Source code for geom.classes.input_class

from geom.classes import parameters
from geom.functions import general, output


[docs]
class input_class:
   """
   Manages user-defined parameters for geometric transformations and structure generation.

   This class stores user inputs related to translation, rotation, structure creation, 
   and other transformations for metal nanoparticles and graphene structures.

   Attributes:
       - Transformation Flags: Enable operations such as translation, rotation, 
         mirroring, and structure generation.
       - Geometry Files: Stores input filenames for molecular structures.
       - Translation & Rotation: Contains direction, distances, angles, and axis information.
       - Structure Generation: Flags and parameters for generating different nanostructures.
       - Miscellaneous: Handles alloy composition, verbosity settings, and file extensions.

   Notes:
       - The full list of attributes is initialized in `__init__()`.
       - Methods validate inputs, read data, and apply transformations.
   """

   def __init__(self):
      """
      Initializes input parameters for geometric transformations and structure generation.
  
      Attributes Initialized:
          - Flags for operations (translation, rotation, mirroring, geometry creation).
          - File handling (input geometry, output file names, temporary directories).
          - Geometric parameters (distances, angles, lattice properties).
          - Structure-specific settings (graphene edge type, core-shell configuration, alloy composition).
      """

      # -- RDKit options

[docs]
      self.rdkit = False


[docs]
      self.rdkit_visualize = False


[docs]
      self.rdkit_visualize_2d = False


[docs]
      self.rdkit_visualize_3d = False


[docs]
      self.rdkit_bw = False


[docs]
      self.rdkit_match = False


[docs]
      self.rdkit_abbreviations = False


[docs]
      self.rdkit_file_conversion = False


[docs]
      self.rdkit_opt = False


[docs]
      self.rdkit_conformers = False

      

[docs]
      self.stereo_annotations = False


[docs]
      self.atom_index = False


[docs]
      self.remove_H = False


[docs]
      self.check_aromaticity = False

      

[docs]
      self.match_smiles = ''


[docs]
      self.rdkit_mol_file = ''


[docs]
      self.rdkit_mol_file_extension = ''


[docs]
      self.rdkit_force_field = ''


[docs]
      self.rdkit_output_file = ''


[docs]
      self.rdkit_confs_ext = '.pdb'



[docs]
      self.rdkit_max_iters = 200


[docs]
      self.rdkit_confs = 50

   

[docs]
      self.rdkit_confs_prune_rms = 0.30      


      # -- Small tasks

[docs]
      self.small_tasks = False

       
      # -- Translate

[docs]
      self.translate = False 


[docs]
      self.translate_controlled_distance = False


[docs]
      self.translate_1 = False


[docs]
      self.translate_center = False

     

[docs]
      self.move_geom_to_000   = False


[docs]
      self.move_geom_1_to_000 = False


[docs]
      self.move_geom_2_to_000 = False



[docs]
      self.distances  = []


[docs]
      self.dir_factor = []



[docs]
      self.file_geom2_translated = ''


[docs]
      self.distances_input = ''


[docs]
      self.geom_file       = ''


[docs]
      self.geom1_file      = ''


[docs]
      self.geom2_file      = ''


[docs]
      self.dir_axis_input  = ''


[docs]
      self.origin_CM       = ''


[docs]
      self.origin_CM_1     = ''


[docs]
      self.origin_CM_2     = '' 



[docs]
      self.direction = 1.0


[docs]
      self.dimer_distance = 0.0


      # -- Minimum distance

[docs]
      self.min_dist = False

      
      # -- Rotate

[docs]
      self.rotate = False


[docs]
      self.rotate_angles = False


[docs]
      self.rotate_1      = False



[docs]
      self.angles = []



[docs]
      self.angles_input = ''


[docs]
      self.file_geom_rotated = ''



