ecearth3/sources/xios-2.5/doc/inputs/user/Axis.lyx

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\begin_body

\begin_layout Chapter
Axis
\end_layout

\begin_layout Standard
Like Domain, Axis is a sub-component of Grid but is one dimension.
 In meteorological applications, axis represents a vertical line with different
 levels.
\end_layout

\begin_layout Section
Working with configuration file
\end_layout

\begin_layout Standard
The way to define an axis with configuration file is similar to define a
 domain.
\end_layout

\begin_layout Subsection
Basic configuration
\end_layout

\begin_layout Standard
Similar to domain, an axis is defined inside its definition part with the
 tag 
\series bold
\color black
axis_definition
\series default
\color inherit
.
 
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<axis_definition>
\end_layout

\begin_layout Plain Layout

  <axis id="axis_A" />
\end_layout

\begin_layout Plain Layout

  <axis axis_ref="axis_A" />
\end_layout

\begin_layout Plain Layout

</axis_definition>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The first one is to specify explicitly identification of an axis with an
 id.
 
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<axis_definition>
\end_layout

\begin_layout Plain Layout

  <axis id="axis_A" />  
\end_layout

\begin_layout Plain Layout

</axis_definition>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
In this way, with id, the axis can be processed, e.x modified its attributes,
 with Fortran interface; besides, it is only possible to reference to a
 axis whose id is explicitly defined.
\end_layout

\begin_layout Standard
To make a reference to an axis, we use axis_ref
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<axis_definition>
\end_layout

\begin_layout Plain Layout

  <axis axis_ref="axis_A" />
\end_layout

\begin_layout Plain Layout

</axis_definition>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
An axis defined by axis_ref will inherit all attributes of the referenced
 one, except its id attribute.
 If there is no id specified, an implicit one is assigned to this new axis.
 The axis with implicit id can only be used inside the scope where it is
 defined, it can not be referenced, nor be processed.
 It is rare to define an axis without id inside axis_definition.
 
\end_layout

\begin_layout Standard
To define a new axis inside a grid, we use the tag 
\series bold
\color black
axis.
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<grid id="grid_A">          
\end_layout

\begin_layout Plain Layout

   <axis axis_ref="axis_A" />
\end_layout

\begin_layout Plain Layout

</grid>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The xml lines above can be translated as: the grid_A composed of an axis_A
 that is defined somewhere else before.
 More precisely, the grid grid_A is constituted of a 
\begin_inset Quotes eld
\end_inset

unknown id
\begin_inset Quotes erd
\end_inset

 axis which has inherited all attributes (and their values) from axis A
 (name, long name, i_index, j_index, ...
 etc).
\end_layout

\begin_layout Subsection
Advanced configuration
\end_layout

\begin_layout Standard
Like domain, there are several transformation which can be defined with
 configuration file.
 All transformations on an axis have form *_axis.
 
\end_layout

\begin_layout Standard
Till now, XIOS supports the following transformation on axis:
\end_layout

\begin_layout Itemize
zoom_axis: Like zoom functionality in XIOS 1.0, the destination grid is the
 zoomed region of the source grid.
\end_layout

\begin_layout Itemize
interpolation_axis: Implement interpolation from an axis to one another.
 For now, only polynominal interpolation is available.
\end_layout

\begin_layout Itemize
inverse_axis: Inverse an axis
\end_layout

\begin_layout Standard
It is not difficult to define a transformation: Include type of transformation
 inside axis definition, as the following
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<axis_definition>
\end_layout

\begin_layout Plain Layout

  <axis id="axis_A" />
\end_layout

\begin_layout Plain Layout

  <axis id="axis_A_zoom" axis_ref="axis_A"> 
\end_layout

\begin_layout Plain Layout

   <zoom_axis zoom_begin="1" zoom_n="3"/>
\end_layout

\begin_layout Plain Layout

  </axis>
\end_layout

\begin_layout Plain Layout

</axis_definition>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The concrete example is translated as: the axis named axis_A_zoom is transformed
 from axis name axis_A with a zoom activity.
 The detailed attributes of zoom_axis can be found in reference document,
 but simply it contains the begining and size of zoomed region.
\end_layout

\begin_layout Standard
One remark is the transformed axis SHOULD have an id, in this case, it's
 axis_A_zoom.
 As mentioned before, a no-id axis or any no-id component of XIOS can only
 be used inside its definition scope.
\end_layout

\begin_layout Standard
To make use of transformation, the grid must contain axis which references
 to transformed ones.
 
