Fixes from Fortitude linter (#190)

* Add fortitude.toml
* Linter fixes (adding intent attributes mostly)
* Ignore S102
* More rule ignores for now
* Apply autofixable fixes
* Fix most of linter errors
* Enable missing-intent rule

fortitude.toml

@@ -0,0 +1,12 @@
+[check]
+ignore = [
+  "S001", # line-too-long
+  "S051", # deprecated-relational-operator (fix available)
+  "S101", # trailing-whitespace
+  "S102", # incorrect-space-before-comment, we should enable this, autofix enable
+  "M011", # use-all (should use "only:")
+  "M001", # procedure-not-in-module (need a per-file ignore for init.F90)
+  "T042", # assumed-size-character-intent TODO: We should fix all instances!
+]
+line-length = 132
+show-fixes = true

src/analysis.F90

@@ -28,7 +28,6 @@ subroutine analysis(x, y, z, vx, vy, vz, fxc, fyc, fzc, eclas)
       use mod_analyze_geometry
       use mod_io
       use mod_system, only: am
-      implicit none
       real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
       real(DP), intent(in) :: fxc(:, :), fyc(:, :), fzc(:, :)
       real(DP), intent(in) :: vx(:, :), vy(:, :), vz(:, :)
@@ -102,7 +101,6 @@ subroutine trajout(x, y, z, time_step)
       use mod_general, only: nwalk, natom, sim_time
       use mod_mpi, only: get_mpi_rank
       use mod_system, only: names
-      implicit none
       real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
       integer, intent(in) :: time_step
       integer :: iat, iw

src/cmdline.F90

@@ -1,12 +1,12 @@
 module mod_cmdline
    use mod_interfaces, only: print_compile_info
+   implicit none
    private
    public :: get_cmdline
 
 contains
 
    subroutine print_help()
-      implicit none
       integer, dimension(8) :: time_data
 
       call date_and_time(values=time_data)

src/ekin.F90

@@ -15,7 +15,6 @@ subroutine temperature(px, py, pz, amt, eclas)
       use mod_nhc, only: inose, get_nhcham
       use mod_gle, only: get_langham
       use mod_shake, only: nshake
-      implicit none
       integer :: iw, iat
       real(DP), intent(in) :: px(:, :), py(:, :), pz(:, :)
       real(DP), intent(in) :: amt(:, :)
@@ -68,7 +67,6 @@ end subroutine temperature
    real(DP) function ekin_v(vx, vy, vz)
       use mod_general, only: nwalk, natom
       use mod_system, only: am
-      implicit none
       real(DP), intent(in) :: vx(:, :), vy(:, :), vz(:, :)
       real(DP) :: temp1, ekin_mom
       integer :: iw, iat

src/en_restraint.F90

@@ -109,7 +109,7 @@ subroutine energy_restraint(x, y, z, px, py, pz, eclas)
 
             !Iterative procedure
             convercrit = 100
-            do while (convercrit > 0.00001)
+            do while (convercrit > 0.00001D0)
                ! deltaE(t+dt) prediction - improves the accuracy
                deltaEnext = 0
                do iat = 1, natom
@@ -166,7 +166,7 @@ subroutine energy_restraint(x, y, z, px, py, pz, eclas)
             eclas = eclas ! + quadratic_restraint_energy
 
             !Output to en_restraint.dat
-            write (UERMD, '(I8,F16.8,E20.10,E20.10,F16.8)') it, excE * AUTOEV, deltaE, 0.0, 0.0
+            write (UERMD, '(I8,F16.8,E20.10,E20.10,F16.8)') it, excE * AUTOEV, deltaE, 0.0D0, 0.0D0
 
          end if
 

src/error.F90

@@ -28,6 +28,7 @@ module mod_error
 
    abstract interface
       subroutine error(filename, line_number, message)
+         implicit none
          character(len=*), intent(in) :: filename
          integer, intent(in) :: line_number
          character(len=*), intent(in) :: message

src/fftw_interface.F90

@@ -38,7 +38,7 @@ subroutine fftw_normalmodes_init(nwalk)
 
       deallocate (x_tmp)
       deallocate (cx_tmp)
-   end subroutine
+   end subroutine fftw_normalmodes_init
 
