diff --git a/Basis/Basis.ml b/Basis/Basis.ml index cae8fd8..e831d8f 100644 --- a/Basis/Basis.ml +++ b/Basis/Basis.ml @@ -101,3 +101,6 @@ let of_nuclei_and_basis_filenames ~nuclei filenames = of_nuclei_and_general_basis nuclei general_basis +let pp ppf t = + Format.fprintf ppf "@[%s@]" (to_string t) + diff --git a/Basis/Basis.mli b/Basis/Basis.mli index 9402864..83f010d 100644 --- a/Basis/Basis.mli +++ b/Basis/Basis.mli @@ -41,5 +41,5 @@ val general_basis : t -> GeneralBasis.t val to_string : t -> string (** Pretty prints the basis set in a string. TODO *) - +val pp : Format.formatter -> t -> unit diff --git a/Notebooks/F12_matrix.ipynb b/Notebooks/F12_matrix.ipynb index 4dee672..94f1983 100644 --- a/Notebooks/F12_matrix.ipynb +++ b/Notebooks/F12_matrix.ipynb @@ -8,9 +8,18 @@ ] }, { - "cell_type": "code", - "execution_count": 7, + "cell_type": "markdown", "metadata": {}, + "source": [ + "## Initialization" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": true + }, "outputs": [ { "name": "stdout", @@ -28,6 +37,57 @@ "\n", "- : unit = ()\n" ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/scemama/qp2/external/opam/4.07.1/lib/bytes: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/base64: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/base64/base64.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ocaml/compiler-libs: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ocaml/compiler-libs/ocamlcommon.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/result: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/result/result.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ppx_deriving/runtime: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ppx_deriving/runtime/ppx_deriving_runtime.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ppx_deriving_yojson/runtime: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ppx_deriving_yojson/runtime/ppx_deriving_yojson_runtime.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ocaml/unix.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/uuidm: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/uuidm/uuidm.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/easy-format: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/easy-format/easy_format.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/biniou: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/biniou/biniou.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/yojson: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/yojson/yojson.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/jupyter: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/jupyter/jupyter.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/jupyter/notebook: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/jupyter/notebook/jupyter_notebook.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ocaml/bigarray.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/lacaml: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/lacaml/lacaml.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/astring: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/astring/astring.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/cmdliner: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/cmdliner/cmdliner.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/seq: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/stdlib-shims: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/stdlib-shims/stdlib_shims.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/fmt: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/fmt/fmt.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/fmt/fmt_cli.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/fmt/fmt_tty.