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Tutorial positron beautified

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2
doc/tutorial/paw1.md
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@ -664,7 +664,7 @@ computed; it is indeed a very good approximation.
Converging a _Self-Consistent Cycle_, or ensuring the global minimum is reached,
with PAW+U is sometimes difficult. Using [[usedmatpu]] and [[dmatpawu]] can help.
See [tutorial on DFT+U](Dftu).
See [tutorial on DFT+U](dftu).
### 8.d. Printing volume for PAW###

237
doc/tutorial/positron.md
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@ -14,9 +14,9 @@ physical properties:
* the lifetime of a positron localized in a vacancy,
* the electron-positron momentum distribution.
For the description of the implementation of TCDFT in ABINIT see [[cite:Wiktor2015]].
For the description of the implementation of TCDFT in `ABINIT` see [[cite:Wiktor2015]].
The user should be familiar with the four basic tutorials of ABINIT and the [first PAW tutorial](paw1).
The user should be familiar with the four basic tutorials of `ABINIT` and the [first PAW tutorial](paw1).
This tutorial should take about 2 hours.
@ -25,14 +25,13 @@ This tutorial should take about 2 hours.
## Computing the positron lifetime in Si lattice
*Before beginning, you might consider to work in a different subdirectory as
for the other tutorials. Why not Work_positron?*
for the other tutorials. Why not* `Work_positron`*?*
```sh
cd $ABI_TESTS/tutorial/Input
mkdir Work_positron
cd Work_positron
cp ../tpositron_x.files . # You will need to edit this file.
cp ../tpositron_1.in .
cp ../tpositron_1.abi .
```
The tutorial begins with a calculation of the positron lifetime in a silicon lattice.
@ -48,48 +47,49 @@ proportional to the inverse of the overlap of the electron and positron
densities. This 2-step calculation, considering the _zero-positron density
limit_, corresponds to the conventional scheme (CONV).
In the `tpositron_1.in` file, you will find two datasets.
In the `tpositron_1.abi` file, you will find two datasets.
{% dialog tests/tutorial/Input/tpositron_1.in %}
{% dialog tests/tutorial/Input/tpositron_1.abi %}
The first dataset is a standard ground-state calculation. The second one introduces a positron into
the system. You can see that in this case we set:
positron2 1 ! Dataset 2 is a positronic GS calculation
getden2 1 ! in presence of the previous electronic density
kptopt2 0 ! Use only k=gamma point
positron2 1 # Dataset 2 is a positronic GS calculation
getden2 1 # in presence of the previous electronic density
ixcpositron2 1 ! We are using the Boronski and Nieminen parametrization
kptopt2 0 # Use only k=gamma point
ixcpositron2 1 # We are using the Boronski and Nieminen parametrization
Here we set [[positron]]=1, which corresponds to a positronic ground-state
calculation, considering that the electrons are not perturbed by the presence
of the positron (_zero-positron density limit_). The electron density is read from the file resulting from
dataset 1. As we consider the positron to be completely delocalized, we only
consider the Γ point in the _Brillouin_ zone. The keyword [[ixcpositron]] selects the electron-
positron correlation functional and enhancement factor. In this calculation we
use the functional parametrized by Boronski and Nieminen [[cite:Boronski1986]], using the data provided by Arponen and Pajanne [[cite:Arponen1979]].
consider the Γ point in the _Brillouin_ zone. The keyword [[ixcpositron]]
selects the **electron-positron correlation functional** and **enhancement factor**.
In this calculation we use the functional parametrized by Boronski and Nieminen
[[cite:Boronski1986]], using the data provided by Arponen and Pajanne [[cite:Arponen1979]].
We can now run the calculation. In the directory
`~abinit/tests/tutorial/Input/Work_positron`, copy the files
`~abinit/tests/tutorial/Input/tpositron_x.files` and `tpositron_1.in`.
We can now run the calculation. In the working directory
`Work_positron`, copy the file `tpositron_1.abi`.
Then, issue:
abinit < tpositron_x.files > log 2> err &
abinit tpositron_1.abi >& log
This calculation should only take a few seconds.
You can look at the *tpositron_1.out* file.
You can look at the `tpositron_1.abo` file.
We find the positron lifetime calculated in the RPA limit:
########## Lifetime computation 2
########## Lifetime computation 2
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
Positron lifetime (ps) = 2.22891945E+02
Positron lifetime (ps) = 2.22879743E+02
The lifetime of 223 ps agrees well with the value of 225 ps calculated with
the same number of valence electrons in [[cite:Wiktor2015]] and
@ -111,61 +111,60 @@ with the experimental value of about 219 ps [[cite:Panda1997]].
We will now perform a positron lifetime calculation for a monovacancy in
silicon in the conventional scheme (which we applied to the perfect lattice
previously). Note that when the positron localizes inside a vacancy, the _zero-
positron density limit_ does not apply anymore. However, in some cases, the
previously). Note that when the positron localizes inside a vacancy, the
_zero-positron density limit_ does not apply anymore. However, in some cases, the
conventional scheme proved to yield results in agreement with experiments.
For the purpose of this tutorial, we generate a defect in a cell containing
only 16 atoms. This supercell is too small to get converged results, but the
calculation is relatively fast.
{% dialog tests/tutorial/Input/tpositron_2.in %}
{% dialog tests/tutorial/Input/tpositron_2.abi %}
You can now, issue (after having replaced *tpositron_1* by *tpositron_2* in the
*tpositron_x.files* file):
You can now, issue:
abinit < tpositron_x.files > log 2> err &
abinit tpositron_2.abi >& log
Once the calculation is finished, look at the *tpositron_2.out* file.
Once the calculation is finished, look at the `tpositron_2.abo` file.
Again, we look at the reported lifetime:
########## Lifetime computation 2
########## Lifetime computation 2
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
Positron lifetime (ps) = 2.46936401E+02
Positron lifetime (ps) = 2.46923233E+02
We observe that when the positron localizes inside the vacancy, its lifetime
increases from 223 to 247 ps. This is because now the majority of the positron
density is localized in the vacancy region, where the electron density is
small. The overlap of the electron and positron densities is reduced, and the lifetime increased.
In the *Work_positron* directory, you will also find a *tpositron_2o_DS2_DEN_POSITRON*
In the `Work_positron` directory, you will also find a `tpositron_2o_DS2_DEN_POSITRON`
file, containing the positron density. Visualizing this file (using e.g.
_cut3d_ and _XcrysDen_ or _VMD_ ) you can see that the positron is localized
_cut3d_ and _XcrysDen_ or _VMD_) you can see that the positron is localized
inside the vacancy. You can see below how the positron (in red, isodensity at
30% of the maximum density) localized the silicon monovacancy looks like:
![](positron_assets/posdensity.png)
![](positron_assets/posdensity.png){width=80%}
## Performing a self-consistent electron-positron calculation for a Si vacancy
We will now perform a self-consistent calculation of the positron and electron
densities. As this calculation will take a few minutes, you can already issue
(putting *tpositron_3.in* in *tpositron_x.files*):
densities. As this calculation will take a few minutes, you can already issue, using
the `tpositron_3.abi` input file:
abinit < tpositron_x.files > log 2> err &
abinit tpositron_3.abi >& log
{% dialog tests/tutorial/Input/tpositron_3.in %}
{% dialog tests/tutorial/Input/tpositron_3.abi %}
This calculation is significantly longer than the previous one, because the
electron and positron steps will be repeated until the convergence criterion is reached.
In *tpositron_3.in* we only have one dataset and we set
In `tpositron_3.abi` we only have one dataset and we set
[[positron]] = -10 to perform an automatic calculation of electrons and positron
densities. The convergence is controlled by [[postoldfe]] = 1d-5. This means
that we will repeat the electron and positron steps until the energy
@ -173,16 +172,16 @@ difference between them is lower than 1d-5 Ha. This value should always be
larger than [[toldfe]]. In this calculation we still use [[ixcpositron]] = 1,
which means that we are using the GGGC scheme (see [[cite:Gilgien1994]] and [[cite:Wiktor2015]]
Once the calculation is finished, look at the positron lifetime in *tpositron_3.out*.
Once the calculation is finished, look at the positron lifetime in `tpositron_3.abo`.
########## Lifetime computation 2
########## Lifetime computation 2
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
Positron lifetime (ps) = 2.55617112E+02
Positron lifetime (ps) = 2.55612619E+02
Including the self-consistency increases the positron lifetime, because its
localization inside the vacancy becomes stronger when the positron and the
@ -193,42 +192,38 @@ electron densities are allowed to relax.
In addition to the self-consistency, the lifetime of a positron inside a
vacancy can be strongly affected by the relaxation of the atoms due to the
forces coming from both the electrons and the positron. You can already start
the relaxation of the vacancy by issuing:
the relaxation (with the `tpositron_4.abi` input file) of the vacancy by issuing:
abinit < tpositron_4.files > log 2> err &
!!! important
Don't forget to put *tpositron_4.in* in *tpositron_x.files*.
abinit tpositron_4.abi >& log
In this calculation we switched on the atomic relaxation by setting
[[ionmov]] = 2. We need to calculate forces to be able to move the atoms, so we
set [[optforces]] = 1. In the provided *tpositron_4.in* file, we only perform 4
set [[optforces]] = 1. In the provided `tpositron_4.abi` file, we only perform 4
relaxation steps ([[ntime]] = 4) to save time, but more steps would be needed to
converge the positron lifetime.
{% dialog tests/tutorial/Input/tpositron_3.in %}
{% dialog tests/tutorial/Input/tpositron_4.abi %}
Look at the positron lifetime in the RPA limit after each ionic step:
Positron lifetime (ps) = 2.55617112E+02
Positron lifetime (ps) = 2.56981105E+02
Positron lifetime (ps) = 2.81986785E+02
Positron lifetime (ps) = 2.82826327E+02
Positron lifetime (ps) = 2.55612619E+02
Positron lifetime (ps) = 2.56978378E+02
Positron lifetime (ps) = 2.82166606E+02
Positron lifetime (ps) = 2.82878399E+02
As the vacancy relaxes outwards, the positron lifetime increases. 4 steps were
not enough to relax the defect completely, as the lifetime still changes.
Indeed, setting [[ntime]] to 10 delivers:
Positron lifetime (ps) = 2.55617112E+02
Positron lifetime (ps) = 2.56981106E+02
Positron lifetime (ps) = 2.81986782E+02
Positron lifetime (ps) = 2.82826326E+02
Positron lifetime (ps) = 2.86660064E+02
Positron lifetime (ps) = 2.87040831E+02
Positron lifetime (ps) = 2.87284438E+02
Positron lifetime (ps) = 2.87360829E+02
Positron lifetime (ps) = 2.87302206E+02
Positron lifetime (ps) = 2.55612619E+02
Positron lifetime (ps) = 2.56978379E+02
Positron lifetime (ps) = 2.82166601E+02
Positron lifetime (ps) = 2.82878398E+02
Positron lifetime (ps) = 2.86515373E+02
Positron lifetime (ps) = 2.86983434E+02
Positron lifetime (ps) = 2.87266489E+02
Positron lifetime (ps) = 2.87359897E+02
Positron lifetime (ps) = 2.87313132E+02
Although the results at ionic steps 3 and 4 differ from each other by less
than one percent, they differ by more from the final result. The one percent
@ -246,13 +241,13 @@ scheme. This type of calculation is much more time and memory consuming than
the _lifetime_ calculation, as it is using the electron and positron
_wavefunctions_ (not only _densities_).
You can already issue (putting *tpositron_5.in* in *tpositron_x.files*):
You can already issue:
abinit < tpositron_5.files > log 2> err &
abinit tpositron_5.abi >& log
Now take a look at the input file *tpositron_5.in*.
Now take a look at the input file `tpositron_5.abi`.
{% dialog tests/tutorial/Input/tpositron_5.in %}
{% dialog tests/tutorial/Input/tpositron_5.abi %}
The momentum distribution calculation is activated by [[posdoppler]] = 1. You can also notice that instead
of having two datasets as in the first part of this tutorial, we now use the
@ -261,18 +256,18 @@ we need to have the full electron and positron wavefunctions in memory, which
is only the case when [[positron]] <= -10. Additionally, the momentum
distribution calculations require using a full k-point grid. In the input file we set:
kptopt 0
istwfk *1
nkpt 8 # This corresponds to a 2x2x2 grid, denser grids may be needed to get converged spectra
kpt
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
kptopt 0 # Option for manual setting of k-points
istwfk *1 # No time-reversal symmetry optimization
nkpt 8 # Corresponds to a 2x2x2 grid
kpt # K-point coordinates in reciprocal space:
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
This grid is used in both electron and positron calculations, but only the
positron _wavefunction_ at the first point is taken in the momentum distribution
@ -281,16 +276,21 @@ calculation, so the $\Gamma$ point should always be given first.
In the calculation of the momentum distribution, we need to include both _core_
and _valence_ electrons. The _wavefunctions_ of the core electrons are read from a
file (one per atom type), which needs to be provided. This _core WF file_ should
be named `<psp_file_name>.corewf` (where `<psp_file_name>` is the name of the
pseudo-potential (or PAW) file) or `corewf.abinit<ityp>` (where `<ityp>` is the
index of the atom type). _Core WF files_ can be obtained with the `atompaw` tool
be named <span style="color:green">&#60;psp_file_name&#62;.corewf.xml</span>
(where `<psp_file_name>` is the name of the PAW atomic dataset file, without `.xml` suffix).
_Core WF files_ can be obtained with the `atompaw` tool
(see [the tutorial on generating PAW datasets (PAW2)](paw2) ) by the use of the
`prtcorewf` keyword. You will find the core wavefunction file used in this calculation in
*$ABI_PSPDIR/Si.LDA-PW-paw.abinit.corewf*.
`$ABI_PSPDIR/Si.LDA-PW-paw.abinit.corewf`.
Once the calculation is complete, you can find a *tpositron_5o_DOPPLER* file
!!! Note
If you use a PAW dataset in _ABINIT legacy proprietary format_ (with the `.abinit` suffix),
the core wavefunction file has to be named `<psp_file_name>.corewf.abinit`.
It also can be obtained with the `atompaw` tool by the use of the `prtcorewf` keyword.
Once the calculation is complete, you can find a `tpositron_5o_DOPPLER` file
containing the _momentum distribution_ on the FFT grid. You can use the
*~abinit/scripts/post_processing/posdopspectra.F90* tool to generate 1D
`$ABI_HOME/scripts/post_processing/posdopspectra.F90` tool to generate 1D
projections (_Doppler spectra_) in (001), (011) and (111) directions and to
calculate the low- and high-momentum contributions to the
momentum distribution (so called `S` and `W` parameters, see [[cite:Wiktor2015]]).
@ -308,25 +308,37 @@ The simplest way to make the **PAW
dataset** more complete is to include `semicore electrons`. It is also possible to
add the `partial waves` corresponding to the `semicore electrons` in the basis
used only for the positron wave function description, while keeping the
initial number of valence electrons (as done in [[cite:Wiktor2015]]). However, this second method is less straightforward.
initial number of valence electrons (as done in [[cite:Wiktor2015]]).
However, this second method is less straightforward.
The previous calculations were done with only **4 valence electrons** (`3s` and `3p`).
We will now see what happens if we include the `2s` and `2p` states in the **PAW dataset**.
In *tpositron_12el_x.files* we have replaced the *Si.LDA-PW-paw.abinit*
dataset with *Si.12el.LDA-PW-paw.abinit*. We can now rerun the lifetime calculation:
We use the `Si_paw_pw_12el.xml` PAW dataset which includes 8 additional valence electrons.
abinit < tpositron_12el_x.files > log 2> err
!!!Tip
To generate the new dataset we use the `atompaw` tool.
To add `semicore states`, the input file is modified
as follows:
- Replace `c` by `v` for the selected orbitals in the _electronic configuration_ section
- Decrease the PAW augmentation radius (because semicore states are more localized)
Don't forget to add `prtcorewf` keyword to create the core orbital file.
We can now rerun the lifetime calculation with the new atomic dataset:
abinit tpositron_6.abi >& log
We now find the positron lifetime calculated in the RPA limit:
########## Lifetime computation 2
########## Lifetime computation 2
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Zero-positron density limit of Arponen and Pajanne provided by Boronski & Nieminen
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
# Enhancement factor of Boronski & Nieminen IN THE RPA LIMIT
Ref.: Boronski and R.M. Nieminen, Phys. Rev. B 34, 3820 (1986)
Positron lifetime (ps) = 2.11481560E+02
Positron lifetime (ps) = 2.11470610E+02
This value is significantly lower than 223 ps achieved with 4 valence
electrons in the first step. **It is, therefore, very important to always test
@ -334,21 +346,22 @@ the PAW dataset completeness for positron calculations**.
The PAW dataset completeness is even more important in the _Doppler spectra_
calculations. We will now recalculate the momentum distribution including 12
_valence electrons_ (using *tpositron_7.in* in *tpositron_12el_x.files*):
_valence electrons_ using `tpositron_7.abi`:
abinit < tpositron_12el_x.files > log 2> err
abinit tpositron_7.abi >& log
Before processing the new *tpositron_7o_DOPPLER file*, you should copy files
Before processing the new `tpositron_7o_DOPPLER file`, you should copy files
`rho_001`, `rho_011`, `rho_111` from the fifth step to for instance `si4el_001`, `si4el_011` and `si4el_111`.
By plotting the _Doppler spectra_ in the (001) direction calculated with 4 and
12 valence electrons, you should obtain a figure like this:
![](positron_assets/doppler.png)
![](positron_assets/doppler.png){width=60%}
The dataset with 4 valence electrons is **not complete enough** to describe the
positron `wavefunction` around the nucleus. This is reflected in the
positron **wavefunction** around the nucleus. This is reflected in the
unphysically high probability at high momenta in the spectrum.
Further explanation of the influence of the PAW dataset on the _Doppler spectra_
can be found in [[cite:Wiktor2015]]. In case you need to generate
your own dataset for momentum distribution calculations, you can follow the [tutorial on generating PAW datasets (PAW2)](paw2).
your own dataset for momentum distribution calculations,
you can follow the [tutorial on generating PAW datasets (PAW2)](paw2).

