| [3493da] | 1 | #key value
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| [cd91bd] | 2 | add_atom "1"
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| 3 | add_empty_boundary "5,5,5"
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| [26cfa51] | 4 | add_potential "Morse"
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| [cd91bd] | 5 | Alignment_Axis "0,0,1"
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| 6 | angle_x "0."
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| 7 | angle_x "0"
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| 8 | angle_y "0."
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| 9 | angle_y "0"
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| 10 | angle_z "0 "
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| 11 | angle_z "0."
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| 12 | angle_z "0"
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| [3493da] | 13 | axis "0 0 1"
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| 14 | axis "0 1 0"
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| 15 | axis "1 2 1"
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| [cd91bd] | 16 | bin_end "10"
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| 17 | bin_end "20"
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| 18 | bin_end "359"
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| 19 | bin_end "359.5"
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| 20 | bin_end "5"
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| 21 | bin_output_file "bin_output-10.csv"
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| 22 | bin_output_file "bin_output-20.csv"
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| 23 | bin_output_file "bin_output-5.csv"
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| 24 | bin_output_file "bin_output.csv"
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| 25 | bin_output_file "emptybox_histogram.dat"
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| 26 | bin_output_file "hydrogenbox_histogram.dat"
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| 27 | bin_output_file "waterbox_histogram.dat"
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| 28 | bin_output_file "waterbox-mirrored_histogram.dat"
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| 29 | bin_start "0"
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| 30 | bin_start "-0.5"
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| 31 | bin_start "10"
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| 32 | bin_start "5"
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| 33 | bin_width "1."
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| 34 | bond_degree "1"
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| 35 | bond_file "bond.dat"
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| [788dce] | 36 | bondside "1"
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| [cd91bd] | 37 | bond_table "table.dat"
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| 38 | calculate_bounding_box ""
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| 39 | calculate_molar_mass ""
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| [2db053] | 40 | center "10. 10. 10."
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| [cd91bd] | 41 | center_in_box "10 0 0 10 0 10"
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| 42 | change_bond_angle "100."
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| 43 | change_box "10 0 0 10 0 10"
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| 44 | change_element "1"
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| 45 | change_molname "water"
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| 46 | convex_envelope "50."
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| 47 | convex_file "convexfile"
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| [987145] | 48 | coordinates "1,0,0"
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| [cd91bd] | 49 | copy_molecule "0"
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| [2db053] | 50 | count "12"
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| [cd91bd] | 51 | create_micelle "200"
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| 52 | damping_factor "0.5"
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| 53 | default_molname "molname"
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| [3493da] | 54 | deltat "0.01"
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| [aa55d0] | 55 | density "1.0"
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| [cd91bd] | 56 | depth_first_search "2."
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| 57 | dipole_angular_correlation "H2O"
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| [3493da] | 58 | distance "1.55"
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| 59 | distances "3.1 3.1 3.1"
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| 60 | distances "3.1 3.1 3.1"
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| [cd91bd] | 61 | distance_to_boundary "1."
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| 62 | distance_to_molecule "1.5"
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| 63 | distance_to_molecule "2.1"
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| 64 | distance_to_vector "named_vector"
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| 65 | domain_position "0. 0. 0."
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| 66 | domain_position "0 0 0"
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| 67 | domain_position "10. 10. 10."
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| [fe0cb8] | 68 | DoCyclesFull "0"
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| [69c733] | 69 | DoLongrange "0"
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| [5f7b95] | 70 | DoOutputEveryStep "0"
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| [b6b21a] | 71 | DoPrintDebug "0"
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| [3493da] | 72 | DoRotate "0"
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| [5ab796] | 73 | DoSaturate "0"
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| [17e4fd] | 74 | DoSmearElectronicCharges "0"
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| [6ff62c] | 75 | DoValenceOnly "0"
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| [cd91bd] | 76 | element_db "./"
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| [3493da] | 77 | elements "1"
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| 78 | elements "1 8"
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| [cd91bd] | 79 | end_step "1"
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| 80 | enforce_net_zero_charge "0"
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| [82e5fb] | 81 | error_file ""
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| [26cfa51] | 82 | evaluate_stability "test"
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| [9291d04] | 83 | ExcludeHydrogen "1"
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| [3493da] | 84 | fastparsing "1"
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| [531f27] | 85 | filename "test.exttypes"
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| [cd91bd] | 86 | fill_molecule "filler.xyz"
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| 87 | fill_void "hydrogen.xyz"
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| 88 | fill_void "water.data"
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| 89 | fill_void "water.xyz"
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| 90 | forces_file "test.forces"
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| [889067e] | 91 | force_overwrite "0"
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| [cd91bd] | 92 | fragment_charges "1 1"
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| 93 | fragment_executable "mpqc"
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| 94 | fragment_jobs "Job00.in"
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| 95 | fragment_molecule "./"
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| 96 | fragment_path "test/"
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| 97 | fragment_prefix "BondFragment"
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| [f5ea10] | 98 | graph6 "B`"
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| [cd91bd] | 99 | grid_level "5"
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| [55feff5] | 100 | help "help"
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| [cd91bd] | 101 | id_mapping "1"
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| [3493da] | 102 | input "test.data"
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| [cd91bd] | 103 | input_to_vector "named_vector"
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| 104 | inter_order "2"
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| 105 | interpolation_degree "5"
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| 106 | interpolation_steps "9"
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| 107 | keep_bondgraph "1"
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| 108 | keep_fixed_CenterOfMass "0"
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| [3493da] | 109 | load "test.data"
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| [cd91bd] | 110 | load_session "test.py"
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| [3493da] | 111 | MaxDistance "-1"
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| [cd91bd] | 112 | max_distance "0"
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| [26cfa51] | 113 | max_hydrogens "1"
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| [cd91bd] | 114 | max_meshwidth "0.3"
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| 115 | mesh_offset "0.5,0.5,0.5"
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| 116 | mesh_size "10,10,10"
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| 117 | min_distance "1."
