mirror of
https://gitlab.com/scemama/QCaml.git
synced 2024-11-07 06:33:39 +01:00
131 lines
4.2 KiB
Org Mode
131 lines
4.2 KiB
Org Mode
#+TITLE: Integrals
|
|
|
|
#+PROPERTY
|
|
|
|
In this example, we write a program that reads the geometry of a
|
|
molecule in =xyz= format and a Gaussian atomic basis set in GAMESS
|
|
format. The output is a set of files containing the one- and two-
|
|
electron integrals.
|
|
|
|
* Header
|
|
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
module Command_line = Qcaml.Common.Command_line
|
|
module Util = Qcaml.Common.Util
|
|
open Qcaml.Linear_algebra
|
|
|
|
let () =
|
|
#+END_SRC
|
|
|
|
* Command-line arguments
|
|
|
|
We use the =Command_line= module to define the following possible
|
|
arguments:
|
|
- =-b --basis= : The name of the file containing the basis set
|
|
- =-x --xyz= : The name of the file containing the atomic coordinates
|
|
- =-u --range-separation= : The value of $\mu$, the range-separation
|
|
parameter in range-separated DFT. If this option is not present,
|
|
no output file will be generated for the range-separated integrals.
|
|
|
|
** Definition
|
|
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let open Command_line in
|
|
begin
|
|
set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
|
|
set_description_doc "Computes the one- and two-electron integrals on the Gaussian atomic basis set.";
|
|
set_specs
|
|
[ { short='b' ; long="basis" ; opt=Mandatory;
|
|
arg=With_arg "<string>";
|
|
doc="Name of the file containing the basis set"; } ;
|
|
|
|
{ short='x' ; long="xyz" ; opt=Mandatory;
|
|
arg=With_arg "<string>";
|
|
doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
|
|
|
|
{ short='u' ; long="range-separation" ; opt=Optional;
|
|
arg=With_arg "<float>";
|
|
doc="Range-separation parameter."; } ;
|
|
]
|
|
end;
|
|
#+END_SRC
|
|
|
|
** Interpretation
|
|
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let basis_file = Util.of_some @@ Command_line.get "basis" in
|
|
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
|
|
|
|
let range_separation =
|
|
match Command_line.get "range-separation" with
|
|
| None -> None
|
|
| Some mu -> Some (float_of_string mu)
|
|
in
|
|
|
|
let operators =
|
|
match range_separation with
|
|
| None -> []
|
|
| Some mu -> [ Qcaml.Operators.Operator.of_range_separation mu ]
|
|
in
|
|
#+END_SRC
|
|
|
|
* Computation
|
|
We first read the =xyz= file to create a molecule:
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let nuclei =
|
|
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
|
|
in
|
|
#+END_SRC
|
|
|
|
Then we create an Gaussian AO basis using the atomic coordinates,
|
|
and we optionally introduce the range-separation parameter via the =operators=:
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let ao_basis =
|
|
Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
|
|
~operators ~cartesian:true ~nuclei basis_file
|
|
in
|
|
#+END_SRC
|
|
|
|
We compute the required one-electron integrals:
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let overlap = Qcaml.Ao.Basis.overlap ao_basis in
|
|
let eN_ints = Qcaml.Ao.Basis.eN_ints ao_basis in
|
|
let kin_ints = Qcaml.Ao.Basis.kin_ints ao_basis in
|
|
let multipole = Qcaml.Ao.Basis.multipole ao_basis in
|
|
let x_mat = multipole "x" in
|
|
let y_mat = multipole "y" in
|
|
let z_mat = multipole "z" in
|
|
#+END_SRC
|
|
|
|
and the two-electron integrals (1/r and long range):
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
let ee_ints = Qcaml.Ao.Basis.ee_ints ao_basis in
|
|
let lr_ints =
|
|
match range_separation with
|
|
| Some _mu -> Some (Qcaml.Ao.Basis.ee_lr_ints ao_basis)
|
|
| None -> None
|
|
in
|
|
#+END_SRC
|
|
|
|
* Output
|
|
|
|
We write the one-electron integrals:
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
Matrix.to_file ~filename:"overlap.dat" ~sym:true overlap;
|
|
Matrix.to_file ~filename:"eN.dat" ~sym:true eN_ints;
|
|
Matrix.to_file ~filename:"kinetic.dat" ~sym:true kin_ints;
|
|
Matrix.to_file ~filename:"x.dat" ~sym:true x_mat;
|
|
Matrix.to_file ~filename:"y.dat" ~sym:true y_mat;
|
|
Matrix.to_file ~filename:"z.dat" ~sym:true z_mat;
|
|
#+END_SRC
|
|
|
|
and the the two-electron integrals:
|
|
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_integrals.ml
|
|
Four_idx_storage.to_file ~filename:"eri.dat" ee_ints;
|
|
match lr_ints with
|
|
| Some integrals -> Four_idx_storage.to_file ~filename:"eri_lr.dat" integrals;
|
|
| None -> ()
|
|
#+END_SRC
|
|
|