1 | #key value
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2 | add-atom "1"
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3 | add-empty-boundary "5,5,5"
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4 | Alignment-Axis "0,0,1"
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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-degree "1"
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34 | bond-file "bond.dat"
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35 | bondside "1"
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36 | bond-table "table.dat"
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37 | calculate-bounding-box ""
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38 | calculate-molar-mass ""
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39 | center "10. 10. 10."
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40 | center-in-box "10 0 0 10 0 10"
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41 | change-bond-angle "100."
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42 | change-box "10 0 0 10 0 10"
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43 | change-element "1"
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44 | change-molname "water"
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45 | convex-envelope "50."
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46 | convex-file "convexfile"
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47 | coordinates "1,0,0"
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48 | copy-molecule "0"
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49 | count "12"
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50 | create-micelle "200"
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51 | default-molname "molname"
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52 | deltat "0.01"
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53 | density "1.0"
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54 | depth-first-search "2."
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55 | dipole-angular-correlation "H2O"
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56 | distance "1.55"
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57 | distances "3.1 3.1 3.1"
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58 | distances "3.1 3.1 3.1"
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59 | distance-to-boundary "1."
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60 | distance-to-molecule "1.5"
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61 | distance-to-molecule "2.1"
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62 | distance-to-vector "named_vector"
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63 | domain-position "0. 0. 0."
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64 | domain-position "0 0 0"
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65 | domain-position "10. 10. 10."
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66 | DoCyclesFull "0"
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67 | DoLongrange "0"
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68 | DoOutputEveryStep "0"
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69 | DoPrintDebug "0"
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70 | DoRotate "0"
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71 | DoSaturate "0"
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72 | DoSmearElectronicCharges "0"
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73 | DoValenceOnly "0"
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74 | element-db "./"
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75 | elements "1"
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76 | elements "1 8"
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77 | end-step "1"
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78 | enforce-net-zero-charge "0"
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79 | ExcludeHydrogen "1"
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80 | fastparsing "1"
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81 | filename "test.exttypes"
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82 | fill-molecule "filler.xyz"
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83 | fill-void "hydrogen.xyz"
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84 | fill-void "water.data"
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85 | fill-void "water.xyz"
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86 | forces-file "test.forces"
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87 | fragment-charges "1 1"
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88 | fragment-executable "mpqc"
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89 | fragment-jobs "Job00.in"
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90 | fragment-molecule "./"
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91 | fragment-path "test/"
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92 | fragment-prefix "BondFragment"
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93 | grid-level "5"
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94 | help "help"
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95 | id-mapping "1"
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96 | input "test.data"
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97 | input-to-vector "named_vector"
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98 | inter-order "2"
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99 | interpolation-degree "5"
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100 | interpolation-steps "9"
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101 | keep-bondgraph "1"
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102 | keep-fixed-CenterOfMass "0"
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103 | load "test.data"
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104 | load-session "test.py"
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105 | MaxDistance "-1"
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106 | max-distance "0"
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107 | max-meshwidth "0.3"
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108 | mesh-offset "0.5,0.5,0.5"
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109 | mesh-size "10,10,10"
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110 | min-distance "1."
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111 | mirror-atoms "1.,1.,1."
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112 | molecule-by-id "0"
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113 | near-field-cells "3"
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114 | nonconvex-envelope "25"
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115 | nonconvex-file "NonConvexEnvelope"
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116 | nonconvex-file "nonconvexfile"
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117 | offset "0"
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118 | offset "1"
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119 | order "2"
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120 | output-as "store.conf"
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121 | output-as "store.data"
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122 | output-as "store.pdb"
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123 | output-as "store.xyz"
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124 | output-as "test.in"
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125 | output-every-step "1"
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126 | output-file "emptybox_values.dat"
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127 | output-file "hydrogenbox_values.dat"
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128 | output-file "output-10.csv"
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129 | output-file "output-20.csv"
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130 | output-file "output-5.csv"
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131 | output-file "output.csv"
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132 | output-file "waterbox-mirrored_values.dat"
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133 | output-file "waterbox_values.dat"
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134 | output-types "xyz"
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135 | output-types "xyz mpqc"
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136 | parse-atom-fragments "atomfragments.dat"
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137 | parse-fragment-results "results.dat"
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138 | parse-homologies "homology.dat"
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139 | parse-particle-parameters "water.particles"
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140 | parse-potentials "water.potentials"
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141 | parse-state-files "1"
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142 | parse-tremolo-potentials "argon.potentials"
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143 | parse-tremolo-potentials "tensid.potentials"
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144 | parser-parameters "mpqc"
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145 | parser-parameters "psi3"
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146 | periodic "0"
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147 | plane-offset "5."
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148 | plane-to-vector "named_vector"
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149 | position "0 0 0"
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150 | position "0 0 1"
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151 | position "0 0 10"
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152 | position "10 10 10"
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153 | position "10. 10. 10."
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154 | position "1 2 1"
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155 | position "5.63 5.71 5.71"
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156 | position "7.283585982 3.275186040 3.535886037"
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157 | position "9.78 2.64 2.64"
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158 | position-to-vector "named_vector"
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159 | potential-charges "1 1"
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160 | potential-type "morse"
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161 | radius "20."
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162 | random-atom-displacement "0."
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163 | random-molecule-displacement "0."
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164 | random-number-distribution-parameters "max=20;"
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165 | random-number-engine-parameters "seed=2;"
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166 | random-perturbation "0.1"
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167 | remove-geometry "named_vector"
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168 | repeat-box "1 1 1"
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169 | reset 1
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170 | reverse "0"
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171 | rotate-around-bond "90."
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172 | rotate-around-origin "180."
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173 | rotate-around-origin "20."
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174 | rotate-around-origin "360."
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175 | rotate-around-origin "90."
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176 | rotate-around-self "180."
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177 | rotate-around-self "180"
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178 | rotate-around-self "20."
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179 | rotate-around-self "360."
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180 | rotate-around-self "90."
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181 | rotate-to-principal-axis-system "0,0,1"
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182 | save-adjacency "test.adj"
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183 | save-bonds "test.bond"
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184 | save-atom-fragments "atomfragments.dat"
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185 | save-fragment-results "results.dat"
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186 | save-homologies "homology.dat"
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187 | save-particle-parameters "water.particles"
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188 | save-potentials "water.potentials"
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189 | save-selected-atoms "testsave.xyz"
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190 | save-selected-atoms-as-exttypes "test.exttypes"
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191 | save-selected-molecules "testsave.xyz"
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192 | save-temperature "test.ekin"
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193 | scale-box "0.5 1. 0.9"
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194 | select-atom-by-element "1"
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195 | select-atom-by-element "4"
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196 | select-atom-by-id "0"
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197 | select-atom-by-order "1"
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198 | select-atoms-inside-cuboid "10 10 10"
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199 | select-atoms-inside-cuboid "2 2 2"
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200 | select-atoms-inside-sphere "0.2"
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201 | select-atoms-inside-sphere "10"
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202 | select-atoms-inside-sphere "7."
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203 | select-molecule-by-id "0"
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204 | select-molecule-by-id "1"
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205 | select-molecule-by-id "4"
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206 | select-molecule-by-order "-1"
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207 | select-molecule-by-order "1"
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208 | select-molecule-by-order "-2"
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209 | select-molecule-by-order "2"
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210 | select-molecules-by-formula "C2H5(OH)"
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211 | select-molecules-by-formula "C6H6"
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212 | select-molecules-by-formula "H2O"
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213 | select-molecules-by-name "water"
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214 | select-shape-by-name "sphere2"
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215 | server-address "127.0.0.1"
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216 | server-port "1026"
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217 | session-type "cli"
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218 | set-bond-degree "1"
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219 | set-boundary-conditions "Wrap, Wrap, Wrap"
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220 | set-max-iterations "10"
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221 | set-parser-parameters "basis = 4-31G"
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222 | set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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223 | set-parser-parameters "maxiter = 499"
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224 | set-parser-parameters "theory=CLKS"
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225 | set-parser-parameters "wfn=scf"
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226 | set-parser-parameters "ref=uhf"
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227 | set-output "tremolo"
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228 | set-random-number-distribution "uniform_int"
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229 | set-random-number-engine "lagged_fibonacci607"
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230 | set-threshold "1e-6"
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231 | set-tremolo-atomdata "ATOMDATA type id x=3"
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232 | set-world-time "10"
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233 | shape-name "sphere1"
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234 | shape-op "AND"
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235 | shape-type "sphere"
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236 | skiplines "1"
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237 | skiplines "2"
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238 | start-step "0"
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239 | steps "5"
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240 | step-world-time "1"
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241 | store-grids "0"
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242 | store-saturated-fragment "BondFragment"
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243 | store-session "test.sh"
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244 | stretch-bond "1.5"
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245 | stretch "1. 1. 1."
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246 | stretch-shapes "1. 2. 3."
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247 | take-best-of "5"
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248 | tesselation-radius "5."
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249 | time-step-zero "0"
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250 | training-file "training.dat"
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251 | translate-atoms "1. 0. 0."
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252 | translate-shapes "1. 2. 3."
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253 | translation "0. 0. 0."
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254 | unselect-atom-by-element "1"
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255 | unselect-atom-by-element "4"
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256 | unselect-atom-by-id "0"
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257 | unselect-atom-by-order "1"
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258 | unselect-atoms-inside-cuboid "10 10 10"
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259 | unselect-atoms-inside-cuboid "2 2 2"
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260 | unselect-atoms-inside-sphere "10"
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261 | unselect-atoms-inside-sphere "7."
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262 | unselect-molecule-by-id "0"
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263 | unselect-molecule-by-id "4"
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264 | unselect-molecule-by-order "-1"
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265 | unselect-molecule-by-order "1"
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266 | unselect-molecule-by-order "-2"
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267 | unselect-molecule-by-order "2"
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268 | unselect-molecules-by-formula "C2H5(OH)"
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269 | unselect-molecules-by-formula "C3H8"
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270 | unselect-molecules-by-formula "C6H6"
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271 | unselect-molecules-by-formula "H2O"
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272 | unselect-molecules-by-name "water"
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273 | unselect-shape-by-name "cube42"
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274 | UseImplicitCharges "1"
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275 | verbose "3"
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276 | verlet-integration "forces.dat"
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