| [3493da] | 1 | #key value
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| 2 | actionname "help"
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| 3 | add-atom "1"
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| 4 | add-empty-boundary ""
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| [cb7676] | 5 | Alignment-Axis "0,0,1"
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| [3493da] | 6 | angle-x "0."
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| 7 | angle-x "0"
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| 8 | angle-y "0."
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| 9 | angle-y "0"
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| 10 | angle-z "0 "
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| 11 | angle-z "0."
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| 12 | angle-z "0"
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| 13 | axis "0 0 1"
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| 14 | axis "0 1 0"
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| 15 | axis "1 2 1"
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| 16 | bin-end "10"
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| 17 | bin-end "20"
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| 18 | bin-end "359"
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| 19 | bin-end "359.5"
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| 20 | bin-end "5"
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| 21 | bin-output-file "bin_output-10.csv"
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| 22 | bin-output-file "bin_output-20.csv"
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| 23 | bin-output-file "bin_output-5.csv"
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| 24 | bin-output-file "bin_output.csv"
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| 25 | bin-output-file "emptybox_histogram.dat"
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| 26 | bin-output-file "hydrogenbox_histogram.dat"
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| 27 | bin-output-file "waterbox_histogram.dat"
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| 28 | bin-output-file "waterbox-mirrored_histogram.dat"
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| 29 | bin-start "0"
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| 30 | bin-start "-0.5"
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| 31 | bin-start "10"
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| 32 | bin-start "5"
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| 33 | bin-width "1."
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| 34 | bond-file "bond.dat"
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| 35 | bond-table "table.dat"
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| [f89b45] | 36 | calculate-bounding-box ""
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| [55f299] | 37 | calculate-molar-mass ""
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| [2db053] | 38 | center "10. 10. 10."
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| [3493da] | 39 | center-in-box "10 0 0 10 0 10"
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| [8b886f] | 40 | change-bond-angle "100."
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| [3493da] | 41 | change-box "10 0 0 10 0 10"
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| 42 | change-element "H"
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| 43 | change-molname "water"
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| 44 | convex-file "convexfile"
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| 45 | copy-molecule "0"
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| [2db053] | 46 | count "12"
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| [5ab796] | 47 | create-micelle "200"
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| [3493da] | 48 | default-molname "molname"
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| 49 | deltat "0.01"
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| 50 | depth-first-search "2."
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| [5ab796] | 51 | dipole-angular-correlation "H2O"
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| [3493da] | 52 | distance "1.55"
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| 53 | distances "3.1 3.1 3.1"
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| 54 | distances "3.1 3.1 3.1"
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| 55 | distance-to-boundary "1."
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| 56 | distance-to-molecule "1.5"
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| 57 | distance-to-molecule "2.1"
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| 58 | domain-position "0. 0. 0."
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| 59 | domain-position "0 0 0"
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| 60 | domain-position "10. 10. 10."
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| [69c733] | 61 | DoLongrange "0"
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| [b6b21a] | 62 | DoPrintDebug "0"
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| [3493da] | 63 | DoRotate "0"
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| [5ab796] | 64 | DoSaturate "0"
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| [6ff62c] | 65 | DoValenceOnly "0"
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| [3493da] | 66 | element-db "./"
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| 67 | elements "1"
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| 68 | elements "1 8"
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| 69 | end-step "1"
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| [9291d04] | 70 | ExcludeHydrogen "1"
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| [3493da] | 71 | fastparsing "1"
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| [531f27] | 72 | filename "test.exttypes"
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| [3493da] | 73 | fill-molecule "filler.xyz"
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| 74 | fill-void "hydrogen.xyz"
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| 75 | fill-void "water.data"
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| 76 | fill-void "water.xyz"
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| [48d20d] | 77 | fit-potential "morse"
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| [4882d5] | 78 | forces-file "test.forces"
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| [48d20d] | 79 | fragment-charges "1 1"
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| [edecba] | 80 | fragment-executable "mpqc"
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| 81 | fragment-jobs "Job00.in"
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| [3493da] | 82 | fragment-molecule "./"
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| [edecba] | 83 | fragment-path "test/"
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| [55e1bc] | 84 | fragment-resultfile "results.dat"
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| [065574] | 85 | grid-level "5"
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| [240c3e] | 86 | homology-file "homology.dat"
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| [3493da] | 87 | id-mapping "1"
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| 88 | input "test.data"
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| [cd2591] | 89 | interpolation-degree "5"
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| [3493da] | 90 | interpolation-steps "9"
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| 91 | keep-fixed-CenterOfMass "0"
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| 92 | load "test.data"
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| 93 | MaxDistance "-1"
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| 94 | MDSteps "1"
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| [a88452] | 95 | mesh-offset "0.5,0.5,0.5"
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| 96 | mesh-size "10,10,10"
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| 97 | min-distance "1."