[docs]
      self.angle = 0.0

      
      # -- Geometrical center

[docs]
      self.geom_center = False


      # -- Specular geometry

[docs]
      self.geom_specular = False


      # -- Generate structure geometry

[docs]
      self.create_dimer = False


[docs]
      self.create_bowtie = False


[docs]
      self.create_geom = False


[docs]
      self.create_ase_bulk = False


[docs]
      self.gen_3d_mesh = False


[docs]
      self.gen_3d_mesh_sphere = False


[docs]
      self.gen_3d_mesh_rod = False


[docs]
      self.gen_graphene = False


[docs]
      self.gen_core_shell = False


[docs]
      self.gen_sphere = False


[docs]
      self.gen_sphere_core_shell = False


[docs]
      self.gen_rod = False


[docs]
      self.gen_rod_core_shell = False


[docs]
      self.gen_tip = False


[docs]
      self.gen_cone = False


[docs]
      self.gen_icosahedra = False


[docs]
      self.gen_cto = False


[docs]
      self.gen_idh = False


[docs]
      self.gen_pyramid = False


[docs]
      self.gen_pentpyramid = False


[docs]
      self.gen_microscope = False


[docs]
      self.gen_bipyramid = False


[docs]
      self.gen_pencil = False


[docs]
      self.gen_pentbipyramid = False


[docs]
      self.pentbipyramid_type = ''


[docs]
      self.alloy = False



[docs]
      self.mesh_size = 1.0


[docs]
      self.alloy_perc = 0.0


[docs]
      self.elliptic_parabola_a = 1.0 # Modifies stepness along x


[docs]
      self.elliptic_parabola_b = 1.0 # Modifies stepness along y


[docs]
      self.elliptic_parabola_c = 0.0 # Fixed for xy parabolloid


[docs]
      self.z_min = 0.0 


[docs]
      self.z_max = 0.0 


[docs]
      self.z_max_paraboloid = 0.0


[docs]
      self.z_max_pyramid = 0.0 


[docs]
      self.rod_length = 0.0


[docs]
      self.rod_length_in = 0.0


[docs]
      self.rod_length_out = 0.0


[docs]
      self.rod_width = 0.0


[docs]
      self.rod_width_in = 0.0


[docs]
      self.rod_width_out = 0.0


[docs]
      self.bipyramid_width = 0.0


[docs]
      self.bipyramid_length = 0.0


[docs]
      self.side_length = 0.0


[docs]
      self.base_width = 0.0


[docs]
      self.radius     = 0.0


[docs]
      self.radius_in  = 0.0


[docs]
      self.radius_out = 0.0


[docs]
      self.X_length = 0.0


[docs]
      self.Y_length = 0.0


[docs]
      self.sphere_center = [0.0,0.0,0.0]



[docs]
      self.xyz_output = ''


[docs]
      self.mesh_output = ''


[docs]
      self.tmp_folder = ''


[docs]
      self.alloy_string = ''


[docs]
      self.atomtype = ''


[docs]
      self.atomtype_in = ''


[docs]
      self.atomtype_out = ''


[docs]
      self.atomtypes_alloys     = ['ag','au']


[docs]
      self.atomtypes_core_shell = ['ag','au']


[docs]
      self.axes = ["x","y","z"]


[docs]
      self.graphene_structures  = ["rib","disk","ring","triangle"]


[docs]
      self.graphene_structure   = ""


[docs]
      self.graphene_edge_types  = ["armchair","zigzag"]


[docs]
      self.graphene_edge_type   = ""


      # -- Merge geometries

[docs]
      self.merge = False


[docs]
      self.merge_cutoff = 0.0 


      # -- Verbose

[docs]
      self.verbose = False


[docs]
      self.verbose_inp = ''


   # -------------------------------- #
   # ------- Check input case ------- #
   

[docs]
   def check_input_case(self):
      """
      Validates and checks input requirements for selected operations.

      Returns:
          None: Performs necessary checks and raises errors if conditions are not met.

      Notes:
          - Ensures input files exist before processing.
          - Checks file extensions for validity.
          - Validates direction axis input.
          - Ensures selected operations are correctly configured.
      """

      if (self.translate_controlled_distance):
         general.check_file_exists(self.distances_input)
         self.read_input(what='distances')

         general.check_file_exists(self.geom1_file)
         general.check_file_exists(self.geom2_file)

         general.check_file_extension(self.geom1_file,'.xyz')
         general.check_file_extension(self.geom2_file,'.xyz')

         general.check_dir_axis(self)

      elif (self.translate_1):
         general.check_file_exists(self.geom_file)
         general.check_file_extension(self.geom_file,'.xyz')

         general.check_dir_axis(self)

      elif (self.rotate_angles):
         general.check_file_exists(self.angles_input)
         self.read_input(what='angles')

         general.check_file_exists(self.geom_file)
         general.check_file_extension(self.geom_file,'.xyz')

