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bjmorgan/lattice_mc

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File lattice.py has 401 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import numpy as np
import random
import itertools
import sys
 
 
Severity: Minor
Found in lattice_mc/lattice.py - About 5 hrs to fix

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

                r = np.array( [ i * sqrt(3) * spacing + sqrt(3)/2 * spacing, ( j * 3 + 1.5 ) * spacing, 0.0 ] )
    Severity: Major
    Found in lattice_mc/init_lattice.py and 1 other location - About 3 hrs to fix
    lattice_mc/init_lattice.py on lines 72..72

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

                r = np.array( [ i * sqrt(3) * spacing + sqrt(3)/2 * spacing, ( j * 3 + 0.5 ) * spacing, 0.0 ] )
    Severity: Major
    Found in lattice_mc/init_lattice.py and 1 other location - About 3 hrs to fix
    lattice_mc/init_lattice.py on lines 78..78

    File simulation.py has 270 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    from lattice_mc import init_lattice, species, lookup_table
     
    class Simulation:
        """
        Simulation class
    Severity: Minor
    Found in lattice_mc/simulation.py - About 2 hrs to fix

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                  neighbours = [ grid[ i, j, 1 ],
                                 grid[ i, j, 3 ],
                                 np.roll( grid, -1, axis=0 )[ i, j, 3 ] ]
      Severity: Major
      Found in lattice_mc/init_lattice.py and 1 other location - About 2 hrs to fix
      lattice_mc/init_lattice.py on lines 73..75

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

                  neighbours = [ grid[ i, j, 0 ], 
                                 grid[ i, j, 2 ], 
                                 np.roll( grid, -1, axis=0 )[ i, j, 0 ] ]
      Severity: Major
      Found in lattice_mc/init_lattice.py and 1 other location - About 2 hrs to fix
      lattice_mc/init_lattice.py on lines 79..81

      Function potential_jumps has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
      Open

          def potential_jumps( self ):
              """
              All nearest-neighbour jumps not blocked by volume exclusion 
              (i.e. from occupied to neighbouring unoccupied sites).
       
       
      Severity: Minor
      Found in lattice_mc/lattice.py - About 1 hr to fix

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

          @property
          def old_tracer_correlation( self ):
              """
              Deprecated tracer correlation factor for this simulation.
      Severity: Major
      Found in lattice_mc/simulation.py and 1 other location - About 1 hr to fix
      lattice_mc/simulation.py on lines 235..255

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

              along_y = any( [ s2 in s1.p_neighbours for s1 in edges[2] for s2 in edges[3] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 96..96
      lattice_mc/cluster.py on lines 98..98

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

          @property
          def old_collective_correlation( self ):
              """
              Returns the collective correlation factor, f_I
       
       
      Severity: Major
      Found in lattice_mc/simulation.py and 1 other location - About 1 hr to fix
      lattice_mc/simulation.py on lines 181..201

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

              along_x = any( [ s2 in s1.p_neighbours for s1 in edges[0] for s2 in edges[1] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 97..97
      lattice_mc/cluster.py on lines 98..98

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

              along_z = any( [ s2 in s1.p_neighbours for s1 in edges[4] for s2 in edges[5] ] )
      Severity: Major
      Found in lattice_mc/cluster.py and 2 other locations - About 1 hr to fix
      lattice_mc/cluster.py on lines 96..96
      lattice_mc/cluster.py on lines 97..97

      Function connected_sites has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

          def connected_sites( self, site_labels=None ):
              """
              Searches the lattice to find sets of sites that are contiguously neighbouring.
              Mutually exclusive sets of contiguous sites are returned as Cluster objects.
       
       
      Severity: Minor
      Found in lattice_mc/lattice.py - About 1 hr to fix

      Function run has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

          def run( self, for_time=None ):
              """
              Run the simulation.
       
              Args:
      Severity: Minor
      Found in lattice_mc/simulation.py - About 1 hr to fix

      Function generate_nearest_neighbour_lookup_table has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

          def generate_nearest_neighbour_lookup_table( self ):
              """
              Construct a look-up table of relative jump probabilities for a nearest-neighbour interaction Hamiltonian.
       
              Args:
      Severity: Minor
      Found in lattice_mc/lookup_table.py - About 1 hr to fix

      Function enforce_periodic_boundary_conditions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def enforce_periodic_boundary_conditions( self ):
              """
              Ensure that all lattice sites are within the central periodic image of the simulation cell.
              Sites that are outside the central simulation cell are mapped back into this cell.
      Severity: Minor
      Found in lattice_mc/lattice.py - About 55 mins to fix

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                  sites.append( lattice_site.Site( grid[ i, j, 3 ], r, neighbours, 0.0, site_labels[3] ) )
      Severity: Major
      Found in lattice_mc/init_lattice.py and 3 other locations - About 45 mins to fix
      lattice_mc/init_lattice.py on lines 70..70
      lattice_mc/init_lattice.py on lines 76..76
      lattice_mc/init_lattice.py on lines 82..82

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                  sites.append( lattice_site.Site( grid[ i, j, 2 ], r, neighbours, 0.0, site_labels[2] ) )
      Severity: Major
      Found in lattice_mc/init_lattice.py and 3 other locations - About 45 mins to fix
      lattice_mc/init_lattice.py on lines 70..70
      lattice_mc/init_lattice.py on lines 76..76
      lattice_mc/init_lattice.py on lines 88..88

      Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__( self, number, coordinates, neighbours, energy, label, cn_energies=None ):
      Severity: Minor
      Found in lattice_mc/lattice_site.py - About 45 mins to fix

        Function connected_site_pairs has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

            def connected_site_pairs( self ):
                """
                Returns a dictionary of all connections between pair of sites (by site label).
                e.g. for a linear lattice A-B-C will return::
        Severity: Minor
        Found in lattice_mc/lattice.py - About 45 mins to fix
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