How to Install WRF-Chem Model

Version 4.4 and KPP

On Ubuntu 22.04.

Compute System

Technological development and Digitization

Hydro Informatics Institute (HII)

Thailand.

Compute System. 22 Jun 2022

CONTENTS
1. Objective. .................................................................................................................................................3
2. Scope. .......................................................................................................................................................3
3. Definition. ..................................................................................................................................................3
4. Device.........................................................................................................................................................3
5. Operating Procedures. ............................................................................................................................4
5.1. open ssh client and connect to your linux ubuntu with username ubuntu. ......................... 4
5.2. update ubuntu software..................................................................................................................... 4
5.3. install preferred software. .................................................................................................................. 4
5.4. install compiler..................................................................................................................................... 5
5.5. Directory Structure. .............................................................................................................................. 5
5.6. Install Preferred Library....................................................................................................................... 5
5.6.1 Install mpich Library. ..............................................................................................................6
5.6.2 install zlib library. ....................................................................................................................7
5.6.3 Install hdf5 Library...................................................................................................................7
5.6.4 install curl library. ....................................................................................................................8
5.6.5. Install netcdf Library. .............................................................................................................9
5.6.6. Install libpng Library............................................................................................................ 10
5.6.7. Install Jasper Library. .......................................................................................................... 11
5.6.8 Install ncl Library. ................................................................................................................. 11
5.7. Install WRF-Chem. .............................................................................................................................. 13
5.7.1 Install WRF-Chem and KPP. ................................................................................................ 13
5.7.2 Install WPS. ............................................................................................................................ 15
5.8. Create Directory for Geography Data. ............................................................................................ 16
5.9. Create directory for Input Data. ...................................................................................................... 17
5.10. Run WRF-Chem................................................................................................................................. 19
5.10.1. Running WPS....................................................................................................................... 19
5.10.2. Running WRF....................................................................................................................... 22
5.10.3. list data inside wrfout. ...................................................................................................... 29
5.10.4. Create pdf from wrfout. ................................................................................................... 29
6. Conclusion. ............................................................................................................................................ 30
 How to Install WRF-Chem Model Version 4.4 and KPP On Ubuntu 22.04.

1. Objective.
To understand about WRF-Chem with KPP installation.

2. Scope.
Installation WRF-Chem Model Version 4.4 and KPP On Ubuntu.

3. Definition.
Ubuntu is linux operating system.
WRF-Chem Model is the Weather Research and Forecasting (WRF) model coupled with Chemistry.
The model simulates the emission, transport, mixing, and chemical transformation of trace gases
and aerosols simultaneously with the meteorology. The model is used for investigation of regional-
scale air quality, field program analysis, and cloud-scale interactions between clouds and
chemistry.
Kinetic PreProcessor(KPP) is a software tool that assists the computer simulation of chemical
kinetic systems. The concentrations of a chemical system evolve in time according to the
differential law of mass action kinetics. A numerical simulation requires an implementation of the
differential laws and a numerical integration in time.

4. Device.
Linux Ubuntu 22.04 type server have available space is 80G and memory more than 32G.
5. Operating Procedures.
5.1. open ssh client and connect to your linux ubuntu with username ubuntu.

ssh ubuntu@192.168.122.229
show ubuntu version.
$ cat /etc/os-release
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04 LTS (Jammy Jellyfish)"
show default home directory.
$ pwd
/home/ubuntu
show user name.
$ whoami
ubuntu

5.2. update ubuntu software.

update repository.
$ sudo apt update

5.3. install preferred software.

Install preferred software by command.
$ sudo apt install csh m4 build-essential nasm cmake unzip libxmu-dev libcairo-dev libbz2-
dev libxaw7-dev libx11-dev xorg-dev flex bison subversion liburi-perl evince tcsh cpp m4
quota cvs libomp-dev python3-pip freeglut3-dev libjpeg-dev file
5.4. install compiler.
install compiler by command.
$ sudo apt install gcc g++ gfortran
and show compiler version.
$ gcc -v
$ g++ -v
$ cpp --version
$ gfortran -v

5.5. Directory Structure.

/ root directory of linux
|--home home directory of linux
|--ubuntu default ubuntu home directory of linux
|--Build_WRF main WRF directory.
|--LIBRARIES WRF library directory.
|--geos Geography Data and mount to /data/geos
|--DATA Directory for Real-time Data.
|--src Directory for Source Code.

5.6. Install Preferred Library.

Preferred Library include
• mpich
• zlib
• hdf5
• curl
• netcdf
• libpng
• Jasper
5.6.1 Install mpich Library.
Create source code directory and change to directory.
$ mkdir -p /home/ubuntu/Build_WRF/src
$ mkdir -p /home/ubuntu/Build_WRF/LIBRARIES
$ cd /home/ubuntu/Build_WRF/src

Download Source Code.

$ wget https://www.mpich.org/static/downloads/4.0.2/mpich-4.0.2.tar.gz

Uncompress Source Code and Compile.

$ tar -xzvf mpich-4.0.2.tar.gz
$ cd mpich-4.0.2

$ FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ./configure --

prefix=/home/ubuntu/Build_WRF/LIBRARIES/mpich

$ make -j4
$ make install

create PATH variable in file .profile.

$ vi /home/ubuntu/.profile

### mpich
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/mpich/bin:$PATH

update PATH variable.

$ source /home/ubuntu/.profile
5.6.2 install zlib library.
change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

download source code.

$ wget http://www.zlib.net/fossils/zlib-1.2.12.tar.gz

uncompress source code and compile.

$ tar xzvf zlib-1.2.12.tar.gz
$ cd zlib-1.2.12
$ ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/zlib
$ make -j4
$ make install

5.6.3 Install hdf5 Library.

change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

Download Source Code

$ wget https://hdf-wordpress-1.s3.amazonaws.com/wp-
content/uploads/manual/HDF5/HDF5_1_12_2/source/hdf5-1.12.2.tar.gz

Uncompress Source Code and Compile.

$ tar xzvf hdf5-1.12.2.tar.gz
$ cd hdf5-1.12.2
$ ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/hdf5 --with-
zlib=/home/ubuntu/Build_WRF/LIBRARIES/zlib --enable-fortran --enable-fortran2003 --
enable-cxx --with-default-api-version=v18

$ make -j4
$ make install
Create PATH variable in file .bash_profile.
$ vi /home/ubuntu/.profile
### hdf5
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/hdf5/bin:$PATH
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/hdf5/lib:$LD_LIBRARY_PATH

update PATH variable.

$ source /home/ubuntu/.profile

5.6.4 install curl library.

change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

download source code.

$ wget https://curl.se/download/curl-7.83.1.tar.gz

uncompress source code and compile.

$ tar xzvf curl-7.83.1.tar.gz
$ cd curl-7.83.1
$ ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/curl --with-
zlib=/home/ubuntu/Build_WRF/LIBRARIES/zlib --without-ssl
$ make -j4
$ make install
5.6.5. Install netcdf Library.
Change to directory.
$ cd /home/ubuntu/Build_WRF/src

Download Source Code.

$ wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.8.0.tar.gz
$ wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.5.3.tar.gz

Uncompress Source Code and Compile.

$ tar xzvf netcdf-c-4.8.0.tar.gz
$ cd netcdf-c-4.8.0

$ CFLAGS=-fPIC CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/hdf5/include -
I/home/ubuntu/Build_WRF/LIBRARIES/curl/include' LDFLAGS='-
L/home/ubuntu/Build_WRF/LIBRARIES/hdf5/lib -
L/home/ubuntu/Build_WRF/LIBRARIES/curl/lib ' ./configure --
prefix=/home/ubuntu/Build_WRF/LIBRARIES/netcdf --enable-netcdf-4 --enable-netcdf4 --
enable-shared --enable-dap

$ make -j4
$ make install
$ cd ..
$ tar xzvf netcdf-fortran-4.5.3.tar.gz
$ cd netcdf-fortran-4.5.3

$ CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/netcdf/include' LDFLAGS='-
L/home/ubuntu/Build_WRF/LIBRARIES/netcdf/lib' FCFLAGS='-m64' ./configure --
prefix=/home/ubuntu/Build_WRF/LIBRARIES/netcdf

$ make -j4
$ make install
Create PATH variable in file .profile.
$ vi /home/ubuntu/.profile
### netcdf
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/netcdf/bin:$PATH
export NETCDF=/home/ubuntu/Build_WRF/LIBRARIES/netcdf
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/netcdf/lib:$LD_LIBRARY_PATH

update PATH variable.

$ source /home/ubuntu/.profile

5.6.6. Install libpng Library.

change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

Download Source Code

$ wget https://jaist.dl.sourceforge.net/project/libpng/libpng16/1.6.37/libpng-1.6.37.tar.gz

Uncompress Source Code and Compile.

$ tar xzvf libpng-1.6.37.tar.gz
$ cd libpng-1.6.37

$ CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/netcdf/include' FCFLAGS='-
m64' ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/libpng

$ make -j4
$ make install
5.6.7. Install Jasper Library.
change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

Download Source Code.

$ wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.10.tar.gz

Uncompress Source Code and Compile.

$ tar -xvzf jasper-2.0.10.tar.gz

$ cmake -G "Unix Makefiles" -H/home/ubuntu/Build_WRF/src/jasper-2.0.10 -

B/home/ubuntu/Build_WRF/src/jasper-2.0.10-build -
DCMAKE_INSTALL_PREFIX=/home/ubuntu/Build_WRF/LIBRARIES/jasper

$ cd /home/ubuntu/Build_WRF/src/jasper-2.0.10-build
$ make install

Create PATH variable in file .profile.

$ vi /home/ubuntu/.profile

#### jasper
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/jasper/bin:$PATH
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib:$LD_LIBRARY_PATH

update PATH variable.

$ source /home/ubuntu/.profile

5.6.8 Install ncl Library.

change to source code directory.
$ cd /home/ubuntu/Build_WRF/src

Install miniconda.
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh ./Miniconda3-latest-Linux-x86_64.sh
Enter…, yes, ENTER, yesl

Install ncl.
$ source /home/ubuntu/.bashrc
$ conda create -n ncl_stable -c conda-forge ncl
$ source activate ncl_stable

Test ncl.
$ ncl -V
Show version 6.6.2 is good.

Create variable in file .profile.

$ vi /home/ubuntu/.bashrc

#### ncl
source activate ncl_stable
5.7. Install WRF-Chem.
5.7.1 Install WRF-Chem and KPP.
Variable setup.

$ ulimit -s unlimited
$ export MALLOC_CHECK_=0
$ export EM_CORE=1
$ export NMM_CORE=0
$ export WRF_CHEM=1
$ export WRF_KPP=1
$ export YACC='/usr/bin/yacc -d'
$ export FLEX=/usr/bin/flex
$ export FLEX_LIB_DIR=/usr/lib/x86_64-linux-gnu
$ export KPP_HOME=/home/ubuntu/Build_WRF/WRFV4.4/chem/KPP/kpp/kpp-2.1
$ export WRF_SRC_ROOT_DIR=/home/ubuntu/Build_WRF/WRFV4.4
$ export PATH=$KPP_HOME/bin:$PATH
$ export SED=/usr/bin/sed
$ export WRFIO_NCD_LARGE_FILE_SUPPORT=1

Change to directory.
$ cd /home/ubuntu/Build_WRF/

Download Source Code.

$ wget -c https://github.com/wrf-model/WRF/releases/download/v4.4/v4.4.tar.gz -O wrf-4.4.tar.gz

Uncompress Source Code and Configure WRF.

$ tar -xvzf wrf-4.4.tar.gz
$ cd WRFV4.4/chem/KPP/kpp/kpp-2.1/src
$ /usr/bin/flex scan.l
$ cd /home/ubuntu/Build_WRF/WRFV4.4
Edit configure file line 919
$ vi configure
Change from To
if [ "$USENETCDFPAR" == "1" ] ; then if [ "$USENETCDFPAR" = "1" ] ; then

Run configure wrf

$ ./configure
select 34. (dmpar) GNU (gfortran/gcc)
Enter selection [1-75] : 34

and nesting is 1
Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]: 1

Complie kpp.
$ ./compile 2>&1 | tee compile_kpp.log
Show message below is good.

Complie em_real mode.

$ ./compile em_real 2>&1 | tee compile_wrf.log

Wait 30-50 minutes for finish test by

$ ls -lah main/*.exe
If you see real.exe and wrf.exe then correct. Else check Error in compile_wrf.log file.
5.7.2 Install WPS.
Change to directory.
$ cd /home/ubuntu/Build_WRF/
$ ln -sf WRFV4.4 WRF

Download Source Code.

$ wget -c https://github.com/wrf-model/WPS/archive/refs/tags/v4.4.tar.gz -O wps-4.4.tar.gz
Uncompress Source Code.
$ tar -xvzf wps-4.4.tar.gz

Define variable.
$ cd WPS-4.4
$ export JASPERLIB=/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib
$ export JASPERINC=/home/ubuntu/Build_WRF/LIBRARIES/jasper/include

Configure WPS.
$ ./configure

select 3. Linux x86_64, gfortran (dmpar)

Enter selection [1-40] : 3

edit configure.wps file. Change DM_FC to mpif90 and Append -lgomp in WRF_LIB.
$ vi configure.wps
COMPRESSION_LIBS = -L/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib -ljasper -lpng -lz
COMPRESSION_INC = -I/home/ubuntu/Build_WRF/LIBRARIES/jasper/include

DM_FC = mpif90
WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \
-L$(WRF_DIR)/external/io_grib_share -lio_grib_share \
-L$(WRF_DIR)/external/io_int -lwrfio_int \
-L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \
-L$(NETCDF)/lib -lnetcdff -lnetcdf -lgomp
Complie WPS.
$ ./compile 2>&1 | tee compile_wps.log

Wait for finish test by

$ ls -lah *.exe
If you see geogrid.exe metgrid.exe and ungrib.exe then correct. Else check Error in
compile_wps.log file.

5.8. Create Directory for Geography Data.

Change Directory.
$ cd /home/ubuntu/Build_WRF/

Downlaod Geography Data.

$ wget http://www2.mmm.ucar.edu/wrf/src/wps_files/albedo_modis.tar.bz2
$ wget http://www2.mmm.ucar.edu/wrf/src/wps_files/geog_complete.tar.gz
$ wget http://www2.mmm.ucar.edu/wrf/src/wps_files/maxsnowalb_modis.tar.bz2
$ wget http://www2.mmm.ucar.edu/wrf/src/wps_files/topo_2m.tar.bz2

Uncompress Geography Data.

$ tar -xvzf geog_complete.tar.gz
$ cd geog
$ tar -xvjf ../albedo_modis.tar.bz2
$ tar -xvjf ../maxsnowalb_modis.tar.bz2
$ tar -xvjf ../topo_2m.tar.bz2
5.9. Create directory for Input Data.
Create Real-time Data Directory and Change to Directory.
$ mkdir -p /home/ubuntu/Build_WRF/data/fnl
$ cd /home/ubuntu/Build_WRF/data/fnl