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/alcotest: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/alcotest/alcotest.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/ocaml/str.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/zarith: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/zarith/zarith.cma: loaded\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/getopt: added to search path\n", + "/home/scemama/qp2/external/opam/4.07.1/lib/getopt/getopt.cma: loaded\n" + ] } ], "source": [ @@ -37,6 +97,8 @@ "\n", "#require \"lacaml\";;\n", "#require \"alcotest\";;\n", + "#require \"str\";;\n", + "#require \"bigarray\";;\n", "#require \"zarith\";;\n", "#require \"getopt\";;\n", "#directory \"_build\";;\n", @@ -47,100 +109,469 @@ "#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" + "#directory \"_build/Utils\";;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Simulation\n" + "### Modules to load" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "#load \"Constants.cmo\";;\n", + "#load_rec \"Util.cma\";;\n", + "#load_rec \"Matrix.cmo\";;\n", + "#load_rec \"Simulation.cmo\";;\n", + "#load_rec \"Simulation.cmo\";;\n", + "#load_rec \"HartreeFock.cmo\";;\n", + "\n", + "open Lacaml.D;;" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Printers" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "#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" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Run" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Simulation\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, "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": [ + "val basis_filename : string = \"/home/scemama/qp2/data/basis/cc-pvdz\"\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" }, { "data": { "text/plain": [ - "- : Simulation.t = \n" + "val aux_basis_filename : string = \"/home/scemama/qp2/data/basis/cc-pvtz\"\n" ] }, - "execution_count": 12, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val nuclei : Nuclei.t = [|(Element.Be, 0.0000 0.0000 0.0000)|]\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val basis : Basis.t =\n", + " \n", + " Atomic Basis set\n", + " ----------------\n", + "\n", + "-----------------------------------------------------------------------\n", + " # Angular Coordinates (Bohr) Exponents Coefficients\n", + " Momentum X Y Z\n", + "-----------------------------------------------------------------------\n", + " 1-3 S 0.0000 0.0000 0.0000 2.94000000e+03 6.80000000e-04\n", + " 4.41200000e+02 5.23600000e-03\n", + " 1.00500000e+02 2.66060000e-02\n", + " 2.84300000e+01 9.99930000e-02\n", + " 9.16900000e+00 2.69702000e-01\n", + " 3.19600000e+00 4.51469000e-01\n", + " 1.15900000e+00 2.95074000e-01\n", + " 1.81100000e-01 1.25870000e-02\n", + " \n", + " 2.94000000e+03 -1.23000000e-04\n", + " 4.41200000e+02 -9.66000000e-04\n", + " 1.00500000e+02 -4.83100000e-03\n", + " 2.84300000e+01 -1.93140000e-02\n", + " 9.16900000e+00 -5.32800000e-02\n", + " 3.19600000e+00 -1.20723000e-01\n", + " 1.15900000e+00 -1.33435000e-01\n", + " 1.81100000e-01 5.30767000e-01\n", + " \n", + " 5.89000000e-02 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + " 4-9 P 0.0000 0.0000 0.0000 3.61900000e+00 2.91110000e-02\n", + " 7.11000000e-01 1.69365000e-01\n", + " 1.95100000e-01 5.13458000e-01\n", + " \n", + " 6.01800000e-02 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + " 10-15 D 0.0000 0.0000 0.0000 2.38000000e-01 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + "\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val aux_basis : Basis.t =\n", + " \n", + " Atomic Basis set\n", + " ----------------\n", + "\n", + "-----------------------------------------------------------------------\n", + " # Angular