# crystod-mol examples (molecular point groups and SALCs of O2, NH3 and CH4)
# Run in this directory: XYZ_O2.xyz, XYZ_NH3.xyz and XYZ_CH4.xyz are copies
# of the files in ../test_XYZs, and --visualize writes its HTML here.

crystod-mol --symmetry --xyz XYZ_O2.xyz

* Molecule *
XYZ_O2.xyz (O2, 2 atoms)

* Point group *
D*h (linear molecule; continuous non-crystallographic group)



crystod-mol --symmetry --xyz XYZ_NH3.xyz

* Molecule *
XYZ_NH3.xyz (H3N, 4 atoms)

* Point group *
C3v (Hermann-Mauguin: 3m)

* Symmetry operations (6) *
E, 2C3, 3sgv



crystod-mol --xyz XYZ_NH3.xyz --element H --orbital s

* Molecule *
XYZ_NH3.xyz (H3N, 4 atoms)

* Point group *
C3v (Hermann-Mauguin: 3m)

* Target sites (H, 3 sites; center-of-mass frame) *
H1: ( 0.807734,  0.466331, -0.298390)
H2: (-0.807709,  0.466374, -0.298391)
H3: (-0.000025, -0.932662, -0.298459)

* Reducible representation (H sites x s orbital) *
class:               E   2C3  3sgv
chi(perm):           3     0     1
chi(s):              1     1     1
chi(total):          3     0     1

* Decomposition *
Gamma = 1(A1) + 1(E)

* SALCs (orbital axes = input Cartesian axes) *
A1: [s(H1) + s(H2) + s(H3)]
E: [s(H1) - s(H3), s(H1) - 2 s(H2) + s(H3)]



crystod-mol --xyz XYZ_CH4.xyz --element H --orbital s

* Molecule *
XYZ_CH4.xyz (H4C, 5 atoms)

* Point group *
Td (Hermann-Mauguin: -43m)

* Target sites (H, 4 sites; center-of-mass frame) *
H1: ( 0.553422,  0.798539,  0.495857)
H2: ( 0.682447, -0.812363, -0.253268)
H3: (-0.777180, -0.373037,  0.668318)
H4: (-0.458693,  0.386865, -0.910906)

* Reducible representation (H sites x s orbital) *
class:               E   8C3   3C2   6S4  6sgd
chi(perm):           4     1     0     0     2
chi(s):              1     1     1     1     1
chi(total):          4     1     0     0     2

* Decomposition *
Gamma = 1(A1) + 1(T2)

* SALCs (orbital axes = input Cartesian axes) *
A1: [s(H1) + s(H2) + s(H3) + s(H4)]
T2: [s(H1) - s(H4), s(H1) - 2 s(H2) + s(H4), s(H1) + s(H2) - 3 s(H3) + s(H4)]



crystod-mol --xyz XYZ_NH3.xyz --element N --orbital p

* Molecule *
XYZ_NH3.xyz (H3N, 4 atoms)

* Point group *
C3v (Hermann-Mauguin: 3m)

* Target sites (N, 1 sites; center-of-mass frame) *
N1: (-0.000000, -0.000003,  0.064423)

* Reducible representation (N sites x p orbital) *
class:               E   2C3  3sgv
chi(perm):           1     1     1
chi(p):              3     0     1
chi(total):          3     0     1

* Decomposition *
Gamma = 1(A1) + 1(E)

* SALCs (orbital axes = input Cartesian axes) *
A1: [pz(N1)]
E: [px(N1), py(N1)]



crystod-mol --xyz XYZ_CH4.xyz --element C --orbital d --align

* Molecule *
XYZ_CH4.xyz (H4C, 5 atoms)

* Point group *
Td (Hermann-Mauguin: -43m)

* Target sites (C, 1 sites; standard point-group frame) *
C1: (-0.000000,  0.000000, -0.000000)

* Reducible representation (C sites x d orbital) *
class:               E   8C3   3C2   6S4  6sgd
chi(perm):           1     1     1     1     1
chi(d):              5    -1     1    -1     1
chi(total):          5    -1     1    -1     1

* Decomposition *
Gamma = 1(E) + 1(T2)

* SALCs (orbital axes = standard point-group axes) *
E: [dz2(C1), dx2-y2(C1)]
T2: [dxy(C1), dyz(C1), dxz(C1)]



crystod-mol --xyz XYZ_NH3.xyz --element H --orbital p --visualize --bond N H 1.2
(output as above, plus:)

* Output files *
  SALC viewer written to SALC_XYZ_NH3_H_p.html
