From 6931f619b7c5d1d97ad8d890d856f96211da5866 Mon Sep 17 00:00:00 2001
From: anphi <anne.philipp@univie.ac.at>
Date: Thu, 9 Jul 2020 00:00:37 +0200
Subject: [PATCH] Update Onlinedocumentation after review of language editing
---
.gitignore | 2 +-
Documentation/html/.buildinfo | 2 +-
Documentation/html/Developers/gen_docu.html | 4 +-
.../html/Documentation/Api/api_fortran.html | 4 +-
.../html/Documentation/Api/api_python.html | 4 +-
.../html/Documentation/Input/changes.html | 4 +-
.../html/Documentation/Input/compilejob.html | 21 ++--
.../html/Documentation/Input/control.html | 4 +-
.../Documentation/Input/control_params.html | 64 ++++++------
.../html/Documentation/Input/ecmwf_env.html | 4 +-
.../html/Documentation/Input/examples.html | 10 +-
.../Documentation/Input/fortran_makefile.html | 4 +-
.../html/Documentation/Input/jobscript.html | 33 +++---
.../html/Documentation/Input/run.html | 55 +++++-----
.../html/Documentation/Input/setup.html | 16 +--
.../html/Documentation/Input/templates.html | 97 ++++++++----------
.../Documentation/Overview/app_modes.html | 4 +-
.../Documentation/Overview/prog_flow.html | 4 +-
Documentation/html/Documentation/api.html | 4 +-
Documentation/html/Documentation/disagg.html | 41 ++++----
Documentation/html/Documentation/input.html | 9 +-
Documentation/html/Documentation/output.html | 30 ++----
.../html/Documentation/overview.html | 4 +-
Documentation/html/Documentation/vertco.html | 20 ++--
Documentation/html/Ecmwf/access.html | 4 +-
Documentation/html/Ecmwf/ec-links.html | 4 +-
Documentation/html/Ecmwf/hintsecmwf.html | 4 +-
Documentation/html/Ecmwf/msdata.html | 4 +-
Documentation/html/Ecmwf/pubdata.html | 4 +-
Documentation/html/Evaluation/metrics.html | 4 +-
Documentation/html/Evaluation/staticcode.html | 4 +-
Documentation/html/Evaluation/testcases.html | 4 +-
Documentation/html/Installation/gateway.html | 8 +-
Documentation/html/Installation/local.html | 28 ++---
Documentation/html/Installation/remote.html | 11 +-
Documentation/html/Support/faq.html | 4 +-
.../html/Support/known_bugs_issues.html | 4 +-
Documentation/html/_modules/ControlFile.html | 4 +-
Documentation/html/_modules/EcFlexpart.html | 4 +-
Documentation/html/_modules/GribUtil.html | 4 +-
.../html/_modules/MarsRetrieval.html | 4 +-
Documentation/html/_modules/UioFiles.html | 4 +-
Documentation/html/_modules/checks.html | 4 +-
.../html/_modules/disaggregation.html | 4 +-
.../html/_modules/get_mars_data.html | 4 +-
Documentation/html/_modules/index.html | 4 +-
Documentation/html/_modules/install.html | 4 +-
.../html/_modules/prepare_flexpart.html | 4 +-
Documentation/html/_modules/submit.html | 4 +-
Documentation/html/_modules/tools.html | 4 +-
.../Documentation/Input/compilejob.rst.txt | 21 ++--
.../Documentation/Input/examples.rst.txt | 4 +-
.../Documentation/Input/jobscript.rst.txt | 25 ++---
.../_sources/Documentation/Input/run.rst.txt | 3 +-
.../Documentation/Input/templates.rst.txt | 83 +++++++--------
.../_sources/Documentation/disagg.rst.txt | 31 +++---
.../html/_sources/Documentation/input.rst.txt | 4 +-
.../_sources/Documentation/output.rst.txt | 14 +--
.../_sources/Documentation/vertco.rst.txt | 6 +-
.../_sources/Installation/gateway.rst.txt | 2 +-
.../html/_sources/Installation/local.rst.txt | 8 +-
.../html/_sources/Installation/remote.rst.txt | 5 +-
Documentation/html/_sources/authors.rst.txt | 14 ++-
Documentation/html/_sources/changelog.rst.txt | 19 ++++
.../html/_sources/installation.rst.txt | 6 +-
.../html/_sources/quick_start.rst.txt | 26 ++---
.../html/_static/documentation_options.js | 2 +-
Documentation/html/authors.html | 16 ++-
Documentation/html/changelog.html | 64 ++++++++----
Documentation/html/dev_guide.html | 4 +-
Documentation/html/documentation.html | 4 +-
Documentation/html/ecmwf_data.html | 4 +-
Documentation/html/evaluation.html | 4 +-
Documentation/html/genindex.html | 4 +-
Documentation/html/index.html | 20 ++--
Documentation/html/installation.html | 10 +-
Documentation/html/objects.inv | Bin 7233 -> 7224 bytes
Documentation/html/py-modindex.html | 4 +-
Documentation/html/quick_start.html | 55 ++++------
Documentation/html/search.html | 4 +-
Documentation/html/searchindex.js | 2 +-
Documentation/html/support.html | 4 +-
Documentation/html/todo.html | 4 +-
For_developers/CONTROLparameter.xls | Bin 33280 -> 33280 bytes
For_developers/InstallationParameter.xls | Bin 9216 -> 9216 bytes
.../Source/Documentation/Input/compilejob.rst | 21 ++--
.../Source/Documentation/Input/examples.rst | 4 +-
.../Source/Documentation/Input/jobscript.rst | 25 ++---
.../Sphinx/Source/Documentation/Input/run.rst | 3 +-
.../Source/Documentation/Input/templates.rst | 83 +++++++--------
.../Sphinx/Source/Documentation/disagg.rst | 31 +++---
.../Sphinx/Source/Documentation/input.rst | 4 +-
.../Sphinx/Source/Documentation/output.rst | 14 +--
.../Sphinx/Source/Documentation/vertco.rst | 6 +-
.../Sphinx/Source/Installation/gateway.rst | 2 +-
.../Sphinx/Source/Installation/local.rst | 8 +-
.../Sphinx/Source/Installation/remote.rst | 5 +-
For_developers/Sphinx/Source/authors.rst | 14 ++-
For_developers/Sphinx/Source/changelog.rst | 19 ++++
For_developers/Sphinx/Source/conf.py | 4 +-
For_developers/Sphinx/Source/installation.rst | 6 +-
For_developers/Sphinx/Source/quick_start.rst | 26 ++---
For_developers/SubmitParameters.xls | Bin 13312 -> 13824 bytes
103 files changed, 643 insertions(+), 691 deletions(-)
diff --git a/.gitignore b/.gitignore
index 79ef1c7..a664ef9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,7 +31,7 @@ Run/Workspace/*
Run/Jobscripts/*sh
Test/Installation/Convert/VERTICAL.EC
Test/Installation/Convert/fort.15
-For_developers/Sphinx/build_temp
+For_developers/Sphinx/Build_temp
# Temporary ignorance of files!!!!
Source/Fortran/Makefile.ecgate
diff --git a/Documentation/html/.buildinfo b/Documentation/html/.buildinfo
index 48a3106..058ef15 100644
--- a/Documentation/html/.buildinfo
+++ b/Documentation/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fddead496515ad2f1960ed379249d24a
+config: cac76732818e0e42f835f525375110ca
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/Documentation/html/Developers/gen_docu.html b/Documentation/html/Developers/gen_docu.html
index de9a15c..a085544 100644
--- a/Documentation/html/Developers/gen_docu.html
+++ b/Documentation/html/Developers/gen_docu.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Updating the documentation — flex_extract 7.1.1 documentation</title>
+ <title>Updating the documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Api/api_fortran.html b/Documentation/html/Documentation/Api/api_fortran.html
index a4d2f92..2c77f4b 100644
--- a/Documentation/html/Documentation/Api/api_fortran.html
+++ b/Documentation/html/Documentation/Api/api_fortran.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation for the Fortran programme — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation for the Fortran programme — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html
index b99d3b9..69fc6c5 100644
--- a/Documentation/html/Documentation/Api/api_python.html
+++ b/Documentation/html/Documentation/Api/api_python.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation for the Python scripts — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation for the Python scripts — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/changes.html b/Documentation/html/Documentation/Input/changes.html
index 264eda3..7f6c03c 100644
--- a/Documentation/html/Documentation/Input/changes.html
+++ b/Documentation/html/Documentation/Input/changes.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>CONTROL file changes — flex_extract 7.1.1 documentation</title>
+ <title>CONTROL file changes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/compilejob.html b/Documentation/html/Documentation/Input/compilejob.html
index 7e3061f..3b9efea 100644
--- a/Documentation/html/Documentation/Input/compilejob.html
+++ b/Documentation/html/Documentation/Input/compilejob.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The compilation job script compilejob.ksh — flex_extract 7.1.1 documentation</title>
+ <title>The compilation job script compilejob.ksh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -194,11 +194,11 @@
<div class="section" id="the-compilation-job-script-compilejob-ksh">
<h1>The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#the-compilation-job-script-compilejob-ksh" title="Permalink to this headline">¶</a></h1>
-<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">compilejob.template</span></code> in the template directory.</p>
+<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code> in the template directory.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
-<p>The job script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
+These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code>.</p>
+<p>The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
<div class="section" id="what-does-the-compilation-script-do">
@@ -210,7 +210,7 @@ server system to load the necessary modules for the environment when submitted t
<li><p>It sets some environment variables for the single session</p></li>
<li><p>It creates the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> path of the user</p></li>
<li><p>It untars the tarball into the root directory.</p></li>
-<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>.</p></li>
+<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">makefile</span></code>.</p></li>
<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
@@ -247,21 +247,18 @@ server system to load the necessary modules for the environment when submitted t
<span class="k">case</span> <span class="si">${</span><span class="nv">HOST</span><span class="si">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
<span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span>makefile_ecgate
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">echo</span> <span class="si">${</span><span class="nv">GROUP</span><span class="si">}</span>
<span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
<span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span> <span class="p">|</span> awk -F / <span class="s1">'{print $1, $2, $3, $4}'</span>
diff --git a/Documentation/html/Documentation/Input/control.html b/Documentation/html/Documentation/Input/control.html
index 4ae1207..a8c5b43 100644
--- a/Documentation/html/Documentation/Input/control.html
+++ b/Documentation/html/Documentation/Input/control.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The CONTROL file — flex_extract 7.1.1 documentation</title>
+ <title>The CONTROL file — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/control_params.html b/Documentation/html/Documentation/Input/control_params.html
index 52af3e4..28ab3ba 100644
--- a/Documentation/html/Documentation/Input/control_params.html
+++ b/Documentation/html/Documentation/Input/control_params.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The CONTROL parameters — flex_extract 7.1.1 documentation</title>
+ <title>The CONTROL parameters — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -278,14 +278,14 @@
<tbody>
<tr class="row-even"><td><p>DEBUG</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>If set to “1” all temporary output files from the mars requests are kept and some extra information is written out to the log file.</p></td>
<td><p>Usually all temporary files except the FLEXPART ready output files are deleted at the end of flex_extract.</p></td>
</tr>
<tr class="row-odd"><td><p>REQUEST</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1,2]</p></td>
+<td><p>0;1;2</p></td>
<td><p>2</p></td>
<td><p>This parameter allows to write out the mars requests in a seperate file.</p></td>
<td><p>The requests are stored in the file “mars_requests.csv”.
@@ -296,34 +296,34 @@ Possible selections are:
</tr>
<tr class="row-even"><td><p>PUBLIC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>This specifies the selection of the kind of ECMWF Web Api access and therefore the kind of available datasets. Public data sets (1) and Memberstate data sets (0).</p></td>
<td><p>Selecting the public access method, the DATASET parameter has explicitly to be set to select the dataset. (CLASS is not enough.) ATTENTION: For public datasets, the user has to accept the license of the dataset to be retrieved. See here for available datasets and their licenses: https://software.ecmwf.int/wiki/display/WEBAPI/ Available+ECMWF+ Public+Datasets</p></td>
</tr>
<tr class="row-odd"><td><p>OPER</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to prepare the operational job script. Start date, end date and basetime will be prepared with environment variables at ecgate.</p></td>
<td><p>This is only necessary if extraction of half-day retrievals should be done automatically. Specific extra feature which is usually not used by normal flex_extract users.</p></td>
</tr>
<tr class="row-even"><td><p>ECSTORAGE</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to store FLEXPART ready output files in the ECFS file system.</p></td>
<td><p>Mind the data limit.</p></td>
</tr>
<tr class="row-odd"><td><p>ECTRANS</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to transfer FLEXPART ready input files to the gateway server.</p></td>
<td><p>The gateway server has to be up and running. A destination has to be installed. See installation instructions for more information.</p></td>
</tr>
<tr class="row-even"><td><p>PREFIX</p></td>
-<td><p>String [xx]</p></td>
+<td><p>String</p></td>
<td><p>anything</p></td>
<td><p>EN</p></td>
<td><p>Prefix of FLEXPART ready input files</p></td>
@@ -339,7 +339,7 @@ Possible selections are:
<tr class="row-even"><td><p>MAILOPS</p></td>
<td><p>list of String [m1, m2, …]</p></td>
<td><p>any number of mail addresses, seperated by comma</p></td>
-<td><p>[‘”${USER}”]</p></td>
+<td><p>${USER}</p></td>
<td><p>Email list for operational log files on ECMWF servers. The email addresses should be seperated by a comma.</p></td>
<td><p>For the ECMWF server it is enough to give ${USER} as input. On local system an actual email is prefered to operate correctly. </p></td>
</tr>
@@ -369,14 +369,14 @@ Possible selections are:
</thead>
<tbody>
<tr class="row-even"><td><p>START_DATE</p></td>
-<td><p>String [YYYYMMDD]</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The first day of the retrieval period.</p></td>
<td><p>If END_DATE is set, START_DATE must be greater than END_DATE.</p></td>
</tr>
<tr class="row-odd"><td><p>END_DATE</p></td>
-<td><p>String [YYYYMMDD]</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The last day of the retrieval period. For a one day retrieval it has to be the same date as START_DATE. If not set, it is automatically equal to START_DATE. </p></td>
@@ -398,7 +398,7 @@ Possible selections are:
</tr>
<tr class="row-even"><td><p>BASETIME</p></td>
<td><p>Integer</p></td>
-<td><p>[0; 12]</p></td>
+<td><p>0; 12</p></td>
<td><p>None</p></td>
<td><p>This parameter is intended for half-day retrievals. Only half a day will be retrieved starting from BASETIME going back 12 hours. E.g. 20180510 with a BASETIME = 00 would lead to a data retrieval of 20180509 12h until 20180510 00h.</p></td>
<td><p>Can be set to 00 or 12 only.</p></td>
@@ -453,14 +453,14 @@ https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets</
<tr class="row-odd"><td><p>EXPVER</p></td>
<td><p>String</p></td>
<td><p>1</p></td>
-<td><p>“1”</p></td>
+<td><p>1</p></td>
<td><p>Experiment number, necessary for R&D experiments, E-suites</p></td>
<td><p></p></td>
</tr>
<tr class="row-even"><td><p>NUMBER</p></td>
-<td><p>String [i/to/i]</p></td>
+<td><p>Integer or String [i/to/i]</p></td>
<td><p>depends on availability</p></td>
-<td><p>“OFF”</p></td>
+<td><p>OFF</p></td>
<td><p>In most cases this can be set to “OFF” but for access to individual ensemble members of ensemble forecasts it is necessary to select numbers. Note, however, that model level data are not stored in MARS for individual ensemble members except the control run. They exist only for a few days before they are discarded. </p></td>
<td><p>For retrieving CERA data, a number has to be selected explicitly. Usually “0” is enough.
