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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 3 - Perfectly Matched Layer (PML)
3.1 - Introduction
In this notebook we describe the Perfectly Matched Layer method, originally proposed by Berenger for electromagnetic waves, a scheme also employing an absorbing layer to reduce the wave reflections coming from the computational boundaries. This is one of the most efficient schemes for this purpose. The formulation that we present here, designed for the wave equation in the form of a second order equation (instead of its formulation as a first order system), is the one proposed By Grote and Sim. 
We will use all the previous set ups employed in the notebooks <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a> and <a href="02_damping.ipynb">Damping</a>, detailling only the new features specific for the
PML method.
3.2 - Acoustic Problem with PML
We again use an extended spatial domain $\Omega=\left[x_{I}-L_{x},x_{F}+L_{x}\right] \times\left[z_{I},z_{F}+L_{z}\right]$, with an absorption region as depicted in blue in the figure bellow.
In the PML scheme, two auxiliary functions are included, which will provide the adequate damping of the wave reflections. The design of the method is such that it would ideally suppress all the reflections in a continuous setting, but since we employ a finite difference discretization some reflections remain, although strongly attenuated.
<img src='domain2.png' width=500>
The set of equations for the acoustic wave equaation with PML, including the auxiliary functions, is given by
Step1:  From Devito's library of examples we import the following structures
Step2:  The mesh parameters that we choose define the domain $\Omega_{0}$ plus the absorption region. For this, we use the following data
Step3:  The number of points of the absorption layer in the directions $x$ and $z$ are given, respectively, by
Step4:  The lengths $L_{x}$ and $L_{z}$ are given, respectively, by
Step5:  We define the grid
Step6:  As in the case of the Damping acoustic equation, we can here split the computations in the two subdomains
Step7:  The blue region is the union of 3 subdomains
Step8:  The figure below represents the division of domains that we did previously
Step9:  The velocity field is needed in both staggered and non-staggered grids. As before, we read the file and interpolate it to the non-staggered grid. From these values we interpolate to the staggered grid.
Step10:  Previously we introduce the local variables x10,x11,z10,z11,xm,zm,pxm and pzm that help us to create a specific velocity field, where we consider the whole domain (including the absorpion region). Below we include a routine to plot the velocity field.
Step11:  Below we include the plot of velocity field.
Step12:  We then define the temporal properties
Step13:  The symbolic values associated with the spatial and temporal grids that are used in the composition of the equations are given by
Step14:  We set the parameters for the Ricker source
Step15:  Below we include the plot of Ricker source.
Step16:  For the receivers
Step17:  The displacement field u is allocated
Step18:  The auxiliary functions $\phi_{1}(x,z,t)$ and $\phi_{2}(x,z,t)$ will be two fields of second order in time and space, which use points of type staggered.
Step19:  We set the velocity on the non-staggered grid
Step20:  and on the staggered one. Notice that the field has one less point in each direction.
Step21:  Taking into account the dimension of the array v1 and the dimension of the field vel1 we will complete the line nptx-1 with information from the line nptx-2 and the column nptz-1 with information from the column nptz-2, information from the v1 array. This copy of information does not alter the properties of the vel1 velocity field in view of its structure of constant profiles on the part. Copying information is done by the following sequence of commands
Step22:  We set the source term and receivers
Step23:  The next step is to create the structures that reproduce the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$ and then assign these functions to fields in non-staggered and staggered grids.
