模式输入文件: 初值数据
================
用于全球模式的初值数据制作
----------------
  初值数据制作前需配置好依赖环境，推荐使用以下几个文件处理软件制作初值数据，括号中为推荐的软件版本：
    - NCO（推荐版本：4.7.6）
    - CDO（推荐版本：2.0.5）

  构建初值数据需要以下几个步骤：
   #.	初值数据前处理
   #.	重命名初值变量
   #.	初值变量后处理


初值数据前处理
~~~~~~~~~~~~~~~~
此步骤需先下载ERA5或GFS再分析数据作为GRIST初值的原始数据，然后将其转化为nc格式，其中初值数据包括：
  1.	气压层数据：T（温度）、U（纬向风）、V（经向风）、比湿（Q）。
  2.	单层数据：PS（气压）、SOILH（重力位势）、SoilMoist（土壤湿度、一般有4层）、SoilTemp（土壤温度、一般有4层）、SKINTEMP（表面温度）、XICE（海冰面积）、SNOW（雪密度）、SNOWH（雪深）。
下载对应数据后，运行step1_convert.sh对数据格式进行转换，以下为step1_convert.sh设置参考（以ERA5数据为例）：

.. code-block:: bash

  pathin=${Path_for_inputfile} #设置原始初值数据读取路径
  pathou=${Path_for_outputfile} #设置初值数据生成路径
  res="G8UR" #网格名
  cdo_grid_file=/path/to/grist_scrip_gridnum.nc #设置模式网格描述文件路径（模式网格描述文件的生成请参考模式网格生成部分）
  cdo -f nc copy ${pathin}/${file} ${pathou}/${file}.tmp0.nc #将GRIB格式文件转化为nc格式
  cdo setmisstoc,0 ${pathou}/${file}.tmp0.nc ${pathou}/${file}.tmp.nc #将缺省值设为0
  cdo -P 6 remapycon,${cdo_grid_file} ${pathou}/${file}.tmp.nc ${pathou}/${file}.${res}.nc #将初始场数据插值到模式网格
  
重命名初值变量
~~~~~~~~~~~~~~~~
此步骤通过运行step2_rename.sh将插值好的初值文件变量名改为模式适用的初值，以下为step2_rename.sh参考设置:

.. code-block:: bash

  res=G8UR #网格分辨率
  pathou=${Path_for_outputfile} #输出文件路径
  lev_type=pl #数据垂直层类型
  cdo chname,var130,T,var131,U,var132,V,var133,Q ${pathin}/ERA5.${lev_type}.${year}${mon}${day}.00.grib.${res}.nc ${pathou}/initial_${res}_${lev_type}_${year}${mon}${day}.nc #将对应变量重命名为模式适用变量名
  cdo chname,var134,PS,var129,SOILH,var235,SKINTEMP,var31,XICE,var39,SoilMoist_lv1,var40,SoilMoist_lv2,var41,SoilMoist_lv3,var42,SoilMoist_lv4,\
  var139,SoilTemp_lv1,var170,SoilTemp_lv2,var183,SoilTemp_lv3,var236,SoilTemp_lv4,var33,SNOW,var141,SNOWH,\ 
  ${pathin}/ERA5.sf.${year}${mon}${day}.00.grib.${res}.nc    ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc #同上，但为单层变量设置
  ncks -v SNOW          ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/snow.nc #选取降雪数据并保存为snow.nc
  ncks -v SNOWH         ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/snowh.nc #选取雪深数据并保存为snowh.nc
  ncks -v SOILH         ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/soilh.nc #选取重力位势数据并保存为soilh.nc
  ncks -x -v SNOW,SOILH ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/newbase.nc #选取降雪，SOILH数据并保存为newbase.nc
  cdo mul ${pathou}/snow.nc      ${pathou}/snowh.nc ${pathou}/snow1.nc #计算得到snow初值
  cdo expr,'SOILH=SOILH/9.80616' ${pathou}/soilh.nc ${pathou}/soilh1.nc #计算得到soilh初值
  ncks -A ${pathou}/snow1.nc ${pathou}/newbase.nc #拼接snow1.nc和newbase.nc文件
  ncks -A ${pathou}/soilh1.nc ${pathou}/newbase.nc #拼接soilh1.nc和newbase.nc文件
  mv ${pathou}/newbase.nc ${pathou}/initial_${res}_sf_${year}${mon}${day}.nc #将newbase.nc重命名为模式初始场读取格式。

初值变量后处理
