Take a peek at Appendix B. Included there are many examples of input
files for
atoms.inp
uses keywords to describe the inputs. With only
a few exceptions, the keywords are allowed to occur in any order in
the file, and usually have transparent meanings. This structure
allows the input file to be easily read and modified. All keywords
use the syntax:
keyword delimiter value(s) delimiter ...
The delimiter can be:
Most keywords take only one value. Many keywords can be put on one
line (though some keywords require their own line). Internal comments
can be written anywhere in atoms.inp
, which help remind
you what the keywords mean, or how you chose the input
values. Keywords can be in upper, lower, or mixed case.
Here is a summary of keywords and their meanings. The following sections give more detailed explanations for each keyword. Where appropriate, default values are given in brackets.
________________________________________________________________________
* or % or ! | Indicates a comment. |
Title | Title line to write to output file. | no title lines
Space | The space group designation. | no default
A | The first lattice constant. | no default
B | The second lattice constant. | [equal to A]
C | The third lattice constant. | [equal to A]
Alpha | The angle between B and C. | [90.0 deg]
Beta | The angle between C and A. | [90.0 deg]
Gamma | The angle between A and B. | [90.0 deg]
Core | Specifies absorbing atom. | no default
Rmax | Radial size of the cluster. | [5.0 A]
Index | Flag controlling indexing of atom list. | [False]
Shift | Shift coordinates of all atoms. | [0,0,0]
Out | Output file name. | [feff.inp]
Edge | Specifies absorption edge. | [K for Z>=57]
Nitrogen | Flag for fluorescence calculations. | [0.0]
Argon | Flag for fluorescence calculations. | [0.0]
Krypton | Flag for fluorescence calculations. | [0.0]
Feff | Flag for writing feff.inp. | [True]
Geom | Flag for writing geom.dat file. | [False]
Unit | Flag for output file with full unit cell | [False]
P1 | Flag for output file as space group p 1 | [False]
Dopant | Symbols of dopant and site replaced + % | [no dopants]
Atom | Begin atom list on next line. |
Basis | Begin basis list on next line. |
-------------------------------------------------------------------------
Everything after one of these characters on a line in the input file
will be ignored by
Indicates a user-chosen title line which will be written to
feff.inp
.
9 title lines of 72 characters each can be used. Everything on a line
after the keyword title will be included in the title. If keywords
are on the line following title, they will be read as part of the
title, not as separate keywords. The word comment
is synonymous with
title
.
This keyword is followed by the Hermann-Maguin or Schoenflies
designation for the space group. Complete lists of these designations
are are found in Appendix A. Because the Hermann-Maguin designation,
as adapted for the keyboard, includes spaces, this keyword is handled
specially by space
should be on its own line or at
the end of a line.
This specifies the first lattice constant. A must always be specified. In a cubic or rhombohedral space groups, where only one lattice parameter is needed, A is the one to specify.
This specifies the second lattice constant. It is set equal to A unless specified.
This specifies the third lattice constant. It is set equal to A unless specified. In tetragonal, or hexagonal space groups, this is the second lattice constant that must be specified.
This specifies the angle between B and C. Specify the angle in degrees. This is the angle that must be specified for rhombohedral space groups. The default value is 90 deg.
This specifies the angle between C and A. Specify the angle in degrees. The default value is 90 deg. This is the angle that must be specified for monoclinic space groups.
This specifies the angle between A and B. Specify the angle in degrees. The default value is 90 deg for orthogonal groups and 120 deg for hexagonal and trigonal groups.
This specifies the absorbing atom. The value of this keyword must be
a site tag. This atom will be placed at the center of the cluster and
will be used as the central atom in the McMaster and fluorescent
correction calculations. The central atom must be specified by this
keyword. This is a change from early versions of central
is synonymous with core
.
This specifies the maximum radial distance in the cluster of calculated atomic coordinates.
This is a logical flag, thus takes a value of true or false. Along
with the coordinates, the atom list in feff.inp
contains the
symbol of each atom. With the index feature turned off, only the two
letter symbol of each atom is printed. With it turned on, atoms of
the same type will be numbered sequentially according to distance. To
enable this feature, the syntax is
index true
An example: in pure copper, the 12 nearest neighbors will be labeled
Cu01, the 6 next neighbors will be labeled Cu02, and so on. Without
indexing, all the atoms will be labeled Cu.
