diff --git a/pr-preview/pr-57/.doctrees/config.doctree b/pr-preview/pr-57/.doctrees/config.doctree
index ca3c46e8..8888fe9d 100644
Binary files a/pr-preview/pr-57/.doctrees/config.doctree and b/pr-preview/pr-57/.doctrees/config.doctree differ
diff --git a/pr-preview/pr-57/.doctrees/environment.pickle b/pr-preview/pr-57/.doctrees/environment.pickle
index 0f578357..80116cf5 100644
Binary files a/pr-preview/pr-57/.doctrees/environment.pickle and b/pr-preview/pr-57/.doctrees/environment.pickle differ
diff --git a/pr-preview/pr-57/_sources/config.rst.txt b/pr-preview/pr-57/_sources/config.rst.txt
index 1e55b24b..3b18046e 100644
--- a/pr-preview/pr-57/_sources/config.rst.txt
+++ b/pr-preview/pr-57/_sources/config.rst.txt
@@ -133,11 +133,14 @@ for the the ``cfg.meteo`` variable::
         inc: 1
 
 These config variables can be accessed via ``cfg.meteo['dir']``, ``cfg.meteo['prefix']``, etc.
-as they are Python dictionaries. However, in :ref:`namelist and runscript template<namelists-section>` files
-(see next section), this accessing does not work because of how the ``.format()`` method is implemented
-in Python. For that reason, the Processing Chain automatically creates new variables in the form of
-``cfg.meteo_dir``, ``cfg.meteo_prefix``, etc. at the start to make them available for namelist
-and runjob templates.
+as they are Python dictionaries. 
+
+.. hint::
+    In :ref:`namelist and runscript template<namelists-section>` files
+    (see next section), this accessing does not work because of how the ``.format()``
+    method is implemented in Python. For that reason, the Processing Chain automatically
+    creates new variables in the form of ``cfg.meteo_dir``, ``cfg.meteo_prefix``, etc.
+    at the start to make them accessible for namelist and runjob templates.
 
 List of dictionary variables
 ****************************
diff --git a/pr-preview/pr-57/config.html b/pr-preview/pr-57/config.html
index 00789a3e..8c282dd3 100644
--- a/pr-preview/pr-57/config.html
+++ b/pr-preview/pr-57/config.html
@@ -344,11 +344,15 @@ <h3>Further variables<a class="headerlink" href="#further-variables" title="Perm
 </pre></div>
 </div>
 <p>These config variables can be accessed via <code class="docutils literal notranslate"><span class="pre">cfg.meteo['dir']</span></code>, <code class="docutils literal notranslate"><span class="pre">cfg.meteo['prefix']</span></code>, etc.
-as they are Python dictionaries. However, in <a class="reference internal" href="namelists.html#namelists-section"><span class="std std-ref">namelist and runscript template</span></a> files
-(see next section), this accessing does not work because of how the <code class="docutils literal notranslate"><span class="pre">.format()</span></code> method is implemented
-in Python. For that reason, the Processing Chain automatically creates new variables in the form of
-<code class="docutils literal notranslate"><span class="pre">cfg.meteo_dir</span></code>, <code class="docutils literal notranslate"><span class="pre">cfg.meteo_prefix</span></code>, etc. at the start to make them available for namelist
-and runjob templates.</p>
+as they are Python dictionaries.</p>
+<div class="admonition hint">
+<p class="admonition-title">Hint</p>
+<p>In <a class="reference internal" href="namelists.html#namelists-section"><span class="std std-ref">namelist and runscript template</span></a> files
+(see next section), this accessing does not work because of how the <code class="docutils literal notranslate"><span class="pre">.format()</span></code>
+method is implemented in Python. For that reason, the Processing Chain automatically
+creates new variables in the form of <code class="docutils literal notranslate"><span class="pre">cfg.meteo_dir</span></code>, <code class="docutils literal notranslate"><span class="pre">cfg.meteo_prefix</span></code>, etc.
+at the start to make them accessible for namelist and runjob templates.</p>
+</div>
 <section id="list-of-dictionary-variables">
 <h4>List of dictionary variables<a class="headerlink" href="#list-of-dictionary-variables" title="Permalink to this heading"></a></h4>
 <p>The following is a list of dictionary variables that exist for the Processing Chain.
diff --git a/pr-preview/pr-57/searchindex.js b/pr-preview/pr-57/searchindex.js
index 36d43c27..d921eb11 100644
--- a/pr-preview/pr-57/searchindex.js
+++ b/pr-preview/pr-57/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["code-structure", "config", "environment", "features", "functions", "howtorun", "index", "jobs", "namelists"], "filenames": ["code-structure.rst", "config.rst", "environment.rst", "features.rst", "functions.rst", "howtorun.rst", "index.rst", "jobs.rst", "namelists.rst"], "titles": ["Code Structure", "Configuration File", "Conda Environment", "Feature Overview", "Jobs", "How to Run", "Processing Chain", "Overview", "Namelist and Runscript Templates"], "terms": {"The": [0, 1, 2, 4, 5, 6, 7, 8], "process": [0, 1, 2, 3, 4, 5, 7], "chain": [0, 1, 2, 4, 7], "i": [0, 1, 2, 4, 5, 6, 7, 8], "follow": [0, 1, 2, 4, 5], "tree": 0, "l": 0, "3": [0, 1, 4, 6], "f": [0, 2, 5], "dirsfirst": 0, "case": [0, 2, 3, 4, 6, 8], "folder": [0, 1, 3, 4], "where": [0, 4, 5], "all": [0, 2, 4, 5, 8], "ar": [0, 1, 2, 4, 5, 7, 8], "store": [0, 4, 6], "cosmo": [0, 3, 4, 5, 6, 7, 8], "ghg": [0, 5, 6, 7], "spinup": [0, 3, 4, 5], "test": [0, 6], "restart": [0, 1, 3, 4, 5], "config": [0, 2, 4, 5, 6, 8], "yaml": [0, 2, 4, 5, 6], "configur": [0, 4, 5, 8], "file": [0, 2, 4, 5, 6, 7, 8], "cfg": [0, 1, 4, 5, 8], "templat": [0, 1, 4, 5, 6], "namelist": [0, 1, 4, 5, 6], "batch": 0, "job": [0, 1, 3, 5, 8], "csv": [0, 