13
shared/libpaw/src/m_pawpsp.F90
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@ -1442,15 +1442,14 @@ subroutine pawpsp_read_corewf(energy_cor,indlmn_core,lcor,lmncmax,ncor,nphicor,r
MSG_ERROR(msg)
end if
oldformat=ex
if (.not.ex) then
! No core WF file found
write(msg, '(3a)' )&
& 'Checks for existence of files corewf.abinit[.xml] or corewf.dat',ch10,&
& 'but INQUIRE finds file does not exist!'
MSG_ERROR(msg)
end if
end if
end if
if (.not.ex) then
write(msg, '(3a)' )&
& 'Checks for existence of file psp-name.corewf[.xml][.abinit] or corewf.dat',ch10,&
& 'but INQUIRE finds file does not exist!'
MSG_ERROR(msg)
end if
end if
!Core WF file is in new XML format

10
src/67_common/m_positron.F90
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@ -2107,11 +2107,11 @@ subroutine posdoppler(cg,cprj,Crystal,dimcprj,dtfil,dtset,electronpositron,&
if (.not.ex) then
write(unit=filename,fmt='(a,i1)') 'corewf.abinit',itypat
inquire(file=filename,exist=ex)
if (.not.ex) then
write(msg,'(4a)') 'Core wave-functions file is missing!',ch10,&
& 'Looking for: ',trim(filename)
MSG_ERROR(msg)
end if
end if
if (.not.ex) then
write(msg,'(3a)') 'Core wave-functions file is missing!',ch10,&
& 'Looking for: psp-name.corewf[.xml][.abinit] or corewf.dat'
MSG_ERROR(msg)
end if
call pawpsp_read_corewf(energycor,indlmncor(itypat)%value,lcor,lmncmax(itypat),&
& ncor,nphicor(itypat),pawrad(itypat),phicor(itypat)%value,&

