code cleaning

Author: danielpeter

DATA/IRIS_EMC/README.md

@@ -49,7 +49,7 @@ Then, select in the `DATA/Par_file`:
 ```
 MODEL            =  EMC_model
 ```
-to read in and use the EMC model. 
+to read in and use the EMC model.
 
 Additionally, for local EMC models the mesher `xmeshfem3D` can use parameters to produce local meshes, with a cut-off depth and local doubling layers.
 In `Par_file`, the following settings could be defined, for example in the Alaska model case:
@@ -95,7 +95,7 @@ which can be used as a guideline to select a stable `DT` size.
 
 ## Implementation
 
-Currently, we support the above mentioned Alaska and CVM model files only. 
+Currently, we support the above mentioned Alaska and CVM model files only.
 Other models might define different parameters and are likely not compatible at the moment.
 
 More general support will hopefully come in future.

src/shared/broadcast_computed_parameters.f90

@@ -367,7 +367,7 @@ subroutine broadcast_computed_parameters()
     EMC_MODEL_TISO = bcast_logical(74)
     EMC_MODEL_QMU = bcast_logical(75)
     FULL_GRAVITY = bcast_logical(76)
-    USE_SINSQ_STF = bcast_logical(77) 
+    USE_SINSQ_STF = bcast_logical(77)
     HDF5_ENABLED = bcast_logical(78)
     HDF5_FOR_MOVIES = bcast_logical(79)
     OUTPUT_SEISMOS_HDF5 = bcast_logical(80)

src/specfem3D/SIEM_prepare_solver.F90

@@ -1636,13 +1636,13 @@ subroutine SIEM_prepare_seismos()
 
   ! additional scaling factors for gravity seismograms
   scale_accel = scale_veloc * scale_t_inv        ! [m / s^2]
-  scale_phi   = scale_displ**2 * scale_t_inv**2  ! [m^2 / s^2] 
-  scale_pgrav = scale_displ * scale_t_inv**2     ! [m / s^2] 
-  
-  ! strain is defined as second time integral 
-  ! of grad grad phi here we just output 
-  ! grad grad phi so scale by units of 1/s^2  
-  scale_hgrav =  scale_t_inv**2     ! [1 / s^2] 
+  scale_phi   = scale_displ**2 * scale_t_inv**2  ! [m^2 / s^2]
+  scale_pgrav = scale_displ * scale_t_inv**2     ! [m / s^2]
+
+  ! strain is defined as second time integral
+  ! of grad grad phi here we just output
+  ! grad grad phi so scale by units of 1/s^2
+  scale_hgrav =  scale_t_inv**2     ! [1 / s^2]
 
 
   ! allocate seismogram array

src/specfem3D/SIEM_solver_petsc.F90

@@ -80,23 +80,23 @@
 !   call VecSetValues(bvec,neq,l2gdof(1:),y,ADD_VALUES,ierr)
 ! well, until a better solution is found.
 
-! 5/12/25 - WE: A further issue with this is the variables ix and y 
-!  for single values e.g. originally 
+! 5/12/25 - WE: A further issue with this is the variables ix and y
+!  for single values e.g. originally
 !  call VecSetValues(interface_gvec1,1,igdof,rval,INSERT_VALUES,ierr)
-!  needs to be written as 
+!  needs to be written as
 !  call VecSetValues(interface_gvec1,1,[igdof],[rval],INSERT_VALUES,ierr)
-!  also for MatSetValues(Mat mat, PetscInt m, const PetscInt idxm[], 
-!                        PetscInt n, const PetscInt idxn[], 
+!  also for MatSetValues(Mat mat, PetscInt m, const PetscInt idxm[],
+!                        PetscInt n, const PetscInt idxn[],
 !                        const PetscScalar v[], InsertMode addv)
 ! the variables idxm, idxn, and v.
-! Other examples in: 
-!   MatMPIAIJSetPreallocation --> requires PETSC_NULL_INTEGER_ARRAY 
+! Other examples in:
+!   MatMPIAIJSetPreallocation --> requires PETSC_NULL_INTEGER_ARRAY
 !   instead of PETSC_NULL_INTEGER
 
