mirror of https://gitlab.com/scemama/QCaml.git
Added a test for Hartree-Fock
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@ -1,6 +1,7 @@
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(executable
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(name ex_integrals)
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(libraries
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qcaml
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))
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(executables
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(names
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ex_integrals
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ex_hartree_fock
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)
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(libraries qcaml))
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@ -0,0 +1,76 @@
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Header][Header:1]] *)
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module Command_line = Qcaml.Common.Command_line
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module Util = Qcaml.Common.Util
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let () =
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(* Header:1 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Definition][Definition:1]] *)
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let open Command_line in
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begin
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set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
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set_description_doc "Computes the one- and two-electron hartree_fock 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='m' ; long="multiplicity" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Spin multiplicity (2S+1). Default is singlet"; } ;
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{ short='c' ; long="charge" ; opt=Optional;
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arg=With_arg "<int>";
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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"; } ;
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]
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end;
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(* Definition:1 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Interpretation][Interpretation:1]] *)
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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 charge =
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match Command_line.get "charge" with
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| Some x -> ( if x.[0] = 'm' then
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~- (int_of_string (String.sub x 1 (String.length x - 1)))
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else
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int_of_string x )
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| None -> 0
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in
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let multiplicity =
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match Command_line.get "multiplicity" with
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| Some x -> int_of_string x
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| None -> 1
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in
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(* Interpretation:1 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:1]] *)
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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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(* Computation:1 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:2]] *)
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let ao_basis =
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Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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(* Computation:2 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:3]] *)
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let simulation = Qcaml.Simulation.make ~charge ~multiplicity ~nuclei ao_basis in
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(* Computation:3 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:4]] *)
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let hf = Qcaml.Mo.Hartree_fock.make ~guess:`Huckel simulation in
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(* Computation:4 ends here *)
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(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Output][Output:1]] *)
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Format.printf "@[%a@]" (Mo.Hartree_fock.pp) hf
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(* Output:1 ends here *)
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@ -0,0 +1,109 @@
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#+TITLE: Hartree-Fock
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#+PROPERTY
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In this example, we write a program that makes a Hartree-Fock
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caculation. The molecule is read in =xyz= format and a Gaussian
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atomic basis set in GAMESS format.
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* Header
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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.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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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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- =-c --charge= : The charge of the molecule
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- =-m --multiplicity= : The spin multiplicity
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** Definition
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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.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) ^ " - QuAcK command");
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set_description_doc "Computes the one- and two-electron hartree_fock 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='m' ; long="multiplicity" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Spin multiplicity (2S+1). Default is singlet"; } ;
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{ short='c' ; long="charge" ; opt=Optional;
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arg=With_arg "<int>";
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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"; } ;
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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_hartree_fock.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 charge =
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match Command_line.get "charge" with
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| Some x -> ( if x.[0] = 'm' then
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~- (int_of_string (String.sub x 1 (String.length x - 1)))
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else
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int_of_string x )
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| None -> 0
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in
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let multiplicity =
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match Command_line.get "multiplicity" with
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| Some x -> int_of_string x
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| None -> 1
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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_hartree_fock.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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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
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let ao_basis =
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Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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#+END_SRC
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We create a simulation from the nuclei and the basis set:
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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
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let simulation = Qcaml.Simulation.make ~nuclei ao_basis in
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#+END_SRC
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and we can make the Hartree-Fock computation:
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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
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let hf = Qcaml.Mo.Hartree_fock.make ~guess:`Huckel simulation in
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#+END_SRC
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* Output
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We print the convergence of the calculation:
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#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
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Format.printf "@[%a@]" (Mo.Hartree_fock.pp) hf
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#+END_SRC
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@ -3,7 +3,7 @@
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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 in =xyz= format and a Gaussian atomic basis set in GAMESS
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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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@ -176,17 +176,17 @@ let gemm ?m ?n ?k ?beta ?c ?(transa=`N) ?(alpha=1.0) a ?(transb=`N) b =
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in
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gemm ?m ?n ?k ?beta ?c ~transa ~alpha a ~transb b
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let gemm_nn ?m ?n ?k ?(beta=0.) ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ~beta ?c ~alpha a b ~transa:`N ~transb:`N
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let gemm_nn ?m ?n ?k ?beta ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ?beta ?c ~alpha a b ~transa:`N ~transb:`N
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let gemm_nt ?m ?n ?k ?(beta=0.) ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ~beta ?c ~alpha a b ~transa:`N ~transb:`T
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let gemm_nt ?m ?n ?k ?beta ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ?beta ?c ~alpha a b ~transa:`N ~transb:`T
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let gemm_tn ?m ?n ?k ?(beta=0.) ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ~beta ?c ~alpha a b ~transa:`T ~transb:`N
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let gemm_tn ?m ?n ?k ?beta ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ?beta ?c ~alpha a b ~transa:`T ~transb:`N
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let gemm_tt ?m ?n ?k ?(beta=0.) ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ~beta ?c ~alpha a b ~transa:`T ~transb:`T
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let gemm_tt ?m ?n ?k ?beta ?c ?(alpha=1.0) a b =
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gemm ?m ?n ?k ?beta ?c ~alpha a b ~transa:`T ~transb:`T
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let gemm_trace ?(transa=`N) a ?(transb=`N) b =
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@ -0,0 +1,24 @@
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open Alcotest
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open Particles
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let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test"
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let tests =
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[ "HF Water", `Quick, fun () ->
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let nuclei =
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wd ^ Filename.dir_sep ^ "water.xyz"
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|> Nuclei.of_xyz_file
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in
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let basis_filename =
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wd ^ Filename.dir_sep ^ "cc-pvdz"
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in
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let ao_basis =
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Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
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~cartesian:false ~nuclei basis_filename
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in
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let simulation = Simulation.make ~nuclei ao_basis in
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let hf = Mo.Hartree_fock.make ~guess:`Huckel simulation in
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Format.printf "%a" (Mo.Hartree_fock.pp) hf;
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check (float 1.e-10) "Energy" (-76.0267987006) (Mo.Hartree_fock.energy hf);
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]
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@ -4,11 +4,13 @@
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(name qcaml)
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(public_name qcaml)
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(libraries
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qcaml.ao
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qcaml.common
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qcaml.particles
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qcaml.gaussian
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qcaml.gaussian_integrals
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qcaml.mo
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qcaml.operators
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qcaml.ao
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qcaml.particles
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qcaml.simulation
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)
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(synopsis "Main QCaml entry point"))
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@ -1,8 +1,9 @@
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module Common = Common
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module Ao = Ao
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module Common = Common
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module Gaussian = Gaussian
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module Gaussian_integrals = Gaussian_integrals
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module Linear_algebra = Linear_algebra
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module Mo = Mo
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module Operators = Operators
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module Particles = Particles
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module Simulation = Simulation
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@ -12,6 +12,7 @@ let test_suites: unit Alcotest.test list = [
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"Ao_basis.Ao_basis_gaussian", Test_ao_basis.Ao_basis_gaussian.tests;
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"Ao_basis.Ao_basis", Test_ao_basis.Ao_basis.tests;
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"Mo_basis.Guess", Test_mo_basis.Guess.tests;
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"Mo_basis.Hartree_Fock", Test_mo_basis.Hf.tests;
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]
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let () = Alcotest.run "QCaml" test_suites
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