3396
tests/Psps_for_tests/Pseudodojo_paw_pw_standard/Si.corewf.xml Normal file
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10289
tests/Psps_for_tests/Si.12el.LDA-PW-paw.abinit
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487
tests/Psps_for_tests/Si.12el.LDA-PW-paw.corewf.abinit
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@ -1,487 +0,0 @@
All-electron core wavefunctions - Paw atomic data for element Si - Generated with atompaw v3.1.0.3
1 1 1 : method,nspinor,nsppol
14.000 2.000 20170718 : zatom,zcore,pspdat
7 7 0 : pspcod,pspxc,lmax
core1 1340 : pspfmt,creatorID
1 1 : norb_core, lmn_size
0 : core_orbitals
1 : number_of_meshes
1 2 1417 4.3309254207421976E-04 6.0632955890390769E-03 : mesh 1, type,size,rad_step[,log_step]
2.3184077508 : r_max(CORE)
===== Core wave functions PHI 1 ===== [phi(r)=PHI(r)/r*Ylm(th,ph)]
1 : radial mesh index
1 0 1 : n,l,spin
-1.30714557E+02 2.00000000E+00 : ene,occ
0.0000000000000000E+00 2.8286746596920014E-04 5.6537099566431970E-04
8.4879000780603597E-04 1.1334003456047999E-03 1.4124026736979209E-03
1.6978690714021451E-03 1.9854904544676722E-03 2.2742669547833275E-03
2.5646640701284494E-03 2.8566364956711448E-03 3.1501958168809129E-03
3.4453728510629427E-03 3.7421872592786902E-03 4.0406578503768831E-03
4.3408024464942430E-03 4.6426378127814071E-03 4.9461799489225241E-03
5.2514442330824926E-03 5.5584455355068667E-03 5.8671983106316217E-03
6.1777166700593550E-03 6.4900144415645598E-03 6.8041052173230263E-03
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6.0029221943263673E-06 5.4738957353196462E-06 4.9886310980536434E-06
4.5437646856493186E-06 4.1361697022747265E-06 3.7629412118927148E-06
3.4213820112108350E-06 3.1089892813339184E-06 2.8234419835972953E-06
2.5625889660449921E-06 2.3244377480096192E-06 2.1071439512464231E-06
1.9090013470706576E-06 1.7284324899426366E-06 1.5639799089362907E-06
1.4142978295127993E-06 1.2781443989987507E-06 1.1543743901366300E-06
1.0419323580324704E-06 9.3984622676963336E-07 8.4722128288755059E-07
7.6323455383845275E-07 6.8712955043249798E-07 6.1821135316118493E-07
5.5584202314954463E-07 4.9943631932849851E-07 4.4845770423921498E-07
4.0241462168063962E-07 3.6085703018909840E-07 3.2337317709453009E-07
2.8958659863113741E-07 2.5915333229081183E-07 2.3175932829538146E-07
2.0711804772847443E-07 1.8496823550953521E-07 1.6507185701132522E-07
1.4721218771818417E-07 1.3119204589558020E-07 1.1683215879225939E-07
1.0396965342487780E-07 9.2456663501679497E-08 8.2159044526924508E-08
7.2955189591760660E-08 6.4734938800506225E-08 5.7398575704313504E-08
5.0855904517405395E-08 4.5025402275021570E-08 3.9833440457400595E-08
3.5213570951103957E-08 3.1105871548308980E-08 2.7456346496926052E-08
2.4216377910103902E-08 2.1342224123452549E-08 1.8794561352716185E-08
1.6538065254250667E-08 1.4541029226079493E-08 1.2775016509096327E-08
1.1214543356719938E-08 9.8367907375548040E-09 8.6213422199221899E-09
7.5499458600488878E-09 6.6062980777701824E-09 5.7758476553430666E-09
5.0456181368876554E-09 4.4040470385763076E-09 3.8408404034558157E-09
3.3468413501870814E-09 2.9139113724736874E-09 2.5348232459643685E-09
2.2031644923781240E-09 1.9132504369219179E-09 1.6600459751412368E-09
1.4390952395387606E-09 1.2464584249757768E-09 1.0786550953786323E-09
9.3261335293672483E-10 8.0562430511213633E-10 6.9530131468168139E-10
5.9954356398269486E-10 5.1650350680259522E-10 4.4455782019325371E-10
3.8228150414480964E-10 3.2842480974678312E-10 2.8189270641119391E-10
2.4172662613447372E-10 2.0708824782179937E-10 1.7724510756706259E-10
1.5155784164092953E-10 1.2946888794460464E-10 1.1049248898415310E-10
9.4205855146013090E-11

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tests/Psps_for_tests/Si.LDA-PW-paw.abinit
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tests/Psps_for_tests/Si.LDA-PW-paw.corewf.abinit
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tests/Psps_for_tests/Si_paw_pw_12el.corewf.xml Normal file
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tests/Psps_for_tests/Si_paw_pw_12el.xml Normal file
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2
tests/tutorial/Input/tpaw1_1.abi
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@ -44,7 +44,7 @@ shiftk # with different shifts:
nstep 20 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions

2
tests/tutorial/Input/tpaw1_2.abi
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@ -55,7 +55,7 @@ shiftk # with different shifts:
nstep 20 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 1 # Print wavefunctions (re-used from one dataset to the other)

2
tests/tutorial/Input/tpaw1_3.abi
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@ -55,7 +55,7 @@ shiftk # with different shifts:
nstep 20 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 1 # Print wavefunctions (re-used from one dataset to the other)

2
tests/tutorial/Input/tpaw1_4.abi
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@ -70,7 +70,7 @@ shiftk # with different shifts:
nstep 20 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions

2
tests/tutorial/Input/tpaw1_5.abi
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@ -54,7 +54,7 @@ shiftk # with different shifts:
nstep 10 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 1 # Print wavefunctions (re-used from one dataset to the other)

2
tests/tutorial/Input/tpaw2_1.abi
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@ -56,7 +56,7 @@ shiftk # with different shifts:
nstep 50 # Maximal number of SCF cycles
tolvrs 1.0d-9 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 1 # Print wavefunctions (re-used from one dataset to the other)

6
tests/tutorial/Input/tpaw2_2.abi
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@ -2,8 +2,8 @@
# Nickel ferromagnetic fcc structure: etotal vs ecut
#Define the different datasets
ndtset 7 # 7 datasets. Uncomment this line for the tutorial
#ndtset 1 # 1 datasets. Comment this line for the tutorial
#ndtset 7 # 7 datasets. Uncomment this line for the tutorial
ndtset 1 # 1 datasets. Comment this line for the tutorial
acell: 3*3.5150 angstrom # The starting values of the cell parameters
acell+ 3*0.0025 angstrom # The increment of acell from one dataset to the other
@ -57,7 +57,7 @@ shiftk # with different shifts:
nstep 50 # Maximal number of SCF cycles
tolvrs 1.0d-12 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 1 # Print wavefunctions (re-used from one dataset to the other)