    ! Simple wrapper functions around the FFTW interface.
    subroutine dft_normalmode2cart(nm, cart)
@@ -72,16 +72,16 @@ subroutine fftw_normalmodes_init(nwalk)
    end subroutine fftw_normalmodes_init
 
    subroutine dft_normalmode2cart(nm, cart)
-      complex(C_DOUBLE_COMPLEX), dimension(:) :: nm
-      real(C_DOUBLE), dimension(:) :: cart
+      complex(C_DOUBLE_COMPLEX), dimension(:), intent(inout) :: nm
+      real(C_DOUBLE), dimension(:), intent(inout) :: cart
       cart = 0.0D0
       nm = (0.0D0, 0.0D0)
       call not_compiled_with('FFTW library')
    end subroutine dft_normalmode2cart
 
    subroutine dft_cart2normalmode(cart, nm)
-      complex(C_DOUBLE_COMPLEX), dimension(:) :: nm
-      real(C_DOUBLE), dimension(:) :: cart
+      complex(C_DOUBLE_COMPLEX), dimension(:), intent(inout) :: nm
+      real(C_DOUBLE), dimension(:), intent(inout) :: cart
       cart = 0.0D0
       nm = (0.0D0, 0.0D0)
       call not_compiled_with('FFTW library')

src/force_abin.F90

@@ -165,7 +165,7 @@ real(DP) function read_energy(engrad_unit, abort) result(energy)
 !$OMP FLUSH(abort)
          return
       end if
-   end function
+   end function read_energy
 
    subroutine read_forces(fx, fy, fz, num_atom, iw, engrad_unit, abort)
       use mod_files, only: stderr
@@ -209,7 +209,6 @@ subroutine force_abin(x, y, z, fx, fy, fz, eclas, chpot, walkmax)
       use mod_lz, only: nstate_lz, tocalc_lz, en_array_lz, istate_lz, write_lz_data
       use mod_qmmm, only: natqm
       use mod_utils, only: toupper, append_rank
-      implicit none
       real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
       real(DP), intent(out) :: fx(:, :), fy(:, :), fz(:, :)
       real(DP), intent(out) :: eclas
@@ -325,7 +324,6 @@ subroutine oniom(x, y, z, fx, fy, fz, eclas, iw, abort)
       use mod_qmmm, only: natqm
       use mod_sh_integ, only: nstate
       use mod_sh, only: en_array, istate
-      implicit none
       real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
       real(DP), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
       real(DP), intent(inout) :: eclas

src/force_bound.F90

@@ -61,7 +61,7 @@ subroutine sbc_init(x, y, z)
          write (*, *) 'Calculating cluster radius from given densty.'
          rho = rho * fact !conversion from g/L to atomic units
          rb_sbc = mass_total / rho * 3 / 4 / PI
-         rb_sbc = rb_sbc**(1 / 3.)
+         rb_sbc = rb_sbc**(1 / 3.0D0)
       end if
 
       if (rmax > rb_sbc) then
@@ -73,7 +73,7 @@ subroutine sbc_init(x, y, z)
 
       write (*, *) 'rb_sbc[A]=', rb_sbc / ang
 
-   end subroutine
+   end subroutine sbc_init
 
    subroutine force_sbc(x, y, z, fx, fy, fz, walkmax)
       use mod_const, only: ANG
@@ -118,7 +118,7 @@ subroutine force_sbc(x, y, z, fx, fy, fz, walkmax)
       end if
 
