Basis Set Library Functions
These basis manipulation functions are designed to allow
a basis set and ECP library to be interrogated by a range of
QM code interfaces,
thus allowing the same results to be obtained
from different QM packages. The specification provided is a nested
Tcl list structure, as described in the next section. It can be
presented using the basisspec= argument to (some of) the
QM interfaces, or the get_basis command can be used to
extract a basis set from the library independently.
The specification takes the form of a list of sublists, each
containing a basis set name and a list of symbols. Here the
newlines have been added for clarity, and ... denotes a variable
length list.
{
{ basis1 { symbol1 symbol2 ... } }
{ basis2 { symbol3 ... } }
...
}
Each target element symbol is checked against each sublist in turn. If
a match is found with any of the symbols, and if the basis set is
available for the element in question, the named basis set is
assigned. If more than one assignment is possible, the last one is
retained.
Tcl "glob-style" pattern matching (see documentation for the string command) is
used for the string comparisons, allowing use of * to match any set of
characters. Also, if a symbol is specified as "all" it will match anything.
Case is ignored in the matching of atom symbols, and in the
presentation of basis set names.
A basis specification of "null" can be used to denote that no basis
set is required (this is needed since it is otherwise a fatal error to
assign an incomplete basis set).
Consider the simplest specification, where the wild card "all" is used
{ { sto-3g all } }
All atoms are assigned as STO-3G. Because pattern matching is used,
the following is equivalent:
{ { sto-3g *} }
To assign all atoms with a name beginning with c or h as 3-21G, and
STO-3G for the remainder, use:
{ { sto-3g all } {3-21g {c* h*} } }
The command list_basis_sets can be used to establish which basis
sets are available in the ChemShell basis set library.
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| elements= |
Tcl list |
no |
all elements |
Elements for which data is required |
| format= |
keyword |
no |
by_basis |
Use by_basis to get a list of elements available for each basis set. Use by_element to list all basis sets available for a given element |
| list_option= |
keyword |
no |
minimal |
How much output, can be "full" or "minimal", in the "full" case with format=by_element the basis set is actually listed |
The command get_basis will generally be invoked
indirectly from within a QM interface
using the basis_spec= argument, but it can be invoked
directly to examine the basis sets.
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| specification= |
Tcl list |
yes |
none |
details of the basis set required |
| coords= |
Fragment tag
|
no |
all elements. |
system for which basis sets are needed. The default is to provide a basis for all supported elements |
Structure of the list returned from get_basis
The list returned from get_basis has the following structure.
[....] denotes that the previous element may be repeated
one or more times.
{
{ atomic-symbol
{ angmom { exp coef [....] } [ ... ] }
[....] }
[....]
}
Where:
| atomic symbol |
An alphabetic element symbol (e.g. H) |
| angmom |
S, P, L, D, F, G etc |
| exp |
Orbital exponent |
| coef |
expansion coefficient In the case of angmom=L
there are two such coefficients |
As an illustration of the structure, the following described the 3-21G
basis assigned to C and H. Note that new-lines have been added for clarity,
they are not part of the return value from get_basis.
{C
{S {172.2560 0.0617669 }
{25.91090 0.358794 }
{5.533350 0.700713}}
{l {3.664980 -0.395897 0.236460}
{0.770545 1.215840 0.860619}}
{l {0.195857 1.000000 1.000000}}}
{H
{S {5.447178 0.156285 }
{0.824547 0.904691}}
{S {0.183192 1.000000}}
}
Examples
The 3-21G C,H sample above was generated using the Tcl command
set bas [ get_basis elements= "c h" specification= {{3-21g all}} ]
To allow for automatic substitution of basis sets that
are not present, the following form could be used.
Here (rather improbably) STO-3G is used for all elements,
except for Z=1,6, where cc-pvdz is selected if available.
set basisspec { {sto-3g all} { cc-pvdz {h he li be b c} } }
set bas [ get_basis coords=c specification= $basisspec ]
The basis set library is stored in the ChemShell source tree, in
the file chemsh/src/basis/load.tcl. It is a collection of Tcl
procedures, one per basis set, with the name load_bas_basname,
where basname is replaced by the required basis name.
