modified on 21 June 2013 at 09:31 ••• 5,109 views

Release66:Geometry examples

From NWChem

Revision as of 09:31, 21 June 2013 by Bert (Talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Contents

Examples of geometries using symmetry

Below are examples of the use of the SYMMETRY directive in the compound GEOMETRY directive. The z axis is always the primary rotation axis. When in doubt about which axes and planes are used for the group elements, the keyword print may be added to the SYMMETRY directive to obtain this information.

Cs methanol

The σh plane is the xy plane.

 geometry units angstroms
   C    0.11931097    -0.66334875     0.00000000
   H    1.20599017    -0.87824237     0.00000000
   H   -0.32267592    -1.15740001     0.89812652
   O   -0.01716588     0.78143468     0.00000000
   H   -1.04379735     0.88169812     0.00000000
   symmetry cs
 end

C2v water

The z axis is the C2 axis and the σv may be either the xz or the yz planes.

 geometry units au
   O     0.00000000    0.00000000    0.00000000
   H     0.00000000    1.43042809   -1.10715266
   symmetry group c2v
 end

D2h acetylene

Although acetylene has symmetry D_{\infty h} the subgroup D2h includes all operations that interchange equivalent atoms which is what determines how much speedup you gain from using symmetry in building a Fock matrix.

The C2 axes are the x, y, and z axes. The σ planes are the xy, xz and yz planes. Generally, the unique atoms are placed to use the z as the primary rotational axis and use the xz or yz planes as the σ plane.

 geometry units au
   symmetry group d2h
   C      0.000000000    0.000000000   -1.115108538
   H      0.000000000    0.000000000   -3.106737425
 end

D2h ethylene

The C2 axes are the x, y, and z axes. The σ planes are the xy, xz and yz planes. Generally, the unique atoms are placed to use the z as the primary rotational axis and use the xz or yz planes as the σ plane.

 geometry units angstroms
   C 0 0 0.659250 
   H 0 0.916366 1.224352 
   symmetry d2h
 end

Td methane

For ease of use, the primary C3 axis should be the x=y=z axis. The 3 C2 axes are the x, y, and z.

 geometry units au
   c   0.0000000      0.0000000      0.0000000
   h   1.1828637      1.1828637      1.1828637
   symmetry group Td
 end

Ih buckminsterfullerene

One of the C5 axes is the z axis and the point of inversion is the origin.

 geometry units angstroms # Bonds = 1.4445, 1.3945
   symmetry group Ih
   c   -1.2287651   0.0   3.3143121
 end

S4 porphyrin

The S4 and C2 rotation axis is the z axis. The reflection plane for the S4 operation is the xy plane.

 geometry units angstroms
    symmetry group s4
    
    fe                0.000  0.000  0.000         
    h                 2.242  6.496 -3.320   
    h                 1.542  4.304 -2.811
    c                 1.947  6.284 -2.433
    c                 1.568  4.987 -2.084
    h                 2.252  8.213 -1.695
    c                 1.993  7.278 -1.458
    h                 5.474 -1.041 -1.143
    c                 1.234  4.676 -0.765
    h                 7.738 -1.714 -0.606
    c                 0.857  3.276 -0.417
    h                 1.380 -4.889 -0.413
    c                 1.875  2.341 -0.234
    h                 3.629  3.659 -0.234
    c                 0.493 -2.964 -0.229
    c                 1.551 -3.933 -0.221
    c                 5.678 -1.273 -0.198
    c                 1.656  6.974 -0.144
    c                 3.261  2.696 -0.100
    n                 1.702  0.990 -0.035
 end

D3h iron penta-carbonyl

The C3 axis is the z axis. The σh plane is the xy plane. One of the perpendicular C2 axes is the x=y axis. One of the σv planes is the plane containing the x=y axis and the z axis. (The other axes and planes are generated by the C3 operation.)

 geometry units au
   symmetry group d3h
  
   fe        0.0         0.0         0.0
   
   c         0.0         0.0         3.414358
   o         0.0         0.0         5.591323
   
   c         2.4417087   2.4417087   0.0
   o         3.9810552   3.9810552   0.0
 end

D3d sodium crown ether

The C3 axis is the z axis. The point of inversion is the origin. One of the perpendicular C2 axes is the x=y axis. One of the σd planes is the plane containing the -x=y axis and the z axis.

