| [3493da] | 1 | #key value
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| 2 | add-atom "1"
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| [afbbfeb] | 3 | add-empty-boundary "5,5,5"
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| [cb7676] | 4 | Alignment-Axis "0,0,1"
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| [3493da] | 5 | angle-x "0."
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| 6 | angle-x "0"
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| 7 | angle-y "0."
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| 8 | angle-y "0"
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| 9 | angle-z "0 "
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| 10 | angle-z "0."
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| 11 | angle-z "0"
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| 12 | axis "0 0 1"
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| 13 | axis "0 1 0"
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| 14 | axis "1 2 1"
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| 15 | bin-end "10"
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| 16 | bin-end "20"
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| 17 | bin-end "359"
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| 18 | bin-end "359.5"
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| 19 | bin-end "5"
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| 20 | bin-output-file "bin_output-10.csv"
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| 21 | bin-output-file "bin_output-20.csv"
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| 22 | bin-output-file "bin_output-5.csv"
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| 23 | bin-output-file "bin_output.csv"
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| 24 | bin-output-file "emptybox_histogram.dat"
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| 25 | bin-output-file "hydrogenbox_histogram.dat"
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| 26 | bin-output-file "waterbox_histogram.dat"
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| 27 | bin-output-file "waterbox-mirrored_histogram.dat"
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| 28 | bin-start "0"
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| 29 | bin-start "-0.5"
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| 30 | bin-start "10"
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| 31 | bin-start "5"
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| 32 | bin-width "1."
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| 33 | bond-file "bond.dat"
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| 34 | bond-table "table.dat"
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| [f89b45] | 35 | calculate-bounding-box ""
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| [55f299] | 36 | calculate-molar-mass ""
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| [2db053] | 37 | center "10. 10. 10."
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| [3493da] | 38 | center-in-box "10 0 0 10 0 10"
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| [8b886f] | 39 | change-bond-angle "100."
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| [3493da] | 40 | change-box "10 0 0 10 0 10"
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| [afbbfeb] | 41 | change-element "1"
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| [3493da] | 42 | change-molname "water"
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| [bcb831] | 43 | convex-envelope "50."
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| [3493da] | 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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| [aa55d0] | 50 | density "1.0"
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| [3493da] | 51 | depth-first-search "2."
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| [5ab796] | 52 | dipole-angular-correlation "H2O"
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| [3493da] | 53 | distance "1.55"
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| 54 | distances "3.1 3.1 3.1"
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| 55 | distances "3.1 3.1 3.1"
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| 56 | distance-to-boundary "1."
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| 57 | distance-to-molecule "1.5"
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| 58 | distance-to-molecule "2.1"
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| 59 | domain-position "0. 0. 0."
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| 60 | domain-position "0 0 0"
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| 61 | domain-position "10. 10. 10."
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| [fe0cb8] | 62 | DoCyclesFull "0"
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| [69c733] | 63 | DoLongrange "0"
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| [5f7b95] | 64 | DoOutputEveryStep "0"
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| [b6b21a] | 65 | DoPrintDebug "0"
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| [3493da] | 66 | DoRotate "0"
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| [5ab796] | 67 | DoSaturate "0"
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| [6ff62c] | 68 | DoValenceOnly "0"
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| [3493da] | 69 | element-db "./"
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| 70 | elements "1"
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| 71 | elements "1 8"
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| 72 | end-step "1"
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| [9291d04] | 73 | ExcludeHydrogen "1"
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| [3493da] | 74 | fastparsing "1"
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| [531f27] | 75 | filename "test.exttypes"
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| [3493da] | 76 | fill-molecule "filler.xyz"
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| 77 | fill-void "hydrogen.xyz"
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| 78 | fill-void "water.data"
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| 79 | fill-void "water.xyz"
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| [4882d5] | 80 | forces-file "test.forces"
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| [48d20d] | 81 | fragment-charges "1 1"
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| [edecba] | 82 | fragment-executable "mpqc"
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| 83 | fragment-jobs "Job00.in"
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| [3493da] | 84 | fragment-molecule "./"
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| [edecba] | 85 | fragment-path "test/"
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| [0588e9] | 86 | fragment-prefix "BondFragment"
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| [55e1bc] | 87 | fragment-resultfile "results.dat"
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| [065574] | 88 | grid-level "5"
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| [55feff5] | 89 | help "help"
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| [3493da] | 90 | id-mapping "1"
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| 91 | input "test.data"
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| [13c5c1] | 92 | inter-order "2"
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| [cd2591] | 93 | interpolation-degree "5"
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| [3493da] | 94 | interpolation-steps "9"
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| [553c54] | 95 | keep-bondgraph "1"
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| [3493da] | 96 | keep-fixed-CenterOfMass "0"
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| 97 | load "test.data"
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| [12d946] | 98 | load-session "test.py"
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| [3493da] | 99 | MaxDistance "-1"
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| [a88452] | 100 | mesh-offset "0.5,0.5,0.5"
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| 101 | mesh-size "10,10,10"
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| 102 | min-distance "1."
