| 1 | #key value
|
|---|
| 2 | actionname "help"
|
|---|
| 3 | add-atom "1"
|
|---|
| 4 | add-empty-boundary ""
|
|---|
| 5 | angle-x "0."
|
|---|
| 6 | angle-x "0"
|
|---|
| 7 | angle-y "0."
|
|---|
| 8 | angle-y "0"
|
|---|
| 9 | angle-z "0 "
|
|---|
| 10 | angle-z "0."
|
|---|
| 11 | angle-z "0"
|
|---|
| 12 | axis "0 0 1"
|
|---|
| 13 | axis "0 1 0"
|
|---|
| 14 | axis "1 2 1"
|
|---|
| 15 | bin-end "10"
|
|---|
| 16 | bin-end "20"
|
|---|
| 17 | bin-end "359"
|
|---|
| 18 | bin-end "359.5"
|
|---|
| 19 | bin-end "5"
|
|---|
| 20 | bin-output-file "bin_output-10.csv"
|
|---|
| 21 | bin-output-file "bin_output-20.csv"
|
|---|
| 22 | bin-output-file "bin_output-5.csv"
|
|---|
| 23 | bin-output-file "bin_output.csv"
|
|---|
| 24 | bin-output-file "emptybox_histogram.dat"
|
|---|
| 25 | bin-output-file "hydrogenbox_histogram.dat"
|
|---|
| 26 | bin-output-file "waterbox_histogram.dat"
|
|---|
| 27 | bin-output-file "waterbox-mirrored_histogram.dat"
|
|---|
| 28 | bin-start "0"
|
|---|
| 29 | bin-start "-0.5"
|
|---|
| 30 | bin-start "10"
|
|---|
| 31 | bin-start "5"
|
|---|
| 32 | bin-width "1."
|
|---|
| 33 | bond-file "bond.dat"
|
|---|
| 34 | bond-table "table.dat"
|
|---|
| 35 | calculate-bounding-box ""
|
|---|
| 36 | calculate-molar-mass ""
|
|---|
| 37 | center-in-box "10 0 0 10 0 10"
|
|---|
| 38 | change-box "10 0 0 10 0 10"
|
|---|
| 39 | change-element "H"
|
|---|
| 40 | change-molname "water"
|
|---|
| 41 | convex-file "convexfile"
|
|---|
| 42 | copy-molecule "0"
|
|---|
| 43 | create-micelle "200"
|
|---|
| 44 | default-molname "molname"
|
|---|
| 45 | deltat "0.01"
|
|---|
| 46 | depth-first-search "2."
|
|---|
| 47 | dipole-angular-correlation "H2O"
|
|---|
| 48 | distance "1.55"
|
|---|
| 49 | distances "3.1 3.1 3.1"
|
|---|
| 50 | distances "3.1 3.1 3.1"
|
|---|
| 51 | distance-to-boundary "1."
|
|---|
| 52 | distance-to-molecule "1.5"
|
|---|
| 53 | distance-to-molecule "2.1"
|
|---|
| 54 | domain-position "0. 0. 0."
|
|---|
| 55 | domain-position "0 0 0"
|
|---|
| 56 | domain-position "10. 10. 10."
|
|---|
| 57 | DoRotate "0"
|
|---|
| 58 | DoSaturate "0"
|
|---|
| 59 | element-db "./"
|
|---|
| 60 | elements "1"
|
|---|
| 61 | elements "1 8"
|
|---|
| 62 | end-step "1"
|
|---|
| 63 | fastparsing "1"
|
|---|
| 64 | fill-molecule "filler.xyz"
|
|---|
| 65 | fill-void "hydrogen.xyz"
|
|---|
| 66 | fill-void "water.data"
|
|---|
| 67 | fill-void "water.xyz"
|
|---|
| 68 | fragment-molecule "./"
|
|---|
| 69 | id-mapping "1"
|
|---|
| 70 | input "test.data"
|
|---|
| 71 | interpolation-steps "9"
|
|---|
| 72 | keep-fixed-CenterOfMass "0"
|
|---|
| 73 | load "test.data"
|
|---|
| 74 | MaxDistance "-1"
|
|---|
| 75 | MDSteps "1"
|
|---|
| 76 | mesh-offset "0.5,0.5,0.5"
|
|---|
| 77 | mesh-size "10,10,10"
|
|---|
| 78 | min-distance "1."