For operational data just one number or a list of number can be selected. You can use the syntax “1/to/9” for example.</p></td>
@@ -468,7 +468,7 @@ For operational data just one number or a list of number can be selected. You ca
<tr class="row-odd"><td><p>FORMAT</p></td>
<td><p>String</p></td>
<td><p>[GRIB1, GRIB2]</p></td>
-<td><p>“GRIB1”</p></td>
+<td><p>GRIB1</p></td>
<td><p>Output format (either GRIB1 or GRIB2). Use GRIB2
only when using FLEXPART versions >9.2 or FLEXPART hast to be adapted for reading GRIB2</p></td>
<td><p>GRIB2 is only available for 3D model level fields, not for surface fields.</p></td>
@@ -500,7 +500,7 @@ only when using FLEXPART versions >9.2 or FLEXPART hast to be adapted for rea
<tbody>
<tr class="row-even"><td><p>TYPE</p></td>
<td><p>list of String [xx xx … xx]</p></td>
-<td><p>[AN, FC, CV, CF, 4V, PF]</p></td>
+<td><p>AN, FC, CV, CF, 4V, PF</p></td>
<td><p>None</p></td>
<td><p>A list of field types for each retrieving hour per day. E.g. AN FC FC FC AN FC FC FC for a day with 3-hourly retrieval DTIME . At 0 and 12 UTC we retrieve analysis fields and at 3, 6, 9, 15, 18 and 21 UTC forecast fields. </p></td>
<td><p>So far flex_extract is using ANalysis (AN), ForeCast (FC), Control Forecast (CF), Perturbed Forecast (PF), Calibration/Validation forecast (CV) and 4D Variational analysis (4V). Other types might be also possible but were not tested. The analysis fields are usually (depending on data set) available at 00/06/12/18 UTC. For better temporal resolution, the time inbetween the AN fields can be filled with forecasts (FC). Additionally, it is recommended to use analysis fields only at 00 and 12 UTC and fill the rest of the times with other field types, such as forecasts. </p></td>
@@ -554,7 +554,7 @@ With MAXSTEP > 24 the forecasts from different days overlap, the naming schem
<tbody>
<tr class="row-even"><td><p>ACCTYPE</p></td>
<td><p>String</p></td>
-<td><p>[FC, CV, CF, 4V, PF] - just one of them</p></td>
+<td><p>FC, CV, CF, 4V, PF - just one of them</p></td>
<td><p>None</p></td>
<td><p>The type of field for accumulated data retrieval. The accumulated data fields are only available from forecast fields. Therefore it is seperated from the normal TYPE parameter to allow, for example, retrievment solely of hourly analysis fields in the Era5 data set. </p></td>
<td><p>For downward compatibility to older versions: if ACCTYPE is not specified, the default value is taken form the second position of the original TYPE parameter (TYPE[2]). NOTE: This is important at the moment the original TYPE parameter is changed from FC to AN for example.</p></td>
@@ -575,7 +575,7 @@ With MAXSTEP > 24 the forecasts from different days overlap, the naming schem
</tr>
<tr class="row-odd"><td><p>RRINT</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>1</p></td>
<td><p>Switch to select method of disaggregation for precipitation fields. Old method (0) with a simple linear disaggregation or new method (1) with 2 additional subsequent intervals per time interval.</p></td>
<td><p>For more information see article:
@@ -702,7 +702,7 @@ depends on data set</p></td>
<tbody>
<tr class="row-even"><td><p>GAUSS</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>A switch to calculate ETADOT from Lat/Lon grid (0) or from Gaussian grid (1)</p></td>
<td><p></p></td>
@@ -716,7 +716,7 @@ depends on data set</p></td>
</tr>
<tr class="row-even"><td><p>OMEGA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Retrieve Omega from MARS and put it to file
OMEGAyymmddhh</p></td>
@@ -724,7 +724,7 @@ OMEGAyymmddhh</p></td>
</tr>
<tr class="row-odd"><td><p>OMEGADIFF</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Calculate Omega and Dps/Dt from continuity
equation for diagnostic purposes and include it in file OMEGAyymmddhh</p></td>
@@ -732,7 +732,7 @@ equation for diagnostic purposes and include it in file OMEGAyymmddhh</p></td>
</tr>
<tr class="row-even"><td><p>ETA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to read ETADOT precalculated by ECMWF and multiply it with DPDETA to be compatible with ETADOT calculated from continuity equation.
ETADOT calculation from continuity equation on either Gaussian or lat/lon grid is disabled unless ETADIFF is set to 1 as well.</p></td>
@@ -740,14 +740,14 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
</tr>
<tr class="row-odd"><td><p>ETADIFF</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to calculate etadot and Dps/Dt from continuity equation for diagnostic purposes and include it in file ETAyymmddhh. Expensive option, only for debugging purposes.</p></td>
<td><p></p></td>
</tr>
<tr class="row-even"><td><p>DPDETA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>1</p></td>
<td><p>Switch to multiply etadot with dpdeta – this is the default. In some future version this may change.</p></td>
<td><p></p></td>
@@ -767,12 +767,12 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<table class="docutils align-default" id="id9">
<caption><span class="caption-text">Additional data parameters in CONTROL file</span><a class="headerlink" href="#id9" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col style="width: 17%" />
+<col style="width: 16%" />
<col style="width: 9%" />
-<col style="width: 13%" />
+<col style="width: 12%" />
<col style="width: 11%" />
-<col style="width: 15%" />
-<col style="width: 35%" />
+<col style="width: 14%" />
+<col style="width: 36%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>PARAMETER</p></th>
@@ -786,14 +786,14 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<tbody>
<tr class="row-even"><td><p>CWC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to retrieve cloud water content (sum of cloud liquid water and cloud ice) (1) or not (0).</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>DOUBLEELDA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to select the calculation of extra ensemble members for the ELDA stream. It doubles the amount of retrieved ensemble members.</p></td>
<td><p>Each ensemble member is used to create a new synthesized ensemble member by subtracting 2 * ( current time step value - last time step value ) from the current time step value</p></td>
diff --git a/Documentation/html/Documentation/Input/ecmwf_env.html b/Documentation/html/Documentation/Input/ecmwf_env.html
index db8373a..46a37c7 100644
--- a/Documentation/html/Documentation/Input/ecmwf_env.html
+++ b/Documentation/html/Documentation/Input/ecmwf_env.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ECMWF user credential file ECMWF_ENV — flex_extract 7.1.1 documentation</title>
+ <title>ECMWF user credential file ECMWF_ENV — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/examples.html b/Documentation/html/Documentation/Input/examples.html
index d9f5d60..c87a5e8 100644
--- a/Documentation/html/Documentation/Input/examples.html
+++ b/Documentation/html/Documentation/Input/examples.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>CONTROL file examples — flex_extract 7.1.1 documentation</title>
+ <title>CONTROL file examples — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -223,9 +223,9 @@ CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
</pre></div>
</div>
-<div class="admonition-todo admonition" id="id1">
-<p class="admonition-title">Todo</p>
-<p>#PS some information to be added.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Further information will follow.</p>
</div>
<div class="toctree-wrapper compound">
</div>
diff --git a/Documentation/html/Documentation/Input/fortran_makefile.html b/Documentation/html/Documentation/Input/fortran_makefile.html
index 3d331fb..aca972b 100644
--- a/Documentation/html/Documentation/Input/fortran_makefile.html
+++ b/Documentation/html/Documentation/Input/fortran_makefile.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Fortran makefile for calc_etadot — flex_extract 7.1.1 documentation</title>
+ <title>The Fortran makefile for calc_etadot — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/jobscript.html b/Documentation/html/Documentation/Input/jobscript.html
index 058dd5e..57ea5ab 100644
--- a/Documentation/html/Documentation/Input/jobscript.html
+++ b/Documentation/html/Documentation/Input/jobscript.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The job script job.ksh — flex_extract 7.1.1 documentation</title>
+ <title>The job script job.ksh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -101,7 +101,7 @@
<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="#what-does-the-job-script-do">What does the job script do?</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#example-jobscript-ksh">Example <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#example-job-ksh">Example <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
@@ -195,11 +195,11 @@
<div class="section" id="the-job-script-job-ksh">
<h1>The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#the-job-script-job-ksh" title="Permalink to this headline">¶</a></h1>
<p>The job script is a Korn-shell script which will be created at runtime for each <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> execution in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
-<p>It is based on the <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> template file stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
-This template is generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">job.template</span></code> template file.</p>
+<p>It is based on the <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code> template file stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
+This template is generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">jobscript.template</span></code> template file.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by <code class="docutils literal notranslate"><span class="pre">$$</span></code> in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
+These individual parameters are marked by <code class="docutils literal notranslate"><span class="pre">$$</span></code> in <code class="docutils literal notranslate"><span class="pre">jobscript.template</span></code>.</p>
<p>The job script has a number of settings for the batch system which are fixed, and differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
@@ -211,14 +211,14 @@ server system to load the necessary modules for the environment when submitted t
<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules.</p></li>
<li><p>It sets some environment variables for the single session.</p></li>
<li><p>It creates the directory structure in the user’s <code class="docutils literal notranslate"><span class="pre">$SCRATCH</span></code> file system.</p></li>
-<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
+<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is started from within the <code class="docutils literal notranslate"><span class="pre">work</span></code> directory of the new directory structure by calling the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script. It sets new paths for input and output directories and the recently generated <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p></li>
<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
</div>
-<div class="section" id="example-jobscript-ksh">
-<h2>Example <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code><a class="headerlink" href="#example-jobscript-ksh" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="example-job-ksh">
+<h2>Example <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#example-job-ksh" title="Permalink to this headline">¶</a></h2>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -249,20 +249,17 @@ server system to load the necessary modules for the environment when submitted t
<span class="k">case</span> <span class="si">${</span><span class="nv">HOST</span><span class="si">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="si">${</span><span class="nv">TMPDIR</span><span class="si">}</span>
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
@@ -288,7 +285,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">dataset None</span>
<span class="s">date_chunk 3</span>
<span class="s">debug 1</span>
-<span class="s">destination annep@genericSftp</span>
+<span class="s">destination <specificname>@genericSftp</span>
<span class="s">doubleelda 0</span>
<span class="s">dpdeta 1</span>
<span class="s">dtime 3</span>
@@ -309,7 +306,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">gaussian</span>
<span class="s">grib2flexpart 0</span>
<span class="s">grid 1.0/1.0</span>
-<span class="s">inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace</span>
+<span class="s">inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace</span>
<span class="s">install_target None</span>
<span class="s">job_chunk 1</span>
<span class="s">job_template job.temp</span>
@@ -326,7 +323,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">omega 0</span>
<span class="s">omegadiff 0</span>
<span class="s">oper 0</span>
-<span class="s">outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace</span>
+<span class="s">outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace</span>
<span class="s">prefix CE</span>
<span class="s">public 0</span>
<span class="s">purefc 0</span>
diff --git a/Documentation/html/Documentation/Input/run.html b/Documentation/html/Documentation/Input/run.html
index 6aa4c57..90abff8 100644
--- a/Documentation/html/Documentation/Input/run.html
+++ b/Documentation/html/Documentation/Input/run.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The executable script - run.sh — flex_extract 7.1.1 documentation</title>
+ <title>The executable script - run.sh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -205,16 +205,16 @@ the command line parameters, and the so-called <code class="docutils literal not
<table class="docutils align-default" id="id1">
<caption><span class="caption-text">Parameters for submission</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col style="width: 12%" />
-<col style="width: 9%" />
-<col style="width: 9%" />
-<col style="width: 9%" />
-<col style="width: 27%" />
-<col style="width: 33%" />
+<col style="width: 13%" />
+<col style="width: 13%" />
+<col style="width: 8%" />
+<col style="width: 8%" />
+<col style="width: 26%" />
+<col style="width: 32%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>PARAMETER</p></th>
-<th class="head"><p>Datatype</p></th>
+<th class="head"><p>Format</p></th>
<th class="head"><p>Possible values</p></th>
<th class="head"><p>Default</p></th>
<th class="head"><p>Description</p></th>
@@ -223,14 +223,14 @@ the command line parameters, and the so-called <code class="docutils literal not
</thead>
<tbody>
<tr class="row-even"><td><p>START_DATE</p></td>
-<td><p>String YYYYMMDD</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The first day of the retrieval period.</p></td>
-<td><p>If END_DATE is set, START_DATE must be greater than END_DATE.</p></td>
+<td><p>If END_DATE is set, START_DATE must be earlier or equal than END_DATE.</p></td>
</tr>
<tr class="row-odd"><td><p>END_DATE</p></td>
-<td><p>String YYYYMMDD</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The last day of the retrieval period. For a one day retrieval it has to be the same date as START_DATE. If not set, it is automatically equal to START_DATE. </p></td>
@@ -259,63 +259,66 @@ the command line parameters, and the so-called <code class="docutils literal not
</tr>
<tr class="row-odd"><td><p>BASETIME</p></td>
<td><p>Integer</p></td>
-<td><p>[0; 12]</p></td>
+<td><p>0; 12</p></td>
<td><p>None</p></td>
<td><p>This parameter is intended for half-day retrievals. Only half a day will be retrieved starting from BASETIME going back 12 hours. E.g. 20180510 with a BASETIME = 00 would lead to a data retrieval of 20180509 12h until 20180510 00h.</p></td>
<td><p>Can be set to 00 or 12 only.</p></td>
</tr>
<tr class="row-even"><td><p>STEP</p></td>
-<td><p>list of String [xx xx … xx] or as String [x/to/x]</p></td>
-<td><p>[00 - max available STEP in data set]</p></td>
+<td><p>blank seperated list of Integers (ii ii … ii) or as String (start/to/end)</p></td>
+<td><p>00 - max available STEP in data set</p></td>
<td><p>None</p></td>
<td><p>This is the forecast time step in hours for each corresponding field type (TYPE). Counting of the steps starts from the forecast times. E.g. In Era-Interim, for forecasts at 3, 6, 9 UTC the STEPS 3,6 and 9 are used and the forecast TIME 00 UTC. </p></td>
<td><p>Has to have the same amount of values as in TYPE and TIME! For analysis (AN) fields the STEP has to be 00 always! It is more easily set in the CONTROL file. For pure forecast modes it might be set here as e.g. 0/to/36</p></td>
</tr>
<tr class="row-odd"><td><p>LEVELIST</p></td>
-<td><p>String [start/to/end]</p></td>
+<td><p>String (start/to/end)</p></td>
<td><p>1/to/137; depends on dataset</p></td>
<td><p>None</p></td>
<td><p>List of vertical levels for MARS request. It can be a subset of levels but it has to include the maximum level (end).</p></td>
<td><p>If full list of levels is needed and parameter LEVEL is set, the LEVELIST parameter is not needed. “end” has to be the maximum number of possible levels and has to be the same as in LEVEL, if specified.</p></td>
</tr>
<tr class="row-even"><td><p>AREA</p></td>
-<td><p>Double [f/f/f/f]</p></td>
+<td><p>Double (f/f/f/f)</p></td>
<td><p>any float within lat and lon boundaries</p></td>
-<td><p>‘’</p></td>
+<td><p>None</p></td>
<td><p>Area defined as north/west/south/east</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>DEBUG</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Debug mode - leave temporary files intact</p></td>
<td><p>Usually only the final FLEXPART inputfiles are saved.</p></td>
</tr>
<tr class="row-even"><td><p>OPER</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Operational mode - prepares dates with environment variables</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>REQUEST</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1,2]</p></td>
+<td><p>0;1;2</p></td>
<td><p>0</p></td>
-<td><p>List all mars requests with its specifc values in file mars_requests.dat</p></td>
+<td><p>List all mars requests with its specifc values in file mars_requests.dat
+0 – no file
+1 – only mars_requests.csv
+2 – file and extraction</p></td>
<td><p>Very useful for documentation or debugging reasons.</p></td>
</tr>
<tr class="row-even"><td><p>PUBLIC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Public mode - retrieves the public datasets</p></td>
<td><p>IMPORTANT: This is necessary to select for each PUBLIC user!</p></td>
</tr>
<tr class="row-odd"><td><p>RRINT</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Selection of old or new precipitation interpolation ;
0 - old method;
@@ -345,8 +348,8 @@ the command line parameters, and the so-called <code class="docutils literal not
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
-<td><p>job.temp</p></td>
-<td><p>job.temp</p></td>
+<td><p>jobscript.template</p></td>
+<td><p>jobscript.template</p></td>
<td><p>The job template file which are adapted to be submitted to the batch system on ECMWF server.</p></td>
<td><p></p></td>
</tr>
diff --git a/Documentation/html/Documentation/Input/setup.html b/Documentation/html/Documentation/Input/setup.html
index 425b45c..9cdd154 100644
--- a/Documentation/html/Documentation/Input/setup.html
+++ b/Documentation/html/Documentation/Input/setup.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The installation script - setup.sh — flex_extract 7.1.1 documentation</title>
+ <title>The installation script - setup.sh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -234,15 +234,15 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<tbody>
<tr class="row-even"><td><p>TARGET</p></td>
<td><p>String</p></td>
-<td><p>local, ecgate, cca</p></td>
+<td><p>local, ecgate, cca, ccb</p></td>
<td><p>None</p></td>
-<td><p>Defines the flex_extract application mode to be used. Local = local mode; egate = Remote or Gateway mode, cca = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
+<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
</tr>
<tr class="row-odd"><td><p>MAKEFILE</p></td>
