Required keywords¶
geometry
{ "atom" : "atom symbol", "xyz" : [x, y, z] }
Please see the end of the file for some examples.basis
df_basis
Note
The use of mixed basis sets and/or density fitting basis sets is possible by specifying a different basis set other than the default for each atom (see example for Basis sets below).
Optional keywords¶
angstrom
true: use Angstromfalse: use Bohrfinite_nucleus
geometry block, the exponent keyword can be used to specify a different exponent for the charge distribution of a particular atom,
where a value of 0.0 indicates a point charge.molden_file
"basis" : "molden" is specified.cfmm
schwarz_thresh
"cfmm" : "true".
For more details, refer to Hartree–Fock section.dkh
magnetic_field
tesla
basis_type
gaussian / giao, londongaussian at zero magnetic field; giao when a field is appliedskip_self_interaction
true: skip the electrostatic interactions between the dummies.false: explicitly calculate the electrostatic interactions between the dummies.Basis sets¶
Orbital basis sets¶
The following basis sets are available in BAGEL library. The basis set name can be used with the basis keyword.
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Density fitting basis sets¶
The following density fitting basis sets are available in BAGEL library. The basis set name can be used with the df_basis keyword.
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Examples¶
{ "bagel" : [
{
"title" : "molecule",
"basis" : "svp",
"df_basis" : "svp-jkfit",
"angstrom" : false,
"geometry" : [
{"atom" : "H", "xyz" : [ -0.22767998367, -0.82511994081, -2.66609980874]; },
{"atom" : "O", "xyz" : [ 0.18572998668, -0.14718998944, -3.25788976629]; },
{"atom" : "H", "xyz" : [ 0.03000999785, 0.71438994875, -2.79590979943]; }
]
},
{
"title" : "hf"
}
]}
Example with mixed basis sets and density fitting basis sets:
{ "bagel" : [
{
"title" : "molecule",
"basis" : "svp",
"df_basis" : "svp-jkfit",
"angstrom" : "false",
"geometry" : [
{ "atom" : "F", "xyz" : [ -0.000000, -0.000000, 2.720616]},
{ "atom" : "H", "xyz" : [ -0.000000, -0.000000, 0.305956],
"basis" : "cc-pvqz", "df_basis" : "cc-pvqz-jkfit" }
]
},
{
"title" : "hf"
}
]}
Example with running a calculation from a molden file using the keyword "basis" : "molden"
and providing a value for "molden_file":
{ "bagel" : [
{
"title" : "molecule",
"basis" : "molden",
"df_basis" : "svp-jkfit",
"cartesian" : true,
"molden_file" : "hf_write_mol_cart.molden"
}
]}
(refer to Molden in Miscellaneous features for more details)
Example with external magnetic field using Gauge-invariant atomic orbitals (GIAO):
{ "bagel" : [
{
"title" : "molecule",
"basis" : "svp",
"df_basis" : "svp-jkfit",
"angstrom" : "false",
"basis_type" : "giao",
"tesla" : "false",
"magnetic_field" : [ 0.2000, 0.3000, -0.1500 ],
"geometry" : [
{ "atom" : "F", "xyz" : [ -1.200000, 2.500000, 2.720616]},
{ "atom" : "H", "xyz" : [ -1.200000, 2.500000, 0.305956]}
]
},
{
"title" : "hf"
}
]}
Auxiliary basis sets¶
The following MP2-fit basis sets are available in BAGEL. The basis set name can be used with the aux_basis keyword
in the method block (refer to Møller–Plesset perturbation theory (MP2) for more details).
cc-pvdz-ri
cc-pvtz-ri
cc-pvqz-ri
cc-pv5z-ri
Example¶
An example using cc-pvdz-ri in MP2 calculation.
{ "bagel" : [
{
"title" : "molecule",
"basis" : "cc-pvdz",
"df_basis" : "cc-pvdz-jkfit",
"angstrom" : "true",
"geometry" : [
{ "atom" : "C", "xyz" : [ -1.20433891360, 0.54285096106, -0.04748199659] },
{ "atom" : "C", "xyz" : [ -1.20543291352, -0.83826393986, 0.12432899108] },
{ "atom" : "C", "xyz" : [ -0.00000600000, -1.52953889027, 0.20833398505] },
{ "atom" : "C", "xyz" : [ 1.20544091352, -0.83825393987, 0.12432799108] },
{ "atom" : "C", "xyz" : [ 1.20433091360, 0.54284396106, -0.04748099659] },
{ "atom" : "C", "xyz" : [ 0.00000400000, 1.23314191154, -0.13372399041] },
{ "atom" : "H", "xyz" : [ -2.13410484690, 1.07591192282, -0.12500499103] },
{ "atom" : "H", "xyz" : [ -2.13651384673, -1.37179190159, 0.18742198655] },
{ "atom" : "H", "xyz" : [ 0.00000000000, -2.59646181374, 0.33932597566] },
{ "atom" : "H", "xyz" : [ 2.13651384673, -1.37179290159, 0.18742198655] },
{ "atom" : "H", "xyz" : [ 2.13410684690, 1.07591292282, -0.12500599103] },
{ "atom" : "H", "xyz" : [ -0.00000000000, 2.29608983528, -0.28688797942] }
]
},
{
"title" : "mp2",
"aux_basis" : "cc-pvdz-ri",
"frozen" : true
}
]}
Effective core potential (ECP) basis sets¶
The following auxiliary basis sets are available in BAGEL library. The basis set name can be used with the basis keyword.
