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Fixes #211
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@ -1,118 +1,56 @@
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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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0 X Dummy 0.000000
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1 H Hydrogen 1.007900
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2 He Helium 4.002600
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3 Li Lithium 6.941000
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4 Be Beryllium 9.012180
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5 B Boron 10.810000
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6 C Carbon 12.011000
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7 N Nitrogen 14.006700
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8 O Oxygen 15.999400
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9 F Fluorine 18.998403
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10 Ne Neon 20.179000
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11 Na Sodium 22.989770
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12 Mg Magnesium 24.305000
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13 Al Aluminum 26.981540
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14 Si Silicon 28.085500
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15 P Phosphorus 30.973760
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16 S Sulfur 32.060000
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17 Cl Chlorine 35.453000
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18 Ar Argon 39.948000
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19 K Potassium 39.098300
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20 Ca Calcium 40.080000
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21 Sc Scandium 44.955900
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22 Ti Titanium 47.900000
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23 V Vanadium 50.941500
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24 Cr Chromium 51.996000
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25 Mn Manganese 54.938000
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26 Fe Iron 55.933200
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27 Co Cobalt 58.933200
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28 Ni Nickel 58.700000
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29 Cu Copper 63.546000
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30 Zn Zinc 65.380000
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31 Ga Gallium 69.720000
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32 Ge Germanium 72.590000
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33 As Arsenic 74.921600
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34 Se Selenium 78.960000
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35 Br Bromine 79.904000
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36 Kr Krypton 83.800000
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37 Rb Rubidium 85.467800
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38 Sr Strontium 87.620000
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39 Y Yttrium 88.905840
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40 Zr Zirconium 91.224000
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41 Nb Niobium 92.906370
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42 Mo Molybdenum 95.950000
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43 Tc Technetium 98.000000
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44 Ru Ruthenium 101.070000
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45 Rh Rhodium 102.905500
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46 Pd Palladium 106.420000
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47 Ag Silver 107.868200
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48 Cd Cadmium 112.414000
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49 In Indium 114.818000
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50 Sn Tin 118.710000
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51 Sb Antimony 121.760000
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52 Te Tellurium 127.600000
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53 I Iodine 126.904470
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54 Xe Xenon 131.293000
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78 Pt Platinum 195.084000
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@ -499,3 +499,4 @@ let mass x =
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result x
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|> Positive_float.of_float
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@ -17,7 +17,7 @@ MLLFILES=$(wildcard *.mll)
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MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml
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MLIFILES=$(wildcard *.mli) git
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ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
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ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native
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ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native element_create_db.byte
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.PHONY: executables default remake_executables
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@ -37,8 +37,9 @@ tests: $(ALL_TESTS)
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executables: $(QP_ROOT)/data/executables
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$(QP_ROOT)/data/executables: remake_executables
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$(QP_ROOT)/data/executables: remake_executables element_create_db.byte Qptypes.ml
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$(QP_ROOT)/scripts/module/create_executables_list.sh
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$(QP_ROOT)/ocaml/element_create_db.byte
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external_libs:
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opam install cryptokit core
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27
ocaml/element_create_db.ml
Normal file
27
ocaml/element_create_db.ml
Normal file
@ -0,0 +1,27 @@
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open Core
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open Qptypes
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open Element
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let () =
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let indices =
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Array.init 78 (fun i -> i)
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in
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Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt")
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~f:(fun out_channel ->
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Array.init 110 ~f:(fun i ->
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let element =
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try
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Some (of_charge (Charge.of_int i))
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with
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| _ -> None
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in
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match element with
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| None -> ""
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| Some x -> Printf.sprintf "%3d %3s %s %f\n"
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i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
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)
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|> Array.to_list
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|> String.concat ~sep:""
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|> Out_channel.output_string out_channel
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)
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@ -1,7 +1,6 @@
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program save_for_qmc
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integer :: iunit
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integer, external :: get_unit_and_open
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logical :: exists
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double precision :: e_ref
