Merge pull request #120 from nekStab/update_docs

Update docs
nekStab · Oct 28, 2024 · ec3c9e8 · ec3c9e8
2 parents b03df82 + 711c021
commit ec3c9e8
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Showing 25 changed files with 1,204 additions and 292 deletions.
diff --git a/.gitignore b/.gitignore
@@ -39,4 +39,6 @@
 *~
 
 # test/debug folder
-debug/
+debug/
+*.css
+doc/
diff --git a/example/roessler/main.f90 b/example/roessler/main.f90
@@ -67,7 +67,7 @@ program demo
    sys%jacobian%X = bf
 
    opts = newton_dp_opts(maxiter=30, ifbisect=.false.)
-   call newton(sys, bf, info, tolerance=tol, options=opts, linear_solver=gmres_rdp, scheduler=constant_atol_dp)
+   call newton(sys, bf, gmres_rdp, info, tolerance=tol, options=opts, scheduler=constant_atol_dp)
 
    call sys%eval(bf, residual, tol)
    print *, ''
@@ -88,7 +88,7 @@ program demo
    print *,''
    sys%jacobian%X = bf
 
-   call newton(sys, bf, info, tolerance=tol, options=opts, linear_solver=gmres_rdp, scheduler=dynamic_tol_dp)
+   call newton(sys, bf, gmres_rdp, info, tolerance=tol, options=opts, scheduler=dynamic_tol_dp)
 
    call sys%eval(bf, residual, tol)
    print *, ''
@@ -214,4 +214,4 @@ program demo
    call rename(file_LE, 'example/roessler/PO-chaos_LE.txt')
    print *, ''
 
-end program demo
+end program demo
diff --git a/example/roessler/roessler_OTD.f90 b/example/roessler/roessler_OTD.f90
@@ -276,7 +276,7 @@ subroutine OTD_map(bf, vec_in, Tend, vec_out, t_FTLE, if_rst)
                FTLE_in = 0.0_wp                                   ! reset FTLE computation
                if (if_rst) call set_pos(bf_bkp, bf)               ! reset orbit to avoid orbit drift
             endif
-            call copy_basis(vec_in, vec_out)
+            call copy(vec_in, vec_out)
          end do
          t_complete = modulo(t2, t1)
          if (t_complete > 1e-4_wp) call OTD_step(OTD_roessler, bf, vec_in, FTLE_in, time, t_complete, vec_out, FTLE_out)
@@ -289,7 +289,7 @@ subroutine OTD_map(bf, vec_in, Tend, vec_out, t_FTLE, if_rst)
             FTLE_in = 0.0_wp                                      ! reset FTLE computation
             if (if_rst) call set_pos(bf_bkp, bf)                  ! reset orbit to avoid orbit drift
          endif
-         call copy_basis(vec_in, vec_out)
+         call copy(vec_in, vec_out)
       end do
       t_complete = modulo(Tend, t2)
       if (t_complete > 1e-4_wp) call OTD_step(OTD_roessler, bf, vec_in, FTLE_in, time, t_complete, vec_out, FTLE_out)
@@ -454,4 +454,4 @@ subroutine write_header_LE()
       return
    end subroutine write_header_LE
 
-end module Roessler_OTD
+end module Roessler_OTD
diff --git a/project-file.md b/project-file.md
@@ -6,6 +6,9 @@ media_dir: ./imgs
 graph: false
 license: bsd
 project_github: https://github.com/nekStab/LightKrylov
+display: public
+sort: permission-alpha
+css: ./bootstrap.min.css
 ---
 