We define the region $\Omega_{0}$ by choosing the values of x0pml and x1pml in the direction $x$ and z0pml and z1pml in the direction $z$. These points satisfy the following relations with the lengths $L_{x}$ and $L_{z}$
Step24:  Having set the boundaries of $\Omega$, we create a function fdamp, which represents $\zeta_{1}(x,z)$ (when $i=1$) and $\zeta_{2}(x,z)$ (when $i=2$).
Step25:  We created the damping function that represents $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$. We now define arrays with the damping function values on grid points (staggered and non-staggered)
Step26:  Below we include a routine to plot the damping fields.
Step27:  Below we include the plot of damping field in $x$ direction.
Step28:  Below we include the plot of damping field in $z$ direction.
Step29:  As pointed out previously, the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$ define  damping in the directions $x$ and $z$ respectively. They will be identified  with the symbolic names of dampx and dampz, respectively.
As damping acts on non-staggered and staggered grids, we will identify dampx0 and dampz0 as being damping on the non-staggered points grid. Similarly, we will identify dampx1 and dampz1 as being the damping on the staggered points grid.
Step30:  In terms of dimensions, the arrays D11 and D12 have dimension $(nptx-1)\times (nptz-1)$. As our grid has $nptx\times nptz$ points, so we complete the line nptx-1 with information from the line nptx-2 and the column nptz-1 with information from the column nptz-2, in fields dampx1 and dampz1 using the arrays D11 and D12, respectively.
Step31:  As we saw previously, the acoustic equation with PML has the formulations
In the white (interior) region
Step32:  Now we define the stencils for each of the pdes that we created previously. The pde01 is defined on subdomain d0.
Step33:  The pdes
Step34:  The boundary conditions  are set
Step35:  We then define the operator (op) that will join the acoustic equation, source term, boundary conditions and receivers.
The acoustic wave equation in the d0 region
Step36:  So that there are no residuals in the variables of interest, we reset the fields u, phi1 and phi2 as follows
Step37:  We assign to op the number of time steps it must execute and the size of the time step in the local variables time and dt, respectively. This assignment is done as in <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a>, where we have the following attribution structure
Step38:  We view the result of the displacement field at the end time using the graph2d routine given by
Step39:  Realize that the solution obtained here has a reduction in the noises when we compared with the results displayed on the notebook <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a>. We plot the result of the Receivers using the graph2drec routine.
<ASSISTANT_TASK:>
Python Code:
# NBVAL_IGNORE_OUTPUT
import numpy                   as np
import matplotlib.pyplot       as plot
import math                    as mt
import matplotlib.ticker       as mticker    
from   mpl_toolkits.axes_grid1 import make_axes_locatable
from   matplotlib              import cm
Explanation: 3 - Perfectly Matched Layer (PML)
3.1 - Introduction
In this notebook we describe the Perfectly Matched Layer method, originally proposed by Berenger for electromagnetic waves, a scheme also employing an absorbing layer to reduce the wave reflections coming from the computational boundaries. This is one of the most efficient schemes for this purpose. The formulation that we present here, designed for the wave equation in the form of a second order equation (instead of its formulation as a first order system), is the one proposed By Grote and Sim. 
We will use all the previous set ups employed in the notebooks <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a> and <a href="02_damping.ipynb">Damping</a>, detailling only the new features specific for the
PML method.
3.2 - Acoustic Problem with PML
We again use an extended spatial domain $\Omega=\left[x_{I}-L_{x},x_{F}+L_{x}\right] \times\left[z_{I},z_{F}+L_{z}\right]$, with an absorption region as depicted in blue in the figure bellow.
