fisidi · fisidi · May 10, 2022 · Apr 19, 2022 · Apr 19, 2022 · Apr 19, 2022
diff --git a/DOCS/Users_Guide/CMAQ_UG_ch13_WRF-CMAQ.md b/DOCS/Users_Guide/CMAQ_UG_ch13_WRF-CMAQ.md
@@ -32,41 +32,10 @@ Hemispheric WRF-CMAQ model simulation over two decades (1990−2010) shows enhan
 
 ## 13.4 Latest WRF-CMAQ Release
 
-The new WRF-CMAQ model is based on WRFv4.3 and CMAQv5.3.3. It supports only RRTMG radiation scheme for short wave aerosol direct effect. It uses core-shell model to perform aerosol optics calculations rather than volume mixing technique as in the previous version of the WRF-CMAQ model. 
+The new WRF-CMAQ model is based on WRF version 4.4 and CMAQ [version 5.3.3.3](https://github.com/USEPA/CMAQ/releases/tag/CMAQv5.3.3.3_10May2022) or later. It supports only RRTMG radiation scheme for short wave aerosol direct effect. It uses core-shell model to perform aerosol optics calculations rather than volume mixing technique as in the previous version of the WRF-CMAQ model. 
 
-The code used to couple the WRFv4.3-CMAQv5.3.3 models is now released as part of the [CMAQ Github Repository](../../../UTIL/wrfcmaq_twoway_coupler).
-
-Build and run instructions are provided in the [WRF-CMAQ Tutorial](Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md).
-
-## 13.5 Benchmarking WRF-CMAQ
-
-Benchmark input and output datasets are available from the CMAS Center Data Warehouse Google Drive.  Beginning with CMAQv5.3.1, the .tar.gz file with benchmark inputs for the base (uncoupled) model also contains a folder (WRF-CMAQ) with the additional input files needed to run the WRF-CMAQ model. A sample runscript ([run_cctm_Bench_2016_12SE1.WRFCMAQ.csh](../../../CCTM/scripts/run_cctm_Bench_2016_12SE1.WRFCMAQ.csh)) is provided as part of the CMAQ Github Repository. Similarly, the .tar.gz file with benchmark output for the base model also contains a folder (WRFv4.3_CMAQv5.3.3_outputs) with reference output for the WRF-CMAQ model with short-wave radiation calculations. These input and output benchmark files have also been posted on the US EPA annoymous ftp server. 
-
-- [Link to WRF-CMAQ Benchmark input and output datasets on Google Drive](https://drive.google.com/drive/u/1/folders/19U1_biDfrEunMlU9W3fCGNFWX5eZmD3Q)
-- WRF-CMAQ Benchmark input and output datasets on EPA annoymous ftp server: https://gaftp.epa.gov/exposure/CMAQ/V5_3_3/Benchmark
-
-WRF-CMAQ output for a two day benchmark case is provided for both the debug mode turned off (.tar.gz files containing "opt") and the debug mode turned on (.tar.gz files containing "rel_debug") version to allow the user to compare their answers to either. To reduce the impact of compiler flags on the model output, it is preferrable to use the debug version. To compare model results obtained while achieving faster run times due to compiler optimization, the Optimized version output is also provided.
-
-Metadata for the CMAQ benchmark test case is posted on the CMAS Center Dataverse site: https://doi.org/10.15139/S3/IQVABD 
-
-Once users have successfully completed installation and users can run a quick test to ensure model installation was truly successful. Users can setup a run base on the provided run script and a benchmark input dataset. Users should consult with the readme file which was accompanied by the test dataset or the release documentation to use the appropriate compiler flags for this quick test. Once the stimulation is completed, users can compare the newly produced result with the provided benchmark output. The comparison should return identical result if users have the same compiler version and system environment. This quick test gives users a peace of mind that the model installation was truly successful.
-
-Users should note, comparing the results of running WRF-CMAQ with the given input to the results of running CMAQ (offline) with the given input, while on the same domain, will include differences from other sources other than just the coupling of WRF and CMAQ. These differences are due to the version and nudging of WRF used to generate input files for CMAQ (offline) through MCIP, as well as the effect of windowing down to the south-east benchmark from the CONUS done for the CMAQ (offline) case. 
-
-
-## 13.6 WRF Namelist Options
-
-New with this version of the coupled model (WRFv4.3-CMAQv5.3.3), all related runtime options are now controlled via the WRF namelist under the &wrf_cmaq section. For convenience these options are set as runscript variables (look for section labeled &wrf_cmaq in the [sample runscript](../../../CCTM/scripts/run_cctm_Bench_2016_12SE1.WRFCMAQ.csh)) and automatically duplicated when creating the WRF namelist. There are five parameters with varying options see below: 
-
-
-| Name | Value | Description | 
-|------|-------|-------------|
-|wrf_cmaq_option| 2 |Dictates how the coupled model execute<br>0 = run WRF only<br>1 = run WRF only producing MCIP like GRID and MET files<br>2 = run WRF-CMAQ coupled model w/o producing MCIP like GRID and MET files<br>3 = run WRF-CMAQ coupled model producing MCIP like GRID and MET files |
-|wrf_cmaq_freq| 5 |Indicates how often WRF and CMAQ interact;<br>For example if set to 5, this means for every 5 WRF steps there will be 1 CMAQ step|
-|met_file_tstep| 10000 |Time step size of MCIP like intermediate output files (HHMMSS)|
-|direct_sw_feedback| .true. |Logical; whether to turn on/off aerosol short ware direct effects|
-|feedback_restart| .false. |Logical; whether aerosol short wave direct effect information is available in the WRF restart file|
-
+Build and run instructions are provided in the [WRF-CMAQ Tutorial](Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_Benchmark.md).
+
 If you have any questions, please contact David Wong at wong.david-c@epa.gov
 
