij')
-                vphi = self.data[0]
-                vr = self.data[1]
-                vtheta = self.data[2]
-
-                vx = vr*np.sin(theta)*np.cos(phi) + vtheta*np.cos(theta)*np.cos(phi) - vphi*np.sin(phi)
-                vy = vr*np.sin(theta)*np.sin(phi) + vtheta*np.cos(theta)*np.sin(phi) + vphi*np.cos(phi)
-                vz = vr*np.cos(theta) - vtheta*np.sin(theta)
-
-                return (Field(vx,coordinates=self.coordinates,domains=self.domains,type='scalar'),
-                        Field(vy,coordinates=self.coordinates,domains=self.domains,type='scalar'),
-                        Field(vz,coordinates=self.coordinates,domains=self.domains,type='scalar'))
-            
-    def get_size(self):
-        return self.data.nbytes/1024**2
-
-    def __str__(self):
-        return str(self.data)
-    
-    def __repr__(self):
-        return str(self.data)
-
-class Simulation(Fargo3d):
-
-    def __init__(self):
-        super().__init__()
-        self.output_dir = None
-        self.set_units(UL=AU,UM=MSUN)
-
-    def set_output_dir(self,dir):
-        if not os.path.isdir(dir):
-            print(f"Directory '{dir}' does not exist.")
-        else:
-            print(f"Now you are connected with output directory '{dir}'")
-        self.output_dir = dir
-
-    def list_outputs(self,quiet=False):
-        if self.output_dir is None:
-            print(f"You have to set forst the outputs directory with <sim>.set_outputs('<directory>')")
-        else:
-            error,output = fargopy.Sys.run(f"ls {self.output_dir}")
-        if error == 0:
-            files = output[:-1]
-            print(f"{len(files)} files in output directory")
-            if not quiet:
-                file_list = ""
-                for i,file in enumerate(files):
-                    file_list += f"{file}, "
-                    if ((i+1)%10) == 0:
-                        file_list += "\n"
-                print(file_list)
-            return files
-
-    def load_properties(self,quiet=False,
-                        varfile='variables.par',
-                        domain_prefix='domain_',
-                        dimsfile='dims.dat'
-                        ):
-        if self.output_dir is None:
-            print(f"You have to set forst the outputs directory with <sim>.set_outputs('<directory>')")
-
-        # Read variables
-        vars = self._load_variables(varfile)
-        print(f"Simulation in {vars.DIM} dimensions")
-        
-        # Read domains 
-        domains = self._load_domains(vars,domain_prefix)
-
-        # Store the variables in the object
-        self.vars = vars
-        self.domains = domains
-
-        # Optionally read dims
-        dims = self._load_dims(dimsfile)
-        if len(dims):
-            self.dims = dims 
-        
-        print("Configuration variables and domains load into the object. See e.g. <sim>.vars")
-    
-    def _load_dims(self,dimsfile):
-        """Parse the dim directory
-        """
-        dimsfile = f"{self.output_dir}/{dimsfile}".replace('//','/')
-        if not os.path.isfile(dimsfile):
-            #print(f"No file with dimensions '{dimsfile}' found.")
-            return []
-        dims = np.loadtxt(dimsfile)
-        return dims
-
-    def _load_variables(self,varfile):
-        """Parse the file with the variables
-        """
-
-        varfile = f"{self.output_dir}/{varfile}".replace('//','/')
-        if not os.path.isfile(varfile):
-            print(f"No file with variables named '{varfile}' found.")