Download Data from

https://rda.ucar.edu/datasets/ds083.2/index.html#sfol-wl-/data/ds083.2?g=22010

Click Web File Listing

Check fnl 2010714_00 to 20100716_00

Select Download Script and copy download_ds083.2.csh to directory

/home/ubuntu/Build_WRF/data/fnl
Change Directory to WPS directory.
$ cp /home/ubuntu/download_ds083.2.csh /home/ubuntu/Build_WRF/data/fnl
$ cd /home/ubuntu/Build_WRF/data/fnl
$ csh ./download_ds083.2.csh
$ ls -al fnl*
-rw-rw-r-- 1 ubuntu ubuntu 14924785 Jun 27 05:53 fnl_20100714_00_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14925135 Jun 27 05:53 fnl_20100714_06_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14828592 Jun 27 05:53 fnl_20100714_12_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14802287 Jun 27 05:53 fnl_20100714_18_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14898435 Jun 27 05:53 fnl_20100715_00_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14708117 Jun 27 05:53 fnl_20100715_06_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14657174 Jun 27 05:53 fnl_20100715_12_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14739475 Jun 27 05:53 fnl_20100715_18_00.grib2
-rw-rw-r-- 1 ubuntu ubuntu 14587482 Jun 27 05:53 fnl_20100716_00_00.grib2
5.10. Run WRF-Chem.
5.10.1. Running WPS
Change Directory to WPS directory.
$ cd /home/ubuntu/Build_WRF/WPS-4.4
Change GEOGRID.TBL
$ cd geogrid
$ rm -rf GEOGRID.TBL
$ ln -svf GEOGRID.TBL.ARW_CHEM GEOGRID.TBL
$ cd ..

Create namelist.wps file.

$ rm -rf namelist.wps
$ vi namelist.wps
&share
wrf_core = 'ARW',
max_dom = 1,
start_date = '2010-07-14_00:00:00',
end_date = '2010-07-16_00:00:00',
interval_seconds = 10800,
io_form_geogrid = 2,
/

&geogrid
parent_id = 1,
parent_grid_ratio = 1,
i_parent_start = 1,
j_parent_start = 1,
e_we = 41,
e_sn = 41,
geog_data_res = '10m',
dx = 100000,
dy = 100000,
map_proj = 'lambert',
 ref_lat = 35.0,
ref_lon = 25.0,
truelat1 = 30.0,
truelat2 = 40.0,
stand_lon = 25.0,
geog_data_path = '/home/ubuntu/Build_WRF/geog'
/
ref_x = 20.5
ref_y = 20.5

&ungrib
out_format = 'WPS',
prefix = 'FILE',
/

&metgrid
fg_name = 'FILE'
io_form_metgrid = 2,
/
opt_ignore_dom_center = .true.,

&mod_levs
press_pa = 201300 , 200100 , 100000 ,
95000 , 90000 ,
85000 , 80000 ,
75000 , 70000 ,
65000 , 60000 ,
55000 , 50000 ,
45000 , 40000 ,
35000 , 30000 ,
25000 , 20000 ,
15000 , 10000 ,
5000 , 1000
/
Create Geography Data.
$ ./geogrid.exe

Wait for finish test by

$ ls -lah geo_em.d01.nc
If you see geo_em.d01.nc is coreect.

link Real-time Data top WPS.

$ ./link_grib.csh /home/ubuntu/Build_WRF/data/fnl/fnl_201007*

link Vtable
$ ln -sf ungrib/Variable_Tables/Vtable.GFS Vtable

create grib file.

$ ./ungrib.exe

Wait for finish test by

$ ls -lah FILE*
If you see FILE* is coreect.

create met file.

$ ./metgrid.exe

Wait for finish test by

$ ls -lah met_em.*
If you see met_em.* is coreect.
5.10.2. Running WRF.
Change Directory to WRF directory.
$ cd /home/ubuntu/Build_WRF/WRF/test/em_real/

link met file from WPS to WRF.

$ ln -sf /home/ubuntu/Build_WRF/WPS-4.4/met_em* .

remove namelist file.

