From 904d44fdbbef80b5d638a9cc214f53df74f56646 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Sun, 25 Aug 2024 16:08:31 -0600
Subject: [PATCH 01/15] New script for WACCM extract. Command-line args only.

---
 tools/waccmToMusicBox.py | 137 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 137 insertions(+)
 create mode 100644 tools/waccmToMusicBox.py

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
new file mode 100644
index 00000000..6e3ddc18
--- /dev/null
+++ b/tools/waccmToMusicBox.py
@@ -0,0 +1,137 @@
+#!/usr/bin/env python3
+# waccmToMusicBox.py
+# MusicBox: Extract variables from WACCM model output,
+# and convert to initial conditions for MusicBox (case TS1).
+#
+# Author: Carl Drews
+# Copyright 2024 by Atomospheric Chemistry Observations & Modeling (UCAR/ACOM)
+
+#import os
+import argparse
+#import numpy
+import datetime
+import xarray
+import sys
+
+import logging
+logger = logging.getLogger(__name__)
+
+
+
+# configure argparse for key-value pairs
+class KeyValueAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        for value in values:
+            key, val = value.split('=')
+            setattr(namespace, key, val)
+
+# Retrieve named arguments from the command line and
+# return in a dictionary of keywords.
+# argPairs = list of arguments, probably from sys.argv[1:]
+#       named arguments are formatted like this=3.14159
+# return dictionary of keywords and values
+def getArgsDictionary(argPairs):
+    parser = argparse.ArgumentParser(
+        description='Process some key=value pairs.')
+    parser.add_argument(
+        'key_value_pairs',
+        nargs='+',  # This means one or more arguments are expected
+        action=KeyValueAction,
+        help="Arguments in key=value format. Example: configFile=my_config.json"
+    )
+
+    argDict = vars(parser.parse_args(argPairs))      # return dictionary
+
+    return (argDict)
+
+
+
+# Convert safely from string to integer (alphas convert to 0).
+def safeInt(intString):
+        intValue = 0
+        try:
+                intValue = int(intString)
+        except ValueError as error:
+                intValue = 0
+
+        return intValue
+
+
+
+# Convert string to number, or 0.0 if not numeric.
+# numString = string that probably can be converted
+def safeFloat(numString):
+	result = -1.0
+	try:
+		result = float(numString)
+	except ValueError:
+		result = 0.0
+
+	return result
+
+
+
+# Build and return dictionary of WACCM variable names
+# and their MusicBox equivalents.
+def getMusicaDictionary():
+   varMap = {
+      "Nairobi": [-1.2921, 36.8219],
+      "Kampala": [0.3476, 32.5825],
+      "Kigali": [-1.9441, 30.0619],
+      "Dodoma": [-6.1630, 35.7516],
+      "Lilongwe": [-13.9626, 33.7741],
+      "Lusaka": [-15.3875, 28.3228]
+   }
+
+   return(dict(sorted(varMap.items())))
+
+
+
+# Main routine begins here.
+def main():
+    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+    logger.info("{}".format(__file__))
+    logger.info("Start time: {}".format(datetime.datetime.now()))
+
+    # retrieve and parse the command-line arguments
+    myArgs = getArgsDictionary(sys.argv[1:])
+    logger.info("Command line = {}".format(myArgs))
+
+    # set up the directories
+    waccmDir = None
+    if ("waccmDir" in myArgs):
+        waccmDir = myArgs.get("waccmDir")
+
+    musicaDir = None
+    if ("musicaDir" in myArgs):
+        musicaDir = myArgs.get("musicaDir")
+
+    # get the geographical location to retrieve
+    lat = None
+    if ("latitude" in myArgs):
+        lat = safeFloat(myArgs.get("latitude"))
+
+    lon = None
+    if ("longitude" in myArgs):
+        lon = safeFloat(myArgs.get("longitude"))
+
+    logger.info("Retrieve WACCM conditions at ({} North, {} East)."
+        .format(lat, lon))
+
+    logger.info("End time: {}".format(datetime.datetime.now()))
+    sys.exit(0)     # no error
+
+
+
+if (__name__ == "__main__"):
+    main()
+
+
+    logger.info("End time: {}".format(datetime.datetime.now()))
+    sys.exit(0)     # no error
+
+
+
+if (__name__ == "__main__"):
+    main()
+

From 529bb186e2e68a7927b0d21c4b64c363fa213c1b Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Sun, 25 Aug 2024 20:24:12 -0600
Subject: [PATCH 02/15] Opening the WACCM file with xarray.