4, 8], "tracer": [0, 4, 8], "inform": [0, 1, 4, 8], "testcas": 0, "standard": [0, 2, 4, 6], "icon": [0, 3, 4, 5, 6, 7, 8], "art": [0, 4, 5, 6, 7], "global": [0, 5, 7], "domain": 0, "icon_runjob": [0, 1], "runjob": [0, 1], "sh": [0, 2, 5], "pre": [0, 3], "script": [0, 2, 4, 5, 6, 8], "mypartab": 0, "oem": [0, 4, 5, 6, 7], "onlin": 0, "emiss": [0, 1, 4, 5, 6, 7], "doc": [0, 7], "sphinx": 0, "document": [0, 2, 4, 7], "_static": 0, "static": 0, "asset": 0, "custom": [0, 3], "css": 0, "style": 0, "png": 0, "ico": 0, "addit": [0, 1, 5, 6], "imag": 0, "tabl": [0, 4, 8], "us": [0, 1, 2, 3, 4, 5, 7, 8], "contain": [0, 1, 4, 5, 7, 8], "data": [0, 1, 4, 5, 6], "conf": 0, "py": [0, 1, 4, 5, 7], "builder": 0, "rst": [0, 7], "restructuredtext": 0, "env": [0, 2], "environ": [0, 1, 6], "yml": [0, 2], "conda": [0, 6], "ext": 0, "other": [0, 4, 5, 7], "spack": [0, 5], "model": [0, 1, 3, 4, 5, 6, 7], "etc": [0, 1, 5], "jenkin": [0, 5], "autom": [0, 5], "individu": [0, 1, 4, 5], "shell": 0, "jenkinsfil": 0, "text": [0, 8], "pipelin": 0, "tool": [0, 5, 6, 8], "licens": 0, "readm": 0, "md": 0, "class": [0, 1, 4], "run_chain": [0, 1, 5, 7], "main": [0, 4, 5, 6, 7, 8], "workflow": [0, 1, 3, 5, 6], "depend": [0, 1, 3, 4, 5, 7], "describ": [1, 7], "simul": [1, 4, 5, 6], "A": [1, 5, 8], "subdirectori": 1, "sever": [1, 4, 5, 6], "e": [1, 2, 4, 6], "g": [1, 2, 4, 6], "int2lm_input": [1, 4, 5], "runscript": [1, 4, 5, 6], "which": [1, 2, 4, 5, 7], "defin": [1, 4, 5, 6], "casenam": [1, 5], "most": [1, 4, 6], "need": [1, 2, 4, 6], "prepar": [1, 4, 6], "run": [1, 2, 3, 4, 6, 8], "exampl": [1, 3, 4, 5, 8], "locat": [1, 2, 4, 8], "input": [1, 4, 5, 6], "thi": [1, 4, 5, 7], "load": [1, 4], "an": [1, 4], "instanc": 1, "non": [1, 4], "exhaust": 1, "import": [1, 4, 7], "descript": 1, "case_path": 1, "path": [1, 2, 4, 8], "directori": [1, 2, 4, 6, 7, 8], "under": 1, "specifi": [1, 4, 5], "name": [1, 4, 5], "deriv": 1, "from": [1, 4, 5, 7, 8], "chain_src_dir": 1, "sourc": [1, 2, 4, 8], "typic": 1, "current": [1, 4], "work": [1, 2, 4, 5], "compute_account": [1, 2], "comput": [1, 3, 4, 6], "account": [1, 2, 5], "base": 1, "user": [1, 4, 5, 6, 8], "constraint": 1, "gpu": 1, "mc": [1, 4], "email": [1, 2], "": [1, 5, 8], "address": [1, 2], "initi": 1, "none": [1, 4, 8], "updat": [1, 2], "set_email": 1, "method": 1, "enddat": 1, "end": 1, "date": [1, 4], "iso": 1, "8601": 1, "format": [1, 4, 8], "yyyi": [1, 4], "mm": 1, "ddthh": 1, "ssz": 1, "execut": [1, 4, 5], "log_finished_dir": [1, 4, 5], "finish": [1, 5], "log": [1, 4], "log_working_dir": [1, 5], "ntasks_per_nod": 1, "number": [1, 4], "task": 1, "per": [1, 4], "node": 1, "type": [1, 2, 4], "restart_step": 1, "step": [1, 2, 3, 5, 6], "restart_step_hour": 1, "hour": [1, 4, 8], "attribut": [1, 4, 8], "run_on": 1, "architectur": 1, "cpu": 1, "spin": [1, 4, 8], "up": [1, 2, 4, 5, 8], "durat": 1, "activ": [1, 2], "behavior": [1, 5], "startdat": [1, 4], "start": 1, "user_mail": [1, 2], "determin": 1, "system": [1, 6], "user_nam": 1, "usernam": 1, "obtain": 1, "self": 1, "one": [1, 4, 5], "work_root": [1, 5], "root": [1, 5], "here": [1, 4, 5, 7], "two": [1, 4], "gener": [1, 4, 5, 8], "should": [1, 2, 4], "12": 1, "pt6h": 1, "2015": 1, "01": 1, "01t00": 1, "00": 1, "00z": 1, "01t18": 1, "compute_queu": 1, "normal": [1, 8], "2018": 1, "01t12": 1, "eccodes_dir": 1, "eccodes_definit": 1, "iconremap_bin": 1, "iconremap": 1, "iconsub_bin": 1, "iconsub": 1, "latbc_filenam": 1, "ifs_": 1, "y": [1, 4], "m": 1, "d": 1, "h": [1, 5], "_lbc": 1, "nc": [1, 4, 5, 8], "inidata_prefix": 1, "ifs_init_": 1, "inidata_nameformat": 1, "inidata_filename_suffix": 1, "output_filenam": 1, "filename_format": 1, "_dom": 1, "physdom": 1, "_": [1, 4], "ddhhmmss": 1, "lateral_boundary_grid_ord": 1, "lateral_boundari": 1, "art_input_fold": 1, "furthermor": 1, "ti": 1, "These": [1, 2, 5, 8], "themselv": 1, "let": 1, "have": [1, 2, 4, 5], "look": [1, 4, 5], "meteo": [1, 4, 5], "dir": [1, 4], "prefix": [1, 2, 4, 8], "laf": [1, 5], "nameformat": 1, "inc": 1, "1": [1, 4, 6], "can": [1, 2, 4, 5, 6, 7], "access": [1, 7], "via": [1, 5], "thei": [1, 4, 5], "python": [1, 4, 5, 6, 8], "howev": 1, "see": [1, 2, 4, 5], "next": 1, "section": [1, 4], "doe": [1, 2, 6], "becaus": 1, "how": [1, 6], "implement": 1, "For": [1, 4, 7], "reason": [1, 4], "automat": [1, 3], "creat": [1, 4, 5, 6, 7, 8], "new": [1, 4, 6], "form": 1, "meteo_dir": 1, "meteo_prefix": 1, "make": [1, 7], "them": [1, 2, 4], "avail": [1, 3, 5, 7], "exist": 1, "element": 1, "those": [1, 2, 4], "pleas": [1, 2], "refer": [1, 4], "within": [1, 2, 5], "prepare_data": [1, 4, 6, 7], "int2lm": [1, 4, 5, 6, 7, 8], "icontools_runjob": [1, 4], "input_fil": 1, "chem": 1, "era5": 1, "cam": [1, 4], "vprm": [1, 4, 5], "bioflux": [1, 4, 5, 6, 7], "online_vprm": [1, 4, 5, 6, 7], "oct": [1, 4, 6, 7], "post_int2lm": [1, 4, 5, 6, 7], "post_cosmo": [1, 4, 5, 6, 7], "reduce_output": [1, 4, 6, 7], "photo_r": [1, 4, 6, 7], "check_output": [1, 4, 6, 7], "obs_nudg": [1, 4, 6, 7], "verify_chain": [1, 4, 6, 7], "allow": 2, "you": [2, 5, 7], "your": [2, 6], "own": [2, 3, 6], "virtual": 2, "we": 2, "recommend": 2, "usag": [2, 4], "provid": [2, 4, 5], "instruct": 2, "onli": [2, 4, 5], "perform": [2, 4], "onc": 2, "home": 2, "default": [2, 4, 5], "itself": 2, "project": [2, 4], "otherwis": [2, 4], "risk": 2, "fill": 2, "below": 2, "To": [2, 4, 5], "latest": 2, "wget": 2, "http": [2, 4], "repo": 2, "anaconda": 2, "com": 2, "miniconda3": 2, "linux": 2, "x86_64": 2, "bash": 2, "further": 2, "detail": [2, 4], "found": [2, 4], "page": [2, 7], "proc": 2, "requir": 2, "abl": [2, 5], "simpli": [2, 5], "instead": [2, 4, 5], "full": [2, 