<td><p>String</p></td>
<td><p>any makefile present in the Fortran source directory</p></td>
<td><p>None</p></td>
-<td><p>Name of the makefile in source/fortran directory to be used for compiling the Fortran program. </p></td>
+<td><p>Name of the makefile in Source/Fortran directory to be used for compiling the Fortran program. </p></td>
</tr>
<tr class="row-even"><td><p>ECUID</p></td>
<td><p>String</p></td>
@@ -272,12 +272,12 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<td><p>String</p></td>
<td><p>a full path </p></td>
<td><p>$HOME on ECMWF server and current flex_extract root path on local machine</p></td>
-<td><p>Root path where flex_extract should be installed. If it is not set, it will be $HOME on ECMWF servers and to the current flex_extract root path on local servers. </p></td>
+<td><p>Root path where flex_extract should be installed. It will always be $HOME on ECMWF servers and if not set for the local mode, it will be the current flex_extract root path on local servers. </p></td>
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
-<td><p>job.template</p></td>
-<td><p>job.template</p></td>
+<td><p>installscript.template</p></td>
+<td><p>installscript.template</p></td>
<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td>
</tr>
<tr class="row-even"><td><p>CONTROLFILE</p></td>
diff --git a/Documentation/html/Documentation/Input/templates.html b/Documentation/html/Documentation/Input/templates.html
index 72a9af3..cf6f391 100644
--- a/Documentation/html/Documentation/Input/templates.html
+++ b/Documentation/html/Documentation/Input/templates.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Templates — flex_extract 7.1.1 documentation</title>
+ <title>Templates — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -106,11 +106,11 @@
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Templates</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#convert-nl">convert.nl</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#ecmwf-env-template">ecmwf_env.template</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#compilejob-template">compilejob.template</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#job-temp">job.temp</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#job-template">job.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#calc-etadot-nml-template">calc_etadot_nml.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#ecmwf-env-template">ECMWF_ENV.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#installscript-template">installscript.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#submitscript-template">submitscript.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#jobscript-template">jobscript.template</a></li>
</ul>
</li>
</ul>
@@ -202,10 +202,10 @@
<p class="admonition-title">Note</p>
<p>Do not change anything in these files unless you understand the effects!</p>
</div>
-<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Kornshell job scripts, where (environment) variables are used, the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled for <cite>escaping</cite>.</p>
+<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Korn shell job scripts, where (environment) variables are used, the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled for <cite>escaping</cite>.</p>
<p>The following templates are used; they can be found in the directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Templates</span></code>:</p>
-<div class="section" id="convert-nl">
-<h2>convert.nl<a class="headerlink" href="#convert-nl" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="calc-etadot-nml-template">
+<h2>calc_etadot_nml.template<a class="headerlink" href="#calc-etadot-nml-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This is the template for a Fortran namelist file called <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> read by <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.
It contains all the parameters <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> needs.</p>
@@ -233,7 +233,7 @@ It contains all the parameters <code class="docutils literal notranslate"><span
</div></blockquote>
</div>
<div class="section" id="ecmwf-env-template">
-<h2>ecmwf_env.template<a class="headerlink" href="#ecmwf-env-template" title="Permalink to this headline">¶</a></h2>
+<h2>ECMWF_ENV.template<a class="headerlink" href="#ecmwf-env-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file in the application modes <strong>gateway</strong> and <strong>remote</strong>. It contains the user credentials and gateway server settings for the file transfers.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ECUID <span class="nv">$user_name</span>
@@ -244,8 +244,8 @@ DESTINATION <span class="nv">$destination_name</span>
</div>
</div></blockquote>
</div>
-<div class="section" id="compilejob-template">
-<h2>compilejob.template<a class="headerlink" href="#compilejob-template" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="installscript-template">
+<h2>installscript.template<a class="headerlink" href="#installscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the job script file called <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code> during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>At the beginning, some directives for the batch system are set.
@@ -283,21 +283,18 @@ For the high-performance computers <strong>cca</strong> and <strong>ccb</strong>
<span class="k">case</span> <span class="nv">$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="nv">$fp_root_scripts</span>
<span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span><span class="nv">$makefile</span>
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>GROUP<span class="o">}</span>
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span> <span class="p">|</span> awk -F / <span class="s1">'{print $1, $2, $3, $4}'</span>
@@ -328,8 +325,8 @@ ls -l <span class="nv">$fortran_program</span> >>flexcompile
</div>
</div></blockquote>
</div>
-<div class="section" id="job-temp">
-<h2>job.temp<a class="headerlink" href="#job-temp" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="submitscript-template">
+<h2>submitscript.template<a class="headerlink" href="#submitscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the actual job script file called <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code> for the execution of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>At the beginning, some directives for the batch system are set.
@@ -367,23 +364,20 @@ for details see <a class="reference external" href="https://confluence.ecmwf.int
<span class="nb">export</span> <span class="nv">VERSION</span><span class="o">=</span><span class="m">7</span>.1
<span class="k">case</span> <span class="nv">$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>/flex_extract_v7.1/Source/Python
- <span class="p">;;</span>
- *cca*<span class="o">)</span>
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- <span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>TMPDIR<span class="o">}</span>
- <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
+ <span class="p">;;</span>
+ *cca*<span class="o">)</span>
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ <span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="si">${</span><span class="nv">TMPDIR</span><span class="si">}</span>
+ <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
<span class="k">esac</span>
@@ -421,10 +415,10 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$</span><span c
</div>
</div></blockquote>
</div>
-<div class="section" id="job-template">
-<h2>job.template<a class="headerlink" href="#job-template" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="jobscript-template">
+<h2>jobscript.template<a class="headerlink" href="#jobscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
-<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>. Several parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
+<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code>. Several parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -454,21 +448,18 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$</span><span c
<span class="nb">export</span> <span class="nv">VERSION</span><span class="o">=</span><span class="nv">$version_number</span>
<span class="k">case</span> <span class="nv">$$$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$fp_root_path</span>
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>TMPDIR<span class="o">}</span>
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$fp_root_path</span>
<span class="p">;;</span>
diff --git a/Documentation/html/Documentation/Overview/app_modes.html b/Documentation/html/Documentation/Overview/app_modes.html
index e29f2fa..462af6b 100644
--- a/Documentation/html/Documentation/Overview/app_modes.html
+++ b/Documentation/html/Documentation/Overview/app_modes.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Application modes — flex_extract 7.1.1 documentation</title>
+ <title>Application modes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Overview/prog_flow.html b/Documentation/html/Documentation/Overview/prog_flow.html
index 42570c4..046be30 100644
--- a/Documentation/html/Documentation/Overview/prog_flow.html
+++ b/Documentation/html/Documentation/Overview/prog_flow.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Program flow — flex_extract 7.1.1 documentation</title>
+ <title>Program flow — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/api.html b/Documentation/html/Documentation/api.html
index fbe7fb5..392d3c1 100644
--- a/Documentation/html/Documentation/api.html
+++ b/Documentation/html/Documentation/api.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/disagg.html b/Documentation/html/Documentation/disagg.html
index 3ad7339..2595125 100644
--- a/Documentation/html/Documentation/disagg.html
+++ b/Documentation/html/Documentation/disagg.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Disaggregation of flux data — flex_extract 7.1.1 documentation</title>
+ <title>Disaggregation of flux data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -200,39 +200,39 @@ pre-processing has to be applied.</p>
<tr class="row-odd"><th class="head"><p>Short Name</p></th>
<th class="head"><p>Name</p></th>
<th class="head"><p>Units</p></th>
-<th class="head"><p>Interpolation Type</p></th>
+<th class="head"><p>Disaggregation</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>LSP</p></td>
<td><p>large-scale precipitation</p></td>
<td><p>m</p></td>
-<td><p>modified linear interpolation</p></td>
+<td><p>precipitation</p></td>
</tr>
<tr class="row-odd"><td><p>CP</p></td>
<td><p>convective precipitation</p></td>
<td><p>m</p></td>
-<td><p>modified linear interpolation</p></td>
+<td><p>precipitation</p></td>
</tr>
<tr class="row-even"><td><p>SSHF</p></td>
<td><p>surface sensible heat flux</p></td>
-<td><p>J m:math:<cite>^{-2}</cite></p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>J m <span class="math notranslate nohighlight">\(^{-2}\)</span></p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-odd"><td><p>EWSS</p></td>
<td><p>eastward turbulent surface stress</p></td>
-<td><p>N m:math:<cite>^{-2}</cite> s</p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>N m <span class="math notranslate nohighlight">\(^{-2}\)</span> s</p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-even"><td><p>NSSS</p></td>
<td><p>northward turbulent surface stress</p></td>
-<td><p>N m:math:<cite>^{-2}</cite> s</p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>N m <span class="math notranslate nohighlight">\(^{-2}\)</span> s</p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-odd"><td><p>SSR</p></td>
<td><p>surface net solar radiation</p></td>
-<td><p>J m:math:<cite>^{-2}</cite></p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>J m <span class="math notranslate nohighlight">\(^{-2}\)</span></p></td>
+<td><p>flux</p></td>
</tr>
</tbody>
</table>
@@ -249,7 +249,7 @@ They are retrieved automatically. Thus, data for flux computation will be reques
<h2>Disaggregation for precipitation in older versions<a class="headerlink" href="#disaggregation-for-precipitation-in-older-versions" title="Permalink to this headline">¶</a></h2>
<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.</p>
<p>In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -311,16 +311,11 @@ The height is thereby determined by the condition of conservation of the integra
<div class="section" id="disaggregation-for-the-other-flux-fields">
<h2>Disaggregation for the other flux fields<a class="headerlink" href="#disaggregation-for-the-other-flux-fields" title="Permalink to this headline">¶</a></h2>
<p>The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (<span class="math notranslate nohighlight">\(p_a, p_b, p_c, p_d\)</span>) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.</p>
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (<span class="math notranslate nohighlight">\(F_0, F_1, F_2, F_3\)</span>) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point <span class="math notranslate nohighlight">\(F\)</span> is used for linear interpolation of the complete timeseries afterwards.</p>
<div class="math notranslate nohighlight">
-\[\begin{split}p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
-p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
-p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
-p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.\end{split}\]</div>
-<p>This new point <span class="math notranslate nohighlight">\(p\)</span> is used for linear interpolation of the complete timeseries afterwards.</p>
-<div class="math notranslate nohighlight">
-\[p = 8. * p_a + 4. * p_b + 2. * p_c + p_d\]</div>
+\[F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3\]</div>
<div class="toctree-wrapper compound">
</div>
</div>
diff --git a/Documentation/html/Documentation/input.html b/Documentation/html/Documentation/input.html
index b799afb..790bb28 100644
--- a/Documentation/html/Documentation/input.html
+++ b/Documentation/html/Documentation/input.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Control & input data — flex_extract 7.1.1 documentation</title>
+ <title>Control & input data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -218,10 +218,7 @@ python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
</pre></div>
</div>
-<dl class="simple">
-<dt>With version 7.1, we provide also wrapper shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a> which set the command-line parameters, do some checks, and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>, respectively.</dt><dd><p>It might be faster and easier for beginners if they are used. See <a class="reference internal" href="../quick_start.html"><span class="doc">Usage</span></a> for information on how to use them.</p>
-</dd>
-</dl>
+<p>With version 7.1, we provide also wrapper shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a> which set the command-line parameters, do some checks, and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>, respectively. It might be faster and easier for beginners if they are used. See <a class="reference internal" href="../quick_start.html"><span class="doc">Usage</span></a> for information on how to use them.</p>
<p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> also creates the Korn shell scripts <a class="reference internal" href="Input/compilejob.html"><span class="doc">The compilation job script compilejob.ksh</span></a> and <a class="reference internal" href="Input/jobscript.html"><span class="doc">The job script job.ksh</span></a> which will be sent to the ECMWF servers in the <strong>remote mode</strong> and the <strong>gateway mode</strong> for starting batch jobs.</p>
<p>The Fortran program is compiled during the installation process using the <a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran makefile for calc_etadot</span></a>.</p>
<p>To sum up, the following scripts control <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
diff --git a/Documentation/html/Documentation/output.html b/Documentation/html/Documentation/output.html
index 463712a..623e913 100644
--- a/Documentation/html/Documentation/output.html
+++ b/Documentation/html/Documentation/output.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Output data — flex_extract 7.1.1 documentation</title>
+ <title>Output data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -98,7 +98,7 @@
<li class="toctree-l2 current"><a class="current reference internal" href="#">Output data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#flexpart-input-files"><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#standard-output-files">Standard output files</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#output-files-for-pure-forecast">Output files for pure forecast</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#output-files-for-long-forecast">Output files for long forecast</a></li>
<li class="toctree-l4"><a class="reference internal" href="#output-files-for-ensemble-predictions">Output files for ensemble predictions</a></li>
<li class="toctree-l4"><a class="reference internal" href="#additional-fields-with-new-precipitation-disaggregation">Additional fields with new precipitation disaggregation</a></li>
</ul>
@@ -106,7 +106,6 @@
<li class="toctree-l3"><a class="reference internal" href="#temporary-files">Temporary files</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#mars-grib-files">MARS grib files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mars-request-file">MARS request file</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#vertical-ec">VERTICAL.EC</a></li>
<li class="toctree-l4"><a class="reference internal" href="#index-file">Index file</a></li>
<li class="toctree-l4"><a class="reference internal" href="#flux-files">Flux files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#fort-files">fort files</a></li>
@@ -277,9 +276,9 @@ edition centre date dataType gridType stepRange ty
</pre></div>
</div>
</div>
-<div class="section" id="output-files-for-pure-forecast">
-<h3>Output files for pure forecast<a class="headerlink" href="#output-files-for-pure-forecast" title="Permalink to this headline">¶</a></h3>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:</p>
+<div class="section" id="output-files-for-long-forecast">
+<h3>Output files for long forecast<a class="headerlink" href="#output-files-for-long-forecast" title="Permalink to this headline">¶</a></h3>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><prefix>YYMMDD.HH.<FORECAST_STEP>
</pre></div>
</div>
@@ -370,18 +369,9 @@ request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist,
</pre></div>
</div>
</div>
-<div class="section" id="vertical-ec">
-<h3>VERTICAL.EC<a class="headerlink" href="#vertical-ec" title="Permalink to this headline">¶</a></h3>
-<p>This file contains information describing the vertical discretisation (model levels)
-in form of the <code class="docutils literal notranslate"><span class="pre">A</span></code> and <code class="docutils literal notranslate"><span class="pre">B</span></code> parameters which allow to calculate the actual pressure of a model level from the surface pressure.</p>
-</div>
<div class="section" id="index-file">
<h3>Index file<a class="headerlink" href="#index-file" title="Permalink to this headline">¶</a></h3>
<p>This file is called <code class="docutils literal notranslate"><span class="pre">date_time_stepRange.idx</span></code>. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.</p>
-<div class="admonition-todo admonition" id="id1">
-<p class="admonition-title">Todo</p>
-<p>#PS NEEDS MORE DESCRIPTION</p>
-</div>
</div>
<div class="section" id="flux-files">
<h3>Flux files<a class="headerlink" href="#flux-files" title="Permalink to this headline">¶</a></h3>
@@ -404,8 +394,8 @@ in form of the <code class="docutils literal notranslate"><span class="pre">A</s
<p>where <code class="docutils literal notranslate"><span class="pre">xx</span></code> is a number which defines the meteorological fields stored in these files.
