mirror of
https://github.com/LCPQ/quantum_package
synced 2024-09-26 19:40:57 +02:00
Renamed qp_create_ezfio
This commit is contained in:
parent
6b18116a7d
commit
dba07af142
@ -1,9 +1,9 @@
|
||||
.. _qp_create_ezfio_from_xyz:
|
||||
.. _qp_create_ezfio:
|
||||
|
||||
qp_create_ezfio_from_xyz
|
||||
========================
|
||||
qp_create_ezfio
|
||||
===============
|
||||
|
||||
.. program:: qp_create_ezfio_from_xyz
|
||||
.. program:: qp_create_ezfio
|
||||
|
||||
This command creates an |EZFIO| directory from a standard `xyz` file or from a
|
||||
`z-matrix` file in Gaussian format.
|
||||
@ -13,7 +13,7 @@ Usage
|
||||
|
||||
.. code:: bash
|
||||
|
||||
qp_create_ezfio_from_xyz [-a] -b <string> [-c <int>] [-d <float>]
|
||||
qp_create_ezfio [-a] -b <string> [-c <int>] [-d <float>]
|
||||
[-h] [-m <int>] [-o EZFIO_DIR] [-p <string>] [-x] [--] FILE
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@ If a file with the same name as the basis set exists, this file will be read.
|
||||
For example, if the file containing the basis set is named ``custom.basis``,
|
||||
and the *xyz* geometry is in ``molecule.xyz``, the following should be used::
|
||||
|
||||
qp_create_ezfio_from_xyz -b custom.basis molecule.xyz
|
||||
qp_create_ezfio -b custom.basis molecule.xyz
|
||||
|
||||
Basis set files should be given in |GAMESS| format, where the full names of the
|
||||
atoms are given, and the basis sets for each element are separated by a blank
|
||||
@ -138,7 +138,7 @@ command should be used
|
||||
|
||||
.. code:: bash
|
||||
|
||||
qp_create_ezfio_from_xyz -b custom.basis -p custom.pseudo molecule.xyz
|
||||
qp_create_ezfio -b custom.basis -p custom.pseudo molecule.xyz
|
||||
|
||||
Pseudo-potential files should be given in a format very close to |GAMESS|
|
||||
format. The first line should be formatted as ``%s GEN %d %d`` where the first
|
||||
|
@ -44,12 +44,12 @@ The file :file:`hcn.xyz` contains::
|
||||
N 0.0 0.0 -1.156
|
||||
|
||||
|
||||
This xyz file is now used with the :ref:`qp_create_ezfio_from_xyz` command to
|
||||
This xyz file is now used with the :ref:`qp_create_ezfio` command to
|
||||
create an |EZFIO| database with the 6-31G basis set:
|
||||
|
||||
.. code:: bash
|
||||
|
||||
qp_create_ezfio_from_xyz -b "6-31G" hcn.xyz -o hcn
|
||||
qp_create_ezfio -b "6-31G" hcn.xyz -o hcn
|
||||
|
||||
The EZFIO database now contains data relative to the nuclear coordinates and the atomic
|
||||
basis set:
|
||||
|
16
etc/qp.rc
16
etc/qp.rc
@ -76,7 +76,7 @@ function qp()
|
||||
qp_reset "$@" ${EZFIO_FILE}
|
||||
;;
|
||||
|
||||
"create_ezfio_from_xyz")
|
||||
"create_ezfio")
|
||||
shift
|
||||
# Replace ':' by spaces
|
||||
for arg in "$@" ; do
|
||||
@ -87,13 +87,13 @@ function qp()
|
||||
_ARGS+=("${arg}") ;;
|
||||
esac
|
||||
done
|
||||
echo qp_create_ezfio_from_xyz "${_ARGS[@]}"
|
||||
NAME=$(qp_create_ezfio_from_xyz "${_ARGS[@]}")
|
||||
echo qp_create_ezfio "${_ARGS[@]}"
|
||||
NAME=$(qp_create_ezfio "${_ARGS[@]}")
|
||||
if [[ -d $NAME ]] ; then
|
||||
[[ -d $EZFIO_FILE ]] && ezfio unset_file
|
||||
ezfio set_file $NAME
|
||||
else
|
||||
qp_create_ezfio_from_xyz -h | more
|
||||
qp_create_ezfio -h | more
|
||||
fi
|
||||
unset _ARGS
|
||||
;;
|
||||
@ -165,7 +165,7 @@ function qp()
|
||||
|
||||
|
||||
function _get_basis_sets () {
|
||||
( qp_create_ezfio_from_xyz -b show \
|
||||
( qp_create_ezfio -b show \
|
||||
| tr ' ' ':' \
|
||||
| while IFS= read -r LINE ; do
|
||||
printf '%s\n' ${LINE}
|
||||
@ -199,9 +199,9 @@ _qp_Complete()
|
||||
COMPREPLY=( $(compgen -W "-o $(\ls)" -- ${cur} ) )
|
||||
return 0
|
||||
;;
|
||||