         general.check_dir_axis(self)

      elif (self.rotate_1):
         general.check_file_exists(self.geom_file)
         general.check_file_extension(self.geom_file,'.xyz')

         general.check_dir_axis(self)

      elif (self.min_dist):
         general.check_file_exists(self.geom1_file)
         general.check_file_exists(self.geom2_file)

         general.check_file_extension(self.geom1_file,'.xyz')
         general.check_file_extension(self.geom2_file,'.xyz')

      elif (self.merge):
         general.check_file_exists(self.geom1_file)
         general.check_file_exists(self.geom2_file)

         general.check_file_extension(self.geom1_file,'.xyz')
         general.check_file_extension(self.geom2_file,'.xyz')

      elif (self.geom_center):
         general.check_file_exists(self.geom_file)
         general.check_file_extension(self.geom_file,'.xyz')

      elif (self.geom_specular):
         general.check_file_exists(self.geom_file)
         general.check_file_extension(self.geom_file,'.xyz')

      elif (self.rdkit):
         general.check_file_exists(self.rdkit_mol_file)

         # Extract parameters to check extension
         param = parameters.parameters()
         general.check_file_extension_rdkit(self.rdkit_mol_file, param.rdkit_file_extensions)

         if (self.rdkit_file_conversion): 
            general.check_file_extension_rdkit(self.rdkit_output_file, param.rdkit_file_extensions)
            general.check_equal_extensions(self.rdkit_mol_file_extension, self.rdkit_output_file)  
         
         if (self.rdkit_opt):
            general.check_accepted_parameters(self.rdkit_force_field, param.rdkit_force_fields, label='Force field')
            general.check_accepted_parameters(self.rdkit_output_file[-4:], param.rdkit_file_extensions_opt, label='Optimization saved to file extension')

      elif (self.create_geom):
         if (not self.gen_graphene          and
             not self.gen_sphere            and
             not self.gen_sphere_core_shell and
             not self.gen_rod               and
             not self.gen_rod_core_shell    and
             not self.gen_tip               and 
             not self.gen_pyramid           and
             not self.gen_pentpyramid       and
             not self.gen_cone              and
             not self.gen_microscope        and
             not self.gen_icosahedra        and
             not self.gen_cto               and
             not self.gen_idh               and 
             not self.gen_3d_mesh_sphere    and
             not self.gen_3d_mesh_rod       and
             not self.gen_bipyramid         and
             not self.gen_pencil            and
             not self.gen_pentbipyramid): output.error("Create geom option not recognised.")

         if self.create_ase_bulk:
            general.check_file_exists(self.geom_file)
            general.check_file_extension(self.geom_file,'.xyz')



   # ------------------------------------------- #
   # ------- Read distances/angles input ------- #


[docs]
   def read_input(self,what):
      """
      Reads an input file containing distances or angles.
  
      Args:
          what (str): Specifies whether to read 'distances' or 'angles'.
  
      Returns:
          None: Populates the respective list attribute (`self.distances` or `self.angles`).
  
      Raises:
          RuntimeError: If a blank line or multiple values are found in a single line.
  
      Notes:
          - Reads a file line by line and converts values to floats.
          - Ensures valid input formatting before processing.
      """

      if (what=='distances'):
         with open(self.distances_input) as infile:
            for line in infile:
               if len(line.split()) == 0: output.error(f'blank line found in distances input file "{self.distances_input}"')
               if len(line.split())  > 1: output.error(f'more than one distance found in a single line of input file "{self.distances_input}"')

               self.distances.append(float(line.split()[0])) 

      elif (what=='angles'):
         with open(self.angles_input) as infile:
            for line in infile:
               if len(line.split()) == 0: output.error(f'blank line found in angles input file "{self.angles_input}"')
               if len(line.split())  > 1: output.error(f'more than one angle found in a single line of input file "{self.angles_input}"')

               self.angles.append(float(line.split()[0])) 


   # ---------------------------------------- #
   # ------- Change translation sense ------- #
   

[docs]
   def change_trans_sense(self):
      """
      Reverses the direction factor for translations.

      Returns:
          input_class: The modified `input_class` instance with updated `dir_factor`.

      Notes:
          - Multiplies all direction factors by -1.
          - Used to invert translation direction dynamically.
      """

      self.dir_factor = [-x for x in self.dir_factor] 

      return(self)