| [3493da] | 1 | #key value
|
|---|
| 2 | actionname "help"
|
|---|
| 3 | add-atom "1"
|
|---|
| 4 | add-empty-boundary ""
|
|---|
| [cb7676] | 5 | Alignment-Axis "0,0,1"
|
|---|
| [3493da] | 6 | angle-x "0."
|
|---|
| 7 | angle-x "0"
|
|---|
| 8 | angle-y "0."
|
|---|
| 9 | angle-y "0"
|
|---|
| 10 | angle-z "0 "
|
|---|
| 11 | angle-z "0."
|
|---|
| 12 | angle-z "0"
|
|---|
| 13 | axis "0 0 1"
|
|---|
| 14 | axis "0 1 0"
|
|---|
| 15 | axis "1 2 1"
|
|---|
| 16 | bin-end "10"
|
|---|
| 17 | bin-end "20"
|
|---|
| 18 | bin-end "359"
|
|---|
| 19 | bin-end "359.5"
|
|---|
| 20 | bin-end "5"
|
|---|
| 21 | bin-output-file "bin_output-10.csv"
|
|---|
| 22 | bin-output-file "bin_output-20.csv"
|
|---|
| 23 | bin-output-file "bin_output-5.csv"
|
|---|
| 24 | bin-output-file "bin_output.csv"
|
|---|
| 25 | bin-output-file "emptybox_histogram.dat"
|
|---|
| 26 | bin-output-file "hydrogenbox_histogram.dat"
|
|---|
| 27 | bin-output-file "waterbox_histogram.dat"
|
|---|
| 28 | bin-output-file "waterbox-mirrored_histogram.dat"
|
|---|
| 29 | bin-start "0"
|
|---|
| 30 | bin-start "-0.5"
|
|---|
| 31 | bin-start "10"
|
|---|
| 32 | bin-start "5"
|
|---|
| 33 | bin-width "1."
|
|---|
| 34 | bond-file "bond.dat"
|
|---|
| 35 | bond-table "table.dat"
|
|---|
| [f89b45] | 36 | calculate-bounding-box ""
|
|---|
| [55f299] | 37 | calculate-molar-mass ""
|
|---|
| [2db053] | 38 | center "10. 10. 10."
|
|---|
| [3493da] | 39 | center-in-box "10 0 0 10 0 10"
|
|---|
| [8b886f] | 40 | change-bond-angle "100."
|
|---|
| [3493da] | 41 | change-box "10 0 0 10 0 10"
|
|---|
| 42 | change-element "H"
|
|---|
| 43 | change-molname "water"
|
|---|
| 44 | convex-file "convexfile"
|
|---|
| 45 | copy-molecule "0"
|
|---|
| [2db053] | 46 | count "12"
|
|---|
| [5ab796] | 47 | create-micelle "200"
|
|---|
| [3493da] | 48 | default-molname "molname"
|
|---|
| 49 | deltat "0.01"
|
|---|
| 50 | depth-first-search "2."
|
|---|
| [5ab796] | 51 | dipole-angular-correlation "H2O"
|
|---|
| [3493da] | 52 | distance "1.55"
|
|---|
| 53 | distances "3.1 3.1 3.1"
|
|---|
| 54 | distances "3.1 3.1 3.1"
|
|---|
| 55 | distance-to-boundary "1."
|
|---|
| 56 | distance-to-molecule "1.5"
|
|---|
| 57 | distance-to-molecule "2.1"
|
|---|
| 58 | domain-position "0. 0. 0."
|
|---|
| 59 | domain-position "0 0 0"
|
|---|
| 60 | domain-position "10. 10. 10."
