Localization

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Anthony Scemama 2020-04-19 23:29:00 +02:00
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"heading_collapsed": true
},
"source": [
"# Installation de QCaml"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"1. Clonage de QCaml:\n",
" ```bash\n",
" git clone https://gitlab.com/scemama/QCaml.git\n",
" ```\n",
"2. Installation des dependances:\n",
" ```bash\n",
" opam install ocamlbuild ocamlfind lacaml gnuplot getopt alcotest zarith\n",
" cd QCaml\n",
" ./configure\n",
" ```\n",
"3. Compilation\n",
" ```bash\n",
" make\n",
" ```"
]
},
{
"cell_type": "markdown",
"metadata": {
"heading_collapsed": true
},
"source": [
"# Initialisation"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Bloc a executer avant de pouvoir utiliser QCaml dans le Notebook"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let png_image = print_endline ;;\n",
"\n",
"(* --------- *)\n",
"\n",
"(*Mettre le bon chemin ici *)\n",
"#cd \"/home/scemama/QCaml\";;\n",
"\n",
"#use \"topfind\";;\n",
"#require \"jupyter.notebook\";;\n",
"\n",
"#require \"gnuplot\";;\n",
"let png_image name = \n",
" Jupyter_notebook.display_file ~base64:true \"image/png\" (\"Notebooks/images/\"^name)\n",
";;\n",
"\n",
"#require \"lacaml.top\";;\n",
"#require \"alcotest\";;\n",
"#require \"str\";;\n",
"#require \"bigarray\";;\n",
"#require \"zarith\";;\n",
"#require \"getopt\";;\n",
"#directory \"_build\";;\n",
"#directory \"_build/Basis\";;\n",
"#directory \"_build/CI\";;\n",
"#directory \"_build/MOBasis\";;\n",
"#directory \"_build/Nuclei\";;\n",
"#directory \"_build/Parallel\";;\n",
"#directory \"_build/Perturbation\";;\n",
"#directory \"_build/SCF\";;\n",
"#directory \"_build/Utils\";;\n",
"\n",
"\n",
"#load \"Constants.cmo\";;\n",
"#load_rec \"Util.cma\";;\n",
"#load_rec \"Matrix.cmo\";;\n",
"#load_rec \"Simulation.cmo\";;\n",
"#load_rec \"Spindeterminant.cmo\";;\n",
"#load_rec \"Determinant.cmo\";;\n",
"#load_rec \"HartreeFock.cmo\";;\n",
"#load_rec \"MOBasis.cmo\";;\n",
"#load_rec \"F12CI.cmo\";;\n",
"\n",
"#install_printer AngularMomentum.pp_string ;;\n",
"#install_printer Basis.pp ;;\n",
"#install_printer Charge.pp ;;\n",
"#install_printer Coordinate.pp ;;\n",
"#install_printer Vector.pp;;\n",
"#install_printer Matrix.pp;;\n",
"#install_printer Util.pp_float_2darray;;\n",
"#install_printer Util.pp_float_array;;\n",
"#install_printer Util.pp_matrix;;\n",
"#install_printer HartreeFock.pp ;;\n",
"#install_printer Fock.pp ;;\n",
"#install_printer MOClass.pp ;;\n",
"#install_printer DeterminantSpace.pp;;\n",
"#install_printer SpindeterminantSpace.pp;;\n",
"#install_printer Bitstring.pp;;\n",
"let pp_mo ppf t = MOBasis.pp ~start:1 ~finish:0 ppf t ;;\n",
"#install_printer pp_mo;;\n",
"\n",
"\n",
"(* --------- *)\n",
"\n",
"open Lacaml.D\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Calculs"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## H_{n}"
]
},
{
"cell_type": "markdown",
"metadata": {
"heading_collapsed": true
},
"source": [
"### Generation du fichier xyz"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Pour faire plusieurs chaines d'hydrogene, il faut d'abord\n",
