Basis, Grid, Dealiasing Function, and Charge Usage for Individual Atoms

  • Overview
  • Examples

The basis keyword allows you to specify the basis sets used to treat particular atoms. The string provided to describe the basis set should be chosen from the first column of the tables in Basis Sets. Lowercase or uppercase letters can be used. Polarization and diffuse functions can be added by appending *, **, +, or ++ immediately after the basis name. The meaning of these symbols is also described in Basis Sets.

Three other keywords shown in Table 1 allow you to specify whether to include grid points, dealiasing functions, or nuclear charges for listed atoms. The values “n,” “no,” “none,” and “only” are not case sensitive. You can use the atomic section to specify counterpoise atoms, and that settings in the atomic section take precedence over Z‑matrix counterpoise input. In the atomic section, counterpoise atoms are indicated by using an entry of “n” in the column entitled “charge” (see Table 1). Also, note that any other word or letter, such as the “Y” entries that may appear in restart files, indicates that the grid, dealiasing function, or charged particles for that atom are included (the usual default for the grid, daf, and charge keywords).

Table 1. Keywords for listing basis, grid, dealiasing function, and charge information for individual atoms in an atomic section

Keyword

Value

Description

basis

n, no, or none

Use no basis functions on atom

 

basis-name

Use basis functions from specified basis set on atom

grid

n, no, or none

Do not include any grid points on atom

 

only

Include grid points on atom, but no basis functions, dealiasing functions, or nuclear charge

daf

n, no, or none

Do not include any dealiasing functions on atom

 

only

Include dealiasing functions on atom, but no basis functions, grid points, or nuclear charge

charge

n, no, or none

Treat atom as a counterpoise atom—do not include nucleus or electrons for atom

 

only

Include nuclear charge on atom, but no basis functions, grid points, or dealiasing functions

Single Point Energy Examples

Example input file (ene-atomdef-0001.in):

&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
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=ene_atomdef_0001 ene-atomdef-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: ene-atomdef-0001.in
Output files

Example input file (ene-atomdef-0002.in):

&gen
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&
&atomic
atom basis
O1   cc-pVDZ
H2   6-31G**
H3   6-31G**
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=ene_atomdef_0002 ene-atomdef-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: ene-atomdef-0002.in
Output files

Note: The cc-pVDZ (for H) and cc-pVDZ-PP (for I) basis sets were individually downloaded from the Basis Set Exchange repository (see https://www.basissetexchange.org) and then placed in the custom basis set file. The cc-pVDZ-PP basis set for I treats core electrons with an effective core potential (ECP). Note that this calculation can be run in Jaguar directly by just setting `basis=cc-pVDZ-PP` in the `&gen` section; this input is just for illustrative purposes. The basis set file may reside anywhere on disk; the path in `BASISFILE` just has to point to it. Note that if a custom basis set set is supplied, than all basis sets must be defined in that file. Last, the pseudospectral approximation is turned off when using a custom basis set (`nops=1` set).

Example input file (ene-custom_basis-0002.in):

BASISFILE:custom.basis
&gen
isymm=0
dftname=b3lyp
&
&zmat
I1      0.0000000000000   0.0000000000000   0.0000000000000
H2      0.1265430000000   0.2665090000000  -1.7002030000000
&
&atomic
atom  basis
I1    cc-pVTZ-PP_BSE
H2    cc-pVTZ_BSE
&

Example input file (custom.basis):

BASIS cc-pVTZ_BSE 5D
H
S 0 1
      3.258000D-01           1.000000D+00
S 0 5
      3.387000D+01           6.068000D-03
      5.095000D+00           4.530800D-02
      1.159000D+00           2.028220D-01
      3.258000D-01           5.039030D-01
      1.027000D-01           3.834210D-01
S 0 1
      1.027000D-01           1.000000D+00
P 0 1
      1.407000D+00           1.000000D+00
P 0 1
      3.880000D-01           1.000000D+00
D 0 1
      1.057000D+00           1.0000000
****
C
S 0 10
      8.236000D+03           5.310000D-04
      1.235000D+03           4.108000D-03
      2.808000D+02           2.108700D-02
      7.927000D+01           8.185300D-02
      2.559000D+01           2.348170D-01
      8.997000D+00           4.344010D-01
      3.319000D+00           3.461290D-01
      9.059000D-01           3.937800D-02
      3.643000D-01          -8.983000D-03
      1.285000D-01           2.385000D-03
S 0 1
      9.059000D-01           1.000000D+00
S 0 10
      8.236000D+03          -1.130000D-04
      1.235000D+03          -8.780000D-04
      2.808000D+02          -4.540000D-03
      7.927000D+01          -1.813300D-02
      2.559000D+01          -5.576000D-02
      8.997000D+00          -1.268950D-01
      3.319000D+00          -1.703520D-01
      9.059000D-01           1.403820D-01
      3.643000D-01           5.986840D-01
      1.285000D-01           3.953890D-01
S 0 1
      1.285000D-01           1.000000D+00
P 0 1
      3.827000D-01           1.000000D+00
P 0 5
      1.871000D+01           1.403100D-02
      4.133000D+00           8.686600D-02
      1.200000D+00           2.902160D-01
      3.827000D-01           5.010080D-01
      1.209000D-01           3.434060D-01
P 0 1
      1.209000D-01           1.000000D+00
D 0 1
      1.097000D+00           1.000000D+00
D 0 1
      3.180000D-01           1.000000D+00
F 0 1
      7.610000D-01           1.0000000
****