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| [bbf6dc] | 103 | mirror-atoms "1.,1.,1."
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| [3493da] | 104 | molecule-by-id "0"
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| [065574] | 105 | near-field-cells "3"
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| [3493da] | 106 | nonconvex-envelope "25"
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| 107 | nonconvex-file "NonConvexEnvelope"
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| 108 | nonconvex-file "nonconvexfile"
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| 109 | offset "0"
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| 110 | offset "1"
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| 111 | order "2"
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| [39986b] | 112 | output-as "store.conf"
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| 113 | output-as "store.data"
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| 114 | output-as "store.pdb"
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| 115 | output-as "store.xyz"
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| 116 | output-as "test.in"
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| 117 | output-every-step "1"
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| [3493da] | 118 | output-file "emptybox_values.dat"
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| 119 | output-file "hydrogenbox_values.dat"
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| 120 | output-file "output-10.csv"
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| 121 | output-file "output-20.csv"
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| 122 | output-file "output-5.csv"
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| 123 | output-file "output.csv"
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| 124 | output-file "waterbox-mirrored_values.dat"
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| 125 | output-file "waterbox_values.dat"
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| [5ab796] | 126 | output-types "xyz"
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| 127 | output-types "xyz mpqc"
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| [d449a9] | 128 | parse-homologies "homology.dat"
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| [f1eabd] | 129 | parse-potentials "water.potentials"
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| [3493da] | 130 | parse-tremolo-potentials "argon.potentials"
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| 131 | parse-tremolo-potentials "tensid.potentials"
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| [5ab796] | 132 | parser-parameters "mpqc"
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| 133 | parser-parameters "psi3"
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| [3493da] | 134 | periodic "0"
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| [bbf6dc] | 135 | plane-offset "5."
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| [3493da] | 136 | position "0 0 0"
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| 137 | position "0 0 1"
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| 138 | position "0 0 10"
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| 139 | position "10 10 10"
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| 140 | position "10. 10. 10."
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| 141 | position "1 2 1"
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| 142 | position "5.63 5.71 5.71"
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| 143 | position "7.283585982 3.275186040 3.535886037"
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| 144 | position "9.78 2.64 2.64"
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| [48d20d] | 145 | potential-charges "1 1"
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| [baccf6] | 146 | potential-file "test.potentials"
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| [a315e8] | 147 | potential-type "morse"
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| [5ab796] | 148 | radius "20."
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| [3493da] | 149 | random-atom-displacement "0."
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| 150 | random-molecule-displacement "0."
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| 151 | random-number-distribution-parameters "max=20;"
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| 152 | random-number-engine-parameters "seed=2;"
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| 153 | repeat-box "1 1 1"
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| [ca331c] | 154 | reset 1
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| [3493da] | 155 | rotate-around-origin "180."
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| 156 | rotate-around-origin "20."
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| 157 | rotate-around-origin "360."
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| 158 | rotate-around-origin "90."
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| 159 | rotate-around-self "180."
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| 160 | rotate-around-self "180"
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| 161 | rotate-around-self "20."
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| 162 | rotate-around-self "360."
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| 163 | rotate-around-self "90."
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| [afbbfeb] | 164 | rotate-to-principal-axis-system "0,0,1"
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| [3493da] | 165 | save-adjacency "test.adj"
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| 166 | save-bonds "test.bond"
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| [d449a9] | 167 | save-homologies "homology.dat"
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| [0ea063] | 168 | save-potentials "water.potentials"
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| [3493da] | 169 | save-selected-atoms "testsave.xyz"
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| [531f27] | 170 | save-selected-atoms-as-exttypes "test.exttypes"
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| [3493da] | 171 | save-selected-molecules "testsave.xyz"
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| 172 | save-temperature "test.ekin"
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| 173 | scale-box "0.5 1. 0.9"
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| 174 | select-atom-by-element "1"
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| 175 | select-atom-by-element "4"
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| 176 | select-atom-by-id "0"
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| [61c364] | 177 | select-atom-by-order "1"
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| [3493da] | 178 | select-atoms-inside-cuboid "10 10 10"
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| 179 | select-atoms-inside-cuboid "2 2 2"
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| 180 | select-atoms-inside-sphere "0.2"
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| 181 | select-atoms-inside-sphere "10"
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| 182 | select-atoms-inside-sphere "7."
