# Tutorial on properties at the nuclei¶

## Observables near the atomic nuclei.¶

The purpose of this tutorial is to show how to compute several observables of interest in Mössbauer, NMR, and NQR spectroscopy, namely:

- the electric field gradient,
- the isomer shift

This tutorial should take about 1 hour.

Note

Supposing you made your own installation of ABINIT, the input files to run the examples
are in the *~abinit/tests/* directory where *~abinit* is the **absolute path** of the abinit top-level directory.
If you have NOT made your own install, ask your system administrator where to find the package,
especially the executable and test files.

In case you work on your own PC or workstation, to make things easier, we suggest you define some handy environment variables by executing the following lines in the terminal:

export ABI_HOME=Replace_with_absolute_path_to_abinit_top_level_dir # Change this line export PATH=$ABI_HOME/src/98_main/:$PATH # Do not change this line: path to executable export ABI_TESTS=$ABI_HOME/tests/ # Do not change this line: path to tests dir export ABI_PSPDIR=$ABI_TESTS/Psps_for_tests/ # Do not change this line: path to pseudos dir

Examples in this tutorial use these shell variables: copy and paste
the code snippets into the terminal (**remember to set ABI_HOME first!**) or, alternatively,
source the `set_abienv.sh`

script located in the *~abinit* directory:

```
source ~abinit/set_abienv.sh
```

The ‘export PATH’ line adds the directory containing the executables to your PATH
so that you can invoke the code by simply typing *abinit* in the terminal instead of providing the absolute path.

To execute the tutorials, create a working directory (`Work*`

) and
copy there the input files of the lesson.

Most of the tutorials do not rely on parallelism (except specific tutorials on parallelism). However you can run most of the tutorial examples in parallel with MPI, see the topic on parallelism.

## Electric field gradient¶

Various spectroscopies, including nuclear magnetic resonance and nuclear quadrupole resonance (NMR and NQR), as well as Mössbauer 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 [Slichter1978]. 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. For charge density n({\mathbf r}), the potential V is given by $$ V({\mathbf r})=\int \frac{n({\mathbf r’})}{ |\mathbf{r}-\mathbf{r’}| } d{\mathbf r’} $$ and the electric field gradient is $$ V_{ij} = -\frac{\partial^2}{\partial x_i\partial x_j}V({\mathbf r}). $$ The gradient is computed at each nuclear site, for each source of charge arising from the PAW decomposition (see the tutorial PAW1 ). This is done in the code as follows [Profeta2003],[Zwanziger2008]:

- 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 SiO_2. 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 atomic sites in stishovite # Stishovite is a polymorph of SiO2 and has the rutile structure. # Computation of EFG requires the use of PAW, Norm-conserving pseudopotentials are # not appropriate for this calculation. # here are the two variables needed to trigger computation of the field gradient prtefg 2 # PRinT the EFG, value of 2 means to also print its components quadmom 0.0 -0.02558 # quadrupole moments of the nuclei (Si-29, O-17 here) # so that couplings as measured in NMR or NQR are also # reported, in MHz frequency units #Definition of the unit cell # stishovite has a primitive tetragonal cell, so two sides are equal, # the third different, and the angles all 90 degrees acell 8.0298189198E+00 8.0298189198E+00 5.1240093322E+00 Bohr rprim 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 #Definition of the atom types and pseudopotentials ntypat 2 # two types of atoms znucl 14 8 # atomic number of atoms, will be cross checked against pseudopotential files # here Silicon (14) and Oxygen (8). Pseudopotentials must be listed in this order. # this order defines type 1 as silicon, type 2 as oxygen pp_dirpath "$ABI_PSPDIR" # pseudopotential directory pseudos "Si.GGA-PBE-rpaw-1.55.abinit, O.GGA-PBE-rpaw-1.45.abinit" #Definition of the atoms natom 6 # 6 atoms in the unit cell typat 1 1 2 2 2 2 # atoms listed as silicons, then oxygens # next are the 6 atomic positions, in order of typat (silicon, then oxygen) # xred gives them in units of the cell translation vectors, as is commonly # done in crystallography xred 3.1301524738E-20 1.2463357829E-20 -8.3403774579E-17 5.0000000000E-01 5.0000000000E-01 5.0000000000E-01 3.0660149474E-01 3.0660149474E-01 -8.3403774579E-17 8.0660149474E-01 1.9339850526E-01 5.0000000000E-01 1.9339850526E-01 8.0660149474E-01 5.0000000000E-01 6.9339850526E-01 6.9339850526E-01 -8.3403774579E-17 #Numerical parameters of the calculation : planewave basis set and k point grid ecut 15 # plane wave cutoff energy, always need to check convergence of ecut in real runs pawecutdg 20 # cutoff energy for PAW fine grid ngkpt 8 8 6 # Parameters of Monkhorst-Pack kpoint grid. Convergence should be checked for # this parameter as well. #Parameters for the SCF procedure nstep 10 tolvrs 1.0D-18 # suppress printing of density, wavefunctions, etc for this tutorial prtden 0 prtwf 0 prteig 0 ############################################################## # This section is used only for regression testing of ABINIT # ############################################################## #%%<BEGIN TEST_INFO> #%% [setup] #%% executable = abinit #%% [files] #%% files_to_test = #%% tnuc_1.abo, tolnlines= 12, tolabs= 1.2e-8 , tolrel= 3.0e-3 #%% [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, in barns, one for each type of atom. A standard source for quadrupole moments is [Pyykko2008]. Here we are considering silicon and oxygen, and in particular Si-29, which has zero quadrupole moment, and O-17, the only stable isotope of oxygen with a non-zero quadrupole moment.

