From 79748da8435bddaf06a17a2551e31319fb77ae73 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 7 Mar 2019 14:15:49 +0100 Subject: [PATCH] from_xyz suppressed --- ...ezfio_from_xyz.rst => qp_create_ezfio.rst} | 0 man/qp_create_ezfio_from_xyz.1 | 235 ------------------ 2 files changed, 235 deletions(-) rename docs/source/users_guide/{qp_create_ezfio_from_xyz.rst => qp_create_ezfio.rst} (100%) delete mode 100644 man/qp_create_ezfio_from_xyz.1 diff --git a/docs/source/users_guide/qp_create_ezfio_from_xyz.rst b/docs/source/users_guide/qp_create_ezfio.rst similarity index 100% rename from docs/source/users_guide/qp_create_ezfio_from_xyz.rst rename to docs/source/users_guide/qp_create_ezfio.rst diff --git a/man/qp_create_ezfio_from_xyz.1 b/man/qp_create_ezfio_from_xyz.1 deleted file mode 100644 index 1c7219f8..00000000 --- a/man/qp_create_ezfio_from_xyz.1 +++ /dev/null @@ -1,235 +0,0 @@ -.\" Man page generated from reStructuredText. -. -.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Mar 06, 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 [\-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 \-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 \-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 -2019, A. Scemama, E. Giner -.\" Generated by docutils manpage writer. -.