11/7/2023 0 Comments Cartesian to zmatrixVariables/parameters can be declared in any order.Ī single blank line separates parameters from the Z-matrix.Īll the following examples are equivalent in the information forwarded to the Q-Chem program.Įxample 3.9 Using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.Įxample 3.10 Not using parameters to define bond lengths and angles, and using numbered symbols to define atoms and indicate connectivity.Įxample 3.11 Using parameters to define bond lengths and angles, and referring to atom connectivities by line number.Įxample 3.12 Referring to atom connectivities by line number, and entering bond length and angles directly. If declared by atomic symbol either number similar atoms ( e.g., H1, H2, O1, O2 etc.) and refer connectivity using this symbol, or indicate connectivity by the line number of the referred atom.īond lengths and angles can be entered either as variables/parameters or real numbers. If declared by atomic number, connectivity needs to be indicated by Z-matrix line number. Line 4 declares the fourth atom and the second hydrogen atom (H2), indicates it is separated from the second oxygen atom (O2) by a distance HO and makes an angle with the first oxygen atom (O1) of hoo and makes a dihedral angle with the first hydrogen atom (H1) of hooh.Ītoms can be declared by either atomic number or symbol. Line 3 declares the first hydrogen atom (H1), indicates it is separated from the first oxygen atom (O1) by a distance HO and makes an angle with the second oxygen atom (O2) of hoo. Line 2 declares the second oxygen atom (O2), followed by a reference to the first atom (O1) and a distance between them denoted oo. Third atom, reference atom A, distance between A and the third atom, reference atom B, angle defined by atoms A, B and the third atom.įourth atom, reference atom A, distance, reference atom B, angle, reference atom C, dihedral angle (A, B, C and the fourth atom).Īll subsequent atoms follow the same basic form as (4)Įxample 3.8 Z-matrix for hydrogen peroxide All subsequent entries begin with an atom declaration, a reference atom and a distance, a second reference atom and an angle, a third reference atom and a dihedral angle. The third line declares the third atom, refers to either the first or second atom, gives the distance between them, refers to the remaining atom and gives the angle between them. The second line of the Z-matrix input declares a second atom, refers to the first atom and gives the distance between them. The first Z-matrix line declares a single atom. The first three atom entries of a Z-matrix are different from the subsequent entries. Note: As with the Cartesian coordinate input method, Q-Chem begins a calculation by taking the user-defined coordinates and translating and rotating them into a Standard Nuclear Orientation. Again, note that all bond lengths and angles must be in Angstroms and degrees. The Z-matrix defines the positions of atoms relative to previously defined atoms using a length, an angle and a dihedral angle. print_out () # print coordinates array to output file geom1py = mat2arr ( geom1psi ) # get coordinates as a Python array print geom1py # print coordinates to screen geom2py =, , [ - 0.8, - 0.3, 0.Z-matrix notation is one of the most common molecular coordinate input forms. geometry () # get coordinates in bohr as a psi4.Matrix geom1psi. print_out () # print molecule to output file geom1psi = formaldehyde. update_geometry () # update the molecule internals since pre-energy()-like call formaldehyde.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |