HEMCO structural updates, including header name changes, build update…

…s, and updates to precision settings.

CMakeScripts/HCO-Helpers.cmake

@@ -0,0 +1,185 @@
+
+#[[ stringify_list
+
+Stringify a list of strings.
+
+Usage:
+    stringify_list(<list>
+        [PRINT]
+        [LINE_LENGTH <length>]
+        [HIGHLIGHT <keyword> ...]
+        [JOIN <token> ...]
+        [AFTER]
+    )
+
+Options:
+    PRINT           Print the stringified list to console. Highlighted text
+                    will also be colorized.
+
+    LINE_LENGTH     When JOINing a list of string, the resulting lines will
+                    be limited to <length> characters. The resulting <list>
+                    will be a list of lines that can then be JOINed with
+                    newlines.
+
+    HIGHLIGHT       A list of keywords to highlight.
+
+    JOIN            A list of tokens that will be used sequentially to join
+                    list items. The last token will be used to join all
+                    remaining items.
+
+    AFTER           Place the JOIN tokens after the item, rather than before.
+
+]]
+function(stringify_list LIST)
+    cmake_parse_arguments(BETTER
+        "PRINT;AFTER"
+        "LINE_LENGTH"
+        "HIGHLIGHT;JOIN"
+        ${ARGN}
+    )
+
+    if(NOT DEFINED BETTER_LINE_LENGTH)
+        set(BETTER_LINE_LENGTH 1000) # Arbitrary big number
+    endif()
+
+    set(STR ${${LIST}})
+
+    # Limit joined line length
+    if(DEFINED BETTER_JOIN)
+        set(TEMP "")
+        set(CUR_LEN "0")
+
+        set(JOIN_IDX "0 - 1")
+        list(LENGTH BETTER_JOIN JOIN_LEN)
+
+        foreach(ITEM ${STR})
+            # Get the join token
+            math(EXPR JOIN_IDX "${JOIN_IDX} + 1")
+            if(${JOIN_IDX} LESS ${JOIN_LEN})
+                list(GET BETTER_JOIN "${JOIN_IDX}" JOIN_TOKEN)
+            endif()
+            string(LENGTH "${JOIN_TOKEN}" SEP_LEN)
+
+            # If a line length was
+            string(LENGTH "${ITEM}" WORD_LEN)
+            math(EXPR POST_LEN "${WORD_LEN} + ${CUR_LEN} + ${SEP_LEN}")
+            if("${POST_LEN}" LESS "${BETTER_LINE_LENGTH}")
+                if(${BETTER_AFTER})
+                    set(TEMP "${TEMP}${ITEM}${JOIN_TOKEN}")
+                else()
+                    set(TEMP "${TEMP}${JOIN_TOKEN}${ITEM}")
+                endif()
+                set(CUR_LEN "${POST_LEN}")
+            else()
+                if(${BETTER_AFTER})
+                    set(TEMP "${TEMP};${ITEM}${JOIN_TOKEN}")
+                else()
+                    set(TEMP "${TEMP};${JOIN_TOKEN}${ITEM}")
+                endif()
+                set(CUR_LEN "0")
+                math(EXPR CUR_LEN "${SEP_LEN} + ${WORD_LEN}")
+            endif()
+        endforeach()
+
+        set(STR "${TEMP}")
+    endif()
+
+    # Highlight selected words
+    if(DEFINED BETTER_HIGHLIGHT)
+        foreach(KEYWORD ${BETTER_HIGHLIGHT})
+            string(REPLACE "${KEYWORD}" "[${KEYWORD}]" STR "${STR}")
+        endforeach()
+    endif()
+
+    if(${BETTER_PRINT})
+        string(ASCII 27 Esc)
+        if(${CMAKE_COLOR_MAKEFILE})
+            string(REGEX REPLACE "\\[([a-zA-Z0-9_\\.]+)\\]" "${Esc}[32m\\1${Esc}[m" COLORIZED "${STR}")
+        else()
+            set(COLORIZED "${STR}")
+        endif()
+	string(REGEX REPLACE "\n$" "" COLORIZED "${COLORIZED}")
+        message("${COLORIZED}")
+    endif()
+
+
+    # Export the new string
+    set(${LIST} "${STR}" PARENT_SCOPE)
+endfunction()
+
+#[[ get_repo_version
+
+Variable with name ${VARNAME} gets set to first 7 characters of the hash
+of the last commit to the repo at ${DIR}.
+
+Usage:
+    get_repo_version(VARNAME DIR)
+
+]]
+macro(get_repo_version VARNAME DIR)
+    execute_process(
+        COMMAND git describe --tags --dirty=.dirty
+        WORKING_DIRECTORY ${DIR}
+        OUTPUT_VARIABLE ${VARNAME}
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+endmacro()
+
+function(hco_pretty_print)
+    cmake_parse_arguments(ARGS
+        "IS_BOOLEAN"
+        "VARIABLE;SECTION"
+        "OPTIONS"
+        ${ARGN}
+    )
+
+    if(DEFINED ARGS_VARIABLE)
+        if(ARGS_IS_BOOLEAN)
+            set(LOGLINE "ON" "OFF")
+            # Split list with "  "
+            stringify_list(LOGLINE
+                JOIN "  "
+                LINE_LENGTH 60
+            )
+            # Wrap lines
+	    stringify_list(LOGLINE
+                JOIN "  * ${ARGS_VARIABLE}:\t" "\n  ...       \t"
+	    )
+            if("${${ARGS_VARIABLE}}")
+                stringify_list(LOGLINE PRINT HIGHLIGHT "ON")
+            else()
+                stringify_list(LOGLINE PRINT HIGHLIGHT "OFF")
+            endif()
+        elseif(DEFINED ARGS_OPTIONS)
+            set(LOGLINE ${ARGS_OPTIONS})
+            # Split list with "  "
+            stringify_list(LOGLINE
+                JOIN "  "
+                LINE_LENGTH 60
+            )
+            # Wrap lines
+            stringify_list(LOGLINE
+                JOIN "  * ${ARGS_VARIABLE}:\t" "\n  ...       \t"
+            )
+            stringify_list(LOGLINE PRINT HIGHLIGHT ${${ARGS_VARIABLE}})
+        else()
+            if(NOT DEFINED ${ARGS_VARIABLE})
+                set(LOGLINE " ") # special case for empty variable
+            else()
+                set(LOGLINE ${${ARGS_VARIABLE}})
+            endif()
+            # Split list with "  "
+            stringify_list(LOGLINE
+                JOIN "  "
+                LINE_LENGTH 60
+            )
+            # Wrap lines
+            stringify_list(LOGLINE
+                JOIN "  + ${ARGS_VARIABLE}:\t" "\n  ...       \t"
+            )
+            stringify_list(LOGLINE PRINT)
+        endif()
+    elseif(DEFINED ARGS_SECTION)
+        message(STATUS "${ARGS_SECTION}:")
+    endif()
+endfunction()

