Merge pull request #1 from NCAR/master

Merging NCAR/DART_dev onto jlsucar/DART_dev

.gitignore

@@ -8,10 +8,11 @@
 .DS_Store
 Gemfile.lock
 _site/
+.cppdefs
 
 # Nuisance files
 
-Makefile
+# Makefile
 dart_log.*
 input.nml.*default
 filter_ics
@@ -20,6 +21,7 @@ obs_kind_mod.f90
 using_mpi_for_*
 check_me.nc
 check_me_interptest.*
+*.orig
 
 # Executables
 
@@ -52,8 +54,6 @@ perturb_single_instance
 preprocess
 restart_file_tool
 system_simulation
-wakeup_filter
-FeoM_time
 
 # Directories to NOT IGNORE ... same as executable names
 # as far as I know, these must be listed after the executables
@@ -88,3 +88,4 @@ FeoM_time
 !restart_file_tool/
 !system_simulation/
 !wakeup_filter/
+

CHANGELOG

@@ -889,4 +889,11 @@ and assim_tools_mod.pf.f90 in sync with assim_tools_mod.f90.
 - added an example of how to use a namelist to the text_to_obs.f90 observation
   converter program.
 
-
+- Removing the clamping messages in 'clamp_variable()' of clamped values
+
+- changed argument names using reserved keywords. 
+  state_vector_io_mod:read_state() 'time' to 'model_time' 
+  random_seq_mod:random_gamma() 'shape' to 'rshape', 'scale' to 'rscale'.
+  random_seq_mod:random_inverse_gamma() 'shape' to 'rshape', 'scale' to 'rscale'.
+  obs_def_mod:init_obs_def() 'kind' to 'obkind', 'time' to 'obtime'
+  obs_utilities_mod: 'start' to 'varstart', 'count' to 'varcount'

README.md

@@ -6,9 +6,9 @@
 [quick-start instructions for the impatient](#QuickStart)
 
 Extensive on-line documentation is available at the GitHub project web pages:
-[https://ncar.github.io/DART](https://ncar.github.io/DART)
+[https://dart.ucar.edu/](https://dart.ucar.edu/)
 or in the repository at [docs/index.md](docs/index.md). It's probably a good idea
-to be familiar with the [GitHub workflow](https://guides.github.com/introduction/flow/).
+to be familiar with the [GitHub flow](https://guides.github.com/introduction/flow/).
 
 <table><tr>
 <td><img height=250, src="./docs/images/DARTspaghettiSquare.gif"></td> 

assimilation_code/location/threed_sphere/location_mod.f90

@@ -2028,7 +2028,7 @@ end function get_maxdist
 
 !----------------------------------------------------------------------------
 
-subroutine distinct_values(in_list, count, values, map)
+subroutine distinct_values(in_list, mycount, values, map)
 
 !> parse an input list of values and return:
 !>  1) the count of distinct values
@@ -2038,7 +2038,7 @@ subroutine distinct_values(in_list, count, values, map)
 !> length as the incoming list length.
 
 real(r8), intent(in)    :: in_list(:)   !< incoming list of all values
-integer,  intent(out)   :: count        !< count of distinct values
+integer,  intent(out)   :: mycount      !< count of distinct values
 real(r8), intent(inout) :: values(:)    !< list of distinct values
 integer,  intent(inout) :: map(:)       !< mapping of in_list to values
 
@@ -2048,7 +2048,7 @@ subroutine distinct_values(in_list, count, values, map)
 
 ! set return values now; if we error out then we can
 ! just return.
-count = 0
+mycount = 0
 values(:) = -1.0_r8
 map(:) = -1
 
@@ -2075,7 +2075,7 @@ subroutine distinct_values(in_list, count, values, map)
   if (foundnew) then
      values(nextslot) = newval
      map(i) = nextslot
-     count = nextslot
+     mycount = nextslot
   endif
 enddo OUTER
 

assimilation_code/location/utilities/location_io_mod.f90

@@ -7,6 +7,8 @@
 !> common routines which can write netcdf arrays no matter which
 !> location module is compiled in.
 
+!>@todo FIXME  there is no documentation for this module.
+
 !>@todo FIXME  define ALL the VERTISXXX here, add a call to has_vertical_choice
 !>to the xxx/location_mod, and if no, return without needing routines
 !>in each of the specific location routines.  if yes, call query and 
@@ -259,17 +261,17 @@ end subroutine nc_get_location_varids
 !> The LocationVarID and WhichVertVarID must be the values returned from
 !> the nc_get_location_varids call.
 