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Note
User-defined ECP basis sets need to contain the keyword “ecp” in the names. Refer to User defined basis sets for more details.
Example¶
Example for CuH2 using cc-pvtz basis set for H and lanl2dz-ecp for the heavy atom Cu
{ "bagel" : [
{
"title" : "molecule",
"basis" : "lanl2dz-ecp",
"df_basis" : "svp-jkfit",
"angstrom" : "true",
"geometry" : [
{ "atom" : "Cu", "xyz" : [ 0.000000, 0.000000, 0.000000]},
{ "atom" : "H", "xyz" : [ 0.000000, 0.000000, -1.560000],
"basis" : "cc-pvtz"},
{ "atom" : "H", "xyz" : [ 0.000000, 0.000000, 1.560000],
"basis" : "cc-pvtz"}
]
},
{
"title" : "hf",
"charge" : "-1"
}
]}
User defined basis sets¶
The basis set file is in the following format
{
"H" : [
{
"angular" : "s",
"prim" : [5.4471780, 0.8245470],
"cont" : [[0.1562850, 0.9046910]]
}, {
"angular" : "s",
"prim" : [0.1831920],
"cont" : [[1.0000000]]
}
],
"He" : [
{
"angular" : "s",
"prim" : [13.6267000, 1.9993500],
"cont" : [[0.1752300, 0.8934830]]
}, {
"angular" : "s",
"prim" : [0.3829930],
"cont" : [[1.0000000]]
}
]
}
The file is essentially one large array, the elements of which are further arrays, each corresponding to the basis set for a given element. The basis set for associated with each element is then made up of further arrays, each of which contains information specifying the properties of a single basis function.
angulardefines the kind of orbital (s,p,d,f…) .
primis a array containing the exponents of the primitive orbitals from which the basis function is composed.
contis an array containing the coefficients associated with each of these primitive orbitals.
The user can specify their own basis set using the above format, or use one of the predefined basis sets listed in Basis sets.
Note
Not all of the the basis sets are defined for all atoms; an error message of form “No such node(X)”, where X is the element, typically means that the relevant element was not found in the basis set file. Refer to the EMSL Basis set exchange library for more basis sets (https://bse.pnl.gov/bse/portal).
To use a user specified basis the explicit path to the basis set file must be specified in the basis set block.
Example¶
{ "bagel" : [
{
"title" : "molecule",
"basis" : "/path/to/my/basis",
"df_basis" : "/path/to/my/basis",
"angstrom" : false,
"geometry" : [
{"atom" : "H", "xyz" : [ -0.22767998367, -0.82511994081, -2.66609980874]; },
{"atom" : "O", "xyz" : [ 0.18572998668, -0.14718998944, -3.25788976629]; },
{"atom" : "H", "xyz" : [ 0.03000999785, 0.71438994875, -2.79590979943]; }
]
},
{
"title" : "hf"
}
]}
Other features¶
Dummy atoms¶
Artificial point charges can be included in the calculation. They introduce a user specified charge into the system, but have no associated basis functions. Introduction of such a charge is accomplished by inclusion of an additional line in the geometry block for an atom of element “Q”.
Example¶
A dihydrogen molecule with a nearby dummy charge of +0.2. Note that the charge specified in the “hf” block does not include the charge associated with the dummy atom.
{ "bagel" : [
{
"title" : "molecule",
"basis" : "tzvpp",
"df_basis" : "tzvpp-jkfit",
"angstrom" : "true",
"geometry" : [
{ "atom" : "Q", "xyz" : [ 0.000000, 0.000000, 2.0000], "charge" : "0.2"},
{ "atom" : "H", "xyz" : [ 0.000000, 0.000000, 0.7414]},
{ "atom" : "H", "xyz" : [ 0.000000, 0.000000, 0.0000]}
]
},
{
"title" : "hf"
}
]}
from which one obtains
=== RHF iteration (tzvpp) ===
o Fock build 0.01
0 -1.12552716 0.00743295 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
1 -1.12987462 0.00139213 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
2 -1.13008781 0.00009095 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
3 -1.13008889 0.00000614 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
4 -1.13008889 0.00000054 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
5 -1.13008889 0.00000007 0.01
o DIIS 0.00
o Diag 0.00
o Post process 0.00
o Fock build 0.01
6 -1.13008889 0.00000000 0.01
* SCF iteration converged.
* Permanent dipole moment:
( 0.000000, -0.000000, -0.427736) a.u.
Updates to Molecule Specification¶
The examples above each provide a complete set of information for the molecule to be constructed from scratch. Alternatively, if a molecule block has already been provided, a new molecule input can be provided with a subset of the required inputs to be altered. This is often useful when optimized orbitals from one calculation are to be used to provide an initial guess for a more difficult calculation.
Useful Parameters to Change¶
geometry
angstrom keyword must be supplied within the same molecule block.basis
geometry block.
The new basis set must be identical to or larger than that used in any previous calculation.
Molecular orbitals will be projected into the expanded space.df_basis
geometry block.magnetic_field
tesla keyword must be supplied within the same molecule block.basis_type
molecule block must be supplied.)References¶
Description of Reference |
Reference |
|---|---|
General text on electronic structure theory |
A. Szabo and N. S. Ostlund, Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory (McGraw-Hill, New York, 1989). |
Gauge invariant atomic orbitals |
R. Ditchfield, Mol. Phys. 27, 789 (1974). |
Finite nuclear charge distribution and default exponents |
L. Visscher and K. G. Dyall, At. Data Nucl. Data Tables 67, 207 (1997). |