% Emacs should use -*- keyval -*- mode. atominfo: ( vdw_radius: ( scale_factor = 1.2 unit = angstrom H = 1.3 Li = 0.1818 ) bragg_radius: ( unit = angstrom H = 0.888 ) atomic_radius: ( unit = angstrom H = 0.999 ) rgb: ( H = [ 0.0 0.0 1.0 ] He:2 = 0.5 ) mass: ( unit = amu H = 2.1 ) ) energy: ( molecule: ( symmetry = c2v { atom_labels atoms geometry } = { O O [0.0 0.0 0.0] H1 H [0.0 1.0 1.0] H2 H [0.0 -1.0 1.0] } ) coordinates: [ : ( atoms = [ 1 2 ] label = "r(OH1)" ) : ( atoms = [ 1 3 ] label = "r(OH2)" ) : ( atoms = [ 2 1 3 ] label = "theta(HOH)" ) ] % force_constants: [ % [ 1 1 4.0 ] % [ 2 2 4.0 ] % [ 3 3 2.0 ] % [ 1 2 1.5 ] % [ 1 3 0.5 ] % [ 2 3 0.5 ] % ] ) % TaylorMolecularEnergy does work with FinDispMolecularHessian xhess: ( energy = $:energy ) freq: ( molecule = $:molecule ) big_molecule: ( angstrom = yes %symmetry=d2h %redundant_atoms=yes xsymmetry_frame = [ [ 1 0 0 ] [ 0 0 1 ] [ 0 1 0 ] ] { atoms geometry } = { n [ 0.000000 0.000000 0.000000 ] c [ 0.000000 0.000000 1.340853 ] c [ 1.276285 0.000000 -0.411067 ] n [ -1.044424 0.000000 2.149457 ] n [ 1.725764 0.000000 -1.653098 ] c [ 1.370758 0.000000 1.856359 ] c [ 2.187205 0.000000 0.735648 ] c [ 1.901357 0.000000 3.136948 ] c [ 3.568793 0.000000 0.848106 ] c [ -2.281309 0.000000 1.747151 ] c [ 0.963636 0.000000 -2.707089 ] n [ -0.394169 0.000000 -2.765670 ] c [ 3.278826 0.000000 3.254057 ] c [ 4.102557 0.000000 2.123344 ] c [ -3.446446 0.000000 2.607232 ] c [ 1.425101 0.000000 -4.079798 ] h [ 1.264025 0.000000 4.001762 ] h [ 4.196577 0.000000 -0.023664 ] n [ -2.753333 0.000000 0.472687 ] h [ -2.168546 0.000000 -0.330035 ] h [ -0.978957 0.000000 -1.962948 ] c [ -4.111141 0.000000 0.414104 ] c [ -0.866194 0.000000 -4.040136 ] c [ -4.572607 0.000000 1.786813 ] c [ 0.298944 0.000000 -4.900217 ] c [ -3.566512 0.000000 3.996510 ] c [ 2.710672 0.000000 -4.619997 ] c [ 5.428715 0.000000 2.285234 ] c [ 3.839479 0.000000 4.466728 ] n [ -4.873266 0.000000 -0.639886 ] n [ -2.103077 0.000000 -4.442443 ] c [ -5.858176 0.000000 2.327010 ] c [ 0.419010 0.000000 -6.289496 ] c [ -4.834777 0.000000 4.525021 ] c [ 2.824921 0.000000 -5.989220 ] h [ -2.693531 0.000000 4.621985 ] h [ 3.573663 0.000000 -3.980803 ] c [ 5.952960 0.000000 3.517888 ] h [ 6.074619 0.000000 1.391664 ] c [ 5.173494 0.000000 4.587840 ] h [ 3.186948 0.000000 5.355469 ] c [ -4.423788 0.000000 -1.881917 ] c [ -3.147503 0.000000 -3.633837 ] c [ -5.972424 0.000000 3.696235 ] c [ 1.687276 0.000000 -6.818005 ] h [ -6.721165 0.000000 1.687817 ] h [ -0.453971 0.000000 -6.914970 ] h [ 7.044639 0.000000 3.672463 ] h [ 5.655300 0.000000 5.579569 ] c [ 4.036295 0.000000 -6.552673 ] c [ -4.999726 0.000000 5.850803 ] n [ -3.147503 0.000000 -2.292984 ] c [ -5.334707 0.000000 -3.028633 ] c [ -4.518262 0.000000 -4.149345 ] c [ 4.154329 0.000000 -7.886964 ] h [ 4.926541 0.000000 -5.902195 ] c [ 1.852220 0.000000 -8.143787 ] c [ -7.183797 0.000000 4.259686 ] c [ -6.233581 0.000000 6.372209 ] h [ -4.107647 0.000000 6.498765 ] c [ -6.716298 0.000000 -3.141092 ] c [ -5.048860 0.000000 -5.429932 ] h [ 5.144938 0.000000 -8.371058 ] c [ 3.086078 0.000000 -8.665193 ] h [ 0.960144 0.000000 -8.791748 ] c [ -7.301831 0.000000 5.593979 ] h [ -8.074043 0.000000 3.609208 ] h [ -6.390672 0.000000 7.463531 ] c [ -7.250060 0.000000 -4.416331 ] c [ -6.426328 0.000000 -5.547041 ] h [ -7.344080 0.000000 -2.269320 ] h [ -4.411528 0.000000 -6.294749 ] h [ 3.243167 0.000000 -9.756515 ] h [ -8.292441 0.000000 6.078073 ] c [ -6.986981 0.000000 -6.759712 ] c [ -8.576216 0.000000 -4.578218 ] c [ -8.320998 0.000000 -6.880823 ] h [ -6.334453 0.000000 -7.648453 ] c [ -9.099795 0.000000 -5.811154 ] h [ -9.222599 0.000000 -3.684999 ] h [ -8.802806 0.000000 -7.872550 ] h [ -10.191392 