5], "add": [2, 7], "bashrc": 2, "export": 2, "conda_envs_path": 2, "If": [2, 4, 5], "alreadi": [2, 5], "want": 2, "prune": 2, "regist": 2, "echo": 2, "your_account_id": 2, "acct": 2, "your_email_address": 2, "forward": 2, "set": [2, 4, 5, 6], "option": [2, 4, 5], "first": [2, 5], "check": [2, 4], "content": [2, 4], "desir": [2, 5], "correspond": [2, 5, 8], "variabl": [2, 4, 6, 8], "overridden": 2, "asynchron": 3, "submiss": 3, "hpc": 3, "queue": [3, 4, 6], "intuit": 3, "definit": [3, 4, 8], "cycl": 3, "over": 3, "time": [3, 4, 5], "period": 3, "includ": 3, "structur": [3, 4, 6], "creation": 3, "variou": 3, "post": [3, 6], "built": 3, "nest": [3, 4, 5], "possibl": 3, "easi": 3, "model_cfg": 4, "copi": [4, 5], "scratch": 4, "object": [4, 8], "hold": [4, 5, 8], "dict": 4, "output": [4, 5, 8], "physic": 4, "plot": 4, "function": [4, 5, 7, 8], "ensur": [4, 5], "rang": 4, "It": [4, 5], "seri": 4, "minimum": 4, "maximum": 4, "mean": 4, "deviat": 4, "panda": 4, "pickl": 4, "also": [4, 5, 6], "setup": [4, 5], "submit": [4, 5, 6], "necessari": [4, 5, 6, 8], "both": [4, 5], "cosmoart": 4, "decid": 4, "soil": 4, "terra": 4, "multi": 4, "layer": 4, "cosmo_run": 4, "cosmo_output": [4, 5], "cosmo_restart_out": [4, 5], "cosmo_bin": 4, "convert": [4, 8], "af": 4, "org": 4, "io": 4, "dyn": 4, "phy": 4, "dia": 4, "ass": 4, "ep": 4, "ini": 4, "netcdf": 4, "string": [4, 8], "char": 4, "multipl": 4, "dataset": [4, 8], "list": [4, 5, 7], "0": [4, 8], "gridnam": 4, "yyyymmdd": 4, "emis_yyyymmdd": 4, "emissions2": 4, "2": [4, 6], "emissions3": 4, "iconart": 4, "icon_work": 4, "icon_output": 4, "icon_restart_out": 4, "icon_binary_fil": 4, "ex": 4, "append": 4, "icon_mast": 4, "icon_namelist_nwp": 4, "binary_fil": 4, "extpar": [4, 5], "extpar_fil": 4, "int2lm_run": 4, "libgrib_api": 4, "renam": 4, "In": [4, 6, 7], "obs_nudging_dir": 4, "save": [4, 8], "yyyymmdd000000": 4, "expect": 4, "x": 4, "noth": 4, "4": 4, "handl": [4, 5, 6], "filenam": [4, 8], "chang": [4, 5], "cosmo_input": 4, "miss": 4, "observ": 4, "ignor": 4, "blacklist": 4, "blklsttmp": 4, "perturb": 4, "bg": 4, "octe_map": 4, "octe_lambda": 4, "background": 4, "field": 4, "do": 4, "read": [4, 5, 8], "lambda": 4, "valu": [4, 8], "last": [4, 5], "along": 4, "nparam": 4, "dimens": 4, "scale": 4, "produc": [4, 5], "each": [4, 5], "ensembl": 4, "profil": 4, "rais": 4, "runtimeerror": 4, "error": [4, 5], "occur": 4, "dure": [4, 8], "modi": 4, "surfac": 4, "reflect": 4, "veget": 4, "fraction": 4, "photolysi": 4, "rate": 4, "photo_rate_fil": 4, "art_photolysi": 4, "posit": 4, "write": [4, 8], "logfil": [4, 5], "output_root": 4, "ha": [4, 5, 7], "been": [4, 5], "befor": 4, "cosmo_output_reduc": 4, "xfer": 4, "combin": 4, "singl": [4, 5], "put": 4, "differ": 4, "post_int2lm_speci": 4, "post_int2lm_species_spinup": 4, "present": 4, "take": [4, 5, 7], "meteorolog": 4, "specif": [4, 6], "icon_input_icbc": 4, "dwd": 4, "remap": 4, "origin": 4, "input_root_meteo": 4, "icon_input": 4, "icbc": [4, 5], "constant": 4, "geosp": 4, "ad": [4, 6], "cdo": 4, "bind": 4, "yyyymmddhh": 4, "lffd": [4, 5], "c": 4, "ani": 4, "subprocess": 4, "return": 4, "zero": 4, "exit": [4, 5], "code": [4, 6], "calcul": 4, "2d": 4, "column": 4, "fix": 4, "level": [4, 5], "consid": 4, "written": 4, "output_level": 4, "gribout": 4, "split": 4, "averag": 4, "dry": 4, "air": 4, "moist": 4, "mole": 4, "separ": [4, 5], "appear": 4, "alphabet": 4, "after": 4, "suffix": [4, 8], "_met": 4, "_trc": 4, "compar": 4, "reference_dir": 4, "output_dir": 4, "els": 4, "goe": 4, "values_to_check": 4, "kei": 4, "temperatur": 4, "o": 4, "join": 4, "input_root": 4, "reference_output": 4, "reference_lffd2015010200": 4, "lffd2015010200": 4, "t": 4, "collect": [4, 6], "well": [4, 5, 8], "mai": [4, 5], "directli": 4, "cams4int2cosmo": [4, 6], "check_model": [4, 6], "comp_nc": [4, 6], "datasets_equ": [4, 6], "ctnoaa4int2cosmo": [4, 6], "mozart2int2lm": [4, 6], "reduce_output_start_end": [4, 6], "string2char": [4, 6], "vprmsplit": [4, 6], "write_cosmo_input_ghg": [4, 6, 8], "write_int2lm_input_art": [4, 6, 8], "inpath": 4, "outpath": 4, "param": 4, "co2": 4, "co": 4, "nox": 4, "boundari": 4, "condit": 4, "int2cosmo": 4, "smartcarb": 4, "consist": 4, "experi": 4, "gf39": 4, "rd": 4, "approx": 4, "15": 4, "km": 4, "resolut": 4, "137": 4, "atmospher": 4, "copernicu": 4, "eu": 4, "NO": 4, "no2": 4, "oper": 4, "product": 4, "exp": 4, "0001": 4, "60": 4, "retriev": 4, "hourli": 4, "mar": 4, "archiv": 4, "ecmwf": 4, "cams_0001_2015010500": 4, "sfc_0001_2015010500": 4, "pressur": 4, "cams_gf39_2015010500": 4, "sfc_gf39_2015010500": 4, "suppli": 4, "invok": 4, "8": 4, "ic": 4, "bc": 4, "cams_nox_yyyymmddhh": 4, "cams_co2_yyyymmddhh": 4, "cams_nox_yyyymmdd00": 4, "cams_nox_yyyymmdd21": 4, "cams_co2_yyyymmdd00": 4, "cams_co2_yyyymmdd21": 4, "str": [4, 8], "match": 4, "prescrib": 4, "capit": 4, "dataset1": 4, "dataset2": 4, "verbos": 4, "true": 4, "numpi": 4, "isclos": 4, "whether": 4, "equal": 4, "No": 4, "bitwis": 4, "numer": 4, "slightli": 4, "essenti": [4, 8], "ident": 4, "rather": 4, "absolut": 4, "rel": 4, "toler": 4, "np": 4, "more": 4, "empti": 4, "netcdf4": 4, "bool": 4, "result": [4, 7, 8], "print": 4, "stdout": 4, "select": 4, "fals": 4, "indir": 4, "outdir": 4, "carbontrack": 4, "compat": 4, "utput": 4, "dictionari": 4, "infil": 4, "extract": 4, "timeslic": 4, "seper": 4, "lev": 4, "transform": 4, "lon": 4, "180": 4, "entri": 4, "_yyyymmddhh": 4, "strdate_start": 4, "strdate_end": 4, "nout_level": 4, "csvfile": 4, "convert_ga": 4, "reduc": 4, "opath": 4, "go": 4, "arrai": 4, "year": 4, "ipath": 4, "dai": 4, "gpp_yyyymmddhh": 4, "ra_yyyymmddhh": 