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| Original file line number | Diff line number | Diff line change |
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| # deformation_utils.py | ||
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| import numpy as np | ||
| from pymatgen.core import Structure, Lattice, Element | ||
| from abipy.core.symmetries import AbinitSpaceGroup | ||
| from pymatgen.symmetry.analyzer import SpacegroupAnalyzer | ||
| from abipy.abio.inputs import AbinitInput | ||
| import re | ||
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| def generate_deformations_volumic(structure, eps_V=0.02, scales=None): | ||
| if scales is None: | ||
| scales = [-1, 0, 1, 2, 3] | ||
| rprim = structure.lattice.matrix | ||
| structures_new = {} | ||
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| for i in scales: | ||
| rprim2 = np.copy(rprim) | ||
| rprim2[:, :] = rprim[:, :] * (1.00 + eps_V * i)**(1/3.) | ||
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| structure2 = structure.copy() | ||
| structure2.lattice = Lattice(rprim2) | ||
| #structure2.scale_lattice(structure2.volume*(1.00 + eps_V * i)) | ||
| namei = int(round(1000 * (1.00 + eps_V * i))) | ||
| formatted_namei = f"{namei:04d}" | ||
| structures_new[formatted_namei] = structure2 | ||
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| return structures_new | ||
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| def generate_deformations(structure , eps=0.005): | ||
| spgrp = AbinitSpaceGroup.from_structure(structure ) | ||
| print (spgrp) | ||
| spgrp_number=spgrp.spgid | ||
| rprim= structure.lattice.matrix | ||
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| rprim2 = np.copy(rprim) | ||
| rprim_new = {} | ||
| structures_new = {} | ||
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| if 1 <= spgrp_number <= 2: | ||
| disp=[[1,1,1,1,1,1], [0,1,1,1,1,1], [2,1,1,1,1,1], [1,0,1,1,1,1], [1,2,1,1,1,1], [1,1,0,1,1,1], | ||
| [1,1,2,1,1,1], [1,1,1,0,1,1], [1,1,1,2,1,1], [1,1,1,1,0,1], [1,1,1,1,2,1], [1,1,1,1,1,0], | ||
| [1,1,1,1,1,2], [0,0,1,1,1,1], [1,0,0,1,1,1], [1,1,0,0,1,1], [1,1,1,0,0,1], [1,1,1,1,0,0], | ||
| [0,1,0,1,1,1], [0,1,1,0,1,1], [0,1,1,1,0,1], [0,1,1,1,1,0], [1,0,1,0,1,1], [1,0,1,1,0,1], | ||
| [1,0,1,1,1,0], [1,1,0,1,0,1], [1,1,0,1,1,0], [1,1,1,0,1,0] , [0 ,0,0,0,0,0]] | ||
| if abs(rprim[1, 0]) > 1e-9 or abs(rprim[2, 0]) > 1e-9 or abs(rprim[2, 1]) > 1e-9: | ||
| print("Warning: The lattice is oriented such that xz =xy =yz =0 .") | ||
| rprim0 = np.copy(rprim) | ||
| a=rprim[0, :] | ||
| b=rprim[1, :] | ||
| c=rprim[2, :] | ||
| norm_a = np.linalg.norm(a) | ||
| norm_b = np.linalg.norm(b) | ||
| norm_c = np.linalg.norm(c) | ||
|
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| # Compute angles between vectors | ||
| cos_ab = np.dot(a, b) / (norm_a * norm_b) | ||
| cos_ac = np.dot(a, c) / (norm_a * norm_c) | ||
| cos_bc = np.dot(b, c) / (norm_b * norm_c) | ||
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| rprim0[0,0] = 1.0 | ||
| rprim0[0,1] = 0.0 | ||
| rprim0[0,2] = 0.0 | ||
| rprim0[1,0] = cos_ab | ||
| rprim0[1,1] = np.sqrt(1-cos_ab**2) | ||
| rprim0[1,2] = 0.0 | ||
| rprim0[2,0] = cos_ac | ||
| rprim0[2,1] = (cos_bc-rprim0[1,0]*rprim0[2,0])/rprim0[1,1] | ||
| rprim0[2,2] = np.sqrt(1.0-rprim0[2,0]**2-rprim0[2,1]**2) | ||
| rprim0[0,:] = rprim0[0,:]*norm_a | ||
| rprim0[1,:] = rprim0[1,:]*norm_b | ||
| rprim0[2,:] = rprim0[2,:]*norm_c | ||
| print("Old rprim:") | ||
| print(rprim) | ||
| print("New rprim:") | ||
| print(rprim0) | ||
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| for pair in disp: | ||
| i,j,k,l,m,n = pair | ||
| rprim2[ :,0] = rprim0[ :,0] * (1.00 + eps * i) + rprim0[ :,1] * (eps * l) +rprim0[ :,2] * (eps * m) | ||
| rprim2[ :,1] = rprim0[ :,1] * (1.00 + eps * j) + rprim0[ :,2] * (eps * n) | ||
| rprim2[ :,2] = rprim0[ :,2] * (1.00 + eps * k) | ||
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| namei = int(round(1000 * (1.00 + eps * i))) | ||
| namej = int(round(1000 * (1.00 + eps * j))) | ||
| namek = int(round(1000 * (1.00 + eps * k))) | ||
| namel = int(round(1000 * (1.00 + eps * l))) | ||
| namem = int(round(1000 * (1.00 + eps * m))) | ||
| namen = int(round(1000 * (1.00 + eps * n))) | ||
| formatted_namei = f"{namei:04d}_{namej:04d}_{namek:04d}_{namel:04d}_{namem:04d}_{namen:04d}" | ||
|
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| structure2=structure.copy() | ||
| structure2.lattice=Lattice(rprim2) | ||
| structures_new[formatted_namei] = structure2 | ||