 

diff --git a/README.md b/README.md
@@ -22,13 +22,15 @@ Potential updates include bugfixes that resolves runtime failures, segmentation
 ### Record of changes to CMAQv5.3.3+
 |      Tag        |   PR Number       |         PR Name          |   Merge Date     | Brief Description |
 | -------------- | ------------------ | ------------------------ | ---------------- | -----------------------|
+| [CMAQv5.3.3.2_7May2022](https://github.com/USEPA/CMAQ/releases/tag/CMAQv5.3.3.2_7May2022)     |  [#171](https://github.com/USEPA/CMAQ/pull/171)|Remove files from chemistry utilities causing problems on MAC and WINDOWS systems | 2022-05-07 | Both the create_ebi and inline_phot_prerproc utilities have files in their source code directories that only differ in letter case in filenames. The property does not cause problems on Linux systems but can cause problems on Window and Macintosh systems. The pull request removes the unneeded files causing the problems.|
 |[CMAQv5.3.3.1_11Feb2022](https://github.com/USEPA/CMAQ/releases/tag/CMAQv5.3.3.1_11Feb2022) | | | | |
 | | [#163](https://github.com/USEPA/CMAQ/pull/163)     | Resolve Bug for reading Emission Stream Families        | 2022-02-09 | Bug fix to avoid errors when processing matches for emission stream families related to capitalization. |
 |                | [#164](https://github.com/USEPA/CMAQ/pull/164)    | Resolve bug in Low-NOx formation of SOA  | 2022-02-09| A typo in the SOA_DEFN data table resulted in high NOx reactions contributing to low-NOx species, which are quite low in volatility. This bug fix has a considerable impact on SOA if using AE6. No impact for AE7.  |
 |                | [#165](https://github.com/USEPA/CMAQ/pull/165)    | Bugfix Speed up emissions processing in PTMET subroutine        | 2022-02-09 | The PTMET subroutine is streamlined so that it is not run for every point source and every stream every time each stream is called. This update drastically reduces runtimes in areas where there happen to be lots of point sources on a particular processor. No impact on results. |
 
 
 
+
 ## CMAQ version 5.3.3 Overview:
 CMAQv5.3.3 is a minor update to CMAQv5.3 that includes multiple bug fixes. These updates include restoration of windowing capability, allowing users to provide gridded input files which were larger in horizontal extent than the simulated domain. This release also includes a new version of the WRF-CMAQ coupled system with a streamlined build process. Users of WRF-CMAQ are strongly encouraged to try the latest version.  Additionally, MCIP users should note that starting with this release we are aligning the version numbering between CMAQ and MCIP, i.e., the MCIP updates included in this release are labeled MCIPv5.3.3. 
 * [CMAQv5.3.3 Release Notes](DOCS/Release_Notes/README.md)   

