fix: Paraview animation feature

examples/glow_discharge/fedm-gd.py

@@ -445,7 +445,7 @@ def Grounded_electrode(x, on_boundary):
     # ============================================================================
     # Solving the coupled equation ussing adaptive solver. The calculated values are assigned to the variables used for postprocessing.
     # ============================================================================
-    t = adaptive_solver(nonlinear_solver, problem, t, dt, dt_old, u_new, u_old, variable_list_new, variable_list_old, assigner, error, files.error_file, max_error, ttol, dt_min, time_dependent_arguments = [Phi_powered], approximation = approximation)
+    t, _ = adaptive_solver(nonlinear_solver, problem, t, dt, dt_old, u_new, u_old, variable_list_new, variable_list_old, assigner, error, files.error_file, max_error, ttol, dt_min, time_dependent_arguments = [Phi_powered], approximation = approximation)
 
     log('time', files.model_log, t)  # Time logging
 

examples/streamer_compare_stab/file_input/benchmark_model/species/electrons.cfg

@@ -0,0 +1,3 @@
+Z    = -1
+Mass = 9.10938215e-31
+Nmom = 3

examples/streamer_compare_stab/file_input/benchmark_model/species/ions.cfg

@@ -0,0 +1,3 @@
+Z   = 1.0
+Mass = 4.6528301e-26
+Nmom = 1

examples/streamer_compare_stab/file_input/benchmark_model/species/neutrals.cfg

@@ -0,0 +1,3 @@
+Z   = 0.0
+Mass = 4.6528301e-26
+Nmom = 1

examples/streamer_compare_stab/file_input/benchmark_model/speclist.cfg

@@ -0,0 +1,3 @@
+neutrals           file: neutrals.cfg
+ions                 file: ions.cfg
+e                     file: electrons.cfg

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/alpha.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: net ionization coefficient
+# Reaction:    neutrals + e -> ions + e + e
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        E_m [V/m]  alpha [1/m]
+# Dependence:  fun:E
+# Comment:
+#
+################################################################################
+
+(1.1944e6 + 4.3666e26 * E_m**(-3))*exp(-2.73e7/E_m)-340.75

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/e_ND.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: diffusion coefficient
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        E_m [V/m]  N*D [m^2/s]
+# Dependence:  fun:E
+# Comment:
+#
+################################################################################
+
+4.3628e-3*E_m**(0.22)

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/e_Nb.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: mobility
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        E_m [V/m]  N*b [1/(m*V*s)]
+# Dependence:  fun:E
+# Comment:
+#
+################################################################################
+
+2.3987*E_m**(-0.26)

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/ions_ND.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: diffusion coefficient
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        const [V/m]  N*b [1/(m*V*s)]
+# Dependence:  const.
+# Comment:
+#
+################################################################################
+
+0.00000E+00

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/ions_Nb.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: mobility
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        const [V/m]  N*b [1/(m*V*s)]
+# Dependence:  const.
+# Comment:
+#
+################################################################################
+
+0.00000E+00

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/neutrals_ND.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: diffusion coefficient
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        const [V/m]  N*b [1/(m*V*s)]
+# Dependence:  const.
+# Comment:
+#
+################################################################################
+
+0.00000E+00

examples/streamer_compare_stab/file_input/benchmark_model/transport_coefficients/neutrals_Nb.dat

@@ -0,0 +1,12 @@
+################################################################################
+#
+# Description: mobility
+# Species:     electrons (field)
+# Data source: B. Bagheri Plasma Sources Sci. Technol. 27 (2018) 095002
+# Data:        const [V/m]  N*b [1/(m*V*s)]
+# Dependence:  const.
+# Comment:
+#
+################################################################################
+
+0.00000E+00

examples/streamer_discharge/fedm-streamer.py

@@ -308,7 +308,7 @@ def Anode(x, on_boundary):
     assigner.assign(variable_list_old, u_old)
 