They are generated by the Python code in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> by splitting the meteorological fields for a unique time stamp from the <code class="docutils literal notranslate"><span class="pre">*.grb</span></code> files, storing them under the names <code class="docutils literal notranslate"><span class="pre">fort.<XX></span></code> where <XX> represents some number.
The following table defines the numbers and the corresponding content:</p>
-<table class="colwidths-given docutils align-default" id="id2">
-<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
+<table class="colwidths-given docutils align-default" id="id1">
+<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
@@ -450,8 +440,8 @@ The following table defines the numbers and the corresponding content:</p>
</table>
<p>Some of the fields are solely retrieved with specific settings, e. g., the eta-coordinate vertical velocity is not available in ERA-Interim datasets, and the total cloud-water content is an optional field which is useful for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span> <span class="pre">v10</span></code> and newer.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> program saves its results in file <code class="docutils literal notranslate"><span class="pre">fort.15</span></code> which typically contains:</p>
-<table class="colwidths-given docutils align-default" id="id3">
-<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
+<table class="colwidths-given docutils align-default" id="id2">
+<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
diff --git a/Documentation/html/Documentation/overview.html b/Documentation/html/Documentation/overview.html
index 7ed1447..868bc61 100644
--- a/Documentation/html/Documentation/overview.html
+++ b/Documentation/html/Documentation/overview.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Overview — flex_extract 7.1.1 documentation</title>
+ <title>Overview — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/vertco.html b/Documentation/html/Documentation/vertco.html
index 369a393..35cf305 100644
--- a/Documentation/html/Documentation/vertco.html
+++ b/Documentation/html/Documentation/vertco.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Vertical wind — flex_extract 7.1.1 documentation</title>
+ <title>Vertical wind — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -184,13 +184,11 @@
<h1>Vertical wind<a class="headerlink" href="#vertical-wind" title="Permalink to this headline">¶</a></h1>
<div class="section" id="calculation-of-vertical-velocity-and-preparation-of-output-files">
<h2>Calculation of vertical velocity and preparation of output files<a class="headerlink" href="#calculation-of-vertical-velocity-and-preparation-of-output-files" title="Permalink to this headline">¶</a></h2>
-<dl class="simple">
-<dt>Two methods are provided in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> for the calculation of the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</dt><dd><ol class="lowerroman simple">
+<p>Two methods are provided in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> for the calculation of the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</p>
+<ol class="lowerroman simple">
<li><p>from the horizontal wind field,</p></li>
<li><p>from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets <strong>ERA5</strong> and <strong>CERA-20C</strong>, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.</p></li>
</ol>
-</dd>
-</dl>
<p>Especially for high resolution data, use of the <code class="docutils literal notranslate"><span class="pre">MARS</span></code> parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
T799. The extraction time, which depends heavily also on the performance of <code class="docutils literal notranslate"><span class="pre">MARS</span></code>, is
@@ -207,18 +205,18 @@ V40_update_protocol.pdf. The computational demand and accuracy of <code class="d
dependent on the specification of parameters <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> and <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>. The
following guidance can be given for choosing the right parameters:</p>
<blockquote>
-<div><ul class="simple">
+<div><ul>
<li><p>For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (<code class="docutils literal notranslate"><span class="pre">RESOL=799</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code>). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on <em>ecgate</em>, the computation of the vertical velocity is feasible only on the lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.</p></li>
-<li><dl class="simple">
-<dt>For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:</dt><dd><ul>
+<li><p>For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:</p>
+<blockquote>
+<div><ul class="simple">
<li><p>For 1.0 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=255</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=179</span></code></p></li>
<li><p>For 0.5 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=399</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=359</span></code></p></li>
<li><p>Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.</p></li>
<li><p>If <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> is set to 1, only the following choices are possible for <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> on <em>ecgate</em>: 159,255,319,399,511,799, (on the HPC also 1279; 2047 in future model versions). This choice is restricted because a reduced Gaussian grid is defined in the ECMWF EMOSLIB only for these spectral resolutions. For <code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> can be any value below the operational resolution.</p></li>
<li><p>For <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>, any resolution lower than <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> is possible. If no smoothing is desired, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code> should be chosen. <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> has no effect if the vertical velocity is calculated on a lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>).</p></li>
</ul>
-</dd>
-</dl>
+</div></blockquote>
</li>
<li><p>The on-demand scripts send an error message for settings where <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> (if set) and <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> are larger than 360./<code class="docutils literal notranslate"><span class="pre">GRID</span></code>/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.</p></li>
<li><p>Regional grids are not cyclic in zonal directions, but global grids are. The software assumes a cyclic grid if <code class="docutils literal notranslate"><span class="pre">RIGHT</span></code>-<code class="docutils literal notranslate"><span class="pre">LEFT</span></code> is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code> or is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code>-360.</p></li>
diff --git a/Documentation/html/Ecmwf/access.html b/Documentation/html/Ecmwf/access.html
index 055965d..381c89f 100644
--- a/Documentation/html/Ecmwf/access.html
+++ b/Documentation/html/Ecmwf/access.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Access modes — flex_extract 7.1.1 documentation</title>
+ <title>Access modes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/ec-links.html b/Documentation/html/Ecmwf/ec-links.html
index 322312f..da98527 100644
--- a/Documentation/html/Ecmwf/ec-links.html
+++ b/Documentation/html/Ecmwf/ec-links.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Link collection — flex_extract 7.1.1 documentation</title>
+ <title>Link collection — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/hintsecmwf.html b/Documentation/html/Ecmwf/hintsecmwf.html
index d749c68..c83ec47 100644
--- a/Documentation/html/Ecmwf/hintsecmwf.html
+++ b/Documentation/html/Ecmwf/hintsecmwf.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Hints for data set selection — flex_extract 7.1.1 documentation</title>
+ <title>Hints for data set selection — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/msdata.html b/Documentation/html/Ecmwf/msdata.html
index 5209689..00ceeb2 100644
--- a/Documentation/html/Ecmwf/msdata.html
+++ b/Documentation/html/Ecmwf/msdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available data sets for member-state users — flex_extract 7.1.1 documentation</title>
+ <title>Available data sets for member-state users — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/pubdata.html b/Documentation/html/Ecmwf/pubdata.html
index 46b69a4..834de86 100644
--- a/Documentation/html/Ecmwf/pubdata.html
+++ b/Documentation/html/Ecmwf/pubdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available data sets for public users — flex_extract 7.1.1 documentation</title>
+ <title>Available data sets for public users — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/metrics.html b/Documentation/html/Evaluation/metrics.html
index 2986296..f821f64 100644
--- a/Documentation/html/Evaluation/metrics.html
+++ b/Documentation/html/Evaluation/metrics.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Metrics — flex_extract 7.1.1 documentation</title>
+ <title>Metrics — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/staticcode.html b/Documentation/html/Evaluation/staticcode.html
index 9d2673e..9a3983c 100644
--- a/Documentation/html/Evaluation/staticcode.html
+++ b/Documentation/html/Evaluation/staticcode.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Static code analysis — flex_extract 7.1.1 documentation</title>
+ <title>Static code analysis — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/testcases.html b/Documentation/html/Evaluation/testcases.html
index 14246cb..30bdf0b 100644
--- a/Documentation/html/Evaluation/testcases.html
+++ b/Documentation/html/Evaluation/testcases.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Test cases — flex_extract 7.1.1 documentation</title>
+ <title>Test cases — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Installation/gateway.html b/Documentation/html/Installation/gateway.html
index ec56114..fefd970 100644
--- a/Documentation/html/Installation/gateway.html
+++ b/Documentation/html/Installation/gateway.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Gateway mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Gateway mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -255,7 +255,7 @@ The job script, send to the job queue via the ECaccess software, loads the requi
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<assoc_name>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -274,7 +274,7 @@ The job script, send to the job queue via the ECaccess software, loads the requi
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<assoc_name>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html
index 650175a..0008fb6 100644
--- a/Documentation/html/Installation/local.html
+++ b/Documentation/html/Installation/local.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Local mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Local mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -207,7 +207,7 @@ and libraries, since the preparation of the extraction and the post-processing i
<li><p><a class="reference external" href="https://www.python.org/">Python3</a></p></li>
<li><p><a class="reference external" href="http://www.numpy.org/">numpy</a></p></li>
<li><p><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></p></li>
-<li><p><a class="reference external" href="https://pypi.org/project/eccodes-python/">eccodes for python</a></p></li>
+<li><p><a class="reference external" href="https://pypi.org/project/eccodes/">eccodes for python</a></p></li>
<li><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</p></li>
<li><p><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5 and member user)</p></li>
</ul>
@@ -273,16 +273,15 @@ and then install the <code class="docutils literal notranslate"><span class="pre
</div>
<div class="section" id="testing-the-local-environment">
<span id="ref-test-local"></span><h2>Testing the local environment<a class="headerlink" href="#testing-the-local-environment" title="Permalink to this headline">¶</a></h2>
-<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell:
-.. code-block:: python</p>
-<blockquote>
-<div><p># check in python3 console
-import eccodes
-import genshi
-import numpy
-import cdsapi
-import ecmwfapi</p>
-</div></blockquote>
+<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
+<span class="kn">import</span> <span class="nn">eccodes</span>
+<span class="kn">import</span> <span class="nn">genshi</span>
+<span class="kn">import</span> <span class="nn">numpy</span>
+<span class="kn">import</span> <span class="nn">cdsapi</span>
+<span class="kn">import</span> <span class="nn">ecmwfapi</span>
+</pre></div>
+</div>
<p>If there are no error messages, you succeeded in setting up the environment.</p>
<div class="section" id="testing-the-web-apis">
<h3>Testing the Web APIs<a class="headerlink" href="#testing-the-web-apis" title="Permalink to this headline">¶</a></h3>
@@ -410,12 +409,13 @@ with an editor and adapt the installation parameters in the section labelled wit
<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
<span class="c1">#</span>
<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'local'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><name_of_your_makefile>
<span class="nv">ECUID</span><span class="o">=</span>None
<span class="nv">ECGID</span><span class="o">=</span>None
<span class="nv">GATEWAY</span><span class="o">=</span>None
<span class="nv">DESTINATION</span><span class="o">=</span>None
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
diff --git a/Documentation/html/Installation/remote.html b/Documentation/html/Installation/remote.html
index 33e7324..baf068e 100644
--- a/Documentation/html/Installation/remote.html
+++ b/Documentation/html/Installation/remote.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Remote mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Remote mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -286,7 +286,7 @@ described in <a class="reference internal" href="../Documentation/Input/setup.ht
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<username>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -305,7 +305,7 @@ described in <a class="reference internal" href="../Documentation/Input/setup.ht
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<username>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="s1">''</span>
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -321,8 +321,7 @@ with your own ones (look at any of your files with ``ls -l’’ to see uid and
<p>If a local gateway server is available, files can be transferred with <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. In that case, a valid <em>GATEWAY</em> and <em>DESTINATION</em> have to be present in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file (even if not used, the lines must not be deleted).</p>
</div>
<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module load python3
-./setup.sh
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./setup.sh
</pre></div>
</div>
<p>to start the installation. You should see the following on standard output.</p>
diff --git a/Documentation/html/Support/faq.html b/Documentation/html/Support/faq.html
index 6a0de91..4d51235 100644
--- a/Documentation/html/Support/faq.html
+++ b/Documentation/html/Support/faq.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>FAQ - Frequently asked questions — flex_extract 7.1.1 documentation</title>
+ <title>FAQ - Frequently asked questions — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Support/known_bugs_issues.html b/Documentation/html/Support/known_bugs_issues.html
index 8f166fd..1bd969f 100644
--- a/Documentation/html/Support/known_bugs_issues.html
+++ b/Documentation/html/Support/known_bugs_issues.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Known Bugs and Issues — flex_extract 7.1.1 documentation</title>
+ <title>Known Bugs and Issues — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/ControlFile.html b/Documentation/html/_modules/ControlFile.html
index 8fad03c..91d39a8 100644
--- a/Documentation/html/_modules/ControlFile.html
+++ b/Documentation/html/_modules/ControlFile.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ControlFile — flex_extract 7.1.1 documentation</title>
+ <title>ControlFile — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/EcFlexpart.html b/Documentation/html/_modules/EcFlexpart.html
index 789f353..a0b36ad 100644
--- a/Documentation/html/_modules/EcFlexpart.html
+++ b/Documentation/html/_modules/EcFlexpart.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>EcFlexpart — flex_extract 7.1.1 documentation</title>
+ <title>EcFlexpart — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/GribUtil.html b/Documentation/html/_modules/GribUtil.html
index 3506e58..a6b59b2 100644
--- a/Documentation/html/_modules/GribUtil.html
+++ b/Documentation/html/_modules/GribUtil.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>GribUtil — flex_extract 7.1.1 documentation</title>
+ <title>GribUtil — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/MarsRetrieval.html b/Documentation/html/_modules/MarsRetrieval.html
index d61076c..3659552 100644
--- a/Documentation/html/_modules/MarsRetrieval.html
+++ b/Documentation/html/_modules/MarsRetrieval.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>MarsRetrieval — flex_extract 7.1.1 documentation</title>
+ <title>MarsRetrieval — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/UioFiles.html b/Documentation/html/_modules/UioFiles.html
index 3c25272..9b059c2 100644
--- a/Documentation/html/_modules/UioFiles.html
+++ b/Documentation/html/_modules/UioFiles.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>UioFiles — flex_extract 7.1.1 documentation</title>
+ <title>UioFiles — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/checks.html b/Documentation/html/_modules/checks.html
index 2bcab08..d592b9a 100644
--- a/Documentation/html/_modules/checks.html
+++ b/Documentation/html/_modules/checks.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>checks — flex_extract 7.1.1 documentation</title>
+ <title>checks — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/disaggregation.html b/Documentation/html/_modules/disaggregation.html
index 001f47a..9cbef22 100644
--- a/Documentation/html/_modules/disaggregation.html
+++ b/Documentation/html/_modules/disaggregation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>disaggregation — flex_extract 7.1.1 documentation</title>
+ <title>disaggregation — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/get_mars_data.html b/Documentation/html/_modules/get_mars_data.html
index d7abc19..c335391 100644
--- a/Documentation/html/_modules/get_mars_data.html
+++ b/Documentation/html/_modules/get_mars_data.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>get_mars_data — flex_extract 7.1.1 documentation</title>
+ <title>get_mars_data — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/index.html b/Documentation/html/_modules/index.html
index e094c37..743fb37 100644
--- a/Documentation/html/_modules/index.html
+++ b/Documentation/html/_modules/index.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Overview: module code — flex_extract 7.1.1 documentation</title>
+ <title>Overview: module code — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html
index 31f7762..bfe349c 100644
--- a/Documentation/html/_modules/install.html
+++ b/Documentation/html/_modules/install.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>install — flex_extract 7.1.1 documentation</title>
+ <title>install — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/prepare_flexpart.html b/Documentation/html/_modules/prepare_flexpart.html
index 86971b2..f032ab5 100644
--- a/Documentation/html/_modules/prepare_flexpart.html
+++ b/Documentation/html/_modules/prepare_flexpart.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>prepare_flexpart — flex_extract 7.1.1 documentation</title>
+ <title>prepare_flexpart — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/submit.html b/Documentation/html/_modules/submit.html
index f61eb0a..1db3ca8 100644
--- a/Documentation/html/_modules/submit.html
+++ b/Documentation/html/_modules/submit.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>submit — flex_extract 7.1.1 documentation</title>
+ <title>submit — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/tools.html b/Documentation/html/_modules/tools.html
index 0222c7c..4d028f0 100644
--- a/Documentation/html/_modules/tools.html
+++ b/Documentation/html/_modules/tools.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>tools — flex_extract 7.1.1 documentation</title>
+ <title>tools — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
index 7eac32c..214a096 100644
--- a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
@@ -1,14 +1,14 @@
-*********************************************
+*************************************************
The compilation job script ``compilejob.ksh``
-*********************************************
+*************************************************
-The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
+The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``installscript.template`` in the template directory.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
+These individual parameters are marked by a doubled ``$`` sign in ``installscript.template``.