---
 tools/waccmToMusicBox.py | 64 +++++++++++++++++++++++++++++++++++-----
 1 file changed, 56 insertions(+), 8 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 6e3ddc18..175109b6 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -75,18 +75,46 @@ def safeFloat(numString):
 # and their MusicBox equivalents.
 def getMusicaDictionary():
    varMap = {
-      "Nairobi": [-1.2921, 36.8219],
-      "Kampala": [0.3476, 32.5825],
-      "Kigali": [-1.9441, 30.0619],
-      "Dodoma": [-6.1630, 35.7516],
-      "Lilongwe": [-13.9626, 33.7741],
-      "Lusaka": [-15.3875, 28.3228]
+      "H2O": "H2O",
+      "TEPOMUC": "jtepo",
+      "BENZENE": "jbenzene",
+      "O3": "O3",
+      "NH3": "NH3",
+      "CH4": "CH4",
+      "O": "O"
    }
 
    return(dict(sorted(varMap.items())))
 
 
 
+# Read array values at a single lat-lon-time point.
+# waccmMusicaDict = mapping from WACCM names to MusicBox
+# latitude, longitude = geo-coordinates of retrieval point
+# when = date and time to extract
+# modelDir = directory containing model output
+# return xarray of variable names and values
+def readWACCM(waccmMusicaDict, latitude, longitude,
+  when, modelDir):
+
+  # create the filename
+  waccmFilename = ("f.e22.beta02.FWSD.f09_f09_mg17.cesm2_2_beta02.forecast.001.cam.h3.{:4d}-{:02d}-{:02}-00000.nc"
+    .format(when.year, when.month, when.day))
+  logger.info("WACCM file = {}".format(waccmFilename))
+
+  # open dataset for reading
+  waccmDataSet = xarray.open_dataset("{}/{}".format(modelDir, waccmFilename))
+  if (True):
+    # diagnostic to look at dataset structure
+    logger.info("WACCM dataset = {}".format(waccmDataSet))
+
+  # close the NetCDF file
+  waccmDataSet.close()
+
+  return(None)
+
+
+
 # Main routine begins here.
 def main():
     logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -106,6 +134,15 @@ def main():
     if ("musicaDir" in myArgs):
         musicaDir = myArgs.get("musicaDir")
 
+    # get the date-time to retrieve
+    dateStr = None
+    if ("date" in myArgs):
+      dateStr = myArgs.get("date")
+
+    timeStr = "00:00"
+    if ("time" in myArgs):
+      timeStr = myArgs.get("time")
+
     # get the geographical location to retrieve
     lat = None
     if ("latitude" in myArgs):
@@ -115,8 +152,19 @@ def main():
     if ("longitude" in myArgs):
         lon = safeFloat(myArgs.get("longitude"))
 
-    logger.info("Retrieve WACCM conditions at ({} North, {} East)."
-        .format(lat, lon))
+    retrieveWhen = datetime.datetime.strptime(
+      "{} {}".format(dateStr, timeStr), "%Y%m%d %H:%M")
+
+    logger.info("Retrieve WACCM conditions at ({} North, {} East)   when {}."
+        .format(lat, lon, retrieveWhen))
+
+    # Read named variables from WACCM model output.
+    varValues = readWACCM(getMusicaDictionary(),
+      lat, lon, retrieveWhen, waccmDir)
+
+    # Perform any conversions needed, or derive variables.
+
+    # Write CSV file for MusicBox initial conditions.
 
     logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)     # no error

From b1df7cd36913d15155abff2f7b0cc40a4ad3e052 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Sun, 25 Aug 2024 21:54:26 -0600
Subject: [PATCH 03/15] Retrieving WACCM values at requested location and time.