4, "vprm_ecmwf_": 4, "_2017": 4, "2017": 4, "flux": 4, "csv_filenam": [4, 8], "namelist_filenam": [4, 8], "input_ghg": [4, 8], "trcr_filenam": [4, 8], "set_filenam": [4, 8], "nml_filenam": [4, 8], "hstart": [4, 8], "input_art": [4, 5, 8], "int": [4, 8], "meteorologi": [4, 8], "command": 5, "line": 5, "respect": [5, 7, 8], "Then": 5, "sbatch": 5, "technic": 5, "achiev": 5, "case1": 5, "case2": 5, "With": 5, "afterward": 5, "There": 5, "argument": [5, 7], "help": 5, "show": 5, "messag": 5, "j": 5, "job_list": 5, "aspect": 5, "launch": 5, "order": [5, 7], "given": 5, "forc": 5, "redo": 5, "even": 5, "were": 5, "previous": 5, "warn": 5, "get": 5, "delet": 5, "effect": 5, "overwritten": 5, "caus": 5, "unexpect": 5, "r": 5, "resum": 5, "unfinish": 5, "call": [5, 7], "restart_run": 5, "divid": 5, "accord": [5, 6], "run_chunk": 5, "part": 5, "chunk": 5, "slurm": 5, "workload": 5, "manag": 5, "compil": 5, "undergo": 5, "regulari": 5, "correctli": 5, "plan": 5, "weekli": 5, "basi": 5, "when": 5, "trigger": 5, "github": 5, "pull": 5, "request": 5, "like": 5, "chain_root": 5, "checkpoint": 5, "cosmo_bas": 5, "cosmo_work": 5, "int2lm_bas": 5, "int2lm_work": 5, "int2lm_output": 5, "As": [5, 7], "preprocessor": 5, "addition": 5, "alwai": 5, "whenev": 5, "successfulli": 5, "sub": 5, "therefor": 5, "four": 5, "deep": 5, "2015010100_2015010106": 5, "prepare_cosmo": 5, "lrff00060000o": 5, "input_": 5, "yu": 5, "lbfd": 5, "2015010106_2015010112": 5, "csc": 6, "appli": 6, "version": 6, "variant": 6, "notabl": 6, "greenhous": 6, "ga": 6, "extens": 6, "aerosol": 6, "reactiv": 6, "trace": 6, "gase": 6, "flexibli": 6, "adapt": 6, "featur": 6, "overview": 6, "instal": 6, "miniconda": 6, "what": 6, "everi": 7, "choos": 7, "some": 7, "indic": 7, "simpl": 7, "jobnam": 7, "same": 7, "sure": 7, "docstr": 7, "__init__": 7, "find": 7, "icontool": 8, "dynam": 8, "paramet": 8, "alongsid": 8, "enclos": 8, "curli": 8, "brace": 8, "runtim": 8, "through": 8, "facilit": 8, "substitut": 8, "subsequ": 8, "actual": 8, "example_namelist": 8, "namelist_var": 8, "pref_suff": 8, "disk": 8, "special": 8}, "objects": {"jobs.biofluxes": [[4, 0, 1, "", "main"]], "jobs.check_output": [[4, 0, 1, "", "main"]], "jobs.cosmo": [[4, 0, 1, "", "main"]], "jobs.emissions": [[4, 0, 1, "", "main"]], "jobs.icon": [[4, 0, 1, "", "main"]], "jobs.int2lm": [[4, 0, 1, "", "main"]], "jobs.obs_nudging": [[4, 0, 1, "", "main"]], "jobs.octe": [[4, 0, 1, "", "main"]], "jobs.oem": [[4, 0, 1, "", "main"]], "jobs.online_vprm": [[4, 0, 1, "", "main"]], "jobs.photo_rate": [[4, 0, 1, "", "main"]], "jobs.post_cosmo": [[4, 0, 1, "", "main"]], "jobs.post_int2lm": [[4, 0, 1, "", "main"]], "jobs.prepare_data": [[4, 0, 1, "", "main"]], "jobs.reduce_output": [[4, 0, 1, "", "main"]], "jobs.tools.cams4int2cosmo": [[4, 0, 1, "", "main"]], "jobs.tools.check_model": [[4, 0, 1, "", "check_model"]], "jobs.tools.comp_nc": [[4, 0, 1, "", "datasets_equal"]], "jobs.tools.ctnoaa4int2cosmo": [[4, 0, 1, "", "main"]], "jobs.tools.mozart2int2lm": [[4, 0, 1, "", "main"]], "jobs.tools.reduce_output_start_end": [[4, 0, 1, "", "main"]], "jobs.tools.string2char": [[4, 0, 1, "", "main"]], "jobs.tools.vprmsplit": [[4, 0, 1, "", "main"]], "jobs.tools.write_cosmo_input_ghg": [[8, 0, 1, "", "main"]], "jobs.tools.write_int2lm_input_art": [[8, 0, 1, "", "main"]], "jobs.verify_chain": [[4, 0, 1, "", "main"]]}, "objtypes": {"0": "py:function"}, "objnames": {"0": ["py", "function", "Python function"]}, "titleterms": {"code": 0, "structur": [0, 5], "configur": [1, 6], "file": 1, "variabl": 1, "set": 1, "config": 1, "yaml": 1, "header": 1, "cosmo": 1, "ghg": 1, "spinup": 1, "test": [1, 5], "case": [1, 5], "icon": 1, "art": 1, "oem": 1, "further": 1, "list": 1, "dictionari": 1, "conda": 2, "environ": 2, "1": 2, "instal": 2, "miniconda": 2, "2": 2, "creat": 2, "3": 2, "store": 2, "user": 2, "specif": 2, "data": 2, "featur": 3, "overview": [3, 7], "job": [4, 6, 7], "tool": 4, "paramet": 4, "todo": 4, "how": 5, "run": 5, "start": [5, 6], "chain": [5, 6], "what": 5, "doe": 5, "directori": 5, "process": 6, "get": 6, "api": 6, "ad": 7, "new": 7, "namelist": 8, "runscript": 8, "templat": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 58}, "alltitles": {"Code Structure": [[0, "code-structure"]], "Configuration File": [[1, "configuration-file"]], "Configuration Variables": [[1, "configuration-variables"]], "Variables to Set in config.yaml": [[1, "variables-to-set-in-config-yaml"]], "Header of config.yaml for the cosmo-ghg-spinup-test case": [[1, "header-of-config-yaml-for-the-cosmo-ghg-spinup-test-case"]], "Header of config.yaml for the icon-art-oem-test case": [[1, "header-of-config-yaml-for-the-icon-art-oem-test-case"]], "Further variables": [[1, "further-variables"]], "List of dictionary variables": [[1, "list-of-dictionary-variables"]], "Conda Environment": [[2, "conda-environment"]], "1. Install Miniconda": [[2, "install-miniconda"]], "2. Create the Conda Environment": [[2, "create-the-conda-environment"]], "3. Store user-specific data": [[2, "store-user-specific-data"]], "Feature Overview": [[3, "feature-overview"]], "Jobs": [[4, "jobs"], [6, null]], "Tools": [[4, "tools"]], "Parameters (TODO)": [[4, "parameters-todo"]], "How to Run": [[5, "how-to-run"]], "Starting the Chain": [[5, "starting-the-chain"]], "What it Does": [[5, "what-it-does"]], "Test Cases": [[5, "test-cases"]], "Directory Structure": [[5, "directory-structure"]], "Processing Chain": [[6, "processing-chain"]], "Getting Started": [[6, null]], "Configuration": [[6, null]], "API": [[6, null]], "Overview": [[7, "overview"]], "Adding New Jobs": [[7, "adding-new-jobs"]], "Namelist