Coordinates (Bohr) Exponents Coefficients\n", + " Momentum X Y Z\n", + "-----------------------------------------------------------------------\n", + " 1-7 S 0.0000 0.0000 0.0000 2.94000000e+03 6.80000000e-04\n", + " 4.41200000e+02 5.23600000e-03\n", + " 1.00500000e+02 2.66060000e-02\n", + " 2.84300000e+01 9.99930000e-02\n", + " 9.16900000e+00 2.69702000e-01\n", + " 3.19600000e+00 4.51469000e-01\n", + " 1.15900000e+00 2.95074000e-01\n", + " 1.81100000e-01 1.25870000e-02\n", + " \n", + " 2.94000000e+03 -1.23000000e-04\n", + " 4.41200000e+02 -9.66000000e-04\n", + " 1.00500000e+02 -4.83100000e-03\n", + " 2.84300000e+01 -1.93140000e-02\n", + " 9.16900000e+00 -5.32800000e-02\n", + " 3.19600000e+00 -1.20723000e-01\n", + " 1.15900000e+00 -1.33435000e-01\n", + " 1.81100000e-01 5.30767000e-01\n", + " \n", + " 5.89000000e-02 1.00000000e+00\n", + " \n", + " 6.86300000e+03 2.36000000e-04\n", + " 1.03000000e+03 1.82600000e-03\n", + " 2.34700000e+02 9.45200000e-03\n", + " 6.65600000e+01 3.79570000e-02\n", + " 2.16900000e+01 1.19965000e-01\n", + " 7.73400000e+00 2.82162000e-01\n", + " 2.91600000e+00 4.27404000e-01\n", + " 1.13000000e+00 2.66278000e-01\n", + " 1.10100000e-01 -7.27500000e-03\n", + " \n", + " 6.86300000e+03 -4.30000000e-05\n", + " 1.03000000e+03 -3.33000000e-04\n", + " 2.34700000e+02 -1.73600000e-03\n", + " 6.65600000e+01 -7.01200000e-03\n", + " 2.16900000e+01 -2.31260000e-02\n", + " 7.73400000e+00 -5.81380000e-02\n", + " 2.91600000e+00 -1.14556000e-01\n", + " 1.13000000e+00 -1.35908000e-01\n", + " 1.10100000e-01 5.77441000e-01\n", + " \n", + " 2.57700000e-01 1.00000000e+00\n", + " \n", + " 4.40900000e-02 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + " 4-18 P 0.0000 0.0000 0.0000 3.61900000e+00 2.91110000e-02\n", + " 7.11000000e-01 1.69365000e-01\n", + " 1.95100000e-01 5.13458000e-01\n", + " \n", + " 6.01800000e-02 1.00000000e+00\n", + " \n", + " 7.43600000e+00 1.07360000e-02\n", + " 1.57700000e+00 6.28540000e-02\n", + " 4.35200000e-01 2.48180000e-01\n", + " \n", + " 1.43800000e-01 1.00000000e+00\n", + " \n", + " 4.99400000e-02 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + " 10-27 D 0.0000 0.0000 0.0000 2.38000000e-01 1.00000000e+00\n", + " \n", + " 3.48000000e-01 1.00000000e+00\n", + " \n", + " 1.80300000e-01 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + " 41-50 F 0.0000 0.0000 0.0000 3.25000000e-01 1.00000000e+00\n", + " \n", + " \n", + "-----------------------------------------------------------------------\n", + "\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val f12 : F12factor.t =\n", + " {F12factor.expo_s = 1.;\n", + " gaussian =\n", + " {GaussianOperator.coef_g =\n", + " [ -0.314400 -0.303700 -0.168100 -0.098110 -0.060240 -0.037260 ];\n", + " expo_sg =\n", + " [ 0.220900 1.004000 3.622000 12.160000 45.870000 254.400000 ];\n", + " expo_sg_inv =\n", + " [ 4.526935 0.996016 0.276091 0.082237 0.021801 0.003931 ]}}\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val charge : int = 0\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val multiplicity : int = 1\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "val simulation : Simulation.t = \n" + ] + }, + "execution_count": 4, "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", + "let basis_filename = \"/home/scemama/qp2/data/basis/cc-pvdz\" \n", + "let aux_basis_filename = \"/home/scemama/qp2/data/basis/cc-pvtz\" \n", + "let nuclei = Nuclei.of_zmt_string \"be\" \n", "\n", - "let multiplicity = 1 in\n", + "let basis = Basis.of_nuclei_and_basis_filenames ~nuclei [basis_filename] \n", + "let aux_basis = Basis.of_nuclei_and_basis_filenames ~nuclei (basis_filename :: aux_basis_filename :: []) \n", + "let