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| [3493da] | 98 | molecule-by-id "0"
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| [065574] | 99 | near-field-cells "3"
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| [3493da] | 100 | nonconvex-envelope "25"
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| 101 | nonconvex-file "NonConvexEnvelope"
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| 102 | nonconvex-file "nonconvexfile"
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| 103 | offset "0"
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| 104 | offset "1"
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| 105 | order "2"
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| 106 | output-file "emptybox_values.dat"
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| 107 | output-file "hydrogenbox_values.dat"
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| 108 | output-file "output-10.csv"
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| 109 | output-file "output-20.csv"
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| 110 | output-file "output-5.csv"
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| 111 | output-file "output.csv"
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| 112 | output-file "waterbox-mirrored_values.dat"
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| 113 | output-file "waterbox_values.dat"
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| [072f0e] | 114 | output-as "store.conf"
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| 115 | output-as "store.data"
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| 116 | output-as "store.pdb"
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| 117 | output-as "store.xyz"
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| 118 | output-as "test.in"
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| [5ab796] | 119 | output-types "xyz"
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| 120 | output-types "xyz mpqc"
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| [3493da] | 121 | parse-tremolo-potentials "argon.potentials"
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| 122 | parse-tremolo-potentials "tensid.potentials"
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| [5ab796] | 123 | parser-parameters "mpqc"
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| 124 | parser-parameters "psi3"
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| [3493da] | 125 | periodic "0"
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| 126 | position "0 0 0"
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| 127 | position "0 0 1"
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| 128 | position "0 0 10"
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| 129 | position "10 10 10"
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| 130 | position "10. 10. 10."
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| 131 | position "1 2 1"
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| 132 | position "5.63 5.71 5.71"
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| 133 | position "7.283585982 3.275186040 3.535886037"
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| 134 | position "9.78 2.64 2.64"
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| [48d20d] | 135 | potential-charges "1 1"
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| [baccf6] | 136 | potential-file "test.potentials"
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| [5ab796] | 137 | radius "20."
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| [3493da] | 138 | random-atom-displacement "0."
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| 139 | random-molecule-displacement "0."
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| 140 | random-number-distribution-parameters "max=20;"
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| 141 | random-number-engine-parameters "seed=2;"
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| 142 | repeat-box "1 1 1"
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| [ca331c] | 143 | reset 1
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| [3493da] | 144 | rotate-around-origin "180."
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| 145 | rotate-around-origin "20."
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| 146 | rotate-around-origin "360."
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| 147 | rotate-around-origin "90."
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| 148 | rotate-around-self "180."
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| 149 | rotate-around-self "180"
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| 150 | rotate-around-self "20."
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| 151 | rotate-around-self "360."
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| 152 | rotate-around-self "90."
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| 153 | rotate-to-principal-axis-system ""
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| 154 | save-adjacency "test.adj"
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| 155 | save-bonds "test.bond"
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| 156 | save-selected-atoms "testsave.xyz"
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| [531f27] | 157 | save-selected-atoms-as-exttypes "test.exttypes"
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| [3493da] | 158 | save-selected-molecules "testsave.xyz"
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| 159 | save-temperature "test.ekin"
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| 160 | scale-box "0.5 1. 0.9"
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| 161 | select-atom-by-element "1"
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| 162 | select-atom-by-element "4"
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| 163 | select-atom-by-id "0"
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| [61c364] | 164 | select-atom-by-order "1"
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| [3493da] | 165 | select-atoms-inside-cuboid "10 10 10"
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| 166 | select-atoms-inside-cuboid "2 2 2"
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| 167 | select-atoms-inside-sphere "0.2"
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| 168 | select-atoms-inside-sphere "10"
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| 169 | select-atoms-inside-sphere "7."
