Question About atomic coordinate

Posted on : May 03, 2015 (Sun) 12:02:44

by Bin

Dear all
I am confused about how to set "natom" and "atmicx" tags in AkaiKRR,In the Mannuel,i was told "natom" tag means number of atoms in unit cell.but in the sample directory,i found some examples confusing.

for example,given the fe2val from the cif file,we are expected to have fe8v4al4,thus "natom" should specified with 16 atoms,but the example writes 4 atom.
c----------------------fe2val----------------------------------
go data/fe2val
c------------------------------------------------------------
c brvtyp a c/a b/a alpha beta gamma
fcc 10.68 , , , , , ,
c------------------------------------------------------------
c edelt ewidth reltyp sdftyp magtyp record
0.001 1.5 sra mjw mag 2nd
c------------------------------------------------------------
c outtyp bzqlty maxitr pmix
update 4 50 0.015
c------------------------------------------------------------
c ntyp
3
c------------------------------------------------------------
c type ncmp rmt field mxl anclr conc
Fe 1 1 0.0 2 26 100
V 1 1 0.0 2 33 100
Al 1 1 0.0 2 13 100
c------------------------------------------------------------
c natm
4
c------------------------------------------------------------
c atmicx atmtyp
0 0 0 Fe
0.25 0.25 0.25 V
0.5 0.5 0.5 Fe
0.75 0.75 0.75 Al
c------------------------------------------------------------
In this case,I think the "natoms" is not the number of atoms in a unit cell,but the number of atoms of basis,and thus the "atmicx" are corresponding to the atomic position of the atoms of basis.

So what do you think? Am i wrong? Thank you!