In the PML scheme, two auxiliary functions are included, which will provide the adequate damping of the wave reflections. The design of the method is such that it would ideally suppress all the reflections in a continuous setting, but since we employ a finite difference discretization some reflections remain, although strongly attenuated.
<img src='domain2.png' width=500>
The set of equations for the acoustic wave equaation with PML, including the auxiliary functions, is given by:
\begin{eqnarray}
        \frac{\partial^2 u(x,z,t)}{\partial t^2}
        + (\zeta_1(x,z)+\zeta_2(x,z))\frac{\partial u(x,z,t)}{\partial t}
    + \zeta_1(x,z) \zeta_2(x,z) u(x,z,t)& = & \
     c^2(x,z)\Delta u(x,z,t) 
    +\frac{\partial \phi_1(x,z,t)}{\partial x}+ 
    \frac{\partial \phi_2(x,z,t)}{\partial z}+  f(x,z,t) & &
\end{eqnarray}
\begin{equation}
        \frac{\partial \phi_1(x,z,t)}{\partial t} =
        - \zeta_1(x,z)\phi_1(x,z,t)+c^2(x,z)(\zeta_2(x,z)-\zeta_1(x,z))
        \frac{\partial u(x,z,t)}{\partial x}
\end{equation}
\begin{equation}
        \frac{\partial \phi_2(x,z,t)}{\partial t} =
        - \zeta_2(x,z)\phi_2(x,z,t)+c^2(x,z)(\zeta_1(x,z)-\zeta_2(x,z))
        \frac{\partial u(x,z,t)}{\partial y}
\end{equation}
where $u(x,z,t):D\rightarrow \mathbb{R}$ is the wave displacement,  $f(x,z,t)$ is the source term, $c(x,z)$ is the wave speed and $\phi_{1}(x,z)$ and $\phi_{2}(x,z)$ are the auxiliary variables, which will be non zero only in the absorption region. The damping functions $\zeta_1(x,z)$ and $\zeta_2(x,z)$ will be defined as in the Damping notebook. The initial and outer boundary conditions for the displacement $u$ are the same as in the previous notebooks. The auxiliary functions will also be kept equal to zero in all the outer boundary of
$\Omega$. The Ricker source term is defined as before.
3.3 - Finite Difference Operators and Discretization of Spatial and Temporal Domains
We employ the same methods as in the previous notebooks.
3.4 - Staggered e non-staggered variables
In the discretization with PML we will use staggering of some variables, which is a convenient way for the centered discretization of the partial derivatives of these variables. 
The staggered spatial domain is $\Omega^{x,y}\Delta={(x{i+1/2},z_{j+1/2}, i=0,\cdots,nx-1,\ j=0,\cdots,nz-1}, \mbox{ with } x_{i+1/2}=(i+\frac{1}{2})\Delta x \mbox{ and } z_{j+1/2}=(j+\frac{1}{2})\Delta z$. Some variables will also be staggered in time, being defined
at intermediary time instantes $t_{k+1/2}=t_k+\Delta t$.
In the formulation of PML that is described here we will define the variables as follows:
The variable $u(x,z,t)$ is a non-staggered variable;
The variables $\phi_{1}(x,z,t)$ and $\phi_{2}(x,z,t)$ are staggered variables;
The functions $\zeta_{1}(x,z)$, $\zeta_{2}(x,z)$, $c(x,z)$ and $f(x,z,t)$ will be used as staggered or non-staggered variables depending on the equation in which they are required.
The direct implication of staggered and non-staggered variables appearing in the same equation is that:
When updating $u(x,z,t)$ we employ averages of neighboring values of $\phi_{1}(x,z,t)$ and $\phi_{2}(x,z,t)$ in order to have them on the non-staggered grid 
When updating $\phi_{1}(x,z,t)$ and $\phi_{2}(x,z,t)$ we use averages of neighboring values of $u(x,z,t)$ to define it on the staggered grid.
The calculation of these averages will be explicit when we write the equations in the Devito code.
3.5 - Standard Problem
Redeeming the Standard Problem definitions discussed on the notebook <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a> we have that:
$x_{I}$ =  0.0 Km;
$x_{F}$ =  1.0 Km = 1000 m;
$z_{I}$ =  0.0 Km;
$z_{F}$ =  1.0 Km = 1000 m;
The spatial discretization parameters are given by:
- $\Delta x$ = 0.01 km = 10m;
- $\Delta z$ = 0.01 km = 10m;
Let's consider a $I$ the time domain with the following limitations:
$t_{I}$ = 0 s = 0 ms;
$t_{F}$ = 1 s = 1000 ms;
The temporal discretization parameters are given by:
$\Delta t$ $\approx$ 0.0016 s = 1.6 ms;
$NT$ = 626.
The source term, velocity model and positioning of receivers will be as in the previous notebooks.
3.6 - Damping Functions
We choose the pair of functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$ as in the  <a href="02_damping.ipynb">Damping</a> notebook. They will act in the directions $x$ and $z$, respectively.
