Upload New File

from mcvine import run_script

import numpy as np

import base.sampleassembly_program as sampleProg

from base.scatterer_xml import grid_sq_kernel

from base.geometry_program import sample_cylinder

from base.xyz_file import generate_xyz_file_H

def run_nomad_cylinder(beam_path, sample_path, cylinder_height, cylinder_radius, sq_path, q_range_start,

                       q_range_end, sampleName, simdir, MS= False, max_scatterering=1,

                       max_interactM_scattering=1,

                       min_neutron_probability=0.03, number_of_neutrons= 1E8,

                       number_of_nodes=10,

                       SE=False, SE_type='cryostat'):

    """

        Run the NOMAD simulation for a cylindrical sample.

        Parameters:

        beam_path (str): Path to the beam file.

        sample_path (str): name of the path where the sample assembly will be created.

        cylinder_height (float): Height of the cylindrical sample.

        cylinder_radius (float): Radius of the cylindrical sample.

        sq_path (str): Path to the S(Q) file.

        q_range_start (float): Starting value of the Q range.

        q_range_end (float): Ending value of the Q range.

        sampleName (str): Name of the sample.

        simdir (str): Directory where the simulation results will be saved.

        max_scatterering (int): Maximum number of scattering loops among scatterers.

        max_interactM_scattering (int): Maximum number of scattering loops for interactM path.

        min_neutron_probability (float): Minimum neutron probability.

        number_of_neutrons (float): Number of neutrons to simulate.

        number_of_nodes (int): Number of nodes to use for the simulation

        SE (bool): Flag to indicate if SE (Sample Environment) is used. Default is False.

        SE_type (str): Type of Sample Environment. Default is 'cryostat'.

        """

    geometry_file_name = f'{sampleName}-geo'

    sample_cylinder(cylinder_radius, cylinder_height, sample_path, geometry_file_name)

    grid_sq_kernel(sq_path, q_range_start, q_range_end, sample_path, sampleName)

    generate_xyz_file_H(sample_path)

    if SE == False:

        scatterers = {

        (f'{sampleName}', f'{sampleName}shape', geometry_file_name, 'H', 'H.xyz', 'xyz'),

        # (name, shape_name, geometry file name, formula, structure file, structurefile type)

    }

    else:

        scatterers = []

        for sampleName in sample_names:

            geometry_file_name = f'{sampleName}-geo'

            scatterers.append((f'{sampleName}', f'{sampleName}shape', geometry_file_name, 'H', 'H.xyz', 'xyz'))

    sampleProg.makeSAXML(sampleName, sample_path, max_scatterering=max_scatterering,

                         max_interactM_scattering=max_interactM_scattering,

                         min_neutron_probability=min_neutron_probability, scatterers=scatterers)

    run_script.run1_mpi(base/Nomad.py, simdir, beam = beam_path, sample_path= sample_path,mutiple_scattering=MS,

                        ncouts =number_of_neutrons, overwrite_datafiles = True, nodes= number_of_nodes)