diff --git a/docs/source/users_guide/qp_create_ezfio_from_xyz.rst b/docs/source/users_guide/qp_create_ezfio_from_xyz.rst index fe980704..71c49982 100644 --- a/docs/source/users_guide/qp_create_ezfio_from_xyz.rst +++ b/docs/source/users_guide/qp_create_ezfio_from_xyz.rst @@ -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 [-c ] [-d ] + qp_create_ezfio [-a] -b [-c ] [-d ] [-h] [-m ] [-o EZFIO_DIR] [-p ] [-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 diff --git a/docs/source/users_guide/quickstart.rst b/docs/source/users_guide/quickstart.rst index e988ef8d..bb702656 100644 --- a/docs/source/users_guide/quickstart.rst +++ b/docs/source/users_guide/quickstart.rst @@ -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: diff --git a/etc/qp.rc b/etc/qp.rc index 832df6e4..ef7489b7 100644 --- a/etc/qp.rc +++ b/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 ) ) diff --git a/man/qp_create_ezfio_from_xyz.1 b/man/qp_create_ezfio_from_xyz.1 deleted file mode 100644 index e51f7aa2..00000000 --- a/man/qp_create_ezfio_from_xyz.1 +++ /dev/null @@ -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 [\-c ] [\-d ] - [\-h] [\-m ] [\-o EZFIO_DIR] [\-p ] [\-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= -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\fP is set to \fBshow\fP, the list of all available basis sets is -displayed. -.UNINDENT -.INDENT 0.0 -.TP -.B \-c, \-\-charge= -Total charge of the molecule. Default is 0. -.UNINDENT -.INDENT 0.0 -.TP -.B \-d, \-\-dummy= -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= -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 , \-\-pseudo= -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. -. diff --git a/ocaml/qp_create_ezfio_from_xyz.ml b/ocaml/qp_create_ezfio.ml similarity index 100% rename from ocaml/qp_create_ezfio_from_xyz.ml rename to ocaml/qp_create_ezfio.ml