Merge branch 'hotfix-v6.2'

This merge addresses minor issues in the MPAS infrastructure with how character
strings are read from netCDF files via PIO, and it adds the 'recursive'
attribute to the mpas_log_write routine to avoid errors raised by several
newer compilers when critical errors are written.

* hotfix-v6.2:
  Add missing 'recursive' attribute to MPAS_log_write(...) routine
  Increment version number to 6.2
  Remove C null characters from strings read by PIO
  Add new MPAS_sanitize_string routine to mpas_c_interfacing
  Change length of xtime variables to ShortStrKIND to match netCDF files

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2013-2018,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
+Copyright (c) 2013-2019,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
 Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
 
 All rights reserved. 

README.md

@@ -1,4 +1,4 @@
-MPAS-v6.1
+MPAS-v6.2
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="6.1">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="6.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_init_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="6.1">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="6.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="6.1">
+<registry model="mpas" core="landice" core_abbrev="li" version="6.2">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="6.1">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="6.2">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_seaice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="seaice" core_abbrev="seaice" version="6.1">
+<registry model="mpas" core="seaice" core_abbrev="seaice" version="6.2">
 
 	<dims>
 		<dim name="nCells"

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="6.1">
+<registry model="mpas" core="sw" core_abbrev="sw" version="6.2">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/core_test/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="test" core_abbrev="test" version="6.1">
+<registry model="mpas" core="test" core_abbrev="test" version="6.2">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/framework/mpas_c_interfacing.F

@@ -4,6 +4,37 @@ module mpas_c_interfacing
     contains
 
 
+    !-----------------------------------------------------------------------
+    !  routine mpas_sanitize_string
+    !
+    !> \brief Converts C null characters in a Fortran string to spaces
+    !> \author Michael Duda
+    !> \date   19 February 2019
+    !> \details
+    !>  Converts all C null characters in a Fortran string to spaces.
+    !>  This may be useful for strings that were provided by C code through other
+    !>  Fortran code external to MPAS.
+    !
+    !-----------------------------------------------------------------------
+    subroutine mpas_sanitize_string(str)
+
+        use iso_c_binding, only : c_null_char
+
+        implicit none
+
+        character(len=*), intent(inout) :: str
+
+        integer :: i
+
+        do i=1,len(str)
+            if (str(i:i) == c_null_char) then
+                str(i:i) = ' '
+            end if
+        end do
+
+    end subroutine mpas_sanitize_string
+
+
     !-----------------------------------------------------------------------
     !  routine mpas_c_to_f_string
     !

src/framework/mpas_io.F

@@ -2187,6 +2187,8 @@ end subroutine MPAS_io_get_var_real5d
 
    subroutine MPAS_io_get_var_char0d(handle, fieldname, val, ierr)
 
+      use mpas_c_interfacing, only : MPAS_sanitize_string
+
       implicit none
 
       type (MPAS_IO_Handle_type), intent(inout) :: handle
@@ -2198,23 +2200,31 @@ subroutine MPAS_io_get_var_char0d(handle, fieldname, val, ierr)
       if (present(ierr)) ierr = MPAS_IO_NOERR
 
       call MPAS_io_get_var_generic(handle, fieldname, charVal=val, ierr=ierr)
+      call MPAS_sanitize_string(val)
 
    end subroutine MPAS_io_get_var_char0d
 
 
    subroutine MPAS_io_get_var_char1d(handle, fieldname, val, ierr)
 
+      use mpas_c_interfacing, only : MPAS_sanitize_string
+
       implicit none
 
       type (MPAS_IO_Handle_type), intent(inout) :: handle
       character (len=*), intent(in) :: fieldname
       character (len=*), dimension(:), intent(out) :: val
       integer, intent(out), optional :: ierr
 
+      integer :: i
+
 !     call mpas_log_write('Called MPAS_io_get_var_char1d()')
       if (present(ierr)) ierr = MPAS_IO_NOERR
 
       call MPAS_io_get_var_generic(handle, fieldname, charArray1d=val, ierr=ierr)
+      do i=1,size(val)
+         call MPAS_sanitize_string(val(i))
+      end do
 
    end subroutine MPAS_io_get_var_char1d
 

src/framework/mpas_io_streams.F

@@ -148,12 +148,12 @@ integer function MPAS_seekStream(stream, seekTime, seekPosition, actualTime, max
       integer :: io_err
       integer :: i
       integer :: timeDim
-      character (len=StrKIND), dimension(:), pointer :: xtimes
-      character (len=StrKIND) :: strTemp
+      character (len=ShortStrKIND), dimension(:), pointer :: xtimes
+      character (len=ShortStrKIND) :: strTemp
       type (MPAS_Time_type) :: sliceTime, startTime
       type (MPAS_TimeInterval_type) :: timeDiff, minTimeDiff
 
-      character (len=StrKIND) :: xtime0, xtime1, xtime2, xtimeGuess
+      character (len=ShortStrKIND) :: xtime0, xtime1, xtime2, xtimeGuess
       type (MPAS_Time_type) :: time0, time1, time2, timeGuess, timeGuessData
       type (MPAS_TimeInterval_type) :: timeInterval
 
@@ -1510,10 +1510,10 @@ subroutine MPAS_streamAddField_0dChar(stream, field, ierr)
       idim = ndims
       allocate(indices(0))
       allocate(dimSizes(1))
-      dimSizes(1) = 64
+      dimSizes(1) = ShortStrKIND
       dimNames(1) = 'StrLen'
-      globalDimSize = 64
-      totalDimSize = 64
+      globalDimSize = ShortStrKIND
+      totalDimSize = ShortStrKIND
 
       
       if (field % isVarArray) then
@@ -1602,7 +1602,7 @@ subroutine MPAS_streamAddField_1dChar(stream, field, ierr)
       idim = ndims
       allocate(indices(1))
       allocate(dimSizes(2))
-      dimSizes(1) = 64
+      dimSizes(1) = ShortStrKIND
       dimNames(1) = 'StrLen'
       dimSizes(2) = field % dimSizes(1)
       dimNames(2) = field % dimNames(1)

src/framework/mpas_log.F

@@ -461,7 +461,7 @@ end subroutine mpas_log_open
 !
 !-----------------------------------------------------------------------
 
-   subroutine mpas_log_write(message, messageType, masterOnly, flushNow, &
+   recursive subroutine mpas_log_write(message, messageType, masterOnly, flushNow, &
                  intArgs, realArgs, logicArgs, err)
 
       use mpas_threading