|
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| return structures_new | ||
| elif 3 <= spgrp_number <= 15: | ||
| disp=[[1,1,1,1], [0,1,1,1], [2,1,1,1], [1,0,1,1], [1,2,1,1], [1,1,0,1], [1,1,2,1], [1,1,1,0], | ||
| [1,1,1,2], [0,0,1,1], [1,0,0,1], [1,1,0,0], [0,1,0,1], [1,0,1,0], [0,1,1,0]] | ||
| if abs(rprim[1, 0]) > 1e-9 or abs(rprim[0, 1]) > 1e-9 or abs(rprim[2, 1]) > 1e-9 or abs(rprim[1, 2]) > 1e-9: | ||
| print("Error: Monoclinic structure with yx=xy=0 and yz=zy=0 lattice required.") | ||
| elif abs(rprim[0, 2]) > 1e-9 : | ||
| print("Warning: The lattice is oriented such that xz = 0.") | ||
| rprim0 = np.copy(rprim) | ||
| a=rprim[0, :] | ||
| b=rprim[1, :] | ||
| c=rprim[2, :] | ||
| norm_a = np.linalg.norm(a) | ||
| norm_b = np.linalg.norm(b) | ||
| norm_c = np.linalg.norm(c) | ||
|
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| # Compute angles between vectors | ||
| cos_ab = np.dot(a, b) / (norm_a * norm_b) | ||
| cos_ac = np.dot(a, c) / (norm_a * norm_c) | ||
| cos_bc = np.dot(b, c) / (norm_b * norm_c) | ||
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| rprim0[0,0] = norm_a | ||
| rprim0[0,2] = 0.0 | ||
| rprim0[1,1] = norm_b | ||
| rprim0[2,0] = norm_c*cos_ac | ||
| rprim0[2,2] = norm_c*np.sqrt(1-cos_ac**2) | ||
| print("Old rprim:") | ||
| print(rprim) | ||
| print("New rprim:") | ||
| print(rprim0) | ||
|
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| for pair in disp: | ||
| i,j,k,l = pair | ||
| rprim2[ :,0] = rprim0[ :,0] * (1.00 + eps * i) +rprim0[ :,2] * (eps * l) | ||
| rprim2[ :,1] = rprim0[ :,1] * (1.00 + eps * j) | ||
| rprim2[ :,2] = rprim0[ :,2] * (1.00 + eps * k) | ||
|
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| namei = int(round(1000 * (1.00 + eps * i))) | ||
| namej = int(round(1000 * (1.00 + eps * j))) | ||
| namek = int(round(1000 * (1.00 + eps * k))) | ||
| namel = int(round(1000 * (1.00 + eps * l))) | ||
| formatted_namei = f"{namei:04d}_{namej:04d}_{namek:04d}_{namel:04d}" | ||
|
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| structure2=structure.copy() | ||
| structure2.lattice=Lattice(rprim2) | ||
| structures_new[formatted_namei] = structure2 | ||
|
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| return structures_new | ||
| elif 16 <= spgrp_number <= 74: | ||
| disp=[[0,0,1],[0,1,0],[1,0,0],[1,1,1],[0,1,1],[2,1,1],[1,0,1],[1,2,1],[1,1,0],[1,1,2]] | ||
| for pair in disp: | ||
| i,j,k = pair | ||
| rprim2[ :,0] = rprim[ :,0] * (1.00 + eps * i) | ||
| rprim2[ :,1] = rprim[ :,1] * (1.00 + eps * j) | ||
| rprim2[ :,2] = rprim[ :,2] * (1.00 + eps * k) | ||
|
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| namei = int(round(1000 * (1.00 + eps * i))) | ||
| namej = int(round(1000 * (1.00 + eps * j))) | ||
| namek = int(round(1000 * (1.00 + eps * k))) | ||
| formatted_namei = f"{namei:04d}_{namej:04d}_{namek:04d}" | ||
|
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| structure2=structure.copy() | ||
| structure2.lattice=Lattice(rprim2) | ||
| structures_new[formatted_namei] = structure2 | ||
|
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| return structures_new | ||
| elif 75 <= spgrp_number <= 194: | ||
| disp=[[0,0],[1,1],[0,1],[2,1],[1,0],[1,2]] | ||
| for pair in disp: | ||
| i, k = pair | ||
| rprim2[ :,0] = rprim[ :,0] * (1.00 + eps * i) | ||
| rprim2[ :,1] = rprim[ :,1] * (1.00 + eps * i) | ||
| rprim2[ :,2] = rprim[ :,2] * (1.00 + eps * k) | ||
|
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| namei = int(round(1000 * (1.00 + eps * i))) | ||
| namek = int(round(1000 * (1.00 + eps * k))) | ||
| formatted_namei = f"{namei:04d}_{namek:04d}" | ||
| rprim_new[formatted_namei] = rprim2 | ||
|
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| structure2=structure.copy() | ||
| structure2.lattice=Lattice(rprim2) | ||
| structures_new[formatted_namei] = structure2 | ||
|
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| return structures_new | ||
| elif 195 <= spgrp_number <= 230: | ||
| for i in range(3): | ||
| rprim2[ :,0] = rprim[ :,0] * (1.00 + eps * i) | ||
| rprim2[ :,1] = rprim[ :,1] * (1.00 + eps * i) | ||
| rprim2[ :,2] = rprim[ :,2] * (1.00 + eps * i) | ||
| namei = int(round(1000 * (1.00 + eps * i))) | ||
| formatted_namei = f"{namei:04d}" | ||
|
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| structure2=structure.copy() | ||
| structure2.lattice=Lattice(rprim2) | ||
| structures_new[formatted_namei] = structure2 | ||
| return structures_new | ||
|
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