 @note

diff --git a/src/AbstractLinops.f90 b/src/AbstractLinops.f90
@@ -402,28 +402,28 @@ subroutine id_matvec_rsp(self, vec_in, vec_out)
         class(Id_rsp), intent(in) :: self
         class(abstract_vector_rsp), intent(in) :: vec_in
         class(abstract_vector_rsp), intent(out) :: vec_out
-        call vec_out%axpby(zero_rsp, vec_in, one_rsp)
+        call copy(vec_out, vec_in)
         return
     end subroutine id_matvec_rsp
     subroutine id_matvec_rdp(self, vec_in, vec_out)
         class(Id_rdp), intent(in) :: self
         class(abstract_vector_rdp), intent(in) :: vec_in
         class(abstract_vector_rdp), intent(out) :: vec_out
-        call vec_out%axpby(zero_rdp, vec_in, one_rdp)
+        call copy(vec_out, vec_in)
         return
     end subroutine id_matvec_rdp
     subroutine id_matvec_csp(self, vec_in, vec_out)
         class(Id_csp), intent(in) :: self
         class(abstract_vector_csp), intent(in) :: vec_in
         class(abstract_vector_csp), intent(out) :: vec_out
-        call vec_out%axpby(zero_csp, vec_in, one_csp)
+        call copy(vec_out, vec_in)
         return
     end subroutine id_matvec_csp
     subroutine id_matvec_cdp(self, vec_in, vec_out)
         class(Id_cdp), intent(in) :: self
         class(abstract_vector_cdp), intent(in) :: vec_in
         class(abstract_vector_cdp), intent(out) :: vec_out
-        call vec_out%axpby(zero_cdp, vec_in, one_cdp)
+        call copy(vec_out, vec_in)
         return
     end subroutine id_matvec_cdp
 

diff --git a/src/AbstractLinops.fypp b/src/AbstractLinops.fypp
@@ -169,7 +169,7 @@ contains
         class(Id_${type[0]}$${kind}$), intent(in) :: self
         class(abstract_vector_${type[0]}$${kind}$), intent(in) :: vec_in
         class(abstract_vector_${type[0]}$${kind}$), intent(out) :: vec_out
-        call vec_out%axpby(zero_${type[0]}$${kind}$, vec_in, one_${type[0]}$${kind}$)
+        call copy(vec_out, vec_in)
         return
     end subroutine id_matvec_${type[0]}$${kind}$
     #:endfor

diff --git a/src/AbstractVectors.f90 b/src/AbstractVectors.f90
@@ -51,7 +51,7 @@ module lightkrylov_AbstractVectors
     public :: linear_combination
     public :: axpby_basis
     public :: zero_basis
-    public :: copy_basis
+    public :: copy
     public :: rand_basis
 
     interface innerprod
@@ -208,7 +208,7 @@ module lightkrylov_AbstractVectors
         module procedure zero_basis_cdp
     end interface
 
-    interface copy_basis
+    interface copy
         !!  This interface provides methods to copy an array `X` of `abstract_vector` into
         !!  another array `Y`. Note that `Y` needs to be pre-allocated.
         !!
@@ -224,9 +224,13 @@ module lightkrylov_AbstractVectors
         !!
         !!      ! ... Your code ...
         !!  ```
+        module procedure copy_vector_rsp
         module procedure copy_basis_rsp
+        module procedure copy_vector_rdp
         module procedure copy_basis_rdp
+        module procedure copy_vector_csp
         module procedure copy_basis_csp
+        module procedure copy_vector_cdp
         module procedure copy_basis_cdp
     end interface
 
@@ -888,6 +892,14 @@ subroutine zero_basis_rsp(X)
         return
     end subroutine zero_basis_rsp
 
+    subroutine copy_vector_rsp(out, from)
+        class(abstract_vector_rsp), intent(in) :: from
+        class(abstract_vector_rsp), intent(out) :: out
+        ! Copy array.
+        call out%axpby(zero_rsp, from, one_rsp)
+        return
+    end subroutine copy_vector_rsp
+
     subroutine copy_basis_rsp(out, from)
         class(abstract_vector_rsp), intent(in) :: from(:)
         class(abstract_vector_rsp), intent(out) :: out(:)
@@ -901,7 +913,7 @@ subroutine copy_basis_rsp(out, from)
 
         ! Copy array.
         do i = 1, size(out)
-            call out(i)%axpby(zero_rsp, from(i), one_rsp)
+            call copy_vector_rsp(out(i), from(i))
         enddo
 
         return
@@ -1068,6 +1080,14 @@ subroutine zero_basis_rdp(X)
         return
     end subroutine zero_basis_rdp
 
+    subroutine copy_vector_rdp(out, from)
+        class(abstract_vector_rdp), intent(in) :: from
+        class(abstract_vector_rdp), intent(out) :: out
+        ! Copy array.
+        call out%axpby(zero_rdp, from, one_rdp)
+        return
+    end subroutine copy_vector_rdp
+
     subroutine copy_basis_rdp(out, from)
         class(abstract_vector_rdp), intent(in) :: from(:)
         class(abstract_vector_rdp), intent(out) :: out(:)
@@ -1081,7 +1101,7 @@ subroutine copy_basis_rdp(out, from)
 
