10
1
mirror of https://gitlab.com/scemama/QCaml.git synced 2024-07-19 01:13:26 +02:00

Makefile OK for notebooks

This commit is contained in:
Anthony Scemama 2019-11-30 10:41:07 +01:00
parent 6dc872bae9
commit 241cd67613
6 changed files with 236 additions and 64 deletions

View File

@ -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";;

View File

@ -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
View 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
}

View File

@ -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"
}

17
_tags
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@ -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)
<odoc-ltxhtml>: not_hygienic
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
View File

@ -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 "'