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Merge branch 'master' of github.com:TApplencourt/quantum_package
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TApplencourt
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b521a8d015
118
data/list_element.txt
Normal file
118
data/list_element.txt
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@ -0,0 +1,118 @@
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1 H Hydrogen
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2 He Helium
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3 Li Lithium
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4 Be Beryllium
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5 B Boron
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6 C Carbon
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7 N Nitrogen
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8 O Oxygen
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9 F Fluorine
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10 Ne Neon
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11 Na Sodium
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12 Mg Magnesium
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13 Al Aluminum
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14 Si Silicon
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15 P Phosphorus
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16 S Sulfur
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17 Cl Chlorine
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18 Ar Argon
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19 K Potassium
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20 Ca Calcium
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21 Sc Scandium
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22 Ti Titanium
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23 V Vanadium
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24 Cr Chromium
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25 Mn Manganese
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26 Fe Iron
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27 Co Cobalt
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28 Ni Nickel
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29 Cu Copper
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30 Zn Zinc
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31 Ga Gallium
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32 Ge Germanium
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33 As Arsenic
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34 Se Selenium
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35 Br Bromine
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36 Kr Krypton
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37 Rb Rubidium
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38 Sr Strontium
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39 Y Yttrium
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40 Zr Zirconium
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41 Nb Niobium
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42 Mo Molybdenum
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43 Tc Technetium
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44 Ru Ruthenium
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45 Rh Rhodium
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46 Pd Palladium
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47 Ag Silver
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48 Cd Cadmium
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49 In Indium
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50 Sn Tin
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51 Sb Antimony
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52 Te Tellurium
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53 I Iodine
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54 Xe Xenon
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55 Cs Cesium
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56 Ba Barium
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57 La Lanthanum
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58 Ce Cerium
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59 Pr Praseodymium
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60 Nd Neodymium
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61 Pm Promethium
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62 Sm Samarium
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63 Eu Europium
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64 Gd Gadolinium
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65 Tb Terbium
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66 Dy Dysprosium
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67 Ho Holmium
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68 Er Erbium
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69 Tm Thulium
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70 Yb Ytterbium
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71 Lu Lutetium
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72 Hf Hafnium
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73 Ta Tantalum
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74 W Tungsten
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75 Re Rhenium
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76 Os Osmium
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77 Ir Iridium
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78 Pt Platinum
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79 Au Gold
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80 Hg Mercury
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81 Tl Thallium
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82 Pb Lead
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83 Bi Bismuth
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84 Po Polonium
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85 At Astatine
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86 Rn Radon
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87 Fr Francium
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88 Ra Radium
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89 Ac Actinium
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90 Th Thorium
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91 Pa Protactinium
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92 U Uranium
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93 Np Neptunium
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94 Pu Plutonium
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95 Am Americium
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96 Cm Curium
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97 Bk Berkelium
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98 Cf Californium
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99 Es Einsteinium
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100 Fm Fermium
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101 Md Mendelevium
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102 No Nobelium
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103 Lr Lawrencium
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104 Rf Rutherfordium
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105 Db Dubnium
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106 Sg Seaborgium
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107 Bh Bohrium
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108 Hs Hassium
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109 Mt Meitnerium
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110 Ds Darmstadtium
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111 Rg Roentgenium
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112 Cn Copernicium
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113 Uut Ununtrium
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114 Fl Flerovium
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115 Uup Ununpentium
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116 Lv Livermorium
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117 Uus Ununseptium
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118 Uuo Ununoctium
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@ -11,7 +11,8 @@ module Determinants_by_hand : sig
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psi_coef : Det_coef.t array;
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psi_det : Determinant.t array;
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} with sexp
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val read : unit -> t option
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val read : unit -> t
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val read_maybe : unit -> t option
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val write : t -> unit
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val to_string : t -> string
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val to_rst : t -> Rst_string.t
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@ -210,13 +211,6 @@ end = struct
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let read () =
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if (Ezfio.has_mo_basis_mo_tot_num ()) then
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let n_det =
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read_n_det ()
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in
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if ( (Det_number.to_int n_det) > n_det_read_max ) then
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None
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else
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Some
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{ n_int = read_n_int () ;
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bit_kind = read_bit_kind () ;
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n_det = read_n_det () ;
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@ -224,6 +218,17 @@ end = struct
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psi_coef = read_psi_coef () ;
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psi_det = read_psi_det () ;
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}
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else
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failwith "No molecular orbitals, so no determinants"
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;;
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let read_maybe () =
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let n_det =