Moves all atoms in the atom list by the specified amount. This keyword takes three real numbers as its values. The syntax is:
shift xvalue yvalue zvalue
The value of the shift vector is simply added to all fractional atomic
coordinates in the atom list. Read the section on Multiple Origins in
section 3.6 for a discussion of the usefulness of this keyword.
This specifies an output file name other than feff.inp
. It can
be up to 72 characters, so can include a directory path as well as the
file name. If out = list
is specified then a file called
atoms.lis
will be written instead of feff.inp
.
atoms.lis
will contain the title lines and the coordinate list
but none of headers or
This specifies the absorption edge of the central atom. If edge is
not specified, the default value is determined from the Z of the
central atom. For central atoms with Z<=57, the K edge is chosen.
For heavier atoms, the L3 edge is chosen. K, L1, L2, and L3 are the
only values for edge recognized by
This number specifies the percentage by pressure of nitrogen gas
in the I0 chamber in a fluorescence XAFS experiment. Specifying
either this keyword or the argon or krypton keywords tells
This number specifies the percentage by pressure of argon gas in
the I0 chamber in a fluorescence XAFS experiment. Specifying either
this keyword or the nitrogen or krypton keywords tells
This number specifies the percentage by pressure of krypton gas
in the I0 chamber in a fluorescence XAFS experiment. Specifying
either this keyword or the nitrogen or argon keywords tells
This is a logical flag, thus takes a value of true or false. If
true, geom.dat
for use in the
path finder module of geom.dat
is written, the
NOGEOM
card will be written to feff.inp
.
This is a logical flag, thus takes a value of true or false. If true,
unit.dat
contining the atomic
coordinates of all atoms in the unit cell as well as all atoms on the
walls, edges, and corners of the unit cell.
This is a logical flag, thus takes a value of true or false. If true,
p1.inp
. This file is a valid
input file for p 1
,
the monoclinic space group of no internal symmetries. All axes and
angles are explicitly specified in p1.inp
, as are core
,
edge
, rmax
, and all of the title lines.
This is a logical flag, thus takes a value of true or false. By
default it is true and will write out feff.inp
. If it is false,
feff.inp
or geom.dat
.
This keyword specifies the type and percent substitution of a dopant material. The syntax is:
dopant dp tag percentage
Where dp
is the atomic symbol of the doping atom, tag
is
the site tag of the site where the dopant resides, and the percentage
is a real number between 0 and 1 specifying the amount of
substitution. If tag
is an atomic symbol rather than a site tag,
then all sites containing that atomic species will affected.
This must be the last keyword in the input file. If it is not the program will almost certainly stop running. This keyword tells the program to go to the next line and begin reading in the unique atom coordinates. The atom list is a five column, structured list. Column one is the two letter atomic symbol (not the Z number). Columns two through four contain the x, y, and z coordinates of each atom. These numbers are entered as fractions of the a, b, and c axes respectively. The fifth column contains the site tag. See section 2.4 for an explanation of the site tags. The keywords atom and basis are incompatible. If both are specified in an input file, the program will stop running.
This must be the last keyword in the input file. If it is not the
program will almost certainly stop running. This keyword tells the
program to go to the next line and begin reading in the basis atom
coordinates. The basis list is a five column, structured list.
Column one is the two letter atomic symbol (not the Z number).
Columns two through four contain the x, y, and z coordinates of each
atom. These numbers are entered as fractions of the a, b, and c axes
respectively. The fifth column contains the site tag. See section 2.4
for an explanation of the site tags. A basis may be constructed
around an empty site. Specify that site with the word null
rather than an atomic symbol. The keywords atom and basis are
incompatible. If both are specified in an input file, the program
will stop running.
The central atom of the cluster written to feff.inp
must
be explicitly specified with the keyword core. To avoid ambiguity in
a situation involving inequivalent crystallographic sites containing
the same atomic species, the value of this keyword must be a site tag.
The site tags are the user supplied character strings which appear in
the fifth column of the atom or basis list.
Users of Atoms 2.41 and prior versions: This is the most
important difference between
The fifth column of the atom list contains the site tag. The user may
label the sites in any way desired and these labels may be up to 10
characters long. The sites must be labeled uniquely or else
THISATOM
is the same as thisatom
and ThisAtom
.
