ENH: Merge content of warnings branch; Start dealing with flake8 warn…

…ings.

assemble/Advection_Diffusion_CG.F90

@@ -234,7 +234,7 @@ subroutine assemble_advection_diffusion_cg(t, matrix, rhs, state, dt, velocity_n
     character(len = *), optional, intent(in) :: velocity_name
 
     character(len = FIELD_NAME_LEN) :: lvelocity_name, velocity_equation_type
-    integer :: i, j, stat
+    integer :: i, stat
     integer, dimension(:), allocatable :: t_bc_types
     type(scalar_field) :: t_bc, t_bc_2
     type(scalar_field), pointer :: absorption, sinking_velocity, source
@@ -255,8 +255,6 @@ subroutine assemble_advection_diffusion_cg(t, matrix, rhs, state, dt, velocity_n
     type(integer_set), dimension(:), pointer :: colours
     integer :: clr, nnid, len, ele
     integer :: num_threads, thread_num
-    !! Did we successfully prepopulate the transform_to_physical_cache?
-    logical :: cache_valid
 
     type(element_type), dimension(:), allocatable :: supg_element
 

assemble/Advection_Diffusion_FV.F90

@@ -164,14 +164,12 @@ subroutine assemble_advection_diffusion_fv(t, matrix, rhs, state)
     type(scalar_field), pointer :: source, absorption
     type(tensor_field), pointer :: diffusivity
 
-    integer :: i, j, stat
+    integer :: stat
 
     !! Coloring  data structures for OpenMP parallization
     type(integer_set), dimension(:), pointer :: colours
     integer :: clr, nnid, len, ele
     integer :: thread_num
-    !! Did we successfully prepopulate the transform_to_physical_cache?
-    logical :: cache_valid
 
     ewrite(1,*) "In assemble_advection_diffusion_fv"
 

assemble/Assemble_CMC.F90

@@ -151,8 +151,6 @@ subroutine assemble_diagonal_schur(schur_diagonal_matrix,u,inner_m,ctp_m,ct_m)
       ! (i.e. DiagonalSchurComplement):
       type(vector_field) :: inner_m_diagonal
 
-      integer :: i
-
       ewrite(1,*) 'Entering assemble_diagonal_schur'
 
       call zero(schur_diagonal_matrix)

assemble/Foam_Drainage.F90

@@ -49,7 +49,7 @@ subroutine calculate_drainage_source_absor(state)
 
     type(state_type), intent(inout) :: state
 
-    integer :: i, stat
+    integer :: i
     type(vector_field), pointer :: K1, foamvel, liquidvelocity, liqcontentvel, source, absor
     type(scalar_field), pointer :: p, liquidcontent, K2
 

assemble/Foam_Flow.F90

@@ -288,15 +288,14 @@ subroutine calculate_foam_velocity(state, foamvel)
 
     type(state_type), intent(inout) :: state
     type(vector_field), pointer, intent(out) :: foamvel
-    type(vector_field), pointer :: liquidvelocity
     type(scalar_field), pointer :: field
     type(csr_sparsity) :: gradient_sparsity
     type(block_csr_matrix) :: C_m
     type(csr_sparsity) :: mass_sparsity
     type(csr_matrix) :: mass
     type(vector_field) :: cfield
 
-    integer :: i, stat
+    integer :: i
 
     foamvel => extract_vector_field(state, foamvel_name)
     if (have_option(trim(foamvel%option_path)//'/diagnostic')) then

