mirror of
https://gitlab.com/scemama/QCaml.git
synced 2024-12-21 20:03:32 +01:00
Makefile OK for notebooks
This commit is contained in:
parent
6dc872bae9
commit
241cd67613
17
.ocamlinit
17
.ocamlinit
@ -5,12 +5,21 @@ let () =
|
||||
|
||||
#use "topfind";;
|
||||
#require "lacaml";;
|
||||
#require "alcotest";;
|
||||
#require "zarith";;
|
||||
#require "getopt";;
|
||||
#directory "_build";;
|
||||
#directory "_build/Utils";;
|
||||
#directory "_build/Nuclei";;
|
||||
#directory "_build/Basis";;
|
||||
#directory "_build/HartreeFock";;
|
||||
#directory "_build/CI";;
|
||||
#directory "_build/MOBasis";;
|
||||
#directory "_build/Nuclei";;
|
||||
#directory "_build/Parallel";;
|
||||
#directory "_build/Perturbation";;
|
||||
#directory "_build/SCF";;
|
||||
#directory "_build/Utils";;
|
||||
|
||||
#load "Constants.cmo";;
|
||||
#load_rec "Util.cma";;
|
||||
|
||||
#use "topfind";;
|
||||
|
||||
|
||||
|
||||
@ -1,9 +1,8 @@
|
||||
.NOPARALLEL:
|
||||
|
||||
INCLUDE_DIRS=Parallel,Nuclei,Utils,Basis,SCF,MOBasis,CI,F12,Perturbation
|
||||
LIBS=
|
||||
PKGS=
|
||||
OCAMLBUILD=ocamlbuild -j 0 -cflags $(ocamlcflags) -lflags $(ocamllflags) $(ocamldocflags) -Is $(INCLUDE_DIRS) -ocamlopt $(ocamloptflags) $(mpi)
|
||||
OCAMLBUILD=ocamlbuild -j 0 -cflags $(ocamlcflags) -lflags $(ocamllflags) $(ocamldocflags) -ocamlopt $(ocamloptflags) $(mpi)
|
||||
|
||||
MLLFILES=$(filter-out $(wildcard _build/*), $(wildcard */*.mll) $(wildcard *.mll)) Utils/math_functions.c
|
||||
MLYFILES=$(filter-out $(wildcard _build/*), $(wildcard */*.mly) $(wildcard *.mly))
|
||||
@ -12,7 +11,7 @@ MLIFILES=$(filter-out $(wildcard Parallel_*/*) $(wildcard _build/*), $(wildcard
|
||||
|
||||
ALL_NATIVE=$(patsubst %.ml,%.native,$(wildcard run_*.ml))
|
||||
ALL_BYTE=$(patsubst %.ml,%.byte,$(wildcard run_*.ml))
|
||||
ALL_EXE=$(ALL_BYTE) $(ALL_NATIVE)
|
||||
ALL_EXE=$(ALL_BYTE) $(ALL_NATIVE) lib
|
||||
|
||||
.PHONY: default doc
|
||||
|
||||
@ -21,8 +20,10 @@ default: $(ALL_EXE)
|
||||
|
||||
tests: run_tests.native
|
||||
|
||||
bytelib:
|
||||
ocamlmklib -o bytelib ./_build/Utils/Util.cmo
|
||||
lib: _build/Utils/Util.cma
|
||||
|
||||
_build/Utils/Util.cma: _build/Utils/Util.cmo _build/Utils/math_functions.o
|
||||
ocamlmklib -o _build/Utils/Util _build/Utils/Util.cmo _build/Utils/math_functions.o
|
||||
|
||||
QCaml.odocl: $(MLIFILES)
|
||||
ls $(MLIFILES) | sed "s/\.mli//" > QCaml.odocl
|
||||
|
||||
159
Notebooks/F12_matrix.ipynb
Normal file
159
Notebooks/F12_matrix.ipynb
Normal file
@ -0,0 +1,159 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# Test of F12 matrix elements"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"- : unit = ()\n",
|
||||
"Findlib has been successfully loaded. Additional directives:\n",
|
||||
" #require \"package\";; to load a package\n",
|
||||
" #list;; to list the available packages\n",
|
||||
" #camlp4o;; to load camlp4 (standard syntax)\n",
|
||||
" #camlp4r;; to load camlp4 (revised syntax)\n",
|
||||
" #predicates \"p,q,...\";; to set these predicates\n",
|
||||
" Topfind.reset();; to force that packages will be reloaded\n",
|
||||
" #thread;; to enable threads\n",
|
||||
"\n",
|
||||
"- : unit = ()\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"#cd \"/home/scemama/QCaml\";;\n",
|
||||
"#use \"topfind\";;\n",
|
||||
"#require \"jupyter.notebook\";;\n",
|
||||
"\n",
|
||||
"#require \"lacaml\";;\n",
|
||||
"#require \"alcotest\";;\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",
|
||||
"#load \"Constants.cmo\";;\n",
|
||||
"#load_rec \"Util.cma\";;\n",
|
||||
"#load_rec \"Matrix.cmo\";;\n",
|
||||
"#load_rec \"Simulation.cmo\";;\n",
|
||||
"\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Simulation\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 12,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"File \"[12]\", line 3, characters 4-22:\n",
|
||||
"Warning 26: unused variable aux_basis_filename.\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"- : Simulation.t = <abstr>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 12,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"let basis_file = \"/home/scemama/qp2/data/basis/6-31g\" in\n",
|
||||
" \n",
|
||||
"let aux_basis_filename = \"/home/scemama/qp2/data/basis/cc-pvdz\" in\n",
|
||||
" \n",
|
||||
"let nuclei_file = \"be.xyz\" in\n",
|
||||
" \n",
|
||||
"let charge = 0 in\n",
|
||||
"\n",
|
||||
"let multiplicity = 1 in\n",
|
||||
"\n",
|
||||