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read_n_det ()
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in
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if ( (Det_number.to_int n_det) < n_det_read_max ) then
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try Some (read ()) with
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| Failure _ -> None
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else
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None
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;;
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@ -36,7 +36,7 @@ let bind_socket ~socket_type ~socket ~address =
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| 0 -> failwith @@ Printf.sprintf
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"Unable to bind the %s socket : %s "
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socket_type address
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| -1 -> ();
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| -1 -> ()
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| i ->
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try
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ZMQ.Socket.bind socket address;
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@ -43,9 +43,7 @@ let psi_det () =
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failwith "Error reading EZFIO file";
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Ezfio.set_file ezfio_filename;
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let psi_det =
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match Input.Determinants_by_hand.read () with
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| Some psi_det -> psi_det
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| _ -> failwith "Error reading the mo set"
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Input.Determinants_by_hand.read ()
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in
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Input.Determinants_by_hand.to_rst psi_det
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|> Rst_string.to_string
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@ -56,5 +54,5 @@ let psi_det () =
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let () =
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basis ();
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mo ();
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psi_det ();
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psi_det ()
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@ -1,7 +1,7 @@
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open Core.Std
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let () =
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Message.of_string "new_job tcp://127.0.0.1 inproc://ao_ints:12345 ao_integrals"
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Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"
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|> Message.to_string
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|> print_endline
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;
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@ -37,7 +37,7 @@ let () =
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;
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try
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Message.of_string "new_job inproc://ao_ints tcp://127.0.0.1:12345 ao_integrals"
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Message.of_string "new_job ao_integrals inproc://ao_ints tcp://127.0.0.1:12345"
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|> Message.to_string
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|> print_endline
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;
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@ -9,6 +9,7 @@ print "#QP -> QMCPACK"
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from ezfio import ezfio
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import os
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import sys
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ezfio_path = sys.argv[1]
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@ -17,7 +18,15 @@ ezfio.set_file(ezfio_path)
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do_pseudo = ezfio.get_pseudo_do_pseudo()
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if do_pseudo:
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print "do_pseudo True"
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print "The charge of nucl will be decreasced for taking into acount the pseudo potentiel"
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from qp_path import QP_ROOT
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l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
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with open(l_ele_path, "r") as f:
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data_raw = f.read()
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l_element_raw = data_raw.split("\n")
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l_element = [element_raw.split() for element_raw in l_element_raw]
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d_z = dict((abr, z) for (z, abr, ele) in l_element)
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else:
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print "do_pseudo False"
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@ -68,7 +77,10 @@ print "nucl_num", len(l_label)
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print "Atomic coord in Bohr"
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for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
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print list_to_string(t)
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t_1 = d_z[t[0]] if do_pseudo else t[1]
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t_new = [t[0],t_1,t[2]]
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print list_to_string(t_new)
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#
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# Call externet process to get the sysmetry
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@ -79,7 +91,6 @@ process = subprocess.Popen(
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stdout=subprocess.PIPE)
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out, err = process.communicate()
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print len(out.split("\n\n\n"))
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basis_raw, sym_raw, _ , det_raw, _ = out.split("\n\n\n")
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# _ __
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@ -310,8 +321,8 @@ if do_pseudo:
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if l_dump:
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l_str.append(l_dump)
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str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE -1 AND LMAX {2} ARE"
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print str_.format(a, i + 1, int(len(l_str) - 1))
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str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
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print str_.format(a, i + 1, int(d_z[a])-int(l_charge[i]), int(len(l_str) - 1))
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for i, l in enumerate(l_str):
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str_ = "FOR L= {0} COEFF N ZETA"
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@ -319,7 +330,8 @@ if do_pseudo:
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for ii, ll in enumerate(l):
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print " ", ii + 1, ll
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str_ = "THE ECP RUN REMOVES -1 CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
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str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
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print str_.format(sum([int(d_z[a])-int(l_charge[i]) for i,a in enumerate(l_label)]))
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print "END_PSEUDO"
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# _
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@ -14,6 +14,12 @@ program qmcpack
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enddo
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enddo
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call ezfio_set_ao_basis_ao_coef(ao_coef)
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do j=1,mo_tot_num
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do i=1,ao_num
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mo_coef(i,j) *= 1.d0/ao_coef_normalization_factor(i)
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enddo
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enddo
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call save_mos
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call system('rm '//trim(ezfio_filename)//'/mo_basis/ao_md5')
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call system('$QP_ROOT/src/qmcpack/qp_convert_qmcpack_to_ezfio.py '//trim(ezfio_filename))
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@ -75,7 +75,7 @@ let get s =
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| Ao_basis ->
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f Ao_basis.(read, to_rst)
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| Determinants_by_hand ->
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f Determinants_by_hand.(read, to_rst)
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f Determinants_by_hand.(read_maybe, to_rst)
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{section_to_rst}
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end
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with
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@ -52,9 +52,6 @@ END_PROVIDER
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enddo
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enddo
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ao_coef_normalization_factor(i) = 1.d0/sqrt(norm)
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do j=1,ao_prim_num(i)
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ao_coef_normalized(i,j) = ao_coef_normalized(i,j) * ao_coef_normalization_factor(i)
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enddo
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enddo
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END_PROVIDER
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