assemble/Hybridized_Helmholtz.F90

@@ -87,18 +87,17 @@ subroutine solve_hybridized_helmholtz(state,D_rhs,U_Rhs,&
     character(len=OPTION_PATH_LEN), intent(in), optional :: solver_option_path
     !
     type(vector_field), pointer :: X, U, down, U_cart
-    type(scalar_field), pointer :: D,f, lambda_nc
+    type(scalar_field), pointer :: D, f
     type(scalar_field) :: lambda
     type(scalar_field), target :: lambda_rhs, u_cpt
     type(csr_sparsity) :: lambda_sparsity, continuity_sparsity
-    type(csr_matrix) :: lambda_mat, continuity_block_mat,continuity_block_mat1
+    type(csr_matrix) :: lambda_mat, continuity_block_mat
     type(block_csr_matrix) :: continuity_mat
     type(mesh_type), pointer :: lambda_mesh
     real :: D0, dt, g, theta
-    integer :: ele,i1, stat, dim1
+    integer :: ele, i1, dim1
     logical :: l_compute_cartesian,l_check_continuity, l_output_dense
     real, dimension(:,:), allocatable :: lambda_mat_dense
-    character(len=OPTION_PATH_LEN) :: constraint_option_string
 
     ewrite(1,*) '  subroutine solve_hybridized_helmholtz('
 
@@ -257,21 +256,20 @@ subroutine assemble_hybridized_helmholtz_ele(D,f,U,X,down,ele, &
          &l_continuity_mat, l_continuity_mat2
     real, allocatable, dimension(:,:) :: helmholtz_loc_mat
     real, allocatable, dimension(:,:,:) :: continuity_face_mat
-    real, allocatable, dimension(:,:) :: scalar_continuity_face_mat
     integer :: ni, face
     integer, dimension(:), pointer :: neigh
-    real, dimension(ele_loc(lambda_rhs,ele)) :: lambda_rhs_loc,lambda_rhs_loc2
+    real, dimension(ele_loc(lambda_rhs,ele)) :: lambda_rhs_loc
     real, dimension(:),allocatable,target :: Rhs_loc
     real, dimension(:,:), allocatable :: local_solver_matrix, local_solver_rhs
     type(element_type) :: U_shape
-    integer :: stat, d_start, d_end, dim1, mdim, uloc,dloc, lloc
+    integer :: d_start, d_end, dim1, mdim, uloc,dloc, lloc
     integer, dimension(mesh_dim(U)) :: U_start, U_end
     type(real_vector), dimension(mesh_dim(U)) :: rhs_u_ptr
     real, dimension(:), pointer :: rhs_d_ptr
     type(real_matrix), dimension(mesh_dim(U)) :: &
          & continuity_mat_u_ptr
     logical :: have_constraint
-    integer :: constraint_choice, n_constraints, constraints_start
+    integer :: n_constraints
 
     !Get some sizes
     lloc = ele_loc(lambda_rhs,ele)
@@ -414,9 +412,6 @@ subroutine reconstruct_U_d_ele(D,f,U,X,down,ele, &
     integer :: d_start, d_end, dim1, mdim, uloc,dloc,lloc
     integer, dimension(mesh_dim(U)) :: U_start, U_end
     type(real_vector), dimension(mesh_dim(U)) :: rhs_u_ptr
-    real, dimension(:), pointer :: rhs_d_ptr
-    type(real_matrix), dimension(mesh_dim(U)) :: &
-         & continuity_mat_u_ptr
     real, dimension(ele_loc(lambda,ele)) :: lambda_val
     real, dimension(:),allocatable,target :: Rhs_loc
     real, dimension(:,:), allocatable :: local_solver_matrix, local_solver_rhs
@@ -573,7 +568,6 @@ subroutine get_local_solver(local_solver_matrix,U,X,down,D,f,ele,&
     real, dimension(mesh_dim(U), X%dim, ele_ngi(U,ele)) :: J
     real, dimension(ele_ngi(x,ele)) :: f_gi
     real, dimension(X%dim, ele_ngi(X,ele)) :: up_gi
-    real, dimension(X%dim) :: up_vec
     real, dimension(mesh_dim(U),ele_loc(U,ele),ele_loc(D,ele)) :: l_div_mat
     real, dimension(mesh_dim(U), mesh_dim(U), ele_ngi(U,ele)) :: Metric, &
          &Metricf
@@ -1091,8 +1085,6 @@ function get_face_normal_manifold(X,ele,face) result (normal)
     real, dimension(X%dim) :: ele_normal_gi, edge_tangent_gi, X_mid_ele,&
          &X_mid_face
     type(element_type) :: X_shape, X_face_shape
-    real, dimension(X%dim,ele_loc(X,ele)) :: X_ele
-    real, dimension(X%dim,face_loc(X,face)) :: X_face
 