Below are the cif file

#(C) 2014 by Fachinformationszentrum Karlsruhe. All rights reserved.
data_57832-ICSD
_database_code_ICSD 57832
_audit_creation_date 2005-04-01
_chemical_name_systematic 'Aluminum iron vanadium (1/2/1)'
_chemical_formula_structural 'Al Fe2 V'
_chemical_formula_sum 'Al1 Fe2 V1'
_chemical_name_structure_type AlCu2Mn
_exptl_crystal_density_diffrn 6.58
_publ_section_title
'Crystal structure of the uranium ternary compound U Fe4 Al8'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Physics Letters A' 1983 98 51 53 PYLAAG
loop_
_publ_author_name
'Stepen' Damm, Yu.'
'Baran, A.'
'Suski, W.'
_cell_length_a 5.762
_cell_length_b 5.762
_cell_length_c 5.762
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 191.3
_cell_formula_units_Z 4
_symmetry_space_group_name_H-M 'F m -3 m'
_symmetry_Int_Tables_number 225
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'z, y, -x'
2 'y, x, -z'
3 'x, z, -y'
4 'z, x, -y'
5 'y, z, -x'
6 'x, y, -z'
7 'z, -y, x'
8 'y, -x, z'
9 'x, -z, y'
10 'z, -x, y'
11 'y, -z, x'
12 'x, -y, z'
13 '-z, y, x'
14 '-y, x, z'
15 '-x, z, y'
16 '-z, x, y'
17 '-y, z, x'
18 '-x, y, z'
19 '-z, -y, -x'
20 '-y, -x, -z'
21 '-x, -z, -y'
22 '-z, -x, -y'
23 '-y, -z, -x'
24 '-x, -y, -z'
25 '-z, -y, x'
26 '-y, -x, z'
27 '-x, -z, y'
28 '-z, -x, y'
29 '-y, -z, x'
30 '-x, -y, z'
31 '-z, y, -x'
32 '-y, x, -z'
33 '-x, z, -y'
34 '-z, x, -y'
35 '-y, z, -x'
36 '-x, y, -z'
37 'z, -y, -x'
38 'y, -x, -z'
39 'x, -z, -y'
40 'z, -x, -y'
41 'y, -z, -x'
42 'x, -y, -z'
43 'z, y, x'
44 'y, x, z'
45 'x, z, y'
46 'z, x, y'
47 'y, z, x'
48 'x, y, z'
49 'z, y+1/2, -x+1/2'
50 'y, x+1/2, -z+1/2'
51 'x, z+1/2, -y+1/2'
52 'z, x+1/2, -y+1/2'
53 'y, z+1/2, -x+1/2'
54 'x, y+1/2, -z+1/2'
55 'z, -y+1/2, x+1/2'
56 'y, -x+1/2, z+1/2'
57 'x, -z+1/2, y+1/2'
58 'z, -x+1/2, y+1/2'
59 'y, -z+1/2, x+1/2'
60 'x, -y+1/2, z+1/2'
61 '-z, y+1/2, x+1/2'
62 '-y, x+1/2, z+1/2'
63 '-x, z+1/2, y+1/2'
64 '-z, x+1/2, y+1/2'
65 '-y, z+1/2, x+1/2'
66 '-x, y+1/2, z+1/2'
67 '-z, -y+1/2, -x+1/2'
68 '-y, -x+1/2, -z+1/2'
69 '-x, -z+1/2, -y+1/2'
70 '-z, -x+1/2, -y+1/2'
71 '-y, -z+1/2, -x+1/2'
72 '-x, -y+1/2, -z+1/2'
73 '-z, -y+1/2, x+1/2'
74 '-y, -x+1/2, z+1/2'
75 '-x, -z+1/2, y+1/2'
76 '-z, -x+1/2, y+1/2'
77 '-y, -z+1/2, x+1/2'
78 '-x, -y+1/2, z+1/2'
79 '-z, y+1/2, -x+1/2'
80 '-y, x+1/2, -z+1/2'
81 '-x, z+1/2, -y+1/2'
82 '-z, x+1/2, -y+1/2'
83 '-y, z+1/2, -x+1/2'
84 '-x, y+1/2, -z+1/2'
85 'z, -y+1/2, -x+1/2'
86 'y, -x+1/2, -z+1/2'
87 'x, -z+1/2, -y+1/2'
88 'z, -x+1/2, -y+1/2'
89 'y, -z+1/2, -x+1/2'
90 'x, -y+1/2, -z+1/2'
91 'z, y+1/2, x+1/2'
92 'y, x+1/2, z+1/2'
93 'x, z+1/2, y+1/2'
94 'z, x+1/2, y+1/2'
95 'y, z+1/2, x+1/2'
96 'x, y+1/2, z+1/2'
97 'z+1/2, y, -x+1/2'
98 'y+1/2, x, -z+1/2'
99 'x+1/2, z, -y+1/2'
100 'z+1/2, x, -y+1/2'
101 'y+1/2, z, -x+1/2'
102 'x+1/2, y, -z+1/2'
