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