vertical data driven scenario 1

xios_examples/shared_testing.py

@@ -111,11 +111,12 @@ def test_resample(self):
                    'differs from the resampled data array\n {res} \n '
                    'with diff \n {diff}\n')
             msg = msg.format(exp=expected, res=result, diff=diff)
-            if np.any(diff):
+            if not np.allclose(result, expected, rtol=cls.rtol):
                 # print message for fail case,
                 # as expected failures do not report msg.
                 print(msg)
             # assert that all of the `diff` varaible values are zero
             # self.assertTrue(not np.any(diff), msg=msg)
-            self.assertTrue(np.allclose(result, expected, rtol=cls.rtol), msg=msg)
+            self.assertTrue(np.allclose(result, expected, rtol=cls.rtol),
+                            msg=msg)
         return test_resample

xios_examples/vertical_stratify_scenarios/Makefile

@@ -0,0 +1,56 @@
+# Make file for the resample demonstartion XIOS programme
+# Targets provided our detailed below...
+#
+# all: (default) Build the resample programme
+# clean: Delete all final products and working files
+# run: run the programme
+#
+# Environment Variables expected by this MakeFile:
+#
+# NETCDF_LIB_DIR: the directories for the netCDF lib files
+#                 encoded as a -L string, e.g.
+#                 "-L/dir1 -L/dir2"
+# NETCDF_INC_DIR: the directories for the netCDF include files
+#                 encoded as a -I string, e.g.
+#                 "-I/dir3 -I/dir4"
+#     (note, this is for consistency with the XIOS build process
+#      required for the CI build machine.
+#      this is not required for other directories)
+#
+# XIOS_INCDIR: The directory for XIOS include files
+# XIOS_LIBDIR: The directory for XIOS lib files
+# XIOS_BINDIR: The directory for XIOS binary files
+
+FCFLAGS = -g -ffree-line-length-none
+
+FC = mpif90       # compiler driver for MPI programs
+
+# compiler flag, includes
+FCFLAGS += -I$(XIOS_INCDIR) $(NETCDF_INCDIR)
+
+# loader flags
+LDFLAGS = \
+	-L$(XIOS_LIBDIR) \
+	$(NETCDF_LIBDIR) \
+	-lxios \
+	-lnetcdf \
+	-lnetcdff \
+	-lstdc++ 
+
+all: resample
+
+# fortran compilation
+%.o: %.F90
+	$(FC) $(FCFLAGS) -c $<
+
+# fortran linking
+resample: resample.o
+	$(FC) -o resample.exe resample.o $(LDFLAGS) \
+		&& ln -fs $(XIOS_BINDIR)/xios_server.exe .
+
+run:
+	mpiexec -n 1 ./resample.exe : -n 1 ./xios_server.exe
+
+# cleanup
+clean:
+	rm -f *.exe *.o *.mod *.MOD *.out *.err *.nc

xios_examples/vertical_stratify_scenarios/axis_check.xml

@@ -0,0 +1,30 @@
+<context id="axis_check">
+
+  <calendar type="Gregorian"/>
+
+
+  <grid_definition>
+    <grid id="mlev_grid">
+      <axis id="xm" />
+      <axis id="ym" />
+      <axis id="mlev" />
+    </grid>
+
+    <grid id="plev_grid">
+      <axis id="xp" />
+      <axis id="yp" />
+      <axis id="plev" />
+    </grid>
+
+  </grid_definition>
+
+  <file_definition type="one_file">
+    <file id="din" name="stratify_input_in_domain_1" output_freq="1ts" mode="read" enabled=".true.">
+      <field id="pressure_in" name="pressure" grid_ref="mlev_grid" operation="instant" />
+      <field id="temperature_in" name="temperature" grid_ref="mlev_grid" operation="instant" />
+      <field id="temponp_in" name="temponP" grid_ref="plev_grid" operation="instant" />
+
+    </file>
+  </file_definition>
+
+</context>

xios_examples/vertical_stratify_scenarios/iodef.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<simulation>
+
+<context id="main" src="main.xml"/>
+<context id="axis_check" src="axis_check.xml"/>
+
+<context id="xios" src="xios.xml"/>
+
+</simulation>