115
tests/tutorial/Input/tpositron_1.abi
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@ -1,58 +1,81 @@
#################################################################
# Input file for the positron tutorial #
# Positron lifetime calculation within PAW #
# #
# Si, 2 atoms in the box #
#################################################################
# Input for Positron tutorial
# First step of the tutorial on electron-positron annihilation
# Positron lifetime calculation within PAW
# Si, 2 atoms in the box
# Datasets definition
ndtset 2
#Define the different datasets
ndtset 2 # 2 datasets
positron1 0 ! Dataset 1 is a simple electronic GS calculation
#FIRST DATASET
positron1 0 # Dataset 1 is a simple electronic GS calculation
positron2 1 ! Dataset 2 is a positronic GS calculation
getden2 1 ! in presence of the previous electronic density
kptopt2 0 ! Use only k=gamma point
#SECOND DATASET
positron2 1 # Dataset 2 is a positronic GS calculation
getden2 1 # in presence of the previous electronic density
ixcpositron2 1 ! We are using the Boronski and Nieminen parametrization
kptopt2 0 # Use only k=gamma point
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
ixcpositron2 1 # We are using the Boronski and Nieminen parametrization
natom 2
ntypat 1
typat 2*1
znucl 14
xred 0.0 0.0 0.0
0.25 0.25 0.25
posocc2 1 # Occupation number for the positron
# (should be set <1 for bulk calculation with a small cell).
# Here the zero positron density limit is used,
# so results do not depend on posocc.
! K-points and occupations
kptopt 1
ngkpt 4 4 4
nshiftk 1
shiftk 0.0 0.0 0.0
occopt 1
nband 6
posocc2 1 ! Occupation number for the positron (should be set <1 for bulk calculation with a small cell).
! Here the zero positron density limit is used, so results do not depend on posocc.
#-------------------------------------------------------------------------------
#Definition of data common to all datasets
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 50 tolvrs 1.d-8
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice)
0.0 1/2 1/2
1/2 0.0 1/2
1/2 1/2 0.0
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Pseudodojo_paw_pw_standard/Si.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 2 # There are two atoms
typat 1 1 # They both are of type 1, that is, Silicon
xred # Location of the atoms:
0.0 0.0 0.0 # Triplet giving the reduced coordinates of atom 1
1/4 1/4 1/4 # Triplet giving the reduced coordinates of atom 2
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.LDA-PW-paw.abinit"
#Definition of bands and occupation numbers
nband 6 # Compute 6 bands
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
kptopt 1 # Automatic generation of k points, taking into account the symmetry
ngkpt 4 4 4 # This is a 4x4x4 grid based on the primitive vectors of the recip. space
nshiftk 1 # We do not shift the grid in order to have Gamma point in it
shiftk 0. 0. 0.
#Parameters for the SCF procedure
nstep 50 # Maximal number of SCF cycles
tolvrs 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 1 # Print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -64,5 +87,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = First step of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% First step of the tutorial on electron-positron annihilation
#%% Positron lifetime calculation within PAW
#%% Si, 2 atoms in the box
#%%<END TEST_INFO>

6
tests/tutorial/Input/tpositron_12el_x.files
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@ -1,6 +0,0 @@
tpositron_6.in
tpositron_6.out
tpositron_6i
tpositron_6o
tpositron_6tmp
../../../Psps_for_tests/Si.12el.LDA-PW-paw.abinit

146
tests/tutorial/Input/tpositron_2.abi
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@ -1,74 +1,96 @@
#################################################################
# Input file for the positron tutorial #
# Positron lifetime calculation within PAW #
# #
# Si monovacancy, "conventional" scheme #
#################################################################
# Input for Positron tutorial
# Second step of the tutorial on electron-positron annihilation
# Positron lifetime calculation within PAW
# Si monovacancy, "conventional" scheme
# Datasets definition
ndtset 2
#Define the different datasets
ndtset 2 # 2 datasets
positron1 0 ! Dataset 1 is a simple electronic GS calculation
#FIRST DATASET
positron1 0 # Dataset 1 is a simple electronic GS calculation
positron2 1 ! Dataset 2 is a positronic GS calculation
getden2 1 ! in presence of the previous electronic density
kptopt2 0 ! Use only k=gamma point
#SECOND DATASET
positron2 1 # Dataset 2 is a positronic GS calculation
getden2 1 # in presence of the previous electronic density
ixcpositron2 1 ! We are using the Boronski and Nieminen parametrization
kptopt2 0 # Use only k=gamma point
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0
natom 15
ntypat 1
typat 15*1
znucl 14
xred
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
ixcpositron2 1 # We are using the Boronski and Nieminen parametrization
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
! 0.625 0.625 0.625 ! We remove one Si atom
posocc2 1 # Occupation number for the positron
# (should be set <1 for bulk calculation with a small cell).
# Here the zero positron density limit is used,
# so results do not depend on posocc.
! K-points and occupations
kptopt 1
ngkpt 2 2 2
nshiftk 1
shiftk 0.0 0.0 0.0
occopt 1
nband 36
posocc2 1.0 ! Occupation number for the positron (should be set <1 for bulk calculation with a small cell).
! Here the zero positron density limit is used, so results do not depend on posocc.
#-------------------------------------------------------------------------------
#Definition of data common to all datasets
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 50 tolvrs 1.d-8
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice, non primitive cell)
0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0 # Do not stop if cell is not primitive
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Pseudodojo_paw_pw_standard/Si.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 15 # There are 15 atoms
typat 15*1 # They all are of type 1, that is, Silicon
xred # Location of the 15 atoms (one triplet per atom):
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
# 0.625 0.625 0.625 # We remove one Si atom
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.LDA-PW-paw.abinit"
#Definition of bands and occupation numbers
nband 36 # Compute 36 bands
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
kptopt 1 # Automatic generation of k points, taking into account the symmetry
ngkpt 2 2 2 # This is a 2 2 2 grid based on the primitive vectors of the recip. space
nshiftk 1 # We do not shift the grid in order to have Gamma point in it
shiftk 0. 0. 0.
#Parameters for the SCF procedure
nstep 50 # Maximal number of SCF cycles
tolvrs 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 1 # Print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -80,5 +102,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Second step of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Second step of the tutorial on electron-positron annihilation
#%% Positron lifetime calculation within PAW
#%% Si monovacancy, "conventional" scheme
#%%<END TEST_INFO>