run/HEMCO_sa_Time.rc

@@ -1,5 +1,5 @@
 # List here simulation start, end, and emission time step (seconds).
 # Dates must have format YYYY-MM-DD hh:mm:ss
-START:   2016-07-01 00:00:00
-END:     2016-08-01 00:00:00
+START:   2019-07-01 00:00:00
+END:     2019-08-01 00:00:00
 TS_EMIS: 3600

run/README

@@ -1,8 +1,10 @@
-This is a HEMCO standalone run directory for a 4x5 simulation. For more
-information on how to download and run the HEMCO standalone model, see:
+This is a HEMCO standalone run directory.
 
-  http://wiki.seg.harvard.edu/geos-chem/index.php/HEMCO_standalone
+For more information on how to download and run the HEMCO standalone model,
+please see:
 
-19 May 2017
+  http://wiki.geos-chem.org/HEMCO_standalone
+
+28 Sep 2020
 GEOS-Chem Support Team
 [email protected]

run/createRunDir.sh

@@ -248,7 +248,7 @@ ln -s ${hemcodir}                            ${rundir}/CodeDir
 sed -i -e "s|{DATA_ROOT}|${GC_DATA_ROOT}|"   ${rundir}/HEMCO_sa_Config.rc
 sed -i -e "s|{GRID_FILE}|${grid_file}|"      ${rundir}/HEMCO_sa_Config.rc
 sed -i -e "s|{MET_NAME}|${met_name}|"        ${rundir}/HEMCO_sa_Config.rc
-sed -i -e "s|{MET_RES}|${grid_res}|"         ${rundir}/HEMCO_sa_Config.rc
+sed -i -e "s|{MET_RES}|${grid_name}|"        ${rundir}/HEMCO_sa_Config.rc
 
 # HEMCO_Config.rc (copied from GEOS-Chem)
 sed -i -e "s|{DATA_ROOT}|${GC_DATA_ROOT}|"   ${rundir}/HEMCO_Config.rc

src/Core/.gitignore

@@ -10,3 +10,4 @@ geosapm
 *.inst.*
 *.continue.*
 *.ppk
+core.*

src/Core/CMakeLists.txt

@@ -27,6 +27,7 @@ add_library(HCO STATIC EXCLUDE_FROM_ALL
 	hcoio_dataread_mod.F90
 	hcoio_diagn_mod.F90
 	hcoio_messy_mod.F90
+	hcoio_util_mod.F90
 	hcoio_read_esmf_mod.F90
 	hcoio_read_std_mod.F90
 	hcoio_write_esmf_mod.F90