$ rm -rf namelist.input

Edit namelist.input
$ vi namelist.input
&time_control
run_days = 2,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2010,
start_month = 07,
start_day = 14,
start_hour = 00,
start_minute = 00,
start_second = 00,
end_year = 2010,
end_month = 07,
end_day = 16,
end_hour = 00,
end_minute = 00,
end_second = 00,
interval_seconds = 10800,
input_from_file = .true.,
history_interval = 60,
frames_per_outfile = 72,
 restart = .false.,
restart_interval = 0,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
auxinput6_inname = 'wrfbiochemi_d01',
auxinput7_inname = 'wrffirechemi_d<domain>',
auxinput8_inname = 'wrfchemi_gocart_bg_d<domain>',
auxinput12_inname = 'wrf_chem_input',
auxinput5_interval_m = 86400,
auxinput7_interval_m = 86400,
auxinput8_interval_m = 86400,
io_form_auxinput2 = 2,
io_form_auxinput5 = 0,
io_form_auxinput6 = 0,
io_form_auxinput7 = 0,
io_form_auxinput8 = 0,
io_form_auxinput12 = 0,
debug_level = 0,
auxinput1_inname = "met_em.d<domain>.<date>",
auxinput13_inname = 'wrfchemv_d<domain>',
auxinput13_interval_m = 86400,
io_form_auxinput13 = 0,
/

&dfi_control
/

&domains
time_step = 600,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
 s_we = 1,
e_we = 41,
s_sn = 1,
e_sn = 41,
e_vert = 31,
num_metgrid_levels = 27,
num_metgrid_soil_levels = 4,
dx = 100000,
dy = 100000,
grid_id = 1,
parent_id = 0,
i_parent_start = 1,
j_parent_start = 1,
parent_grid_ratio = 1,
parent_time_step_ratio = 1,
p_top_requested = 10000,
feedback = 1,
smooth_option = 0,
p_top_requested = 10000,
zap_close_levels = 50,
interp_type = 1,
t_extrap_type = 2,
force_sfc_in_vinterp = 0,
use_levels_below_ground = .true.,
use_surface = .true.,
lagrange_order = 1,
sfcp_to_sfcp = .true.,
/

&physics
num_land_cat = 21,
mp_physics = 4,
progn = 0,
ra_lw_physics = 1,
 ra_sw_physics = 2,
radt = 30,
sf_sfclay_physics = 1,
sf_surface_physics = 2,
bl_pbl_physics = 1,
bldt = 0,
cu_physics = 5,
cu_diag = 1,
cudt = 0,
ishallow = 0,
isfflx = 1,
ifsnow = 1,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0,
mp_zero_out = 2,
mp_zero_out_thresh = 1.e-12,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
cu_rad_feedback = .true.,
/

&fdda
/

&dynamics
rk_ord = 3,
w_damping = 1,
diff_opt = 1,
km_opt = 4,
 diff_6th_opt = 0,
diff_6th_factor = 0.12,
base_temp = 290.
damp_opt = 0,
zdamp = 5000.,
dampcoef = 0.01,
khdif = 0,
kvdif = 0,
non_hydrostatic = .true.,
moist_adv_opt = 2,
scalar_adv_opt = 2,
chem_adv_opt = 2,
tke_adv_opt = 2,
time_step_sound = 4,
h_mom_adv_order = 5,
v_mom_adv_order = 3,
h_sca_adv_order = 5,
v_sca_adv_order = 3,
/

&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true.,
nested = .false.,
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