"construire une fonction qui genere un fichier xyz pour\n",
"une chaine de `n` hydrogenes avec une distance H-H de `d` bohr.\n",
"Le fichier xyz est en Angstrom, donc il faut utiliser\n",
"`Constants.a0` pour convertir les bohr en Angstroms.\n",
"\n",
"Voila un exemple de ce qu'on doit obtenir pour 20 hydrogenes:\n",
"\n",
"```\n",
" 20\n",
"Hydrogen chain, d=1.8 Bohr\n",
"H -4.286335 0.000000 0.000000\n",
"H -3.333816 0.000000 0.000000\n",
"H -2.381297 0.000000 0.000000\n",
"H -1.428778 0.000000 0.000000\n",
"H -0.476259 0.000000 0.000000\n",
"H 0.476259 0.000000 0.000000\n",
"H 1.428778 0.000000 0.000000\n",
"H 2.381297 0.000000 0.000000\n",
"H 3.333816 0.000000 0.000000\n",
"H 4.286335 0.000000 0.000000\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let string_of_xyz d n =\n",
"\" 10\n",
"Hydrogen chain, d=1.8 Bohr\n",
"H -4.286335 0.000000 0.000000\n",
"H -3.333816 0.000000 0.000000\n",
"H -2.381297 0.000000 0.000000\n",
"H -1.428778 0.000000 0.000000\n",
"H -0.476259 0.000000 0.000000\n",
"H 0.476259 0.000000 0.000000\n",
"H 1.428778 0.000000 0.000000\n",
"H 2.381297 0.000000 0.000000\n",
"H 3.333816 0.000000 0.000000\n",
"H 4.286335 0.000000 0.000000\n",
"\"\n",
"\n",
"let xyz_string =\n",
" string_of_xyz 1.8 10"
]
},
{
"cell_type": "markdown",
"metadata": {
"heading_collapsed": true
},
"source": [
"### Base atomique"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Les bases atomiques sont telechargeables ici: https://www.basissetexchange.org/\n",
"\n",
"Voila la base STO-6G pour l'hydrogene:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let basis_string = \n",
"\"\n",
"HYDROGEN\n",
"S 6\n",
"1 0.3552322122E+02 0.9163596281E-02\n",
"2 0.6513143725E+01 0.4936149294E-01\n",
"3 0.1822142904E+01 0.1685383049E+00\n",
"4 0.6259552659E+00 0.3705627997E+00\n",
"5 0.2430767471E+00 0.4164915298E+00\n",
"6 0.1001124280E+00 0.1303340841E+00\n",
"\n",
"\""
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Une orbitale atomique STO-6G centree sur l'atome A est composee d'une contraction de 6 Gaussiennes:\n",
"$$\n",
"\\chi(r) = \\sum_{i=1}^6 a_i \\exp \\left( -\\alpha_i |r-r_A|^2 \\right)\n",
"$$\n",
"Dans le fichier de base, la 2ieme colonne represente l'exposant $\\alpha_i$ et la 3ieme colonne le coefficient de contraction $a_i$."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let nuclei =\n",
" Nuclei.of_xyz_string xyz_string\n",
" \n",
"let basis = \n",
" Basis.of_nuclei_and_basis_string nuclei basis_string\n",
" \n",
"let simulation = \n",
" Simulation.make ~charge:0 ~multiplicity:1 ~nuclei basis\n",
" \n",
"let ao_basis = \n",
" Simulation.ao_basis simulation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Plot des orbitales atomiques"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"let plot data filename = \n",
" let output = Gnuplot.Output.create (`Png filename) in\n",
" let gp = Gnuplot.create () in\n",
" Gnuplot.set gp ~use_grid:true;\n",
" List.map Gnuplot.Series.lines_xy data\n",
" |> Gnuplot.plot_many gp ~output;\n",
" Gnuplot.close gp ;\n",
