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