     ## Solving problem with adaptive time step
-    t = adaptive_solver(nonlinear_solver, problem, t, dt, dt_old, u_new, u_old, variable_list_new, variable_list_old, assigner, error, files.error_file, max_error, ttol, dt_min, time_dependent_arguments = [], approximation = approximation)
+    t, _ = adaptive_solver(nonlinear_solver, problem, t, dt, dt_old, u_new, u_old, variable_list_new, variable_list_old, assigner, error, files.error_file, max_error, ttol, dt_min, time_dependent_arguments = [], approximation = approximation)
 
     ## For the constant time step, comment previous and  uncomment following code block
     # t += dt.time_step

examples/time_of_flight/fedm-tof.py

@@ -42,6 +42,11 @@
 M = me
 charge = -elementary_charge
 equation_type = ['drift-diffusion-reaction'] # Defining the type of the equation (reaction | diffusion-reaction | drift-diffusion-reaction)
+wez = 1.7e5 # electron velocity 
+De = 0.12 # electron diffusion coefficient
+alpha_e = 5009.51 # reaction coefficient 
+
+
 log('properties', files.model_log, gas, model, particle_species_type, M, charge) # Writting particle properties into a log file
 vtkfile_u = output_files('pvd', 'number density', particle_species_type) # Setting-up output files
 
@@ -99,20 +104,20 @@
 u_old1 = Function(V) # Defining function for storing the data at k-2 time step
 u_new = Function(V) # Defining function for storing the data at k time step
 
-u_analytical  = Expression('std::log(exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)/pow(4*D*t*pi,1.5))', D = 0.12, w = 1.7e5, alpha = 5009.51, t = t, pi=pi,  degree = 3) # Analytical solution of the particle balance equation.
+u_analytical  = Expression('std::log(exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)/pow(4*D*t*pi,1.5))', D = De, w = wez, alpha = alpha_e, t = t, pi=pi,  degree = 3) # Analytical solution of the particle balance equation.
 u_old.assign(interpolate(u_analytical , V)) # Setting up value at k-1 time step
 u_old1.assign(interpolate(u_analytical , V)) # Setting up value at k-2 time step
 
-w = interpolate(Constant(('0','1.7e5')), W) # Electron drift velocity [m/s]
-D = interpolate(Constant(0.12), V) # Diffusion coefficient [m^2/s]
-alpha_eff = interpolate(Constant(5009.51), V) #Effective ionization coefficient [1/m]
+w = interpolate(Constant(('0', wez)), W) # Electron drift velocity [m/s]
+D = interpolate(Constant(De), V) # Diffusion coefficient [m^2/s]
+alpha_eff = interpolate(Constant(alpha_e), V) #Effective ionization coefficient [1/m]
 
 Gamma = -grad(D*exp(u)) + w*exp(u) # Defining electron flux [m^{-2} s^{-1}]
-f = Expression('exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)*(w*alpha)/(8*pow(pi,1.5)*pow(D*t, 1.5))', D = 0.12, w = 1.7e5, alpha = 5009.51, t = t, pi=pi,  degree = 2) # Defining source term
+f = Expression('exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)*(w*alpha)/(8*pow(pi,1.5)*pow(D*t, 1.5))', D = De, w = wez, alpha = alpha_e, t = t, pi=pi,  degree = 2) # Defining source term
 
 F = weak_form_balance_equation_log_representation(equation_type[0], dt, dt_old, dx, u, u_old, u_old1, v, f, Gamma, r) # Definition of variational formulation of the balance equation for the electrons
 
-u_new.assign(interpolate(Expression('std::log(exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)/pow(4.0*D*t*pi,1.5) + DOLFIN_EPS)', D = 0.12, w = 1.7e5, alpha = 5009.51, t = t, pi=pi,  degree = 2), V)) # Setting up initial guess for nonlinear solver
+u_new.assign(interpolate(Expression('std::log(exp(-(pow(x[1]-w*t, 2)+pow(x[0], 2))/(4.0*D*t)+alpha*w*t)/pow(4.0*D*t*pi,1.5) + DOLFIN_EPS)', D = De, w = wez, alpha = alpha_e, t = t, pi=pi,  degree = 2), V)) # Setting up initial guess for nonlinear solver
 