" Jupyter_notebook.display_file ~base64:true \"image/png\" filename\n",
";;\n",
"\n",
"let x_values = \n",
" let n = 1000 in\n",
" \n",
" let xmin, xmax =\n",
" let coord =\n",
" Array.map snd nuclei\n",
" |> Array.map (fun a -> Coordinate.(get X) a)\n",
" in\n",
" Array.sort compare coord;\n",
" coord.(0) -. 4. ,\n",
" coord.(Array.length coord -1) +. 4.\n",
" in\n",
"\n",
" let dx =\n",
" (xmax -. xmin) /. (float_of_int n -. 1.)\n",
" in\n",
" Array.init n (fun i -> xmin +. (float_of_int i)*.dx)\n",
"in\n",
"\n",
"let data = \n",
" Array.map (fun x -> \n",
" let point = Coordinate.make_angstrom\n",
" { Coordinate.\n",
" x ; y = 0. ; z = 0.\n",
" } in\n",
" AOBasis.values ao_basis point\n",
" ) x_values\n",
" |> Mat.of_col_vecs\n",
" |> Mat.transpose_copy\n",
" |> Mat.to_col_vecs\n",
" |> Array.map Vec.to_list\n",
" |> Array.map (fun l -> List.mapi (fun i y -> (x_values.(i),y)) l)\n",
" |> Array.to_list\n",
"in\n",
"plot data \"test_data.png\""
]
},
{
"cell_type": "markdown",
"metadata": {
"heading_collapsed": true
},
"source": [
"### Calcul Hartree-Fock pour generer des orbitales moleculaires"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let hf = HartreeFock.make simulation"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let mo_basis = MOBasis.of_hartree_fock hf"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Orbitales moleculaires :\n",
"$$\n",
"\\phi_j(r) = \\sum_{i=1}^{N_b} C_{ij} \\chi_i(r)\n",
"$$\n",
"\n",
"* $i$: lignes\n",
"* $j$: colonnes"
]
},
{
"cell_type": "markdown",
"metadata": {
"hidden": true
},
"source": [
"Extraction des OM de la structure de donnees `mo_basis` comme une matrice $C$ utilisable avec Lacaml:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"hidden": true
},
"outputs": [],
"source": [
"let mo_coef = MOBasis.mo_coef mo_basis"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"let plot data filename = \n",
" let output = Gnuplot.Output.create (`Png filename) in\n",
" let gp = Gnuplot.create () in\n",
" Gnuplot.set gp ~use_grid:true;\n",
" List.map Gnuplot.Series.lines_xy data\n",
" |> Gnuplot.plot_many gp ~output;\n",
" Gnuplot.close gp ;\n",
" Jupyter_notebook.display_file ~base64:true \"image/png\" filename\n",
";;\n",
"\n",
"let x_values = \n",
" let n = 1000 in\n",
" \n",
" let xmin, xmax =\n",
" let coord =\n",
" Array.map snd nuclei\n",
" |> Array.map (fun a -> Coordinate.(get X) a)\n",
" in\n",
" Array.sort compare coord;\n",
" coord.(0) -. 4. ,\n",
" coord.(Array.length coord -1) +. 4.\n",
" in\n",
"\n",
" let dx =\n",
" (xmax -. xmin) /. (float_of_int n -. 1.)\n",
" in\n",
" Array.init n (fun i -> xmin +. (float_of_int i)*.dx)\n",
"in\n",
"\n",
"let data = \n",
" let result = \n",
" Array.map (fun x -> \n",
" let point = Coordinate.make_angstrom\n",
" { Coordinate.\n",
" x ; y = 0. ; z = 0.\n",
" } in\n",
" MOBasis.values mo_basis point\n",
" ) x_values\n",
" |> Mat.of_col_vecs\n",
" |> Mat.transpose_copy\n",
" |> Mat.to_col_vecs\n",
" |> Array.map Vec.to_list\n",
" |> Array.map (fun l -> List.mapi (fun i y -> (x_values.(i),y)) l)\n",
" in\n",
" [ result.(0) ; result.(1) ]\n",
"in\n",
"\n",