     call compute_jacobian(X, ele, J=J, detwei=detwei)
     call compute_jacobian(X,face, J=J_f, detwei=detwei_f, facet=.true.)
@@ -1692,7 +1684,6 @@ subroutine set_coriolis_term_ele(Coriolis_term,f,down,U_local,X,ele)
     real, dimension(mesh_dim(U_local)*ele_loc(U_local,ele)) :: coriolis_rhs
     real, dimension(mesh_dim(U_local), ele_ngi(U_local,ele)) :: U_gi
     real, dimension(mesh_dim(U_local), ele_ngi(U_local,ele)) :: coriolis_gi
-    real, dimension(X%dim) :: up_vec
     integer :: dim1, dim2,uloc,gi
     type(element_type) :: u_shape
 

assemble/Hydrostatic_Pressure.F90

@@ -115,7 +115,7 @@ end subroutine calculate_hydrostatic_pressure
   subroutine calculate_hydrostatic_pressure_gradient(state)
     type(state_type), intent(inout) :: state
 
-    integer :: i, stat
+    integer :: stat
     type(vector_field), pointer :: hpg
 
     hpg => extract_vector_field(state, hpg_name, stat = stat)

assemble/Makefile.dependencies

@@ -691,14 +691,13 @@ Sam_integration.o ../include/sam_integration.mod: Sam_integration.F90 \
    ../include/elements.mod ../include/fdebug.h ../include/field_options.mod \
    ../include/fields.mod ../include/fldebug.mod ../include/futils.mod \
    ../include/global_parameters.mod ../include/halos.mod \
-   ../include/ieee_arithmetic.mod ../include/memory_diagnostics.mod \
-   ../include/metric_tools.mod ../include/mpi_interfaces.mod \
-   ../include/node_boundary.mod ../include/parallel_tools.mod \
-   ../include/pickers.mod ../include/populate_state_module.mod \
-   ../include/quadrature.mod ../include/reference_counting.mod \
-   ../include/reserve_state_module.mod ../include/state_module.mod \
-   ../include/surface_id_interleaving.mod ../include/surfacelabels.mod \
-   ../include/tictoc.mod
+   ../include/memory_diagnostics.mod ../include/metric_tools.mod \
+   ../include/mpi_interfaces.mod ../include/node_boundary.mod \
+   ../include/parallel_tools.mod ../include/pickers.mod \
+   ../include/populate_state_module.mod ../include/quadrature.mod \
+   ../include/reference_counting.mod ../include/reserve_state_module.mod \
+   ../include/state_module.mod ../include/surface_id_interleaving.mod \
+   ../include/surfacelabels.mod ../include/tictoc.mod
 
 ../include/shallow_water_equations.mod: Shallow_Water_Equations.o
 	@true
@@ -717,10 +716,9 @@ Slope_limiters_DG.o ../include/slope_limiters_dg.mod: Slope_limiters_DG.F90 \
    ../include/bound_field_module.mod ../include/elements.mod \
    ../include/eventcounter.mod ../include/fdebug.h \
    ../include/field_options.mod ../include/fields.mod ../include/fldebug.mod \
-   ../include/ieee_arithmetic.mod ../include/sparse_tools.mod \
-   ../include/state_fields_module.mod ../include/state_module.mod \
-   ../include/transform_elements.mod ../include/vector_tools.mod \
-   ../include/vtk_interfaces.mod
+   ../include/sparse_tools.mod ../include/state_fields_module.mod \
+   ../include/state_module.mod ../include/transform_elements.mod \
+   ../include/vector_tools.mod ../include/vtk_interfaces.mod
 
