Lesson on properties at the nuclei¶
Observables near the atomic nuclei.¶
The purpose of this lesson is to show how to compute several observables of interest in Moessbauer, NMR, and NQR spectroscopy, namely:
- the electric field gradient,
- the isomer shift (not yet available),
- and the electronic density itself (not yet available).
This lesson should take about 1 hour.
1 Electric field gradient¶
Various spectroscopies, including nuclear magnetic resonance and nuclear quadrupole resonance (NMR and NQR), as well as Moessbauer spectroscopy, show spectral features arising from the electric field gradient at the nuclear sites. Note that the electric field gradient (EFG) considered here arises from the distribution of charge within the solid, not due to any external electric fields.
The way that the EFG is observed in spectroscopic experiments is through its coupling to the nuclear electric quadrupole moment. The physics of this coupling is described in various texts, for example Principles of Magnetic Resonance, 3rd ed., C. P. Slichter (Springer, New York, 1989). ABINIT computes the field gradient at each site, and then reports the gradient and its coupling based on input values of the nuclear quadrupole moments.
The electric field and its gradient at each nuclear site arises from the distribution of charge, both electronic and ionic, in the solid. The gradient especially is quite sensitive to the details of the distribution at short range, and so it is necessary to use the PAW formalism to compute the gradient accurately. The various sources of charge in the PAW decomposition are summarized in the following equation:
Here the “v” subscript indicates valence, “c” indicates core, and “Z” indicates the ions. Essentially the gradient must be computed for each source of charge, which is done in the code as follows:
- Valence space described by planewaves: expression for gradient is Fourier-transformed at each nuclear site.
- Ion cores: gradient is computed by an Ewald sum method
- On-site PAW contributions: moments of densities are integrated in real space around each atom, weighted by the gradient operator
The code reports each contribution separately if requested.
The electric field gradient computation is performed at the end of a ground- state calculation, and takes almost no additional time. The tutorial file is for stishovite, a polymorph of SiO2. In addition to typical ground state variables, only two additional variables are added:
prtefg 2
quadmom 0.0 -0.02558
# computation of the electric field gradient at the atoms in stishovite prtefg 2 quadmom 0.0 -0.02558 nstep 10 ecut 20 pawecutdg 25 prtden 0 prtwf 0 prteig 0 tolvrs 1.0D-18 ngkpt 8 8 6 spgroup 136 # space group number acell 4.1790 4.1790 2.6649 angstrom # cell sides, angstrom units angdeg 90.0 90.0 90.0 # cell angles (this is the default by the way) znucl 14 8 # atomic number of atoms, will be cross checked against pseudopotential files natom 6 # 6 atoms in the unit cell (remember Z = 2 here) natrd 2 # only read two atoms in, this is the asymmetric unit ntypat 2 # two types of atoms typat 1 2 # read atom type 1 then type 2, order is set by znucl above xred # here come the fractional coordinates from the cif file 0 0 0 # first atom type 0.3062 0.3062 0 # second atom type ## After modifying the following section, one might need to regenerate the pickle database with runtests.py -r #%%<BEGIN TEST_INFO> #%% [setup] #%% executable = abinit #%% [files] #%% files_to_test = #%% tnuc_1.out, tolnlines= 0, tolabs= 0.000e+00, tolrel= 0.000e+00 #%% psp_files = Si.GGA-PBE-rpaw-1.55.abinit, O.GGA-PBE-rpaw-1.45.abinit #%% [paral_info] #%% max_nprocs = 4 #%% [extra_info] #%% authors = J. Zwanziger #%% keywords = PAW #%% description = #%% topics = SmartSymm #%%<END TEST_INFO>
The first variable instructs Abinit to compute and print the electric field gradient, and the second gives the quadrupole moments of the nuclei, one for each type of atom. Here we are considering silicon and oxygen, and in particular Si-29, which as zero quadrupole moment, and O-17, the only stable isotope of oxygen with a non-zero quadrupole moment.
After running the file tnuc_1.in through abinit, you can find the following near the end of the output file:
Electric Field Gradient Calculation
Atom 1, typat 1: Cq = 0.000000 MHz eta = 0.000000
efg eigval : -0.165960
- eigvec : -0.000001 -0.000001 -1.000000
efg eigval : -0.042510
- eigvec : 0.707107 -0.707107 0.000000
efg eigval : 0.208470
- eigvec : 0.707107 0.707107 -0.000002
total efg : 0.082980 0.125490 -0.000000
total efg : 0.125490 0.082980 -0.000000
total efg : -0.000000 -0.000000 -0.165960
This fragment gives the gradient at the first atom, which was silicon. Note that the gradient is not zero, but the coupling is—that’s because the quadrupole moment of Si-29 is zero, so although there’s a gradient there’s nothing in the nucleus for it to couple to.
Atom 2 is an oxygen atom, and its entry in the output is:
Atom 2, typat 2: Cq = 6.603688 MHz eta = 0.140953
efg eigval : -1.098710
- eigvec : -0.707107 0.707107 0.000000
efg eigval : 0.471922
- eigvec : -0.000270 -0.000270 1.000000
efg eigval : 0.626789
- eigvec : 0.707107 0.707107 0.000382
total efg : -0.235961 0.862750 0.000042
total efg : 0.862750 -0.235961 0.000042
total efg : 0.000042 0.000042 0.471922
efg_el : -0.044260 -0.065290 0.000042
efg_el : -0.065290 -0.044260 0.000042
efg_el : 0.000042 0.000042 0.088520
efg_ion : -0.017255 0.306132 -0.000000
efg_ion : 0.306132 -0.017255 -0.000000
efg_ion : -0.000000 -0.000000 0.034509
efg_paw : -0.174446 0.621908 0.000000
efg_paw : 0.621908 -0.174446 0.000000
efg_paw : 0.000000 0.000000 0.348892
Now we see the electric field gradient coupling, in frequency units, along with the asymmetry of the coupling tensor, and, finally, the three contributions to the total. Note that the valence part, efg_el, is quite small, while the ionic part and the on-site PAW part are larger. In fact, the PAW part is largest – this is why these calculations give very poor results with norm-conserving pseudopotentials, and need the full accuracy of PAW.