BASIS cc-pVTZ-PP_BSE 5D ECP
I
S 0 11
      5.546500D+03           1.560000D-04
      8.382140D+02           9.860000D-04
      1.821870D+02           2.792000D-03
      3.121230D+01          -4.325100D-02
      1.953140D+01           2.341340D-01
      8.240990D+00          -7.509430D-01
      2.194550D+00           8.829680D-01
      1.109110D+00           4.620610D-01
      3.746410D-01           2.228600D-02
      1.770800D-01          -4.353000D-03
      8.106100D-02           1.102000D-03
S 0 1
      3.746410D-01           1.000000D+00
S 0 1
      1.770800D-01           1.000000D+00
S 0 11
      5.546500D+03          -7.300000D-05
      8.382140D+02          -5.080000D-04
      1.821870D+02          -1.158000D-03
      3.121230D+01           1.219300D-02
      1.953140D+01          -8.785400D-02
      8.240990D+00           3.382000D-01
      2.194550D+00          -5.765500D-01
      1.109110D+00          -4.092980D-01
      3.746410D-01           5.674590D-01
      1.770800D-01           6.124890D-01
      8.106100D-02           1.432310D-01
S 0 1
      1.001000D-01           1.000000D+00
P 0 9
      1.889880D+02           5.850000D-04
      2.128680D+01           3.692300D-02
      1.003960D+01          -2.353240D-01
      3.451800D+00           3.414830D-01
      1.974560D+00           5.347880D-01
      1.024200D+00           2.651410D-01
      4.494370D-01           2.578700D-02
      1.866480D-01           5.220000D-04
      7.348100D-02           6.060000D-04
P 0 1
      5.981000D-01           1.000000D+00
P 0 9
      1.889880D+02          -2.560000D-04
      2.128680D+01          -1.168200D-02
      1.003960D+01           8.319200D-02
      3.451800D+00          -1.569700D-01
      1.974560D+00          -2.245180D-01
      1.024200D+00          -1.144510D-01
      4.494370D-01           3.753560D-01
      1.866480D-01           5.751360D-01
      7.348100D-02           2.459170D-01
P 0 1
      9.618000D-02           1.000000D+00
D 0 9
      1.326620D+02           5.720000D-04
      3.760540D+01           4.402000D-03
      1.038910D+01          -4.092200D-02
      6.490170D+00           9.966100D-02
      3.454510D+00           3.226630D-01
      1.844130D+00           4.003430D-01
      9.624780D-01           2.683060D-01
      4.728530D-01           8.484700D-02
      1.932000D-01           7.632000D-03
D 0 1
      4.728530D-01           1.000000D+00
D 0 1
      1.932000D-01           1.000000D+00
F 0 1
      4.064000D-01           1.000000D+00
**
I 4 28
G_AND_UP
2      1.00000000             0.00000000
S-G
2     40.03337600            49.98964900
2     17.30057600           281.00655600
2      8.85172000            61.41673900
P-G
2     15.72014100            67.41623900
2     15.20822200           134.80769600
2      8.29418600            14.56654800
2      7.75394900            28.96842200
D-G
2     13.81775100            35.53875600
2     13.58780500            53.33975900
2      6.94763000             9.71646600
2      6.96009900            14.97750000
F-G
2     18.52295000           -20.17661800
2     18.25103500           -26.08807700
2      7.55790100            -0.22043400
2      7.59740400            -0.22164600
****

To submit the job from the command line, download the input files (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=ene_custom_basis_0002 ene-custom_basis-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: ene-custom_basis-0002.in
Input : custom.basis
Output files

Calculation of Molecular Properties Examples

Note: To properly model density around the Fe nucleus, a special partridge-1 basis set is defined in the &atomic section. Additional definitions are employed in the input to improve convergence behavior, including (1) charge and spins of several atoms in the &atomic section, and (2) nops=1 and vhift=0.0 in the &gen section.

Example input file (prop-moessbauer-0001.in):

&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
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0001 prop-moessbauer-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: prop-moessbauer-0001.in
Output files

Note: To properly model density around the Fe nucleus, a special partridge-1 basis set is defined in the &atomic section. Additional definitions are employed in the input to improve convergence behavior, including (1) charge and spins of several atoms in the &atomic section, and (2) nops=1 and vhift=0.0 in the &gen section.

Example input file (prop-moessbauer-0002.in):

&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
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=prop_moessbauer_0002 prop-moessbauer-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: prop-moessbauer-0002.in
Output files