~~~~~~~~~~~~~~~~
此步骤通过运行step3_post.sh脚本进一步对初值文件进行整理，使其符合GRIST模式的读取需求，以下是step3_post.sh脚本的设置参考：

.. code-block:: bash

  lvname=plev #垂直坐标变量名
  ncks -d time,0 ${pathin}/initial_${res}_${lev_type}_${year}${mon}${day}.nc  initial_${res}.dim1.nc #选取第一个时间维度的变量作为初始场（如果有多个时间维度）
  ncwa -a time initial_${res}.dim1.nc tmp.nc #去除时间维度
  ncpdq -a ncells,${lvname} tmp.nc ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc #调换ncells和垂直坐标位置。
  cdo selname,SoilTemp_lv1 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st1.nc #提取SoilTemp_lv1变量
  ncrename -v SoilTemp_lv1,SoilTemp tmp.st1.nc #将SoilTemp_lv1 重命名为SoilTemp
  … …
  cdo selname,SoilTemp_lv4 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st4.nc #同上但为第四层
  ncrename -v SoilTemp_lv4,SoilTemp tmp.st4.nc #同上但为第四层
  cdo merge tmp.st?.nc tmp.st.nc #将四层土壤温度合并到depth维度
  ncpdq -a ncells,depth tmp.st.nc tmp.st.ncpdq.nc #将ncells和depth维度位置调换
  cdo selname,XICE,SOILH,SNOWH,SNOW,SKINTEMP,PS grist.initial.${res}_sf_${year}${mon}${day}.nc grist.init.${res}_sf_${year}${mon}${day}.nc #选取单层变量并存为GRIST模式读取格式文件
  ncks -A tmp.sn.ncpdq.nc grist.init.${res}_sf_${year}${mon}${day}.nc #拼接计算得到的土壤湿度变量
  ncks -A grist.init.${res}_sf_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc #将单层变量和气压层变量拼接为一个初始场文件。

大初值文件制作
^^^^^^^^^^^^^^^^^^^^^
需指出，GRIST模式在读取比G9网格更细的初值文件时，由于netcdf对文件容量的限制，需单独制作气压层的各变量，并逐一读取。以下为大初值文件的制作参考：

.. code-block:: bash

  cdo selname,U ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.U.${lev_type}.${res}_${year}${mon}${day}.nc #提取U变量并单独存放
  … …
  cdo selname,Q ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.Q.${lev_type}.${res}_${year}${mon}${day}.nc #提取Q变量并单独存放

相应的需要修改namelist中的初值文件读取模式，以下为namelist设置参考：

.. code-block:: bash

  large_atm_file_on      = .true. #开启大文件选项
  initialAtmUFilePath    = ${Path_for_AtmUFile} #单独读取U
  initialAtmVFilePath    = ${Path_for_AtmVFile} #单独读取V
  initialAtmTFilePath    = ${Path_for_AtmTFile} #单独读取T
  initialAtmQFilePath    = ${Path_for_AtmQFile} #单独读取Q

用于有限区域模式的初值数据制作
----------------
  产生有限区域模式初值数据的方式，与全球模式类似。仅需将CDO插值采用的SCRIP模版文件替换为有限区域网格的对应文件即可。
  如果已经产生了全球模式初值数据，也可以直接基于全球模式数据插值到有限区域网格，例如：
  cdo remapdis,${lam_scrip_file} ${global_fileName} ${lam_fileName}

初值制作脚本参考样例（使用G8分辨率网格）
----------------
**1.step1_convert.sh**

.. code-block:: bash

  pathin=${Path_for_inputfile}
  pathou=${Path_for_outputfile}
  mkdir -p ${pathou}

  hres="G8UR"
  cdo_grid_file=${Path_for_gridfile}

  for file in `ls ${pathin}` ;do
  if [ "${file##*.}"x = "grib"x ] ;then
  echo ${file}
  echo "1) convert grib to netcdf"
  cdo -f nc copy ${pathin}/${file} ${pathou}/${file}.tmp0.nc
  # only sea ice fraction has missing, just set to 0
  cdo setmisstoc,0                 ${pathou}/${file}.tmp0.nc ${pathou}/${file}.tmp.nc