Here is an example. Note that the the value of core is a tag, not an element symbol.
title YBCO: Y Ba2 Cu3 O7 (1-2-3 structure)
space P M M M
core = Cu1
rmax=5.2 a 3.823 b 3.886 c 11.681
atom
! At.type x y z tag
Y 0.5 0.5 0.5
Ba 0.5 0.5 0.184
Cu 0 0 0 Cu1
Cu 0 0 0.356 Cu2
O 0 0.5 0 O1
O 0 0 0.158 O2
O 0 0.5 0.379 O3
O 0.5 0 0.377 O4
--------------------------------------------
This is the atoms.inp
for superconducting Y Ba2 Cu3 O7. Notice
that the copper and oxygen sites are tagged with unique labels. The
central atom is specified with one of these labels -- the Cu1
site will be at the center of the cluster written to feff.inp
.
The yttrium and barium sites are tagged with the atomic symbol by
default. Since each of these species occupies only one site, there is
no ambiguity in using the atomic symbol as the tag.
In feff.inp
each atom will be identified by its tag, not by its
atomic symbol. Assignment of unique potentials, however, is based on
atomic species. If you wish to assign unique potentials based on
crystallographic considerations, you will need to edit feff.inp
.
The best use of this feature would be to generate an atom list for a structure that is described by a periodic repetition of some large, complex local structure. Clathrates are an excellent example of this.
One very important rule must be followed when using a basis list. The
first atom in the list must correctly represent the desired
translation symmetry. In the case of silicon, the basis must be
translated like the point (0,0,0) in space group F m 3 m
(the
space group of FCC crystals) to yield the diamond structure. Thus the
first atom in the basis list for silicon must be at (0,0,0) or
else the basis will not be expanded correctly.
A basis can be constructed around an empty site, by specifying the
coordinates of the empty site as the first entry in the basis list and
entering the word null
instead of an atomic symbol. The null site
will not appear in the atom list in feff.inp
. The keyword core
may not take null
as a value.
To finish the example of silicon, here are two input files that give the same output:
title Si, fcc with a two atom basis
a = 6.485 space F m 3 m ! space group of fcc
rmax=6.5 core=si1
basis
Si 0.0 0.0 0.0 si1
Si 0.25 0.25 0.25 si2
-----------------------------------------
title Si, diamond structure
a = 6.485 space F d 3 m ! space group of diamond
rmax 6.5
atom
Si 0.125 0.125 0.125
-----------------------------------------
See section 3.7 for an explanation of why the silicon atom in the second example must be at (1/8, 1/8, 1/8) rather than at (0,0,0).
feff.inp
is the list for the undoped structure.
The syntax is:
dopant dp tag percentage
where dp
and tag
are character strings and percentage is a
number between 0 and 1. The value of dp
is the atomic symbol of
the dopant. The value of tag
is the site tag of the site where
the dopant resides. If the value of tag
is an atomic symbol then
all sites containing that atomic species will be doped.
The atomic species specified for a site by the dopant keyword need not
be the minority component. This might be useful for uniquely
specifying the core atom. Vacancies may be introduced by doping
sites with null
.
Analyzing a doped material in fine structure spectroscopies is
complicated. The simple scheme that I describe in this section is
useful for several of the calculations in the code, but is clearly
insufficient for the task of resolving the local structure of a doped
material. That feff.inp
using
the undoped structure is indicative of this.
The path finder in geom.dat
containing
special flags specifying the relevant symmetries. Setting geom =
true
in atoms.inp
will tell geom.dat
file and to place the card NOGEOM
in feff.inp
. This leads
to a large reduction of computation time only in crystals of high
symmetry. In an fcc structure, the reduction in time can be as high
as a factor of about 50. In a structure of lower symmetry, the
savings will rarely be more than a factor of about 4. Use of the
geom.dat generated by geom.dat
file has the same atom
list as the feff.inp
file.
To use the geom.dat
file, it must be located in the directory in
which NOGEOM
card is in
feff.inp
, geom.dat
file and
the atom list in feff.inp
should both remain unmodified, or else
RMAX
can be
changed to limit the extent of the