f12 = F12factor.gaussian_geminal 1.0 \n", + "let charge = 0 \n", + "let multiplicity = 1 \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" + " Simulation.make \n", + " ~f12 ~charge ~multiplicity ~nuclei\n", + " ~cartesian:true\n", + " basis\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Hartree-Fock" ] }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 7, "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\u001b[0m in \u001b[0;36m\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" + "name": "stdout", + "output_type": "stream", + "text": [ + "MOs =\n", + "\n", + "\n", + " -- 1 -- -- 2 -- -- 3 -- -- 4 -- -- 5 --\n", + " 1 1.0006 0.00028918 -0 -0 0\n", + " 2 0.00576322 1.00367 -7.13815E-16 -0 0\n", + " 3 -0.00181801 0.582215 4.68436E-16 -6.48338E-16 0\n", + " ... ... ... ... ...\n", + " 13 -0.00209072 -0.00172308 -0 -0 0\n", + " 14 -0 -0 -0 -0 0\n", + " 15 -0.00209072 -0.00172308 -0 -8.65517E-16 0\n", + " \n", + "\n", + " -- 6 -- -- 7 -- -- 8 -- -- 9 -- -- 10 --\n", + " 1 0.549926 -7.88204E-16 0 0 -5.10457E-16\n", + " 2 2.77214 -4.20928E-15 0 -8.18142E-16 -6.26457E-16\n", + " 3 -1.826 2.68321E-15 0 0 4.82834E-15\n", + " ... ... ... ... ...\n", + " 13 0.224421 0 0 0 -0.995373\n", + " 14 -0 0 0 0 -0.00304009\n", + " 15 0.224421 0 0 0 0.534433\n", + " \n", + "\n", + " -- 11 -- -- 12 -- -- 13 -- -- 14 -- -- 15 --\n", + " 1 -8.47272E-16 4.18722E-16 0 0 0.516133\n", + " 2 -7.29877E-15 3.26085E-15 -5.13582E-16 0 4.52711\n", + " 3 -1.53999E-15 0 0 0 1.08073\n", + " ... ... ... ... ...\n", + " 13 0.0741226 0.0584492 -0.01795 0.000120624 -1.45115\n", + " 14 0.00668622 0.201298 0.848372 -0.489582 0\n", + " 15 0.750441 -0.380516 0.0792247 -0.0122393 -1.45115\n", + " \n" ] + }, + { + "data": { + "text/plain": [ + "val hf : HartreeFock.t = \n", + "======================================================================\n", + " Restricted Hartree-Fock \n", + "======================================================================\n", + "\n", + " ------------------------------------------------------------\n", + " # HF energy Convergence HOMO-LUMO\n", + " ------------------------------------------------------------\n", + " 1 -14.05142130 8.0958e-01 0.2991\n", + " 2 -14.51982122 2.7933e-01 0.3600\n", + " 3 -14.56519147 8.3990e-02 0.3674\n", + " 4 -14.57117146 2.6217e-02 0.3679\n", + " 5 -14.57214606 1.0744e-02 0.3676\n", + " 6 -14.57232209 5.0392e-03 0.3675\n", + " 7 -14.57235521 2.2956e-03 0.3674\n", + " 8 -14.57236154 1.0293e-03 0.3673\n", + " 9 -14.57236304 4.1738e-08 0.3673\n", + " 10 -14.57236304 4.9181e-09 0.3673\n", + " ------------------------------------------------------------\n", + "\n", + "\n", + " ============================================================\n", + " One-electron energy -19.0610711155\n", + " Kinetic 14.5598880887\n", + " Potential -33.6209592042\n", + " -------------------------------------------------------- \n", + " Two-electron energy 4.4887080772\n", + " Coulomb 7.1543328046\n", + " Exchange -2.6656247274\n", + " -------------------------------------------------------- \n", + " HF HOMO -8.4100296422\n", + " HF LUMO 1.5842692336\n", + " HF LUMO-LUMO 9.9942988758\n", + " -------------------------------------------------------- \n", + " Electronic energy -14.5723630383\n", + " Nuclear repulsion 0.0000000000\n", + " Hartree-Fock energy -14.5723630383\n", + " ============================================================\n", + " \n", + "\n" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" } ], - "source": [] + "source": [ + "let hf = \n", + " HartreeFock.make ~guess:`Hcore simulation \n" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "val ints : ERI.t = \n" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "text/plain": [ + "- : float = 0.