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@ -1,119 +1,15 @@
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name_to_elec = {"X": 0,
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"H": 1,
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"He": 2,
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"Li": 3,
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"Be": 4,
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"B": 5,
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"C": 6,
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"N": 7,
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"O": 8,
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"F": 9,
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"Ne": 10,
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"Na": 11,
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"Mg": 12,
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"Al": 13,
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"Si": 14,
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"P": 15,
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"S": 16,
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"Cl": 17,
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"Ar": 18,
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"K": 19,
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"Ca": 20,
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"Sc": 21,
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"Ti": 22,
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"V": 23,
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"Cr": 24,
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"Mn": 25,
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"Fe": 26,
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"Co": 27,
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"Ni": 28,
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"Cu": 29,
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"Zn": 30,
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"Ga": 31,
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"Ge": 32,
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"As": 33,
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"Se": 34,
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"Br": 35,
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"Kr": 36,
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"Rb": 37,
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"Sr": 38,
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"Y": 39,
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"Zr": 40,
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"Nb": 41,
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"Mo": 42,
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"Tc": 43,
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"Ru": 44,
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"Rh": 45,
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"Pd": 46,
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"Ag": 47,
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"Cd": 48,
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"In": 49,
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"Sn": 50,
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"Sb": 51,
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"Te": 52,
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"I": 53,
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"Xe": 54,
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"Cs": 55,
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"Ba": 56,
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"La": 57,
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"Ce": 58,
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"Pr": 59,
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"Nd": 60,
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"Pm": 61,
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"Sm": 62,
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"Eu": 63,
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"Gd": 64,
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"Tb": 65,
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"Dy": 66,
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"Ho": 67,
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"Er": 68,
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"Tm": 69,
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"Yb": 70,
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"Lu": 71,
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"Hf": 72,
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"Ta": 73,
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"W": 74,
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"Re": 75,
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"Os": 76,
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"Ir": 77,
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"Pt": 78,
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"Au": 79,
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"Hg": 80,
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"Tl": 81,
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"Pb": 82,
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"Bi": 83,
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"Po": 84,
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"At": 85,
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"Rn": 86,
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"Fr": 87,
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"Ra": 88,
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"Ac": 89,
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"Th": 90,
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"Pa": 91,
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"U": 92,
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"Np": 93,
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"Pu": 94,
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"Am": 95,
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"Cm": 96,
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"Bk": 97,
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"Cf": 98,
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"Es": 99,
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"Fm": 100,
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"Md": 101,
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"No": 102,
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"Lr": 103,
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"Rf": 104,
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"Db": 105,
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"Sg": 106,
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"Bh": 107,
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"Hs": 108,
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"Mt": 109,
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"Ds": 110,
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"Rg": 111,
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"Cn": 112,
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"Uut": 113,
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"Fl": 114,
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"Uup": 115,
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"Lv": 116,
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"Uus": 117,
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"Uuo": 118}
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#!/usr/bin/env python
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import os
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QP_ROOT=os.environ["QP_ROOT"]
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name_to_elec = {}
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with open(QP_ROOT+"/data/list_element.txt","r") as f:
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data = f.readlines()
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for line in data:
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b = line.split()
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name_to_elec[b[1]] = int(b[0])
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if __name__ == '__main__':
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print name_to_elec
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@ -6,12 +6,12 @@ BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ]
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integer :: i,j,k
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inertia_tensor = 0.d0
