Index: ThirdParty/mpqc_open/src/lib/chemistry/molecule/moltest.in
===================================================================
--- ThirdParty/mpqc_open/src/lib/chemistry/molecule/moltest.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/src/lib/chemistry/molecule/moltest.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,365 @@
+% 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
