| 1 | #key value
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| 2 | add_atom "1"
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| 3 | add_selected_atoms_as_fragment "BondFragment"
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| 4 | add_empty_boundary "5,5,5"
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| 5 | add_potential "Morse"
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| 6 | Alignment_Axis "0,0,1"
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| 7 | angle_x "0."
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| 8 | angle_x "0"
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| 9 | angle_y "0."
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| 10 | angle_y "0"
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| 11 | angle_z "0 "
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| 12 | angle_z "0."
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| 13 | angle_z "0"
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| 14 | axis "0 0 1"
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| 15 | axis "0 1 0"
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| 16 | axis "1 2 1"
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| 17 | bin_end "10"
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| 18 | bin_end "20"
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| 19 | bin_end "359"
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| 20 | bin_end "359.5"
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| 21 | bin_end "5"
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| 22 | bin_output_file "bin_output-10.csv"
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| 23 | bin_output_file "bin_output-20.csv"
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| 24 | bin_output_file "bin_output-5.csv"
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| 25 | bin_output_file "bin_output.csv"
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| 26 | bin_output_file "emptybox_histogram.dat"
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| 27 | bin_output_file "hydrogenbox_histogram.dat"
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| 28 | bin_output_file "waterbox_histogram.dat"
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| 29 | bin_output_file "waterbox-mirrored_histogram.dat"
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| 30 | bin_start "0"
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| 31 | bin_start "-0.5"
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| 32 | bin_start "10"
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| 33 | bin_start "5"
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| 34 | bin_width "1."
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| 35 | bond_degree "1"
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| 36 | bond_file "bond.dat"
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| 37 | bondside "1"
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| 38 | bond_table "table.dat"
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| 39 | calculate_bounding_box ""
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| 40 | calculate_molar_mass ""
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| 41 | center "10. 10. 10."
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| 42 | center_in_box "10 0 0 10 0 10"
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| 43 | change_bond_angle "100."
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| 44 | change_box "10 0 0 10 0 10"
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| 45 | change_element "1"
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| 46 | change_molname "water"
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| 47 | convex_envelope "50."
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| 48 | convex_file "convexfile"
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| 49 | coordinates "1,0,0"
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| 50 | copy_molecule "0"
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| 51 | count "12"
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| 52 | create_micelle "200"
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| 53 | damping_factor "0.5"
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| 54 | default_molname "molname"
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| 55 | deltat "0.01"
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| 56 | density "1.0"
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| 57 | depth_first_search "2."
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| 58 | dipole_angular_correlation "H2O"
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| 59 | distance "1.55"
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| 60 | distances "3.1 3.1 3.1"
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| 61 | distances "3.1 3.1 3.1"
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| 62 | distance_to_boundary "1."
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| 63 | distance_to_molecule "1.5"
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| 64 | distance_to_molecule "2.1"
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| 65 | distance_to_vector "named_vector"
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| 66 | domain_position "0. 0. 0."
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| 67 | domain_position "0 0 0"
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| 68 | domain_position "10. 10. 10."
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| 69 | DoCyclesFull "0"
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| 70 | DoLongrange "0"
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| 71 | DoOutputEveryStep "0"
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| 72 | DoPrintDebug "0"
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| 73 | DoRotate "0"
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| 74 | DoSaturate "0"
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| 75 | DoSmearElectronicCharges "0"
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| 76 | DoValenceOnly "0"
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| 77 | element_db "./"
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| 78 | elements "1"
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| 79 | elements "1 8"
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| 80 | end_step "1"
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| 81 | enforce_net_zero_charge "0"
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| 82 | error_file ""
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| 83 | evaluate_stability "test"
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| 84 | ExcludeHydrogen "1"
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| 85 | fastparsing "1"
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| 86 | filename "test.exttypes"
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| 87 | fill_molecule "filler.xyz"
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| 88 | fill_void "hydrogen.xyz"
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| 89 | fill_void "water.data"
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| 90 | fill_void "water.xyz"
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| 91 | forces_file "test.forces"
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| 92 | force_overwrite "0"
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| 93 | fragment_charges "1 1"
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| 94 | fragment_executable "mpqc"
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| 95 | fragment_jobs "Job00.in"
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| 96 | fragment_molecule "./"
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| 97 | fragment_path "test/"
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| 98 | fragment_prefix "BondFragment"
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| 99 | graph6 "B`"
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| 100 | grid_level "5"
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| 101 | help "help"
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| 102 | id_mapping "1"
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| 103 | input "test.data"
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| 104 | input_to_vector "named_vector"
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| 105 | inter_order "2"
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| 106 | interpolation_degree "5"
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| 107 | interpolation_steps "9"
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| 108 | keep_bondgraph "1"
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| 109 | keep_fixed_CenterOfMass "0"
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| 110 | load "test.data"
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| 111 | load_session "test.py"
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| 112 | MaxDistance "-1"
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| 113 | max_distance "0"
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| 114 | max_hydrogens "1"
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| 115 | max_meshwidth "0.3"
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| 116 | mesh_offset "0.5,0.5,0.5"
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| 117 | mesh_size "10,10,10"
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| 118 | min_distance "1."