After running the file *tnuc_1.abi* 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 : -0.152323 - eigvec : 0.000000 0.000000 -1.000000 efg eigval : -0.054274 - eigvec : 0.707107 -0.707107 -0.000000 efg eigval : 0.206597 - eigvec : 0.707107 0.707107 0.000000 total efg : 0.076161 0.130436 0.000000 total efg : 0.130436 0.076161 0.000000 total efg : 0.000000 0.000000 -0.152323

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 3 is an oxygen atom, and its entry in the output is:

Atom 3, typat 2: Cq = 6.615041 MHz eta = 0.140313 efg eigval : -1.100599 - eigvec : 0.707107 -0.707107 0.000000 efg eigval : 0.473085 - eigvec : -0.000000 -0.000000 -1.000000 efg eigval : 0.627514 - eigvec : 0.707107 0.707107 -0.000000 total efg : -0.236543 0.864057 -0.000000 total efg : 0.864057 -0.236543 -0.000000 total efg : -0.000000 -0.000000 0.473085 efg_el : -0.036290 -0.075078 -0.000000 efg_el : -0.075078 -0.036290 -0.000000 efg_el : -0.000000 -0.000000 0.072579 efg_ion : -0.016807 0.291185 -0.000000 efg_ion : 0.291185 -0.016807 -0.000000 efg_ion : -0.000000 -0.000000 0.033615 efg_paw : -0.183446 0.647950 0.000000 efg_paw : 0.647950 -0.183446 0.000000 efg_paw : 0.000000 0.000000 0.366891

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 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 to capture the behavior near the nucleus. Experimentally, the nuclear quadrupole coupling for O-17 in stishovite is reported as 6.5\pm 0.1 MHz, with asymmetry 0.125\pm 0.05 [Xianyuxue1994]. It is not uncommon for PAW-based EFG calculations to give coupling values a few percent too large; often this can be improved by using PAW datasets with smaller PAW radii, at the expense of more expensive calculations [Zwanziger2016].

## Fermi contact interaction¶

The Fermi contact interaction arises from overlap of the electronic wavefunctions with the atomic nucleus, and is an observable for example in Mössbauer spectroscopy [Greenwood1971]. In Mössbauer spectra, the isomer shift \delta is expressed in (SI) velocity units as $$ \delta = \frac{2\pi}{3}\frac{c}{E_\gamma}\frac{Z e^2}{ 4\pi\epsilon_0} ( |\Psi (R)_A|^2 - |\Psi (R)_S|^2 )\Delta\langle r^2\rangle $$ where \Psi(R) is the electronic wavefunction at nuclear site R, for the absorber (A) and source (S) respectively; c is the speed of light, E_\gamma is the nuclear transition energy, and Z the atomic number; and \Delta\langle r^2\rangle the change in the nuclear size squared. All these quantities are assumed known in the Mössbauer spectrum of interest, except |\Psi(R)|^2, the Fermi contact term.

Abinit computes the Fermi contact term in the PAW formalism by using as observable \delta(R), that is, the Dirac delta function at the nuclear site [Zwanziger2009]. Like the electric field gradient computation, the Fermi contact calculation is performed at the end of a ground- state calculation, and takes almost no time. There is a tutorial file for SnO_2, which, like stishovite studied above, has the rutile structure. In addition to typical ground state variables, only one additional variable is needed:

prtfc 1

# Computation of the Fermi contact term at the atomic sites in SnO2 # SnO2 has the rutile structure prtfc 1 # requests Fermi contact at each nuclear site #Definition of the unit cell acell 3*8.9535222618 # each primitive vector in rprim is scaled # by its value in acell, to give internally # cell vectors dimensioned as length in atomic units # SnO2 has a primitive tetragonal cell, so two sides are equal, # the third different, and the angles all 90 degrees rprim 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.672541156606163 #Definition of the atom types and pseudopotentials ntypat 2 # two types of atoms znucl 50 8 # atomic number of atoms, will be cross checked against pseudopotential files # here Tin (50) and Oxygen (8). Pseudopotentials must be listed in this order. # this order defines type 1 as tin, type 2 as oxygen pp_dirpath "$ABI_PSPDIR" # pseudopotential directory pseudos "Pseudodojo_paw_pbe_standard/Sn-sp.xml, Pseudodojo_paw_pbe_standard/O.xml" #Definition of the atoms natom 6 # 6 atoms in the unit cell typat 1 1 2 2 2 2 # atoms listed as silicons, then oxygens # next are the 6 atomic positions, in order of typat (silicon, then oxygen) # xred gives them in units of the cell translation vectors, as is commonly # done in crystallography xred 0.000000000000000 0.000000000000000 0.000000000000000 0.500000000000000 0.500000000000000 0.500000000000000 0.307100000000000 0.307100000000000 0.000000000000000 0.807100000000000 0.192900000000000 0.500000000000000 0.192900000000000 0.807100000000000 0.500000000000000 0.692900000000000 0.692900000000000 0.000000000000000 #Numerical parameters of the calculation : planewave basis set and k point grid ecut 15 # plane wave cutoff energy, always need to check convergence of ecut in real runs pawecutdg 20 # cutoff energy for PAW fine grid ngkpt 8 8 6 # Parameters of Monkhorst-Pack kpoint grid. Convergence should be checked for # this parameter as well. #Parameters for the SCF procedure nstep 10 tolvrs 1.0D-18 # suppress printing of density, wavefunctions, etc for this tutorial prtden 0 prtwf 0 prteig 0 ############################################################## # This section is used only for regression testing of ABINIT # ############################################################## #%%<BEGIN TEST_INFO> #%% [setup] #%% executable = abinit #%% [files] #%% files_to_test = #%% tnuc_2.abo, tolnlines= 12, tolabs= 4.1e-09, tolrel= 3.000e-03 #%% [paral_info] #%% max_nprocs = 4 #%% [extra_info] #%% authors = J. Zwanziger #%% keywords = PAW #%% description = #%% topics = SmartSymm #%%<END TEST_INFO>

After running this file, inspect the output and look for the phrase “Fermi-contact Term Calculation”. There you’ll find the FC output for each atom; in this case, the Sn atoms, typat 1, yield a contact term of 71.6428 (density in atomic units, a^{-3}_0).

To interpret Mössbauer spectra you need really both a source and an absorber; in the tutorial we provide also a file for \alpha-Sn (grey tin, which is non-metallic).

# Computation of the Fermi contact term at the atomic sites in \alpha-Sn # Nonmetallic form of tin prtfc 1 # requests Fermi contact at each nuclear site #Definition of the unit cell acell 3*12.262810608 # each primitive vector in rprim is scaled # by its value in acell, to give internally # cell vectors dimensioned as length in atomic units # a-Sn has a cubic conventional cell, so the primitive cell # has 60 deg angles rprim 0.000000000000000 0.500000000000000 0.500000000000000 0.500000000000000 0.000000000000000 0.500000000000000 0.500000000000000 0.500000000000000 0.000000000000000 #Definition of the atom types and pseudopotentials ntypat 1 # one types of atom znucl 50 # atomic number of atoms, will be cross checked against pseudopotential files # here Tin (50) is the atom type pp_dirpath "$ABI_PSPDIR" # pseudopotential directory pseudos "Pseudodojo_paw_pbe_standard/Sn-sp.xml" #Definition of the atoms natom 2 # 2 atoms in the primitive unit cell typat 1 1 # atoms listed as Sn Sn # next are the atomic positions # xred gives them in units of the cell translation vectors, as is commonly # done in crystallography xred 0.000000000000000 0.000000000000000 0.000000000000000 0.250000000000000 0.250000000000000 0.250000000000000 #Numerical parameters of the calculation : planewave basis set and k point grid ecut 15 # plane wave cutoff energy, always need to check convergence of ecut in real runs pawecutdg 20 # cutoff energy for PAW fine grid ngkpt 4 4 4 # Parameters of Monkhorst-Pack kpoint grid. Convergence should be checked for # this parameter as well. nshiftk 4 # the default M-P shift of 1/2, 1/2, 1/2 breaks the symmetry of the # reciprocal lattice but these shifts preserve it. See the abinit # documentation for the shiftk input variable shiftk 0.5 0.5 0.5 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 #Parameters for the SCF procedure nstep 10 tolvrs 1.0D-18 # suppress printing of density, wavefunctions, etc for this tutorial prtden 0 prtwf 0 prteig 0 ############################################################## # This section is used only for regression testing of ABINIT # ############################################################## #%%<BEGIN TEST_INFO> #%% [setup] #%% executable = abinit #%% [files] #%% files_to_test = #%% tnuc_3.abo, tolnlines= 3, tolabs= 6.000e-10, tolrel= 3.000e-10 #%% [paral_info] #%% max_nprocs = 4 #%% [extra_info] #%% authors = J. Zwanziger #%% keywords = PAW #%% description = #%% topics = SmartSymm #%%<END TEST_INFO>

If you run this file, you should find a contact term of 102.0748.

To check your results, you can use experimental data for the isomer shift \delta for known compounds to compute \Delta\langle r^2\rangle in the above equation (see [Zwanziger2009]). Using our results above together with standard tin Mössbauer parameters of E_\gamma = 23.875 keV and an experimental shift of 2.2 mm/sec for \alpha-Sn relative to SnO_2, we find \Delta\langle r^2\rangle = 5.67\times 10^{-3}\mathrm{fm}^2, in decent agreement with other calculations of 6–7\times 10^{-3}\mathrm{fm}^2 [Svane1987], [Svane1997].