3.7 - Numerical Simulations
For the numerical simulations of this notebook we use several parts the notebook codes <a href="02_damping.ipynb">Damping</a>. We will highlight only the significant changes and comment on the most relevant operations, since the computational structure of the acoustic equation with PML is very similar to the case of the acoustic equation with Damping.
We import the following Python and Devito packages:
End of explanation
# NBVAL_IGNORE_OUTPUT
%matplotlib inline
from   examples.seismic  import TimeAxis
from   examples.seismic  import RickerSource
from   examples.seismic  import Receiver
from   devito            import SubDomain, Grid, NODE, TimeFunction, Function, Eq, solve, Operator
Explanation: From Devito's library of examples we import the following structures:
End of explanation
nptx   =  101
nptz   =  101
x0     =  0.
x1     =  1000. 
compx  =  x1-x0
z0     =  0.
z1     =  1000.
compz  =  z1-z0;
hxv    =  (x1-x0)/(nptx-1)
hzv    =  (z1-z0)/(nptz-1)
Explanation: The mesh parameters that we choose define the domain $\Omega_{0}$ plus the absorption region. For this, we use the following data:
End of explanation
npmlx  = 20
npmlz  = 20
Explanation: The number of points of the absorption layer in the directions $x$ and $z$ are given, respectively, by:
End of explanation
lx = npmlx*hxv
lz = npmlz*hzv
Explanation: The lengths $L_{x}$ and $L_{z}$ are given, respectively, by:
End of explanation
nptx   =  nptx + 2*npmlx
nptz   =  nptz + 1*npmlz
x0     =  x0 - hxv*npmlx
x1     =  x1 + hxv*npmlx
compx  =  x1-x0
z0     =  z0
z1     =  z1 + hzv*npmlz
compz  =  z1-z0
origin  = (x0,z0)
extent  = (compx,compz)
shape   = (nptx,nptz)
spacing = (hxv,hzv)
Explanation: We define the grid:
End of explanation
class d0domain(SubDomain):
    name = 'd0'
    def define(self, dimensions):
        x, z = dimensions
        return {x: ('middle', npmlx, npmlx), z: ('middle', 0, npmlz)}
d0_domain = d0domain()
Explanation: As in the case of the Damping acoustic equation, we can here split the computations in the two subdomains:
In the blue region:
\begin{eqnarray}
        \frac{\partial^2 u(x,z,t)}{\partial t^2}
        + (\zeta_1(x,z)+\zeta_2(x,z))\frac{\partial u(x,z,t)}{\partial t}
    + \zeta_1(x,z) \zeta_2(x,z) u(x,z,t)& = & \
     c^2(x,z)\Delta u(x,z,t) 
    +\frac{\partial \phi_1(x,z,t)}{\partial x}+ 
    \frac{\partial \phi_2(x,z,t)}{\partial z}+  f(x,z,t) & &
\end{eqnarray}
\begin{equation}
        \frac{\partial \phi_1(x,z,t)}{\partial t} =
        - \zeta_1(x,z)\phi_1(x,z,t)+c^2(x,z)(\zeta_2(x,z)-\zeta_1(x,z))
        \frac{\partial u(x,z,t)}{\partial x}
\end{equation}
\begin{equation}
        \frac{\partial \phi_2(x,z,t)}{\partial t} =
        - \zeta_2(x,z)\phi_2(x,z,t)+c^2(x,z)(\zeta_1(x,z)-\zeta_2(x,z))
        \frac{\partial u(x,z,t)}{\partial y}
\end{equation}
In the white region:
\begin{equation}
u(x,z,t)_{tt}-c^2(x,z)\Delta(u(x,z,t))=c^2(x,z)f(x,z,t).
\end{equation}
We use the structure of the subdomains to represent the white region and the blue region.
First, we define the white region, naming it as *d0
End of explanation
class d1domain(SubDomain):
    name = 'd1'
    def define(self, dimensions):
        x, z = dimensions
        return {x: ('left',npmlx), z: z}
d1_domain = d1domain()
class d2domain(SubDomain):
    name = 'd2'
    def define(self, dimensions):
        x, z = dimensions
        return {x: ('right',npmlx), z: z}
d2_domain = d2domain()
class d3domain(SubDomain):
    name = 'd3'
    def define(self, dimensions):
        x, z = dimensions
        return {x: ('middle', npmlx, npmlx), z: ('right',npmlz)}
d3_domain = d3domain()
Explanation: The blue region is the union of 3 subdomains:
End of explanation
grid = Grid(origin=origin, extent=extent, shape=shape, subdomains=(d0_domain,d1_domain,d2_domain,d3_domain), dtype=np.float64)
Explanation: The figure below represents the division of domains that we did previously:
<img src='domain3.png' width=500>
The spatial grid is then defined:
End of explanation
v0 = np.zeros((nptx,nptz))
v1 = np.zeros((nptx-1,nptz-1))
X0 = np.linspace(x0,x1,nptx)
Z0 = np.linspace(z0,z1,nptz)
    