---
 tools/waccmToMusicBox.py | 34 +++++++++++++++++++++++++++++++---
 1 file changed, 31 insertions(+), 3 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 175109b6..0a77e630 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -81,7 +81,7 @@ def getMusicaDictionary():
       "O3": "O3",
       "NH3": "NH3",
       "CH4": "CH4",
-      "O": "O"
+      "O": "O"          # test var not in WACCM
    }
 
    return(dict(sorted(varMap.items())))
@@ -93,7 +93,7 @@ def getMusicaDictionary():
 # latitude, longitude = geo-coordinates of retrieval point
 # when = date and time to extract
 # modelDir = directory containing model output
-# return xarray of variable names and values
+# return dictionary of MUSICA variable names, values, and units
 def readWACCM(waccmMusicaDict, latitude, longitude,
   when, modelDir):
 
@@ -108,10 +108,37 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
     # diagnostic to look at dataset structure
     logger.info("WACCM dataset = {}".format(waccmDataSet))
 
+  # retrieve all vars at a single point
+  whenStr = when.strftime("%Y-%m-%d %H:%M:%S")
+  logger.info("whenStr = {}".format(whenStr))
+  singlePoint = waccmDataSet.sel(lon=longitude, lat=latitude, lev=1000.0,
+    time=whenStr, method="nearest")
+  if (True):
+    # diagnostic to look at single point structure
+    logger.info("WACCM singlePoint = {}".format(singlePoint))
+
+  # loop through vars and build another dictionary
+  musicaDict = {}
+  for waccmKey, musicaName in waccmMusicaDict.items():
+    logger.info("WACCM Chemical = {}".format(waccmKey))
+    if not waccmKey in singlePoint:
+      logger.warning("Requested variable {} not found in WACCM model output."
+        .format(waccmKey))
+      musicaTuple = (waccmKey, None, None)
+      musicaDict[musicaName] = musicaTuple
+      continue
+
+    chemSinglePoint = singlePoint[waccmKey]
+    if (True):
+      logger.info("{} = {}".format(waccmKey, chemSinglePoint))
+      logger.info("{} = {} {}".format(waccmKey, chemSinglePoint.values, chemSinglePoint.units))
+    musicaTuple = (waccmKey, chemSinglePoint.values, chemSinglePoint.units)
+    musicaDict[musicaName] = musicaTuple
+
   # close the NetCDF file
   waccmDataSet.close()
 
-  return(None)
+  return(musicaDict)
 
 
 
@@ -161,6 +188,7 @@ def main():
     # Read named variables from WACCM model output.
     varValues = readWACCM(getMusicaDictionary(),
       lat, lon, retrieveWhen, waccmDir)
+    logger.info("WACCM varValues = {}".format(varValues))
 
     # Perform any conversions needed, or derive variables.
 

From 595001dbfd21085cfc89ae3764e2056b5464e8e2 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Sun, 25 Aug 2024 22:11:26 -0600
Subject: [PATCH 04/15] Added example conversion.

---
 tools/waccmToMusicBox.py | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 0a77e630..a9b5598a 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -76,12 +76,12 @@ def safeFloat(numString):
 def getMusicaDictionary():
    varMap = {
       "H2O": "H2O",
-      "TEPOMUC": "jtepo",
+      "TEPOMUC": "jtepo",   # test var not in WACCM
       "BENZENE": "jbenzene",
       "O3": "O3",
       "NH3": "NH3",
       "CH4": "CH4",
-      "O": "O"          # test var not in WACCM
+      "O": "O"             # test var not in WACCM
    }
 
    return(dict(sorted(varMap.items())))
@@ -142,6 +142,21 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
 
 
 
+# Perform any numeric conversion needed.
+# varDict = originally read from WACCM, tuples are (musicaName, value, units)
+# return varDict with values modified
+def convertWaccm(varDict):
+   # set up indexes for the tuple
+   musicaIndex = 0
+   valueIndex = 1
+   unitIndex = 2
+
+   nh3Tuple = varDict["NH3"]
+   varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[2])
+   return(varDict)
+
+
+
 # Main routine begins here.
 def main():
     logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -188,9 +203,11 @@ def main():
     # Read named variables from WACCM model output.
     varValues = readWACCM(getMusicaDictionary(),
       lat, lon, retrieveWhen, waccmDir)
-    logger.info("WACCM varValues = {}".format(varValues))
+    logger.info("Original WACCM varValues = {}".format(varValues))
 
     # Perform any conversions needed, or derive variables.
+    convertWaccm(varValues)
+    logger.info("Converted WACCM varValues = {}".format(varValues))
 
     # Write CSV file for MusicBox initial conditions.
 

From a556e70248350ca6a3a1397100e10d67ab647d8d Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Sun, 25 Aug 2024 22:49:55 -0600
Subject: [PATCH 05/15] Writing initial values to CSV file.

