pencil.pipelines.clonesimulations
=================================

.. py:module:: pencil.pipelines.clonesimulations


Functions
---------

.. autoapisummary::

   pencil.pipelines.clonesimulations.clone_sims
   pencil.pipelines.clonesimulations.clone_sims_from_obj


Module Contents
---------------

.. py:function:: clone_sims(simset, simsdir=None)

   clone_sims(simset, simsdir=None)

   Create a set of simulation directories from a dictionary object, simset,
   which contains the list of parameters to combine across set of clones.

   :param simset: Parameters to combine across set of clones.
   :type simset: dictionary
   :param simsdir: Root directory for collection of clone simulations.
   :type simsdir: string

   :returns: * *Set of uncompiled and unexecuted simulation run directories with*
             * *parameters updated.*

   .. rubric:: Notes

   It is assumed that the user is working in the compiled source directory.

   .. rubric:: Examples

   >>> simsdir = '/path/to/set_of_clones'
   >>> params = pencil.pipelines.parameter_table('example_filename.txt')
   >>> params = user_own_trim_table(params)#See pc.pipelines.trim_table
   >>> simset = pencil.pipelines.make_sims_dict(params)
   >>> clone_sims(simset,simsdir=simsdir)


.. py:function:: clone_sims_from_obj(simset, simsdir='..', template_sim=None, specify_nml=True)

   clone_sims_from_obj(simset, simsdir="..", template_sim=None, specify_nml=True):

   Create a set of simulation directories from a dictionary object, simset,
   which contains the list of parameters to combine across set of clones.
   This differs from the clone_sims function in that it is more configurable,
   and uses the native Python way of copying the sim.

   :param simset: Parameters to combine across set of clones.
   :type simset: dictionary
   :param simsdir: Root directory for collection of clone simulations.
   :type simsdir: string
   :param template_sim: A pencil simulation object (returned by pc.get_sim).
                        If not specified, the simulation in the current directory will be used.
   :type template_sim: obj
   :param specify_nml: Whether, for files like run.in, you also specify the namelist in simset.
                       If so, f90nml will be directly used to write the value. If not, the
                       change_value_in_file function will be used even for these files.
   :type specify_nml: bool

   :returns: * *Set of unexecuted simulation run directories with*
             * *parameters updated.*

   .. rubric:: Example

   >>> template_sim = pc.get_sim("simulation_to_clone")
   >>> template_sim.optionals.append("job.pbs") #A job submission script which
   ... #one wants to copy along with the other simulation files.
   >>> params = pc.pipelines.parameter_table("example_filename.txt")
   >>> simset = pc.pipelines.make_sims_dict(params)
   >>> pc.pipelines.clone_sims_from_obj(simset, template_sim=template_sim, simsdir=".")