|
|---|
| 79 | molecule-by-id "0"
|
|---|
| 80 | nonconvex-envelope "25"
|
|---|
| 81 | nonconvex-file "NonConvexEnvelope"
|
|---|
| 82 | nonconvex-file "nonconvexfile"
|
|---|
| 83 | offset "0"
|
|---|
| 84 | offset "1"
|
|---|
| 85 | order "2"
|
|---|
| 86 | output-file "emptybox_values.dat"
|
|---|
| 87 | output-file "hydrogenbox_values.dat"
|
|---|
| 88 | output-file "output-10.csv"
|
|---|
| 89 | output-file "output-20.csv"
|
|---|
| 90 | output-file "output-5.csv"
|
|---|
| 91 | output-file "output.csv"
|
|---|
| 92 | output-file "waterbox-mirrored_values.dat"
|
|---|
| 93 | output-file "waterbox_values.dat"
|
|---|
| 94 | output "store.conf"
|
|---|
| 95 | output "store.data"
|
|---|
| 96 | output "store.pdb"
|
|---|
| 97 | output "store.xyz"
|
|---|
| 98 | output "test.in"
|
|---|
| 99 | output-types "xyz"
|
|---|
| 100 | output-types "xyz mpqc"
|
|---|
| 101 | parse-tremolo-potentials "argon.potentials"
|
|---|
| 102 | parse-tremolo-potentials "tensid.potentials"
|
|---|
| 103 | parser-parameters "mpqc"
|
|---|
| 104 | parser-parameters "psi3"
|
|---|
| 105 | periodic "0"
|
|---|
| 106 | position "0 0 0"
|
|---|
| 107 | position "0 0 1"
|
|---|
| 108 | position "0 0 10"
|
|---|
| 109 | position "10 10 10"
|
|---|
| 110 | position "10. 10. 10."
|
|---|
| 111 | position "1 2 1"
|
|---|
| 112 | position "5.63 5.71 5.71"
|
|---|
| 113 | position "7.283585982 3.275186040 3.535886037"
|
|---|
| 114 | position "9.78 2.64 2.64"
|
|---|
| 115 | radius "20."
|
|---|
| 116 | random-atom-displacement "0."
|
|---|
| 117 | random-molecule-displacement "0."
|
|---|
| 118 | random-number-distribution-parameters "max=20;"
|
|---|
| 119 | random-number-engine-parameters "seed=2;"
|
|---|
| 120 | repeat-box "1 1 1"
|
|---|
| 121 | rotate-around-origin "180."
|
|---|
| 122 | rotate-around-origin "20."
|
|---|
| 123 | rotate-around-origin "360."
|
|---|
| 124 | rotate-around-origin "90."
|
|---|
| 125 | rotate-around-self "180."
|
|---|
| 126 | rotate-around-self "180"
|
|---|
| 127 | rotate-around-self "20."
|
|---|
| 128 | rotate-around-self "360."
|
|---|
| 129 | rotate-around-self "90."