143
tests/tutorial/Input/tpositron_3.abi
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@ -1,71 +1,94 @@
#################################################################
# Input file for the positron tutorial #
# Positron lifetime calculation within PAW #
# #
# Si monovacancy, self-consistent scheme #
#################################################################
# Input for Positron tutorial
# Third step of the tutorial on electron-positron annihilation
# Positron lifetime calculation within PAW
# Si monovacancy, self-consistent scheme
# Self-consistent positron lifetime calculation
#To perform a self-consistent electron-positron calculation, we need only one dataset
positron -10 ! We perform automatic calculation of electrons and positron densities in the two-component DFT context
postoldfe 1d-5 ! We will repeat the electon and positron steps until the energy difference is lower than 1d-5
posnstep 20 ! Maximum number of electon and positron steps
#-------------------------------------------------------------------------------
#Definition of variables specific to electron-positron calculation
ixcpositron 1 ! We are using the Boronski and Nieminen parametrization
#TC-DFT Self-consistent cycle
positron -10 # We perform automatic calculation of electrons and positron densities
# in the two-component DFT context (storing wavefunctions in memory)
posnstep 20 # Maximum number of electon and positron steps
postoldfe 1d-5 # We will repeat the electon and positron steps
# until the energy difference is lower than 1d-5
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0
natom 15
ntypat 1
typat 15*1
znucl 14
xred
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
! 0.625 0.625 0.625 ! We remove one Si atom
ixcpositron 1 # We are using the Boronski and Nieminen parametrization
! K-points and occupations
kptopt 1
ngkpt 2 2 2
nshiftk 1
shiftk 0.0 0.0 0.0
occopt 1
nband 36
posocc 1.0 # Occupation number for the positron
# (we have only one positron in the cell)
posocc 1.0 ! Occupation number for the positron (we have one positron in the cell).
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 500 ! We increase nstep
toldfe 1.d-8
#-------------------------------------------------------------------------------
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice, non primitive cell)
0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0 # Do not stop if cell is not primitive
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.LDA-PW-paw.abinit"
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Pseudodojo_paw_pw_standard/Si.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 15 # There are 15 atoms
typat 15*1 # They all are of type 1, that is, Silicon
xred # Location of the 15 atoms (one triplet per atom):
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
# 0.625 0.625 0.625 # We remove one Si atom
#Definition of bands and occupation numbers
nband 36 # Compute 36 bands
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
kptopt 1 # Automatic generation of k points, taking into account the symmetry
ngkpt 2 2 2 # This is a 2 2 2 grid based on the primitive vectors of the recip. space
nshiftk 1 # We do not shift the grid in order to have Gamma point in it
shiftk 0. 0. 0.
#Parameters for the SCF procedure
nstep 500 # Maximal number of SCF cycles. We increase it!
toldfe 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of energy
# differ by less than toldfe
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 0 # Do not print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -77,5 +100,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Third step of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Third step of the tutorial on electron-positron annihilation
#%% Positron lifetime calculation within PAW
#%% Si monovacancy, self-consistent scheme
#%%<END TEST_INFO>

155
tests/tutorial/Input/tpositron_4.abi
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@ -1,75 +1,104 @@
#################################################################
# Input file for the positron tutorial #
# Positron lifetime calculation within PAW #
# #
# Si monovacancy, relaxation effect #
#################################################################
# Input for Positron tutorial
# Fourth step of the tutorial on electron-positron annihilation
# Positron lifetime calculation within PAW
# Si monovacancy, relaxation effect
# Self-consistent positron lifetime calculation
#To perform a self-consistent electron-positron calculation, we need only one dataset
positron -10 ! We perform automatic calculation of electrons and positron densities in the two-component DFT context
postoldfe 1.0d-5 ! We will repeat the electron and positron steps until the energy difference is lower than 1.0d-5
posnstep 20 ! Maximum number of electon and positron steps
#-------------------------------------------------------------------------------
#Definition of variables specific to electron-positron calculation
ixcpositron 1 ! We are using the Boronski and Nieminen parametrization
optforces 1 optstress 0 ! We need to calculate forces to perform relaxation
#TC-DFT Self-consistent cycle
positron -10 # We perform automatic calculation of electrons and positron densities
# in the two-component DFT context (storing wavefunctions in memory)
posnstep 20 # Maximum number of electon and positron steps
postoldfe 1d-5 # We will repeat the electon and positron steps
# until the energy difference is lower than 1d-5
# We now include the effect of the atomic relaxation
ionmov 2
ntime 4 ! We will perform only 4 steps of relaxation, in reality more steps are required
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0
natom 15
ntypat 1
typat 15*1
znucl 14
xred
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
ixcpositron 1 # We are using the Boronski and Nieminen parametrization
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
! 0.625 0.625 0.625 ! We remove one Si atom
posocc 1.0 # Occupation number for the positron
# (we have only one positron in the cell)
! K-points and occupations
kptopt 1
ngkpt 2 2 2
nshiftk 1
shiftk 0.0 0.0 0.0
occopt 1
nband 36
#-------------------------------------------------------------------------------
#Definition of variables specific to atomic relaxation
posocc 1.0 ! Occupation number for the positron (we have one positron in the cell).
ionmov 2 # We now include the effect of the atomic relaxation
# (BFGS relaxation algorithm)
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 500 ! We increase nstep
toldfe 1.d-8
ntime 4 # We will perform only 4 steps of relaxation
# in reality more steps are required
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 1 # Forces computation done at each (electronic or positronic) SCF step
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.LDA-PW-paw.abinit"
#-------------------------------------------------------------------------------
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice, non primitive cell)
0.0 1.0 1.0
1.0 0.0 1.0
1.0 1.0 0.0
chkprim 0 # Do not stop if cell is not primitive
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Pseudodojo_paw_pw_standard/Si.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 15 # There are 15 atoms
typat 15*1 # They all are of type 1, that is, Silicon
xred # Location of the 15 atoms (one triplet per atom):
0.0 0.0 0.0
0.0 0.0 0.5
0.0 0.5 0.0
0.5 0.0 0.0
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
0.125 0.125 0.125
0.125 0.125 0.625
0.125 0.625 0.125
0.625 0.125 0.125
0.125 0.625 0.625
0.625 0.125 0.625
0.625 0.625 0.125
# 0.625 0.625 0.625 # We remove one Si atom
#Definition of bands and occupation numbers
nband 36 # Compute 36 bands
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
kptopt 1 # Automatic generation of k points, taking into account the symmetry
ngkpt 2 2 2 # This is a 2 2 2 grid based on the primitive vectors of the recip. space
nshiftk 1 # We do not shift the grid in order to have Gamma point in it
shiftk 0. 0. 0.
#Parameters for the SCF procedure
nstep 500 # Maximal number of SCF cycles. We increase it!
toldfe 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of energy
# differ by less than toldfe
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 0 # Do not print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -81,5 +110,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Fourth step of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Fourth step of the tutorial on electron-positron annihilation
#%% Positron lifetime calculation within PAW
#%% Si monovacancy, relaxation effect
#%%<END TEST_INFO>

