.\" Man page generated from reStructuredText. . .TH "QP_CREATE_EZFIO" "1" "Jun 15, 2019" "2.0" "Quantum Package" .SH NAME qp_create_ezfio \- | 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. .