---
 tools/waccmToMusicBox.py | 51 +++++++++++++++++++++++++++++++++-------
 1 file changed, 43 insertions(+), 8 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index a9b5598a..a9957f7c 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -142,18 +142,51 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
 
 
 
+# set up indexes for the tuple
+musicaIndex = 0
+valueIndex = 1
+unitIndex = 2
+
 # Perform any numeric conversion needed.
 # varDict = originally read from WACCM, tuples are (musicaName, value, units)
 # return varDict with values modified
 def convertWaccm(varDict):
-   # set up indexes for the tuple
-   musicaIndex = 0
-   valueIndex = 1
-   unitIndex = 2
+  # convert Ammonia to milli-moles
+  nh3Tuple = varDict["NH3"]
+  varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[2])
+  return(varDict)
+
+
+
+# Write CSV file suitable for initial_conditions.csv in MusicBox
+# initValues = dictionary of Musica varnames and (WACCM name, value, units)
+def writeInitCSV(initValues, filename):
+  fp = open(filename, "w")
+
+  # write the column titles
+  firstColumn = True
+  for key, value in initValues.items():
+    if (firstColumn):
+      firstColumn = False
+    else:
+      fp.write(",")
+
+    fp.write(key)
+  fp.write("\n")
+
+  # write the variable values
+  firstColumn = True
+  for key, value in initValues.items():
+    if (firstColumn):
+      firstColumn = False
+    else:
+      fp.write(",")
+
+    fp.write("{}".format(value[valueIndex]))
+  fp.write("\n")
 
-   nh3Tuple = varDict["NH3"]
-   varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[2])
-   return(varDict)
+  fp.close()
+  return
 
 
 
@@ -206,10 +239,12 @@ def main():
     logger.info("Original WACCM varValues = {}".format(varValues))
 
     # Perform any conversions needed, or derive variables.
-    convertWaccm(varValues)
+    varValues = convertWaccm(varValues)
     logger.info("Converted WACCM varValues = {}".format(varValues))
 
     # Write CSV file for MusicBox initial conditions.
+    csvName = "{}/{}".format(musicaDir, "initial_conditions.csv")
+    writeInitCSV(varValues, csvName)
 
     logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)     # no error

From 3308858235295adcff48c131337c29635d80b2e5 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 26 Aug 2024 13:56:05 -0600
Subject: [PATCH 06/15] Added temperature and pressure.

---
 tools/waccmToMusicBox.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index a9957f7c..da72a34b 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -75,6 +75,8 @@ def safeFloat(numString):
 # and their MusicBox equivalents.
 def getMusicaDictionary():
    varMap = {
+      "T": "temperature",
+      "PS": "pressure",
       "H2O": "H2O",
       "TEPOMUC": "jtepo",   # test var not in WACCM
       "BENZENE": "jbenzene",

From c3c9e641de685137133b3dafdc92b1ee33c321fb Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 26 Aug 2024 14:08:59 -0600
Subject: [PATCH 07/15] Stub function for writing JSON output.

---
 tools/waccmToMusicBox.py | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index da72a34b..3b3c5044 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -160,7 +160,7 @@ def convertWaccm(varDict):
 
 
 
-# Write CSV file suitable for initial_conditions.csv in MusicBox
+# Write CSV file suitable for initial_conditions.csv in MusicBox.
 # initValues = dictionary of Musica varnames and (WACCM name, value, units)
 def writeInitCSV(initValues, filename):
   fp = open(filename, "w")
@@ -192,6 +192,18 @@ def writeInitCSV(initValues, filename):
 
 
 
+# Write JSON fragment suitable for my_config.json in MusicBox.
+# initValues = dictionary of Musica varnames and (WACCM name, value, units)
+def writeInitJSON(initValues, filename):
+  fp = open(filename, "w")
+
+  fp.write("Hello, JSON World!\n")
+
+  fp.close()
+  return
+
+
+
 # Main routine begins here.
 def main():
     logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -244,9 +256,15 @@ def main():
     varValues = convertWaccm(varValues)
     logger.info("Converted WACCM varValues = {}".format(varValues))
 