|
|---|
| [69c733] | 61 | DoLongrange "0"
|
|---|
| [b6b21a] | 62 | DoPrintDebug "0"
|
|---|
| [3493da] | 63 | DoRotate "0"
|
|---|
| [5ab796] | 64 | DoSaturate "0"
|
|---|
| [6ff62c] | 65 | DoValenceOnly "0"
|
|---|
| [3493da] | 66 | element-db "./"
|
|---|
| 67 | elements "1"
|
|---|
| 68 | elements "1 8"
|
|---|
| 69 | end-step "1"
|
|---|
| [9291d04] | 70 | ExcludeHydrogen "1"
|
|---|
| [3493da] | 71 | fastparsing "1"
|
|---|
| [531f27] | 72 | filename "test.exttypes"
|
|---|
| [3493da] | 73 | fill-molecule "filler.xyz"
|
|---|
| 74 | fill-void "hydrogen.xyz"
|
|---|
| 75 | fill-void "water.data"
|
|---|
| 76 | fill-void "water.xyz"
|
|---|
| [4882d5] | 77 | forces-file "test.forces"
|
|---|
| [48d20d] | 78 | fragment-charges "1 1"
|
|---|
| [edecba] | 79 | fragment-executable "mpqc"
|
|---|
| 80 | fragment-jobs "Job00.in"
|
|---|
| [3493da] | 81 | fragment-molecule "./"
|
|---|
| [edecba] | 82 | fragment-path "test/"
|
|---|
| [55e1bc] | 83 | fragment-resultfile "results.dat"
|
|---|
| [065574] | 84 | grid-level "5"
|
|---|
| [3493da] | 85 | id-mapping "1"
|
|---|
| 86 | input "test.data"
|
|---|
| [13c5c1] | 87 | inter-order "2"
|
|---|
| [cd2591] | 88 | interpolation-degree "5"
|
|---|
| [3493da] | 89 | interpolation-steps "9"
|
|---|
| 90 | keep-fixed-CenterOfMass "0"
|
|---|
| 91 | load "test.data"
|
|---|
| 92 | MaxDistance "-1"
|
|---|
| [a88452] | 93 | mesh-offset "0.5,0.5,0.5"
|
|---|
| 94 | mesh-size "10,10,10"
|
|---|
| 95 | min-distance "1."
|
|---|
| [3493da] | 96 | molecule-by-id "0"
|
|---|
| [065574] | 97 | near-field-cells "3"
|
|---|
| [3493da] | 98 | nonconvex-envelope "25"
|
|---|
| 99 | nonconvex-file "NonConvexEnvelope"
|
|---|
| 100 | nonconvex-file "nonconvexfile"
|
|---|
| 101 | offset "0"
|
|---|
| 102 | offset "1"
|
|---|
| 103 | order "2"
|
|---|
| [39986b] | 104 | output-as "store.conf"
|
|---|
| 105 | output-as "store.data"
|
|---|
| 106 | output-as "store.pdb"
|
|---|
| 107 | output-as "store.xyz"
|
|---|
| 108 | output-as "test.in"
|
|---|
| 109 | output-every-step "1"
|
|---|
| [3493da] | 110 | output-file "emptybox_values.dat"
|
|---|
| 111 | output-file "hydrogenbox_values.dat"
|
|---|
| 112 | output-file "output-10.csv"
|
|---|
| 113 | output-file "output-20.csv"
|
|---|
| 114 | output-file "output-5.csv"
|
|---|
| 115 | output-file "output.csv"
|
|---|
| 116 | output-file "waterbox-mirrored_values.dat"
|
|---|
| 117 | output-file "waterbox_values.dat"
|
|---|
| [5ab796] | 118 | output-types "xyz"
|
|---|
| 119 | output-types "xyz mpqc"
|
|---|
| [d449a9] | 120 | parse-homologies "homology.dat"
|
|---|
| [3493da] | 121 | parse-tremolo-potentials "argon.potentials"
|
|---|
| 122 | parse-tremolo-potentials "tensid.potentials"
|
|---|
| [5ab796] | 123 | parser-parameters "mpqc"
|
|---|
| 124 | parser-parameters "psi3"
|
|---|
| [3493da] | 125 | periodic "0"
|
|---|
| 126 | position "0 0 0"
|
|---|
| 127 | position "0 0 1"
|
|---|
| 128 | position "0 0 10"
|
|---|
| 129 | position "10 10 10"
|
|---|
| 130 | position "10. 10. 10."