-The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
+The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
@@ -23,7 +23,7 @@ What does the compilation script do?
#. It sets some environment variables for the single session
#. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
#. It untars the tarball into the root directory.
- #. It compiles the Fortran program using ``Makefile``.
+ #. It compiles the Fortran program using ``makefile``.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
@@ -66,21 +66,18 @@ Example ``compilejob.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=${HOME}
export MAKEFILE=makefile_ecgate
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo ${GROUP}
echo ${HOME}
echo ${HOME} | awk -F / '{print $1, $2, $3, $4}'
diff --git a/Documentation/html/_sources/Documentation/Input/examples.rst.txt b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
index f69fd02..8ed3c76 100644
--- a/Documentation/html/_sources/Documentation/Input/examples.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
@@ -35,9 +35,9 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
-.. todo::
+.. note::
- #PS some information to be added.
+ Further information will follow.
.. toctree::
:hidden:
diff --git a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
index 6a8b760..a1f43b2 100644
--- a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
@@ -4,12 +4,12 @@ The job script ``job.ksh``
The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
-It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
-This template is generated in the installation process from a ``job.template`` template file.
+It is based on the ``submitscript.template`` template file stored in the ``Templates`` directory.
+This template is generated in the installation process from a ``jobscript.template`` template file.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by ``$$`` in ``job.temp``.
+These individual parameters are marked by ``$$`` in ``jobscript.template``.
The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
@@ -25,14 +25,14 @@ What does the job script do?
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
#. It sets some environment variables for the single session.
#. It creates the directory structure in the user's ``$SCRATCH`` file system.
- #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
+ #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``job.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
#. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
-Example ``jobscript.ksh``
+Example ``job.ksh``
-------------------------
.. code-block:: bash
@@ -67,20 +67,17 @@ Example ``jobscript.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=${TMPDIR}
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
@@ -106,7 +103,7 @@ Example ``jobscript.ksh``
dataset None
date_chunk 3
debug 1
- destination annep@genericSftp
+ destination <specificname>@genericSftp
doubleelda 0
dpdeta 1
dtime 3
@@ -127,7 +124,7 @@ Example ``jobscript.ksh``
gaussian
grib2flexpart 0
grid 1.0/1.0
- inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
install_target None
job_chunk 1
job_template job.temp
@@ -144,7 +141,7 @@ Example ``jobscript.ksh``
omega 0
omegadiff 0
oper 0
- outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
prefix CE
public 0
purefc 0
diff --git a/Documentation/html/_sources/Documentation/Input/run.rst.txt b/Documentation/html/_sources/Documentation/Input/run.rst.txt
index 1e3ad68..21b1ddb 100644
--- a/Documentation/html/_sources/Documentation/Input/run.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/run.rst.txt
@@ -30,8 +30,7 @@ Content of ``run.sh``
.. literalinclude:: ../../../../../Run/run.sh
:language: bash
- :caption: run.sh
-
+ :caption: run.sh
diff --git a/Documentation/html/_sources/Documentation/Input/templates.rst.txt b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
index 786679e..4a26a54 100644
--- a/Documentation/html/_sources/Documentation/Input/templates.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
@@ -7,12 +7,12 @@ In ``flex_extract``, the Python package `genshi <https://genshi.edgewall.org/>`_
.. note::
Do not change anything in these files unless you understand the effects!
-Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
+Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Korn shell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
-convert.nl
-----------
+calc_etadot_nml.template
+-------------------------
This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
It contains all the parameters ``calc_etadot`` needs.
@@ -39,7 +39,7 @@ convert.nl
mdpdeta = $mdpdeta
/
-ecmwf_env.template
+ECMWF_ENV.template
------------------
This template is used to create the ``ECMWF_ENV`` file in the application modes **gateway** and **remote**. It contains the user credentials and gateway server settings for the file transfers.
@@ -51,8 +51,8 @@ ecmwf_env.template
GATEWAY $gateway_name
DESTINATION $destination_name
-compilejob.template
--------------------
+installscript.template
+----------------------
This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
@@ -96,21 +96,18 @@ compilejob.template
case $${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo $${GROUP}
echo $${HOME}
echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
@@ -139,8 +136,8 @@ compilejob.template
fi
-job.temp
---------
+submitscript.template
+---------------------
This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**.
@@ -184,23 +181,20 @@ job.temp
export VERSION=7.1
case $${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
- ;;
- *cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- export SCRATCH=$${TMPDIR}
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
esac
@@ -236,10 +230,10 @@ job.temp
fi
-job.template
-------------
+jobscript.template
+------------------
- This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
+ This template is used to create the template for the execution job script ``submitscript.template`` for ``flex_extract`` in the installation process. A description of the file can be found under ``submitscript.template``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
.. code-block:: ksh
@@ -272,21 +266,18 @@ job.template
export VERSION=$version_number
case $$$${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export PATH=$$$${PATH}:$fp_root_path
;;
*cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=$$$${TMPDIR}
export PATH=$$$${PATH}:$fp_root_path
;;
diff --git a/Documentation/html/_sources/Documentation/disagg.rst.txt b/Documentation/html/_sources/Documentation/disagg.rst.txt
index 64a3e3d..9a51e6b 100644
--- a/Documentation/html/_sources/Documentation/disagg.rst.txt
+++ b/Documentation/html/_sources/Documentation/disagg.rst.txt
@@ -12,16 +12,16 @@ pre-processing has to be applied.
.. _ref-table-fluxpar:
.. csv-table:: Flux fields
- :header: "Short Name", "Name", "Units", "Interpolation Type"
+ :header: "Short Name", "Name", "Units", "Disaggregation"
:align: center
:widths: 5,15,5,10
- LSP, "large-scale precipitation", "m", "modified linear interpolation"
- CP, "convective precipitation", "m", "modified linear interpolation"
- SSHF, "surface sensible heat flux", "J m:math:`^{-2}`", "bicubic interpolation"
- EWSS, "eastward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- SSR, "surface net solar radiation", "J m:math:`^{-2}`", "bicubic interpolation"
+ LSP, "large-scale precipitation", "m", "precipitation "
+ CP, "convective precipitation", "m", "precipitation"
+ SSHF, "surface sensible heat flux", "J m :math:`^{-2}`", "flux"
+ EWSS, "eastward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ NSSS, "northward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ SSR, "surface net solar radiation", "J m :math:`^{-2}`", "flux "
The first step is to *de-accumulate* the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
@@ -42,7 +42,7 @@ Disaggregation for precipitation in older versions
In ``flex_extract`` up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.
In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -160,21 +160,14 @@ Disaggregation for the other flux fields
----------------------------------------------
The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (:math:`F_0, F_1, F_2, F_3`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point :math:`F` is used for linear interpolation of the complete timeseries afterwards.
.. math::
-
- p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
- p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
- p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
- p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.
-
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards.
-.. math::
- p = 8. * p_a + 4. * p_b + 2. * p_c + p_d
+ F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3
diff --git a/Documentation/html/_sources/Documentation/input.rst.txt b/Documentation/html/_sources/Documentation/input.rst.txt
index 0a0e11d..64f3366 100644
--- a/Documentation/html/_sources/Documentation/input.rst.txt
+++ b/Documentation/html/_sources/Documentation/input.rst.txt
@@ -35,8 +35,8 @@ Controlling
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
- With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
- It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
+
+ With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively. It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.
diff --git a/Documentation/html/_sources/Documentation/output.rst.txt b/Documentation/html/_sources/Documentation/output.rst.txt
index 8a25f25..4f6aebf 100644
--- a/Documentation/html/_sources/Documentation/output.rst.txt
+++ b/Documentation/html/_sources/Documentation/output.rst.txt
@@ -80,10 +80,10 @@ Here is an example output which lists the meteorological fields in a single file
35 of 35 messages in CE00010800
-Output files for pure forecast
+Output files for long forecast
------------------------------
-``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
+``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:
.. code-block:: bash
@@ -193,22 +193,12 @@ Example output of a one-day retrieval of CERA-20C data:
4, 24, 40.0/-5.0/30.0/5.0, None, 20000108/to/20000108, 1, , 1.0/1.0, 1, SFC, EP, 000, 141.128/151.128/164.128/165.128/166.128/167.128/168.128/129.128/172.128/027.128/028.128/186.128/187.128/188.128/235.128/139.128/039.128/173.128, , 159, 00, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/ANOG__SL.20000108.23903.23904.grb, 00/03/06/09/12/15/18/21, AN
-VERTICAL.EC
------------
-
-This file contains information describing the vertical discretisation (model levels)
-in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
-
Index file
----------
This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
-.. todo::
-
- #PS NEEDS MORE DESCRIPTION
-
Flux files
----------
diff --git a/Documentation/html/_sources/Documentation/vertco.rst.txt b/Documentation/html/_sources/Documentation/vertco.rst.txt
index fcc1d14..2196482 100644
--- a/Documentation/html/_sources/Documentation/vertco.rst.txt
+++ b/Documentation/html/_sources/Documentation/vertco.rst.txt
@@ -6,8 +6,9 @@ Calculation of vertical velocity and preparation of output files
================================================================
Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
- (i) from the horizontal wind field,
- (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
+
+(i) from the horizontal wind field,
+(ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
@@ -30,6 +31,7 @@ following guidance can be given for choosing the right parameters:
* For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
* For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
+
- For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
- For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
- Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.
diff --git a/Documentation/html/_sources/Installation/gateway.rst.txt b/Documentation/html/_sources/Installation/gateway.rst.txt
index 34764c8..06f50a9 100644
--- a/Documentation/html/_sources/Installation/gateway.rst.txt
+++ b/Documentation/html/_sources/Installation/gateway.rst.txt
@@ -128,7 +128,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<assoc_name>@genericSftp' | DESTINATION='<assoc_name>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR=None |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
index 5e20d27..9f9c012 100644
--- a/Documentation/html/_sources/Installation/local.rst.txt
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -16,8 +16,8 @@ Local mode installation
.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
.. _genshi: https://genshi.edgewall.org/
-.. _eccodes for python: https://pypi.org/project/eccodes-python/
-.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _eccodes for python: https://pypi.org/project/eccodes/
+.. _eccodes for conda: https://anaconda.org/conda-forge/python-eccodes
.. _gfortran: https://gcc.gnu.org/wiki/GFortran
.. _fftw3: http://www.fftw.org
.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
@@ -119,6 +119,7 @@ Testing the local environment
=============================
Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell:
+
.. code-block:: python
# check in python3 console
@@ -286,12 +287,13 @@ with an editor and adapt the installation parameters in the section labelled wit
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
+ MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
- JOB_TEMPLATE='job.template'
+ JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
diff --git a/Documentation/html/_sources/Installation/remote.rst.txt b/Documentation/html/_sources/Installation/remote.rst.txt
index 95f0c63..127e2b7 100644
--- a/Documentation/html/_sources/Installation/remote.rst.txt
+++ b/Documentation/html/_sources/Installation/remote.rst.txt
@@ -137,7 +137,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<username>@genericSftp' | DESTINATION='<username>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
@@ -152,8 +152,7 @@ with your own ones (look at any of your files with ``ls -l'' to see uid and gid)
Afterwards, type:
.. code-block:: bash
-
- module load python3
+
./setup.sh
to start the installation. You should see the following on standard output.