-    # Write CSV file for MusicBox initial conditions.
-    csvName = "{}/{}".format(musicaDir, "initial_conditions.csv")
-    writeInitCSV(varValues, csvName)
+    if (False):
+      # Write CSV file for MusicBox initial conditions.
+      csvName = "{}/{}".format(musicaDir, "initial_conditions.csv")
+      writeInitCSV(varValues, csvName)
+
+    else:
+      # Write JSON file for MusicBox initial conditions.
+      jsonName = "{}/{}".format(musicaDir, "initial_config.json")
+      writeInitJSON(varValues, jsonName)
 
     logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)     # no error

From ed34d79874a362073d4d48c5125ef1cb9f7a8474 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 26 Aug 2024 15:53:16 -0600
Subject: [PATCH 08/15] Writing initial concentrations to JSON file.

---
 tools/waccmToMusicBox.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 3b3c5044..196b8fc5 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -8,9 +8,9 @@
 
 #import os
 import argparse
-#import numpy
 import datetime
 import xarray
+import json
 import sys
 
 import logging
@@ -132,9 +132,9 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
 
     chemSinglePoint = singlePoint[waccmKey]
     if (True):
-      logger.info("{} = {}".format(waccmKey, chemSinglePoint))
-      logger.info("{} = {} {}".format(waccmKey, chemSinglePoint.values, chemSinglePoint.units))
-    musicaTuple = (waccmKey, chemSinglePoint.values, chemSinglePoint.units)
+      logger.info("{} = object {}".format(waccmKey, chemSinglePoint))
+      logger.info("{} = value {} {}".format(waccmKey, chemSinglePoint.values, chemSinglePoint.units))
+    musicaTuple = (waccmKey, float(chemSinglePoint.values.mean()), chemSinglePoint.units)
     musicaDict[musicaName] = musicaTuple
 
   # close the NetCDF file
@@ -195,11 +195,22 @@ def writeInitCSV(initValues, filename):
 # Write JSON fragment suitable for my_config.json in MusicBox.
 # initValues = dictionary of Musica varnames and (WACCM name, value, units)
 def writeInitJSON(initValues, filename):
-  fp = open(filename, "w")
 
-  fp.write("Hello, JSON World!\n")
+  # set up dictionary of vars and initial values
+  dictName = "chemical species"
+  initConfig = {dictName: {} }
 
-  fp.close()
+  for key, value in initValues.items():
+    initConfig[dictName][key] = {
+      "initial value [{}]".format(value[unitIndex]): value[valueIndex]}
+
+  # write JSON content to the file
+  fpJson = open(filename, "w")
+
+  json.dump(initConfig, fpJson, indent=2)
+  fpJson.close()
+
+  fpJson.close()
   return
 
 

From 717c079c248e20f8065b79ad2917265afe5664ac Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 26 Aug 2024 16:06:58 -0600
Subject: [PATCH 09/15] Comment for 0-dim array.

---
 tools/waccmToMusicBox.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 196b8fc5..f7ab5867 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -134,7 +134,7 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
     if (True):
       logger.info("{} = object {}".format(waccmKey, chemSinglePoint))
       logger.info("{} = value {} {}".format(waccmKey, chemSinglePoint.values, chemSinglePoint.units))
-    musicaTuple = (waccmKey, float(chemSinglePoint.values.mean()), chemSinglePoint.units)
+    musicaTuple = (waccmKey, float(chemSinglePoint.values.mean()), chemSinglePoint.units)   # from 0-dim array
     musicaDict[musicaName] = musicaTuple
 
   # close the NetCDF file

From cecd5bcb1f0bd6783e07e855f9ae2aa3e0e4173b Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 26 Aug 2024 17:05:53 -0600
Subject: [PATCH 10/15] More realistic example species.

---
 tools/waccmToMusicBox.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index f7ab5867..7868c85d 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -77,13 +77,11 @@ def getMusicaDictionary():
    varMap = {
       "T": "temperature",
       "PS": "pressure",
-      "H2O": "H2O",
-      "TEPOMUC": "jtepo",   # test var not in WACCM
-      "BENZENE": "jbenzene",
+      "N2O": "N2O",
+      "H2O2": "H2O2",
       "O3": "O3",
       "NH3": "NH3",
-      "CH4": "CH4",
-      "O": "O"             # test var not in WACCM
+      "CH4": "CH4"
    }
 
    return(dict(sorted(varMap.items())))
@@ -155,7 +153,8 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
 def convertWaccm(varDict):
   # convert Ammonia to milli-moles
   nh3Tuple = varDict["NH3"]
-  varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[2])
+  varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[unitIndex])
+
   return(varDict)
 
 

From b032ba8b639f05da9ae5aecd5ad9c16018ff664e Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 27 Aug 2024 15:15:51 -0600
Subject: [PATCH 11/15] Copy template directory; no insertion or compression
 yet.

