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.TH "QP_CREATE_EZFIO_FROM_XYZ" "1" "Jan 14, 2019" "2.0" "Quantum Package"
.SH NAME
qp_create_ezfio_from_xyz \-  | Quantum Package >
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.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 [FLAGS] (<xyz_file> | <zmt_file>)
Flags :
   \-b [\-au] [\-c int] [\-cart] [\-d float]
   [\-m int] [\-o file] [\-p string] [\-help]
.ft P
.fi
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.UNINDENT
.INDENT 0.0
.TP
.B \-b <basis_name>
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
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.sp
By default, the basis set is obtained from the local database of the \fIQuantum Package\fP\&.
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.TP
.B \-au
If present, input geometry is in atomic units.
.UNINDENT
.INDENT 0.0
.TP
.B \-c <float>
Total charge of the molecule. Default is 0.
.UNINDENT
.INDENT 0.0
.TP
.B \-cart
Compute AOs in the Cartesian basis set (6d, 10f, …)
.UNINDENT
.INDENT 0.0
.TP
.B \-d <float>
Add dummy atoms. x * (covalent radii of the atoms)
.UNINDENT
.INDENT 0.0
.TP
.B \-m <int>
Spin multiplicity (2S+1) of the molecule. Default is 1.
.UNINDENT
.INDENT 0.0
.TP
.B \-o <EZFIO_DIRECTORY>
Name of the created \fI\%EZFIO\fP directory.
.UNINDENT
.INDENT 0.0
.TP
.B \-p <string>
Name of the pseudo\-potential
.UNINDENT
.INDENT 0.0
.TP
.B \-help, \-?
Print the help text and exit
.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:
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.sp
.nf
.ft C
qp_create_ezfio_from_xyz \-b custom.basis molecule.xyz
.ft P
.fi
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.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
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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
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.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
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.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
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.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2018, A. Scemama, E. Giner
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