147
tests/tutorial/Input/tpositron_5.abi
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@ -1,70 +1,103 @@
#################################################################
# Input file for the positron tutorial #
# Doppler spectrum calculation within PAW #
# #
# Si, 2 atoms in the box #
#################################################################
# Input for Positron tutorial
# Fifth step of the tutorial on electron-positron annihilation
# Doppler spectrum calculation within PAW
# Si, 2 atoms in the box
positron -10 ! Electron/positron GS calculation
! Automatic electron-positron loop has to be switched on in Doppler calculations
! to have both electron and positron wavefunctions in memory
#To perform a self-consistent electron-positron calculation, we need only one dataset
posnstep 2 ! We simulate a delocalized positron, so we only perform two steps of electon-positron calculations.
! It means that the electronic wavefunction is not affected by the positron.
posdoppler 1 ! Activation of Doppler broadening calculation
#-------------------------------------------------------------------------------
#Definition of variables specific to electron-positron calculation
ixcpositron 1 ! We are using the Boronski and Nieminen parametrization
#TC-DFT Self-consistent cycle
positron -10 # We perform automatic calculation of electrons and positron densities
# in the two-component DFT context (storing wavefunctions in memory)
# Automatic electron-positron loop has to be switched on in Doppler calculations
# to have both electron and positron wavefunctions in memory
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
posnstep 2 # Maximum number of electon and positron steps = 2
# We simulate a delocalized positron, so we only perform two steps
# of electon-positron calculations. It means that the electronic
# wavefunction is not affected by the positron.
posdoppler 1 # Activation of Doppler broadening calculation
natom 2
ntypat 1
typat 2*1
znucl 14
xred 0.0 0.0 0.0
0.25 0.25 0.25
ixcpositron 1 # We are using the Boronski and Nieminen parametrization
! K-points and occupations
! In Doppler calculation we need to have a uniform
! grid in the momentum space. Symmetries are not used,
! so the full grid needs to be specified.
posocc 1.0 # Occupation number for the positron
# (should be set <1 for bulk calculation with a small cell).
# Here the zero positron density limit is used,
# so results do not depend on posocc.
kptopt 0
istwfk *1
nkpt 8 ! This corresponds to a 2x2x2 grid, denser grids may be needed to get converged spectra
kpt
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
# Note about Brillouin zone sampling:
# In Doppler calculation we need to have a uniform k-point grid
# in the momentum space. Symmetries are not used,
# so the full grid needs to be specified.
occopt 1
nband 6
posocc 1.0 ! Occupation number for the positron (should be set <1 for bulk calculation with a small cell).
! Here the zero positron density limit is used, so results do not depend on posocc.
#-------------------------------------------------------------------------------
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 50 tolvrs 1.d-8
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice)
0.0 1/2 1/2
1/2 0.0 1/2
1/2 1/2 0.0
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Pseudodojo_paw_pw_standard/Si.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 2 # There are two atoms
typat 1 1 # They both are of type 1, that is, Silicon
xred # Location of the atoms:
0.0 0.0 0.0 # Triplet giving the reduced coordinates of atom 1
1/4 1/4 1/4 # Triplet giving the reduced coordinates of atom 2
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.LDA-PW-paw.abinit"
#Definition of bands and occupation numbers
nband 6 # Compute 6 bands
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
# In Doppler broadening calculation we need to have a uniform
# k-point grid in the momentum space. Symmetries are not used,
# so the full grid needs to be specified.
kptopt 0 # - Option for manual setting of k-points
istwfk *1 # - No time-reversal symmetry optimization
nkpt 8 # - Corresponds to a 2x2x2 grid, denser grids may be needed to get converged spectra
kpt # - K-point coordinates in reciprocal space:
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
#Parameters for the SCF procedure
nstep 50 # Maximal number of SCF cycles.
tolvrs 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential/density
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 0 # Do not print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -76,5 +109,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Fifth step of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Fifth step of the tutorial on electron-positron annihilation
#%% Doppler spectrum calculation within PAW
#%% Si, 2 atoms in the box
#%%<END TEST_INFO>

120
tests/tutorial/Input/tpositron_6.abi
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@ -1,58 +1,84 @@
#################################################################
# Input file for the positron tutorial #
# Positron lifetime calculation within PAW #
# (12 valence electrons) #
# Si, 2 atoms in the box #
#################################################################
# Input for Positron tutorial
# Sixth step (part 1) of the tutorial on electron-positron annihilation
# Positron lifetime calculation within PAW - 12 valence electrons
# Si, 2 atoms in the box
# Datasets definition
ndtset 2
# This input file is similar to tpositron_1.abi, except:
# - the number of bands, because of the additional 8 electrons states
positron1 0 ! Dataset 1 is a simple electronic GS calculation
#Define the different datasets
ndtset 2 # 2 datasets
positron2 1 ! Dataset 2 is a positronic GS calculation
getden2 1 ! in presence of the previous electronic density
kptopt2 0 ! Use only k=gamma point
#FIRST DATASET
positron1 0 # Dataset 1 is a simple electronic GS calculation
ixcpositron2 1 ! We are using the Boronski and Nieminen parametrization
#SECOND DATASET
positron2 1 # Dataset 2 is a positronic GS calculation
getden2 1 # in presence of the previous electronic density
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
kptopt2 0 # Use only k=gamma point
natom 2
ntypat 1
typat 2*1
znucl 14
xred 0.0 0.0 0.0
0.25 0.25 0.25
ixcpositron2 1 # We are using the Boronski and Nieminen parametrization
! K-points and occupations
kptopt 1
ngkpt 4 4 4
nshiftk 1
shiftk 0.0 0.0 0.0
occopt 1
nband 14
posocc2 1 ! Occupation number for the positron (should be set <1 for bulk calculation with a small cell).
! Here the zero positron density limit is used, so results do not depend on posocc.
posocc2 1 # Occupation number for the positron
# (should be set <1 for bulk calculation with a small cell).
# Here the zero positron density limit is used,
# so results do not depend on posocc.
! Convergence parameters
ecut 8. pawecutdg 15.
iscf 17
nstep 50 tolvrs 1.d-8
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#-------------------------------------------------------------------------------
#Definition of data common to all datasets
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.12el.LDA-PW-paw.abinit"
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice)
0.0 1/2 1/2
1/2 0.0 1/2
1/2 1/2 0.0
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Si_paw_pw_12el.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 2 # There are two atoms
typat 1 1 # They both are of type 1, that is, Silicon
xred # Location of the atoms:
0.0 0.0 0.0 # Triplet giving the reduced coordinates of atom 1
1/4 1/4 1/4 # Triplet giving the reduced coordinates of atom 2
#Definition of bands and occupation numbers
nband 14 # Compute 14 bands (we have semicore states)
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 8. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
kptopt 1 # Automatic generation of k points, taking into account the symmetry
ngkpt 4 4 4 # This is a 4x4x4 grid based on the primitive vectors of the recip. space
nshiftk 1 # We do not shift the grid in order to have Gamma point in it
shiftk 0. 0. 0.
#Parameters for the SCF procedure
nstep 50 # Maximal number of SCF cycles
tolvrs 1.0d-8 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 1 # Print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -64,5 +90,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Sixth step (part 1) of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Sixth step (part 1) of the tutorial on electron-positron annihilation
#%% Positron lifetime calculation within PAW - 12 valence electrons
#%% Si, 2 atoms in the box
#%%<END TEST_INFO>