---
 tools/waccmToMusicBox.py | 36 ++++++++++++++++++++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 7868c85d..5f4173ab 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -12,6 +12,8 @@
 import xarray
 import json
 import sys
+import os
+import shutil
 
 import logging
 logger = logging.getLogger(__name__)
@@ -214,6 +216,28 @@ def writeInitJSON(initValues, filename):
 
 
 
+# Reproduce the MusicBox configuration with new initial values.
+# initValues = dictionary of Musica varnames and (WACCM name, value, units)
+# templateDir = directory containing configuration files and camp_data
+# destDir = the template will be created in this directory
+def insertIntoTemplate(initValues, templateDir, destDir):
+
+  # copy the template directory to working area
+  destPath = os.path.basename(os.path.normpath(templateDir))
+  destPath = os.path.join(destDir, destPath)
+  logger.info("Create new configuration in = {}".format(destPath))
+
+  # remove directory if it already exists
+  if os.path.exists(destPath):
+    shutil.rmtree(destPath)
+
+  # copy the template directory
+  shutil.copytree(templateDir, destPath)
+
+  return
+
+
+
 # Main routine begins here.
 def main():
     logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -254,6 +278,10 @@ def main():
     retrieveWhen = datetime.datetime.strptime(
       "{} {}".format(dateStr, timeStr), "%Y%m%d %H:%M")
 
+    template = None
+    if ("template" in myArgs):
+        template = myArgs.get("template")
+
     logger.info("Retrieve WACCM conditions at ({} North, {} East)   when {}."
         .format(lat, lon, retrieveWhen))
 
@@ -266,16 +294,20 @@ def main():
     varValues = convertWaccm(varValues)
     logger.info("Converted WACCM varValues = {}".format(varValues))
 
-    if (False):
+    if (True):
       # Write CSV file for MusicBox initial conditions.
       csvName = "{}/{}".format(musicaDir, "initial_conditions.csv")
       writeInitCSV(varValues, csvName)
 
-    else:
+    if (True):
       # Write JSON file for MusicBox initial conditions.
       jsonName = "{}/{}".format(musicaDir, "initial_config.json")
       writeInitJSON(varValues, jsonName)
 
+    if (True and template is not None):
+      logger.info("Insert values into template {}".format(template))
+      insertIntoTemplate(varValues, template, musicaDir)
+
     logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)     # no error
 

From aca12fcdd9bed9f70970d2e2fef6147aa136b6c3 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 27 Aug 2024 16:58:25 -0600
Subject: [PATCH 12/15] Inserted chemical concentrations into the JSON.

---
 tools/waccmToMusicBox.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 5f4173ab..8415127c 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -234,6 +234,44 @@ def insertIntoTemplate(initValues, templateDir, destDir):
   # copy the template directory
   shutil.copytree(templateDir, destPath)
 
+  # find the standard configuration file and parse it
+  myConfigFile = os.path.join(destPath, "my_config.json")
+  with open(myConfigFile) as jsonFile:
+    myConfig = json.load(jsonFile)
+
+  # locate the section for chemical concentrations
+  chemSpeciesTag = "chemical species"
+  chemSpecies = myConfig[chemSpeciesTag]
+  logger.info("chemSpecies = {}".format(chemSpecies))
+  del myConfig[chemSpeciesTag]     # delete the existing section
+
+  # set up dictionary of chemicals and initial values
+  chemValueDict = {}
+  temperature = 0.0
+  pressure = 0.0
+  for key, value in initValues.items():
+    if (key == "temperature"):
+      temperature = safeFloat(value[valueIndex])
+      continue
+    if (key == "pressure"):
+      pressure = safeFloat(value[valueIndex])
+      continue
+
+    chemValueDict[key] = {
+      "initial value [{}]".format(value[unitIndex]): value[valueIndex]}
+
+  myConfig[chemSpeciesTag] = chemValueDict
+
+  # replace the values of temperature and pressure
+  envConditionsTag = "environmental conditions"
+  envConfig = myConfig[envConditionsTag]
+  envConfig["temperature"]["initial value [K]"] = temperature
+  envConfig["pressure"]["initial value [Pa]"] = pressure
+
+  # save over the former json file
+  with open(myConfigFile, "w") as myConfigFile:
+    json.dump(myConfig, myConfigFile, indent=2)
+
   return
 
 

From 2e8722aaf699d7e13c34d4075f299b4eb93188be Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 27 Aug 2024 17:30:44 -0600
Subject: [PATCH 13/15] Added unit conversion from mol/mol to mol m-3.

---
 tools/waccmToMusicBox.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 8415127c..9b6d9b75 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -153,9 +153,14 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
 # varDict = originally read from WACCM, tuples are (musicaName, value, units)
 # return varDict with values modified
 def convertWaccm(varDict):
-  # convert Ammonia to milli-moles
-  nh3Tuple = varDict["NH3"]
-  varDict["NH3"] = (nh3Tuple[0], nh3Tuple[valueIndex] * 1000, "milli" + nh3Tuple[unitIndex])
+
+  moleToM3 = 1000 / 22.4
+
+  for key, vTuple in varDict.items():
+    # convert moles / mole to moles / cubic meter
+    units = vTuple[unitIndex]
+    if (units == "mol/mol"):
+      varDict[key] = (vTuple[0], vTuple[valueIndex] * moleToM3, "mol m-3")
 
   return(varDict)
 
@@ -242,7 +247,7 @@ def insertIntoTemplate(initValues, templateDir, destDir):
   # locate the section for chemical concentrations
   chemSpeciesTag = "chemical species"
   chemSpecies = myConfig[chemSpeciesTag]
-  logger.info("chemSpecies = {}".format(chemSpecies))
+  logger.info("Replace chemSpecies = {}".format(chemSpecies))
   del myConfig[chemSpeciesTag]     # delete the existing section
 
   # set up dictionary of chemicals and initial values

From b5204f88ce1f3481d2402a17f229880079810eae Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 27 Aug 2024 20:13:36 -0600
Subject: [PATCH 14/15] Compressed into zip file, still need to copy into TS1
 dir.

---
 tools/waccmToMusicBox.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index 9b6d9b75..fed11e8d 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -228,8 +228,8 @@ def writeInitJSON(initValues, filename):
 def insertIntoTemplate(initValues, templateDir, destDir):
 
   # copy the template directory to working area
-  destPath = os.path.basename(os.path.normpath(templateDir))
-  destPath = os.path.join(destDir, destPath)
+  destZip = os.path.basename(os.path.normpath(templateDir))
+  destPath = os.path.join(destDir, destZip)
   logger.info("Create new configuration in = {}".format(destPath))
 
   # remove directory if it already exists
@@ -274,8 +274,14 @@ def insertIntoTemplate(initValues, templateDir, destDir):
   envConfig["pressure"]["initial value [Pa]"] = pressure
 
   # save over the former json file
-  with open(myConfigFile, "w") as myConfigFile:
-    json.dump(myConfig, myConfigFile, indent=2)
+  with open(myConfigFile, "w") as myConfigFp:
+    json.dump(myConfig, myConfigFp, indent=2)
+
+  # compress the written directory as a zip file
+  shutil.make_archive(destPath, "zip",
+    root_dir=destDir, base_dir=destZip)
+
+  # move into the created directory
 
   return
 

From 6c25d00564609c7e3d93926082efef6cdd830544 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 27 Aug 2024 20:28:19 -0600
Subject: [PATCH 15/15] Copy zip archive to example directory.

---
 tools/waccmToMusicBox.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/waccmToMusicBox.py b/tools/waccmToMusicBox.py
index fed11e8d..8fadcd23 100644
--- a/tools/waccmToMusicBox.py
+++ b/tools/waccmToMusicBox.py
@@ -282,6 +282,7 @@ def insertIntoTemplate(initValues, templateDir, destDir):
     root_dir=destDir, base_dir=destZip)
 
   # move into the created directory
+  shutil.move(destPath + ".zip", destPath)
 
   return