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| 119 | mirror_atoms "1.,1.,1."
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| 120 | molecule_by_id "0"
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| 121 | name "test"
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| 122 | near_field_cells "3"
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| 123 | nonconvex_envelope "25"
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| 124 | nonconvex_file "NonConvexEnvelope"
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| 125 | nonconvex_file "nonconvexfile"
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| 126 | offset "0"
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| 127 | offset "1"
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| 128 | order "2"
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| 129 | output_as "store.conf"
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| 130 | output_as "store.data"
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| 131 | output_as "store.pdb"
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| 132 | output_as "store.xyz"
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| 133 | output_as "test.in"
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| 134 | output_every_step "1"
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| 135 | output_file "emptybox_values.dat"
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| 136 | output_file "hydrogenbox_values.dat"
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| 137 | output_file "output-10.csv"
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| 138 | output_file "output-20.csv"
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| 139 | output_file "output-5.csv"
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| 140 | output_file "output.csv"
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| 141 | output_file "waterbox-mirrored_values.dat"
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| 142 | output_file "waterbox_values.dat"
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| 143 | output_types "xyz"
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| 144 | output_types "xyz mpqc"
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| 145 | parse_atom_fragments "atomfragments.dat"
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| 146 | parse_fragment_results "results.dat"
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| 147 | parse_homologies "homology.dat"
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| 148 | parse_particle_parameters "water.particles"
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| 149 | parse_potentials "water.potentials"
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| 150 | parse_state_files "1"
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| 151 | parse_tremolo_potentials "argon.potentials"
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| 152 | parse_tremolo_potentials "tensid.potentials"
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| 153 | parser_parameters "mpqc"
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| 154 | parser_parameters "psi3"
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| 155 | periodic "0"
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| 156 | plane_offset "5."
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| 157 | plane_to_vector "named_vector"
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| 158 | position "0 0 0"
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| 159 | position "0 0 1"
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| 160 | position "0 0 10"
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| 161 | position "10 10 10"
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| 162 | position "10. 10. 10."
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| 163 | position "1 2 1"
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| 164 | position "5.63 5.71 5.71"
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| 165 | position "7.283585982 3.275186040 3.535886037"
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| 166 | position "9.78 2.64 2.64"
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| 167 | position_to_vector "named_vector"
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| 168 | potential_charges "1 1"
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| 169 | potential_type "morse"
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| 170 | potential_list "angle harmonic_bond"
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| 171 | radius "20."
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| 172 | random_atom_displacement "0."
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| 173 | random_molecule_displacement "0."
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| 174 | random_number_distribution_parameters "max=20;"
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| 175 | random_number_engine_parameters "seed=2;"
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| 176 | random_perturbation "0.1"
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| 177 | remove_geometry "named_vector"
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| 178 | remove_potential "Morse"
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| 179 | repeat_box "1 1 1"
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| 180 | reset 1
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| 181 | reverse "0"
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| 182 | rotate_around_bond "90."
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| 183 | rotate_around_origin "180."
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| 184 | rotate_around_origin "20."
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| 185 | rotate_around_origin "360."
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| 186 | rotate_around_origin "90."
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| 187 | rotate_around_self "180."
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| 188 | rotate_around_self "180"
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| 189 | rotate_around_self "20."
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| 190 | rotate_around_self "360."
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| 191 | rotate_around_self "90."
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| 192 | rotate_to_principal_axis_system "0,0,1"
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| 193 | save_adjacency "test.adj"
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| 194 | save_bonds "test.bond"
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| 195 | save_atom_fragments "atomfragments.dat"
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| 196 | save_fragment_results "results.dat"
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| 197 | save_homologies "homology.dat"
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| 198 | save_particle_parameters "water.particles"
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| 199 | save_potentials "water.potentials"
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| 200 | save_selected_atoms "testsave.xyz"
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| 201 | save_selected_atoms_as_exttypes "test.exttypes"
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| 202 | save_selected_molecules "testsave.xyz"
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| 203 | save_energies "test.ekin"
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| 204 | scale_box "0.5 1. 0.9"
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| 205 | select_atom_by_element "1"
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| 206 | select_atom_by_element "4"
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| 207 | select_atom_by_id "0"
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| 208 | select_atom_by_name "H1"
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| 209 | select_atom_by_order "1"
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| 210 | select_atom_by_random "4"
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| 211 | select_atoms_inside_cuboid "10 10 10"
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| 212 | select_atoms_inside_cuboid "2 2 2"
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| 213 | select_atoms_inside_sphere "0.2"
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| 214 | select_atoms_inside_sphere "10"
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| 215 | select_atoms_inside_sphere "7."