       return
-   end subroutine
+   end subroutine force_sbc
 
    ! TODO: This could be a general purpose routine,
    ! move to utils

src/force_h2o.F90

@@ -129,6 +129,13 @@ subroutine force_h2o_cvrqd(x, y, z, fx, fy, fz, Eclas, natom, nbeads)
       ! TODO: Given the small difference between the Schwenke potential,
       ! we might not need to implement numerical forces here.
       ! call numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
+      ! Just to squash compiler warnings
+      if (.false.) then
+         print*,natom
+         fx = 0.0D0
+         fy = 0.0D0
+         fz = 0.0D0
+      end if
 
    end subroutine force_h2o_cvrqd
 
@@ -159,7 +166,7 @@ subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
       real(DP) :: Epot_delta(1)
 
       real(DP) :: Eclas_orig
-      real(DP) :: delta = 5.0E-5_DP
+      real(DP), parameter :: DELTA = 5.0E-5_DP
       integer :: i, j, k
 
       ! Calculate forces numerically using central differences
@@ -180,11 +187,11 @@ subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
                ! Move the atom forwards
                select case (k)
                case (1)
-                  x_new_forward(i, j) = x_new_forward(i, j) + delta
+                  x_new_forward(i, j) = x_new_forward(i, j) + DELTA
                case (2)
-                  y_new_forward(i, j) = y_new_forward(i, j) + delta
+                  y_new_forward(i, j) = y_new_forward(i, j) + DELTA
                case (3)
-                  z_new_forward(i, j) = z_new_forward(i, j) + delta
+                  z_new_forward(i, j) = z_new_forward(i, j) + DELTA
                end select
 
                ! Calculate the energy for the forward perturbed geometry
@@ -197,11 +204,11 @@ subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
                ! Calculate the numerical force
                select case (k)
                case (1)
-                  fx(i, j) = -(Epot_delta(1) - Eclas_orig) / delta
+                  fx(i, j) = -(Epot_delta(1) - Eclas_orig) / DELTA
                case (2)
-                  fy(i, j) = -(Epot_delta(1) - Eclas_orig) / delta
+                  fy(i, j) = -(Epot_delta(1) - Eclas_orig) / DELTA
                case (3)
-                  fz(i, j) = -(Epot_delta(1) - Eclas_orig) / delta
+                  fz(i, j) = -(Epot_delta(1) - Eclas_orig) / DELTA
                end select
             end do
          end do

src/force_spline.F90

@@ -87,7 +87,7 @@ subroutine finalize_spline()
       if (allocated(second_derivatives)) then
          deallocate (second_derivatives)
       end if
-   end subroutine
+   end subroutine finalize_spline
 
    subroutine read_grid(fname, x_grid, y_grid, grid_size)
       use mod_files, only: stdout
@@ -122,7 +122,7 @@ subroutine read_grid(fname, x_grid, y_grid, grid_size)
       end do
       close (u)
 
-   end subroutine
+   end subroutine read_grid
 
    subroutine validate_grid(x_grid, ngrid)
       real(DP), dimension(ngrid), intent(in) :: x_grid
@@ -141,7 +141,7 @@ subroutine validate_grid(x_grid, ngrid)
             return
          end if
       end do
-   end subroutine
+   end subroutine validate_grid
 
    subroutine print_splined_potential(fname, x_grid, grid_size)
       character(len=*), intent(in) :: fname
@@ -158,6 +158,6 @@ subroutine print_splined_potential(fname, x_grid, grid_size)
          x = x + dx
       end do
       close (u)
-   end subroutine
+   end subroutine print_splined_potential
 
-end module
+end module mod_splined_grid

src/force_tcpb.F90

@@ -33,7 +33,7 @@ module mod_force_tcpb
       character(len=1024) :: input_file = ''
       ! This make TC reuse WF from previous step.
       integer :: globaltreatment = 0
-   end type
+   end type tcpb_params
    type(tcpb_params) :: tcpb
    character(len=5), allocatable :: qmattypes(:)
    save