 ../include/solenoidal_interpolation_module.mod: Solenoidal_interpolation.o
 	@true
@@ -844,7 +842,7 @@ Zoltan_global_variables.o ../include/zoltan_global_variables.mod: \
 
 Zoltan_integration.o ../include/zoltan_integration.mod: Zoltan_integration.F90 \
    ../include/adapt_integration.mod ../include/boundary_conditions.mod \
-   ../include/boundary_conditions_from_options.mod ../include/c_interfaces.mod \
+   ../include/boundary_conditions_from_options.mod \
    ../include/data_structures.mod ../include/detector_data_types.mod \
    ../include/detector_parallel.mod ../include/detector_tools.mod \
    ../include/element_numbering.mod ../include/elements.mod \

assemble/Manifold_Projections.F90

@@ -162,7 +162,6 @@ subroutine project_cartesian_to_local_transpose_ele(ele, X, U_cartesian, U_local
     real, dimension(mesh_dim(U_local), X%dim, ele_ngi(X,ele)) :: J
     real, dimension(ele_ngi(X,ele)) :: detwei, detJ
     real, dimension(U_cartesian%dim, ele_ngi(X,ele)) :: U_quad
-    real, dimension(mesh_dim(U_local)*ele_loc(U_local,ele)) :: l_rhs
     real, dimension(mesh_dim(U_local), mesh_dim(U_local), ele_loc(U_local,ele), ele_loc(U_local,ele)) :: l_mass
     real, dimension(mesh_dim(U_local)*ele_loc(U_local,ele), mesh_dim(U_local)*ele_loc(U_local,ele)) :: l_big_mat
     real, dimension(mesh_dim(U_local)*ele_loc(U_local,ele)) :: tmp
@@ -172,7 +171,7 @@ subroutine project_cartesian_to_local_transpose_ele(ele, X, U_cartesian, U_local
     real, dimension(X%dim, ele_loc(U_cartesian,ele)) :: rhs
     type(element_type), pointer :: U_shape
     integer, dimension(:), pointer :: U_ele
-    integer :: dim, dim1, dim2, gi, loc, nloc
+    integer :: dim, dim1, dim2, gi, nloc
 
     dim=U_local%dim
 
@@ -318,12 +317,9 @@ subroutine project_local_to_cartesian_transpose_ele(ele, X, U_local, U_cartesian
     real, dimension(ele_loc(U_cartesian,ele), ele_loc(U_cartesian,ele)) :: mass
     real, dimension(mesh_dim(U_local), X%dim, ele_ngi(X,ele)) :: J
     real, dimension(ele_ngi(U_local,ele)) :: detwei
-    real, dimension(U_local%dim, ele_ngi(X,ele)) :: U_quad
-    real, dimension(X%dim, ele_ngi(X,ele)) :: U_cartesian_gi
-    real, dimension(X%dim, ele_loc(U_cartesian,ele)) :: rhs
     real, dimension(U_cartesian%dim, ele_loc(U_cartesian, ele)) :: tmp, U_cartesian_ele
     type(element_type), pointer :: U_shape
-    integer :: d, gi
+    integer :: d
 
     call compute_jacobian(X, ele, J=J, detwei=detwei)
 

assemble/MeshMovement.F90

@@ -26,7 +26,6 @@ module meshmovement
   use sparsity_patterns_meshes
 
   implicit none
-  integer,save :: MeshCount=0
 
   interface
 

assemble/Momentum_Diagnostic_Fields.F90

@@ -67,8 +67,7 @@ subroutine calculate_momentum_diagnostics(state, istate, submaterials, submateri
     type(state_type), dimension(size(state)) :: calculated_state
     type(state_type), dimension(size(submaterials)) :: calculated_submaterials
     type(scalar_field), pointer :: bulk_density, buoyancy_density, sfield
-    type(vector_field), pointer :: vfield, x, velocity
-    type(vector_field) :: prescribed_source
+    type(vector_field), pointer :: vfield, velocity
     type(tensor_field), pointer :: tfield
 