and Runscript Templates": [[8, "namelist-and-runscript-templates"]]}, "indexentries": {"check_model() (in module jobs.tools.check_model)": [[4, "jobs.tools.check_model.check_model"]], "datasets_equal() (in module jobs.tools.comp_nc)": [[4, "jobs.tools.comp_nc.datasets_equal"]], "main() (in module jobs.biofluxes)": [[4, "jobs.biofluxes.main"]], "main() (in module jobs.check_output)": [[4, "jobs.check_output.main"]], "main() (in module jobs.cosmo)": [[4, "jobs.cosmo.main"]], "main() (in module jobs.emissions)": [[4, "jobs.emissions.main"]], "main() (in module jobs.icon)": [[4, "jobs.icon.main"]], "main() (in module jobs.int2lm)": [[4, "jobs.int2lm.main"]], "main() (in module jobs.obs_nudging)": [[4, "jobs.obs_nudging.main"]], "main() (in module jobs.octe)": [[4, "jobs.octe.main"]], "main() (in module jobs.oem)": [[4, "jobs.oem.main"]], "main() (in module jobs.online_vprm)": [[4, "jobs.online_vprm.main"]], "main() (in module jobs.photo_rate)": [[4, "jobs.photo_rate.main"]], "main() (in module jobs.post_cosmo)": [[4, "jobs.post_cosmo.main"]], "main() (in module jobs.post_int2lm)": [[4, "jobs.post_int2lm.main"]], "main() (in module jobs.prepare_data)": [[4, "jobs.prepare_data.main"]], "main() (in module jobs.reduce_output)": [[4, "jobs.reduce_output.main"]], "main() (in module jobs.tools.cams4int2cosmo)": [[4, "jobs.tools.cams4int2cosmo.main"]], "main() (in module jobs.tools.ctnoaa4int2cosmo)": [[4, "jobs.tools.ctnoaa4int2cosmo.main"]], "main() (in module jobs.tools.mozart2int2lm)": [[4, "jobs.tools.mozart2int2lm.main"]], "main() (in module jobs.tools.reduce_output_start_end)": [[4, "jobs.tools.reduce_output_start_end.main"]], "main() (in module jobs.tools.string2char)": [[4, "jobs.tools.string2char.main"]], "main() (in module jobs.tools.vprmsplit)": [[4, "jobs.tools.vprmsplit.main"]], "main() (in module jobs.tools.write_cosmo_input_ghg)": [[4, "jobs.tools.write_cosmo_input_ghg.main"], [8, "jobs.tools.write_cosmo_input_ghg.main"]], "main() (in module jobs.tools.write_int2lm_input_art)": [[4, "jobs.tools.write_int2lm_input_art.main"], [8, "jobs.tools.write_int2lm_input_art.main"]], "main() (in module jobs.verify_chain)": [[4, "jobs.verify_chain.main"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["code-structure", "config", "environment", "features", "functions", "howtorun", "index", "jobs", "namelists"], "filenames": ["code-structure.rst", "config.rst", "environment.rst", "features.rst", "functions.rst", "howtorun.rst", "index.rst", "jobs.rst", "namelists.rst"], "titles": ["Code Structure", "Configuration File", "Conda Environment", "Feature Overview", "Jobs", "How to Run", "Processing Chain", "Overview", "Namelist and Runscript Templates"], "terms": {"The": [0, 1, 2, 4, 5, 6, 7, 8], "process": [0, 1, 2, 3, 4, 5, 7], "chain": [0, 1, 2, 4, 7], "i": [0, 1, 2, 4, 5, 6, 7, 8], "follow": [0, 1, 2, 4, 5], "tree": 0, "l": 0, "3": [0, 1, 4, 6], "f": [0, 2, 5], "dirsfirst": 0, "case": [0, 2, 3, 4, 6, 8], "folder": [0, 1, 3, 4], "where": [0, 4, 5], "all": [0, 2, 4, 5, 8], "ar": [0, 1, 2, 4, 5, 7, 8], "store": [0, 4, 6], "cosmo": [0, 3, 4, 5, 6, 7, 8], "ghg": [0, 5, 6, 7], "spinup": [0, 3, 4, 5], "test": [0, 6], "restart": [0, 1, 3, 4, 5], "config": [0, 2, 4, 5, 6, 8], "yaml": [0, 2, 4, 5, 6], "configur": [0, 4, 5, 8], "file": [0, 2, 4, 5, 6, 7, 8], "cfg": [0, 1, 4, 5, 8], "templat": [0, 1, 4, 5, 6], "namelist": [0, 1, 4, 5, 6], "batch": 0, "job": [0, 1, 3, 5, 8], "csv": [0, 4, 8], "tracer": [0, 4, 8], "inform": [0, 1, 4, 8], "testcas": 0, "standard": [0, 2, 4, 6], "icon": [0, 3, 4, 5, 6, 7, 8], "art": [0, 4, 5, 6, 7], "global": [0, 5, 7], "domain": 0, "icon_runjob": [0, 1], "runjob": [0, 1], "sh": [0, 2, 5], "pre": [0, 3], "script": [0, 2, 4, 5, 6, 8], "mypartab": 0, "oem": [0, 4, 5, 6, 7], "onlin": 0, "emiss": [0, 1, 4, 5, 6, 7], "doc": [0, 7], "sphinx": 0, "document": [0, 2, 4, 7], "_static": 0, "static": 0, "asset": 0, "custom": [0, 3], "css": 0, "style": 0, "png": 0, "ico": 0, "addit": [0, 1, 5, 6], "imag": 0, "tabl": [0, 4, 8], "us": [0, 1, 2, 3, 4, 5, 7, 8], "contain": [0, 1, 4, 5, 7, 8], "data": [0, 1, 4, 5, 6], "conf": 0, "py": [0, 1, 4, 5, 7], "builder": 0, "rst": [0, 7], "restructuredtext": 0, "env": [0, 2], "environ": [0, 1, 6], "yml": [0, 2], "conda": [0, 6], "ext": 0, "other": [0, 4, 5, 7], "spack": [0, 5], "model": [0, 1, 3, 4, 5, 6, 7], "etc": [0, 1, 5], "jenkin": [0, 5], "autom": [0, 5], "individu": [0, 1, 4, 5], "shell": 0, "jenkinsfil": 0, "text": [0, 8], "pipelin": 0, "tool": [0, 5, 6, 8], "licens": 0, "readm": 0, "md": 0, "class": [0, 1, 4], "run_chain": [0, 1, 5, 7], "main": [0, 4, 5, 6, 7, 8], "workflow": [0, 1, 3, 5, 6], "depend": [0, 1, 3, 4, 5, 7], "describ": [1, 7], "simul": [1, 4, 5, 6], "A": [1, 5, 8], "subdirectori": 1, "sever": [1, 4, 5, 6], "e": [1, 2, 4, 6], "g": [1, 2, 4, 6], "int2lm_input": [1, 4, 5], "runscript": [1, 4, 5, 6], "which": [1, 2, 4, 5, 7], "defin": [1, 4, 5, 6], "casenam": [1, 5], "most": [1, 4, 6], "need": [1, 2, 4, 6], "prepar": [1, 4, 6], "run": [1, 2, 3, 4, 6, 8], "exampl": [1, 3, 4, 5, 8], "locat": [1, 2, 4, 8], "input": [1, 4, 5, 6], "thi": [1, 4, 5, 7], "load": [1, 4], "an": [1, 4], "instanc": 1, "non": [1, 4], "exhaust": 1, "import": [1, 4, 7], "descript": 1, "case_path": 1, "path": [1, 2, 4, 8], "directori": [1, 2, 4, 6, 7, 8], "under": 1, "specifi": [1, 4, 5], "name": [1, 4, 5], "deriv": 1, "from": [1, 4, 5, 7, 8], "chain_src_dir": 1, "sourc": [1, 2, 4, 8], "typic": 1, "current": [1, 4], "work": [1, 2, 4, 5], "compute_account": [1, 2], "comput": [1, 3, 4, 6], "account": [1, 2, 5], "base": 1, "user": [1, 4, 5, 6, 8], "constraint": 1, "gpu": 1, "mc": [1, 4], "email": [1, 