create_ezfio_from_xyz)
|
||||
create_ezfio)
|
||||
case "${prev}" in
|
||||
create_ezfio_from_xyz)
|
||||
create_ezfio)
|
||||
COMPREPLY=( $(compgen -W "-b -a -c -d -h -m -o -p -x" -- $cur ) )
|
||||
return 0
|
||||
;;
|
||||
@ -254,7 +254,7 @@ _qp_Complete()
|
||||
*)
|
||||
COMPREPLY=( $(compgen -W 'plugins \
|
||||
man \
|
||||
create_ezfio_from_xyz \
|
||||
create_ezfio \
|
||||
convert_output_to_ezfio \
|
||||
-h update' -- $cur ) )
|
||||
|
||||
|
@ -1,234 +0,0 @@
|
||||
.\" Man page generated from reStructuredText.
|
||||
.
|
||||
.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 16, 2019" "2.0" "Quantum Package"
|
||||
.SH NAME
|
||||
qp_create_ezfio_from_xyz \- | Quantum Package >
|
||||
.
|
||||
.nr rst2man-indent-level 0
|
||||
.
|
||||
.de1 rstReportMargin
|
||||
\\$1 \\n[an-margin]
|
||||
level \\n[rst2man-indent-level]
|
||||
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
-
|
||||
\\n[rst2man-indent0]
|
||||
\\n[rst2man-indent1]
|
||||
\\n[rst2man-indent2]
|
||||
..
|
||||
.de1 INDENT
|
||||
.\" .rstReportMargin pre:
|
||||
. RS \\$1
|
||||
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
|
||||
. nr rst2man-indent-level +1
|
||||
.\" .rstReportMargin post:
|
||||
..
|
||||
.de UNINDENT
|
||||
. RE
|
||||
.\" indent \\n[an-margin]
|
||||
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.nr rst2man-indent-level -1
|
||||
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
|
||||
..
|
||||
.sp
|
||||
This command creates an \fI\%EZFIO\fP directory from a standard \fIxyz\fP file or from a
|
||||
\fIz\-matrix\fP file in Gaussian format.
|
||||
.SH USAGE
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
qp_create_ezfio_from_xyz [\-a] \-b <string> [\-c <int>] [\-d <float>]
|
||||
[\-h] [\-m <int>] [\-o EZFIO_DIR] [\-p <string>] [\-x] [\-\-] FILE
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-a, \-\-au
|
||||
If present, input geometry is in atomic units.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-b, \-\-basis=<string>
|
||||
Name of basis set. The basis set is defined as a single string if all the
|
||||
atoms are taken from the same basis set, otherwise specific elements can be
|
||||
defined as follows:
|
||||
.INDENT 7.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
\-b "cc\-pcvdz | H:cc\-pvdz | C:6\-31g"
|
||||
\-b "cc\-pvtz | 1,H:sto\-3g | 3,H:6\-31g"
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.sp
|
||||
By default, the basis set is obtained from the local database of the \fIQuantum Package\fP\&.
|
||||
This option is mandatory.
|
||||
.sp
|
||||
If \fB<string>\fP is set to \fBshow\fP, the list of all available basis sets is
|
||||
displayed.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-c, \-\-charge=<int>
|
||||
Total charge of the molecule. Default is 0.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-d, \-\-dummy=<float>
|
||||
Add dummy atoms (X) between atoms when the distance between two atoms
|
||||
is less than x \etimes \esum R_\emathrm{cov}, the covalent radii
|
||||
of the atoms. The default is x=0, so no dummy atom is added.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-h, \-\-help
|
||||
Print the help text and exit
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-m, \-\-multiplicity=<int>
|
||||
Spin multiplicity 2S+1 of the molecule. Default is 1.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-o, \-\-output=EZFIO_DIR
|
||||
Name of the created \fI\%EZFIO\fP directory.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-p <string>, \-\-pseudo=<string>
|
||||
Name of the pseudo\-potential. Follows the same conventions as the basis set.