     integer :: stat, i

assemble/Momentum_Equation.F90

@@ -210,8 +210,6 @@ subroutine solve_momentum(state, at_first_timestep, timestep)
 
          ! Change in pressure
          type(scalar_field) :: delta_p
-         ! Change in velocity
-         type(vector_field) :: delta_u
 
          ! Dummy fields
          type(scalar_field), pointer :: dummyscalar, dummydensity, dummypressure

assemble/Multiphase.F90

@@ -289,7 +289,7 @@ subroutine add_fluid_particle_drag(state, istate, u, x, big_m, mom_rhs)
 
          integer :: i, dim
          logical :: not_found ! Error flag. Have we found the fluid phase?
-         integer :: istate_fluid, istate_particle
+         integer :: istate_fluid
 
          ! Types of drag correlation
          integer, parameter :: DRAG_CORRELATION_TYPE_STOKES = 1, DRAG_CORRELATION_TYPE_WEN_YU = 2, DRAG_CORRELATION_TYPE_ERGUN = 3, DRAG_CORRELATION_TYPE_SCHILLER_NAUMANN = 4, DRAG_CORRELATION_TYPE_LAIN_1_1999= 5, DRAG_CORRELATION_TYPE_LAIN_2_2002 = 6
@@ -701,7 +701,7 @@ subroutine add_heat_transfer(state, istate, internal_energy, matrix, rhs)
 
          logical :: is_particle_phase
          logical :: not_found ! Error flag. Have we found the fluid phase?
-         integer :: i, istate_fluid, istate_particle
+         integer :: i, istate_fluid
 
 
          ewrite(1, *) "Entering add_heat_transfer"

assemble/Particle_Diagnostics.F90

@@ -68,9 +68,8 @@ subroutine initialise_constant_particle_diagnostics(state)
     type(state_type), dimension(:), intent(inout) :: state
 
     character(len = OPTION_PATH_LEN) :: group_path, subgroup_path
-    type(scalar_field), pointer :: s_field
     integer :: i, j
-    integer :: particle_groups, list_counter, particle_materials
+    integer :: particle_groups, list_counter
     integer, dimension(:), allocatable :: particle_arrays
 
     type(detector_type), pointer :: particle
@@ -199,14 +198,14 @@ subroutine calculate_field_from_particles(states, state_index, s_field)
     character(len=OPTION_PATH_LEN) :: lgroup, lattribute
     type(vector_field), pointer :: xfield
     type(detector_type), pointer :: particle
-    integer :: i, j
+    integer :: i
     real, allocatable, dimension(:) :: node_values
     real, allocatable, dimension(:) :: node_part_count ! real instead of integer, so we can use halo_accumulate
     integer :: element, node_number
     real, allocatable, dimension(:) :: local_crds
     integer, dimension(:), pointer :: nodes
     integer :: nprocs, att_n
-    real :: att_value, ratio_val
+    real :: att_value
     character(len= OPTION_PATH_LEN) :: lmethod
     logical :: from_particles
 