x10 = x0+lx
x11 = x1-lx
        
z10 = z0
z11 = z1 - lz
xm = 0.5*(x10+x11)
zm = 0.5*(z10+z11)
        
pxm = 0
pzm = 0
        
for i in range(0,nptx):
    if(X0[i]==xm): pxm = i
            
for j in range(0,nptz):
    if(Z0[j]==zm): pzm = j
            
p0 = 0    
p1 = pzm
p2 = nptz
v0[0:nptx,p0:p1] = 1.5
v0[0:nptx,p1:p2] = 2.5
p0 = 0    
p1 = pzm
p2 = nptz-1
v1[0:nptx-1,p0:p1] = 1.5
v1[0:nptx-1,p1:p2] = 2.5
Explanation: The velocity field is needed in both staggered and non-staggered grids. As before, we read the file and interpolate it to the non-staggered grid. From these values we interpolate to the staggered grid.
End of explanation
def graph2dvel(vel):
        plot.figure()
        plot.figure(figsize=(16,8))
        fscale =  1/10**(3)
        scale  = np.amax(vel[npmlx:-npmlx,0:-npmlz])
        extent = [fscale*(x0+lx),fscale*(x1-lx), fscale*(z1-lz), fscale*(z0)]
        fig = plot.imshow(np.transpose(vel[npmlx:-npmlx,0:-npmlz]), vmin=0.,vmax=scale, cmap=cm.seismic, extent=extent)
        plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
        plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
        plot.title('Velocity Profile')
        plot.grid()
        ax = plot.gca()
        divider = make_axes_locatable(ax)
        cax = divider.append_axes("right", size="5%", pad=0.05)
        cbar = plot.colorbar(fig, cax=cax, format='%.2e')
        cbar.set_label('Velocity [km/s]')
        plot.show()
Explanation: Previously we introduce the local variables x10,x11,z10,z11,xm,zm,pxm and pzm that help us to create a specific velocity field, where we consider the whole domain (including the absorpion region). Below we include a routine to plot the velocity field.
End of explanation
# NBVAL_IGNORE_OUTPUT
graph2dvel(v0)
Explanation: Below we include the plot of velocity field.
End of explanation
t0    = 0.
tn    = 1000.   
CFL   = 0.4
vmax  = np.amax(v0) 
dtmax = np.float64((min(hxv,hzv)*CFL)/(vmax))
ntmax = int((tn-t0)/dtmax)+1
dt0   = np.float64((tn-t0)/ntmax)
time_range = TimeAxis(start=t0,stop=tn,num=ntmax+1)
nt         = time_range.num - 1
Explanation: We then define the temporal properties:
End of explanation
(hx,hz) = grid.spacing_map  
(x, z)  = grid.dimensions     
t       = grid.stepping_dim
dt      = grid.stepping_dim.spacing
Explanation: The symbolic values associated with the spatial and temporal grids that are used in the composition of the equations are given by:
End of explanation
f0      = 0.01
nsource = 1
xposf   = 0.5*(compx-2*npmlx*hxv)
zposf   = hzv
src = RickerSource(name='src',grid=grid,f0=f0,npoint=nsource,time_range=time_range,staggered=NODE,dtype=np.float64)
src.coordinates.data[:, 0] = xposf
src.coordinates.data[:, 1] = zposf
Explanation: We set the parameters for the Ricker source:
End of explanation
# NBVAL_IGNORE_OUTPUT
src.show()
Explanation: Below we include the plot of Ricker source.
End of explanation
nrec   = nptx
nxpos  = np.linspace(x0,x1,nrec)
nzpos  = hzv
rec = Receiver(name='rec',grid=grid,npoint=nrec,time_range=time_range,staggered=NODE,dtype=np.float64)
rec.coordinates.data[:, 0] = nxpos
rec.coordinates.data[:, 1] = nzpos
Explanation: For the receivers:
End of explanation
u = TimeFunction(name="u",grid=grid,time_order=2,space_order=2,staggered=NODE,dtype=np.float64)
Explanation: The displacement field u is allocated
End of explanation
phi1 = TimeFunction(name="phi1",grid=grid,time_order=2,space_order=2,staggered=(x,z),dtype=np.float64)
phi2 = TimeFunction(name="phi2",grid=grid,time_order=2,space_order=2,staggered=(x,z),dtype=np.float64)
Explanation: The auxiliary functions $\phi_{1}(x,z,t)$ and $\phi_{2}(x,z,t)$ will be two fields of second order in time and space, which use points of type staggered.
End of explanation
vel0 = Function(name="vel0",grid=grid,space_order=2,staggered=NODE,dtype=np.float64)
vel0.data[:,:] = v0[:,:]
Explanation: We set the velocity on the non-staggered grid
End of explanation
vel1 = Function(name="vel1", grid=grid,space_order=2,staggered=(x,z),dtype=np.float64)
vel1.data[0:nptx-1,0:nptz-1] = v1
Explanation: and on the staggered one. Notice that the field has one less point in each direction.
End of explanation
vel1.data[nptx-1,0:nptz-1] = vel1.data[nptx-2,0:nptz-1]
vel1.data[0:nptx,nptz-1]   = vel1.data[0:nptx,nptz-2]
Explanation: Taking into account the dimension of the array v1 and the dimension of the field vel1 we will complete the line nptx-1 with information from the line nptx-2 and the column nptz-1 with information from the column nptz-2, information from the v1 array. This copy of information does not alter the properties of the vel1 velocity field in view of its structure of constant profiles on the part. Copying information is done by the following sequence of commands:
End of explanation
src_term = src.inject(field=u.forward,expr=src*dt**2*vel0**2)
rec_term = rec.interpolate(expr=u)
Explanation: We set the source term and receivers
End of explanation
x0pml  = x0 + npmlx*hxv 
x1pml  = x1 - npmlx*hxv 
z0pml  = z0            
z1pml  = z1 - npmlz*hzv 
Explanation: The next step is to create the structures that reproduce the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$ and then assign these functions to fields in non-staggered and staggered grids.
We define the region $\Omega_{0}$ by choosing the values of x0pml and x1pml in the direction $x$ and z0pml and z1pml in the direction $z$. These points satisfy the following relations with the lengths $L_{x}$ and $L_{z}$:
x0pml = x0 + $L_{x}$;
x1pml = x1 - $L_{x}$;
z0pml = z0;
z1pml = z1 - $L_{z}$;
In terms of program variables, we have the following definitions:
End of explanation
def fdamp(x,z,i):
    