 # ============================================================================
 # Setting-up nonlinear solver
@@ -129,6 +134,9 @@
 nonlinear_solver.parameters['maximum_iterations'] = maximum_iterations # Setting up maximum number of iterations
 # nonlinear_solver.parameters["preconditioner"]="hypre_amg" # Setting the preconditioner, uncomment if iterative solver is used
 
+n_exact = Function(V) # Defining function for storing the data (analytical solution)
+n_num = Function(V) # Defining function for storing the data (numerical solution)
+
 while abs(t-T_final)/T_final > 1e-6:
     t_old = t # Updating old time steps
     u_old1.assign(u_old) # Updating variable value in k-2 time step
@@ -144,8 +152,8 @@
     nonlinear_solver.solve(problem, u_new.vector()) # Solving the system of equations
 
     if abs(t-t_output)/t_output <= 1e-6:
-        n_exact = project(exp(u_analytical), V, solver_type='mumps')
-        n_num = project(exp(u_new), V, solver_type='mumps')
+        n_exact.assign(project(exp(u_analytical), V, solver_type='mumps'))
+        n_num.assign(project(exp(u_new), V, solver_type='mumps'))
         relative_error = errornorm(n_num, n_exact, 'l2')/norm(n_exact, 'l2') # Calculating relative difference between exact analytical and numerical solution
         with open(files.error_file, "a") as f_err:
             f_err.write('h_max = ' + str(h) + '\t dt = ' + str(dt.time_step) + '\t relative_error = ' + str(relative_error) + '\n')