-            return
-
-        print(f"Loading variables")
-        variables = np.genfromtxt(
-            varfile,dtype={'names': ("parameters","values"),
-            'formats': ("|S30","|S300")}
-        ).tolist()
-        
-        vars = dict()
-        for posicion in variables:
-            str_value = posicion[1].decode("utf-8")
-            try:
-                value = int(str_value)
-            except:
-                try:
-                    value = float(str_value)
-                except:
-                    value = str_value
-            vars[posicion[0].decode("utf-8")] = value
-        
-        vars = fargopy.Dictobj(dict=vars)
-        print(f"{len(vars.__dict__.keys())} variables loaded")
-
-        # Create additional variables
-        variables = ['x', 'y', 'z']
-        if vars.COORDINATES == 'cylindrical':
-            variables = ['phi', 'r', 'z']
-        elif vars.COORDINATES == 'spherical':
-            variables = ['phi', 'r', 'theta']
-        vars.VARIABLES = variables
-
-        vars.__dict__[f'N{variables[0].upper()}'] = vars.NX
-        vars.__dict__[f'N{variables[1].upper()}'] = vars.NY
-        vars.__dict__[f'N{variables[2].upper()}'] = vars.NZ
-
-        # Dimension of the domain
-        vars.DIM = 2 if vars.NZ == 1 else 3
-        
-        return vars
-
-    def _load_domains(self,vars,domain_prefix,
-                      borders=[[],[3,-3],[3,-3]],
-                      middle=True):
-
-        # Coordinates
-        variable_suffixes = ['x', 'y', 'z']
-        print(f"Loading domain in {vars.COORDINATES} coordinates:")
-
-        # Correct dims in case of 2D
-        if vars.DIM == 2:
-            borders[-1] = []
-
-        # Load domains
-        domains = dict()
-        domains['extrema'] = dict()
-
-        for i,variable_suffix in enumerate(variable_suffixes):
-            domain_file = f"{self.output_dir}/{domain_prefix}{variable_suffix}.dat".replace('//','/')
-            if os.path.isfile(domain_file):
-
-                # Load data from file
-                domains[vars.VARIABLES[i]] = np.genfromtxt(domain_file)
-
-                if len(borders[i]) > 0:
-                    # Drop the border of the domain
-                    domains[vars.VARIABLES[i]] = domains[vars.VARIABLES[i]][borders[i][0]:borders[i][1]]
-
-                if middle:
-                    # Average between domain cell coordinates
-                    domains[vars.VARIABLES[i]] = 0.5*(domains[vars.VARIABLES[i]][:-1]+domains[vars.VARIABLES[i]][1:])
-                
-                # Show indices and value map
-                domains['extrema'][vars.VARIABLES[i]] = [[0,domains[vars.VARIABLES[i]][0]],[-1,domains[vars.VARIABLES[i]][-1]]]
-                
-                print(f"\tVariable {vars.VARIABLES[i]}: {len(domains[vars.VARIABLES[i]])} {domains['extrema'][vars.VARIABLES[i]]}")
-            else:
-                print(f"\tDomain file {domain_file} not found.")
-        domains = fargopy.Dictobj(dict=domains)
-
-        return domains        
-
-    def load_field(self,field,snapshot=None,type='scalar'):
-
-        if not self.has('vars'):
-            # If the simulation has not loaded the variables
-            dims, vars, domains = self.load_properties()
-        
-        # In case no snapshot has been provided use 0
-        snapshot = 0 if snapshot is None else snapshot
-
-        field_data = []
-        if type == 'scalar':
-            file_name = f"{field}{str(snapshot)}.dat"
-            file_field = f"{self.output_dir}/{file_name}".replace('//','/')
-            field_data = self._load_field_scalar(file_field)
-        elif type == 'vector':
-            field_data = []
-            variables = ['x','y'] 
-            if self.vars.DIM == 3:
-                variables += ['z'] 
-            for i,variable in enumerate(variables):
-                file_name = f"{field}{variable}{str(snapshot)}.dat"
-                file_field = f"{self.output_dir}/{file_name}".replace('//','/')
-                field_data += [self._load_field_scalar(file_field)]
-        else:
-            raise ValueError(f"Field type '{type}' not recognized.")
-
-        field = Field(data=np.array(field_data), coordinates=self.vars.COORDINATES, domains=self.domains, type=type)
-        return field
-    
-    def _load_field_scalar(self,file):
-        """Load scalar field from file a file.