xios_examples/vertical_stratify_scenarios/main.xml

@@ -0,0 +1,52 @@
+<context id="main">
+
+  <calendar type="Gregorian"/>
+
+    <axis_definition>
+      <axis id="model_levels" unit="1" name="levels"/>
+      <axis id="pressure_levels1" positive="down" long_name="Air Pressure" standard_name="air_pressure" unit="Pa">
+        <interpolate_axis type="polynomial" order="1" coordinate="pressure" />
+      </axis>
+
+    </axis_definition>
+
+    <domain_definition>
+      <domain id="latlon_domain" type="rectilinear" nvertex="2"/>
+
+    </domain_definition>
+
+    <grid_definition>
+      <grid id="model">
+        <domain domain_ref="latlon_domain" />
+        <axis axis_ref="model_levels" />
+      </grid>
+      <grid id="model_plev">
+        <domain domain_ref="latlon_domain" />
+        <axis axis_ref="pressure_levels1" />
+      </grid>
+    </grid_definition>
+
+    <field_definition freq_op="1ts" enabled=".TRUE." operation="instant" >
+      <field id="pressure" name="pressure" long_name="Air Pressure" standard_name="air_pressure" unit="Pa" grid_ref="model" />
+      <field id="temperature" name="temperature" long_name="Air Temperature" standard_name="air_temperature" unit="K" grid_ref="model" />
+      <field id="temperature_on_P" name="resampled_data" long_name="Air Temperature" standard_name="air_temperature" unit="K" field_ref="temperature" grid_ref="model_plev" />
+      <field id="expected" name="resample_data" long_name="Expected Air Temperature" standard_name="air_temperature" unit="K" grid_ref="model_plev" />
+      <field id="diff" name="resampled_minus_resample" long_name="Air Temperature difference" unit="K" grid_ref="model_plev">temperature_on_P - expected</field>
+
+    </field_definition>
+
+
+  <file_definition type="one_file">
+    <file id="pressure_stratify" output_freq="1ts">
+      <field_group operation="once">
+        <field field_ref="pressure" />
+        <field field_ref="temperature"/>
+        <field field_ref="temperature_on_P"/>
+        <field field_ref="expected"/>
+        <field field_ref="diff"/>
+
+      </field_group>
+    </file>
+  </file_definition>
+
+</context>