|
|---|
| 131 | position "1 2 1"
|
|---|
| 132 | position "5.63 5.71 5.71"
|
|---|
| 133 | position "7.283585982 3.275186040 3.535886037"
|
|---|
| 134 | position "9.78 2.64 2.64"
|
|---|
| [48d20d] | 135 | potential-charges "1 1"
|
|---|
| [baccf6] | 136 | potential-file "test.potentials"
|
|---|
| [a315e8] | 137 | potential-type "morse"
|
|---|
| [5ab796] | 138 | radius "20."
|
|---|
| [3493da] | 139 | random-atom-displacement "0."
|
|---|
| 140 | random-molecule-displacement "0."
|
|---|
| 141 | random-number-distribution-parameters "max=20;"
|
|---|
| 142 | random-number-engine-parameters "seed=2;"
|
|---|
| 143 | repeat-box "1 1 1"
|
|---|
| [ca331c] | 144 | reset 1
|
|---|
| [3493da] | 145 | rotate-around-origin "180."
|
|---|
| 146 | rotate-around-origin "20."
|
|---|
| 147 | rotate-around-origin "360."
|
|---|
| 148 | rotate-around-origin "90."
|
|---|
| 149 | rotate-around-self "180."
|
|---|
| 150 | rotate-around-self "180"
|
|---|
| 151 | rotate-around-self "20."
|
|---|
| 152 | rotate-around-self "360."
|
|---|
| 153 | rotate-around-self "90."
|
|---|
| 154 | rotate-to-principal-axis-system ""
|
|---|
| 155 | save-adjacency "test.adj"
|
|---|
| 156 | save-bonds "test.bond"
|
|---|
| [d449a9] | 157 | save-homologies "homology.dat"
|
|---|
| [3493da] | 158 | save-selected-atoms "testsave.xyz"
|
|---|
| [531f27] | 159 | save-selected-atoms-as-exttypes "test.exttypes"
|
|---|
| [3493da] | 160 | save-selected-molecules "testsave.xyz"
|
|---|
| 161 | save-temperature "test.ekin"
|
|---|
| 162 | scale-box "0.5 1. 0.9"
|
|---|
| 163 | select-atom-by-element "1"
|
|---|
| 164 | select-atom-by-element "4"
|
|---|
| 165 | select-atom-by-id "0"
|
|---|
| [61c364] | 166 | select-atom-by-order "1"
|
|---|
| [3493da] | 167 | select-atoms-inside-cuboid "10 10 10"
|
|---|
| 168 | select-atoms-inside-cuboid "2 2 2"
|
|---|
| 169 | select-atoms-inside-sphere "0.2"
|
|---|
| 170 | select-atoms-inside-sphere "10"
|
|---|
| 171 | select-atoms-inside-sphere "7."