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-x, \-\-cart
|
||||
Compute AOs in the Cartesian basis set (6d, 10f, …)
|
||||
.UNINDENT
|
||||
.SH USING CUSTOM ATOMIC BASIS SETS
|
||||
.sp
|
||||
If a file with the same name as the basis set exists, this file will be read.
|
||||
For example, if the file containing the basis set is named \fBcustom.basis\fP,
|
||||
and the \fIxyz\fP geometry is in \fBmolecule.xyz\fP, the following should be used:
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
qp_create_ezfio_from_xyz \-b custom.basis molecule.xyz
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.sp
|
||||
Basis set files should be given in \fI\%GAMESS\fP format, where the full names of the
|
||||
atoms are given, and the basis sets for each element are separated by a blank
|
||||
line. Here is an example
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
HYDROGEN
|
||||
S 3
|
||||
1 13.0100000 0.0196850
|
||||
2 1.9620000 0.1379770
|
||||
3 0.4446000 0.4781480
|
||||
S 1
|
||||
1 0.1220000 1.0000000
|
||||
P 1
|
||||
1 0.7270000 1.0000000
|
||||
|
||||
BORON
|
||||
S 8
|
||||
1 4570.0000000 0.0006960
|
||||
2 685.9000000 0.0053530
|
||||
3 156.5000000 0.0271340
|
||||
4 44.4700000 0.1013800
|
||||
5 14.4800000 0.2720550
|
||||
6 5.1310000 0.4484030
|
||||
7 1.8980000 0.2901230
|
||||
8 0.3329000 0.0143220
|
||||
S 8
|
||||
1 4570.0000000 \-0.0001390
|
||||
2 685.9000000 \-0.0010970
|
||||
3 156.5000000 \-0.0054440
|
||||
4 44.4700000 \-0.0219160
|
||||
5 14.4800000 \-0.0597510
|
||||
6 5.1310000 \-0.1387320
|
||||
7 1.8980000 \-0.1314820
|
||||
8 0.3329000 0.5395260
|
||||
S 1
|
||||
1 0.1043000 1.0000000
|
||||
P 3
|
||||
1 6.0010000 0.0354810
|
||||
2 1.2410000 0.1980720
|
||||
3 0.3364000 0.5052300
|
||||
P 1
|
||||
1 0.0953800 1.0000000
|
||||
D 1
|
||||
1 0.3430000 1.0000000
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.SH USING CUSTOM PSEUDO-POTENTIALS
|
||||
.sp
|
||||
As for the basis set, if a file with the same name as the pseudo\-potential
|
||||
exists, this file will be read. For example, if the file containing the custom
|
||||
pseudo\-potential is named \fBcustom.pseudo\fP, the basis set is named
|
||||
\fBcustom.basis\fP, and the \fIxyz\fP geometry is in \fBmolecule.xyz\fP, the following
|
||||
command should be used
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
qp_create_ezfio_from_xyz \-b custom.basis \-p custom.pseudo molecule.xyz
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.sp
|
||||
Pseudo\-potential files should be given in a format very close to \fI\%GAMESS\fP
|
||||
format. The first line should be formatted as \fB%s GEN %d %d\fP where the first
|
||||
string is the chemical symbol, the first integer is the number of core
|
||||
electrons to be removed and the second integer is LMAX+1 as in \fI\%GAMESS\fP format.
|
||||
The pseudo\-potential for each element are separated by a blank line. Here is
|
||||
an example
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
Ne GEN 2 1
|
||||
3
|
||||
8.00000000 1 10.74945199
|
||||
85.99561593 3 10.19801460
|
||||
\-56.79004456 2 10.18694048
|
||||
1
|
||||
55.11144535 2 12.85042963
|
||||
|
||||
F GEN 2 1
|
||||
3
|
||||
7.00000000 1 11.39210685
|
||||
79.74474797 3 10.74911370
|
||||
\-49.45159098 2 10.45120693
|
||||
1
|
||||
50.25646328 2 11.30345826
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.SH AUTHOR
|
||||
A. Scemama, E. Giner
|
||||
.SH COPYRIGHT
|
||||
2018, A. Scemama, E. Giner
|
||||
.\" Generated by docutils manpage writer.
|
||||
.
|
Loading…
Reference in New Issue
Block a user