xios_examples/vertical_stratify_scenarios/resample.F90

@@ -0,0 +1,169 @@
+!-----------------------------------------------------------------------------
+! (C) Crown copyright 2020 Met Office. All rights reserved.
+! The file LICENCE, distributed with this code, contains details of the terms
+! under which the code may be used.
+!-----------------------------------------------------------------------------
+!> Read 2D data on a domain and resample using the axis_input.nc file
+!>
+program resample
+  use xios
+  use mpi
+
+  implicit none
+
+  integer :: comm = -1
+  integer :: rank = -1
+  integer :: npar = 0
+
+  call initialise()
+  call simulate()
+  call finalise()
+contains
+
+  subroutine initialise()
+
+    type(xios_date) :: origin
+    type(xios_date) :: start
+    type(xios_duration) :: tstep
+    integer :: mpi_error
+    integer :: lenx
+    integer :: lenrx
+    integer :: leny
+    integer :: lenry
+    integer :: lenz
+    integer :: lenrz
+    double precision, dimension (:), allocatable :: latvals, lonvals, plvals, mlvals
+    double precision, dimension (:,:), allocatable :: latb, lonb
+
+    ! Arbitrary datetime setup, required for XIOS but unused
+    origin = xios_date(2022, 2, 2, 12, 0, 0)
+    start = xios_date(2022, 12, 13, 12, 0, 0)
+    tstep = xios_hour
+
+    ! Initialise MPI and XIOS
+    call MPI_INIT(mpi_error)
+
+    call xios_initialize('client', return_comm=comm)
+
+    call MPI_Comm_rank(comm, rank, mpi_error)
+    call MPI_Comm_size(comm, npar, mpi_error)
+
+    ! use the axis_check context to obtain sizing information on all arrays
+    ! for use in defining the main context interpretation
+    call xios_context_initialize('axis_check', comm)
+    call xios_set_time_origin(origin)
+    call xios_set_start_date(start)
+    call xios_set_timestep(tstep)
+
+    call xios_close_context_definition()
+
+    call xios_get_axis_attr('xm', n_glo=lenx)
+    call xios_get_axis_attr('xp', n_glo=lenrx)
+    call xios_get_axis_attr('ym', n_glo=leny)
+    call xios_get_axis_attr('yp', n_glo=lenry)
+    call xios_get_axis_attr('mlev', n_glo=lenz)
+    call xios_get_axis_attr('plev', n_glo=lenrz)
+
+    allocate ( mlvals(lenz) )
+    allocate ( plvals(lenrz) )
+    allocate ( lonvals(lenx) )
+    allocate ( latvals(leny) )
+    allocate ( lonb(2, lenx) )
+    allocate ( latb(2, leny) )
+
+    lonb = reshape((/-6.0, -3.0/), shape(lonb))
+    latb = reshape((/50.0, 53.0/), shape(latb))
+
+
+    call xios_get_axis_attr('xm', value=lonvals)
+    call xios_get_axis_attr('ym', value=latvals)
+    call xios_get_axis_attr('mlev', value=mlvals)
+    call xios_get_axis_attr('plev', value=plvals)
+
+
+    ! initialize the main context for interacting with the data.
+    call xios_context_initialize('main', comm)
+
+    call xios_set_time_origin(origin)
+    call xios_set_start_date(start)
+    call xios_set_timestep(tstep)
+
+    !call xios_set_axis_attr('model_levels', n_glo=lenz)
+    call xios_set_axis_attr('model_levels', n_glo=lenz, value=mlvals)
+    call xios_set_axis_attr('pressure_levels1', n_glo=lenrz, value=plvals)
+
+    call xios_set_domain_attr('latlon_domain', ni_glo=lenx, nj_glo=leny, ni=lenx, nj=leny, ibegin=0, jbegin=0)
+    call xios_set_domain_attr('latlon_domain', lonvalue_1d=lonvals, latvalue_1d=latvals, bounds_lon_1d=lonb, bounds_lat_1d=latb)
+
+
+    call xios_close_context_definition()
+
+  end subroutine initialise
+
+  subroutine finalise()
+
+    integer :: mpi_error
+
+    ! Finalise all XIOS contexts and MPI
+    call xios_set_current_context('axis_check')
+    call xios_context_finalize()
+    call xios_set_current_context('main')
+    call xios_context_finalize()
+    call MPI_Comm_free(comm, mpi_error)
+    call xios_finalize()
+    call MPI_Finalize(mpi_error)
+
+  end subroutine finalise
+
+  subroutine simulate()
+
+    type(xios_date) :: current
+    integer :: ts
+    integer :: lenx
+    integer :: leny
+    integer :: lenmlz
+    integer :: lenplz
+
+    ! Allocatable arrays, size is taken from input file
+    double precision, dimension (:,:,:), allocatable :: inpdata
+    double precision, dimension (:,:,:), allocatable :: intdata
+    double precision, dimension (:,:,:), allocatable :: intonpdata
+
+    call xios_get_domain_attr('latlon_domain', ni_glo=lenx, nj_glo=leny)
+    call xios_get_axis_attr('model_levels', n_glo=lenmlz)
+    call xios_get_axis_attr('pressure_levels1', n_glo=lenplz)
+
+    allocate ( inpdata(lenmlz, leny, lenx) )
+    allocate ( intdata(lenmlz, leny, lenx) )
+    allocate ( intonpdata(lenplz, leny, lenx) )
+
+    call xios_set_current_context('axis_check')
+
+
+    ! Load data from the input file
+    call xios_recv_field('pressure_in', inpdata)
+    call xios_recv_field('temperature_in', intdata)
+    call xios_recv_field('temponp_in', intonpdata)
+
+    call xios_set_current_context('main')
+
+    do ts=1, 1
+      call xios_update_calendar(ts)
+      call xios_get_current_date(current)
+      ! Send the pressure data to the output file.
+      call xios_send_field('pressure', inpdata)
+      ! Send the pressure data to the output file.
+      ! The interpolate_axis and field-ref in main.xml will
+      ! also write the interpolated data into the output file.
+      call xios_send_field('temperature', intdata)
+      call xios_send_field('expected', intonpdata)
+    enddo
+
+
+    deallocate (inpdata)
+    deallocate (intdata)
+    deallocate (intonpdata)
+
+  end subroutine simulate
+
+end program resample