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| 118 | mirror_atoms "1.,1.,1."
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| 119 | molecule_by_id "0"
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| 120 | near_field_cells "3"
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| 121 | nonconvex_envelope "25"
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| 122 | nonconvex_file "NonConvexEnvelope"
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| 123 | nonconvex_file "nonconvexfile"
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| [3493da] | 124 | offset "0"
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| 125 | offset "1"
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| 126 | order "2"
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| [cd91bd] | 127 | output_as "store.conf"
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| 128 | output_as "store.data"
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| 129 | output_as "store.pdb"
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| 130 | output_as "store.xyz"
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| 131 | output_as "test.in"
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| 132 | output_every_step "1"
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| 133 | output_file "emptybox_values.dat"
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| 134 | output_file "hydrogenbox_values.dat"
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| 135 | output_file "output-10.csv"
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| 136 | output_file "output-20.csv"
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| 137 | output_file "output-5.csv"
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| 138 | output_file "output.csv"
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| 139 | output_file "waterbox-mirrored_values.dat"
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| 140 | output_file "waterbox_values.dat"
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| 141 | output_types "xyz"
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| 142 | output_types "xyz mpqc"
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| 143 | parse_atom_fragments "atomfragments.dat"
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| 144 | parse_fragment_results "results.dat"
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| 145 | parse_homologies "homology.dat"
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| 146 | parse_particle_parameters "water.particles"
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| 147 | parse_potentials "water.potentials"
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| 148 | parse_state_files "1"
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| 149 | parse_tremolo_potentials "argon.potentials"
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| 150 | parse_tremolo_potentials "tensid.potentials"
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| 151 | parser_parameters "mpqc"
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| 152 | parser_parameters "psi3"
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| [3493da] | 153 | periodic "0"
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| [cd91bd] | 154 | plane_offset "5."
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| 155 | plane_to_vector "named_vector"
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| [3493da] | 156 | position "0 0 0"
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| 157 | position "0 0 1"
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| 158 | position "0 0 10"
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| 159 | position "10 10 10"
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| 160 | position "10. 10. 10."
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| 161 | position "1 2 1"
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| 162 | position "5.63 5.71 5.71"
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| 163 | position "7.283585982 3.275186040 3.535886037"
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| 164 | position "9.78 2.64 2.64"
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| [cd91bd] | 165 | position_to_vector "named_vector"
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| 166 | potential_charges "1 1"
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| 167 | potential_type "morse"
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| [9b0dcd] | 168 | potential_list "angle harmonic_bond"
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| [5ab796] | 169 | radius "20."
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| [cd91bd] | 170 | random_atom_displacement "0."
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| 171 | random_molecule_displacement "0."
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| 172 | random_number_distribution_parameters "max=20;"
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| 173 | random_number_engine_parameters "seed=2;"
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| 174 | random_perturbation "0.1"
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| 175 | remove_geometry "named_vector"
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| [26cfa51] | 176 | remove_potential "Morse"
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| [cd91bd] | 177 | repeat_box "1 1 1"
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| [ca331c] | 178 | reset 1
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| [987145] | 179 | reverse "0"
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| [cd91bd] | 180 | rotate_around_bond "90."
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| 181 | rotate_around_origin "180."
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| 182 | rotate_around_origin "20."
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| 183 | rotate_around_origin "360."
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| 184 | rotate_around_origin "90."
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| 185 | rotate_around_self "180."
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| 186 | rotate_around_self "180"
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| 187 | rotate_around_self "20."
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| 188 | rotate_around_self "360."
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| 189 | rotate_around_self "90."