 ! For MatSetValues - flattening
 !   MatSetValues documentation suggests in f90 varray needs to be flattened
-!   note that F90 is column major but C is row major. 
-! It appears petsc updated VecGetArrayF90 back to VecGetArray in 
+!   note that F90 is column major but C is row major.
+! It appears petsc updated VecGetArrayF90 back to VecGetArray in
 ! 3.23 (https://petsc.org/release/changes/323/)
 
 module siem_solver_petsc
@@ -228,7 +228,7 @@ module siem_solver_petsc
 #define API_F90_SUFFIX 0
 #endif
 
-! In version 3.23 
+! In version 3.23
 ! MatInfo changed from arrays to derived data types
 #if PETSC_VERSION_GE(3,22,0)
 #define PETSC_INFO_DERIVED_TYPE 1
@@ -282,7 +282,7 @@ module siem_solver_petsc
   type(tPC)               :: pc
   PetscErrorCode          :: ierr
   PetscInt                :: nzeros_max,nzeros_min
-  PetscInt                :: ig0,ig1, ONE 
+  PetscInt                :: ig0,ig1, ONE
 #endif
 
   ! public function
@@ -312,7 +312,7 @@ subroutine petsc_initialize1()
   use specfem_par, only: ADD_TRINF,SIMULATION_TYPE
 
   use specfem_par_full_gravity, only: ggdof_ic1,ggdof_oc1,ggdof_cm1,ggdof_trinf1,ggdof_inf1
-  
+
   implicit none
   type(tVec) :: nzeror_gvec1,nzeror_dvec1,nzeror_ovec1,iproc_gvec1, &
                 interface_gvec1,ninterface_dvec1,ninterface_ovec1,nself_gvec1
@@ -618,9 +618,9 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecGetArrayF90(nself_gvec1,rnself_array1,ierr)
-#else 
+#else
   call VecGetArray(nself_gvec1,rnself_array1,ierr)
-#endif 
+#endif
 
   allocate(nself_array1(n))
   nself_array1 = int(rnself_array1(1:n))
@@ -629,9 +629,9 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(nself_gvec1,rnself_array1,ierr)
-#else 
+#else
   call VecRestoreArray(nself_gvec1,rnself_array1,ierr)
-#endif 
+#endif
 
   call VecDestroy(nself_gvec1,ierr)
 
@@ -749,9 +749,9 @@ subroutine petsc_initialize1()
   call VecGetLocalSize(nzeror_dvec1,n,ierr)
 #if API_F90_SUFFIX
   call VecGetArrayF90(nzeror_dvec1,nzeror_darray1,ierr)
-#else 
+#else
   call VecGetArray(nzeror_dvec1,nzeror_darray1,ierr)
-#endif 
+#endif
 
 
   allocate(nnzero_diag1(n))
@@ -765,28 +765,28 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(nzeror_dvec1,nzeror_darray1,ierr)
-#else 
+#else
   call VecRestoreArray(nzeror_dvec1,nzeror_darray1,ierr)
-#endif 
+#endif
 
   call VecDestroy(nzeror_dvec1,ierr)
 
   ! off-diagonal matrix
 #if API_F90_SUFFIX
   call VecGetArrayF90(nzeror_ovec1,nzeror_oarray1,ierr)
-#else 
+#else
   call VecGetArray(nzeror_ovec1,nzeror_oarray1,ierr)
-#endif 
+#endif
 
 
   allocate(nnzero_offdiag1(n))
   nnzero_offdiag1(:) = int(nzeror_oarray1(1:n))
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(nzeror_ovec1,nzeror_oarray1,ierr)
-#else 
+#else
   call VecRestoreArray(nzeror_ovec1,nzeror_oarray1,ierr)
-#endif 
+#endif
 
   call VecDestroy(nzeror_ovec1,ierr)
 
