General Format of the atomic Section of the Jaguar Input File
- Overview
- Examples
After the &atomic line, the atomic section should list sets of atomic input values. Each of these sets is a free-format table. The first row of the table lists the keywords whose values are to be set for each atom. This row is the column heading row. Subsequent rows list the values for the keywords for each relevant atom. For instance, in the following atomic section:
&atomic atom mass vdw2 H1 2.00 1.20 H2 2.00 1.20 atom vdw2 O 1.55 &
the keywords are atom (the atom label or number), mass (the nuclear mass in amu), and vdw2 (the van der Waals radii for PBF solvation), and the lines for the atoms H1 and H2 specify that these atoms have a nuclear mass of 2.00 amu (deuterium) and solvation van der Waals radii of 1.2 Å, while the line for atom O specifies a solvation van der Waals radius of 1.55 Å for this atom. It is not necessary to list information for atoms that are to be treated in the default manner. Keywords are case insensitive. Columns can be given in any order. All entries in a row should be separated by one or more spaces or tabs, but columns do not need to be aligned.
The atom column must be included in every set of atomic input values. The atom identifiers can be either atom labels (such as H1 or O in the example above) or atom index numbers (such as 2 for the second atom listed in the zmat input). Atom label input is case sensitive.
If you do not want to set a value for a given atom, you can use a “?” or “–” to indicate that the default value should be used. You may leave the values blank for values at the end of the row. For instance, either of the sections below has the same effect as the first atomic section example listed above.
&atomic atom mass vdw2 H1 2.00 1.20 H2 2.00 1.20 O ? 1.55 & &atomic atom vdw2 mass H1 1.20 2.00 H2 1.20 2.00 O 1.55 &
Atoms may be described in more than one set of atomic input values, but the same keyword cannot be used more than once for the same atom. Thus, the following syntax is supported:
&atomic atom basis C1 6-31g* atom formal C1 1 &
but the following syntax is not supported:
&atomic atom basis C1 6-31g* atom basis C1 cc-pVTZ &
To print an atomic section in the restart file that contains information for all atoms, not just some, set the output keyword ip29 to 2. If an atomic section exists or if ip29=2 in the input file, the atomic section is echoed in the output from the program pre.
Single Point Energy Examples
Example: B3LYP-D3/LACV3P single point energy for transition metal complex FeC8S4O4. User-defined charge and multiplicity of the total molecule. Use of the &atomic section to set charge and multiplicity of individual atoms
&gen dftname=b3lyp-d3 basis=lacv3p iuhf=1 molchg=-2 multip=5 & &zmat Fe1 4.2790000000 1.6230000000 0.9160000000 S2 5.1260000000 0.2170000000 -0.8060000000 S3 3.9930000000 -0.1270000000 2.5250000000 S4 5.4270000000 3.5210000000 1.8230000000 S5 2.2710000000 2.7920000000 0.3720000000 O6 1.0340000000 5.8730000000 1.7610000000 O7 3.9540000000 6.5300000000 3.2050000000 O8 5.2370000000 -3.4260000000 -0.9770000000 O9 4.2860000000 -3.6930000000 2.1560000000 C10 4.0070000000 4.4170000000 1.8550000000 C11 2.7590000000 4.1370000000 1.2760000000 C12 2.1290000000 5.3630000000 1.8060000000 C13 3.4980000000 5.6900000000 2.4770000000 C14 4.9190000000 -1.1840000000 0.1370000000 C15 4.4790000000 -1.3210000000 1.4470000000 C16 4.5460000000 -2.8020000000 1.3920000000 C17 4.9880000000 -2.6590000000 -0.0770000000 & &atomic atom formal multip Fe1 +2 5 S2 -1 1 S3 -1 1 S4 -1 1 S5 -1 1 &
$SCHRODINGER/jaguar run -jobname=ene_atomdef_0001 ene-atomdef-0001.in
Calculation of Molecular Properties Examples
Example: Moessbauer spectrum calculation of FeCl5(H2O)2- with B3LYP
&gen mossbauer=1 dftname=b3lyp basis=cc-pvdz multip=6 molchg=-2 nops=1 vshift=0.0 & &zmat Fe1 5.3897000000 2.9179000000 3.3439000000 Cl2 7.0882000000 1.4535000000 4.1314000000 Cl3 3.7609000000 1.4064000000 4.1734000000 Cl4 3.6737000000 4.5069000000 2.9302000000 Cl5 7.0474000000 4.4650000000 2.7828000000 Cl6 5.3231000000 2.0080000000 1.2007000000 O7 5.4927000000 3.7637000000 5.3506000000 H8 5.3019000000 3.2697000000 6.1216000000 H9 4.9612000000 4.5148000000 5.4634000000 & &atomic atom formal multip Fe1 +3 6 Cl2 -1 1 Cl3 -1 1 Cl4 -1 1 Cl5 -1 1 Cl6 -1 1 atom basis Fe1 partridge-1 &
$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0001 prop-moessbauer-0001.in
Example: Moessbauer spectrum calculation of FeCl5(H2O)2- with B3LYP. Use of a non-default value for moss_nuc_quadrupole of 0.18
&gen mossbauer=1 moss_nuc_quadrupole=0.18 dftname=b3lyp basis=cc-pvdz multip=6 molchg=-2 nops=1 vshift=0.0 & &zmat Fe1 5.3897000000 2.9179000000 3.3439000000 Cl2 7.0882000000 1.4535000000 4.1314000000 Cl3 3.7609000000 1.4064000000 4.1734000000 Cl4 3.6737000000 4.5069000000 2.9302000000 Cl5 7.0474000000 4.4650000000 2.7828000000 Cl6 5.3231000000 2.0080000000 1.2007000000 O7 5.4927000000 3.7637000000 5.3506000000 H8 5.3019000000 3.2697000000 6.1216000000 H9 4.9612000000 4.5148000000 5.4634000000 & &atomic atom formal multip Fe1 +3 6 Cl2 -1 1 Cl3 -1 1 Cl4 -1 1 Cl5 -1 1 Cl6 -1 1 atom basis Fe1 partridge-1 &
$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0002 prop-moessbauer-0002.in