When executed, the procedure should set the array variable bas
in the calling procedure so that bas(1) contains the basis set for z=1,
etc..
As an example, consider the following routine that would set up the
first three entries in the 3-21G basis.
proc load_bas_3-21g {} {
upvar bas bas
array set bas {
1 {{S {5.447178 0.156285} {0.824547 0.904691}} {S {0.183192 1.000000}}}
2 {{S {13.62670 0.175230} {1.999350 0.893483}} {S {0.382993 1.000000}}}
3 {{S {36.83820 0.0696686} {5.481720 0.381346} {1.113270 0.681702}}
{L {0.540205 -0.263127 0.161546} {0.102255 1.14339 0.915663}}
{L {0.028565 1.000000 1.000000}}}
}
}
It is important to ensure that the procedure is defined
before it is to be used (rather than relying on Tcl autoloading
procedures) since the scripts rely on the a set of
procedure definitions
of the form load_bas_basname to provide a complete
list of available basis sets. For basis sets stored in the
load.tcl file mentioned above this is achieved by forcing a
load via a dummy procedure. For user-added basis sets, the files
can be sourced.
ECPs are handled in a corresponding way. The quantum interfaces should
load ECPs as a required for the selected basis sets so no specific ECP
selection string should be needed. It is actually generated by
prepending the entry { null * } to the basis specification,
which means that if there are no ECPs stored for a given basis set choice,
a null ECP will be assigned.
The command to access the library directly is get_ecp.
The ECPs are output in a form analogous to that basis sets, an
example is given below (again new lines are added for clarity).
An initial 2-element list (indicating lmax and ncore) precedes
the basis set expansion.
As an example, consider the return value from the following command:
get_ecp elements=pt specification= {{ stuttgart_rsc * }}
{78
{ 5 60}
{5 {H POTENTIAL} {2 1.000000000 .000000000}}
{0 {S-H POTENTIAL} {2 13.428651000 579.223861000} {2 6.714326000 29.669491000}}
{1 {P-H POTENTIAL} {2 10.365944000 280.860774000} {2 5.182972000 26.745382000}}
{2 {D-H POTENTIAL} {2 7.600479000 120.396444000} {2 3.800240000 15.810921000}}
{3 {F-H POTENTIAL} {2 3.309569000 24.314376000}}
{4 {G-H POTENTIAL} {2 5.277289000 -24.218675000}}
}
The structure of the ECP procedures is similar to that of the basis sets,
as indicated in the following example:
proc load_ecp_stuttgart_rlc {} {
upvar bas bas
array set bas {
35 {
{ 4 28}
{4 {G POTENTIAL} {2 1.000000000 .000000000}}
{0 {S-G POTENTIAL} {2 5.021800000 61.513721000} {2 2.510900000 9.021493000}}
{1 {P-G POTENTIAL} {2 4.281400000 53.875864000} {2 2.140700000 4.629402000}}
{2 {D-G POTENTIAL} {2 2.880000000 20.849677000} {2 1.440000000 2.965444000}}
{3 {F-G POTENTIAL} {2 2.720700000 -8.161493000}}
}
36 {
{ 5 28}
{5 {H POTENTIAL} {2 1.000000000 .000000000}}
{0 {S-H POTENTIAL} {2 5.877718000 73.915693900} {2 3.084622000 16.168250800}}
{1 {P-H POTENTIAL} {2 5.164110000 58.517691010} {2 2.358302000 8.259100730}}
...
}
...
}
- It may be possible to generate a basis set specification
that contains a mix of ECP and non-ecp basis sets such that
when get_basis is called a non-ecp basis is assigned, and
when get_ecp is called, the ECP is also chosen. This can
be avoided by always placing ECP basis sets after non-ecp ones in
the basis set specification listing.
|