diff --git a/Documentation/html/_sources/authors.rst.txt b/Documentation/html/_sources/authors.rst.txt
index 3992e33..5636f8d 100644
--- a/Documentation/html/_sources/authors.rst.txt
+++ b/Documentation/html/_sources/authors.rst.txt
@@ -8,18 +8,24 @@ Developer Team
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: anne.philipp [at] univie.ac.at
+| e-mail: anne.philipp [at] univie.ac.at
-
| Leopold Haimberger
| Department of Meteorology and Geophysics
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: leopold.haimberger [at] univie.ac.at
+| e-mail: leopold.haimberger [at] univie.ac.at
-
+
+| Petra Seibert
+| Institute of Meteorology (BOKU-Met)
+| University of Natural Resources & Life Sciences (BOKU)
+| Gregor-Mendel-Str. 33
+| 1180 Wien, Austria
+| e-mail: petra.seibert ./at/. boku.ac.at
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/Documentation/html/_sources/changelog.rst.txt b/Documentation/html/_sources/changelog.rst.txt
index b3f98e0..ed72fc1 100644
--- a/Documentation/html/_sources/changelog.rst.txt
+++ b/Documentation/html/_sources/changelog.rst.txt
@@ -10,6 +10,25 @@ Changelog
.. _new algorithm: https://www.geosci-model-dev.net/11/2503/2018/
+.. _ref-v712:
+
+Release v7.1.2
+--------------
+
+Changes
+#########
+ * changed naming of template files
+ * separate loading of Python3 module in remote mode is no longer necessary
+ * updated module versions for ECMWF servers
+ * changed names of working directories on ECMWF servers
+ * select makefile automatically regarding application mode if it was not set in ``setup.sh``
+ * updated online documentation
+ * converted most important Fortran code documentation from German to English
+ * deactivate writing of VERTICAL.EC file by Fortran code
+ * adapt and improve Fortran regression test scripts
+ * remove jasper lib from Fortran makefiles
+
+
.. _ref-v711:
Release v7.1.1
diff --git a/Documentation/html/_sources/installation.rst.txt b/Documentation/html/_sources/installation.rst.txt
index 6a0c8a5..97c5cb8 100644
--- a/Documentation/html/_sources/installation.rst.txt
+++ b/Documentation/html/_sources/installation.rst.txt
@@ -139,7 +139,7 @@ The software required to run ``flex_extract`` depends on the :doc:`Documentation
Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
-Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example:
+Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system) ``rpm -q <package_name>``. For example:
.. code-block:: sh
@@ -197,14 +197,14 @@ Fortran program test
To check whether the Fortran program ``calc_etadot`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
-For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
+For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Calc_etadot/`` directory and execute the Fortran program.
.. note::
Remember that you might have to log in at the ECMWF server if you used the installation for the **remote** or **gateway** mode. There you find the ``flex_extract`` root directory in your ``$HOME`` directory.
.. code-block:: bash
- cd Testing/Installation/Convert
+ cd Testing/Installation/Calc_etadot
# execute the Fortran progam without arguments
../../../Source/Fortran/calc_etadot
diff --git a/Documentation/html/_sources/quick_start.rst.txt b/Documentation/html/_sources/quick_start.rst.txt
index baa36ca..3816442 100644
--- a/Documentation/html/_sources/quick_start.rst.txt
+++ b/Documentation/html/_sources/quick_start.rst.txt
@@ -64,7 +64,6 @@ Remote mode
.. code-block:: bash
# On ECMWF server
- [<ecuid>@ecgb11 ~]$ module load python3
[<ecuid>@ecgb11 ~]$ cd flex_extract_vX.X/Run
@@ -103,7 +102,7 @@ Therefore open the ``run.sh`` file and modify the parameter block marked in the
INPUTDIR=None
OUTPUTDIR=None
PP_ID=None
- JOB_TEMPLATE='job.temp'
+ JOB_TEMPLATE='jobscript.template'
CONTROLFILE='CONTROL_CERA'
DEBUG=0
REQUEST=2
@@ -137,12 +136,12 @@ In case the job fails you will receive an email with the subject ``ERROR!`` and
cd $SCRATCH
ls -rthl
-The last command lists the most recent logs and temporary retrieval directories (usually ``pythonXXXXX``, where XXXXX is the process id). Under ``pythonXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
+The last command lists the most recent logs and temporary retrieval directories (usually ``extractXXXXX``, where XXXXX is the process id). Under ``extractXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
.. code-block:: bash
:caption: "Example structure of ``flex_extract`` output directory on ECMWF servers."
- pythonXXXXX
+ extractXXXXX
├── CONTROL
├── prot
├── work
@@ -357,8 +356,8 @@ These files defines the minimum number of parameters necessary to retrieve a dai
Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ for hints about retrieval efficiency and troubleshooting.
-Pure forecast
- It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
+Long forecast
+ It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today (1-hourly). *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!
@@ -417,10 +416,6 @@ Field type and time
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
- .. todo::
-
- #PS needs to be rephrased
-
.. code-block:: bash
:caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
@@ -450,9 +445,6 @@ Grid resolution and domain
The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
- .. todo::
-
- #PS shouldn't we explain how to define a domain??
The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
@@ -469,12 +461,8 @@ Grid resolution and domain
Flux data
- Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
-
- .. todo::
-
- #PS for which application would this be typical?
-
+ Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a ``CONTROL`` file.
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
diff --git a/Documentation/html/_static/documentation_options.js b/Documentation/html/_static/documentation_options.js
index 3efa030..bc92269 100644
--- a/Documentation/html/_static/documentation_options.js
+++ b/Documentation/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '7.1.1',
+ VERSION: '7.1.2',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/Documentation/html/authors.html b/Documentation/html/authors.html
index 1ca2cbc..08ad4e8 100644
--- a/Documentation/html/authors.html
+++ b/Documentation/html/authors.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Developer Team — flex_extract 7.1.1 documentation</title>
+ <title>Developer Team — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -173,7 +173,7 @@
<div class="line">University of Vienna</div>
<div class="line">Althanstraße 14 / UZA II</div>
<div class="line">1090 Vienna, Austria</div>
-<div class="line">mail: anne.philipp [at] univie.ac.at</div>
+<div class="line">e-mail: anne.philipp [at] univie.ac.at</div>
</div>
<div class="line-block">
<div class="line">Leopold Haimberger</div>
@@ -181,7 +181,15 @@
<div class="line">University of Vienna</div>
<div class="line">Althanstraße 14 / UZA II</div>
<div class="line">1090 Vienna, Austria</div>
-<div class="line">mail: leopold.haimberger [at] univie.ac.at</div>
+<div class="line">e-mail: leopold.haimberger [at] univie.ac.at</div>
+</div>
+<div class="line-block">
+<div class="line">Petra Seibert</div>
+<div class="line">Institute of Meteorology (BOKU-Met)</div>
+<div class="line">University of Natural Resources & Life Sciences (BOKU)</div>
+<div class="line">Gregor-Mendel-Str. 33</div>
+<div class="line">1180 Wien, Austria</div>
+<div class="line">e-mail: petra.seibert ./at/. boku.ac.at</div>
</div>
<div class="toctree-wrapper compound">
</div>
diff --git a/Documentation/html/changelog.html b/Documentation/html/changelog.html
index a0eab66..0f47633 100644
--- a/Documentation/html/changelog.html
+++ b/Documentation/html/changelog.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Changelog — flex_extract 7.1.1 documentation</title>
+ <title>Changelog — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -96,27 +96,31 @@
<li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="dev_guide.html">Developer Guide</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#release-v7-1-2">Release v7.1.2</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#changes">Changes</a></li>
+</ul>
+</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-1-1">Release v7.1.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#bug-fixes">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-1">Release v7.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#new-features">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#changes">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id1">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-4">Release v7.0.4</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id1">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id2">Bug fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id2">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id3">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-3">Release v7.0.3</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id3">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id4">New Features</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-2">Release v7.0.2</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id4">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id5">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id5">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id6">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v0-1-v6-0">Release v0.1 - v6.0</a></li>
@@ -193,6 +197,26 @@
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
+<div class="section" id="release-v7-1-2">
+<span id="ref-v712"></span><h2>Release v7.1.2<a class="headerlink" href="#release-v7-1-2" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="changes">
+<h3>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h3>
+<blockquote>
+<div><ul class="simple">
+<li><p>changed naming of template files</p></li>
+<li><p>separate loading of Python3 module in remote mode is no longer necessary</p></li>
+<li><p>updated module versions for ECMWF servers</p></li>
+<li><p>changed names of working directories on ECMWF servers</p></li>
+<li><p>select makefile automatically regarding application mode if it was not set in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></p></li>
+<li><p>updated online documentation</p></li>
+<li><p>converted most important Fortran code documentation from German to English</p></li>
+<li><p>deactivate writing of VERTICAL.EC file by Fortran code</p></li>
+<li><p>adapt and improve Fortran regression test scripts</p></li>
+<li><p>remove jasper lib from Fortran makefiles</p></li>
+</ul>
+</div></blockquote>
+</div>
+</div>
<div class="section" id="release-v7-1-1">
<span id="ref-v711"></span><h2>Release v7.1.1<a class="headerlink" href="#release-v7-1-1" title="Permalink to this headline">¶</a></h2>
<div class="section" id="bug-fixes">
@@ -221,8 +245,8 @@
</ul>
</div></blockquote>
</div>
-<div class="section" id="changes">
-<h3>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id1">
+<h3>Changes<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>upgraded to Python3</p></li>
@@ -239,16 +263,16 @@
</div>
<div class="section" id="release-v7-0-4">
<span id="ref-v704"></span><h2>Release v7.0.4<a class="headerlink" href="#release-v7-0-4" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id1">
-<h3>New Features<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id2">
+<h3>New Features<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>Ensemble retrieval for ENFO and ELDA stream (ZAMG specific with extra synthesized ensembles for ELDA stream)</p></li>
</ul>
</div></blockquote>
</div>
-<div class="section" id="id2">
-<h3>Bug fixes<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id3">
+<h3>Bug fixes<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>various problems with ERA 5 retrieval</p></li>
@@ -263,8 +287,8 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span
</div>
<div class="section" id="release-v7-0-3">
<span id="ref-v703"></span><h2>Release v7.0.3<a class="headerlink" href="#release-v7-0-3" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id3">
-<h3>New Features<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id4">
+<h3>New Features<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>output of MARS requests to an extra file (debugging and documentation)</p></li>
@@ -278,16 +302,16 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span
</div>
<div class="section" id="release-v7-0-2">
<span id="ref-v702"></span><h2>Release v7.0.2<a class="headerlink" href="#release-v7-0-2" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id4">
-<h3>New Features<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id5">
+<h3>New Features<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>Python-based version</p></li>
</ul>
</div></blockquote>
</div>
-<div class="section" id="id5">
-<h3>Changes<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id6">
+<h3>Changes<a class="headerlink" href="#id6" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>korn shell scripts substituted by Python scripts</p></li>
diff --git a/Documentation/html/dev_guide.html b/Documentation/html/dev_guide.html
index 0c8112c..56d7d21 100644
--- a/Documentation/html/dev_guide.html
+++ b/Documentation/html/dev_guide.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Developer Guide — flex_extract 7.1.1 documentation</title>
+ <title>Developer Guide — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/documentation.html b/Documentation/html/documentation.html
index 9d1a864..3fc7d93 100644
--- a/Documentation/html/documentation.html
+++ b/Documentation/html/documentation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Code-Level Documentation — flex_extract 7.1.1 documentation</title>
+ <title>Code-Level Documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/ecmwf_data.html b/Documentation/html/ecmwf_data.html
index b5ca88a..2f8f1fc 100644
--- a/Documentation/html/ecmwf_data.html
+++ b/Documentation/html/ecmwf_data.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ECMWF Data — flex_extract 7.1.1 documentation</title>
+ <title>ECMWF Data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/evaluation.html b/Documentation/html/evaluation.html
index 5e5e020..b3771fc 100644
--- a/Documentation/html/evaluation.html
+++ b/Documentation/html/evaluation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Evaluation — flex_extract 7.1.1 documentation</title>
+ <title>Evaluation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/genindex.html b/Documentation/html/genindex.html
index 7aa6b98..2bea1d4 100644
--- a/Documentation/html/genindex.html
+++ b/Documentation/html/genindex.html
@@ -9,7 +9,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Index — flex_extract 7.1.1 documentation</title>
+ <title>Index — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/index.html b/Documentation/html/index.html
index 97ce63a..452dcf1 100644
--- a/Documentation/html/index.html
+++ b/Documentation/html/index.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Welcome to the flex_extract Documentation! — flex_extract 7.1.1 documentation</title>
+ <title>Welcome to the flex_extract Documentation! — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -318,27 +318,31 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p>
<li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="dev_guide.html">Developer Guide</a></li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1-2">Release v7.1.2</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#changes">Changes</a></li>
+</ul>
+</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1-1">Release v7.1.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#bug-fixes">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1">Release v7.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#new-features">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#changes">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id1">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-4">Release v7.0.4</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id1">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id2">Bug fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id2">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id3">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-3">Release v7.0.3</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id3">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id4">New Features</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-2">Release v7.0.2</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id4">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id5">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id5">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id6">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v0-1-v6-0">Release v0.1 - v6.0</a></li>
diff --git a/Documentation/html/installation.html b/Documentation/html/installation.html
index 1985aa7..84574bf 100644
--- a/Documentation/html/installation.html
+++ b/Documentation/html/installation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Installation — flex_extract 7.1.1 documentation</title>
+ <title>Installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -285,7 +285,7 @@
<p>The software required to run <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application modes</span></a> and therefore is described in the respective specific installation sections.</p>
<p>Generally speaking, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> requires <a class="reference external" href="https://docs.python.org/3/">Python 3</a> and Fortran together with certain modules / libraries.