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do k=1,nucl_num
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inertia_tensor(1,1) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2)
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inertia_tensor(2,2) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2)
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inertia_tensor(3,3) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2)
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inertia_tensor(1,2) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) )
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inertia_tensor(1,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) )
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inertia_tensor(2,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) )
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inertia_tensor(1,1) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2)
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inertia_tensor(2,2) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2)
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inertia_tensor(3,3) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2)
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inertia_tensor(1,2) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) )
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inertia_tensor(1,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) )
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inertia_tensor(2,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) )
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enddo
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inertia_tensor(2,1) = inertia_tensor(1,2)
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inertia_tensor(3,1) = inertia_tensor(1,3)
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@ -27,6 +27,6 @@ END_PROVIDER
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integer :: k
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call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3)
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print *, 'Rotational constants (GHZ):'
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print *, (1805.65468542d0/inertia_tensor_eigenvalues(k), k=3,1,-1)
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print *, (1805.65468542d0/(inertia_tensor_eigenvalues(k)+1.d-32), k=3,1,-1)
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END_PROVIDER
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@ -260,155 +260,33 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
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endif
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END_PROVIDER
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BEGIN_PROVIDER [ character*(128), element_name, (78)]
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BEGIN_PROVIDER [ character*(4), element_name, (0:128)]
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&BEGIN_PROVIDER [ double precision, element_mass, (0:128) ]
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BEGIN_DOC
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! Array of the name of element, sorted by nuclear charge (integer)
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END_DOC
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element_name(1) = 'H'
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element_name(2) = 'He'
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element_name(3) = 'Li'
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element_name(4) = 'Be'
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element_name(5) = 'B'
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element_name(6) = 'C'
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element_name(7) = 'N'
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element_name(8) = 'O'
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element_name(9) = 'F'
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element_name(10) = 'Ne'
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element_name(11) = 'Na'
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element_name(12) = 'Mg'
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element_name(13) = 'Al'
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element_name(14) = 'Si'
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element_name(15) = 'P'
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element_name(16) = 'S'
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element_name(17) = 'Cl'
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element_name(18) = 'Ar'
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element_name(19) = 'K'
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element_name(20) = 'Ca'
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element_name(21) = 'Sc'
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element_name(22) = 'Ti'
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element_name(23) = 'V'
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element_name(24) = 'Cr'
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element_name(25) = 'Mn'
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element_name(26) = 'Fe'
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element_name(27) = 'Co'
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element_name(28) = 'Ni'
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element_name(29) = 'Cu'
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element_name(30) = 'Zn'
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element_name(31) = 'Ga'
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element_name(32) = 'Ge'
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element_name(33) = 'As'
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element_name(34) = 'Se'
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element_name(35) = 'Br'
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element_name(36) = 'Kr'
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element_name(37) = 'Rb'
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element_name(38) = 'Sr'
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element_name(39) = 'Y'
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element_name(40) = 'Zr'
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element_name(41) = 'Nb'
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element_name(42) = 'Mo'
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element_name(43) = 'Tc'
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element_name(44) = 'Ru'
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element_name(45) = 'Rh'
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element_name(46) = 'Pd'
|
||||
element_name(47) = 'Ag'
|
||||
element_name(48) = 'Cd'
|
||||
element_name(49) = 'In'
|
||||
element_name(50) = 'Sn'
|
||||
element_name(51) = 'Sb'
|
||||
element_name(52) = 'Te'
|
||||
element_name(53) = 'I'
|
||||
element_name(54) = 'Xe'
|
||||
element_name(55) = 'Cs'
|
||||
element_name(56) = 'Ba'
|
||||
element_name(57) = 'La'
|
||||
element_name(58) = 'Ce'
|
||||
element_name(59) = 'Pr'
|
||||
element_name(60) = 'Nd'
|
||||
element_name(61) = 'Pm'
|
||||
element_name(62) = 'Sm'
|
||||
element_name(63) = 'Eu'
|
||||
element_name(64) = 'Gd'
|
||||
element_name(65) = 'Tb'
|
||||
element_name(66) = 'Dy'
|
||||
element_name(67) = 'Ho'
|
||||
element_name(68) = 'Er'
|
||||
element_name(69) = 'Tm'
|
||||
element_name(70) = 'Yb'
|
||||
element_name(71) = 'Lu'
|
||||
element_name(72) = 'Hf'
|
||||
element_name(73) = 'Ta'
|
||||
element_name(74) = 'W'
|
||||
element_name(75) = 'Re'
|
||||
element_name(76) = 'Os'
|
||||
element_name(77) = 'Ir'
|
||||
element_name(78) = 'Pt'
|
||||
integer :: iunit
|
||||
integer, external :: getUnitAndOpen
|
||||
character*(128) :: filename
|
||||
call getenv('QP_ROOT',filename)
|
||||
filename = trim(filename)//'/data/list_element.txt'
|
||||
iunit = getUnitAndOpen(filename,'r')
|
||||
element_mass(:) = 0.d0
|
||||
do i=0,128
|
||||
write(element_name(i),'(I4)') i
|
||||
enddo
|
||||
character*(80) :: buffer, dummy
|
||||
do
|
||||
read(iunit,'(A80)',end=10) buffer
|
||||
read(buffer,*) i ! First read i
|
||||
read(buffer,*) i, element_name(i), dummy, element_mass(i)
|
||||
print *, i, element_name(i), element_mass(i)
|
||||
enddo
|
||||
10 continue
|
||||
close(10)
|
||||
|
||||
END_PROVIDER
|
||||
|
||||
BEGIN_PROVIDER [ double precision, mass, (0:110) ]
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! Atomic masses
|
||||
END_DOC
|
||||
|
||||
mass( 0 ) = 0.