158
tests/tutorial/Input/tpositron_7.abi
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@ -1,72 +1,112 @@
#################################################################
# Input file for the positron tutorial #
# Doppler spectrum calculation within PAW #
# #
# Si, 2 atoms in the box #
#################################################################
# Input for Positron tutorial
# Sixth step (part 2) of the tutorial on electron-positron annihilation
# Doppler spectrum calculation within PAW - 12 valence electrons
# Si, 2 atoms in the box
positron -10 ! Electron/positron GS calculation
! Automatic electron-positron loop has to be switched on in Doppler calculations
! to have both electron and positron wavefunctions in memory
# This input file is similar to tpositron_5.abi, except:
# - the number of bands, because of the additional 8 electrons states
# - the plane wave cut-off energy because additional PAW basis functions are localized
posnstep 2 ! We simulate a delocalized positron, so we only perform two steps of electon-positron calculations.
! It means that the electronic wavefunction is not affected by the positron.
posdoppler 1 ! Activation of Doppler broadening calculation
#-------------------------------------------------------------------------------
#Definition of variables specific to electron-positron calculation
ixcpositron 1 ! We are using the Boronski and Nieminen parametrization
#TC-DFT Self-consistent cycle
positron -10 # We perform automatic calculation of electrons and positron densities
# in the two-component DFT context (storing wavefunctions in memory)
# Automatic electron-positron loop has to be switched on in Doppler calculations
# to have both electron and positron wavefunctions in memory
# Common input parameters
! Unit cell
acell 3*5.43 angstrom
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
posnstep 2 # Maximum number of electon and positron steps = 2
# We simulate a delocalized positron, so we only perform two steps
# of electon-positron calculations. It means that the electronic
# wavefunction is not affected by the positron.
posdoppler 1 # Activation of Doppler broadening calculation
natom 2
ntypat 1
typat 2*1
znucl 14
xred 0.0 0.0 0.0
0.25 0.25 0.25
ixcpositron 1 # We are using the Boronski and Nieminen parametrization
! K-points and occupations
! In Doppler calculation we need to have a uniform
! grid in the momentum space. Symmetries are not used,
! so the full grid needs to be specified.
posocc 1.0 # Occupation number for the positron
# (should be set <1 for bulk calculation with a small cell).
# Here the zero positron density limit is used,
# so results do not depend on posocc.
kptopt 0
istwfk *1
nkpt 8 ! This corresponds to a 2x2x2 grid, denser grids may be needed to get converged spectra
kpt
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
# Note about Brillouin zone sampling:
# In Doppler calculation we need to have a uniform k-point grid
# in the momentum space. Symmetries are not used,
# so the full grid needs to be specified.
# so results do not depend on posocc.
occopt 1
nband 16
posocc 1.0 ! Occupation number for the positron (should be set <1 for bulk calculation with a small cell).
! Here the zero positron density limit is used, so results do not depend on posocc.
#-------------------------------------------------------------------------------
#Definition of data common to all datasets
! Convergence parameters
ecut 12. pawecutdg 15.
iscf 17
nstep 100 tolvrs 1.d-10
nline 8 nnsclo 2 ! This is to help the convergency
nbdbuf 16 ! This is to make the test portable (don't use this usually)
#Definition of the unit cell
acell 3*5.43 angstrom # Lengths of the primitive vectors (exp. param. in angstrom)
rprim # 3 orthogonal primitive vectors (FCC lattice)
0.0 1/2 1/2
1/2 0.0 1/2
1/2 1/2 0.0
! Miscelaneous
prtwf 0 prteig 0 ! To save disk space
optforces 0 optstress 0 ! Not relevant here
#Definition of the atom types and pseudopotentials
ntypat 1 # There is only one type of atom
znucl 14 # Atomic number of the possible type(s) of atom. Here silicon.
pp_dirpath "$ABI_PSPDIR" # Path to the directory were
# pseudopotentials for tests are stored
pseudos "Si_paw_pw_12el.xml" # Name and location of the pseudopotential
#Definition of the atoms
natom 2 # There are two atoms
typat 1 1 # They both are of type 1, that is, Silicon
xred # Location of the atoms:
0.0 0.0 0.0 # Triplet giving the reduced coordinates of atom 1
1/4 1/4 1/4 # Triplet giving the reduced coordinates of atom 2
pp_dirpath "$ABI_PSPDIR"
pseudos "Si.12el.LDA-PW-paw.abinit"
#Definition of bands and occupation numbers
nband 16 # Compute 16 bands (we have semicore states)
occopt 1 # Automatic generation of occupation numbers, as a semiconductor
#Numerical parameters of the calculation : planewave basis set and k point grid
ecut 12. # Maximal plane-wave kinetic energy cut-off, in Hartree
pawecutdg 15. # Max. plane-wave kinetic energy cut-off, in Ha, for the PAW double grid
# In Doppler broadening calculation we need to have a uniform
# k-point grid in the momentum space. Symmetries are not used,
# so the full grid needs to be specified.
kptopt 0 # - Option for manual setting of k-points
istwfk *1 # - No time-reversal symmetry optimization
nkpt 8 # - Corresponds to a 2x2x2 grid, denser grids may be needed to get converged spectra
kpt # - K-point coordinates in reciprocal space:
0 0 0
0 0 0.5
0 0.5 0
0.5 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.5 0.5 0.5
#Parameters for the SCF procedure
nstep 100 # Maximal number of SCF cycles
tolvrs 1.0d-10 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of potential residual
# differ by less than tolvrs
# We need additional parameters to imporve the convergency:
nline 8 # - increase the number of iterations of the minimization algorithm
nnsclo 2 # - perform 2 non-self-consistent loop per SCF cycle
nbdbuf 16 # This is to make the test portable (don't use this usually)
#Miscelaneous parameters
prtwf 0 # Do not print wavefunctions
prtden 1 # Print density (electronic and/or positronic)
prteig 0 # Do not print eigenvalues
optforces 0 # Forces computation is not relevant here
optstress 0 # Stress tensor computation is not relevant here
##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
@ -78,5 +118,9 @@
#%% [extra_info]
#%% authors = J. Wiktor
#%% keywords = POSITRON,PAW
#%% description = Sixth step (part 2) of the tutorial on electron-positron annihilation
#%% description =
#%% Input for Positron tutorial
#%% Sixth step (part 2) of the tutorial on electron-positron annihilation
#%% Doppler spectrum calculation within PAW - 12 valence electrons
#%% Si, 2 atoms in the box
#%%<END TEST_INFO>

6
tests/tutorial/Input/tpositron_x.files
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@ -1,6 +0,0 @@
tpositron_1.in
tpositron_1.out
tpositron_1i
tpositron_1o
tpositron_1tmp
../../../Psps_for_tests/Si.LDA-PW-paw.abinit