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| 183 | select-molecule-by-id "0"
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| 184 | select-molecule-by-id "1"
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| 185 | select-molecule-by-id "4"
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| 186 | select-molecule-by-order "-1"
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| 187 | select-molecule-by-order "1"
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| 188 | select-molecule-by-order "-2"
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| 189 | select-molecule-by-order "2"
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| 190 | select-molecules-by-formula "C2H5(OH)"
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| 191 | select-molecules-by-formula "C6H6"
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| 192 | select-molecules-by-formula "H2O"
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| 193 | select-molecules-by-name "water"
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| [663606] | 194 | select-shape-by-name "sphere2"
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| [edecba] | 195 | server-address "127.0.0.1"
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| 196 | server-port "1026"
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| [9e4655] | 197 | session-type "cli"
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| [c52e08] | 198 | set-boundary-conditions "Wrap, Wrap, Wrap"
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| [5ab796] | 199 | set-parser-parameters "basis = 4-31G"
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| 200 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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| 201 | set-parser-parameters "maxiter = 499"
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| 202 | set-parser-parameters "theory=CLKS"
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| 203 | set-parser-parameters "wfn=scf"
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| 204 | set-parser-parameters "ref=uhf"
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| [3493da] | 205 | set-output "tremolo"
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| 206 | set-random-number-distribution "uniform_int"
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| 207 | set-random-number-engine "lagged_fibonacci607"
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| [4792ab] | 208 | set-threshold "1e-6"
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| [3493da] | 209 | set-tremolo-atomdata "ATOMDATA type id x=3"
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| 210 | set-world-time "10"
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| [6131d8] | 211 | shape-name "sphere1"
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| [d475a6] | 212 | shape-op "AND"
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| [4dc309] | 213 | shape-type "sphere"
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| [3493da] | 214 | skiplines "1"
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| 215 | skiplines "2"
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| 216 | start-step "0"
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| [39986b] | 217 | steps "5"
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| [bf1d1b] | 218 | store-grids "0"
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| [5589e7e] | 219 | store-saturated-fragment "BondFragment"
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| [bad589] | 220 | store-session "test.sh"
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| [3a51bd] | 221 | stretch-bond "1.5"
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| [4dc309] | 222 | stretch "1. 1. 1."
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| [29ea65] | 223 | stretch-shapes "1. 2. 3."
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| [48d20d] | 224 | take-best-of "5"
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| [345eda] | 225 | tesselation-radius "5."
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| [5ab796] | 226 | time-step-zero "0"
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| [a504946] | 227 | training-file "training.dat"
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| [3493da] | 228 | translate-atoms "1. 0. 0."
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| [0b5057] | 229 | translate-shapes "1. 2. 3."
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| [4dc309] | 230 | translation "0. 0. 0."
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| [3493da] | 231 | unselect-atom-by-element "1"
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| 232 | unselect-atom-by-element "4"
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| 233 | unselect-atom-by-id "0"
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| [61c364] | 234 | unselect-atom-by-order "1"
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| [3493da] | 235 | unselect-atoms-inside-cuboid "10 10 10"
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| 236 | unselect-atoms-inside-cuboid "2 2 2"
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| 237 | unselect-atoms-inside-sphere "10"
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| 238 | unselect-atoms-inside-sphere "7."
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| 239 | unselect-molecule-by-id "0"
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| 240 | unselect-molecule-by-id "4"
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| 241 | unselect-molecule-by-order "-1"
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| 242 | unselect-molecule-by-order "1"
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| 243 | unselect-molecule-by-order "-2"
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| 244 | unselect-molecule-by-order "2"
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| 245 | unselect-molecules-by-formula "C2H5(OH)"
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| 246 | unselect-molecules-by-formula "C3H8"
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| 247 | unselect-molecules-by-formula "C6H6"
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| 248 | unselect-molecules-by-formula "H2O"
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| 249 | unselect-molecules-by-name "water"
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| [2c004d] | 250 | unselect-shape-by-name "cube42"
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| [3493da] | 251 | verbose "3"
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| 252 | verlet-integration "forces.dat"
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