From 91c866eee7b0b0024c27f5394eaab366fcc45c8e Mon Sep 17 00:00:00 2001 From: lakshenoy Date: Tue, 15 Aug 2023 16:38:30 +0100 Subject: [PATCH] code feedback corrections --- matscipy/fracture_mechanics/crack.py | 10 +++++----- matscipy/fracture_mechanics/meson.build | 3 +-- matscipy/meson.build | 1 + .../{fracture_mechanics/solvers.py => optimize.py} | 0 matscipy/surface.py | 6 +++--- 5 files changed, 10 insertions(+), 10 deletions(-) rename matscipy/{fracture_mechanics/solvers.py => optimize.py} (100%) diff --git a/matscipy/fracture_mechanics/crack.py b/matscipy/fracture_mechanics/crack.py index 4dfc97a5..6a80aef4 100644 --- a/matscipy/fracture_mechanics/crack.py +++ b/matscipy/fracture_mechanics/crack.py @@ -44,7 +44,7 @@ Voigt_6_to_full_3x3_stress) from matscipy.surface import MillerDirection, MillerPlane from matscipy.neighbours import neighbour_list -from matscipy.fracture_mechanics.solvers import ode12r +from matscipy.optimize import ode12r import matplotlib.pyplot as plt from ase.optimize.precon import Exp, PreconLBFGS @@ -736,7 +736,7 @@ class SinclairCrack: def __init__(self, crk, cryst, calc, k, alpha=0.0, vacuum=6.0, variable_alpha=True, variable_k=False, alpha_scale=None, k_scale=None, - extended_far_field=False,rI=0.0,rIII=0.0,cutoff=0.0): + extended_far_field=False, rI=0.0, rIII=0.0, cutoff=0.0): """ Parameters @@ -1700,9 +1700,9 @@ def strain_err(self,cutoff,seperate_surface=False): mid_cell_x = self.cryst.cell.diagonal()[0] / 2.0 mid_cell_y = self.cryst.cell.diagonal()[1] / 2.0 I_positions = self.cryst.get_positions()[I] - x_criteria = ((I_positions[:,0]-mid_cell_x)<0.5) - y_criteria = ((I_positions[:,1]-mid_cell_y)<((1.5*self.cutoff)))&\ - ((I_positions[:,1]-mid_cell_y)>(-1.5*self.cutoff)) + x_criteria = ((I_positions[:,0] - mid_cell_x) < 0.5) + y_criteria = ((I_positions[:,1] - mid_cell_y) < ((1.5 * self.cutoff)))&\ + ((I_positions[:,1] - mid_cell_y) > (-1.5 * self.cutoff)) surface_mask_full = np.logical_and(x_criteria,y_criteria) bulk_mask_full = np.logical_not(surface_mask_full) surface_mask = np.logical_and(surface_mask_full,mask) diff --git a/matscipy/fracture_mechanics/meson.build b/matscipy/fracture_mechanics/meson.build index 7a01e6df..9cef288d 100644 --- a/matscipy/fracture_mechanics/meson.build +++ b/matscipy/fracture_mechanics/meson.build @@ -7,8 +7,7 @@ python_sources = [ 'crack.py', 'crackpathsel.py', 'energy_release.py', - 'idealbrittlesolid.py', - 'solvers.py' + 'idealbrittlesolid.py' ] # Install pure Python diff --git a/matscipy/meson.build b/matscipy/meson.build index dc597d26..a8e6f488 100644 --- a/matscipy/meson.build +++ b/matscipy/meson.build @@ -28,6 +28,7 @@ python_sources = [ 'numerical.py', 'numpy_tricks.py', 'opls.py', + 'optimize.py', 'precon.py', 'pressurecoupling.py', 'rings.py', diff --git a/matscipy/fracture_mechanics/solvers.py b/matscipy/optimize.py similarity index 100% rename from matscipy/fracture_mechanics/solvers.py rename to matscipy/optimize.py diff --git a/matscipy/surface.py b/matscipy/surface.py index 4fbbd271..dc1abee5 100644 --- a/matscipy/surface.py +++ b/matscipy/surface.py @@ -26,6 +26,7 @@ import numpy as np from numpy.linalg import norm, inv +from ase import units def gcd(a, b): """Calculate the greatest common divisor of a and b""" @@ -327,11 +328,10 @@ def find_surface_energy(symbol,calc,a0,surface,size=(8,1,1),vacuum=10,fmax=0.000 if unit == 'ASE': return [gamma_ase,'ase_units'] else: - from ase import units gamma_SI = (gamma_ase / units.J ) * (units.m)**2 if unit =='J/m^2': - return [gamma_SI,'J/m^2'] + return gamma_SI elif unit == '0.1J/m^2': - return [10*gamma_SI,'0.1J/m^2'] # units required for the fracture code + return 10*gamma_SI # units required for the fracture code else: print('Error: Unsupported unit of surface energy.')