Simulation with molecules only in the pore
=======================================

.. code:: ipython3

    import poresim as ps

Set job inputs for your working station
---------------------------------------

Example Bash file for Horeka:

::

   #!/bin/bash 
   #SBATCH --nodes=SIMULATIONNODES 
   #SBATCH --ntasks-per-node=SIMULATIONPROCS 
   #SBATCH --time=SIMULATIONTIME 
   #SBATCH --job-name=SIMULATIONLABEL 
   #SBATCH --error=SIMULATIONLABEL.e.%J 
   #SBATCH --output=SIMULATIONLABEL.o.%J 

   module load chem/gromacs/2019.6_cpu 

   COMMANDCHANGEDIR

   COMMANDGROMACS

Simulation inputs

.. code:: ipython3

    cpu = 75
    job = {"min": {"file": "data/bash.sh", "nodes": 1, "np": cpu, "wall": "24:00:00"},
           "nvt": {"file": "data/bash.sh", "nodes": 5, "np": cpu, "wall": "24:00:00"},
           "run": {"file": "data/bash.sh", "maxh": 24, "nodes": 5, "np": cpu, "runs": 15, "wall": "24:00:00"}}
    
    param = {"min": {"file": "../Simulation_Inputs/Pore/pore_eq_min.mdp"},
             "nvt": {"file": "../Simulation_Inputs/Pore/pore_eq_nvt.mdp", "param": {"NUMBEROFSTEPS": 500000, "TEMPERATURE_VAL": 353.15}},
             "run": {"file": "../Simulation_Inputs/Pore/pore_prod_run.mdp", "param": {"NUMBEROFSTEPS": 200000000, "TEMPERATURE_VAL": 353.15}}}
    
    cluster_horeka = {"address": "",                    
                      "directory": "xxx",        
                      "queuing": {"add_np": False, "mpi": "$DO_PARALLEL", "shell": "horeka.sh", "submit": "sbatch -p cpuonly "}}

Create a box object with the molecules contained in your system
---------------------------------------------------------------

.. code:: ipython3

    pores = ps.Box("conf4")
    pores.set_label("conf4")
    pores.add_box("../PoreMS/pore.gro")
    pores.add_pore("../PoreMS/pore.yml")
    pores.add_struct("mol_list", "../PoreMS/pore.obj")
    
    # Add gro files 
    pores.add_mol("CAT", "../Molecules/cat.gro", inp=4, section="pore",  kwargs_gmx={"-try": 1000})
    pores.add_mol("EDC", "../Molecules/edc.gro", inp=18, section="res",  kwargs_gmx={"-try": 1000})
    pores.add_mol("IM", "../Molecules/im.gro", inp=311, section="pore", kwargs_gmx={"-try": 50000} )
    pores.add_mol("BF4", "../Molecules/bf4.gro", inp=600, section="pore",  kwargs_gmx={"-try": 50000})
    pores.add_mol("HEP", "../Molecules/1-heptane.gro", inp="fill", mass = 100.21, auto_dens=629.595, section = "res", kwargs_gmx={"-try":1000} )
    
    
    # Add top files 
    pores.add_topol("../PoreMS/master_topol_pore.top", "master")
    pores.add_topol("../Topologies/forcefield_new_red.itp","top")
    pores.add_topol("../Topologies/ffnonbonded_new_red.itp","top")
    pores.add_topol("../Topologies/ffbonded_new.itp","top")
    pores.add_topol("../Surfaces_Molecules/tms.itp","top")
    pores.add_topol("../Surfaces_Molecules/tmsg.itp", "top")
    pores.add_topol("../PoreMS/grid.itp", "top")
    pores.add_topol("../Topologies/cat.itp", "top")
    pores.add_topol("../Topologies/bf4.itp", "top")
    pores.add_topol("../Topologies/im.itp", "top")
    pores.add_topol("../Surfaces_Molecules/im_img_surface.itp", "top")
    pores.add_topol("../Topologies/1-heptane.itp", "top")
    pores.add_topol("../Topologies/educt_oplsaa.itp", "top")
    
    pores.set_job(job)
    pores.set_param(param)

.. note::

   If you only want to put molecules into the pore, it is better to add the larger molecules first 
   to make sure that Gromacs can get them into the pore.


Create simulation objects and generate folder structure
--------------------------------------------------------

.. code:: ipython3

    sim = ps.Simulate("Simulation/pore/conf4-r", pores)  # Single
    sim.set_cluster(cluster_horeka)
    sim.generate()


``Finished simulation folder - conf4-r ...``

Image of the system after filling the box
-----------------------------------------

Inside view of the pore after running construct.sh.
Colour code: catalyst, red; ionic anion, orange; ionic kation (on pore surface), green; ionic kation, blue; rectant, grey; heptane not shown.

.. figure::  /pics/pore_il.pdf
      :align: center
      :width: 70%
      :name: fig1