QCaml/examples/ex_hartree_fock.org

#+TITLE: Hartree-Fock

#+PROPERTY

In this example, we write a program that makes a Hartree-Fock
caculation.  The molecule is read in =xyz= format and a Gaussian
atomic basis set in GAMESS format. 

* Header 

#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
module Command_line = Qcaml.Common.Command_line
module Util = Qcaml.Common.Util

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
  - =-c --charge=  : The charge of the molecule
  - =-m --multiplicity= : The spin multiplicity

** Definition

   #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
let open Command_line in
begin
  set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
  set_description_doc "Computes the one- and two-electron hartree_fock 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='m' ; long="multiplicity" ; opt=Optional;
        arg=With_arg "<int>";
        doc="Spin multiplicity (2S+1). Default is singlet"; } ;
      
      { short='c' ; long="charge" ; opt=Optional;
        arg=With_arg "<int>";
        doc="Total charge of the molecule. Specify negative charges with 'm' instead of the minus sign, for example m1 instead of -1. Default is 0"; } ;
      
    ]
end;
   #+END_SRC

** Interpretation

   #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
let basis_file  = Util.of_some @@ Command_line.get "basis" in
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in

let charge =
  match Command_line.get "charge" with
  | Some x -> ( if x.[0] = 'm' then
                  ~- (int_of_string (String.sub x 1 (String.length x - 1)))
                else
                  int_of_string x )
  | None   -> 0
in
    
let multiplicity =
  match Command_line.get "multiplicity" with
  | Some x -> int_of_string x
  | None -> 1
in
   #+END_SRC

* Computation
  We first read the =xyz= file to create a molecule:
  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.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:
  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
let ao_basis =
  Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
in
  #+END_SRC

  We create a simulation from the nuclei and the basis set:
  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
let simulation = Qcaml.Simulation.make ~nuclei ao_basis in
  #+END_SRC

  and we can make the Hartree-Fock computation:
  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
let hf = Qcaml.Mo.Hartree_fock.make ~guess:`Huckel simulation in
  #+END_SRC

* Output

  We print the convergence of the calculation:
  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
Format.printf "@[%a@]" (Mo.Hartree_fock.pp) hf
  #+END_SRC