-        """
-        if os.path.isfile(file):
-            field_data = np.fromfile(file).reshape(int(self.vars.NZ),int(self.vars.NY),int(self.vars.NX))
-            """
-            if self.vars.NZ > 1:
-                # 3D field
-                field_data = np.fromfile(file).reshape(int(self.vars.NZ),int(self.vars.NY),int(self.vars.NX))
-            else:
-                # 2D field
-                field_data = np.fromfile(file).reshape(int(self.vars.NY),int(self.vars.NX))
-            """
-            return field_data
-        else:
-            raise AssertionError(f"File with field '{file}' not found")
-        
-    def load_allfields(self,fluid,snapshot=None,type='scalar'):
-        """Load all fields in the output
-        """
-        qall = False
-        if snapshot is None:
-            qall = True
-            fields = fargopy.Dictobj()
-        else:
-            fields = fargopy.Dictobj()
-        
-        # Search for field files
-        pattern = f"{self.output_dir}/{fluid}*.dat"
-        error,output = fargopy.Sys.run(f"ls {pattern}")
-
-        if not error:
-            size = 0
-            for file_field in output[:-1]:
-                comps = Simulation._parse_file_field(file_field)
-                if comps:
-                    if qall:
-                        # Store all snapshots
-                        field_name = comps[0]
-                        field_snap = int(comps[1])
-
-                        if type == 'scalar':
-                            field_data = self._load_field_scalar(file_field)
-                        elif type == 'vector':
-                            field_data = []
-                            variables = ['x','y'] 
-                            if self.vars.DIM == 3:
-                                variables += ['z'] 
-                            for i,variable in enumerate(variables):
-                                file_name = f"{fluid}{variable}{str(field_snap)}.dat"
-                                file_field = f"{self.output_dir}/{file_name}".replace('//','/')
-                                field_data += [self._load_field_scalar(file_field)]
-                            field_data = np.array(field_data)
-                            field_name = field_name[:-1]
-
-                        if str(field_snap) not in fields.keys():
-                            fields.__dict__[str(field_snap)] = fargopy.Dictobj()
-                        size += field_data.nbytes
-                        (fields.__dict__[str(field_snap)]).__dict__[f"{field_name}"] = Field(data=field_data, coordinates=self.vars.COORDINATES, domains=self.domains, type=type)
-
-                    else:
-                        # Store a specific snapshot
-                        if int(comps[1]) == snapshot:
-                            field_name = comps[0]
-
-                            if type == 'scalar':
-                                field_data = self._load_field_scalar(file_field)
-                            elif type == 'vector':
-                                field_data = []
-                                variables = ['x','y'] 
-                                if self.vars.DIM == 3:
-                                    variables += ['z'] 
-                                for i,variable in enumerate(variables):
-                                    file_name = f"{fluid}{variable}{str(field_snap)}.dat"
-                                    file_field = f"{self.output_dir}/{file_name}".replace('//','/')
-                                    field_data += [self._load_field_scalar(file_field)]
-                                field_data = np.array(field_data)
-                                field_name = field_name[:-1]
-
-                            size += field_data.nbytes
-                            fields.__dict__[f"{field_name}"] = Field(data=field_data, coordinates=self.vars.COORDINATES, domains=self.domains, type=type)
-
-        else:
-            raise ValueError(f"No field found with pattern '{pattern}'. Change the fluid")
-    
-        if qall:
-            fields.snapshots = sorted([int(s) for s in fields.keys() if s != 'size'])
-        fields.size = size/1024**2
-        return fields
-
-    @staticmethod
-    def _parse_file_field(file_field):
-        basename = os.path.basename(file_field)
-        comps = None
-        match = re.match('([a-zA-Z]+)(\d+).dat',basename)
-        if match is not None:
-            comps = [match.group(i) for i in range(1,match.lastindex+1)]
-        return comps
-    
-    def set_units(self,UM=MSUN,UL=AU,G=1,mu=2.35):
-        """Set units of simulation
-        """
-        # Basic
-        self.UM = UM
-        self.UL = UL
-        self.G = G
-        self.UT = (G*self.UL**3/(GCONST*self.UM))**0.5 # In seconds
-
-        # Thermodynamics
-        self.UTEMP = (GCONST*MP*mu/KB)*self.UM/self.UL # In K
-        
-        # Derivative
-        self.USIGMA = self.UM/self.UL**2 # In g/cm^2
-        self.URHO = self.UM/self.UL**3 # In kg/m^3
-        self.UEPS = self.UM/(self.UL*self.UT**2)  # In J/m^3
-        self.UV = self.UL/self.UT
-
-    
-