    quibar  = 0.05
          
    if(i==1):
        a = np.where(x<=x0pml,(np.abs(x-x0pml)/lx),np.where(x>=x1pml,(np.abs(x-x1pml)/lx),0.))
        fdamp = quibar*(a-(1./(2.*np.pi))*np.sin(2.*np.pi*a))
    if(i==2):
        a = np.where(z<=z0pml,(np.abs(z-z0pml)/lz),np.where(z>=z1pml,(np.abs(z-z1pml)/lz),0.))
        fdamp = quibar*(a-(1./(2.*np.pi))*np.sin(2.*np.pi*a))
      
    return fdamp
Explanation: Having set the boundaries of $\Omega$, we create a function fdamp, which represents $\zeta_{1}(x,z)$ (when $i=1$) and $\zeta_{2}(x,z)$ (when $i=2$).
End of explanation
def generatemdamp():
    
    X0     = np.linspace(x0,x1,nptx)    
    Z0     = np.linspace(z0,z1,nptz)
    X0grid,Z0grid = np.meshgrid(X0,Z0)
    X1   = np.linspace((x0+0.5*hxv),(x1-0.5*hxv),nptx-1)
    Z1   = np.linspace((z0+0.5*hzv),(z1-0.5*hzv),nptz-1)
    X1grid,Z1grid = np.meshgrid(X1,Z1)
   
    D01 = np.zeros((nptx,nptz))
    D02 = np.zeros((nptx,nptz))
    D11 = np.zeros((nptx,nptz))
    D12 = np.zeros((nptx,nptz))
    
    D01 = np.transpose(fdamp(X0grid,Z0grid,1))
    D02 = np.transpose(fdamp(X0grid,Z0grid,2))
  
    D11 = np.transpose(fdamp(X1grid,Z1grid,1))
    D12 = np.transpose(fdamp(X1grid,Z1grid,2))
    
    return D01, D02, D11, D12
D01, D02, D11, D12 = generatemdamp();
Explanation: We created the damping function that represents $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$. We now define arrays with the damping function values on grid points (staggered and non-staggered): c
The arrays D01 and D02 are associated with points of type staggered and represent the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$, respectively. 
The arrays D11 and D12 are associated with points of type non-staggered and represent the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$, respectively.
End of explanation
def graph2damp(D):     
    plot.figure()
    plot.figure(figsize=(16,8))
    fscale = 1/10**(-3)
    fscale = 10**(-3)
    scale  = np.amax(D)
    extent = [fscale*x0,fscale*x1, fscale*z1, fscale*z0]
    fig = plot.imshow(np.transpose(D), vmin=0.,vmax=scale, cmap=cm.seismic, extent=extent)
    plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
    plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
    plot.title('Absorbing Layer Function')
    plot.grid()
    ax = plot.gca()
    divider = make_axes_locatable(ax)
    cax = divider.append_axes("right", size="5%", pad=0.05)
    cbar = plot.colorbar(fig, cax=cax, format='%.2e')
    cbar.set_label('Damping')
    plot.show()
Explanation: Below we include a routine to plot the damping fields.
End of explanation
# NBVAL_IGNORE_OUTPUT
graph2damp(D01)
Explanation: Below we include the plot of damping field in $x$ direction.
End of explanation
# NBVAL_IGNORE_OUTPUT
graph2damp(D02)
Explanation: Below we include the plot of damping field in $z$ direction.
End of explanation
dampx0 = Function(name="dampx0", grid=grid,space_order=2,staggered=NODE ,dtype=np.float64)
dampz0 = Function(name="dampz0", grid=grid,space_order=2,staggered=NODE ,dtype=np.float64)
dampx0.data[:,:] = D01
dampz0.data[:,:] = D02
dampx1 = Function(name="dampx1", grid=grid,space_order=2,staggered=(x,z),dtype=np.float64)
dampz1 = Function(name="dampz1", grid=grid,space_order=2,staggered=(x,z),dtype=np.float64)
dampx1.data[0:nptx-1,0:nptz-1] = D11
dampz1.data[0:nptx-1,0:nptz-1] = D12
Explanation: As pointed out previously, the functions $\zeta_{1}(x,z)$ and $\zeta_{2}(x,z)$ define  damping in the directions $x$ and $z$ respectively. They will be identified  with the symbolic names of dampx and dampz, respectively.
As damping acts on non-staggered and staggered grids, we will identify dampx0 and dampz0 as being damping on the non-staggered points grid. Similarly, we will identify dampx1 and dampz1 as being the damping on the staggered points grid.
End of explanation
dampx1.data[nptx-1,0:nptz-1]   = dampx1.data[nptx-2,0:nptz-1]
dampx1.data[0:nptx,nptz-1]     = dampx1.data[0:nptx,nptz-2]
dampz1.data[nptx-1,0:nptz-1]   = dampz1.data[nptx-2,0:nptz-1]
dampz1.data[0:nptx,nptz-1]     = dampz1.data[0:nptx,nptz-2]
Explanation: In terms of dimensions, the arrays D11 and D12 have dimension $(nptx-1)\times (nptz-1)$. As our grid has $nptx\times nptz$ points, so we complete the line nptx-1 with information from the line nptx-2 and the column nptz-1 with information from the column nptz-2, in fields dampx1 and dampz1 using the arrays D11 and D12, respectively.
End of explanation
# White Region
pde01   = Eq(u.dt2-u.laplace*vel0**2) 
# Blue Region
pde02a  = u.dt2   + (dampx0+dampz0)*u.dtc + (dampx0*dampz0)*u - u.laplace*vel0*vel0 
pde02b  = - (0.5/hx)*(phi1[t,x,z-1]+phi1[t,x,z]-phi1[t,x-1,z-1]-phi1[t,x-1,z])
pde02c  = - (0.5/hz)*(phi2[t,x-1,z]+phi2[t,x,z]-phi2[t,x-1,z-1]-phi2[t,x,z-1])
pde02   = Eq(pde02a + pde02b + pde02c)
pde10 = phi1.dt + dampx1*0.5*(phi1.forward+phi1)
a1    = u[t+1,x+1,z] + u[t+1,x+1,z+1] - u[t+1,x,z] - u[t+1,x,z+1] 
a2    = u[t,x+1,z]   + u[t,x+1,z+1]   - u[t,x,z]   - u[t,x,z+1] 
pde11 = -(dampz1-dampx1)*0.5*(0.5/hx)*(a1+a2)*vel1**2
pde1  = Eq(pde10+pde11)
                                                    