src/forces.F90

@@ -260,9 +260,9 @@ subroutine force_quantum(fx, fy, fz, x, y, z, amg, quantum_energy)
             fz(j, i) = (z(j, i) - z(j, kplus))
             fz(j, i) = fz(j, i) + (z(j, i) - z(j, kminus))
             fz(j, i) = -fz(j, i) * ak(j, i)
-            equant = equant + 0.5 * ak(j, i) * (x(j, i) - x(j, kplus))**2
-            equant = equant + 0.5 * ak(j, i) * (y(j, i) - y(j, kplus))**2
-            equant = equant + 0.5 * ak(j, i) * (z(j, i) - z(j, kplus))**2
+            equant = equant + 0.5D0 * ak(j, i) * (x(j, i) - x(j, kplus))**2
+            equant = equant + 0.5D0 * ak(j, i) * (y(j, i) - y(j, kplus))**2
+            equant = equant + 0.5D0 * ak(j, i) * (z(j, i) - z(j, kplus))**2
          end do
       end do
    end if

src/fortran_interfaces.F90

@@ -6,18 +6,22 @@
 module mod_interfaces
    use, intrinsic :: iso_c_binding, only: C_INT, C_INT32_T
    use mod_const, only: DP
+   implicit none
    public
    interface
 
       subroutine print_compile_info()
+         implicit none
       end subroutine print_compile_info
 
       subroutine finish(error_code)
+         implicit none
          integer, intent(in) :: error_code
       end subroutine finish
 
       subroutine force_clas(fx, fy, fz, x, y, z, eclas, chpot)
          import :: DP
+         implicit none
          real(DP), intent(inout) :: x(:, :), y(:, :), z(:, :)
          real(DP), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
          real(DP), intent(out) :: eclas
@@ -26,6 +30,7 @@ end subroutine force_clas
 
       subroutine force_quantum(fx, fy, fz, x, y, z, amg, energy)
          import :: DP
+         implicit none
          real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
          real(DP), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
          real(DP), intent(in) :: amg(:, :)
@@ -34,6 +39,7 @@ end subroutine force_quantum
 
       subroutine force_wrapper(x, y, z, fx, fy, fz, eclas, chpot, walkmax)
          import :: DP
+         implicit none
          real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
          real(DP), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
          real(DP), intent(out) :: eclas
@@ -42,13 +48,15 @@ subroutine force_wrapper(x, y, z, fx, fy, fz, eclas, chpot, walkmax)
       end subroutine force_wrapper
 
       subroutine omp_set_num_threads(nthreads)
+         implicit none
          integer, intent(in) :: nthreads
       end subroutine omp_set_num_threads
 
       ! TODO: This interface currently doesn't work, probably because
       ! of how we pass the 2D arrays...
       !subroutine force_water(x, y, z, fx, fy, fz, eclas, natom, walkmax, watpot) !bind(C)
       !   use, intrinsic :: iso_c_binding
+      !   implicit none
       !   real(C_DOUBLE), intent(in) :: x(:, :), y(:, :), z(:, :)
       !   real(C_DOUBLE), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
       !   real(C_DOUBLE), intent(inout) :: eclas
@@ -59,21 +67,24 @@ end subroutine omp_set_num_threads
       ! int usleep(useconds_t useconds)
       function usleep(useconds) bind(c, name='usleep')
          import :: C_INT, C_INT32_T
-         integer(kind=C_INT32_T), value :: useconds
+         implicit none
+         integer(kind=C_INT32_T), intent(in), value :: useconds
          integer(kind=C_INT) :: usleep
       end function usleep
 
       ! Computes potential energy of a water molecule
       ! using Schwenke potential, see h2o_schwenke.f
       subroutine h2o_pot_schwenke(rij, v, n)
          import :: DP
+         implicit none
          integer, intent(in) :: n
          real(DP), intent(in) :: rij(n, 3)
          real(DP), intent(out) :: v(n)
       end subroutine h2o_pot_schwenke
 
       subroutine h2o_pot_cvrqd(V, rOH1, rOH2, aHOH, mH, mO)
          import :: DP
+         implicit none
          real(DP), intent(out) :: V
          real(DP), intent(in) :: rOH1, rOH2, aHOH, mH, mO
       end subroutine h2o_pot_cvrqd