Merge branch 'master' of gitlab.com:scemama/QCaml

.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";;
 
 

Makefile.include

@@ -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:
+lib: _build/Utils/Util.cma
-	ocamlmklib -o bytelib ./_build/Utils/Util.cmo 
+
+_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

Notebooks/F12_matrix.ipynb

@@ -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
+}

_tags

@@ -1,4 +1,13 @@
-true: package(str,unix,bigarray,lacaml,alcotest,zarith,getopt)
+not <**/*.cma>   : linkdep(Utils/math_functions.o),  package(str,unix,bigarray,lacaml,alcotest,zarith,getopt)
-<*.byte>  : linkdep(Utils/math_functions.o), custom
+<**/*.byte>      : custom
-<*.native>: linkdep(Utils/math_functions.o)
+<**/*.native>    : linkdep(Utils/math_functions.o)
-<odoc-ltxhtml>: not_hygienic
+<odoc-ltxhtml>   : not_hygienic
+<Parallel>       : include
+<Nuclei>         : include
+<Utils>          : include
+<Basis>          : include
+<SCF>            : include
+<MOBasis>        : include
+<CI>             : include
+<F12>            : include
+<Perturbation>   : include

configure

@@ -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 "'