Changeset 1084 for XIOS/trunk/doc/inputs/user/Domain.lyx

Timestamp:

04/10/17 18:46:02 (7 years ago)

Author:

mhnguyen

Message:

Update user guide and reference guide

File:

• XIOS/trunk/doc/inputs/user/Domain.lyx (modified) (21 diffs)

XIOS/trunk/doc/inputs/user/Domain.lyx

@@ -1 @@
-#LyX 2.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 474
+#LyX 2.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 508
 \begin_document
 \begin_header
+\save_transient_properties true
+\origin unavailable
 \textclass book
 \use_default_options true
@@ -11 +13 @@
 \inputencoding auto
 \fontencoding global
-\font_roman default
-\font_sans default
-\font_typewriter default
-\font_math auto
+\font_roman "default" "default"
+\font_sans "default" "default"
+\font_typewriter "default" "default"
+\font_math "auto" "auto"
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
 \font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
+\font_sf_scale 100 100
+\font_tt_scale 100 100
 \graphics default
 \default_output_format default
@@ -143 +145 @@
 \color inherit
  among this kind of components.
- It is not allowed to have two domains with a same id, but it is permitted
- a domain and a grid, for example, to share a same one.
+ Domains defined by a same Id always represent only one domain.
 \end_layout
 
@@ -181 +182 @@
 \begin_layout Standard
 Very often, after a domain is defined, it may be referenced many times.
- To make a reference to a domain, we use domain_ref
+ To make a reference to a domain, we use 
+\shape italic
+domain_ref
 \end_layout
 
@@ -216 +219 @@
  The domain 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 a domain without id inside domain_definition.
- However, the domain_ref is utilized widely outside the scope of domain_definiti
-on.
+ It is useless to define a domain without id inside domain_definition.
+ Meanwhile, the domain_ref is utilized widely outside the scope of domain_defini
+tion.
 \end_layout
 
@@ -230 +233 @@
 \series default
 \color inherit
-Moreover it is the only region where we can define a new domain outside
+However, it is the only region where we can define a new domain outside
  domain_definition.
 \end_layout
@@ -286 +289 @@
 
 \begin_layout Standard
-One of a new concept which differenciates XIOS 2.0 from its precedent is
- transformation.
- In a simple case, zoom feature is now considered to be a transformation.
- It can be more complicated for other geometric transformation such as inversion
- or interpolation.
- All transformation are taken place on grid level.
- It means that it is neccessary to define a grid source and a grid destination
- as well as a transformation or list of transformation which we'd like to
- have.
- In order to transform a grid to one another, we need to specify a transformatio
-n on its sub-component: domain or axis.
-\end_layout
-
-\begin_layout Standard
-Because transformation on a domain is different from one on an axis, we
- differenciate two categories of transformation: transformation_domain and
- transformation_axis.
-\end_layout
-
-\begin_layout Standard
-Till now, XIOS supports the following transformation on domain:
-\end_layout
-
-\begin_layout Itemize
-zoom_domain: Like zoom functionality in XIOS 1.0, the destination grid is
- the zoomed region of the source grid.
-\end_layout
-
-\begin_layout Itemize
-interpolation_domain: Implement interpolation from a domain to one another,
- for now XIOS can only do interpolation by reading calculated weight values
- from a file or calculate the weights on the fly.
-\end_layout
-
-\begin_layout Itemize
-generate_rectilinear_domain: auto generating, distributing a rectilinear
- domain then filling all mandatory attributes.
-\end_layout
-
-\begin_layout Standard
-It is not difficult to define a transformation: Include type of transformation
- inside domain 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
-
-<domain_definition>
-\end_layout
-
-\begin_layout Plain Layout
-
-  <domain id="domain_A" />
-\end_layout
-
-\begin_layout Plain Layout
-
-  <domain id="domain_A_zoom" domain_ref="domain_A"> 
-\end_layout
-
-\begin_layout Plain Layout
-
-   <zoom_domain zoom_ibegin="1" zoom_ni="3" zoom_jbegin="0" zoom_nj="2"/>
-\end_layout
-
-\begin_layout Plain Layout
-
-  </domain>
-\end_layout
-
-\begin_layout Plain Layout
-
-</domain_definition>
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The concrete example above tells many things: a domain named domain_A_zoom
- is transformed from domain name domain_A with a zoom activity.
- The domain_A_zoom is the zoomed region of domain_A.
- The detailed attributes of zoom_domain 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 domain SHOULD have an id, in this case, it's
- domain_A_zoom.
- As mentioned before, a no-id domain or any no-id component of XIOS can
- only be used inside its definition scope.
- It exists but is useless.
- So care about that.
-\end_layout
-
-\begin_layout Standard
-To make use of transformation, the grid must contain domains which reference
- 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
-
-   <domain domain_ref="domain_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
-
-   <domain domain_ref="domain_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 is not convenient
- to customize attributes of domain.
- So it's the turn of Fortran interface.
+One of a new concept which differentiates XIOS 2.0 from its precedent is
+ (spatial) transformation, which can be defined inside a domain.
+ All transformations on a domain have form *_domain.
+ See Chapter 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "chap:Transformation"
+
+\end_inset
+
+ for more details.
 \end_layout
 
