.. |br| raw:: html

   <br/>

.. _run-checklist:

###############################
Complete this pre-run checklist
###############################

Now that you have created a :ref:`run script <run-script>` for
GEOS-Chem Classic, take a moment to make sure that you have completed
all required setup steps before running your simulation.

.. _run-checklist-first:

================
First-time setup
================

#. If this is your first-time using GEOS-Chem, make sure that you
   :ref:`registered as a new user <rundir-registration>` when you
   created the run directory. |br|
   |br|

#. Make sure that your computational environment meets all of the
   :ref:`hardware <req-hard>` and
   :ref:`software <req-soft>` requirements for GEOS-Chem Classic.

.. _run-checklist-each:

===============
Each-time setup
===============

#. Make sure that you have :ref:`properly configured your
   login environment <env>` (i.e. load necessary software modules
   after login, etc.) |br|
   |br|

#. Create a :ref:`GEOS-Chem Classic run directory <rundir>`,
   and make sure that it is correct for the simulation you wish to
   perform.

   .. attention::

      The initial :ref:`restart file that is included with your run
      directory <restart-files>` does not reflect the actual
      atmospheric state and should only be used to "spin-up" the
      model. We recommend a spin-up period of 6 months to 1 year
      (depending on the type of simulation you are using).

#. :ref:`Edit configuration files <cfg>` to specify the runtime
   behavior of GEOS-Chem Classic..

   .. attention::

      Be aware that GEOS-FP meteorology is an operational
      (i.e. evolving) product that is subject to assimilation
      system updates.

      On the other hand, the MERRA-2 meteorology is a 40+
      year reanalysis product performed with a "frozen" version of the
      NASA GEOS assimilation system.  Thus, `MERRA-2
      <http://wiki.geos-chem.org/MERRA-2>`_ is preferable for studies
      ranging over multiple years or decades.

   .. attention::

      The convection scheme used to generate archived GEOS-FP
      meteorology files changed from RAS to Grell-Freitas starting 01
      June 2020 with impact on vertical transport. Discussion and
      analysis of the impact is available at
      https://github.com/geoschem/geos-chem/issues/1409.

      To fix this issue, different GEOS-Chem convection schemes are
      called based on simulation start time. This ensures
      comparability in GEOS-Chem runs using GEOS-FP fields generated
      using the RAS convection scheme and fields generated using
      Grell-Freitas, but only if the simulation does not cross the 01
      June 2020 boundary. We therefore recommend splitting up GEOS-FP
      runs in time such that a single simulation does not span this
      date. For example, configure one run to end on 01 June 2020 and
      then use its output restart to start another run on 01 June
      2020.. Alternatively consider using MERRA2 which was entirely
      generated with RAS, or GEOS-IT which was entirely generated with
      Grell-Freitas. If you wish to use a GEOS-FP meteorology year
      different from your simulation year please create a GEOS-Chem
      GitHub issue for assistance to avoid accidentally using zero
      convective precipitation flux.

#. :ref:`Configure and build <compile>` the source code into an
   executable file. |br|
   |br|

#. Create a :ref:`GEOS-Chem Classic run script <run-script>` to
   your run directory and edit it for the particulars of your
   simulation and computer system. |br|
   |br|

#. Make sure that your run script contains the proper settings for
   :ref:`OpenMP parallelization <env-files-envvars-parallel>`, either
   by sourcing an environment file, or by manually adding the settings
   to the run script. |br|
   |br|

#. Be aware of :ref:`ways in which you can speed up your GEOS-Chem
   Classic simulations <run-speedup>`.