FCI example

ci/lib/ci.ml

@@ -11,6 +11,7 @@ module Ci_matrix_element = Ci_matrix_element
 
 module Ds = Determinant_space
 module Sd = Spindeterminant
+module Si = Simulation
 
 
 type num_states
@@ -23,8 +24,11 @@ type t =
     m_S2        : (Determinant.t, Determinant.t) Matrix.t lazy_t ;
     eigensystem : ((Determinant.t, num_states) Matrix.t * num_states Vector.t) lazy_t;
     n_states    : int;
+    simulation  : Simulation.t;
   }
 
+let simulation   t = t.simulation
+
 let det_space    t = t.det_space
 
 let n_states     t = t.n_states
@@ -620,8 +624,10 @@ let create_matrix_spin_computed ?(nmax=2) f det_space =
   )
 
 
+let nuclear_repulsion t =
+  Si.nuclear_repulsion (simulation t)
 
-let make ?(n_states=1) ?(algo=`Direct) det_space =
+let make ?(n_states=1) ?(algo=`Direct) ~det_space simulation =
 
   let mo_basis = Ds.mo_basis det_space in
 
@@ -635,7 +641,7 @@ let make ?(n_states=1) ?(algo=`Direct) det_space =
       Ds.determinant_stream det_space
       |> Stream.next
     in
-    h_ij_non_zero mo_basis 0 0 d0 d0
+    (h_ij_non_zero mo_basis 0 0 d0 d0)
   in
 
   let m_H =
@@ -680,11 +686,14 @@ let make ?(n_states=1) ?(algo=`Direct) det_space =
     let eigenvectors, eigenvalues =
       Davidson.make ~threshold:1.e-6  ~n_states diagonal matrix_prod
     in
-    let eigenvalues = Vector.map (fun x -> x +. e_shift) eigenvalues in
+    let nuclear_repulsion =
+      Si.nuclear_repulsion simulation
+    in
+    let eigenvalues = Vector.map (fun x -> x +. e_shift  +. nuclear_repulsion) eigenvalues in
     (Conventions.rephase eigenvectors), eigenvalues
   )
   in
-  { det_space ; e_shift ; m_H ; m_S2 ; eigensystem ; n_states }
+  { det_space ; e_shift ; m_H ; m_S2 ; eigensystem ; n_states ; simulation }
 
 
 

examples/dune

@@ -1,5 +1,6 @@
 (executables
   (names
+        ex_fci
         ex_integrals
         ex_hartree_fock
         ex_localization

examples/ex_fci.ml

@@ -0,0 +1,102 @@
+(* [[file:ex_fci.org::*Header][Header:1]] *)
+open Qcaml
+open Common
+open Linear_algebra
+
+let () =
+(* Header:1 ends here *)
+
+(* [[file:ex_fci.org::*Definition][Definition:1]] *)
+let open Command_line in
+begin
+  set_header_doc (Sys.argv.(0));
+  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;
+(* Definition:1 ends here *)
+
+(* [[file:ex_fci.org::*Interpretation][Interpretation:1]] *)
+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
+(* Interpretation:1 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:1]] *)
+let nuclei =
+  Particles.Nuclei.of_xyz_file nuclei_file
+in
+(* Computation:1 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:2]] *)
+let ao_basis =
+  Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
+in
+(* Computation:2 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:3]] *)
+let simulation =
+  Simulation.make ~multiplicity ~charge ~nuclei ao_basis
+in
+(* Computation:3 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:4]] *)
+let hf =
+  Mo.Hartree_fock.make ~guess:`Huckel simulation
+in
+(* Computation:4 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:5]] *)
+let mo_basis =
+  Mo.Basis.of_hartree_fock hf
+in
+
+let frozen_core =
+  Mo.Frozen_core.(make Large nuclei)
+in
+
+let det_space =
+  Ci.Determinant_space.fci_of_mo_basis ~frozen_core mo_basis
+in
+(* Computation:5 ends here *)
+
+(* [[file:ex_fci.org::*Computation][Computation:6]] *)
+let ci =
+  Ci.make ~det_space simulation
+in
+(* Computation:6 ends here *)
+
+(* [[file:ex_fci.org::*Output][Output:1]] *)
+Format.printf "@[HF  energy : %f@]\n" (Mo.Hartree_fock.energy hf) ;
+Format.printf "@[FCI energy : %a@]\n" Vector.pp (Ci.eigenvalues ci)
+(* Output:1 ends here *)

