Molecular coordinates
Molecular coordinates can be provided in the vmc or dmc input files a text file or a separate .xyz file in one of the following ways:
1. Geometry in the (XYZ in Bohr units) format to be read from a separate .xyz file.
load molecule molecule.xyz
load molecule $pool/molecule.xyz
The following are the valid examples (molecule.xyz)
2. Geometry in the (XYZ in Bohr units) format with automatic Zvalence
10
# molecular complex (Symbol, X,Y,Z in Bohr)
Si -0.59659972 0.06162019 0.21100680
S -2.60025162 -2.54807062 -2.52884266
S 2.14594449 2.17606672 -2.44253887
S 1.75703132 -2.78062975 2.53564756
S -1.40663455 3.06742023 3.14712509
H -3.50597461 0.49044059 0.39864337
H 0.96753971 3.57914102 3.86259992
H -0.57825615 -3.70197321 -3.52433897
H 0.37416575 3.66039924 -3.47898554
H -0.21164931 -3.70953211 3.82669513
3. Geometry in the (XYZ in Bohr units) format with explicit Zvalence. This also allows different labels for the same element.
10
# molecular complex (Symbol, X,Y,Z in Bohr, Zvalence)
Si -0.59659972 0.06162019 0.21100680 4.0
S -2.60025162 -2.54807062 -2.52884266 6.0
S 2.14594449 2.17606672 -2.44253887 6.0
S 1.75703132 -2.78062975 2.53564756 6.0
S -1.40663455 3.06742023 3.14712509 6.0
H1 -3.50597461 0.49044059 0.39864337 1.0
H2 0.96753971 3.57914102 3.86259992 1.0
H2 -0.57825615 -3.70197321 -3.52433897 1.0
H2 0.37416575 3.66039924 -3.47898554 1.0
H2 -0.21164931 -3.70953211 3.82669513 1.0
4. Geometry in the (XYZ in Bohr units) format to be read from a separate .xyz file.
%block molecule < molecule.xyz
Note the coordinates are in Bohr units.