pde20 = phi2.dt + dampz1*0.5*(phi2.forward+phi2) 
b1    = u[t+1,x,z+1] + u[t+1,x+1,z+1] - u[t+1,x,z] - u[t+1,x+1,z] 
b2    = u[t,x,z+1]   + u[t,x+1,z+1]   - u[t,x,z]   - u[t,x+1,z] 
pde21 = -(dampx1-dampz1)*0.5*(0.5/hz)*(b1+b2)*vel1**2
pde2  = Eq(pde20+pde21)
Explanation: As we saw previously, the acoustic equation with PML has the formulations
In the white (interior) region:
eq1 = u.dt2 - vel0 * vel0 * u.laplace;
And in the blue (absorption) region:
eq2  = u.dt2 + (dampx0+dampz0) * u.dtc + (dampx0 * dampz0) * u - u.laplace * vel0 * vel0 + $\bar{phi1}$[t,x,z] + $\bar{phi2}$[t,x,z];
eq3 = phi1.dt + dampx1 * 0.5 * (phi1.forward+phi1) -(dampz1-dampx1) * $\bar{u}$[t,x,z] * vel1 * vel1
eq4 = phi2.dt + dampz1 * 0.5 * (phi2.forward+phi2) -(dampx1-dampz1) * $\bar{u}$[t,x,z] * vel1 * vel1
In the equation eq2 the term $\bar{phi1}$[t,x,z] is given by following expression:
-(0.5/hx) * (phi1[t,x,z-1]+phi1[t,x,z]-phi1[t,x-1,z-1]-phi1[t,x-1,z]);
And the term $\bar{phi2}$[t,x,z] in the equation eq2 is given by:
-(0.5/hz) * (phi2[t,x-1,z]+phi2[t,x,z]-phi2[t,x-1,z-1]-phi2[t,x,z-1]);
In the equation eq3 the term $\bar{u}$[t,x,z] is given by:
a1 = u[t+1,x+1,z] + u[t+1,x+1,z+1] - u[t+1,x,z] - u[t+1,x,z+1]; 
a2 = u[t,x+1,z]   + u[t,x+1,z+1]   - u[t,x,z]   - u[t,x,z+1]; 
$\bar{u}$[t,x,z] = 0.5 * (0.5/hx) * (a1+a2);
In the equation eq4 the term $\bar{u}$[t,x,z] is given by:
b1 = u[t+1,x,z+1] + u[t+1,x+1,z+1] - u[t+1,x,z] - u[t+1,x+1,z]; 
b2 = u[t,x,z+1]   + u[t,x+1,z+1]   - u[t,x,z]   - u[t,x+1,z]; 
$\bar{u}$[t,x,z] = 0.5 * (0.5/hz) * (b1+b2)
Then, using the operator Eq(eq) and the equation in the format associated with Devito we create the pdes that represent the acoustic equations with PML without the external force term in the white and blue regions, respectively by:
End of explanation
stencil01 =  Eq(u.forward,solve(pde01,u.forward) ,subdomain = grid.subdomains['d0'])
Explanation: Now we define the stencils for each of the pdes that we created previously. The pde01 is defined on subdomain d0.
End of explanation
subds = ['d1','d2','d3']
stencil02 = [Eq(u.forward,solve(pde02, u.forward),subdomain = grid.subdomains[subds[i]]) for i in range(0,len(subds))]
stencil1 = [Eq(phi1.forward, solve(pde1,phi1.forward),subdomain = grid.subdomains[subds[i]]) for i in range(0,len(subds))]
stencil2 = [Eq(phi2.forward, solve(pde2,phi2.forward),subdomain = grid.subdomains[subds[i]]) for i in range(0,len(subds))]
Explanation: The pdes: pde02, pde1 and pde2 are defined on the union of the subdomains d1, d2 and d3.
End of explanation
bc  = [Eq(u[t+1,0,z],0.),Eq(u[t+1,nptx-1,z],0.),Eq(u[t+1,x,nptz-1],0.),Eq(u[t+1,x,0],u[t+1,x,1])]
Explanation: The boundary conditions  are set
End of explanation
# NBVAL_IGNORE_OUTPUT
op = Operator([stencil01,stencil02] + src_term + bc + [stencil1,stencil2] + rec_term,subs=grid.spacing_map)
Explanation: We then define the operator (op) that will join the acoustic equation, source term, boundary conditions and receivers.
The acoustic wave equation in the d0 region: [stencil01];