0.000000 -5.966319 ] } ) small_molecule: ( angstrom = no { atoms geometry } = { O [ 0.000000 0.000000 0.000000 ] H [ 0.000000 1.000000 1.000000 ] H [ 0.000000 -1.000000 1.000000 ] } ) linear_molecule: ( angstrom = no { atoms geometry } = { H [ 0.000000 0.100000 2.000000 ] C [ 0.000000 0.000000 1.000000 ] C [ 0.000000 0.000000 -1.000000 ] H [ 0.000000 0.200000 -2.000000 ] } ) enediyne: ( symmetry = C2V angstroms = no { atoms geometry } = { H [ -5.3870492639 -0.0000000000 1.3995052531 ] H [ 5.3870492639 -0.0000000000 1.3995052531 ] C [ -4.1906139895 -0.0000000000 -0.2149062043 ] C [ 4.1906139895 -0.0000000000 -0.2149062043 ] C [ -2.8240829859 0.0000000000 -2.0097148495 ] C [ 2.8240829859 -0.0000000000 -2.0097148495 ] C [ -1.2579864521 -0.0000000000 -4.2267821010 ] C [ 1.2579864521 0.0000000000 -4.2267821010 ] H [ -2.2391693577 -0.0000000000 -6.0205520984 ] H [ 2.2391693577 -0.0000000000 -6.0205520984 ] } atom_labels:1 = "H2" ) molecule = $:small_molecule big_molcoor: ( molecule = $:big_molecule scale_bonds = 16.0 scale_bends = 4.0 simple_tolerance = 0.05 update_bmatrix = yes given_fixed_values = yes fixed: [ : ( atoms = [ 1 2 ] label = "r(OH)" value = 1.0 ) % = [ "r(OH)" 1 2 ] % = [ "a(HOH)" 2 1 3 ] ] extra_bonds = [ 1 3 2 4 1 4 ] ) small_molcoor: ( molecule = $:small_molecule scale_bonds = 16.0 scale_bends = 4.0 simple_tolerance = 0.05 update_bmatrix = yes have_fixed_values = yes max_update_steps = 100 max_update_disp = 100.0 fixed: [ : ( atoms = [ 2 3 ] label = "r(HH)" value = 1.5 ) %: ( atoms = [ 1 3 ] label = "r(OH)" value = 2.2 ) ] ) small_redund_molcoor: ( molecule = $:small_molecule ) medium_molcoor: ( molecule: ( angstrom = yes { atoms geometry } = { C [ -1.481978 1.137918 0.053920] C [ -2.377552 -0.058848 0.015422] N [ -0.256358 0.721189 0.007050] H [ -1.754455 2.190795 0.079781] C [ -0.326866 -0.730249 -0.014562] C [ 1.043217 1.561636 -0.056035] N [ -1.671068 -1.129599 -0.036351] H [ -3.465237 -0.021159 0.023663] H [ 1.063541 2.111989 0.901108] H [ 0.887902 2.255657 -0.891111] N [ 0.656762 -1.486673 0.005244] H [ 2.056209 0.795245 -0.136829] H [ 0.425921 -2.467905 -0.021317] H [ 1.917997 -1.027989 0.094573] O [ 2.866992 -0.212573 -0.043377] H [ 3.685907 -0.333218 0.473075] } ) scale_bonds = 16.0 scale_bends = 4.0 simple_tolerance = 0.05 update_bmatrix = yes max_update_steps = 200 max_update_disp = 0.5 have_fixed_values = yes fixed: [ : ( unit = bohr value = 0.1 label = "Reaction Coordinate" coor: [ : (atoms = [ 6 12] label = "r(CH)") : (atoms = [12 15] label = "r(HO)") : (atoms = [15 14] label = "r(OH)") : (atoms = [14 11] label = "r(HN)") ] coef = [ 1.0 -1.0 1.0 -1.0 ] ) ] extra_bonds = [ 12 6 12 15 14 15 11 14 ] ) molcoor = $:small_redund_molcoor custom_simp: [ = [ "st____1" 1 2 ] = [ "st2" 1 3 ] : ( label = "lin1" value = 1.1 { coef coor } = { 1.0 $:simp:0 -1.0 $:simp:1 } ) = ["st2_again" 1 3] : ( label = "lin2" value = 1.1 { coef coor } = { 1.0 $:simp:0 -1.0 $:simp:1 -1.0 $:simp:2 -1.0 $:simp:3 } ) ] generator: ( molecule = $:molecule linear_bend = no linear_bend_threshold = 10.0 linear_tors = no linear_tors_threshold = 10.0 ) generated_simp: ( generator = $:generator ) simp = $:generated_simp bmat_test = $:simp renderer: ( filename = "moltest.oogl" ) ball: ( appearance: ( level = 3 ) molecule = $..:molecule atominfo = $..:atominfo ) surf: ( surface: ( surface: ( verbose = yes ) vdw: ( molecule = $:molecule atominfo = $:atominfo ) con: ( molecule = $:molecule probe_radius = 2.6456173 atominfo = $:atominfo ) volume = $con resolution = 0.5 remove_short_edges = 1 remove_slender_triangles = 1 short_edge_factor = 0.4 slender_triangle_factor = 0.2 initialize = yes ) molecule = $:molecule atominfo = $:atominfo ) renderedmolecule = $:surf