examples/time_of_flight_1D/fedm-tof_1d.py

@@ -0,0 +1,176 @@
+"""
+This small example presents modelling of time-of-flight experiment and is used for verification purpose.
+Namely, for this particular test case the exact analytical solution for the electron number density exists,
+so it is used to verify the accuracy of the code using the method of exact solutions. L2 norm is used to
+quantify the difference between the solutions and to determine the mesh and time order-of-accuracy of the
+code for solving the balance equation.
+"""
+from dolfin import *
+import numpy as np
+from timeit import default_timer as timer
+import time
+import sys
+from fedm.physical_constants import *
+from fedm.file_io import *
+from fedm.functions import *
+
+# Optimization parameters.
+parameters["form_compiler"]["optimize"]     = True
+parameters["form_compiler"]["cpp_optimize"] = True
+parameters['krylov_solver']['nonzero_initial_guess'] = True
+
+# Defining tye of used solver and its parameters.
+linear_solver = "mumps" # Setting linear solver: mumps | gmres | lu
+maximum_iterations = 50 # Setting up maximum number of nonlinear solver iterations
+relative_tolerance = 1e-10 # Setting up relative tolerance
+
+# ============================================================================
+# Definition of the simulation conditions, model and coordinates
+# ============================================================================
+model = 'Time_of_flight' # Model name
+coordinates = 'cylindrical' # Coordinates choice
+gas = 'Air'
+Tgas = 300.0 # Gas temperature in [K]
+p0 = 760.0 # Pressure in [Torr]
+N0 = p0*3.21877e22 # Number density in [m^-3]
+
+
+# ============================================================================
+# Defining number of species for which the problem is solved, their properties and creating output files.
+# ============================================================================
+number_of_species = 1
+particle_species_type = ['electrons', 'analytical solution'] # Defining particle species types, where the values are used as names for output files
+M = me
+charge = -elementary_charge
+equation_type = ['drift-diffusion-reaction'] # Defining the type of the equation (reaction | diffusion-reaction | drift-diffusion-reaction)
+wez = 1.7e5 # Electron drift velocity z component [m/s] 
+De = 0.12 # Electron Diffusion coefficient [m^2/s]
+alpha_e = 5009.51 # Effective ionization coefficient [1/m]
+x0 =3e-4
+l = 0.00004 # 0.04 # Gaussian characteristic width
+
+log('properties', files.model_log, gas, model, particle_species_type, M, charge) # Writting particle properties into a log file
+vtkfile_u = output_files('pvd', 'number density', particle_species_type) # Setting-up output files
+
+# ============================================================================
+# Definition of the time variables.
+# ============================================================================
+t_old = None # Previous time step
+t0 = 0 # Initial time step
+t = t0 # Current time step
+T_final = 3e-9 # Simulation time end [s]
+
+dt_init = 1e-11 # Initial time step size
+dt = Expression("time_step", time_step = dt_init, degree = 0) # Time step size [s]
+dt_old = Expression("time_step", time_step = 1e30, degree = 0) # Time step size [s] set up as a large value to reduce the order of BDF.
+
+t_output_step =10* dt_init #0.5e-9 # Time step intervals at which the results are printed to file
+t_output = t0 + 10*dt_init # Initial output time step
+
+
+# ============================================================================
+# Defining the geometry of the problem and corresponding boundaries.
+# ============================================================================
+if coordinates == 'cylindrical':
+    #r = Expression('x[0]', degree = 1)
+    z = Expression('x[0]', degree = 1)
+
+# Gap length and width
+box_height = 1e-3 # [m]
+
+boundaries = [['point', 0.0, 0.0],\
+                ['point', 0.0, box_height]] # Defining list of boundaries lying between z0 and z1
+
+# ============================================================================
+# Mesh setup. Structured mesh is generated using built-in mesh generator.
+# ============================================================================
+mesh = IntervalMesh(4000, 0. , box_height) # Generating structured mesh.
+mesh_statistics(mesh) # Prints number of elements, minimal and maximal cell diameter.
+h = MPI.max(MPI.comm_world, mesh.hmax()) # Maximuml cell size in mesh.
+
+log('conditions', files.model_log, dt.time_step, 'None', p0, box_height, N0, Tgas)
+log('initial time', files.model_log, t)
+
+# ============================================================================
+# Defining type of elements and function space, test functions, trial functions and functions for storing variables, and weak form