|
|---|
| 130 | rotate-to-principal-axis-system ""
|
|---|
| 131 | save-adjacency "test.adj"
|
|---|
| 132 | save-bonds "test.bond"
|
|---|
| 133 | save-selected-atoms "testsave.xyz"
|
|---|
| 134 | save-selected-molecules "testsave.xyz"
|
|---|
| 135 | save-temperature "test.ekin"
|
|---|
| 136 | scale-box "0.5 1. 0.9"
|
|---|
| 137 | select-atom-by-element "1"
|
|---|
| 138 | select-atom-by-element "4"
|
|---|
| 139 | select-atom-by-id "0"
|
|---|
| 140 | select-atoms-inside-cuboid "10 10 10"
|
|---|
| 141 | select-atoms-inside-cuboid "2 2 2"
|
|---|
| 142 | select-atoms-inside-sphere "0.2"
|
|---|
| 143 | select-atoms-inside-sphere "10"
|
|---|
| 144 | select-atoms-inside-sphere "7."
|
|---|
| 145 | select-molecule-by-id "0"
|
|---|
| 146 | select-molecule-by-id "1"
|
|---|
| 147 | select-molecule-by-id "4"
|
|---|
| 148 | select-molecule-by-order "-1"
|
|---|
| 149 | select-molecule-by-order "1"
|
|---|
| 150 | select-molecule-by-order "-2"
|
|---|
| 151 | select-molecule-by-order "2"
|
|---|
| 152 | select-molecules-by-formula "C2H5(OH)"
|
|---|
| 153 | select-molecules-by-formula "C6H6"
|
|---|
| 154 | select-molecules-by-formula "H2O"
|
|---|
| 155 | select-molecules-by-name "water"
|
|---|
| 156 | set-boundary-conditions "Wrap, Wrap, Wrap"
|
|---|
| 157 | set-parser-parameters "basis = 4-31G"
|
|---|
| 158 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
|
|---|
| 159 | set-parser-parameters "maxiter = 499"
|
|---|
| 160 | set-parser-parameters "theory=CLKS"
|
|---|
| 161 | set-parser-parameters "wfn=scf"
|
|---|
| 162 | set-parser-parameters "ref=uhf"
|
|---|
| 163 | set-output "tremolo"
|
|---|
| 164 | set-random-number-distribution "uniform_int"
|
|---|
| 165 | set-random-number-engine "lagged_fibonacci607"
|
|---|
| 166 | set-tremolo-atomdata "ATOMDATA type id x=3"
|
|---|
| 167 | set-world-time "10"
|
|---|
| 168 | skiplines "1"
|
|---|
| 169 | skiplines "2"
|
|---|
| 170 | start-step "0"
|
|---|
| 171 | suspend-in-water "1.0"
|
|---|
| 172 | tesselation-radius "5."
|
|---|
| 173 | time-step-zero "0"
|
|---|
| 174 | translate-atoms "1. 0. 0."
|
|---|
| 175 | unselect-atom-by-element "1"
|
|---|
| 176 | unselect-atom-by-element "4"
|
|---|
| 177 | unselect-atom-by-id "0"
|
|---|
| 178 | unselect-atoms-inside-cuboid "10 10 10"
|
|---|
| 179 | unselect-atoms-inside-cuboid "2 2 2"
|
|---|
| 180 | unselect-atoms-inside-sphere "10"
|
|---|
| 181 | unselect-atoms-inside-sphere "7."
|
|---|
| 182 | unselect-molecule-by-id "0"
|
|---|
| 183 | unselect-molecule-by-id "4"
|
|---|
| 184 | unselect-molecule-by-order "-1"
|
|---|
| 185 | unselect-molecule-by-order "1"
|
|---|
| 186 | unselect-molecule-by-order "-2"
|
|---|
| 187 | unselect-molecule-by-order "2"
|
|---|
| 188 | unselect-molecules-by-formula "C2H5(OH)"
|
|---|
| 189 | unselect-molecules-by-formula "C3H8"
|
|---|
| 190 | unselect-molecules-by-formula "C6H6"
|
|---|
| 191 | unselect-molecules-by-formula "H2O"
|
|---|
| 192 | unselect-molecules-by-name "water"
|
|---|
| 193 | verbose "3"
|
|---|
| 194 | verlet-integration "forces.dat"
|
|---|