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<grid id="grid_A">          
\end_layout

\begin_layout Plain Layout

  <axis axis_ref="axis_A" />
\end_layout

\begin_layout Plain Layout

</grid>
\end_layout

\begin_layout Plain Layout

<grid id="grid_A_zoom">          
\end_layout

\begin_layout Plain Layout

  <axis axis_ref="axis_A_zoom" />
\end_layout

\begin_layout Plain Layout

</grid>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
On defining this way, we tell XIOS to establish a connection between two
 grids by a transformation (zoom) with: grid source - grid_A, grid destination
 - grid_A_zoom.
\end_layout

\begin_layout Standard
As mentioned in Grid Chapter, in order to use transformed grid, just reference
 to it in field_definition
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

<field_definition level="1" enabled=".TRUE." default_value="9.96921e+36">
\end_layout

\begin_layout Plain Layout

  <field id="field_A"  operation="average" freq_op="3600s" grid_ref="grid_A"
 />
\end_layout

\begin_layout Plain Layout

  <field id="field_A_zoom"  operation="average" freq_op="3600s" grid_ref="grid_A
_zoom" />
\end_layout

\begin_layout Plain Layout

 </field_definition>
\end_layout

\end_inset


\end_layout

\begin_layout Standard
Although xml is helpful to define several configurations, it can not be
 used to customize attributes of axis.
 So it's the turn of Fortran interface.
\end_layout

\begin_layout Section
Working with FORTRAN code
\end_layout

\begin_layout Standard
Although axis is not as complexe as domain, there are some mandatory attributes
 to define.
 Different from precedent version, XIOS 2.0 supports distribution of data
 on a axis.
 The followings describe the essential parts of axis.
 Details of its attributes and operations can be found in XIOS reference
 guide.
\end_layout

\begin_layout Subsection
Local axis index
\end_layout

\begin_layout Standard
Axis is often used with domain, which is broken into several distributed
 pieces, to make a 3 dimension grid.
 However, there are cases in which data on axis are distributed among processes.
 Following we consider a simple case: a axis with global size 9 and its
 data are distributed evenly among 3 client processes, each of which has
 size 3.
\end_layout

\begin_layout Standard
\begin_inset Float figure
placement !tbph
wide false
sideways false
status open

\begin_layout Plain Layout
\begin_inset Graphics
	filename ../images/Distributed_Axis.pdf
	lyxscale 50
	scale 60

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout
Global axis data
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "globalAxis"

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
The local axis can be described by the following way.
\end_layout

\begin_layout Standard
Specify the the beginning and size of local axis with:
\end_layout

\begin_layout Itemize
n_glo: global size of axis.
 
\end_layout

\begin_layout Itemize
begin: global position where a local axis begin
\end_layout

\begin_layout Itemize
n: local size of axis on each process 
\end_layout

\begin_layout Standard
For example, the local axis in the middle (the yellow one) can be specified
 with:
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

CALL xios_set_axis_attr("axis_A",n_glo=9, begin=3, n=3)
\end_layout

\end_inset


\end_layout

\begin_layout Subsection
Local axis data
\end_layout

\begin_layout Standard
Simpler than local domain data, data on axis is always on-dimension.
 Like local domain data, local axis data represent the data offset from
 local axis, and it can be defined in two ways.
\end_layout

\begin_layout Standard
Specify the begining and size of data on the local axis:
\end_layout

\begin_layout Itemize
data_begin: the local position of data on axis where data begins
\end_layout

\begin_layout Itemize
data_n: size of data on each local axis
\end_layout

\begin_layout Standard
Or specify data with its position in the local axis:
\end_layout

\begin_layout Itemize
data_index: array of local position of data in the local axis.
\end_layout

\begin_layout Standard
Although the valid data must be inside a local axis, it is not neccessary
 for data to have same size.
 In fact, data can have larger size than local axis.
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

CALL xios_set_axis_attr("axis_A", data_begin=-1, data_n=n+2)
\end_layout

\end_inset


\end_layout

\begin_layout Standard
For local axis_A, the negative value of data_begin indicates that data is
 larger than local axis, the valid part of data needs extracted from the
 real data.
 If data_begin has a positive value, that means data size is smaller than
 local axis.
 The default value of data_begin is 0, which implies that local data fit
 into local axis properly.
 
\end_layout

\begin_layout Standard
Loal data can be defined with:
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

CALL xios_set_axis_attr("axis_A",data_index=data)
\end_layout

\end_inset


\end_layout

\begin_layout Standard
with
\end_layout

\begin_layout Itemize
data = {-1,0,1,2,3}
\end_layout

\begin_layout Subsection
Value
\end_layout

\begin_layout Standard
Value of axis plays a same role as longitude and latitude of domain.
 As local data, it can be distributed among processes.
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

CALL xios_set_axis_attr("axis_A", value=valueAxis)
\end_layout

\end_inset


\end_layout

\begin_layout Standard
with
\end_layout

\begin_layout Itemize
valueAxis = {30, 40, 50}
\end_layout

\begin_layout Standard
Because there is a need of direction of an axis, then comes the attribute
 positive
\end_layout

\begin_layout Standard
\begin_inset listings
lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}"
inline false
status open

\begin_layout Plain Layout

CALL xios_set_axis_attr("axis_A", positive='up')
\end_layout

\end_inset


\end_layout

\begin_layout Standard
All attributes of axis can be found in Reference Guide.
\end_layout

\begin_layout Standard

\end_layout

\end_body
\end_document