103 'z+1/2, -y, x+1/2'
104 'y+1/2, -x, z+1/2'
105 'x+1/2, -z, y+1/2'
106 'z+1/2, -x, y+1/2'
107 'y+1/2, -z, x+1/2'
108 'x+1/2, -y, z+1/2'
109 '-z+1/2, y, x+1/2'
110 '-y+1/2, x, z+1/2'
111 '-x+1/2, z, y+1/2'
112 '-z+1/2, x, y+1/2'
113 '-y+1/2, z, x+1/2'
114 '-x+1/2, y, z+1/2'
115 '-z+1/2, -y, -x+1/2'
116 '-y+1/2, -x, -z+1/2'
117 '-x+1/2, -z, -y+1/2'
118 '-z+1/2, -x, -y+1/2'
119 '-y+1/2, -z, -x+1/2'
120 '-x+1/2, -y, -z+1/2'
121 '-z+1/2, -y, x+1/2'
122 '-y+1/2, -x, z+1/2'
123 '-x+1/2, -z, y+1/2'
124 '-z+1/2, -x, y+1/2'
125 '-y+1/2, -z, x+1/2'
126 '-x+1/2, -y, z+1/2'
127 '-z+1/2, y, -x+1/2'
128 '-y+1/2, x, -z+1/2'
129 '-x+1/2, z, -y+1/2'
130 '-z+1/2, x, -y+1/2'
131 '-y+1/2, z, -x+1/2'
132 '-x+1/2, y, -z+1/2'
133 'z+1/2, -y, -x+1/2'
134 'y+1/2, -x, -z+1/2'
135 'x+1/2, -z, -y+1/2'
136 'z+1/2, -x, -y+1/2'
137 'y+1/2, -z, -x+1/2'
138 'x+1/2, -y, -z+1/2'
139 'z+1/2, y, x+1/2'
140 'y+1/2, x, z+1/2'
141 'x+1/2, z, y+1/2'
142 'z+1/2, x, y+1/2'
143 'y+1/2, z, x+1/2'
144 'x+1/2, y, z+1/2'
145 'z+1/2, y+1/2, -x'
146 'y+1/2, x+1/2, -z'
147 'x+1/2, z+1/2, -y'
148 'z+1/2, x+1/2, -y'
149 'y+1/2, z+1/2, -x'
150 'x+1/2, y+1/2, -z'
151 'z+1/2, -y+1/2, x'
152 'y+1/2, -x+1/2, z'
153 'x+1/2, -z+1/2, y'
154 'z+1/2, -x+1/2, y'
155 'y+1/2, -z+1/2, x'
156 'x+1/2, -y+1/2, z'
157 '-z+1/2, y+1/2, x'
158 '-y+1/2, x+1/2, z'
159 '-x+1/2, z+1/2, y'
160 '-z+1/2, x+1/2, y'
161 '-y+1/2, z+1/2, x'
162 '-x+1/2, y+1/2, z'
163 '-z+1/2, -y+1/2, -x'
164 '-y+1/2, -x+1/2, -z'
165 '-x+1/2, -z+1/2, -y'
166 '-z+1/2, -x+1/2, -y'
167 '-y+1/2, -z+1/2, -x'
168 '-x+1/2, -y+1/2, -z'
169 '-z+1/2, -y+1/2, x'
170 '-y+1/2, -x+1/2, z'
171 '-x+1/2, -z+1/2, y'
172 '-z+1/2, -x+1/2, y'
173 '-y+1/2, -z+1/2, x'
174 '-x+1/2, -y+1/2, z'
175 '-z+1/2, y+1/2, -x'
176 '-y+1/2, x+1/2, -z'
177 '-x+1/2, z+1/2, -y'
178 '-z+1/2, x+1/2, -y'
179 '-y+1/2, z+1/2, -x'
180 '-x+1/2, y+1/2, -z'
181 'z+1/2, -y+1/2, -x'
182 'y+1/2, -x+1/2, -z'
183 'x+1/2, -z+1/2, -y'
184 'z+1/2, -x+1/2, -y'
185 'y+1/2, -z+1/2, -x'
186 'x+1/2, -y+1/2, -z'
187 'z+1/2, y+1/2, x'
188 'y+1/2, x+1/2, z'
189 'x+1/2, z+1/2, y'
190 'z+1/2, x+1/2, y'
191 'y+1/2, z+1/2, x'
192 'x+1/2, y+1/2, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Al0+ 0
Fe0+ 0
V0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
Al1 Al0+ 4 a 0 0 0 . 1. 0
Fe1 Fe0+ 8 c 0.25 0.25 0.25 . 1. 0
V1 V0+ 4 b 0.5 0.5 0.5 . 1. 0
#End of TTdata_57832-ICSD

[Re:01] Question About atomic coordinate

Posted on : May 04, 2015 (Mon) 08:26:47

by Hitoshi

> In this case,I think the "natoms" is not the number of atoms in a unit cell,but the number of atoms of basis,and thus the "atmicx" are corresponding to the atomic position of the atoms of basis.

I think so too.

This arctlie went ah

Posted on : July 09, 2015 (Thu) 08:15:11

by Navid

This arctlie went ahead and made my day.