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| 216 | select_molecule_by_id "0"
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| 217 | select_molecule_by_id "1"
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| 218 | select_molecule_by_id "4"
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| 219 | select_molecule_by_order "-1"
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| 220 | select_molecule_by_order "1"
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| 221 | select_molecule_by_order "-2"
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| 222 | select_molecule_by_order "2"
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| 223 | select_molecules_by_formula "C2H5(OH)"
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| 224 | select_molecules_by_formula "C6H6"
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| 225 | select_molecules_by_formula "H2O"
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| 226 | select_molecules_by_name "water"
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| 227 | select_shape_by_name "sphere2"
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| 228 | server_address "127.0.0.1"
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| 229 | server_port "1026"
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| 230 | session_type "cli"
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| 231 | set_bond_degree "1"
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| 232 | set_boundary_conditions "Wrap, Wrap, Wrap"
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| 233 | set_max_iterations "10"
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|---|
| 234 | use_outer_shell "1"
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| 235 | set_parser_parameters "basis = 4-31G"
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| 236 | set_parser_parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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| 237 | set_parser_parameters "maxiter = 499"
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| 238 | set_parser_parameters "theory=CLKS"
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| 239 | set_parser_parameters "wfn=scf"
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| 240 | set_parser_parameters "ref=uhf"
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| 241 | set_output "tremolo"
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| 242 | set_random_number_distribution "uniform_int"
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| 243 | set_random_number_engine "lagged_fibonacci607"
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| 244 | set_threshold "1e-6"
|
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| 245 | set_tremolo_atomdata "ATOMDATA type id x=3"
|
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| 246 | set_undo_mark "1"
|
|---|
| 247 | set_world_time "10"
|
|---|
| 248 | shape_name "sphere1"
|
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| 249 | shape_op "AND"
|
|---|
| 250 | shape_type "sphere"
|
|---|
| 251 | skiplines "1"
|
|---|
| 252 | skiplines "2"
|
|---|
| 253 | start_step "0"
|
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| 254 | steps "5"
|
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| 255 | step_world_time "1"
|
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| 256 | store_grids "0"
|
|---|
| 257 | store_saturated_fragment "BondFragment"
|
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| 258 | store_session "test.sh"
|
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| 259 | stretch_bond "1.5"
|
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| 260 | stretch "1. 1. 1."
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| 261 | stretch_shapes "1. 2. 3."
|
|---|
| 262 | take_best_of "5"
|
|---|
| 263 | tesselation_radius "5."
|
|---|
| 264 | till-mark "0"
|
|---|
| 265 | time_step_zero "0"
|
|---|
| 266 | training_file "training.dat"
|
|---|
| 267 | translate_atoms "1. 0. 0."
|
|---|
| 268 | translate_shapes "1. 2. 3."
|
|---|
| 269 | translation "0. 0. 0."
|
|---|
| 270 | undo-mark "0"
|
|---|
| 271 | unselect_atom_by_element "1"
|
|---|
| 272 | unselect_atom_by_element "4"
|
|---|
| 273 | unselect_atom_by_id "0"
|
|---|
| 274 | unselect_atom_by_name "H1"
|
|---|
| 275 | unselect_atom_by_order "1"
|
|---|
| 276 | unselect_atoms_inside_cuboid "10 10 10"
|
|---|
| 277 | unselect_atoms_inside_cuboid "2 2 2"
|
|---|
| 278 | unselect_atoms_inside_sphere "10"
|
|---|
| 279 | unselect_atoms_inside_sphere "7."
|
|---|
| 280 | unselect_molecule_by_id "0"
|
|---|
| 281 | unselect_molecule_by_id "4"
|
|---|
| 282 | unselect_molecule_by_order "-1"
|
|---|
| 283 | unselect_molecule_by_order "1"
|
|---|
| 284 | unselect_molecule_by_order "-2"
|
|---|
| 285 | unselect_molecule_by_order "2"
|
|---|
| 286 | unselect_molecules_by_formula "C2H5(OH)"
|
|---|
| 287 | unselect_molecules_by_formula "C3H8"
|
|---|
| 288 | unselect_molecules_by_formula "C6H6"
|
|---|
| 289 | unselect_molecules_by_formula "H2O"
|
|---|
| 290 | unselect_molecules_by_name "water"
|
|---|
| 291 | unselect_shape_by_name "cube42"
|
|---|
| 292 | use_bondgraph "1"
|
|---|
| 293 | UseImplicitCharges "1"
|
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| 294 | verbose "3"
|
|---|
| 295 | verlet_integration "forces.dat"
|
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