|
||||
mass( 1 ) = 1.0079
|
||||
mass( 2 ) = 4.00260
|
||||
mass( 3 ) = 6.941
|
||||
mass( 4 ) = 9.01218
|
||||
mass( 5 ) = 10.81
|
||||
mass( 6 ) = 12.011
|
||||
mass( 7 ) = 14.0067
|
||||
mass( 8 ) = 15.9994
|
||||
mass( 9 ) = 18.998403
|
||||
mass( 10 ) = 20.179
|
||||
mass( 11 ) = 22.98977
|
||||
mass( 12 ) = 24.305
|
||||
mass( 13 ) = 26.98154
|
||||
mass( 14 ) = 28.0855
|
||||
mass( 15 ) = 30.97376
|
||||
mass( 16 ) = 32.06
|
||||
mass( 17 ) = 35.453
|
||||
mass( 18 ) = 39.948
|
||||
mass( 19 ) = 39.0983
|
||||
mass( 20 ) = 40.08
|
||||
mass( 21 ) = 44.9559
|
||||
mass( 22 ) = 47.90
|
||||
mass( 23 ) = 50.9415
|
||||
mass( 24 ) = 51.996
|
||||
mass( 25 ) = 54.9380
|
||||
mass( 26 ) = 55.9332
|
||||
mass( 27 ) = 58.9332
|
||||
mass( 28 ) = 58.70
|
||||
mass( 29 ) = 63.546
|
||||
mass( 30 ) = 65.38
|
||||
mass( 31 ) = 69.72
|
||||
mass( 32 ) = 72.59
|
||||
mass( 33 ) = 74.9216
|
||||
mass( 34 ) = 78.96
|
||||
mass( 35 ) = 79.904
|
||||
mass( 36 ) = 83.80
|
||||
mass( 37 ) = 85.4678
|
||||
mass( 38 ) = 87.62
|
||||
mass( 39 ) = 88.90584
|
||||
mass( 40 ) = 91.224
|
||||
mass( 41 ) = 92.90637
|
||||
mass( 42 ) = 95.95
|
||||
mass( 43 ) = 98.
|
||||
mass( 44 ) = 101.07
|
||||
mass( 45 ) = 102.90550
|
||||
mass( 46 ) = 106.42
|
||||
mass( 47 ) = 107.8682
|
||||
mass( 48 ) = 112.414
|
||||
mass( 49 ) = 114.818
|
||||
mass( 50 ) = 118.710
|
||||
mass( 51 ) = 121.760
|
||||
mass( 52 ) = 127.60
|
||||
mass( 53 ) = 126.90447
|
||||
mass( 54 ) = 131.293
|
||||
mass( 78 ) = 195.084
|
||||
END_PROVIDER
|
||||
|
||||
BEGIN_PROVIDER [ double precision, center_of_mass, (3) ]
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
@ -420,9 +298,9 @@ BEGIN_PROVIDER [ double precision, center_of_mass, (3) ]
|
||||
s = 0.d0
|
||||
do i=1,nucl_num
|
||||
do j=1,3
|
||||
center_of_mass(j) += nucl_coord_input(i,j)* mass(int(nucl_charge(i)))
|
||||
center_of_mass(j) += nucl_coord_input(i,j)* element_mass(int(nucl_charge(i)))
|
||||
enddo
|
||||
s += mass(int(nucl_charge(i)))
|
||||
s += element_mass(int(nucl_charge(i)))
|
||||
enddo
|
||||
s = 1.d0/s
|
||||
center_of_mass(:) = center_of_mass(:)*s
|
||||
|
||||
Loading…
Reference in New Issue
Block a user