@@ -693,7 +692,7 @@ subroutine spawn_particles(node_part_count, node_particles, group_arrays, xfield
     integer :: id, group_spawn, ele_spawn, proc_num
     integer :: j, i, k, l, m, dim
     logical :: spawn_group, coords_set, rand_set
-    real :: max_lcoord, rand_lcoord, sum_coords, rand_val
+    real :: max_lcoord, rand_lcoord, rand_val
     real, dimension(:), allocatable :: rand_lcoords
 
     proc_num = getprocno()

assemble/Sam_integration.F90

@@ -1191,7 +1191,7 @@ subroutine allocate_remaining_fields(states)
 
        type(state_type), dimension(:), intent(inout) :: states
 
-       integer :: i, j, k
+       integer :: i, j
        type(scalar_field), pointer :: s_field
        type(tensor_field), pointer :: t_field
        type(vector_field), pointer :: v_field
@@ -1252,7 +1252,6 @@ subroutine sam_init(states, options, max_coplanar_id, metric, external_mesh_name
        integer, dimension(:), pointer :: ndglno
        integer, dimension(:), allocatable :: surfid, sndgln
        integer :: nloc, snloc
-       real, dimension(:), pointer :: x, y, z
        real, dimension(:), allocatable :: metric_handle
        integer :: nfields
        real, dimension(:), pointer :: fields
@@ -1703,9 +1702,6 @@ end subroutine check_sam_linear_remap_validity
 
   subroutine sam_integration_check_options
 
-    integer :: i
-    character (len=OPTION_PATH_LEN) :: continuity_var
-
     !!< Check libsam integration related options
 
     if(.not. isparallel()) then

assemble/Slope_limiters_DG.F90

@@ -1461,16 +1461,15 @@ subroutine limit_fpn(state, t)
     type(scalar_field) :: lowerbound, upperbound, inverse_lumped_mass
     type(csr_matrix), pointer :: mass
 
-    type(csr_sparsity), pointer :: eelist
-    integer :: ele, i, j, k, row, column
+    integer :: ele, i, j, row, column
     integer :: rows, columns
-    real :: node_max, node_min, extra_val, extra_val2
+    real :: node_max, node_min
 
-    integer, dimension(:), pointer :: nodelist, faces, neighbouring_ele_nodes
-    integer, dimension(:), allocatable :: face_nodes, neighbouring_nodes
+    integer, dimension(:), pointer :: nodelist, faces
+    integer, dimension(:), allocatable :: neighbouring_nodes
     integer :: neighbouring_face, neighbouring_ele
     logical, save :: first=.true.
-    logical :: midpoint, extrapolate, pre_dist_mass
+    logical :: midpoint, extrapolate
 
     real :: beta=1.0, mean_val
     type(vector_field), pointer :: position
@@ -1480,9 +1479,7 @@ subroutine limit_fpn(state, t)
     real, dimension(:,:), allocatable :: grad_t
     real :: grad, e_dist
 
-    real, dimension(ele_loc(t,1)) :: weight, tracer_val
-    logical, dimension(ele_loc(t,1)) :: nweight, pweight
-    real :: nodeval, nodemin, nodemax, adjust
+    real, dimension(ele_loc(t,1)) :: tracer_val
 
     integer, dimension(:,:,:), allocatable, save :: nodes_array
 !     real, dimension(2,4) :: local_values

assemble/Timeloop_utilities.F90

@@ -264,11 +264,11 @@ subroutine relax_to_nonlinear(state)
        velocity=>extract_vector_field(state(s), "Velocity", stat)
        if(stat==0) then
           if (have_option(trim(velocity%option_path)//"/prognostic")) then
-             call get_option(trim(velocity%option_path)//"/prognostic/temporal_discretisation/relaxation", itheta, default=0.5)
+            call get_option(trim(velocity%option_path)//"/prognostic/temporal_discretisation/relaxation", itheta, default=0.5)
           else if (have_option(trim(velocity%option_path)//"/prescribed")) then
-             call get_option(trim(velocity%option_path)//"/prescribed/temporal_discretisation/relaxation", itheta, default=1.0)
+            call get_option(trim(velocity%option_path)//"/prescribed/temporal_discretisation/relaxation", itheta, default=1.0)
           else
-	     itheta = 0.5
+            itheta = 0.5
           end if
        else
          itheta = 0.5