2], "": [1, 5, 8], "address": [1, 2], "initi": 1, "none": [1, 4, 8], "updat": [1, 2], "set_email": 1, "method": 1, "enddat": 1, "end": 1, "date": [1, 4], "iso": 1, "8601": 1, "format": [1, 4, 8], "yyyi": [1, 4], "mm": 1, "ddthh": 1, "ssz": 1, "execut": [1, 4, 5], "log_finished_dir": [1, 4, 5], "finish": [1, 5], "log": [1, 4], "log_working_dir": [1, 5], "ntasks_per_nod": 1, "number": [1, 4], "task": 1, "per": [1, 4], "node": 1, "type": [1, 2, 4], "restart_step": 1, "step": [1, 2, 3, 5, 6], "restart_step_hour": 1, "hour": [1, 4, 8], "attribut": [1, 4, 8], "run_on": 1, "architectur": 1, "cpu": 1, "spin": [1, 4, 8], "up": [1, 2, 4, 5, 8], "durat": 1, "activ": [1, 2], "behavior": [1, 5], "startdat": [1, 4], "start": 1, "user_mail": [1, 2], "determin": 1, "system": [1, 6], "user_nam": 1, "usernam": 1, "obtain": 1, "self": 1, "one": [1, 4, 5], "work_root": [1, 5], "root": [1, 5], "here": [1, 4, 5, 7], "two": [1, 4], "gener": [1, 4, 5, 8], "should": [1, 2, 4], "12": 1, "pt6h": 1, "2015": 1, "01": 1, "01t00": 1, "00": 1, "00z": 1, "01t18": 1, "compute_queu": 1, "normal": [1, 8], "2018": 1, "01t12": 1, "eccodes_dir": 1, "eccodes_definit": 1, "iconremap_bin": 1, "iconremap": 1, "iconsub_bin": 1, "iconsub": 1, "latbc_filenam": 1, "ifs_": 1, "y": [1, 4], "m": 1, "d": 1, "h": [1, 5], "_lbc": 1, "nc": [1, 4, 5, 8], "inidata_prefix": 1, "ifs_init_": 1, "inidata_nameformat": 1, "inidata_filename_suffix": 1, "output_filenam": 1, "filename_format": 1, "_dom": 1, "physdom": 1, "_": [1, 4], "ddhhmmss": 1, "lateral_boundary_grid_ord": 1, "lateral_boundari": 1, "art_input_fold": 1, "furthermor": 1, "ti": 1, "These": [1, 2, 5, 8], "themselv": 1, "let": 1, "have": [1, 2, 4, 5], "look": [1, 4, 5], "meteo": [1, 4, 5], "dir": [1, 4], "prefix": [1, 2, 4, 8], "laf": [1, 5], "nameformat": 1, "inc": 1, "1": [1, 4, 6], "can": [1, 2, 4, 5, 6, 7], "access": [1, 7], "via": [1, 5], "thei": [1, 4, 5], "python": [1, 4, 5, 6, 8], "In": [1, 4, 6, 7], "see": [1, 2, 4, 5], "next": 1, "section": [1, 4], "doe": [1, 2, 6], "becaus": 1, "how": [1, 6], "implement": 1, "For": [1, 4, 7], "reason": [1, 4], "automat": [1, 3], "creat": [1, 4, 5, 6, 7, 8], "new": [1, 4, 6], "form": 1, "meteo_dir": 1, "meteo_prefix": 1, "make": [1, 7], "them": [1, 2, 4], "exist": 1, "element": 1, "those": [1, 2, 4], "pleas": [1, 2], "refer": [1, 4], "within": [1, 2, 5], "prepare_data": [1, 4, 6, 7], "int2lm": [1, 4, 5, 6, 7, 8], "icontools_runjob": [1, 4], "input_fil": 1, "chem": 1, "era5": 1, "cam": [1, 4], "vprm": [1, 4, 5], "bioflux": [1, 4, 5, 6, 7], "online_vprm": [1, 4, 5, 6, 7], "oct": [1, 4, 6, 7], "post_int2lm": [1, 4, 5, 6, 7], "post_cosmo": [1, 4, 5, 6, 7], "reduce_output": [1, 4, 6, 7], "photo_r": [1, 4, 6, 7], "check_output": [1, 4, 6, 7], "obs_nudg": [1, 4, 6, 7], "verify_chain": [1, 4, 6, 7], "allow": 2, "you": [2, 5, 7], "your": [2, 6], "own": [2, 3, 6], "virtual": 2, "we": 2, "recommend": 2, "usag": [2, 4], "provid": [2, 4, 5], "instruct": 2, "onli": [2, 4, 5], "perform": [2, 4], "onc": 2, "home": 2, "default": [2, 4, 5], "itself": 2, "project": [2, 4], "otherwis": [2, 4], "risk": 2, "fill": 2, "below": 2, "To": [2, 4, 5], "latest": 2, "wget": 2, "http": [2, 4], "repo": 2, "anaconda": 2, "com": 2, "miniconda3": 2, "linux": 2, "x86_64": 2, "bash": 2, "further": 2, "detail": [2, 4], "found": [2, 4], "page": [2, 7], "proc": 2, "requir": 2, "abl": [2, 5], "simpli": [2, 5], "instead": [2, 4, 5], "full": [2, 5], "add": [2, 7], "bashrc": 2, "export": 2, "conda_envs_path": 2, "If": [2, 4, 5], "alreadi": [2, 5], "want": 2, "prune": 2, "regist": 2, "echo": 2, "your_account_id": 2, "acct": 2, "your_email_address": 2, "forward": 2, "set": [2, 4, 5, 6], "option": [2, 4, 5], "first": [2, 5], "check": [2, 4], "content": [2, 4], "desir": [2, 5], "correspond": [2, 5, 8], "variabl": [2, 4, 6, 8], "overridden": 2, "asynchron": 3, "submiss": 3, "hpc": 3, "queue": [3, 4, 6], "intuit": 3, "definit": [3, 4, 8], "cycl": 3, "over": 3, "time": [3, 4, 5], "period": 3, "includ": 3, "structur": [3, 4, 6], "creation": 3, "variou": 3, "post": [3, 6], "built": 3, "nest": [3, 4, 5], "possibl": 3, "easi": 3, "avail": [3, 5, 7], "model_cfg": 4, "copi": [4, 5], "scratch": 4, "object": [4, 8], "hold": [4, 5, 8], "dict": 4, "output": [4, 5, 8], "physic": 4, "plot": 4, "function": [4, 5, 7, 8], "ensur": [4, 5], "rang": 4, "It": [4, 5], "seri": 4, "minimum": 4, "maximum": 4, "mean": 4, "deviat": 4, "panda": 4, "pickl": 4, "also": [4, 5, 6], "setup": [4, 5], "submit": [4, 5, 6], "necessari": [4, 5, 6, 8], "both": [4, 5], "cosmoart": 4, "decid": 4, "soil": 4, "terra": 4, "multi": 4, "layer": 4, "cosmo_run": 4, "cosmo_output": [4, 5], "cosmo_restart_out": [4, 5], "cosmo_bin": 4, "convert": [4, 8], "af": 4, "org": 4, "io": 4, "dyn": 4, "phy": 4, "dia": 4, "ass": 4, "ep": 4, "ini": 4, "netcdf": 4, "string": [4, 8], "char": 4, "multipl": 4, "dataset": [4, 8], "list": [4, 5, 7], "0": [4, 8], "gridnam": 4, "yyyymmdd": 4, "emis_yyyymmdd": 4, "emissions2": 4, "2": [4, 6], "emissions3": 4, "iconart": 4, "icon_work": 4, "icon_output": 4, "icon_restart_out": 4, "icon_binary_fil": 4, "ex": 4, "append": 4, "icon_mast": 4, "icon_namelist_nwp": 4, "binary_fil": 4, "extpar": [4, 5], "extpar_fil": 4, "int2lm_run": 4, "libgrib_api": 4, "renam": 4, "obs_nudging_dir": 4, "save": [4, 8], "yyyymmdd000000": 4, "expect": 4, "x": 4, "noth": 4, "4": 4, "handl": [4, 5, 6], "filenam": [4, 8], "chang": [4, 5], "cosmo_input": 4, "miss": 4, "observ": 4, "ignor": 4, "blacklist": 4, "blklsttmp": 4, "perturb": 4, "bg": 4, "octe_map": 4, "octe_lambda": 4, "background": 4, "field": 4, "do": 4, "read": [4, 5, 8], "lambda": 4, "valu": [4, 8], "last": [4, 