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| 190 | rotate_to_principal_axis_system "0,0,1"
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| 191 | save_adjacency "test.adj"
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| 192 | save_bonds "test.bond"
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| 193 | save_atom_fragments "atomfragments.dat"
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| 194 | save_fragment_results "results.dat"
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| 195 | save_homologies "homology.dat"
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| 196 | save_particle_parameters "water.particles"
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| 197 | save_potentials "water.potentials"
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| 198 | save_selected_atoms "testsave.xyz"
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| 199 | save_selected_atoms_as_exttypes "test.exttypes"
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| 200 | save_selected_molecules "testsave.xyz"
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| [d40189] | 201 | save_energies "test.ekin"
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| [cd91bd] | 202 | scale_box "0.5 1. 0.9"
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| 203 | select_atom_by_element "1"
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| 204 | select_atom_by_element "4"
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| 205 | select_atom_by_id "0"
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| 206 | select_atom_by_name "H1"
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| 207 | select_atom_by_order "1"
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| [26cfa51] | 208 | select_atom_by_random "4"
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| [cd91bd] | 209 | select_atoms_inside_cuboid "10 10 10"
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| 210 | select_atoms_inside_cuboid "2 2 2"
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| 211 | select_atoms_inside_sphere "0.2"
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| 212 | select_atoms_inside_sphere "10"
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| 213 | select_atoms_inside_sphere "7."
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| 214 | select_molecule_by_id "0"
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| 215 | select_molecule_by_id "1"
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| 216 | select_molecule_by_id "4"
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| 217 | select_molecule_by_order "-1"
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| 218 | select_molecule_by_order "1"
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| 219 | select_molecule_by_order "-2"
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| 220 | select_molecule_by_order "2"
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| 221 | select_molecules_by_formula "C2H5(OH)"
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| 222 | select_molecules_by_formula "C6H6"
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| 223 | select_molecules_by_formula "H2O"
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| 224 | select_molecules_by_name "water"
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| 225 | select_shape_by_name "sphere2"
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| 226 | server_address "127.0.0.1"
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| 227 | server_port "1026"
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| 228 | session_type "cli"
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| 229 | set_bond_degree "1"
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| 230 | set_boundary_conditions "Wrap, Wrap, Wrap"
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| 231 | set_max_iterations "10"
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| [26cfa51] | 232 | use_outer_shell "1"
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| [cd91bd] | 233 | set_parser_parameters "basis = 4-31G"
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| 234 | set_parser_parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
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| 235 | set_parser_parameters "maxiter = 499"
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| 236 | set_parser_parameters "theory=CLKS"
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| 237 | set_parser_parameters "wfn=scf"
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| 238 | set_parser_parameters "ref=uhf"
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| 239 | set_output "tremolo"
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| 240 | set_random_number_distribution "uniform_int"
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| 241 | set_random_number_engine "lagged_fibonacci607"
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| 242 | set_threshold "1e-6"
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| 243 | set_tremolo_atomdata "ATOMDATA type id x=3"
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| [26cfa51] | 244 | set_undo_mark "1"
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| [cd91bd] | 245 | set_world_time "10"
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| 246 | shape_name "sphere1"
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| 247 | shape_op "AND"
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| 248 | shape_type "sphere"
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| [3493da] | 249 | skiplines "1"
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| 250 | skiplines "2"
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| [cd91bd] | 251 | start_step "0"
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| [39986b] | 252 | steps "5"
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| [cd91bd] | 253 | step_world_time "1"
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| 254 | store_grids "0"
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| 255 | store_saturated_fragment "BondFragment"
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| 256 | store_session "test.sh"
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| 257 | stretch_bond "1.5"
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| [4dc309] | 258 | stretch "1. 1. 1."
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| [cd91bd] | 259 | stretch_shapes "1. 2. 3."
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| 260 | take_best_of "5"
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| 261 | tesselation_radius "5."
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| [0ec9f5] | 262 | till-mark "0"
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| [cd91bd] | 263 | time_step_zero "0"
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| 264 | training_file "training.dat"
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| 265 | translate_atoms "1. 0. 0."
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| 266 | translate_shapes "1. 2. 3."
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| [4dc309] | 267 | translation "0. 0. 0."
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| [0ec9f5] | 268 | undo-mark "0"
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| [cd91bd] | 269 | unselect_atom_by_element "1"
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| 270 | unselect_atom_by_element "4"
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| 271 | unselect_atom_by_id "0"
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| 272 | unselect_atom_by_name "H1"
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| 273 | unselect_atom_by_order "1"
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| 274 | unselect_atoms_inside_cuboid "10 10 10"
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| 275 | unselect_atoms_inside_cuboid "2 2 2"
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| 276 | unselect_atoms_inside_sphere "10"
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| 277 | unselect_atoms_inside_sphere "7."
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| 278 | unselect_molecule_by_id "0"
|
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| 279 | unselect_molecule_by_id "4"
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| 280 | unselect_molecule_by_order "-1"
|
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| 281 | unselect_molecule_by_order "1"
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| 282 | unselect_molecule_by_order "-2"
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| 283 | unselect_molecule_by_order "2"
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| 284 | unselect_molecules_by_formula "C2H5(OH)"
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| 285 | unselect_molecules_by_formula "C3H8"
|
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| 286 | unselect_molecules_by_formula "C6H6"
|
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| 287 | unselect_molecules_by_formula "H2O"
|
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| 288 | unselect_molecules_by_name "water"
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| 289 | unselect_shape_by_name "cube42"
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| 290 | use_bondgraph "1"
|
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| [666e9e] | 291 | UseImplicitCharges "1"
|
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| [3493da] | 292 | verbose "3"
|
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| [cd91bd] | 293 | verlet_integration "forces.dat"
|
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