Notations and notes

Package-wise notations

• 1(N)=IdentityMatrix(N), T+=HermitianTranspose(T)
• el,element::{posint,string} element number, symbol, or name.
• A,Atoms::list([symbol,<X,Y,Z>,optional_entries]) list of atoms, sometimes internal coordinates are allowed as [symbol,[i1,r,i2,theta,i3,phi]] or as incomplete form of the latter.
• M::Matrix(3,nt) unit cell matrix whose columns are translation vectors Tvs=list(Tv::["Tv",Vector(3)]).
• C,Cell::[a,b,c,alpha,beta,gamma,optional_entries] unit cell parameters recognizable by cryst2M command.
• SG::string Symmetry Group recognizable by FiniteGroup[SymmetryGroup] command.
• ev::Vector(no) eigenvalues.
• evc,mo,lmo::Matrix(N,no) right eigenvectors (MO, LMO) as columns.
• S::Matrix(N,N) basis set overlap matrix.
• evr,evcS,moS,lmoS::Matrix(no,N)=evc+.S left eigenvectors as rows multiplied by S so that evr.evc=1.
• AO Atomic Orbitals
• BS Basis Set
• psi::list(AO) wave-function
• na=|A|, nt=|Tvs|, N=|BS|, no,n=|ev|
• i,j=1..na, k=1..N, o=1..no

Units

• Electronic wave-function – bohrs
• Atomic coordinates – Ao
• Energy – eV
• Temperature – K or eV
• Pressure – GPa (10 kbar)
• Gradient – eV/Ao
• Dipole (l-pole) – e*Ao (e*Ao^l)
• See also list of conversion constants printed by Setup command.

Notes

• When reading a file, its extension can be omitted if there will be no confusion.
• Fully supported external programs are Gaussian, VASP, MOPAC, LAMMPS.
• Partially supported are TINKER, Firefly, and also Abinit, Molpro, FHI-aims, GROMACS.
• Some commands and applications use global variable CurrentDataFolder if that variable is defined.
• Some commands accept two types of geometry input: if atoms are provided as pair Atoms,Cell then the coordinates are assumed to be lattice, if Cell is not provided then cartesian coordinates are assumed, see also Atoms2Cell command.