5], "along": 4, "nparam": 4, "dimens": 4, "scale": 4, "produc": [4, 5], "each": [4, 5], "ensembl": 4, "profil": 4, "rais": 4, "runtimeerror": 4, "error": [4, 5], "occur": 4, "dure": [4, 8], "modi": 4, "surfac": 4, "reflect": 4, "veget": 4, "fraction": 4, "photolysi": 4, "rate": 4, "photo_rate_fil": 4, "art_photolysi": 4, "posit": 4, "write": [4, 8], "logfil": [4, 5], "output_root": 4, "ha": [4, 5, 7], "been": [4, 5], "befor": 4, "cosmo_output_reduc": 4, "xfer": 4, "combin": 4, "singl": [4, 5], "put": 4, "differ": 4, "post_int2lm_speci": 4, "post_int2lm_species_spinup": 4, "present": 4, "take": [4, 5, 7], "meteorolog": 4, "specif": [4, 6], "icon_input_icbc": 4, "dwd": 4, "remap": 4, "origin": 4, "input_root_meteo": 4, "icon_input": 4, "icbc": [4, 5], "constant": 4, "geosp": 4, "ad": [4, 6], "cdo": 4, "bind": 4, "yyyymmddhh": 4, "lffd": [4, 5], "c": 4, "ani": 4, "subprocess": 4, "return": 4, "zero": 4, "exit": [4, 5], "code": [4, 6], "calcul": 4, "2d": 4, "column": 4, "fix": 4, "level": [4, 5], "consid": 4, "written": 4, "output_level": 4, "gribout": 4, "split": 4, "averag": 4, "dry": 4, "air": 4, "moist": 4, "mole": 4, "separ": [4, 5], "appear": 4, "alphabet": 4, "after": 4, "suffix": [4, 8], "_met": 4, "_trc": 4, "compar": 4, "reference_dir": 4, "output_dir": 4, "els": 4, "goe": 4, "values_to_check": 4, "kei": 4, "temperatur": 4, "o": 4, "join": 4, "input_root": 4, "reference_output": 4, "reference_lffd2015010200": 4, "lffd2015010200": 4, "t": 4, "collect": [4, 6], "well": [4, 5, 8], "mai": [4, 5], "directli": 4, "cams4int2cosmo": [4, 6], "check_model": [4, 6], "comp_nc": [4, 6], "datasets_equ": [4, 6], "ctnoaa4int2cosmo": [4, 6], "mozart2int2lm": [4, 6], "reduce_output_start_end": [4, 6], "string2char": [4, 6], "vprmsplit": [4, 6], "write_cosmo_input_ghg": [4, 6, 8], "write_int2lm_input_art": [4, 6, 8], "inpath": 4, "outpath": 4, "param": 4, "co2": 4, "co": 4, "nox": 4, "boundari": 4, "condit": 4, "int2cosmo": 4, "smartcarb": 4, "consist": 4, "experi": 4, "gf39": 4, "rd": 4, "approx": 4, "15": 4, "km": 4, "resolut": 4, "137": 4, "atmospher": 4, "copernicu": 4, "eu": 4, "NO": 4, "no2": 4, "oper": 4, "product": 4, "exp": 4, "0001": 4, "60": 4, "retriev": 4, "hourli": 4, "mar": 4, "archiv": 4, "ecmwf": 4, "cams_0001_2015010500": 4, "sfc_0001_2015010500": 4, "pressur": 4, "cams_gf39_2015010500": 4, "sfc_gf39_2015010500": 4, "suppli": 4, "invok": 4, "8": 4, "ic": 4, "bc": 4, "cams_nox_yyyymmddhh": 4, "cams_co2_yyyymmddhh": 4, "cams_nox_yyyymmdd00": 4, "cams_nox_yyyymmdd21": 4, "cams_co2_yyyymmdd00": 4, "cams_co2_yyyymmdd21": 4, "str": [4, 8], "match": 4, "prescrib": 4, "capit": 4, "dataset1": 4, "dataset2": 4, "verbos": 4, "true": 4, "numpi": 4, "isclos": 4, "whether": 4, "equal": 4, "No": 4, "bitwis": 4, "numer": 4, "slightli": 4, "essenti": [4, 8], "ident": 4, "rather": 4, "absolut": 4, "rel": 4, "toler": 4, "np": 4, "more": 4, "empti": 4, "netcdf4": 4, "bool": 4, "result": [4, 7, 8], "print": 4, "stdout": 4, "select": 4, "fals": 4, "indir": 4, "outdir": 4, "carbontrack": 4, "compat": 4, "utput": 4, "dictionari": 4, "infil": 4, "extract": 4, "timeslic": 4, "seper": 4, "lev": 4, "transform": 4, "lon": 4, "180": 4, "entri": 4, "_yyyymmddhh": 4, "strdate_start": 4, "strdate_end": 4, "nout_level": 4, "csvfile": 4, "convert_ga": 4, "reduc": 4, "opath": 4, "go": 4, "arrai": 4, "year": 4, "ipath": 4, "dai": 4, "gpp_yyyymmddhh": 4, "ra_yyyymmddhh": 4, "vprm_ecmwf_": 4, "_2017": 4, "2017": 4, "flux": 4, "csv_filenam": [4, 8], "namelist_filenam": [4, 8], "input_ghg": [4, 8], "trcr_filenam": [4, 8], "set_filenam": [4, 8], "nml_filenam": [4, 8], "hstart": [4, 8], "input_art": [4, 5, 8], "int": [4, 8], "meteorologi": [4, 8], "command": 5, "line": 5, "respect": [5, 7, 8], "Then": 5, "sbatch": 5, "technic": 5, "achiev": 5, "case1": 5, "case2": 5, "With": 5, "afterward": 5, "There": 5, "argument": [5, 7], "help": 5, "show": 5, "messag": 5, "j": 5, "job_list": 5, "aspect": 5, "launch": 5, "order": [5, 7], "given": 5, "forc": 5, "redo": 5, "even": 5, "were": 5, "previous": 5, "warn": 5, "get": 5, "delet": 5, "effect": 5, "overwritten": 5, "caus": 5, "unexpect": 5, "r": 5, "resum": 5, "unfinish": 5, "call": [5, 7], "restart_run": 5, "divid": 5, "accord": [5, 6], "run_chunk": 5, "part": 5, "chunk": 5, "slurm": 5, "workload": 5, "manag": 5, "compil": 5, "undergo": 5, "regulari": 5, "correctli": 5, "plan": 5, "weekli": 5, "basi": 5, "when": 5, "trigger": 5, "github": 5, "pull": 5, "request": 5, "like": 5, "chain_root": 5, "checkpoint": 5, "cosmo_bas": 5, "cosmo_work": 5, "int2lm_bas": 5, "int2lm_work": 5, "int2lm_output": 5, "As": [5, 7], "preprocessor": 5, "addition": 5, "alwai": 5, "whenev": 5, "successfulli": 5, "sub": 5, "therefor": 5, "four": 5, "deep": 5, "2015010100_2015010106": 5, "prepare_cosmo": 5, "lrff00060000o": 5, "input_": 5, "yu": 5, "lbfd": 5, "2015010106_2015010112": 5, "csc": 6, "appli": 6, "version": 6, "variant": 6, "notabl": 6, "greenhous": 6, "ga": 6, "extens": 6, "aerosol": 6, "reactiv": 6, "trace": 6, "gase": 6, "flexibli": 6, "adapt": 6, "featur": 6, "overview": 6, "instal": 6, "miniconda": 6, "what": 6, "everi": 7, "choos": 7, "some": 7, "indic": 7, "simpl": 7, "jobnam": 7, "same": 7, "sure": 7, "docstr": 7, "__init__": 7, "find": 7, "icontool": 8, "dynam": 8, "paramet": 8, "alongsid": 8, "enclos": 8, "curli": 8, "brace": 8, "runtim": 8, "through": 8, "facilit": 8, "substitut": 8, "subsequ": 8, "actual": 8, "example_namelist": 8, "namelist_var": 8, "pref_suff": 8, "disk": 8, "special": 8}, "objects": {"jobs.biofluxes": [[4, 0, 1, "", "main"]], "jobs.check_output": [[4, 0, 1, "", "main"]], "jobs.cosmo": [[4, 0, 