| [3493da] | 1 | #key value
|
|---|
| [cd91bd] | 2 | add_atom "1"
|
|---|
| 3 | add_empty_boundary "5,5,5"
|
|---|
| 4 | Alignment_Axis "0,0,1"
|
|---|
| 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"
|
|---|
| [3493da] | 12 | axis "0 0 1"
|
|---|
| 13 | axis "0 1 0"
|
|---|
| 14 | axis "1 2 1"
|
|---|
| [cd91bd] | 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_degree "1"
|
|---|
| 34 | bond_file "bond.dat"
|
|---|
| [788dce] | 35 | bondside "1"
|
|---|
| [cd91bd] | 36 | bond_table "table.dat"
|
|---|
| 37 | calculate_bounding_box ""
|
|---|
| 38 | calculate_molar_mass ""
|
|---|
| [2db053] | 39 | center "10. 10. 10."
|
|---|
| [cd91bd] | 40 | center_in_box "10 0 0 10 0 10"
|
|---|
| 41 | change_bond_angle "100."
|
|---|
| 42 | change_box "10 0 0 10 0 10"
|
|---|
| 43 | change_element "1"
|
|---|
| 44 | change_molname "water"
|
|---|
| 45 | convex_envelope "50."
|
|---|
| 46 | convex_file "convexfile"
|
|---|
| [987145] | 47 | coordinates "1,0,0"
|
|---|
| [cd91bd] | 48 | copy_molecule "0"
|
|---|
| [2db053] | 49 | count "12"
|
|---|
| [cd91bd] | 50 | create_micelle "200"
|
|---|
| 51 | damping_factor "0.5"
|
|---|
| 52 | default_molname "molname"
|
|---|
| [3493da] | 53 | deltat "0.01"
|
|---|
| [aa55d0] | 54 | density "1.0"
|
|---|
| [cd91bd] | 55 | depth_first_search "2."
|
|---|
| 56 | dipole_angular_correlation "H2O"
|
|---|
| [3493da] | 57 | distance "1.55"
|
|---|
| 58 | distances "3.1 3.1 3.1"
|
|---|
| 59 | distances "3.1 3.1 3.1"
|
|---|
| [cd91bd] | 60 | distance_to_boundary "1."
|
|---|
| 61 | distance_to_molecule "1.5"
|
|---|
| 62 | distance_to_molecule "2.1"
|
|---|
| 63 | distance_to_vector "named_vector"
|
|---|
| 64 | domain_position "0. 0. 0."
|
|---|
| 65 | domain_position "0 0 0"
|
|---|
| 66 | domain_position "10. 10. 10."
|
|---|
| [fe0cb8] | 67 | DoCyclesFull "0"
|
|---|
| [69c733] | 68 | DoLongrange "0"
|
|---|
| [5f7b95] | 69 | DoOutputEveryStep "0"
|
|---|
| [b6b21a] | 70 | DoPrintDebug "0"
|
|---|
| [3493da] | 71 | DoRotate "0"
|
|---|
| [5ab796] | 72 | DoSaturate "0"
|
|---|
| [17e4fd] | 73 | DoSmearElectronicCharges "0"
|
|---|
| [6ff62c] | 74 | DoValenceOnly "0"
|
|---|
| [cd91bd] | 75 | element_db "./"
|
|---|
| [3493da] | 76 | elements "1"
|
|---|
| 77 | elements "1 8"
|
|---|
| [cd91bd] | 78 | end_step "1"
|
|---|
| 79 | enforce_net_zero_charge "0"
|
|---|
| [9291d04] | 80 | ExcludeHydrogen "1"
|
|---|
| [3493da] | 81 | fastparsing "1"
|
|---|
| [531f27] | 82 | filename "test.exttypes"
|
|---|
| [cd91bd] | 83 | fill_molecule "filler.xyz"
|
|---|
| 84 | fill_void "hydrogen.xyz"
|
|---|
| 85 | fill_void "water.data"
|
|---|
| 86 | fill_void "water.xyz"
|
|---|
| 87 | forces_file "test.forces"
|
|---|
| 88 | fragment_charges "1 1"
|
|---|
| 89 | fragment_executable "mpqc"
|
|---|
| 90 | fragment_jobs "Job00.in"
|
|---|
| 91 | fragment_molecule "./"
|
|---|
| 92 | fragment_path "test/"
|
|---|
| 93 | fragment_prefix "BondFragment"
|
|---|
| [f5ea10] | 94 | graph6 "B`"
|
|---|
| [cd91bd] | 95 | grid_level "5"
|
|---|
| [55feff5] | 96 | help "help"
|
|---|
| [cd91bd] | 97 | id_mapping "1"
|
|---|
| [3493da] | 98 | input "test.data"
|
|---|
| [cd91bd] | 99 | input_to_vector "named_vector"
|
|---|
| 100 | inter_order "2"
|
|---|
| 101 | interpolation_degree "5"
|
|---|
| 102 | interpolation_steps "9"
|
|---|
| 103 | keep_bondgraph "1"
|
|---|
| 104 | keep_fixed_CenterOfMass "0"
|
|---|
| [3493da] | 105 | load "test.data"
|
|---|
| [cd91bd] | 106 | load_session "test.py"
|
|---|
| [3493da] | 107 | MaxDistance "-1"
|
|---|
| [cd91bd] | 108 | max_distance "0"
|
|---|
| 109 | max_meshwidth "0.3"
|
|---|
| 110 | mesh_offset "0.5,0.5,0.5"
|
|---|
| 111 | mesh_size "10,10,10"
|
|---|
| 112 | min_distance "1."
|
|---|
| 113 | mirror_atoms "1.,1.,1."
|
|---|
| 114 | molecule_by_id "0"
|
|---|
| 115 | near_field_cells "3"
|
|---|
| 116 | nonconvex_envelope "25"
|
|---|
| 117 | nonconvex_file "NonConvexEnvelope"
|
|---|
| 118 | nonconvex_file "nonconvexfile"
|
|---|
| [3493da] | 119 | offset "0"
|
|---|
| 120 | offset "1"
|
|---|
| 121 | order "2"
|
|---|
| [cd91bd] | 122 | output_as "store.conf"
|
|---|
| 123 | output_as "store.data"
|
|---|
| 124 | output_as "store.pdb"
|
|---|
| 125 | output_as "store.xyz"
|
|---|
| 126 | output_as "test.in"
|
|---|
| 127 | output_every_step "1"
|
|---|
| 128 | output_file "emptybox_values.dat"
|
|---|
| 129 | output_file "hydrogenbox_values.dat"
|
|---|
| 130 | output_file "output-10.csv"
|
|---|
| 131 | output_file "output-20.csv"
|
|---|
| 132 | output_file "output-5.csv"
|
|---|
| 133 | output_file "output.csv"
|
|---|
| 134 | output_file "waterbox-mirrored_values.dat"
|
|---|
| 135 | output_file "waterbox_values.dat"
|
|---|
| 136 | output_types "xyz"
|
|---|
| 137 | output_types "xyz mpqc"
|
|---|
| 138 | parse_atom_fragments "atomfragments.dat"
|
|---|
| 139 | parse_fragment_results "results.dat"
|
|---|
| 140 | parse_homologies "homology.dat"
|
|---|
| 141 | parse_particle_parameters "water.particles"
|
|---|
| 142 | parse_potentials "water.potentials"
|
|---|
| 143 | parse_state_files "1"
|
|---|
| 144 | parse_tremolo_potentials "argon.potentials"
|
|---|
| 145 | parse_tremolo_potentials "tensid.potentials"
|
|---|
| 146 | parser_parameters "mpqc"
|
|---|
| 147 | parser_parameters "psi3"
|
|---|
| [3493da] | 148 | periodic "0"
|
|---|
| [cd91bd] | 149 | plane_offset "5."
|
|---|
| 150 | plane_to_vector "named_vector"
|
|---|
| [3493da] | 151 | position "0 0 0"
|
|---|
| 152 | position "0 0 1"
|
|---|
| 153 | position "0 0 10"
|
|---|
| 154 | position "10 10 10"
|
|---|
| 155 | position "10. 10. 10."
|
|---|
| 156 | position "1 2 1"
|
|---|
| 157 | position "5.63 5.71 5.71"
|
|---|
| 158 | position "7.283585982 3.275186040 3.535886037"
|
|---|
| 159 | position "9.78 2.64 2.64"
|
|---|
| [cd91bd] | 160 | position_to_vector "named_vector"
|
|---|
| 161 | potential_charges "1 1"
|
|---|
| 162 | potential_type "morse"
|
|---|
| [5ab796] | 163 | radius "20."
|
|---|
| [cd91bd] | 164 | random_atom_displacement "0."
|
|---|
| 165 | random_molecule_displacement "0."
|
|---|
| 166 | random_number_distribution_parameters "max=20;"
|
|---|
| 167 | random_number_engine_parameters "seed=2;"
|
|---|
| 168 | random_perturbation "0.1"
|
|---|
| 169 | remove_geometry "named_vector"
|
|---|
| 170 | repeat_box "1 1 1"
|
|---|
| [ca331c] | 171 | reset 1
|
|---|
| [987145] | 172 | reverse "0"
|
|---|
| [cd91bd] | 173 | rotate_around_bond "90."
|
|---|
| 174 | rotate_around_origin "180."
|
|---|
| 175 | rotate_around_origin "20."
|
|---|
| 176 | rotate_around_origin "360."
|
|---|
| 177 | rotate_around_origin "90."
|
|---|
| 178 | rotate_around_self "180."
|
|---|
| 179 | rotate_around_self "180"
|
|---|
| 180 | rotate_around_self "20."
|
|---|
| 181 | rotate_around_self "360."
|
|---|
| 182 | rotate_around_self "90."
|
|---|
| 183 | rotate_to_principal_axis_system "0,0,1"
|
|---|
| 184 | save_adjacency "test.adj"
|
|---|
| 185 | save_bonds "test.bond"
|
|---|
| 186 | save_atom_fragments "atomfragments.dat"
|
|---|
| 187 | save_fragment_results "results.dat"
|
|---|
| 188 | save_homologies "homology.dat"
|
|---|
| 189 | save_particle_parameters "water.particles"
|
|---|
| 190 | save_potentials "water.potentials"
|
|---|
| 191 | save_selected_atoms "testsave.xyz"
|
|---|
| 192 | save_selected_atoms_as_exttypes "test.exttypes"
|
|---|
| 193 | save_selected_molecules "testsave.xyz"
|
|---|
| [d40189] | 194 | save_energies "test.ekin"
|
|---|
| [cd91bd] | 195 | scale_box "0.5 1. 0.9"
|
|---|
| 196 | select_atom_by_element "1"
|
|---|
| 197 | select_atom_by_element "4"
|
|---|
| 198 | select_atom_by_id "0"
|
|---|
| 199 | select_atom_by_name "H1"
|
|---|
| 200 | select_atom_by_order "1"
|
|---|
| 201 | select_atoms_inside_cuboid "10 10 10"
|
|---|
| 202 | select_atoms_inside_cuboid "2 2 2"
|
|---|
| 203 | select_atoms_inside_sphere "0.2"
|
|---|
| 204 | select_atoms_inside_sphere "10"
|
|---|
| 205 | select_atoms_inside_sphere "7."
|
|---|
| 206 | select_molecule_by_id "0"
|
|---|
| 207 | select_molecule_by_id "1"
|
|---|
| 208 | select_molecule_by_id "4"
|
|---|
| 209 | select_molecule_by_order "-1"
|
|---|
| 210 | select_molecule_by_order "1"
|
|---|
| 211 | select_molecule_by_order "-2"
|
|---|
| 212 | select_molecule_by_order "2"
|
|---|
| 213 | select_molecules_by_formula "C2H5(OH)"
|
|---|
| 214 | select_molecules_by_formula "C6H6"
|
|---|
| 215 | select_molecules_by_formula "H2O"
|
|---|
| 216 | select_molecules_by_name "water"
|
|---|
| 217 | select_shape_by_name "sphere2"
|
|---|
| 218 | server_address "127.0.0.1"
|
|---|
| 219 | server_port "1026"
|
|---|
| 220 | session_type "cli"
|
|---|
| 221 | set_bond_degree "1"
|
|---|
| 222 | set_boundary_conditions "Wrap, Wrap, Wrap"
|
|---|
| 223 | set_max_iterations "10"
|
|---|
| 224 | set_parser_parameters "basis = 4-31G"
|
|---|
| 225 | set_parser_parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
|
|---|
| 226 | set_parser_parameters "maxiter = 499"
|
|---|
| 227 | set_parser_parameters "theory=CLKS"
|
|---|
| 228 | set_parser_parameters "wfn=scf"
|
|---|
| 229 | set_parser_parameters "ref=uhf"
|
|---|
| 230 | set_output "tremolo"
|
|---|
| 231 | set_random_number_distribution "uniform_int"
|
|---|
| 232 | set_random_number_engine "lagged_fibonacci607"
|
|---|
| 233 | set_threshold "1e-6"
|
|---|
| 234 | set_tremolo_atomdata "ATOMDATA type id x=3"
|
|---|
| 235 | set_world_time "10"
|
|---|
| 236 | shape_name "sphere1"
|
|---|
| 237 | shape_op "AND"
|
|---|
| 238 | shape_type "sphere"
|
|---|
| [3493da] | 239 | skiplines "1"
|
|---|
| 240 | skiplines "2"
|
|---|
| [cd91bd] | 241 | start_step "0"
|
|---|
| [39986b] | 242 | steps "5"
|
|---|
| [cd91bd] | 243 | step_world_time "1"
|
|---|
| 244 | store_grids "0"
|
|---|
| 245 | store_saturated_fragment "BondFragment"
|
|---|
| 246 | store_session "test.sh"
|
|---|
| 247 | stretch_bond "1.5"
|
|---|
| [4dc309] | 248 | stretch "1. 1. 1."
|
|---|
| [cd91bd] | 249 | stretch_shapes "1. 2. 3."
|
|---|
| 250 | take_best_of "5"
|
|---|
| 251 | tesselation_radius "5."
|
|---|
| [0ec9f5] | 252 | till-mark "0"
|
|---|
| [cd91bd] | 253 | time_step_zero "0"
|
|---|
| 254 | training_file "training.dat"
|
|---|
| 255 | translate_atoms "1. 0. 0."
|
|---|
| 256 | translate_shapes "1. 2. 3."
|
|---|
| [4dc309] | 257 | translation "0. 0. 0."
|
|---|
| [0ec9f5] | 258 | undo-mark "0"
|
|---|
| [cd91bd] | 259 | unselect_atom_by_element "1"
|
|---|
| 260 | unselect_atom_by_element "4"
|
|---|
| 261 | unselect_atom_by_id "0"
|
|---|
| 262 | unselect_atom_by_name "H1"
|
|---|
| 263 | unselect_atom_by_order "1"
|
|---|
| 264 | unselect_atoms_inside_cuboid "10 10 10"
|
|---|
| 265 | unselect_atoms_inside_cuboid "2 2 2"
|
|---|
| 266 | unselect_atoms_inside_sphere "10"
|
|---|
| 267 | unselect_atoms_inside_sphere "7."
|
|---|
| 268 | unselect_molecule_by_id "0"
|
|---|
| 269 | unselect_molecule_by_id "4"
|
|---|
| 270 | unselect_molecule_by_order "-1"
|
|---|
| 271 | unselect_molecule_by_order "1"
|
|---|
| 272 | unselect_molecule_by_order "-2"
|
|---|
| 273 | unselect_molecule_by_order "2"
|
|---|
| 274 | unselect_molecules_by_formula "C2H5(OH)"
|
|---|
| 275 | unselect_molecules_by_formula "C3H8"
|
|---|
| 276 | unselect_molecules_by_formula "C6H6"
|
|---|
| 277 | unselect_molecules_by_formula "H2O"
|
|---|
| 278 | unselect_molecules_by_name "water"
|
|---|
| 279 | unselect_shape_by_name "cube42"
|
|---|
| 280 | use_bondgraph "1"
|
|---|
| [666e9e] | 281 | UseImplicitCharges "1"
|
|---|
| [3493da] | 282 | verbose "3"
|
|---|
| [cd91bd] | 283 | verlet_integration "forces.dat"
|
|---|