We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python’s own package manager <code class="docutils literal notranslate"><span class="pre">pip</span></code> (this may mess up some aspects of your python installation, especially if you use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as root. Think about using virtual environments.).</p>
-<p>Before installing the system packages check the availability with (Debian-based system) <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or (Redhat-based system)``rpm -q <package_name>``. For example:</p>
+<p>Before installing the system packages check the availability with (Debian-based system) <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or (Redhat-based system) <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>. For example:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status
<span class="c1"># or</span>
$ rpm -q libeccodes-dev
@@ -317,12 +317,12 @@ installation has to be done. At the users local side not all software has to be
<div class="section" id="fortran-program-test">
<h3>Fortran program test<a class="headerlink" href="#fortran-program-test" title="Permalink to this headline">¶</a></h3>
<p>To check whether the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> has been compiled and runs properly, it can be applied to a prepared minimal dataset.</p>
-<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Convert/</span></code> directory and execute the Fortran program.</p>
+<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Calc_etadot/</span></code> directory and execute the Fortran program.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Remember that you might have to log in at the ECMWF server if you used the installation for the <strong>remote</strong> or <strong>gateway</strong> mode. There you find the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in your <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory.</p>
</div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Convert
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Calc_etadot
<span class="c1"># execute the Fortran progam without arguments</span>
../../../Source/Fortran/calc_etadot
</pre></div>
diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv
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diff --git a/Documentation/html/py-modindex.html b/Documentation/html/py-modindex.html
index c1f0bff..b68f278 100644
--- a/Documentation/html/py-modindex.html
+++ b/Documentation/html/py-modindex.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Python Module Index — flex_extract 7.1.1 documentation</title>
+ <title>Python Module Index — flex_extract 7.1.2 documentation</title>
@@ -68,7 +68,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/quick_start.html b/Documentation/html/quick_start.html
index 1addb35..651f61a 100644
--- a/Documentation/html/quick_start.html
+++ b/Documentation/html/quick_start.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Usage — flex_extract 7.1.1 documentation</title>
+ <title>Usage — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -226,7 +226,6 @@ ssh -X <ecuid>@ecaccess.ecmwf.int
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># On ECMWF server</span>
-<span class="o">[</span><ecuid>@ecgb11 ~<span class="o">]</span>$ module load python3
<span class="o">[</span><ecuid>@ecgb11 ~<span class="o">]</span>$ <span class="nb">cd</span> flex_extract_vX.X/Run
</pre></div>
</div>
@@ -259,7 +258,7 @@ ssh <user>@<gatewayserver>
<span class="nv">INPUTDIR</span><span class="o">=</span>None
<span class="nv">OUTPUTDIR</span><span class="o">=</span>None
<span class="nv">PP_ID</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.temp'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'jobscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_CERA'</span>
<span class="nv">DEBUG</span><span class="o">=</span><span class="m">0</span>
<span class="nv">REQUEST</span><span class="o">=</span><span class="m">2</span>
@@ -284,10 +283,10 @@ FLEX_EXTRACT JOB SCRIPT IS SUBMITED!
ls -rthl
</pre></div>
</div>
-<p>The last command lists the most recent logs and temporary retrieval directories (usually <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code>, where XXXXX is the process id). Under <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code> a copy of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored under the name <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>, the protocol is stored in the file <code class="docutils literal notranslate"><span class="pre">prot</span></code> and the temporary files as well as the resulting files are stored in a directory <code class="docutils literal notranslate"><span class="pre">work</span></code>. The original name of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored in this new file under parameter <code class="docutils literal notranslate"><span class="pre">controlfile</span></code>.</p>
-<div class="literal-block-wrapper docutils container" id="id5">
-<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pythonXXXXX
+<p>The last command lists the most recent logs and temporary retrieval directories (usually <code class="docutils literal notranslate"><span class="pre">extractXXXXX</span></code>, where XXXXX is the process id). Under <code class="docutils literal notranslate"><span class="pre">extractXXXXX</span></code> a copy of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored under the name <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>, the protocol is stored in the file <code class="docutils literal notranslate"><span class="pre">prot</span></code> and the temporary files as well as the resulting files are stored in a directory <code class="docutils literal notranslate"><span class="pre">work</span></code>. The original name of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored in this new file under parameter <code class="docutils literal notranslate"><span class="pre">controlfile</span></code>.</p>
+<div class="literal-block-wrapper docutils container" id="id2">
+<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id2" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>extractXXXXX
├── CONTROL
├── prot
├── work
@@ -398,8 +397,8 @@ ls -rthl
<p>Additionally, you can find a lot of helpful links to dataset documentations, direct links to specific dataset web catalogues or further general information at the <a class="reference external" href="Ecmwf/ec-links.html">link collection</a> in the ECMWF data section.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is specialised to retrieve a limited number of datasets, namely <em>ERA-Interim</em>, <em>CERA-20C</em>, <em>ERA5</em> and <em>HRES (operational data)</em> as well as the <em>ENS (operational data, 15-day forecast)</em>. The limitation relates mainly to the dataset itself, the stream (what kind of forecast or what subset of dataset) and the experiment number. Mostly, the experiment number is equal to <code class="docutils literal notranslate"><span class="pre">1</span></code> to signal that the actual version should be used.</p>
<p>The next level of differentiation would be the field type, level type and time period. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> currently only supports the main streams for the re-analysis datasets and provides extraction of different streams for the operational dataset. The possibilities of compositions of dataset and stream selection are represented by the current list of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. You can see this in the naming of the example files:</p>
-<div class="literal-block-wrapper docutils container" id="id6">
-<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id3">
+<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id3" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_CERA
CONTROL_CERA.global
CONTROL_CERA.public
@@ -489,7 +488,7 @@ CONTROL_OD.OPER.FC.gauss.highres
<p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency">Information about MARS retrievement</a> for hints about retrieval efficiency and troubleshooting.</p>
</div>
<dl>
-<dt>Pure forecast</dt><dd><p>It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
+<dt>Long forecast</dt><dd><p>It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
The <em>CV</em> field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the <em>CF</em> type since this is available from 1992 (3-hourly) on up to today (1-hourly). <em>CV</em> and <em>CF</em> field types belong to the <em>Ensemble prediction system (ENFO)</em> which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.ENFO.CF.36hours
@@ -540,12 +539,8 @@ CONTROL_OD.ENFO.PF.ens
<dt>Field type and time</dt><dd><p>This combination is very important. It defines the temporal resolution and which field type is extracted on each time step.
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be <code class="docutils literal notranslate"><span class="pre">0</span></code>.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of <code class="docutils literal notranslate"><span class="pre">TYPE</span></code>, <code class="docutils literal notranslate"><span class="pre">TIME</span></code> and <code class="docutils literal notranslate"><span class="pre">STEP</span></code> because the temporal (hourly) resolution with the <code class="docutils literal notranslate"><span class="pre">DTIME</span></code> parameter will select the correct combinations.</p>
-<div class="admonition-todo admonition" id="id2">
-<p class="admonition-title">Todo</p>
-<p>#PS needs to be rephrased</p>
-</div>
-<div class="literal-block-wrapper docutils container" id="id7">
-<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id4">
+<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.</span><a class="headerlink" href="#id4" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
TYPE AN FC FC FC AN FC FC FC
TIME <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span>
@@ -557,8 +552,8 @@ The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of
<dt>Vertical velocity</dt><dd><p>The vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> is not directly available from MARS and has to be calculated.
There are several options for this, and the following parameters are responsible for the selection. See <a class="reference internal" href="Documentation/vertco.html"><span class="doc">Vertical wind</span></a> for a detailed explanation. Using <code class="docutils literal notranslate"><span class="pre">ETADIFF</span> <span class="pre">1</span></code>, <code class="docutils literal notranslate"><span class="pre">OMEGA</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span> <span class="pre">1</span></code> is recommended for debugging and testing only.
Usually, one has to decide between <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code>. <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> where possible, as there is a substantial computational overhead for solving the continuity equation.</p>
-<div class="literal-block-wrapper docutils container" id="id8">
-<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).</span><a class="headerlink" href="#id8" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id5">
+<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GAUSS <span class="m">0</span>
ETA <span class="m">1</span>
ETADIFF <span class="m">0</span>
@@ -571,15 +566,9 @@ OMEGADIFF <span class="m">0</span>
</dd>
<dt>Grid resolution and domain</dt><dd><p>The grid and domain parameters depends on each other. <code class="docutils literal notranslate"><span class="pre">grid</span></code> refers to the grid resolution. It can be given as decimal values (e.g., <code class="docutils literal notranslate"><span class="pre">1.</span></code> meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., <code class="docutils literal notranslate"><span class="pre">1000</span></code> means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the <code class="docutils literal notranslate"><span class="pre">domain</span></code> has to be defined. The extension in longitude or latitude direction must be an integer multiple of <code class="docutils literal notranslate"><span class="pre">grid</span></code>.</p>
-<blockquote>
-<div><div class="admonition-todo admonition" id="id3">
-<p class="admonition-title">Todo</p>
-<p>#PS shouldn’t we explain how to define a domain??</p>
-</div>
-</div></blockquote>
<p>The horizontal resolution for spectral fields is set by the parameter <code class="docutils literal notranslate"><span class="pre">RESOL</span></code>. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol">in this entry of the ECMWF on-line documentation</a> and <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation">this table (also ECMWF documentation)</a>.</p>
-<div class="literal-block-wrapper docutils container" id="id9">
-<div class="code-block-caption"><span class="caption-text">Example setting for a domain covering the northern hemisphere domain with a grid resolution of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id9" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id6">
+<div class="code-block-caption"><span class="caption-text">Example setting for a domain covering the northern hemisphere domain with a grid resolution of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GRID <span class="m">0</span>.25
RESOL <span class="m">799</span>
SMOOTH <span class="m">0</span>
@@ -591,15 +580,9 @@ RIGHT <span class="m">180</span>.
</div>
</div>
</dd>
-<dt>Flux data</dt><dd><p>Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code> is the field type (must be a type of forecast), <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> the forecast starting time, and <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code> the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.</p>
-<blockquote>
-<div><div class="admonition-todo admonition" id="id4">
-<p class="admonition-title">Todo</p>
-<p>#PS for which application would this be typical?</p>
-</div>
-</div></blockquote>
-<div class="literal-block-wrapper docutils container" id="id10">
-<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id10" title="Permalink to this code">¶</a></div>
+<dt>Flux data</dt><dd><p>Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code> is the field type (must be a type of forecast), <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> the forecast starting time, and <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code> the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p>
+<div class="literal-block-wrapper docutils container" id="id7">
+<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
ACCTYPE FC
ACCTIME <span class="m">00</span>/12
diff --git a/Documentation/html/search.html b/Documentation/html/search.html
index 9a1d204..533e755 100644
--- a/Documentation/html/search.html
+++ b/Documentation/html/search.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Search — flex_extract 7.1.1 documentation</title>
+ <title>Search — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js
index a19a783..f73bd59 100644
--- a/Documentation/html/searchindex.js
+++ b/Documentation/html/searchindex.js
@@ -1 +1 @@
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the documentation","Auto-generated documentation for the Fortran programme","Auto-generated documentation for the Python scripts","CONTROL file changes","The compilation job script <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF user credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran makefile for <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The job script <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The installation script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application modes","Program flow","Auto-generated documentation","Disaggregation of flux data","Control & input data","Output data","Overview","Vertical wind","Access modes","Link collection","Hints for data set selection","Available data sets for member-state users","Available data sets for public users","Metrics","Static code analysis","Test cases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Code-Level Documentation","ECMWF Data","Evaluation","Welcome to the <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code> Documentation!","Installation","Usage","Support","ToDos"],titleterms:{"case":29,"class":2,"long":19,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],accept:42,access:22,addit:[0,6,19],adjust:43,agreement:[],analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calc_etadot_nml:13,calcul:21,can:[24,33],cera:43,certain:43,chang:[3,36],changelog:36,check:2,code:[28,34,38],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:4,content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:[],coordin:[],credenti:7,data:[6,17,18,19,24,25,26,34,39,43],dataset:[42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:[],fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],installscript:13,interim:43,issu:[34,44],job:[4,10,43],jobscript:13,known:[34,44],ksh:[4,10],level:[25,38],librari:33,licenc:42,line:0,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:[],oper:43,option:[11,12],other:17,out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],programm:1,proper:43,pure:[],python:2,question:33,quick:[],registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:[],retriev:[],run:11,script:[2,4,10,11,12],section:6,select:[24,43],sequenc:0,set:[15,24,25,26],setup:12,softwar:0,some:[],specif:43,specifi:[],sphinx:0,standard:19,start:[],state:25,submiss:11,submit:[2,11],submitscript:13,support:44,surfac:25,system:44,team:35,temp:[],templat:13,temporari:19,test:[29,30,31,42],testcas:[],third:33,ticket:44,time:6,todo:45,tool:2,uiofil:2,updat:0,usag:[11,12,43],user:[6,7,15,25,26],using:21,veloc:21,version:17,vertic:[6,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}})
\ No newline at end of file
diff --git a/Documentation/html/support.html b/Documentation/html/support.html
index 666510c..aca09f4 100644
--- a/Documentation/html/support.html
+++ b/Documentation/html/support.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Support — flex_extract 7.1.1 documentation</title>
+ <title>Support — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/todo.html b/Documentation/html/todo.html
index 4d320bf..4a64ede 100644
--- a/Documentation/html/todo.html
+++ b/Documentation/html/todo.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ToDos — flex_extract 7.1.1 documentation</title>
+ <title>ToDos — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/For_developers/CONTROLparameter.xls b/For_developers/CONTROLparameter.xls
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diff --git a/For_developers/InstallationParameter.xls b/For_developers/InstallationParameter.xls
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diff --git a/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst b/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
index 7eac32c..214a096 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
@@ -1,14 +1,14 @@
-*********************************************
+*************************************************
The compilation job script ``compilejob.ksh``
-*********************************************
+*************************************************
-The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
+The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``installscript.template`` in the template directory.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
+These individual parameters are marked by a doubled ``$`` sign in ``installscript.template``.
-The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
+The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
@@ -23,7 +23,7 @@ What does the compilation script do?
#. It sets some environment variables for the single session
#. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
#. It untars the tarball into the root directory.
- #. It compiles the Fortran program using ``Makefile``.
+ #. It compiles the Fortran program using ``makefile``.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
@@ -66,21 +66,18 @@ Example ``compilejob.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=${HOME}
export MAKEFILE=makefile_ecgate
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo ${GROUP}
echo ${HOME}
echo ${HOME} | awk -F / '{print $1, $2, $3, $4}'
diff --git a/For_developers/Sphinx/Source/Documentation/Input/examples.rst b/For_developers/Sphinx/Source/Documentation/Input/examples.rst
index f69fd02..8ed3c76 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/examples.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/examples.rst
@@ -35,9 +35,9 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
-.. todo::
+.. note::
- #PS some information to be added.
+ Further information will follow.
.. toctree::
:hidden:
diff --git a/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst b/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
index 6a8b760..a1f43b2 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
@@ -4,12 +4,12 @@ The job script ``job.ksh``
The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
-It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
-This template is generated in the installation process from a ``job.template`` template file.
+It is based on the ``submitscript.template`` template file stored in the ``Templates`` directory.
+This template is generated in the installation process from a ``jobscript.template`` template file.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by ``$$`` in ``job.temp``.
+These individual parameters are marked by ``$$`` in ``jobscript.template``.
The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
@@ -25,14 +25,14 @@ What does the job script do?
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
#. It sets some environment variables for the single session.
#. It creates the directory structure in the user's ``$SCRATCH`` file system.
