Migration from Py2 -> Py3 (Maxwell_vc_1d)

Dockerfile

@@ -0,0 +1,31 @@
+# Use the official Miniconda3 image as the base image
+FROM continuumio/miniconda3
+
+# Update package list and install necessary tools
+RUN apt-get update && \
+    apt-get install -y gfortran libblas-dev liblapack-dev
+
+# Set up an example Conda environment and install packages
+RUN conda create -n myenv python=3.8 -y && \
+    echo "source activate myenv" > ~/.bashrc
+
+# Set up the environment for running commands
+SHELL ["/bin/bash", "-c", "source activate myenv"]
+
+# Install packages within the Conda environment
+RUN conda install -c conda-forge numpy scipy matplotlib petsc4py -y
+
+# Set the environment variable
+ENV EMCLAW_PATH /home/$USER/emclaw
+
+# Clone the repository and navigate to the riemann directory
+RUN git clone https://github.com/MaxwellGEMS/emclaw.git $EMCLAW_PATH && \
+    cd $EMCLAW_PATH/emclaw/riemann
+
+# Activate the Conda environment and build/install the package
+RUN source activate myenv && \
+    python setup.py build_ext -i && \
+    conda develop -n myenv $EMCLAW_PATH
+
+# Set the default command to activate the Conda environment
+CMD ["bash", "-i"]

examples/maxwell_vc_1d/_convergence_sint.py

@@ -1,14 +1,17 @@
+# Import necessary libraries
 import sys
 import os
 import numpy as np
 
+# Adding paths to custom modules
 sys.path.append(os.path.realpath('../utils'))
 sys.path.append(os.path.realpath('../'))
 
-
+# Import custom modules
 from utils.materials import Material1D
 from utils.sources import Source1D
 
+# Defining some constants and initialize material properties
 x_lower = 0.
 x_upper = 100.
 
@@ -19,35 +22,40 @@
 material.setup()
 material.delta_length = x_upper
 material.delta_corner = x_lower
-material.delta_omega  = 12.0*np.pi/200.0
+material.delta_omega = 12.0 * np.pi / 200.0
 
-source = Source1D(material,shape='off',wavelength=2.0)
+# Create a source object
+source = Source1D(material, shape='off', wavelength=2.0)
 source.setup()
 source.offset = 10.0
 source.pulse_width = 2.0
 
-def grid_basic(x_lower,x_upper,mx,cfl):
-    dx = (x_upper-x_lower)/mx
-    dt = 0.9*cfl/(material.co*np.sqrt(1.0/(dx**2)))
+# Define a function for grid calculations
+def grid_basic(x_lower, x_upper, mx, cfl):
+    dx = (x_upper - x_lower) / mx
+    dt = 0.9 * cfl / (material.co * np.sqrt(1.0 / (dx ** 2)))
     tf = 100.0
 
-    return dx,dt,tf
+    return dx, dt, tf
 
-def dq_source(solver,state,dt):
+# Define a function for source terms
+def dq_source(solver, state, dt):
     """
     Source terms for Maxwell's equations in one spatial dimension.
     Assume aux values are averages on the cell i
     """
 
-    dq = -dt*state.q*state.aux[2:4,:]/state.aux[0:2,:]
+    dq = -dt * state.q * state.aux[2:4, :] / state.aux[0:2, :]
 
     return dq
 
-def em1D(mx=1024,num_frames=5,cfl=1.0,outdir='./_output',before_step=True,debug=False,chi3=0.0,chi2=0.0,nl=False,psi=True,em=True,homogeneous=True):
+# Define the main simulation function
+def em1D(mx=1024, num_frames=5, cfl=1.0, outdir='./_output', before_step=True, debug=False, chi3=0.0, chi2=0.0, nl=False, psi=True, em=True, homogeneous=True):
 
     import clawpack.petclaw as pyclaw
     import petsc4py.PETSc as MPI
 
+    # Set material properties if not homogeneous
     if not homogeneous:
         if nl:
             material.chi3_e = chi3
@@ -56,46 +64,48 @@ def em1D(mx=1024,num_frames=5,cfl=1.0,outdir='./_output',before_step=True,debug=
                 material.chi3_m = chi3
                 material.chi2_m = chi2
 
-    if MPI.COMM_WORLD.rank==0:
+    if MPI.COMM_WORLD.rank == 0:
         material._outdir = outdir
-        source._outdir   = outdir
+        source._outdir = outdir
         material._dump_to_latex()
         source._dump_to_latex()
 
-    num_eqn   = 2
+    num_eqn = 2
     num_waves = 2
-    num_aux   = 4
+    num_aux = 4
 