+# of equation.
+# ============================================================================
+V = FunctionSpace(mesh, 'P', 2) # Defining function space
+W = VectorFunctionSpace(mesh, 'P', 1) # Defining vector function space
+
+u = TrialFunction(V) # Defining trial function
+v = TestFunction(V) # Defining test function
+u_old = Function(V) # Defining function for storing the data at k-1 time step
+u_old1 = Function(V) # Defining function for storing the data at k-2 time step
+u_new = Function(V) # Defining function for storing the data at k time step
+
+u_analytical  = Expression('std::log(exp(-(pow((x[0] - x0 -w*t)/l, 2))/(1 + 4.0*D*t/pow(l,2))+alpha*w*t)/pow(1 + 4*D*t/pow(l,2),0.5))', x0=x0, D = De, w = wez, alpha = alpha_e, t = t, pi=pi, l=l, degree = 3) # Analytical solution of the particle balance equation.
+u_old.assign(interpolate(u_analytical , V)) # Setting up value at k-1 time step
+u_old1.assign(interpolate(u_analytical , V)) # Setting up value at k-2 time step
+
+w = interpolate(Constant((wez, )), W)
+D = interpolate(Constant(De), V) # Diffusion coefficient [m^2/s]
+alpha_eff = interpolate(Constant(alpha_e), V) #Effective ionization coefficient [1/m]
+
+Gamma = -grad(D*exp(u)) + w*exp(u) # Defining electron flux [m^{-2} s^{-1}]
+f = Expression('exp(-(pow((x[0] - x0 -w*t)/l, 2))/(1 + 4.0*D*t/pow(l,2))+alpha*w*t)*(w*alpha)/pow(1 + 4*D*t/pow(l,2),0.5)', x0=x0, D = De, w = wez, alpha = alpha_e, t = t, pi=pi, l=l,  degree = 2) # Defining source term
+
+F = weak_form_balance_equation_log_representation(equation_type[0], dt, dt_old, dx, u, u_old, u_old1, v, f, Gamma) # Definition of variational formulation of the balance equation for the electrons
+
+#u_new.assign(interpolate(Expression('std::log(exp(-(pow((x[0] - x0)/l, 2))) + DOLFIN_EPS)', x0=x0, l=l, degree = 2), V)) # Setting up initial guess for nonlinear solver
+u_new.assign(interpolate(Expression('std::log(exp(-(pow((x[0] - x0 -w*t)/l, 2))/(1 + 4.0*D*t/pow(l,2))+alpha*w*t)/pow(1 + 4*D*t/pow(l,2),0.5) + DOLFIN_EPS)', x0=x0, D = De, w = wez, alpha = alpha_e, t = t, pi=pi, l=l, degree = 3), V)) # Setting up initial guess for nonlinear solver
+
+# ============================================================================
+# Setting-up nonlinear solver
+# ============================================================================
+# Defining the problem
+F = action(F, u_new)
+J = derivative(F, u_new, u)
+problem = Problem(J, F, [])
+
+# Initializing nonlinear solver and setting up the parameters
+nonlinear_solver = PETScSNESSolver() # Nonlinear solver initialization
+nonlinear_solver.parameters['relative_tolerance'] = relative_tolerance # Setting up relative tolerance of the nonlinear solver
+nonlinear_solver.parameters["linear_solver"]= linear_solver # Setting up linear solver
+nonlinear_solver.parameters['maximum_iterations'] = maximum_iterations # Setting up maximum number of iterations
+# nonlinear_solver.parameters["preconditioner"]="hypre_amg" # Setting the preconditioner, uncomment if iterative solver is used
+
+n_exact = Function(V) # Defining function for storing the data at k-2 time step
+n_num = Function(V) # Defining function for storing the data at k time step
+
+while abs(t-T_final)/T_final > 1e-6:
+    t_old = t # Updating old time steps
+    u_old1.assign(u_old) # Updating variable value in k-2 time step
+    u_old.assign(u_new) # Updating variable value in k-1 time step
+    t += dt.time_step # Updating the new  time steps
+
+    log('time', files.model_log, t) # Time logging
+    print_time(t) # Printing out current time step
+
+    f.t=t # Updating the source term for the current time step
+    u_analytical.t = t # Updating the analytical solution for the current time step
+
+    nonlinear_solver.solve(problem, u_new.vector()) # Solving the system of equations
+
+    if abs(t-t_output)/t_output <= 1e-6:
+
+        n_exact.assign(project(exp(u_analytical), V, solver_type='mumps'))
+        n_num.assign(project(exp(u_new), V, solver_type='mumps'))
+
+        relative_error = errornorm(n_num, n_exact, 'l2')/norm(n_exact, 'l2') # Calculating relative difference between exact analytical and numerical solution
+        with open(files.error_file, "a") as f_err:
+            f_err.write('h_max = ' + str(h) + '\t dt = ' + str(dt.time_step) + '\t relative_error = ' + str(relative_error) + '\n')
+        if(MPI.rank(MPI.comm_world)==0):
+            print(relative_error)
+        vtkfile_u[0] <<  (n_num, t)
+        vtkfile_u[1] << (n_exact, t)
+        t_output += t_output_step
+        print("Saved")
+
+    if t > (t0 + dt_init):
+        dt_old.time_step = dt.time_step # For initialization BDF1 is used and after initial step BDF2 is activated
+        if(MPI.rank(MPI.comm_world)==0):
+            print(str(dt_old.time_step) + '\t' + str(dt.time_step) +'\n')
+
+
+print("Finished")