examples/ex_fci.org

@@ -0,0 +1,142 @@
+#+TITLE: Full-CI
+
+#+PROPERTY: header-args :tangle ex_fci.ml :comments link :exports code 
+
+
+In this example, we write a program that makes a valence Full CI calculation with
+Hartree-Fock orbitals. The molecule is read in =xyz= format and a Gaussian
+atomic basis set in GAMESS format. 
+
+* Header 
+
+#+BEGIN_SRC ocaml
+open Qcaml
+open Common
+open 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
+  - =-c --charge=  : The charge of the molecule
+  - =-m --multiplicity= : The spin multiplicity
+
+** Definition
+
+   #+BEGIN_SRC ocaml
+let open Command_line in
+begin
+  set_header_doc (Sys.argv.(0));
+  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
+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
+let nuclei =
+  Particles.Nuclei.of_xyz_file nuclei_file
+in
+  #+END_SRC
+
+  Then we create a Gaussian AO basis using the atomic coordinates:
+  #+BEGIN_SRC ocaml
+let ao_basis =
+  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
+let simulation =
+  Simulation.make ~multiplicity ~charge ~nuclei ao_basis
+in
+  #+END_SRC
+
+  and we make the Hartree-Fock computation:
+  #+BEGIN_SRC ocaml
+let hf =
+  Mo.Hartree_fock.make ~guess:`Huckel simulation
+in
+  #+END_SRC
+
+  We define the FCI determinant space:
+  #+BEGIN_SRC ocaml
+let mo_basis =
+  Mo.Basis.of_hartree_fock hf
+in
+
+let frozen_core =
+  Mo.Frozen_core.(make Large nuclei)
+in
+
+let det_space =
+  Ci.Determinant_space.fci_of_mo_basis ~frozen_core mo_basis
+in
+  #+END_SRC
+
+  And we run the FCI calculation:
+  #+BEGIN_SRC ocaml
+let ci =
+  Ci.make ~det_space simulation
+in
+  #+END_SRC
+
+* Output
+
+  We print the FCI energy: 
+  #+BEGIN_SRC ocaml
+Format.printf "@[HF  energy : %f@]\n" (Mo.Hartree_fock.energy hf) ;
+Format.printf "@[FCI energy : %a@]\n" Vector.pp (Ci.eigenvalues ci)
+  #+END_SRC
+
+  

examples/ex_hartree_fock.org

@@ -1,6 +1,7 @@
 #+TITLE: Hartree-Fock
 
-#+PROPERTY
+#+PROPERTY: header-args :tangle ex_hartree_fock.ml :comments link :exports code
+
 
 In this example, we write a program that makes a Hartree-Fock
 calculation.  The molecule is read in =xyz= format and a Gaussian
@@ -8,7 +9,7 @@ atomic basis set in GAMESS format.
 
 * Header 
 
-#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
+#+BEGIN_SRC ocaml
 module Command_line = Qcaml.Common.Command_line
 module Util = Qcaml.Common.Util
 
@@ -26,7 +27,7 @@ let () =
 
 ** Definition
 
-   #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
+   #+BEGIN_SRC ocaml
 let open Command_line in
 begin
   set_header_doc (Sys.argv.(0));
@@ -54,7 +55,7 @@ end;
 
 ** Interpretation
 
-   #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
+   #+BEGIN_SRC ocaml
 let basis_file  = Util.of_some @@ Command_line.get "basis" in
 let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
 
@@ -78,33 +79,33 @@ in
 
   We first read the =xyz= file to create a molecule:
 
-  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
+  #+BEGIN_SRC ocaml
 let nuclei =
   Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
 in
   #+END_SRC
 
   Then we create a Gaussian AO basis using the atomic coordinates:
-  #+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml  
+  #+BEGIN_SRC ocaml
 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  
+  #+BEGIN_SRC ocaml
 let simulation = Qcaml.Simulation.make ~multiplicity ~charge ~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  
+  #+BEGIN_SRC ocaml
 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  
+  #+BEGIN_SRC ocaml
 Format.printf "@[%a@]" (Mo.Hartree_fock.pp) hf
   #+END_SRC
 

qcaml/lib/qcaml.ml

@@ -9,3 +9,7 @@ module Operators = Operators
 module Particles = Particles
 module Perturbation = Perturbation
 module Simulation = Simulation
+
+let (%.) = Linear_algebra.Vector.(%.) ;;
+let (%:) = Linear_algebra.Matrix.(%:) ;;
+