"plot data \"test_data.png\""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Calcul des integrales necessaires"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"let dx, x_values = \n",
" let n = 101 in\n",
" \n",
" let xmin, xmax =\n",
" let coord =\n",
" Array.map snd nuclei\n",
" |> Array.map (fun a -> Coordinate.(get X) a)\n",
" in\n",
" Array.sort compare coord;\n",
" coord.(0) -. 10. ,\n",
" coord.(Array.length coord -1) +. 10.\n",
" in\n",
"\n",
" let dx =\n",
" (xmax -. xmin) /. (float_of_int n -. 1.)\n",
" in\n",
" dx, Array.init n (fun i -> xmin +. (float_of_int i)*.dx)\n",
"in\n",
"\n",
"let dy, y_values = \n",
" let n = 51 in\n",
" \n",
" let ymin, ymax =\n",
" let coord =\n",
" Array.map snd nuclei\n",
" |> Array.map (fun a -> Coordinate.(get Y) a)\n",
" in\n",
" Array.sort compare coord;\n",
" coord.(0) -. 10. ,\n",
" coord.(Array.length coord -1) +. 10.\n",
" in\n",
"\n",
" let dy =\n",
" (ymax -. ymin) /. (float_of_int n -. 1.)\n",
" in\n",
" dy, Array.init n (fun i -> ymin +. (float_of_int i)*.dy)\n",
"in\n",
"\n",
"\n",
"let dz, z_values = \n",
" let n = 51 in\n",
" \n",
" let zmin, zmax =\n",
" let coord =\n",
" Array.map snd nuclei\n",
" |> Array.map (fun a -> Coordinate.(get Z) a)\n",
" in\n",
" Array.sort compare coord;\n",
" coord.(0) -. 10. ,\n",
" coord.(Array.length coord -1) +. 10.\n",
" in\n",
"\n",
" let dz =\n",
" (zmax -. zmin) /. (float_of_int n -. 1.)\n",
" in\n",
" dz, Array.init n (fun i -> zmin +. (float_of_int i)*.dz)\n",
"in\n",
"\n",
"\n",
"let points = \n",
" Array.map (fun x -> \n",
" Array.map (fun y -> \n",
" Array.map (fun z -> \n",
" Coordinate.make_angstrom\n",
" { Coordinate.\n",
" x ; y ; z \n",
" } \n",
" ) x_values\n",
" ) y_values\n",
" ) z_values\n",
" |> Array.map Array.to_list\n",
" |> Array.to_list\n",
" |> List.concat\n",
" |> Array.concat\n",
"in\n",
"\n",
"let dv = dx *. dy *. dz in\n",
"Printf.printf \"%f %f %f %f\\n%!\" dx dy dz dv;\n",
"\n",
"let ao_val = \n",
" Array.map (fun point -> \n",
" AOBasis.values ao_basis point\n",
" ) points\n",
" |> Mat.of_col_vecs\n",
"in\n",
"\n",
"(*\n",
"let r = \n",
" gemm ~transb:`T ao_val ao_val \n",
"in\n",
"Mat.scal dv r;\n",
"r;;\n",
"AOBasis.overlap ao_basis |> Overlap.matrix ;;\n",
"*)\n",
"\n",
"let ao_x_val = \n",
" Array.map (fun point -> \n",
" let r = AOBasis.values ao_basis point in\n",
" scal (Coordinate.(get X) point) r;\n",
" r\n",
" ) points\n",
" |> Mat.of_col_vecs\n",
"in\n",
"\n",
"let r = \n",
" gemm ~transb:`T ao_val ao_x_val \n",
"in\n",
"Mat.scal dv r;\n",
"r;;\n",
"AOBasis.multipole ao_basis |> Multipole.matrix_x ;;"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Localisation des orbitales"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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"kernelspec": {
"display_name": "OCaml 4.10.0",
"language": "OCaml",
"name": "ocaml-jupyter"
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"language_info": {
"codemirror_mode": "text/x-ocaml",
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"mimetype": "text/x-ocaml",
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