  echo "2) convert lat-lon to unstructured"
  cdo -P 6 remapycon,${cdo_grid_file} ${pathou}/${file}.tmp.nc ${pathou}/${file}.${hres}.nc
  echo "3) clean"
  rm -rf ${pathou}/${file}.tmp.nc ${pathou}/${file}.tmp0.nc
  echo "done"
  fi
  done

**2.step2_rename.sh**

.. code-block:: bash

  res=G8UR
  pathou=${Path_for_outputfile}
  lev_type=pl
  mkdir -p ${pathou}
  for year in 2008 ;do
  for mon in 07 ;do
  for day in 14 ;do
  pathin=${Path_for_netcdf_file}/${year}${mon}${day}/
  echo ${year} ${mon} ${day} 
  if true ;then
    cdo chname,var130,T,var131,U,var132,V,var133,Q ${pathin}/ERA5.${lev_type}.${year}${mon}${day}.00.grib.${res}.nc ${pathou}/initial_${res}_${lev_type}_${year}${mon}${day}.nc
    cdo chname,var134,PS,var129,SOILH,var235,SKINTEMP,var31,XICE,\
        var39,SoilMoist_lv1,var40,SoilMoist_lv2,var41,SoilMoist_lv3,var42,SoilMoist_lv4,\
        var139,SoilTemp_lv1,var170,SoilTemp_lv2,var183,SoilTemp_lv3,var236,SoilTemp_lv4,\
        var33,SNOW,var141,SNOWH \
        ${pathin}/ERA5.sf.${year}${mon}${day}.00.grib.${res}.nc    ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc
  fi
  if  true ; then 
    ncks -v SNOW          ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/snow.nc 
    ncks -v SNOWH         ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/snowh.nc
    ncks -v SOILH         ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/soilh.nc
    ncks -x -v SNOW,SOILH ${pathou}/initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/newbase.nc

    cdo mul ${pathou}/snow.nc      ${pathou}/snowh.nc ${pathou}/snow1.nc
    cdo expr,'SOILH=SOILH/9.80616' ${pathou}/soilh.nc ${pathou}/soilh1.nc
    mv ${pathou}/snow1.nc  ${pathou}/snow.nc
    mv ${pathou}/soilh1.nc ${pathou}/soilh.nc

    ncks -A ${pathou}/snow.nc ${pathou}/newbase.nc
    ncks -A ${pathou}/soilh.nc ${pathou}/newbase.nc
    mv ${pathou}/newbase.nc ${pathou}/initial_${res}_sf_${year}${mon}${day}.nc
    rm -rf initial_${res}_sf_${year}${mon}${day}.tmp.nc ${pathou}/snow.nc ${pathou}/snowh.nc ${pathou}/soilh.nc
  fi
  done
  done
  done
**3.step3_post.sh**

.. code-block:: bash

  res=G8UR
  pathin=${Path_for_inputfile}
  pathou=${Path_for_outputfile}
  lev_type=pl
  lvname=plev
  mkdir -p ${pathou}
  for year in 2008 ;do
  for mon in 07 ;do
  for day in 14 ;do
  echo ${year}${mon}${day}
  #2d
  ncks -d time,0 ${pathin}/initial_${res}_${lev_type}_${year}${mon}${day}.nc  initial_${res}.dim1.nc
  ncwa -a time initial_${res}.dim1.nc tmp.nc
  ncpdq -a ncells,${lvname} tmp.nc ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc
  cdo selname,U ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.U.${lev_type}.${res}_${year}${mon}${day}.nc
  cdo selname,V ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.V.${lev_type}.${res}_${year}${mon}${day}.nc
  cdo selname,T ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.T.${lev_type}.${res}_${year}${mon}${day}.nc
  cdo selname,Q ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.Q.${lev_type}.${res}_${year}${mon}${day}.nc
  rm -rf initial_${res}.dim1.nc tmp.nc
  #1d
  ncks -d time,0 ${pathin}/initial_${res}_sf_${year}${mon}${day}.nc  initial_${res}.dim1.nc
  ncwa -a time initial_${res}.dim1.nc grist.initial.${res}_sf_${year}${mon}${day}.nc
  cdo selname,PS grist.initial.${res}_sf_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.PS.${lev_type}.${res}_${year}${mon}${day}.nc
  cdo selname,SoilTemp_lv1 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st1.nc
  ncrename -v SoilTemp_lv1,SoilTemp tmp.st1.nc
  cdo selname,SoilTemp_lv2 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st2.nc
  ncrename -v SoilTemp_lv2,SoilTemp tmp.st2.nc
  cdo selname,SoilTemp_lv3 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st3.nc  
  ncrename -v SoilTemp_lv3,SoilTemp tmp.st3.nc
  cdo selname,SoilTemp_lv4 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.st4.nc
  ncrename -v SoilTemp_lv4,SoilTemp tmp.st4.nc
  cdo merge tmp.st?.nc tmp.st.nc
  ncpdq -a ncells,depth tmp.st.nc tmp.st.ncpdq.nc
  cdo selname,SoilMoist_lv1 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.sn1.nc
  ncrename -v SoilMoist_lv1,SoilMoist tmp.sn1.nc
  cdo selname,SoilMoist_lv2 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.sn2.nc
  ncrename -v SoilMoist_lv2,SoilMoist tmp.sn2.nc
  cdo selname,SoilMoist_lv3 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.sn3.nc
  ncrename -v SoilMoist_lv3,SoilMoist tmp.sn3.nc
  cdo selname,SoilMoist_lv4 grist.initial.${res}_sf_${year}${mon}${day}.nc tmp.sn4.nc
  ncrename -v SoilMoist_lv4,SoilMoist tmp.sn4.nc
  cdo merge tmp.sn?.nc tmp.sn.nc
  ncpdq -a ncells,depth tmp.sn.nc tmp.sn.ncpdq.nc
  cdo selname,XICE,SOILH,SNOWH,SNOW,SKINTEMP,PS grist.initial.${res}_sf_${year}${mon}${day}.nc grist.init.${res}_sf_${year}${mon}${day}.nc
  ncks -A tmp.sn.ncpdq.nc grist.init.${res}_sf_${year}${mon}${day}.nc
  ncks -A tmp.st.ncpdq.nc grist.init.${res}_sf_${year}${mon}${day}.nc
  cp grist.init.${res}_sf_${year}${mon}${day}.nc ${pathou}/grist.init.${res}_sf_${year}${mon}${day}.nc
  #append  
  ncks -A grist.init.${res}_sf_${year}${mon}${day}.nc ${pathou}/grist.era5.ini.${lev_type}.${res}_${year}${mon}${day}.nc
  rm -rf initial_${res}.dim1.nc grist.initial.${res}_sf_${year}${mon}${day}.nc
  rm -rf tmp*.nc
  done
  done
  done