- #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
+ #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``job.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
#. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
-Example ``jobscript.ksh``
+Example ``job.ksh``
-------------------------
.. code-block:: bash
@@ -67,20 +67,17 @@ Example ``jobscript.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=${TMPDIR}
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
@@ -106,7 +103,7 @@ Example ``jobscript.ksh``
dataset None
date_chunk 3
debug 1
- destination annep@genericSftp
+ destination <specificname>@genericSftp
doubleelda 0
dpdeta 1
dtime 3
@@ -127,7 +124,7 @@ Example ``jobscript.ksh``
gaussian
grib2flexpart 0
grid 1.0/1.0
- inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
install_target None
job_chunk 1
job_template job.temp
@@ -144,7 +141,7 @@ Example ``jobscript.ksh``
omega 0
omegadiff 0
oper 0
- outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
prefix CE
public 0
purefc 0
diff --git a/For_developers/Sphinx/Source/Documentation/Input/run.rst b/For_developers/Sphinx/Source/Documentation/Input/run.rst
index 1e3ad68..21b1ddb 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/run.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/run.rst
@@ -30,8 +30,7 @@ Content of ``run.sh``
.. literalinclude:: ../../../../../Run/run.sh
:language: bash
- :caption: run.sh
-
+ :caption: run.sh
diff --git a/For_developers/Sphinx/Source/Documentation/Input/templates.rst b/For_developers/Sphinx/Source/Documentation/Input/templates.rst
index 786679e..4a26a54 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/templates.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/templates.rst
@@ -7,12 +7,12 @@ In ``flex_extract``, the Python package `genshi <https://genshi.edgewall.org/>`_
.. note::
Do not change anything in these files unless you understand the effects!
-Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
+Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Korn shell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
-convert.nl
-----------
+calc_etadot_nml.template
+-------------------------
This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
It contains all the parameters ``calc_etadot`` needs.
@@ -39,7 +39,7 @@ convert.nl
mdpdeta = $mdpdeta
/
-ecmwf_env.template
+ECMWF_ENV.template
------------------
This template is used to create the ``ECMWF_ENV`` file in the application modes **gateway** and **remote**. It contains the user credentials and gateway server settings for the file transfers.
@@ -51,8 +51,8 @@ ecmwf_env.template
GATEWAY $gateway_name
DESTINATION $destination_name
-compilejob.template
--------------------
+installscript.template
+----------------------
This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
@@ -96,21 +96,18 @@ compilejob.template
case $${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo $${GROUP}
echo $${HOME}
echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
@@ -139,8 +136,8 @@ compilejob.template
fi
-job.temp
---------
+submitscript.template
+---------------------
This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**.
@@ -184,23 +181,20 @@ job.temp
export VERSION=7.1
case $${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
- ;;
- *cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- export SCRATCH=$${TMPDIR}
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
esac
@@ -236,10 +230,10 @@ job.temp
fi
-job.template
-------------
+jobscript.template
+------------------
- This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
+ This template is used to create the template for the execution job script ``submitscript.template`` for ``flex_extract`` in the installation process. A description of the file can be found under ``submitscript.template``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
.. code-block:: ksh
@@ -272,21 +266,18 @@ job.template
export VERSION=$version_number
case $$$${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export PATH=$$$${PATH}:$fp_root_path
;;
*cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=$$$${TMPDIR}
export PATH=$$$${PATH}:$fp_root_path
;;
diff --git a/For_developers/Sphinx/Source/Documentation/disagg.rst b/For_developers/Sphinx/Source/Documentation/disagg.rst
index 64a3e3d..9a51e6b 100644
--- a/For_developers/Sphinx/Source/Documentation/disagg.rst
+++ b/For_developers/Sphinx/Source/Documentation/disagg.rst
@@ -12,16 +12,16 @@ pre-processing has to be applied.
.. _ref-table-fluxpar:
.. csv-table:: Flux fields
- :header: "Short Name", "Name", "Units", "Interpolation Type"
+ :header: "Short Name", "Name", "Units", "Disaggregation"
:align: center
:widths: 5,15,5,10
- LSP, "large-scale precipitation", "m", "modified linear interpolation"
- CP, "convective precipitation", "m", "modified linear interpolation"
- SSHF, "surface sensible heat flux", "J m:math:`^{-2}`", "bicubic interpolation"
- EWSS, "eastward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- SSR, "surface net solar radiation", "J m:math:`^{-2}`", "bicubic interpolation"
+ LSP, "large-scale precipitation", "m", "precipitation "
+ CP, "convective precipitation", "m", "precipitation"
+ SSHF, "surface sensible heat flux", "J m :math:`^{-2}`", "flux"
+ EWSS, "eastward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ NSSS, "northward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ SSR, "surface net solar radiation", "J m :math:`^{-2}`", "flux "
The first step is to *de-accumulate* the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
@@ -42,7 +42,7 @@ Disaggregation for precipitation in older versions
In ``flex_extract`` up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.
In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -160,21 +160,14 @@ Disaggregation for the other flux fields
----------------------------------------------
The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (:math:`F_0, F_1, F_2, F_3`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point :math:`F` is used for linear interpolation of the complete timeseries afterwards.
.. math::
-
- p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
- p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
- p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
- p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.
-
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards.
-.. math::
- p = 8. * p_a + 4. * p_b + 2. * p_c + p_d
+ F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3
diff --git a/For_developers/Sphinx/Source/Documentation/input.rst b/For_developers/Sphinx/Source/Documentation/input.rst
index 0a0e11d..64f3366 100644
--- a/For_developers/Sphinx/Source/Documentation/input.rst
+++ b/For_developers/Sphinx/Source/Documentation/input.rst
@@ -35,8 +35,8 @@ Controlling
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
- With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
- It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
+
+ With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively. It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.
diff --git a/For_developers/Sphinx/Source/Documentation/output.rst b/For_developers/Sphinx/Source/Documentation/output.rst
index 8a25f25..4f6aebf 100644
--- a/For_developers/Sphinx/Source/Documentation/output.rst
+++ b/For_developers/Sphinx/Source/Documentation/output.rst
@@ -80,10 +80,10 @@ Here is an example output which lists the meteorological fields in a single file
35 of 35 messages in CE00010800
-Output files for pure forecast
+Output files for long forecast
------------------------------
-``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
+``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:
.. code-block:: bash
@@ -193,22 +193,12 @@ Example output of a one-day retrieval of CERA-20C data:
4, 24, 40.0/-5.0/30.0/5.0, None, 20000108/to/20000108, 1, , 1.0/1.0, 1, SFC, EP, 000, 141.128/151.128/164.128/165.128/166.128/167.128/168.128/129.128/172.128/027.128/028.128/186.128/187.128/188.128/235.128/139.128/039.128/173.128, , 159, 00, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/ANOG__SL.20000108.23903.23904.grb, 00/03/06/09/12/15/18/21, AN
-VERTICAL.EC
------------
-
-This file contains information describing the vertical discretisation (model levels)
-in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
-
Index file
----------
This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
-.. todo::
-
- #PS NEEDS MORE DESCRIPTION
-
Flux files
----------
diff --git a/For_developers/Sphinx/Source/Documentation/vertco.rst b/For_developers/Sphinx/Source/Documentation/vertco.rst
index fcc1d14..2196482 100644
--- a/For_developers/Sphinx/Source/Documentation/vertco.rst
+++ b/For_developers/Sphinx/Source/Documentation/vertco.rst
@@ -6,8 +6,9 @@ Calculation of vertical velocity and preparation of output files
================================================================
Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
- (i) from the horizontal wind field,
- (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
+
+(i) from the horizontal wind field,
+(ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
@@ -30,6 +31,7 @@ following guidance can be given for choosing the right parameters:
* For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
* For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
+
- For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
- For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
- Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.
diff --git a/For_developers/Sphinx/Source/Installation/gateway.rst b/For_developers/Sphinx/Source/Installation/gateway.rst
index 34764c8..06f50a9 100644
--- a/For_developers/Sphinx/Source/Installation/gateway.rst
+++ b/For_developers/Sphinx/Source/Installation/gateway.rst
@@ -128,7 +128,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<assoc_name>@genericSftp' | DESTINATION='<assoc_name>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR=None |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
diff --git a/For_developers/Sphinx/Source/Installation/local.rst b/For_developers/Sphinx/Source/Installation/local.rst
index 5e20d27..9f9c012 100644
--- a/For_developers/Sphinx/Source/Installation/local.rst
+++ b/For_developers/Sphinx/Source/Installation/local.rst
@@ -16,8 +16,8 @@ Local mode installation
.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
.. _genshi: https://genshi.edgewall.org/
-.. _eccodes for python: https://pypi.org/project/eccodes-python/
-.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _eccodes for python: https://pypi.org/project/eccodes/
+.. _eccodes for conda: https://anaconda.org/conda-forge/python-eccodes
.. _gfortran: https://gcc.gnu.org/wiki/GFortran
.. _fftw3: http://www.fftw.org
.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
@@ -119,6 +119,7 @@ Testing the local environment
=============================
Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell:
+
.. code-block:: python
# check in python3 console
@@ -286,12 +287,13 @@ with an editor and adapt the installation parameters in the section labelled wit
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
+ MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
- JOB_TEMPLATE='job.template'
+ JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
diff --git a/For_developers/Sphinx/Source/Installation/remote.rst b/For_developers/Sphinx/Source/Installation/remote.rst
index 95f0c63..127e2b7 100644
--- a/For_developers/Sphinx/Source/Installation/remote.rst
+++ b/For_developers/Sphinx/Source/Installation/remote.rst
@@ -137,7 +137,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<username>@genericSftp' | DESTINATION='<username>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
@@ -152,8 +152,7 @@ with your own ones (look at any of your files with ``ls -l'' to see uid and gid)
Afterwards, type:
.. code-block:: bash
-
- module load python3
+
./setup.sh
to start the installation. You should see the following on standard output.
diff --git a/For_developers/Sphinx/Source/authors.rst b/For_developers/Sphinx/Source/authors.rst
index 3992e33..5636f8d 100644
--- a/For_developers/Sphinx/Source/authors.rst
+++ b/For_developers/Sphinx/Source/authors.rst
@@ -8,18 +8,24 @@ Developer Team
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: anne.philipp [at] univie.ac.at
+| e-mail: anne.philipp [at] univie.ac.at
-
| Leopold Haimberger
| Department of Meteorology and Geophysics
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: leopold.haimberger [at] univie.ac.at
+| e-mail: leopold.haimberger [at] univie.ac.at
-
+
+| Petra Seibert
+| Institute of Meteorology (BOKU-Met)
+| University of Natural Resources & Life Sciences (BOKU)
+| Gregor-Mendel-Str. 33
+| 1180 Wien, Austria
+| e-mail: petra.seibert ./at/. boku.ac.at
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/For_developers/Sphinx/Source/changelog.rst b/For_developers/Sphinx/Source/changelog.rst
index b3f98e0..ed72fc1 100644
--- a/For_developers/Sphinx/Source/changelog.rst
+++ b/For_developers/Sphinx/Source/changelog.rst
@@ -10,6 +10,25 @@ Changelog
.. _new algorithm: https://www.geosci-model-dev.net/11/2503/2018/
+.. _ref-v712:
+
+Release v7.1.2
+--------------
+
+Changes
+#########
+ * changed naming of template files
+ * separate loading of Python3 module in remote mode is no longer necessary
+ * updated module versions for ECMWF servers
+ * changed names of working directories on ECMWF servers
+ * select makefile automatically regarding application mode if it was not set in ``setup.sh``
+ * updated online documentation
+ * converted most important Fortran code documentation from German to English
+ * deactivate writing of VERTICAL.EC file by Fortran code
+ * adapt and improve Fortran regression test scripts
+ * remove jasper lib from Fortran makefiles
+
+
.. _ref-v711:
Release v7.1.1
diff --git a/For_developers/Sphinx/Source/conf.py b/For_developers/Sphinx/Source/conf.py
index 2a07796..7110349 100644
--- a/For_developers/Sphinx/Source/conf.py
+++ b/For_developers/Sphinx/Source/conf.py
@@ -31,9 +31,9 @@ copyright = u'2020, Anne Philipp, Leopold Haimberger and Petra Seibert'
author = u'Anne Philipp, Leopold Haimberger and Petra Seibert'
# The short X.Y version
-version = u'7.1.1'
+version = u'7.1.2'
# The full version, including alpha/beta/rc tags
-release = u'7.1.1'
+release = u'7.1.2'
# -- General configuration ---------------------------------------------------
diff --git a/For_developers/Sphinx/Source/installation.rst b/For_developers/Sphinx/Source/installation.rst
index 6a0c8a5..97c5cb8 100644
--- a/For_developers/Sphinx/Source/installation.rst
+++ b/For_developers/Sphinx/Source/installation.rst
@@ -139,7 +139,7 @@ The software required to run ``flex_extract`` depends on the :doc:`Documentation
Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
-Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example:
+Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system) ``rpm -q <package_name>``. For example:
.. code-block:: sh
@@ -197,14 +197,14 @@ Fortran program test
To check whether the Fortran program ``calc_etadot`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
-For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
+For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Calc_etadot/`` directory and execute the Fortran program.
.. note::
Remember that you might have to log in at the ECMWF server if you used the installation for the **remote** or **gateway** mode. There you find the ``flex_extract`` root directory in your ``$HOME`` directory.
.. code-block:: bash
- cd Testing/Installation/Convert
+ cd Testing/Installation/Calc_etadot
# execute the Fortran progam without arguments
../../../Source/Fortran/calc_etadot
diff --git a/For_developers/Sphinx/Source/quick_start.rst b/For_developers/Sphinx/Source/quick_start.rst
index baa36ca..3816442 100644
--- a/For_developers/Sphinx/Source/quick_start.rst
+++ b/For_developers/Sphinx/Source/quick_start.rst
@@ -64,7 +64,6 @@ Remote mode
.. code-block:: bash
# On ECMWF server
- [<ecuid>@ecgb11 ~]$ module load python3
[<ecuid>@ecgb11 ~]$ cd flex_extract_vX.X/Run
@@ -103,7 +102,7 @@ Therefore open the ``run.sh`` file and modify the parameter block marked in the
INPUTDIR=None
OUTPUTDIR=None
PP_ID=None
- JOB_TEMPLATE='job.temp'
+ JOB_TEMPLATE='jobscript.template'
CONTROLFILE='CONTROL_CERA'
DEBUG=0
REQUEST=2
@@ -137,12 +136,12 @@ In case the job fails you will receive an email with the subject ``ERROR!`` and
cd $SCRATCH
ls -rthl
-The last command lists the most recent logs and temporary retrieval directories (usually ``pythonXXXXX``, where XXXXX is the process id). Under ``pythonXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
+The last command lists the most recent logs and temporary retrieval directories (usually ``extractXXXXX``, where XXXXX is the process id). Under ``extractXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
.. code-block:: bash
:caption: "Example structure of ``flex_extract`` output directory on ECMWF servers."
- pythonXXXXX
+ extractXXXXX
├── CONTROL
├── prot
├── work
@@ -357,8 +356,8 @@ These files defines the minimum number of parameters necessary to retrieve a dai
Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ for hints about retrieval efficiency and troubleshooting.
-Pure forecast
- It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
+Long forecast
+ It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today (1-hourly). *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!
@@ -417,10 +416,6 @@ Field type and time
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
- .. todo::
-
- #PS needs to be rephrased
-
.. code-block:: bash
:caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
@@ -450,9 +445,6 @@ Grid resolution and domain
The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
- .. todo::
-
- #PS shouldn't we explain how to define a domain??
The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
@@ -469,12 +461,8 @@ Grid resolution and domain
Flux data
- Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
-
- .. todo::
-
- #PS for which application would this be typical?
-
+ Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a ``CONTROL`` file.
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
diff --git a/For_developers/SubmitParameters.xls b/For_developers/SubmitParameters.xls
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--
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