&chem
kemit = 1,
chem_opt = 401,
bioemdt = 0,
photdt = 0,
chemdt = 10,
io_style_emissions = 0,
emiss_opt = 3,
emiss_opt_vol = 0,
emiss_ash_hgt = 20000.,
chem_in_opt = 0,
phot_opt = 0,
gas_drydep_opt = 0,
aer_drydep_opt = 1,
bio_emiss_opt = 0,
ne_area = 0,
dust_opt = 1,
dmsemis_opt = 0,
seas_opt = 0,
depo_fact = 0.25,
gas_bc_opt = 0,
gas_ic_opt = 0,
aer_bc_opt = 1,
aer_ic_opt = 1,
gaschem_onoff = 0,
aerchem_onoff = 1,
wetscav_onoff = 0,
cldchem_onoff = 0,
vertmix_onoff = 1,
chem_conv_tr = 0,
conv_tr_wetscav = 0,
 conv_tr_aqchem = 0,
biomass_burn_opt = 0,
plumerisefire_frq = 30,
have_bcs_chem = .false.,
aer_ra_feedback = 0,
aer_op_opt = 0,
opt_pars_out = 0,
diagnostic_chem = 0,
/

create real case.

$ mpirun -np 1 ./real.exe

Wait for finish test by

$ tail rsl.error.0000
If you see real_em: SUCCESS COMPLETE REAL_EM INIT is coreect.

And see file wrfbdy_d01 wrfinput_d01.

$ ls -alh wrfbdy_d01 wrfinput_d01
If you see wrfbdy_d01 and wrfinput_d01 is coreect.

Run WRF
$ mpirun -np 2 ./wrf.exe

Wait for finish test by

$ tail rsl.error.0000
If you see wrf: SUCCESS COMPLETE WRF is coreect.

And see file wrfout_*

$ ls -alh wrfout_*
If you see wrfout_* is coreect.
5.10.3. list data inside wrfout.
$ ncdump -h wrfout_d01*
$ ncdump -v DUST_5 wrfout_d01*

5.10.4. Create pdf from wrfout.

Change Directory
$ cd /home/ubuntu/Build_WRF/WRF/test/em_real

Create ncl script.

$ vi plot_dust_5.ncl
;*************************************************
; WRF: DUST_5
;************************************************
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRF_contributed.ncl"

begin
f = addfile ("wrfout_d01_2010-07-14_00:00:00", "r")

wks = gsn_open_wks("pdf" ,"WRF_DUST_5") ; ps,pdf,x11,ncgm,eps

gsn_define_colormap(wks,"BlAqGrYeOrReVi200") ; select color map

res = True ; plot mods desired

res@gsnMaximize = True ; uncomment to maximize size
res@gsnSpreadColors = True ; use full range of colormap
res@cnFillOn = True ; color plot desired
res@cnLinesOn = False ; turn off contour lines
res@cnLineLabelsOn = False ; turn off contour labels
 WRF_map_c(f, res, 0) ; reads info from file

res@tfDoNDCOverlay = True
res@pmTickMarkDisplayMode = "Always" ; turn on tickmarks

times = wrf_user_getvar(f,"times",-1) ; get all times in the file

ntimes = dimsizes(times) ; number of times in the file

do nt=0,ntimes,6
x = f->DUST_5(nt,0,:,:) ; (Time,level, south_north, west_east)
res@tiMainString = "WRF-CHEM (DUST_5) " + times(nt)
res@gsnLeftString = x@description
plot = gsn_csm_contour_map(wks,x(:,:),res)
end do
end

Create PDF
$ ncl plot_dust_5.ncl
Output is WRF_DUST_5.pdf, you can open pdf file from pdf viewer or download to your laptop or
type “evince WRF_DUST_5.pdf”.

6. Conclusion.
We can setup WRF-Chem and KPP. And thank you website

• https://wiki.harvard.edu/confluence/pages/viewpage.action?pageId=228526205

• https://github.com/whatheway/WRFCHEM-4.4-install-script-linux-
64bit/blob/main/WRF_CHEMKPP_INSTALL_64BIT.sh

• https://ruc.noaa.gov/wrf/wrf-chem/tutorialexercises/tutorialexercises001.html

• https://www.ncl.ucar.edu/Training/Tutorials/WRF_Users_Workshop/WRF_NCL.shtml

for information.

Thank you.