@@ -526 +343 @@
 rectilinear: a simple 2-dimensional Cartesian coordinates with two perpendicular
  axes.
- Latitude represents the y-axe while longitude represents the x-axe.
+ Latitude represents the y-axis while longitude represents the x-axe.
 \end_layout
 
@@ -537 +354 @@
 
 \begin_layout Itemize
-unstructured: not any of two above, the latitutude and longitude, as curvilinear
-, are reprensented with the help of boundaries.
+unstructured: not any of two above, the latitude and longitude, as curvilinear,
+ are represented with the help of boundaries.
  
 \end_layout
@@ -564 +381 @@
 
 \begin_layout Standard
-Althoug there are different domain types, they share the similar patterns
+Although there are different domain types, they share the similar patterns
  to settle local data on a client process: There are some essential attributes
  to define.
@@ -578 +395 @@
 It is not uncommon that a global domain is broken into several pieces, each
  of which is distributed to one process.
- Following we consider a simple case: a domain of rectilinear type with
+ Following, we consider a simple case: a domain of rectilinear type with
  global size 9 x 9 and its data is distributed evenly among 9 client processes,
  each of which has 3x3.
@@ -634 +451 @@
 
 \begin_layout Itemize
+ibegin, jbegin: global position on x-axis and y-axis where a local domain
+ begin
+\end_layout
+
+\begin_layout Itemize
+ni, nj: local size of domain of each process on x-axis and y-axis
+\end_layout
+
+\begin_layout Itemize
 ni_glo, nj_glo: global size of x-axis and y-axis correspondingly.
  
 \end_layout
 
-\begin_layout Itemize
-ibegin, jbegin: global position on x-axis and y-axis where a local domain
- begin
-\end_layout
-
-\begin_layout Itemize
-ni, nj: local size of domain of each process on x-axis and y-axis
-\end_layout
-
 \begin_layout Standard
 Or tell XIOS exactly the global position of each point in the local domain,
@@ -717 +534 @@
 
 \begin_layout Standard
-Specify the begining and size of data on the local domain:
+Specify the beginning and size of data on the local domain:
 \end_layout
 
 \begin_layout Itemize
 data_ibegin, data_jbegin: the local position of data on x-axis and y-axis
- where data begins
+ where data begins inside the local domain
 \end_layout
 
@@ -772 +589 @@
 
 \begin_layout Standard
-In order to be processed correctly, data must be specified with the begining
+In order to be processed correctly, data must be specified with the beginning
  and size of its block .
  For two-dimensional data, it can be done with data_ibegin, data_ni for
@@ -778 +595 @@
  In case of one-dimensional data, it is only necessary to determine data_ibegin
  and data_ni.
- Although the valid data must be inside a local domain, it is not neccessary
+ Although the valid data must be inside a local domain, it is not necessary
  for data to have same size as local domain.
  In fact, data can have larger size than domain on each dimension, this
@@ -857 +674 @@
 
 \begin_layout Standard
-With the secon way, data can be represented with:
+With the second way, data can be represented with:
 \end_layout
 
@@ -891 +708 @@
 \begin_layout Standard
 As mentioned, data on a domain are two-dimensional but in some cases, there
- is a need to write data continously, there comes one-dimensional data.
+ is a need to write data continuously, there comes one-dimensional data.
  With the precedent example, we can define one dimensional data with:
 \end_layout
@@ -921 +738 @@
 \begin_layout Standard
 Above are the mandatory attributes to define local domain.
- There are some auxilliary attributes which make data meaningful, especially
+ There are some auxiliary attributes which make data meaningful, especially
  for meteorological one.
- The next section disscuses these attributes.
+ The next section discuses these attributes.
 \end_layout
 
@@ -931 +748 @@
 
 \begin_layout Standard
-Different from the previous version, in XIOS 2.0, lonngitude and latitude
+Different from the previous version, in XIOS 2.0, longitude and latitude
  are optional.
  Moreover, to be coherent to the data_dim concept, there are more ways to
@@ -1025 +842 @@
 \begin_layout Standard
 For unstructured mesh, a cell can have different number of vertices than
- rectinlinear, in this case, longitude and latitude value of the vertex
- of cell are specified with bounds_lon_1d and bounds_lat_1d.
+ rectilinear, in this case, longitude and latitude value of the vertex of
+ cell are specified with bounds_lon_1d and bounds_lat_1d.
 \end_layout
 
@@ -1038 +855 @@
 \begin_layout Standard
 One thing to remind, only *_1d or *_2d attributes are used, if *_1d and
- *_2d of a same attribute are provides, there will be runtime error.
+ *_2d of a same attribute are provides, there will be run-time error.
 \end_layout