Note that the oxygen atom is rotated in the x-y plane 15 degrees away from the y-axis so that it lies in a mirror plane. There is a total of six atoms generated from the unique oxygen, in contrast to twelve from each of the carbon and hydrogen atoms.

 geometry units au
   symmetry D3d
   
  NA     .0000000000    .0000000000   .0000000000
  O     1.3384771885   4.9952647969   .1544089284
  H     6.7342048019  -0.6723850379  2.6581562148
  C     6.7599180056  -0.4844977035   .6136583870
  H     8.6497577017   0.0709194071   .0345361934
   
 end

C3v ammonia

The C3 axis is the z axis. One of the σv planes is the plane containing the x=y axis and the z axis.

 geometry units angstroms
   N 0     0     -0.055 
   H 0.665 0.665 -0.481 
   symmetry c3v
 end

D6h benzene

The C6 axis is the z axis. The point of inversion is the origin. One of the 6 perpendicular C2' axes is the x=y axis. (-x=y works as a C2'' axis.) The σh plane is the xy plane. The σd planes contain the C2'' axis and the z axis. The σv planes contain the C2' axis and the z axis.

 geometry units au
   C 1.855 1.855 0 
   H 3.289 3.289 0 
   symmetry D6h
 end

C3h BO3H3

The C3 axis is the z axis. The σh plane is the xy plane.

 geometry units au
   b 0 0 0 
   o 2.27238285 1.19464491 0.00000000 
   h 2.10895420 2.97347707 0.00000000 
  symmetry C3h
 end

D5d ferrocene

The C5 axis is the z axis. The center of inversion is the origin. One of the perpendicular C2 axes is the x axis. One of the σd planes is the yz plane.

 geometry units angstroms
   symmetry d5d
  
   fe 0 0     0 
   c  0 1.194 1.789 
   h  0 2.256 1.789 
 end

C4v SF5Cl

The C4 axis is the z axis. The σv planes are the yz and the xz planes. The σd planes are: 1) the plane containing the x=y axis and the z axis and 2) the plane containing the -x=y axis and the z axis.

 geometry units au
   S  0.00000000 0.00000000 -0.14917600 
   Cl 0.00000000 0.00000000  4.03279700 
   F  3.13694200 0.00000000 -0.15321800 
   F  0.00000000 0.00000000 -3.27074500 
  
   symmetry C4v
 end

C2h trans-dichloroethylene

The C2 axis is the z axis. The origin is the inversion center. The σh plane is the xy plane.

 geometry units angstroms
   C  0.65051239 -0.08305064 0 
   Cl 1.75249381  1.30491767 0 
   H  1.14820954 -1.04789741 0 
   symmetry C2h
 end

D2d CH2CCH2

The C2 axis is the z axis (z is also the S4 axis). The x and y axes are the perpendicular C2's. The σd planes are: 1) the plane containing the x=y axis and the z axis and 2) the plane containing the -x=y axis and the z axis.

 geometry units angstroms
   symmetry d2d
   c 0     0     0 
   c 0     0     1.300 
   h 0.656 0.656 1.857 
 end

D5h cyclopentadiene anion

The C5 axis is the z axis (z is also the S5 axis). The y axis is one of the perpendicular C2 axes. The σh plane is the xy plane and one of the σd planes is the yz plane.

 charge -1
 geometry units angstroms
   symmetry d5h
   c 0 1.1853 0 
   h 0 2.2654 0 
 end

D4h gold tetrachloride

The C4 axis is the z axis (z is also the S4 axis). The C2' axes are the x and y axes and the C2'' axes are the x=y axis and the x=-y axis. The inversion center is the origin. The σh plane is the xy plane. The σv planes are the xz and yz planes and the σd planes are 1) the plane containing the x=-y axis and the z axis and 2) the plane containing the x=y axis and the z axis.

 geometry units au
   Au 0 0     0 
   Cl 0 4.033 0
   symmetry D4h
 end