View source for Atomic positions file format

BigDFT supports atomic files which are of three types.
The first one is a particular generalisation of the traditional <tt>.xyz</tt> format and can be obtained from this via simple modifications. 
The second one permits to define the atomic positions with internal coordinates (bond lengths, angles, ...)
The third one (<tt>.ascii</tt>) is peculiar of BigDFT and [//inac.cea.fr/L_Sim/V_Sim V_Sim]. All these formats work with the two codes.
Compiled with the library [//openbabel.org/wiki/Main_Page Open Babel], BigDFT can accept many various formats as <tt>.cif</tt> (see [//openbabel.org/wiki/List_of_extensions the list of extensions]).


== The <tt>.xyz</tt> format==
By default the atomic input coordinates are in the file <tt>posinp.xyz</tt>. All the input and output files for atomic coordinates are in the <tt>.xyz</tt> format, ''i.e.'' they can be visualized with any standard visualization package and in particular with [//inac.cea.fr/L_Sim/V_Sim V_Sim].

The '''first line contains the number of atoms and then the units''', which are specified by &rsquo;atomic&rsquo;, &rsquo;atomicd0&rsquo; &rsquo;bohr&rsquo; or &rsquo;bohrd0&rsquo; if atomic units are used or by &rsquo;angstroem&rsquo; or &rsquo;angstroemd0&rsquo; if the angström unit is used. &rsquo;d0&rsquo; formats (<tt>1pe24.17</tt> in Fortran) guarantee that not a single bit is lost during write and read of the numbers.

The '''second line contains the boundary conditions''' specified by the keywords &rsquo;free&rsquo; for free boundary conditions, &rsquo;periodic&rsquo; for periodic boundary conditions or &rsquo;surface&rsquo; for surface boundary conditions where the x and z direction have periodic boundary conditions and the y direction free boundary conditions. The keywords &rsquo;periodic and &rsquo;surface&rsquo; have to be followed by 3 real numbers giving the length of the orthorhombic periodic cell. In the case of surface boundary condition the second of these numbers is ignored.

The '''following lines contain the name of the chemical element followed by the 3 Cartesian coordinates'''. The 3 Cartesian coordinates can be followed by optional additional information.

Here is a simple example of an isolated water molecule:
<pre>3  angstroem
free 
O   0.000000    0.000000   -0.065587 
H   0.000000   -0.757136    0.520545
H   0.000000    0.757136    0.520545
</pre>

and an example for a periodic Ag bulk system:
<pre>4   angstroem           
periodic       4.08600000000000030E+00    4.08600000000000030E+00    4.08600000000000030E+00
Ag       0.00000000000000000E+00    0.00000000000000000E+00    0.00000000000000000E+00
Ag       2.04309999999999992E+00    2.04309999999999992E+00    0.00000000000000000E+00
Ag      -0.00000000000000000E+00    2.04309999999999992E+00    2.04309999999999992E+00
Ag       2.04309999999999992E+00   -0.00000000000000000E+00    2.04309999999999992E+00
</pre>

In the case of spin-polarized calculation, the polarization in the region around the atom can be given by an integer. In addition the charge in the region around the atom can be specified. Finally it can be specified if the atom is fully or partially fixed during a geometry optimization. &rsquo;<tt>f</tt>&rsquo; or &rsquo;<tt>fxyz</tt>&rsquo; stands for completely frozen, &rsquo;<tt>fxz</tt>&rsquo; if the atom can only move along the y axis and &rsquo;<tt>fy</tt>&rsquo; if the atom can only move in the XZ plane.
&rsquo;<tt>fx</tt>&rsquo;, &rsquo;<tt>fz</tt>&rsquo;, &rsquo;<tt>fxy</tt>&rsquo;, &rsquo;<tt>fyz</tt>&rsquo; are also some possible choices.
It also possible to specify a plane given by some positive Miller indices where the atom can move as &rsquo;<tt>f110</tt>&rsquo;.
Finally, it is also possible to specify two blocks of atoms (&rsquo;<tt>fb1</tt>&rsquo; and &rsquo;<tt>fb2</tt>&rsquo;) where only the center of mass can move.
Below are some examples:

This hydrogen atom is frozen during the geometry optimization

<pre>  H  1.2  3.4  5.6   f</pre>
This hydrogen atom has a spin up polarization

<pre>  H  1.2  3.4  5.6   1</pre>
This chlorine atom has an additional electron and no spin polarization

<pre>  Cl  1.2  3.4  5.6   0  -1</pre>
Same as above, but also frozen

<pre>  Cl  1.2  3.4  5.6   0  -1   fz</pre>

For each atom, you can also add a [[posinp.xyz#Dictionary | dictionary]] specifying any property you like as for the Mn2 molecule:

<pre>2  atomicd0
Manganese
Mn  0.0 0.0 0.00000 {IGmom: [0.0, 0.0, 1.0]}
Mn  0.0 0.0 5.19674  {IGmom: [0.0, 0.0, -1.0]}
</pre>

== The <tt>.int</tt> format==

The first line contains the number of atoms (mandatory) and the units
(<tt>bohr></tt>

== The <tt>.ascii</tt> format ==

BigDFT can also use another text file format for input (and thus output) atomic positions. Here is its structure:

* 1st line is arbitrary
* 2nd line must contain dxx dyx dyy values
* 3rd line must contain dzx dzy dzz values other lines may contain:
** keywords, with the syntax [#!]keyword: followed by a list of keywords, separated by commas or blank spaces.
** comments beginning with &rsquo;#&rsquo; or &rsquo;!&rsquo;
** x y z name [label] for atomic position and optional labels


dxx dyx dyy dzx dzy dzz values define the box that contains the atoms. The format allows non-orthogonal boxes, but '''BigDFT supports only orthorhombic super-cells, so dyx, dzx and dzy must be zeros'''. When the keyword angdeg is used, the six values contains the three lengths of basis vectors in dxx dyx and dyy, and the three angles (bc, ac, ab) in dzx dzy and dzz.

After the three first mandatory lines, all subsequent lines can be comment lines (ignored), ''i.e.'' empty, containing only blanks, or beginning with ! or with #. '''A non comment line must contain &rsquo;x y z name&rsquo;''', giving the 3 coordinates and the name of the atom. The coordinates of the atoms are given in the orthonormal basis not in the box basis. In case the keyword reduced has been specified, the three coordinates x, y and z are given in the box basis.

The keywords can be positionned anywhere after the first three lines. The following list summurises all available keywords:

* <tt>reduced</tt>: All atomic coordinates are given in reduced coordinates with respect to the box definition.
* <tt>angdeg</tt>: The box definition contains three distances and three angles instead of the classical six projection values.
* <tt>bohr</tt> or <tt>bohrd0</tt>: The units for the distance are Bohr.
* <tt>angstroem</tt> or <tt>angstroemd0</tt>: The units for the distance are Angströms.
* <tt>atomic</tt> or <tt>atomicd0</tt>: The units for the distance are Bohr.
* <tt>periodic</tt>, <tt>surface</tt> or <tt>freeBC</tt>: The periodicity of the system is either 3D, 2D (free direction is y) or 0D.

Additional informations can be provided after the atom names, like for the <tt>.xyz</tt> format.

As for the posinp format, for each atom, you can also add a [[posinp.xyz#Dictionary | dictionary]] specifying any property you like.

here is a example for the graphene sheet with some lines of comments starting with #:
<pre>4.61388         0         40.00
0               0         7.99146
#keyword: reduced
#keyword: atomic
#keyword: surface
# Statistics are valid for all nodes (hidden or not).
# Hidden nodes are printed, but commented.
# Box contains 1 element(s).
# Box contains 4 nodes.
#  | 4 nodes for element 'C'.
 0             0.5               0 C
 0             0.5        0.3333333333 C
 0.5             0.5             0.5 C
 0.5             0.5        0.8333333333 C
</pre>

[[category:manual]]
[[category:input files]]
[[category:output files]]

== Dictionary ==
in order to indicate different quantities as 'IGSpin' (Input Guess Spin with nspin=2) or 'IGmom' (Input Guess moment with nspin=4), it is possible to add a dictionary in yaml format at each atom as:
<pre>
 2  atomicd0
Manganese
Mn  0.0 0.0 0.00000 {IGmom: [0.0, 0.0, 1.0]}
Mn  0.0 0.0 5.19674  {IGmom: [0.0, 0.0, -1.0]}
</pre>

== Pseudo-potentials ==
Chemical elements are identified by their pseudopotential. If an element is for instance denoted by &rsquo;Si&rsquo; in the input file, the element will be described by the file &rsquo;psppar.Si&rsquo; which may be present in the working directory of the BigDFT run. A silicon atom could however also be denoted by &rsquo;Si_lda&rsquo; if there is file &rsquo;psppar.Si_lda. BigDFT supports the GTH and HGH pseudopotentials in the format which can be downloaded from the [//www.abinit.org ABINIT website].

Pseudo-potentials files are not mandatory. If not present, some hard-coded values will be used. Hard-coded values are available for LDA and PBE only.