"let f12 = F12factor.gaussian_geminal 1.0 in\n",
|
||||
"\n",
|
||||
"let simulation =\n",
|
||||
" Simulation.of_filenames ~f12 ~charge ~multiplicity ~nuclei:nuclei_file basis_file \n",
|
||||
"in\n",
|
||||
"simulation\n",
|
||||
" \n",
|
||||
"\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"ename": "NameError",
|
||||
"evalue": "name 'version' is not defined",
|
||||
"output_type": "error",
|
||||
"traceback": [
|
||||
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
|
||||
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
|
||||
"\u001b[0;32m<ipython-input-10-605b5d1778ad>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mversion\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
|
||||
"\u001b[0;31mNameError\u001b[0m: name 'version' is not defined"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"\n",
|
||||
"\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "OCaml default",
|
||||
"language": "OCaml",
|
||||
"name": "ocaml-jupyter"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": "text/x-ocaml",
|
||||
"file_extension": ".ml",
|
||||
"mimetype": "text/x-ocaml",
|
||||
"name": "OCaml",
|
||||
"nbconverter_exporter": null,
|
||||
"pygments_lexer": "OCaml",
|
||||
"version": "4.07.1"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 2
|
||||
}
|
||||
@ -74,19 +74,6 @@
|
||||
"----------------"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"A sparse vector is a structure made of:\n",
|
||||
"* The dimension of the vector space\n",
|
||||
"* The number of non-zeros\n",
|
||||
"* An array of indices\n",
|
||||
"* An array of values\n",
|
||||
"\n",
|
||||
"The indices are stored in an ``int Bigarray`` and the values are stored in a ``Lacaml.Vec.t``\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
@ -147,7 +134,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 32,
|
||||
"execution_count": 3,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -156,7 +143,7 @@
|
||||
"val pp : Format.formatter -> t -> unit = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 32,
|
||||
"execution_count": 3,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -189,7 +176,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"execution_count": 4,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -198,7 +185,7 @@
|
||||
"val make0 : int -> t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 5,
|
||||
"execution_count": 4,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -214,7 +201,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"execution_count": 5,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -223,7 +210,7 @@
|
||||
"val of_vec : ?threshold:float -> Lacaml.D.vec -> t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 6,
|
||||
"execution_count": 5,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -262,7 +249,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"execution_count": 6,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -271,7 +258,7 @@
|
||||
"val of_array : ?threshold:float -> float array -> t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 7,
|
||||
"execution_count": 6,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -284,7 +271,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 8,
|
||||
"execution_count": 7,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -293,7 +280,7 @@
|
||||
"val copy : t -> t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 8,
|
||||
"execution_count": 7,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -312,7 +299,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 37,
|
||||
"execution_count": 8,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -321,7 +308,7 @@
|
||||
"val map : ?threshold:float -> (float -> float) -> t -> t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 37,
|
||||
"execution_count": 8,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -361,16 +348,20 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"val x : t = {dim: 10 }\n"
|
||||
"val x : t =\n",
|
||||
" {dim = 10; nnz = 0; indices = <abstr>;\n",
|
||||
" values =\n",
|
||||
" R1 R2 R3 R30 R31 R32\n",
|
||||
" 6.91705E-310 6.91705E-310 0 ... 6.91705E-310 6.91705E-310 6.91705E-310}\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -381,17 +372,20 @@
|
||||
" 1 -2 0 ... 0 3 0\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"val sparse_a : t = {dim: 9 (1, 1) (2, -2) (5, 0.5) (6, 1e-08) (8, 3) }\n"
|
||||
"val sparse_a : t =\n",
|
||||