@@ -795,9 +795,9 @@ subroutine petsc_initialize1()
   ! 8 therefore to be safe we need to subtract this from all
 #if API_F90_SUFFIX
   call VecGetArrayF90(ninterface_dvec1,rninterface_darray1,ierr)
-#else 
+#else
   call VecGetArray(ninterface_dvec1,rninterface_darray1,ierr)
-#endif 
+#endif
 
 
   !where(rninterface_darray1>0.0 .and. rninterface_darray1 < 1.0)rninterface_darray1=1.0
@@ -807,9 +807,9 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(ninterface_dvec1,rninterface_darray1,ierr)
-#else 
+#else
   call VecRestoreArray(ninterface_dvec1,rninterface_darray1,ierr)
-#endif 
+#endif
 
   call VecDestroy(ninterface_dvec1,ierr)
 
@@ -818,9 +818,9 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecGetArrayF90(ninterface_ovec1,rninterface_oarray1,ierr)
-#else 
+#else
   call VecGetArray(ninterface_ovec1,rninterface_oarray1,ierr)
-#endif 
+#endif
 
 
   !where(rninterface_oarray1>0.0 .and. rninterface_oarray1 < 1.0)rninterface_oarray1=1.0
@@ -830,9 +830,9 @@ subroutine petsc_initialize1()
 
 #if API_F90_SUFFIX
   call VecGetArrayF90(ninterface_ovec1,rninterface_oarray1,ierr)
-#else 
+#else
   call VecGetArray(ninterface_ovec1,rninterface_oarray1,ierr)
-#endif 
+#endif
 
   call VecDestroy(ninterface_ovec1,ierr)
 
@@ -867,18 +867,18 @@ subroutine petsc_initialize1()
   ! non-zero array for diagonal/off-diagonal matrix?
 #if API_F90_SUFFIX
   call VecGetArrayF90(nzeror_gvec1,nzeror_array1,ierr); CHECK_PETSC_ERROR(ierr)
-#else 
+#else
   call VecGetArray(nzeror_gvec1,nzeror_array1,ierr); CHECK_PETSC_ERROR(ierr)
-#endif 
+#endif
 
   allocate(inzeror_array1(n))
   inzeror_array1(:) = int(nzeror_array1(1:n))
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(nzeror_gvec1,nzeror_array1,ierr); CHECK_PETSC_ERROR(ierr)
-#else 
+#else
   call VecRestoreArray(nzeror_gvec1,nzeror_array1,ierr); CHECK_PETSC_ERROR(ierr)
-#endif 
+#endif
 
   call VecDestroy(nzeror_gvec1,ierr); CHECK_PETSC_ERROR(ierr)
 
@@ -914,8 +914,8 @@ subroutine petsc_initialize1()
   !
   !        this seems to lead to a much faster petsc_set_matrix1() routine without the re-allocations.
   !        however, the diagonal and in particular the off-diagonal estimate with nzeros_max might be still off.
-  
-  
+
+
 #if PETSC_ARRAY_NULL_API
   ! Later version uses integer array
   call MatMPIAIJSetPreallocation(Amat1,nzeros_max, PETSC_NULL_INTEGER_ARRAY, &
@@ -1195,7 +1195,7 @@ subroutine petsc_set_matrix1()
   !debugging
   logical, parameter :: DEBUG_FILE_OUTPUT = .false.
 