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| 170 | select-molecule-by-id "0"
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| 171 | select-molecule-by-id "1"
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| 172 | select-molecule-by-id "4"
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| 173 | select-molecule-by-order "-1"
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| 174 | select-molecule-by-order "1"
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| 175 | select-molecule-by-order "-2"
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| 176 | select-molecule-by-order "2"
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| 177 | select-molecules-by-formula "C2H5(OH)"
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| 178 | select-molecules-by-formula "C6H6"
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| 179 | select-molecules-by-formula "H2O"
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| 180 | select-molecules-by-name "water"
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| [663606] | 181 | select-shape-by-name "sphere2"
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| [edecba] | 182 | server-address "127.0.0.1"
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| 183 | server-port "1026"
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| [c52e08] | 184 | set-boundary-conditions "Wrap, Wrap, Wrap"
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| [5ab796] | 185 | set-parser-parameters "basis = 4-31G"
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| 186 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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| 187 | set-parser-parameters "maxiter = 499"
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| 188 | set-parser-parameters "theory=CLKS"
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| 189 | set-parser-parameters "wfn=scf"
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| 190 | set-parser-parameters "ref=uhf"
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| [3493da] | 191 | set-output "tremolo"
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| 192 | set-random-number-distribution "uniform_int"
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| 193 | set-random-number-engine "lagged_fibonacci607"
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| 194 | set-tremolo-atomdata "ATOMDATA type id x=3"
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| 195 | set-world-time "10"
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| [6131d8] | 196 | shape-name "sphere1"
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| [d475a6] | 197 | shape-op "AND"
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| [4dc309] | 198 | shape-type "sphere"
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| [3493da] | 199 | skiplines "1"
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| 200 | skiplines "2"
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| 201 | start-step "0"
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| [5589e7e] | 202 | store-saturated-fragment "BondFragment"
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| [3a51bd] | 203 | stretch-bond "1.5"
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| [4dc309] | 204 | stretch "1. 1. 1."
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| [29ea65] | 205 | stretch-shapes "1. 2. 3."
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| [3493da] | 206 | suspend-in-water "1.0"
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| [48d20d] | 207 | take-best-of "5"
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| [345eda] | 208 | tesselation-radius "5."
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| [5ab796] | 209 | time-step-zero "0"
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| [a504946] | 210 | training-file "training.dat"
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| [3493da] | 211 | translate-atoms "1. 0. 0."
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| [0b5057] | 212 | translate-shapes "1. 2. 3."
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| [4dc309] | 213 | translation "0. 0. 0."
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| [3493da] | 214 | unselect-atom-by-element "1"
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| 215 | unselect-atom-by-element "4"
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| 216 | unselect-atom-by-id "0"
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| [61c364] | 217 | unselect-atom-by-order "1"
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| [3493da] | 218 | unselect-atoms-inside-cuboid "10 10 10"
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| 219 | unselect-atoms-inside-cuboid "2 2 2"
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| 220 | unselect-atoms-inside-sphere "10"
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| 221 | unselect-atoms-inside-sphere "7."
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| 222 | unselect-molecule-by-id "0"
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| 223 | unselect-molecule-by-id "4"
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| 224 | unselect-molecule-by-order "-1"
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| 225 | unselect-molecule-by-order "1"
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| 226 | unselect-molecule-by-order "-2"
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| 227 | unselect-molecule-by-order "2"
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| 228 | unselect-molecules-by-formula "C2H5(OH)"
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| 229 | unselect-molecules-by-formula "C3H8"
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| 230 | unselect-molecules-by-formula "C6H6"
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| 231 | unselect-molecules-by-formula "H2O"
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| 232 | unselect-molecules-by-name "water"
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| [2c004d] | 233 | unselect-shape-by-name "cube42"
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| [3493da] | 234 | verbose "3"
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| 235 | verlet-integration "forces.dat"
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