The acoustic wave equation in the d1, d2 and d3 regions: [stencil02];
Source term: src_term;
Boundary Condition: bc;
Auxiliary function $\phi_{1}(x,z,t)$ in the d1, d2 and d3 regions: [stencil1];
Auxiliary function $\phi_{2}(x,z,t)$ in the d1, d2 and d3 regions: [stencil2];
Receivers: rec_term;
We then define the following op:
End of explanation
u.data[:]     = 0.
phi1.data[:]  = 0.
phi2.data[:]  = 0.
Explanation: So that there are no residuals in the variables of interest, we reset the fields u, phi1 and phi2 as follows:
End of explanation
# NBVAL_IGNORE_OUTPUT
op(time=nt,dt=dt0)
Explanation: We assign to op the number of time steps it must execute and the size of the time step in the local variables time and dt, respectively. This assignment is done as in <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a>, where we have the following attribution structure:
End of explanation
def graph2d(U):    
    plot.figure()
    plot.figure(figsize=(16,8))
    fscale =  1/10**(3)
    scale  = np.amax(U[npmlx:-npmlx,0:-npmlz])/10.
    extent = [fscale*x0pml,fscale*x1pml,fscale*z1pml,fscale*z0pml]
    fig = plot.imshow(np.transpose(U[npmlx:-npmlx,0:-npmlz]),vmin=-scale, vmax=scale, cmap=cm.seismic, extent=extent)
    plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
    plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
    plot.axis('equal')
    plot.title('Map - Acoustic Problem PML Devito')
    plot.grid()
    ax = plot.gca()
    divider = make_axes_locatable(ax)
    cax = divider.append_axes("right", size="5%", pad=0.05)
    cbar = plot.colorbar(fig, cax=cax, format='%.2e')
    cbar.set_label('Displacement [km]')
    plot.draw()
    plot.show()
# NBVAL_IGNORE_OUTPUT
graph2d(u.data[0,:,:])
Explanation: We view the result of the displacement field at the end time using the graph2d routine given by:
End of explanation
def graph2drec(rec):    
        plot.figure()
        plot.figure(figsize=(16,8))
        fscaled = 1/10**(3)
        fscalet = 1/10**(3)
        scale   = np.amax(rec[:,npmlx:-npmlx])/10.
        extent  = [fscaled*x0pml,fscaled*x1pml, fscalet*tn, fscalet*t0]
        fig = plot.imshow(rec[:,npmlx:-npmlx], vmin=-scale, vmax=scale, cmap=cm.seismic, extent=extent)
        plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))
        plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f s'))
        plot.axis('equal')
        plot.title('Receivers Signal Profile with PML - Devito')
        ax = plot.gca()
        divider = make_axes_locatable(ax)
        cax = divider.append_axes("right", size="5%", pad=0.05)
        cbar = plot.colorbar(fig, cax=cax, format='%.2e')
        plot.show()
# NBVAL_IGNORE_OUTPUT
graph2drec(rec.data)
assert np.isclose(np.linalg.norm(rec.data), 990, rtol=1)
Explanation: Realize that the solution obtained here has a reduction in the noises when we compared with the results displayed on the notebook <a href="01_introduction.ipynb">Introduction to Acoustic Problem</a>. We plot the result of the Receivers using the graph2drec routine.
End of explanation
<END_TASK>