\n" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "let ints = Simulation.ao_basis simulation\n", + "|> AOBasis.ee_ints ;;\n", + "ERI.get_phys ints 1 1 1 4" + ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], - "source": [ - "\n", - "\n" - ] + "source": [] } ], "metadata": { "kernelspec": { - "display_name": "OCaml default", + "display_name": "OCaml 4.07.1", "language": "OCaml", "name": "ocaml-jupyter" }, diff --git a/Notebooks/SpVec.ipynb b/Notebooks/SpVec.ipynb index 4070396..72b1b75 100644 --- a/Notebooks/SpVec.ipynb +++ b/Notebooks/SpVec.ipynb @@ -1746,7 +1746,7 @@ "metadata": { "celltoolbar": "Raw Cell Format", "kernelspec": { - "display_name": "OCaml default", + "display_name": "OCaml 4.07.1", "language": "OCaml", "name": "ocaml-jupyter" }, diff --git a/Parallel_serial/SharedMemory.ml b/Parallel_serial/SharedMemory.ml index 5d89c91..134d6b5 100644 --- a/Parallel_serial/SharedMemory.ml +++ b/Parallel_serial/SharedMemory.ml @@ -1,3 +1,7 @@ let create ?(temp_dir="/dev/shm") data_type size_array = - Bigarray.Genarray.create data_type Bigarray.fortran_layout size_array + let result = + Bigarray.Genarray.create data_type Bigarray.fortran_layout size_array + in + Bigarray.Genarray.fill result 0.; + result diff --git a/SCF/Fock.ml b/SCF/Fock.ml index 194d18f..e8986fd 100644 --- a/SCF/Fock.ml +++ b/SCF/Fock.ml @@ -234,7 +234,7 @@ let scale alpha f1 = -let pp_fock ppf a = +let pp ppf a = Format.fprintf ppf "@[<2>"; Format.fprintf ppf "@[ Fock matrix:@[<2>@[%a@]@.]@]" pp_matrix a.fock; Format.fprintf ppf "@[ Core Hamiltonian:@[<2>@[%a@]@.]@]" pp_matrix a.core; diff --git a/SCF/Fock.mli b/SCF/Fock.mli index 21da4e8..cf87500 100644 --- a/SCF/Fock.mli +++ b/SCF/Fock.mli @@ -46,5 +46,5 @@ val sub : t -> t -> t (** {1 Printers} *) -val pp_fock : Format.formatter -> t -> unit +val pp : Format.formatter -> t -> unit diff --git a/SCF/HartreeFock.ml b/SCF/HartreeFock.ml index 7d8c126..c43111d 100644 --- a/SCF/HartreeFock.ml +++ b/SCF/HartreeFock.ml @@ -192,7 +192,7 @@ let make ?kind ?guess:(guess=`Huckel) ?max_scf:(max_scf=64) - ?level_shift:(level_shift=0.1) + ?level_shift:(level_shift=0.2) ?threshold_SCF:(threshold_SCF=1.e-8) simulation = @@ -223,6 +223,7 @@ let make (* Orthogonalization matrix *) let m_X = Ao.ortho ao_basis + |> Util.remove_epsilons in (* Overlap matrix *) @@ -276,6 +277,7 @@ let make (* Density matrix over nocc occupied MOs *) let m_P = gemm ~alpha:2. ~transb:`T ~k:nocc m_C m_C + |> Util.remove_epsilons in (* Fock matrix in AO basis *) @@ -698,7 +700,7 @@ let pp_summary ppf t = -let pp_hf ppf t = +let pp ppf t = Format.fprintf ppf "@.@[%s@]@." (Printing.line ~c:'=' 70); Format.fprintf ppf "@[%34s %-34s@]@." (match t.kind with | UHF -> "Unrestricted" diff --git a/SCF/HartreeFock.mli b/SCF/HartreeFock.mli index 3384e2a..9197046 100644 --- a/SCF/HartreeFock.mli +++ b/SCF/HartreeFock.mli @@ -65,7 +65,7 @@ val make : (** {1 Printers} *) -val pp_hf : Format.formatter -> t -> unit +val pp : Format.formatter -> t -> unit val pp_iterations : Format.formatter -> t -> unit diff --git a/Utils/Matrix.ml b/Utils/Matrix.ml index 95188f8..21e6133 100644 --- a/Utils/Matrix.ml +++ b/Utils/Matrix.ml @@ -624,10 +624,10 @@ let parallel_mm ?(transa=`N) ?(transb=`N) ?