|
|---|
| 172 | select-molecule-by-id "0"
|
|---|
| 173 | select-molecule-by-id "1"
|
|---|
| 174 | select-molecule-by-id "4"
|
|---|
| 175 | select-molecule-by-order "-1"
|
|---|
| 176 | select-molecule-by-order "1"
|
|---|
| 177 | select-molecule-by-order "-2"
|
|---|
| 178 | select-molecule-by-order "2"
|
|---|
| 179 | select-molecules-by-formula "C2H5(OH)"
|
|---|
| 180 | select-molecules-by-formula "C6H6"
|
|---|
| 181 | select-molecules-by-formula "H2O"
|
|---|
| 182 | select-molecules-by-name "water"
|
|---|
| [663606] | 183 | select-shape-by-name "sphere2"
|
|---|
| [edecba] | 184 | server-address "127.0.0.1"
|
|---|
| 185 | server-port "1026"
|
|---|
| [9e4655] | 186 | session-type "cli"
|
|---|
| [c52e08] | 187 | set-boundary-conditions "Wrap, Wrap, Wrap"
|
|---|
| [5ab796] | 188 | set-parser-parameters "basis = 4-31G"
|
|---|
| 189 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
|
|---|
| 190 | set-parser-parameters "maxiter = 499"
|
|---|
| 191 | set-parser-parameters "theory=CLKS"
|
|---|
| 192 | set-parser-parameters "wfn=scf"
|
|---|
| 193 | set-parser-parameters "ref=uhf"
|
|---|
| [3493da] | 194 | set-output "tremolo"
|
|---|
| 195 | set-random-number-distribution "uniform_int"
|
|---|
| 196 | set-random-number-engine "lagged_fibonacci607"
|
|---|
| [4792ab] | 197 | set-threshold "1e-6"
|
|---|
| [3493da] | 198 | set-tremolo-atomdata "ATOMDATA type id x=3"
|
|---|
| 199 | set-world-time "10"
|
|---|
| [6131d8] | 200 | shape-name "sphere1"
|
|---|
| [d475a6] | 201 | shape-op "AND"
|
|---|
| [4dc309] | 202 | shape-type "sphere"
|
|---|
| [3493da] | 203 | skiplines "1"
|
|---|
| 204 | skiplines "2"
|
|---|
| 205 | start-step "0"
|
|---|
| [39986b] | 206 | steps "5"
|
|---|
| [bf1d1b] | 207 | store-grids "0"
|
|---|
| [5589e7e] | 208 | store-saturated-fragment "BondFragment"
|
|---|
| [bad589] | 209 | store-session "test.sh"
|
|---|
| [3a51bd] | 210 | stretch-bond "1.5"
|
|---|
| [4dc309] | 211 | stretch "1. 1. 1."
|
|---|
| [29ea65] | 212 | stretch-shapes "1. 2. 3."
|
|---|
| [3493da] | 213 | suspend-in-water "1.0"
|
|---|
| [48d20d] | 214 | take-best-of "5"
|
|---|
| [345eda] | 215 | tesselation-radius "5."
|
|---|
| [5ab796] | 216 | time-step-zero "0"
|
|---|
| [a504946] | 217 | training-file "training.dat"
|
|---|
| [3493da] | 218 | translate-atoms "1. 0. 0."
|
|---|
| [0b5057] | 219 | translate-shapes "1. 2. 3."
|
|---|
| [4dc309] | 220 | translation "0. 0. 0."
|
|---|
| [3493da] | 221 | unselect-atom-by-element "1"
|
|---|
| 222 | unselect-atom-by-element "4"
|
|---|
| 223 | unselect-atom-by-id "0"
|
|---|
| [61c364] | 224 | unselect-atom-by-order "1"
|
|---|
| [3493da] | 225 | unselect-atoms-inside-cuboid "10 10 10"
|
|---|
| 226 | unselect-atoms-inside-cuboid "2 2 2"
|
|---|
| 227 | unselect-atoms-inside-sphere "10"
|
|---|
| 228 | unselect-atoms-inside-sphere "7."
|
|---|
| 229 | unselect-molecule-by-id "0"
|
|---|
| 230 | unselect-molecule-by-id "4"
|
|---|
| 231 | unselect-molecule-by-order "-1"
|
|---|
| 232 | unselect-molecule-by-order "1"
|
|---|
| 233 | unselect-molecule-by-order "-2"
|
|---|
| 234 | unselect-molecule-by-order "2"
|
|---|
| 235 | unselect-molecules-by-formula "C2H5(OH)"
|
|---|
| 236 | unselect-molecules-by-formula "C3H8"
|
|---|
| 237 | unselect-molecules-by-formula "C6H6"
|
|---|
| 238 | unselect-molecules-by-formula "H2O"
|
|---|
| 239 | unselect-molecules-by-name "water"
|
|---|
| [2c004d] | 240 | unselect-shape-by-name "cube42"
|
|---|
| [3493da] | 241 | verbose "3"
|
|---|
| 242 | verlet-integration "forces.dat"
|
|---|
