pre-finalized validation ntbk

validation/helper.py

@@ -5,21 +5,29 @@ import os
 
 
 
-file_location = "../potentials/AlLi.eam.fs"
+#file_location = "../potentials/AlLi.eam.fs"
 
-with open(file_location, "r") as f:
-    lines = f.readlines()
+#with open(file_location, "r") as f:
+#    lines = f.readlines()
     
-pot_atomcrex = pd.DataFrame({
+pot_eam = pd.DataFrame({
     'Name': ['LiAl_eam'],
-    'Filename': [[os.path.abspath(file_location)]],
+    'Filename': [[os.path.abspath("../potentials/AlLi.eam.fs")]],
     'Model': ["EAM"],
     'Species': [['Li', 'Al']],
     'Config': [['pair_style eam/fs\n', 'pair_coeff * * AlLi.eam.fs Li Al\n']]
 })
 
+pot_ace = pd.DataFrame({
+    'Name': ['LiAl_yace'],
+    'Filename': [[os.path.abspath("../potentials/AlLi.yace")]],
+    'Model': ["ACE"],
+    'Species': [['Al', 'Li']],
+    'Config': [['pair_style pace\n', 'pair_coeff * * AlLi.yace Li Al\n']]
+})
+
 
-potentials_list = [pot_atomcrex]
+potentials_list = [pot_eam,pot_ace]
 
 
 def get_clean_project_name(pot):    

validation/mp_structures/Al2Li3-6021.cif

+# Generated by Catalysthub (Web: http://www.catalysthub.net/)
+data_Al2Li3 
+_symmetry_space_group_name_H-M          'P 1'
+_cell_length_a      4.418698 
+_cell_length_b      4.418698 
+_cell_length_c      5.296002 
+_cell_angle_alpha     65.343769 
+_cell_angle_beta    114.656235 
+_cell_angle_gamma    119.999997 
+loop_ 
+  _space_group_symop_operation_xyz 
+  'x, y, z' 
+loop_ 
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_type_symbol
+    0.801868     0.198134     0.405600 Al
+    0.198133     0.801867     0.594400 Al
+    0.000000     0.000000     0.000000 Li
+    0.402534     0.597467     0.207602 Li
+    0.597467     0.402534     0.792398 Li
\ No newline at end of file

validation/mp_structures/Li9Al4_mp-568404_primitive.cif

+# generated using pymatgen
+data_Li9Al4
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   9.60870096
+_cell_length_b   9.60870096
+_cell_length_c   5.36843891
+_cell_angle_alpha   75.18806097
+_cell_angle_beta   104.81193903
+_cell_angle_gamma   153.09324779
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Li9Al4
+_chemical_formula_sum   'Li9 Al4'
+_cell_volume   216.41468194
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li  Li0  1  0.76710500  0.23289500  0.15740600  1
+  Li  Li1  1  0.69205900  0.30794100  0.52711500  1
+  Li  Li2  1  0.30794100  0.69205900  0.47288500  1
+  Li  Li3  1  0.45644800  0.54355200  0.67414000  1
+  Li  Li4  1  0.23289500  0.76710500  0.84259400  1
+  Li  Li5  1  0.54355200  0.45644800  0.32586000  1
+  Li  Li6  1  0.00000000  0.00000000  0.00000000  1
+  Li  Li7  1  0.08590200  0.91409800  0.64065300  1
+  Li  Li8  1  0.91409800  0.08590200  0.35934700  1
+  Al  Al9  1  0.38570600  0.61429400  0.06594200  1
+  Al  Al10  1  0.61429400  0.38570600  0.93405800  1
+  Al  Al11  1  0.84918000  0.15082000  0.78331600  1
+  Al  Al12  1  0.15082000  0.84918000  0.21668400  1
\ No newline at end of file

validation/mp_structures/LiAl3_mp-10890_primitive.cif

+# generated using pymatgen
+data_LiAl3
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.02558300
+_cell_length_b   4.02558300
+_cell_length_c   4.02558300
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiAl3
+_chemical_formula_sum   'Li1 Al3'
+_cell_volume   65.23585462
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li  Li0  1  0.00000000  0.00000000  0.00000000  1
+  Al  Al1  1  0.50000000  0.50000000  0.00000000  1
+  Al  Al2  1  0.50000000  0.00000000  0.50000000  1
+  Al  Al3  1  0.00000000  0.50000000  0.50000000  1
\ No newline at end of file

validation/mp_structures/LiAl3_mp-975906_primitive.cif

+# generated using pymatgen
+data_LiAl3
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.97579348
+_cell_length_b   4.97579348
+_cell_length_c   4.97579348
+_cell_angle_alpha   132.62107882
+_cell_angle_beta   132.62107882
+_cell_angle_gamma   69.24985159
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiAl3
+_chemical_formula_sum   'Li1 Al3'
+_cell_volume   65.45813345
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li  Li0  1  0.00000000  0.00000000  0.00000000  1
+  Al  Al1  1  0.75000000  0.25000000  0.50000000  1
+  Al  Al2  1  0.25000000  0.75000000  0.50000000  1
+  Al  Al3  1  0.50000000  0.50000000  0.00000000  1
\ No newline at end of file

validation/mp_structures/LiAl_mp-1067_primitive.cif

+# generated using pymatgen
+data_LiAl
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.49468324
+_cell_length_b   4.49468324
+_cell_length_c   4.49468324
+_cell_angle_alpha   60.00000000
+_cell_angle_beta   60.00000000
+_cell_angle_gamma   60.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiAl
+_chemical_formula_sum   'Li2 Al2'
+_cell_volume   64.20698462
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li  Li0  1  0.50000000  0.50000000  0.50000000  1
+  Li  Li1  1  0.75000000  0.75000000  0.75000000  1
+  Al  Al2  1  1.00000000  0.00000000  0.00000000  1
+  Al  Al3  1  0.25000000  0.25000000  0.25000000  1
\ No newline at end of file

validation/mp_structures/LiAl_mp-1079240_primitive.cif

+# generated using pymatgen
+data_LiAl
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.46800190
+_cell_length_b   4.46800190
+_cell_length_c   8.60409900
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiAl
+_chemical_formula_sum   'Li4 Al4'
+_cell_volume   148.75197078
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li  Li0  1  0.66666667  0.33333333  0.91638100  1
+  Li  Li1  1  0.33333333  0.66666667  0.08361900  1
+  Li  Li2  1  0.33333333  0.66666667  0.41638100  1
+  Li  Li3  1  0.66666667  0.33333333  0.58361900  1
+  Al  Al4  1  0.00000000  0.00000000  0.75000000  1
+  Al  Al5  1  0.00000000  0.00000000  0.25000000  1
+  Al  Al6  1  0.66666667  0.33333333  0.25000000  1
+  Al  Al7  1  0.33333333  0.66666667  0.75000000  1
\ No newline at end of file