(threshold=epsilon) a b = (* ------------ Printers ------------ *) -let rec pp_matrix ppf = function +let rec pp ppf = function | Dense m -> Util.pp_matrix ppf m - | Sparse m -> pp_matrix ppf @@ dense_of_sparse (Sparse m) - | Computed m -> pp_matrix ppf @@ dense_of_computed (Computed m) + | Sparse m -> pp ppf @@ dense_of_sparse (Sparse m) + | Computed m -> pp ppf @@ dense_of_computed (Computed m) diff --git a/Utils/Matrix.mli b/Utils/Matrix.mli index cbf5a0c..971b3f3 100644 --- a/Utils/Matrix.mli +++ b/Utils/Matrix.mli @@ -93,7 +93,7 @@ val parallel_mm : ?transa:trans3 -> ?transb:trans3 -> ?threshold:float -> t -> t (** {1 Printers } *) -val pp_matrix : Format.formatter -> t -> unit +val pp : Format.formatter -> t -> unit (** {1 Unit testing} *) diff --git a/Utils/Range.ml b/Utils/Range.ml index e20c240..f424717 100644 --- a/Utils/Range.ml +++ b/Utils/Range.ml @@ -40,7 +40,7 @@ let to_string l = "]" -let pp_range ppf t = +let pp ppf t = Format.fprintf ppf "@[%s@]" (to_string t) diff --git a/Utils/Range.mli b/Utils/Range.mli index 8afabbd..8a18174 100644 --- a/Utils/Range.mli +++ b/Utils/Range.mli @@ -26,5 +26,5 @@ val to_int_list : t -> int list (** {2 Printers} *) -val pp_range : Format.formatter -> t -> unit +val pp : Format.formatter -> t -> unit diff --git a/Utils/Vector.ml b/Utils/Vector.ml index b881ed8..756b1bd 100644 --- a/Utils/Vector.ml +++ b/Utils/Vector.ml @@ -186,7 +186,7 @@ let add = axpy ~alpha:1. let sub ?(threshold=epsilon) x y = add ~threshold x @@ neg y -let pp_vector ppf = function +let pp ppf = function | Dense m -> Util.pp_float_array ppf @@ Vec.to_array m | Sparse {n ; v} -> begin diff --git a/Utils/Vector.mli b/Utils/Vector.mli index 304a906..5c3b537 100644 --- a/Utils/Vector.mli +++ b/Utils/Vector.mli @@ -70,7 +70,7 @@ val norm : t -> float (** {1 Printers } *) -val pp_vector : Format.formatter -> t -> unit +val pp : Format.formatter -> t -> unit (** {1 Unit testing} *) diff --git a/run_cas.ml b/run_cas.ml index 436ff94..573548c 100644 --- a/run_cas.ml +++ b/run_cas.ml @@ -60,7 +60,7 @@ let () = in let hf = HartreeFock.make s in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf; + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf; let mos = MOBasis.of_hartree_fock hf diff --git a/run_fci.ml b/run_fci.ml index 1d1c886..6b3dc4a 100644 --- a/run_fci.ml +++ b/run_fci.ml @@ -49,7 +49,7 @@ let () = in let hf = HartreeFock.make s in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf; + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf; let mos = MOBasis.of_hartree_fock hf diff --git a/run_fci_f12.ml b/run_fci_f12.ml index 91e03c9..6d06b06 100644 --- a/run_fci_f12.ml +++ b/run_fci_f12.ml @@ -47,7 +47,10 @@ let () = let charge = match Command_line.get "charge" with - | Some x -> int_of_string x + | 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 diff --git a/run_hartree_fock.ml b/run_hartree_fock.ml index bb67a14..2a9f8df 100644 --- a/run_hartree_fock.ml +++ b/run_hartree_fock.ml @@ -59,7 +59,7 @@ let () = let s_guess = Simulation.of_filenames ~charge ~multiplicity ~nuclei:nuclei_file filename in let hf = HartreeFock.make s_guess in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf; + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf; let guess_mos = MOBasis.of_hartree_fock hf |> MOBasis.of_mo_basis s @@ -69,7 +69,7 @@ let () = let hf = HartreeFock.make ~guess s in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf (* ; let mos = MOBasis.of_hartree_fock hf in Format.fprintf ppf "@[%a@]@." (fun ppf x -> MOBasis.pp_mo ppf x) mos diff --git a/run_mp2.ml b/run_mp2.ml index 458caa2..adc5ffc 100644 --- a/run_mp2.ml +++ b/run_mp2.ml @@ -59,7 +59,7 @@ let () = let s_guess = Simulation.of_filenames ~charge ~multiplicity ~nuclei:nuclei_file filename in let hf = HartreeFock.make s_guess in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf; + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf; let guess_mos = MOBasis.of_hartree_fock hf |> MOBasis.of_mo_basis s @@ -69,7 +69,7 @@ let () = let hf = HartreeFock.make ~guess s in - Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf; + Format.fprintf ppf "@[%a@]@." HartreeFock.pp hf; let e_hf = HartreeFock.energy hf in