diff --git a/UTIL/README.md b/UTIL/README.md
@@ -12,4 +12,3 @@ The CMAQ release includes several optional utilities for model developers. Chemi
 * **[inline_phot_preproc](inline_phot_preproc/README.md)**: creates photolysis reaction parameter tables for the CCTM inline photlysis module
 * **[nml](nml/README.md)**: converts chemical mechanism csv output files from chemmech to the namelist files required by the CMAQ programs
 * **[jproc](jproc/README.md)**: calculates daily look-up tables containing clear-sky photolysis rates that are used by the tabular method for calculate photolysis rates in CMAQ CCTM
-* **[wrfcmaq_twoway_coupler](wrfcmaq_twoway_coupler/README.md)**: WRF-CMAQ code to couple WRFv4.3 and CMAQv5.3.3
diff --git a/UTIL/create_ebi/makefile.v50XX b/UTIL/create_ebi/makefile.v50XX
@@ -113,8 +113,8 @@ driver.o:  $(SRCDIR)/driver.F
 set_glbldata.o:  $(SRCDIR)/set_glbldata.F 
 	$(LOAD) -c $(INCLUDES) $(SRCDIR)/set_glbldata.F
 
-junit.o:  $(SRCDIR)/junit.f
-	$(LOAD) -c $(INCLUDES) $(SRCDIR)/junit.f
+junit.o:  $(SRCDIR)/junit.F
+	$(LOAD) -c $(INCLUDES) $(SRCDIR)/junit.F
 
 name_index.o:  $(SRCDIR)/name_index.f
 	$(LOAD) -c $(INCLUDES) $(SRCDIR)/name_index.f

diff --git a/UTIL/create_ebi/scripts/bldrun_create_ebi.csh b/UTIL/create_ebi/scripts/bldrun_create_ebi.csh
@@ -2,7 +2,7 @@
 # C-shell script to run CR_EBI_SOLVER 
 
  date; set timestamp; set echo 
-# current working directory assumed ${CMAQ_REPO}/UTIL/create_ebi;change if otherwise
+# current working directory assumed ${CMAQ_REPO}/UTIL/create_ebi/scripts; change if otherwise
  set BASE            = $cwd          
  set EXDIR           = ${BASE}/BLD  
  set EXEC            = cr_ebi_solver 
@@ -14,7 +14,7 @@
 # RXNS_DATA is the input directory containing the mechanism's data module
 # value will change based on user's goals
 set MECH             = 'cb6r3_ae7_aq'
-set RXNS_DATA        = ${BASE}/../../CCTM/src/MECHS/${MECH}
+set RXNS_DATA        = ${BASE}/../../../CCTM/src/MECHS/${MECH}
 setenv RXNS_DATA_SRC   ${RXNS_DATA}/RXNS_DATA_MODULE.F90
 
 if ( ! ( -e ${RXNS_DATA_SRC} ) )then
@@ -23,9 +23,9 @@ if ( ! ( -e ${RXNS_DATA_SRC} ) )then
 endif 
 
 # Define templates and scource code  directories
- setenv TMPLDIR         ${BASE}/template_RXNSU_OPT
- setenv DEGRADE_CODES   ${BASE}/degrade_codes_serial-RXNST
- setenv SRCDIR          ${BASE}/src_RXNSU
+ setenv TMPLDIR         ${BASE}/../template_RXNSU_OPT
+ setenv DEGRADE_CODES   ${BASE}/../degrade_codes_serial-RXNST
+ setenv SRCDIR          ${BASE}/../src_RXNSU
 
 # Define output directory;value will change based on user's goals
  set day = ` date "+%b-%d-%Y" `
@@ -67,7 +67,7 @@ endif
 
  mkdir BLD
 
- cp makefile.v50XX  ./BLD/Makefile
+ cp ../makefile.v50XX  ./BLD/Makefile
 
  cd BLD
 

diff --git a/UTIL/create_ebi/src_RXNSU/junit.f b/UTIL/create_ebi/src_RXNSU/junit.f
diff --git a/UTIL/inline_phot_preproc/bldrun.inline_phot_preproc.csh b/UTIL/inline_phot_preproc/bldrun.inline_phot_preproc.csh
@@ -1,8 +1,9 @@
 #!/bin/csh -fx
 
  set echo
-#set REPO  = /home/username/CMAQ_repo
- set REPO  = /home/cnolte/cmaq/dev-repo/CMAQ_Dev
+#set REPOsitory path 
+#commands assumes that current direct is UTIL/inline_phot_preproc subdirectory
+ cd ../.. ; set REPO = $cwd ; cd -
  set MECHS = $REPO/CCTM/src/MECHS
 
 #> CMAQ Mechanism under Repository directory CCTM/src/MECHS or