" {dim = 9; nnz = 5; indices = <abstr>;\n",
|
||||
" values = R1 R2 R3 R4 R5\n",
|
||||
" 1 -2 0.5 1E-08 3}\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -401,7 +395,7 @@
|
||||
"- : bool = true\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -411,7 +405,7 @@
|
||||
"- : bool = false\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 38,
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -440,7 +434,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -449,7 +443,7 @@
|
||||
"val dim : t -> int = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -459,7 +453,7 @@
|
||||
"val nnz : t -> int = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -471,7 +465,7 @@
|
||||
" <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -481,7 +475,7 @@
|
||||
"val values : t -> L.Vec.t = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -491,7 +485,7 @@
|
||||
"val density : t -> float = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 39,
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -506,7 +500,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 40,
|
||||
"execution_count": 11,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -515,7 +509,7 @@
|
||||
"val get : t -> int -> float = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 40,
|
||||
"execution_count": 11,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -549,7 +543,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 41,
|
||||
"execution_count": 12,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -558,7 +552,7 @@
|
||||
"val iter : (int -> float -> 'a) -> t -> unit = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 41,
|
||||
"execution_count": 12,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -579,7 +573,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 42,
|
||||
"execution_count": 13,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -588,7 +582,7 @@
|
||||
"- : bool = true\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 42,
|
||||
"execution_count": 13,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -609,7 +603,7 @@
|
||||
"- : unit = ()\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 42,
|
||||
"execution_count": 13,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
@ -628,7 +622,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 43,
|
||||
"execution_count": 14,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
@ -637,7 +631,7 @@
|
||||
"val to_assoc_list : t -> (int * float) list = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 43,
|
||||
"execution_count": 14,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
},
|
||||
@ -647,7 +641,7 @@
|
||||
"val to_vec : t -> Lacaml.D.vec = <fun>\n"
|
||||
]
|
||||
},
|
||||
"execution_count": 43,
|
||||
"execution_count": 14,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
|
||||
15
_tags
15
_tags
@ -1,4 +1,13 @@
|
||||
true: package(str,unix,bigarray,lacaml,alcotest,zarith,getopt)
|
||||
<*.byte> : linkdep(Utils/math_functions.o), custom
|
||||
<*.native>: linkdep(Utils/math_functions.o)
|
||||
not <**/*.cma> : linkdep(Utils/math_functions.o), package(str,unix,bigarray,lacaml,alcotest,zarith,getopt)
|
||||
<**/*.byte> : custom
|
||||
<**/*.native> : linkdep(Utils/math_functions.o)
|
||||
<odoc-ltxhtml> : not_hygienic
|
||||
<Parallel> : include
|
||||
<Nuclei> : include
|
||||
<Utils> : include
|
||||
<Basis> : include
|
||||
<SCF> : include
|
||||
<MOBasis> : include
|
||||
<CI> : include
|
||||
<F12> : include
|
||||
<Perturbation> : include
|
||||
|
||||
4
configure
vendored
4
configure
vendored
@ -11,9 +11,9 @@ doc='$(prefix)/doc'
|
||||
share='$(prefix)/share'
|
||||
man='$(prefix)/man'
|
||||
etc='$(prefix)/etc'
|
||||
ocamlcflags='"-g -warn-error A -cc gcc -ccopt -Ofast -ccopt -march=native "'
|
||||
ocamlcflags='"-g -warn-error A -cc gcc -ccopt -Ofast -ccopt -march=native -ccopt=-fPIC "'
|
||||
ocamllflags='"-g -warn-error A"'
|
||||
ocamloptflags='"opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100 -cc gcc -ccopt -Ofast -ccopt -march=native"'
|
||||
ocamloptflags='"opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100 -cc gcc -ccopt -Ofast -ccopt -march=native -ccopt=-fPIC "'
|
||||
ocamldocflags='-docflags "-g ltxhtml.cma -sort -css-style $(PWD)/style.css -colorize-code"'
|
||||
mpi=''
|
||||
ocamloptflags_profile='"opt -p -cc gcc -ccopt -Ofast -ccopt -march=native -ccopt -no-pie "'
|
||||
|
||||
Loading…
Reference in New Issue
Block a user