moltest.in

大型并行量子化学软件；支持密度泛函（DFT）。可以进行各种量子化学计算。支持CHARMM并行计算。非常具有应用价值。

% Emacs should use -*- keyval -*- mode.

atominfo<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<TaylorMolecularEnergy>: (
  molecule<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<SetIntCoor>: [
       <StreSimpleCo>: ( atoms = [ 1 2 ] label = "r(OH1)" )
       <StreSimpleCo>: ( atoms = [ 1 3 ] label = "r(OH2)" )
       <BendSimpleCo>: ( 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<FinDispMolecularHessian>: (
    energy = $:energy
  )

freq<MolecularFrequencies>: (
    molecule = $:molecule
  )

big_molecule<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<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<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<Molecule>: (
  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<SymmMolecularCoor>: (
  molecule = $:big_molecule
  scale_bonds = 16.0
  scale_bends = 4.0
  simple_tolerance = 0.05
  update_bmatrix = yes
  given_fixed_values = yes
  fixed<SetIntCoor>: [
    <StreSimpleCo>: ( atoms = [ 1 2 ] label = "r(OH)" value = 1.0 )
    %<StreSimpleCo> = [ "r(OH)" 1 2 ]
    %<BendSimpleCo> = [ "a(HOH)" 2 1 3 ]
    ]
  extra_bonds = [ 1 3  2 4  1 4 ]
  )

small_molcoor<SymmMolecularCoor>: (
  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<SetIntCoor>: [
    <StreSimpleCo>: ( atoms = [ 2 3 ] label = "r(HH)" value = 1.5 )
    %<StreSimpleCo>: ( atoms = [ 1 3 ] label = "r(OH)" value = 2.2 )
    ]
  )

small_redund_molcoor<RedundMolecularCoor>: (
  molecule = $:small_molecule
  )

medium_molcoor<SymmMolecularCoor>: (
  molecule<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<SetIntCoor>: [
    <SumIntCoor>: (
        unit = bohr
        value = 0.1
        label = "Reaction Coordinate"
        coor: [
            <StreSimpleCo>: (atoms = [ 6 12] label = "r(CH)")
            <StreSimpleCo>: (atoms = [12 15] label = "r(HO)")
            <StreSimpleCo>: (atoms = [15 14] label = "r(OH)")
            <StreSimpleCo>: (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<SetIntCoor>: [
    <StreSimpleCo> = [ "st____1" 1 2 ]
    <StreSimpleCo> = [ "st2" 1 3 ]
    <SumIntCoor>: (
        label = "lin1"
        value = 1.1
        { coef  coor } = {
          1.0   $:simp:0
         -1.0   $:simp:1
         }
       )
    <StreSimpleCo> = ["st2_again" 1 3]
    <SumIntCoor>: (
        label = "lin2"
        value = 1.1
        { coef  coor } = {
          1.0   $:simp:0
         -1.0   $:simp:1
         -1.0   $:simp:2
         -1.0   $:simp:3
         }
       )
  ]

generator<IntCoorGen>: (
    molecule = $:molecule
    linear_bend = no
    linear_bend_threshold = 10.0
    linear_tors = no
    linear_tors_threshold = 10.0
  )

generated_simp<SetIntCoor>: (
  generator = $:generator
  )

simp = $:generated_simp

bmat_test = $:simp

renderer<OOGLRender>: (
    filename = "moltest.oogl"
  )

ball<RenderedBallMolecule>: (
    appearance<Appearance>: (
        level = 3
      )
    molecule = $..:molecule
    atominfo = $..:atominfo
  )

surf<RenderedMolecularSurface>: (
    surface<TriangulatedImplicitSurface>: (
        surface<TriangulatedSurface>: (
            verbose = yes
          )
        vdw<VDWShape>: (
            molecule = $:molecule
            atominfo = $:atominfo
          )
        con<ConnollyShape>: (
            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