-subroutine nc_write_single_location(ncFileID, loc, locindex, do_vert, fname)
+subroutine nc_write_single_location(ncFileID, location, locindex, do_vert, fname)
 
 integer,                    intent(in) :: ncFileID
-type(location_type),        intent(in) :: loc
+type(location_type),        intent(in) :: location
 integer,                    intent(in) :: locindex
 logical, optional,          intent(in) :: do_vert
 character(len=*), optional, intent(in) :: fname       ! file name (for error printing purposes)
 
 integer :: LocationVarID
 integer :: WhichVertVarID
-real(r8), dimension(LocationDims) :: locations
+real(r8), dimension(LocationDims) :: location_array
 integer,  dimension(1) :: intval
 logical :: write_vert
 integer :: rc
@@ -285,13 +287,13 @@ subroutine nc_write_single_location(ncFileID, loc, locindex, do_vert, fname)
 rc = nf90_inq_varid(ncFileID, 'location', varid=LocationVarID)
 call nc_check(rc, context, 'location', fname)
 
-locations = get_location( loc ) 
+location_array = get_location( location ) 
 
 if (LocationDims > 1) then
-   rc = nf90_put_var(ncFileID, LocationVarId, locations, &
+   rc = nf90_put_var(ncFileID, LocationVarId, location_array, &
                      start=(/ 1, locindex /), count=(/ LocationDims, 1 /) )
 else
-   rc = nf90_put_var(ncFileID, LocationVarId, locations, &
+   rc = nf90_put_var(ncFileID, LocationVarId, location_array, &
                      start=(/ locindex /), count=(/ 1 /) )
 endif
 call nc_check(rc, context, 'put_var:location', fname)
@@ -300,7 +302,7 @@ subroutine nc_write_single_location(ncFileID, loc, locindex, do_vert, fname)
    rc = nf90_inq_varid(ncFileID, 'which_vert', varid=WhichVertVarID)
    call nc_check(rc, context, 'inq_varid:which_vert', fname)
 
-   intval = query_location(loc, 'WHICH_VERT')
+   intval = query_location(location, 'WHICH_VERT')
    rc = nf90_put_var(ncFileID, WhichVertVarID, intval, &
                      start=(/ locindex /), count=(/ 1 /) )
    call nc_check(rc, context, 'put_var:which_vert', fname)
@@ -313,18 +315,18 @@ end subroutine nc_write_single_location
 !> The LocationVarID and WhichVertVarID must be the values returned from
 !> the nc_get_location_varids call.
 
-subroutine nc_write_multiple_locations(ncFileID, loc, loccount, startlocindex, do_vert, fname)
+subroutine nc_write_multiple_locations(ncFileID, locations, loccount, startlocindex, do_vert, fname)
 
 integer,             intent(in) :: ncFileID
-type(location_type), intent(in) :: loc(:)
+type(location_type), intent(in) :: locations(:)
 integer,             intent(in) :: loccount
 integer, optional,   intent(in) :: startlocindex
 logical, optional,   intent(in) :: do_vert
 character(len=*), optional, intent(in) :: fname       ! file name (for error printing purposes)
 
 integer :: LocationVarID
 integer :: WhichVertVarID
-real(r8), allocatable :: locations(:,:)
+real(r8), allocatable :: location_array(:,:)
 integer,  allocatable :: intvals(:)
 logical :: write_vert
 integer :: rc, i, starthere
@@ -343,19 +345,19 @@ subroutine nc_write_multiple_locations(ncFileID, loc, loccount, startlocindex, d
 rc = nf90_inq_varid(ncFileID, 'location', varid=LocationVarID)
 call nc_check(rc, context, 'location', fname)
 
-allocate(locations(LocationDims,loccount))
+allocate(location_array(LocationDims,loccount))
 if (write_vert) allocate(intvals(loccount))
 
 do i=1, loccount
-   locations(:,i) = get_location( loc(i) ) 
-   if (write_vert) intvals(i) = query_location(loc(i), 'WHICH_VERT')
+   location_array(:,i) = get_location( locations(i) ) 
+   if (write_vert) intvals(i) = query_location(locations(i), 'WHICH_VERT')
 enddo
 
 if (LocationDims > 1) then
-   rc = nf90_put_var(ncFileID, LocationVarId, locations, &
+   rc = nf90_put_var(ncFileID, LocationVarId, location_array, &
                      start=(/ 1, starthere /), count=(/ LocationDims, loccount /) )
 else
-   rc = nf90_put_var(ncFileID, LocationVarId, locations, &
+   rc = nf90_put_var(ncFileID, LocationVarId, location_array, &
                      start=(/ starthere /), count=(/ loccount /) )
 endif
 call nc_check(rc, context, 'put_var:location', fname)
@@ -369,7 +371,7 @@ subroutine nc_write_multiple_locations(ncFileID, loc, loccount, startlocindex, d
    call nc_check(rc, context, 'put_var:which_vert', fname)
 endif
 
-deallocate(locations)
+deallocate(location_array)
 if (write_vert) deallocate(intvals)
 
 end subroutine nc_write_multiple_locations