-#   grid pre calculations and domain setup
-    dx,dt,tf = grid_basic(x_lower,x_upper,mx,cfl)
-    x = pyclaw.Dimension('x',x_lower,x_upper,mx)
+    # Grid pre-calculations and domain setup
+    dx, dt, tf = grid_basic(x_lower, x_upper, mx, cfl)
+    x = pyclaw.Dimension('x', x_lower, x_upper, mx)
     domain = pyclaw.Domain([x])
 
-#   Solver settings
-    solver=pyclaw.SharpClawSolver1D()
-    solver.num_waves  = num_waves
-    solver.num_eqn    = num_eqn
+    # Solver settings
+    solver = pyclaw.SharpClawSolver1D()
+    solver.num_waves = num_waves
+    solver.num_eqn = num_eqn
     solver.weno_order = 5
 
     solver.dt_variable = True
-    solver.dt_initial  = dt/2.0
-    solver.dt_max      = dt
-    solver.max_steps   = int(2*tf/dt)
+    solver.dt_initial = dt / 2.0
+    solver.dt_max = dt
+    solver.max_steps = int(2 * tf / dt)
 
-#   Set the source
+    # Set the source
     if not psi:
-        print 'using dq_src'
+        # Python 2-style print statement
+        # print 'using dq_src'
+        print('using dq_src')  
         solver.dq_src = dq_source
 
-#   Import Riemann and Tfluct solvers
+    # Import Riemann and Tfluct solvers
     if homogeneous:
         import maxwell_1d_rp
     else:
         import maxwell_1d_nl_rp as maxwell_1d_rp
 
     solver.tfluct_solver = False
-    solver.fwave         = True
-    
+    solver.fwave = True
+
     solver.rp = maxwell_1d_rp
 
     if solver.tfluct_solver:
@@ -105,11 +115,11 @@ def em1D(mx=1024,num_frames=5,cfl=1.0,outdir='./_output',before_step=True,debug=
             import maxwell_1d_nl_tfluct as maxwell_1d_tfluct
 
         solver.tfluct = maxwell_1d_tfluct
-    
-    solver.cfl_max     = cfl+0.05
+
+    solver.cfl_max = cfl + 0.05
     solver.cfl_desired = cfl
 
-#   boundary conditions
+    # Boundary conditions
     solver.bc_lower[0] = pyclaw.BC.wall
     solver.bc_upper[0] = pyclaw.BC.wall
 
@@ -118,47 +128,47 @@ def em1D(mx=1024,num_frames=5,cfl=1.0,outdir='./_output',before_step=True,debug=
 
     solver.reflect_index = [0]
 
-#   before step configure
+    # Before step configure
     if before_step:
         solver.call_before_step_each_stage = True
         solver.before_step = material.update_aux
 
-#   state setup
-    state = pyclaw.State(domain,num_eqn,num_aux)
-    
+    # State setup
+    state = pyclaw.State(domain, num_eqn, num_aux)
+
     state.problem_data['chi2_e'] = material.chi2_e
     state.problem_data['chi3_e'] = material.chi3_e
     state.problem_data['chi2_m'] = material.chi2_m
     state.problem_data['chi3_m'] = material.chi3_m
-    state.problem_data['eo']     = material.eo
-    state.problem_data['mo']     = material.mo
-    state.problem_data['co']     = material.co
-    state.problem_data['zo']     = material.zo
-    state.problem_data['dx']     = state.grid.x.delta
-    state.problem_data['nl']     = nl
-    state.problem_data['psi']    = psi
-
-    source._dx   = state.grid.x.delta
+    state.problem_data['eo'] = material.eo
+    state.problem_data['mo'] = material.mo
+    state.problem_data['co'] = material.co
+    state.problem_data['zo'] = material.zo
+    state.problem_data['dx'] = state.grid.x.delta
+    state.problem_data['nl'] = nl
+    state.problem_data['psi'] = psi
+
+    source._dx = state.grid.x.delta
     material._dx = state.grid.x.delta
 
-#   array initialization
+    # Array initialization
     source.init(state)
     material.init(state)
 
-    state.q = state.q*state.aux[0:2,:]
-  
-#   controller
+    state.q = state.q * state.aux[0:2, :]
+
+    # Controller
     claw = pyclaw.Controller()
     claw.tfinal = tf
     claw.num_output_times = num_frames
     claw.solver = solver
-    claw.solution = pyclaw.Solution(state,domain)
+    claw.solution = pyclaw.Solution(state, domain)
     claw.outdir = outdir
     claw.write_aux_always = True
 
     return claw
 
-if __name__=="__main__":
+if __name__ == "__main__":
     import sys
     from clawpack.pyclaw.util import run_app_from_main
-    output = run_app_from_main(em1D)
+    output = run_app_from_main(em1D)