1, "", "main"]], "jobs.emissions": [[4, 0, 1, "", "main"]], "jobs.icon": [[4, 0, 1, "", "main"]], "jobs.int2lm": [[4, 0, 1, "", "main"]], "jobs.obs_nudging": [[4, 0, 1, "", "main"]], "jobs.octe": [[4, 0, 1, "", "main"]], "jobs.oem": [[4, 0, 1, "", "main"]], "jobs.online_vprm": [[4, 0, 1, "", "main"]], "jobs.photo_rate": [[4, 0, 1, "", "main"]], "jobs.post_cosmo": [[4, 0, 1, "", "main"]], "jobs.post_int2lm": [[4, 0, 1, "", "main"]], "jobs.prepare_data": [[4, 0, 1, "", "main"]], "jobs.reduce_output": [[4, 0, 1, "", "main"]], "jobs.tools.cams4int2cosmo": [[4, 0, 1, "", "main"]], "jobs.tools.check_model": [[4, 0, 1, "", "check_model"]], "jobs.tools.comp_nc": [[4, 0, 1, "", "datasets_equal"]], "jobs.tools.ctnoaa4int2cosmo": [[4, 0, 1, "", "main"]], "jobs.tools.mozart2int2lm": [[4, 0, 1, "", "main"]], "jobs.tools.reduce_output_start_end": [[4, 0, 1, "", "main"]], "jobs.tools.string2char": [[4, 0, 1, "", "main"]], "jobs.tools.vprmsplit": [[4, 0, 1, "", "main"]], "jobs.tools.write_cosmo_input_ghg": [[8, 0, 1, "", "main"]], "jobs.tools.write_int2lm_input_art": [[8, 0, 1, "", "main"]], "jobs.verify_chain": [[4, 0, 1, "", "main"]]}, "objtypes": {"0": "py:function"}, "objnames": {"0": ["py", "function", "Python function"]}, "titleterms": {"code": 0, "structur": [0, 5], "configur": [1, 6], "file": 1, "variabl": 1, "set": 1, "config": 1, "yaml": 1, "header": 1, "cosmo": 1, "ghg": 1, "spinup": 1, "test": [1, 5], "case": [1, 5], "icon": 1, "art": 1, "oem": 1, "further": 1, "list": 1, "dictionari": 1, "conda": 2, "environ": 2, "1": 2, "instal": 2, "miniconda": 2, "2": 2, "creat": 2, "3": 2, "store": 2, "user": 2, "specif": 2, "data": 2, "featur": 3, "overview": [3, 7], "job": [4, 6, 7], "tool": 4, "paramet": 4, "todo": 4, "how": 5, "run": 5, "start": [5, 6], "chain": [5, 6], "what": 5, "doe": 5, "directori": 5, "process": 6, "get": 6, "api": 6, "ad": 7, "new": 7, "namelist": 8, "runscript": 8, "templat": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 58}, "alltitles": {"Code Structure": [[0, "code-structure"]], "Configuration File": [[1, "configuration-file"]], "Configuration Variables": [[1, "configuration-variables"]], "Variables to Set in config.yaml": [[1, "variables-to-set-in-config-yaml"]], "Header of config.yaml for the cosmo-ghg-spinup-test case": [[1, "header-of-config-yaml-for-the-cosmo-ghg-spinup-test-case"]], "Header of config.yaml for the icon-art-oem-test case": [[1, "header-of-config-yaml-for-the-icon-art-oem-test-case"]], "Further variables": [[1, "further-variables"]], "List of dictionary variables": [[1, "list-of-dictionary-variables"]], "Conda Environment": [[2, "conda-environment"]], "1. Install Miniconda": [[2, "install-miniconda"]], "2. Create the Conda Environment": [[2, "create-the-conda-environment"]], "3. Store user-specific data": [[2, "store-user-specific-data"]], "Feature Overview": [[3, "feature-overview"]], "Jobs": [[4, "jobs"], [6, null]], "Tools": [[4, "tools"]], "Parameters (TODO)": [[4, "parameters-todo"]], "How to Run": [[5, "how-to-run"]], "Starting the Chain": [[5, "starting-the-chain"]], "What it Does": [[5, "what-it-does"]], "Test Cases": [[5, "test-cases"]], "Directory Structure": [[5, "directory-structure"]], "Processing Chain": [[6, "processing-chain"]], "Getting Started": [[6, null]], "Configuration": [[6, null]], "API": [[6, null]], "Overview": [[7, "overview"]], "Adding New Jobs": [[7, "adding-new-jobs"]], "Namelist and Runscript Templates": [[8, "namelist-and-runscript-templates"]]}, "indexentries": {"check_model() (in module jobs.tools.check_model)": [[4, "jobs.tools.check_model.check_model"]], "datasets_equal() (in module jobs.tools.comp_nc)": [[4, "jobs.tools.comp_nc.datasets_equal"]], "main() (in module jobs.biofluxes)": [[4, "jobs.biofluxes.main"]], "main() (in module jobs.check_output)": [[4, "jobs.check_output.main"]], "main() (in module jobs.cosmo)": [[4, "jobs.cosmo.main"]], "main() (in module jobs.emissions)": [[4, "jobs.emissions.main"]], "main() (in module jobs.icon)": [[4, "jobs.icon.main"]], "main() (in module jobs.int2lm)": [[4, "jobs.int2lm.main"]], "main() (in module jobs.obs_nudging)": [[4, "jobs.obs_nudging.main"]], "main() (in module jobs.octe)": [[4, "jobs.octe.main"]], "main() (in module jobs.oem)": [[4, "jobs.oem.main"]], "main() (in module jobs.online_vprm)": [[4, "jobs.online_vprm.main"]], "main() (in module jobs.photo_rate)": [[4, "jobs.photo_rate.main"]], "main() (in module jobs.post_cosmo)": [[4, "jobs.post_cosmo.main"]], "main() (in module jobs.post_int2lm)": [[4, "jobs.post_int2lm.main"]], "main() (in module jobs.prepare_data)": [[4, "jobs.prepare_data.main"]], "main() (in module jobs.reduce_output)": [[4, "jobs.reduce_output.main"]], "main() (in module jobs.tools.cams4int2cosmo)": [[4, "jobs.tools.cams4int2cosmo.main"]], "main() (in module jobs.tools.ctnoaa4int2cosmo)": [[4, "jobs.tools.ctnoaa4int2cosmo.main"]], "main() (in module jobs.tools.mozart2int2lm)": [[4, "jobs.tools.mozart2int2lm.main"]], "main() (in module jobs.tools.reduce_output_start_end)": [[4, "jobs.tools.reduce_output_start_end.main"]], "main() (in module jobs.tools.string2char)": [[4, "jobs.tools.string2char.main"]], "main() (in module jobs.tools.vprmsplit)": [[4, "jobs.tools.vprmsplit.main"]], "main() (in module jobs.tools.write_cosmo_input_ghg)": [[4, "jobs.tools.write_cosmo_input_ghg.main"], [8, "jobs.tools.write_cosmo_input_ghg.main"]], "main() (in module jobs.tools.write_int2lm_input_art)": [[4, "jobs.tools.write_int2lm_input_art.main"], [8, "jobs.tools.write_int2lm_input_art.main"]], "main() (in module jobs.verify_chain)": [[4, "jobs.verify_chain.main"]]}})
\ No newline at end of file