-  ! For the MatGetRow call 
+  ! For the MatGetRow call
   !integer :: ncols
   !integer,dimension(:),allocatable :: cols
   PetscInt :: ncols
@@ -1213,9 +1213,9 @@ subroutine petsc_set_matrix1()
    ! matrix info
 #if PETSC_INFO_DERIVED_TYPE
 MatInfo :: info
-#else 
+#else
   double precision :: info(MAT_INFO_SIZE)
-#endif 
+#endif
 double precision :: mallocsval
 
 
@@ -1459,9 +1459,9 @@ subroutine petsc_set_matrix1()
 
 #if PETSC_INFO_DERIVED_TYPE
 mallocsval = info%mallocs
-#else 
+#else
 mallocsval = info(MAT_INFO_MALLOCS)               ! number of mallocs during MatSetValues()
-#endif 
+#endif
   !memval = info(MAT_INFO_MEMORY)                   ! memory allocated - not provided
   !nonzeros_allocated = info(MAT_INFO_NZ_ALLOCATED) ! nonzero entries allocated
 
@@ -1751,18 +1751,18 @@ subroutine scatter_globalvec1(global_vec,larray)
 
 #if API_F90_SUFFIX
   call VecGetArrayF90(local_vec1,array_data,ierr); CHECK_PETSC_ERROR(ierr)
-#else 
+#else
   call VecGetArray(local_vec1,array_data,ierr); CHECK_PETSC_ERROR(ierr)
-#endif 
+#endif
 
 
   larray(1:n) = array_data(1:n)
 
 #if API_F90_SUFFIX
   call VecRestoreArrayF90(local_vec1,array_data,ierr); CHECK_PETSC_ERROR(ierr)
-#else 
+#else
   call VecRestoreArray(local_vec1,array_data,ierr); CHECK_PETSC_ERROR(ierr)
-#endif 
+#endif
 
   end subroutine scatter_globalvec1
 
@@ -2140,9 +2140,9 @@ subroutine petsc_set_matrix()
   ! matrix info
 #if PETSC_INFO_DERIVED_TYPE
 MatInfo :: info
-#else 
+#else
   double precision :: info(MAT_INFO_SIZE)
-#endif 
+#endif
 double precision :: mallocsval
 
   PetscLogDouble :: bytes
@@ -2252,7 +2252,7 @@ subroutine petsc_set_matrix()
     do iflat = 1, ncount
       do jflat = 1, ncount
         varr((iflat-1)*ncount + jflat) = storekmat_crust_mantle(idof(iflat), idof(jflat), i_elmt)
-      enddo !jflat 
+      enddo !jflat
     enddo !iflat
 
     call MatSetValues(Amat,ncount,igdof(1:ncount),ncount,igdof(1:ncount),varr,ADD_VALUES,ierr); CHECK_PETSC_ERROR(ierr)
@@ -2295,7 +2295,7 @@ subroutine petsc_set_matrix()
       do iflat = 1, ncount
         do jflat = 1, ncount
           varr((iflat-1)*ncount + jflat) = storekmat_trinfinite(idof(iflat), idof(jflat), i_elmt)
-        enddo !jflat 
+        enddo !jflat
       enddo !iflat
       call MatSetValues(Amat,ncount,igdof(1:ncount),ncount,igdof(1:ncount),varr,ADD_VALUES,ierr); CHECK_PETSC_ERROR(ierr)
       deallocate(varr)
@@ -2334,7 +2334,7 @@ subroutine petsc_set_matrix()
     do iflat = 1, ncount
       do jflat = 1, ncount
         varr((iflat-1)*ncount + jflat) = storekmat_infinite(idof(iflat), idof(jflat), i_elmt)
-      enddo !jflat 
+      enddo !jflat
     enddo !iflat
     call MatSetValues(Amat,ncount,igdof(1:ncount),ncount,igdof(1:ncount),varr,ADD_VALUES,ierr); CHECK_PETSC_ERROR(ierr)
     deallocate(varr)
@@ -2357,9 +2357,9 @@ subroutine petsc_set_matrix()
 
 #if PETSC_INFO_DERIVED_TYPE
 mallocsval = info%mallocs
-#else 
+#else
 mallocsval = info(MAT_INFO_MALLOCS)               ! number of mallocs during MatSetValues()
-#endif 
+#endif
 
   ! memory usage
   call PetscMemoryGetCurrentUsage(bytes, ierr); CHECK_PETSC_ERROR(ierr)