         ! Copy array.
         do i = 1, size(out)
-            call out(i)%axpby(zero_rdp, from(i), one_rdp)
+            call copy_vector_rdp(out(i), from(i))
         enddo
 
         return
@@ -1248,6 +1268,14 @@ subroutine zero_basis_csp(X)
         return
     end subroutine zero_basis_csp
 
+    subroutine copy_vector_csp(out, from)
+        class(abstract_vector_csp), intent(in) :: from
+        class(abstract_vector_csp), intent(out) :: out
+        ! Copy array.
+        call out%axpby(zero_csp, from, one_csp)
+        return
+    end subroutine copy_vector_csp
+
     subroutine copy_basis_csp(out, from)
         class(abstract_vector_csp), intent(in) :: from(:)
         class(abstract_vector_csp), intent(out) :: out(:)
@@ -1261,7 +1289,7 @@ subroutine copy_basis_csp(out, from)
 
         ! Copy array.
         do i = 1, size(out)
-            call out(i)%axpby(zero_csp, from(i), one_csp)
+            call copy_vector_csp(out(i), from(i))
         enddo
 
         return
@@ -1428,6 +1456,14 @@ subroutine zero_basis_cdp(X)
         return
     end subroutine zero_basis_cdp
 
+    subroutine copy_vector_cdp(out, from)
+        class(abstract_vector_cdp), intent(in) :: from
+        class(abstract_vector_cdp), intent(out) :: out
+        ! Copy array.
+        call out%axpby(zero_cdp, from, one_cdp)
+        return
+    end subroutine copy_vector_cdp
+
     subroutine copy_basis_cdp(out, from)
         class(abstract_vector_cdp), intent(in) :: from(:)
         class(abstract_vector_cdp), intent(out) :: out(:)
@@ -1441,7 +1477,7 @@ subroutine copy_basis_cdp(out, from)
 
         ! Copy array.
         do i = 1, size(out)
-            call out(i)%axpby(zero_cdp, from(i), one_cdp)
+            call copy_vector_cdp(out(i), from(i))
         enddo
 
         return

diff --git a/src/AbstractVectors.fypp b/src/AbstractVectors.fypp
@@ -53,7 +53,7 @@ module lightkrylov_AbstractVectors
     public :: linear_combination
     public :: axpby_basis
     public :: zero_basis
-    public :: copy_basis
+    public :: copy
     public :: rand_basis
 
     interface innerprod
@@ -200,7 +200,7 @@ module lightkrylov_AbstractVectors
         #:endfor
     end interface
 
-    interface copy_basis
+    interface copy
         !!  This interface provides methods to copy an array `X` of `abstract_vector` into
         !!  another array `Y`. Note that `Y` needs to be pre-allocated.
         !!
@@ -217,6 +217,7 @@ module lightkrylov_AbstractVectors
         !!      ! ... Your code ...
         !!  ```
         #:for kind, type in RC_KINDS_TYPES
+        module procedure copy_vector_${type[0]}$${kind}$
         module procedure copy_basis_${type[0]}$${kind}$
         #:endfor
     end interface
@@ -529,6 +530,14 @@ contains
         return
     end subroutine zero_basis_${type[0]}$${kind}$
 
+    subroutine copy_vector_${type[0]}$${kind}$(out, from)
+        class(abstract_vector_${type[0]}$${kind}$), intent(in) :: from
+        class(abstract_vector_${type[0]}$${kind}$), intent(out) :: out
+        ! Copy array.
+        call out%axpby(zero_${type[0]}$${kind}$, from, one_${type[0]}$${kind}$)
+        return
+    end subroutine copy_vector_${type[0]}$${kind}$
+
     subroutine copy_basis_${type[0]}$${kind}$(out, from)
         class(abstract_vector_${type[0]}$${kind}$), intent(in) :: from(:)
         class(abstract_vector_${type[0]}$${kind}$), intent(out) :: out(:)
@@ -542,7 +551,7 @@ contains
 
         ! Copy array.
         do i = 1, size(out)
-            call out(i)%axpby(zero_${type[0]}$${kind}$, from(i), one_${type[0]}$${kind}$)
+            call copy_vector_${type[0]}$${kind}$(out(i), from(i))
         enddo
 
         return
-Original file line number
+Diff line change
@@ Expand Up / @@ -39,4 +39,6 @@ @@
     *~
     # test/debug folder
-    debug/
+    debug/
+    *.css
+    doc/