# Second (basic) tutorial¶

## The H2 molecule, with convergence studies.¶

This tutorial aims at showing how to get converged values for the following physical properties:

• the bond length
• the atomisation energy

You will learn about the numerical quality of the calculations, then make convergence studies with respect to the number of planewaves and the size of the supercell, and finally consider the effect of the XC functional. The problems related to the use of different pseudopotential are not examined. You will also finish to read the abinit help file.

This tutorial should take about 1 hour.

Note

Supposing you made your own install 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.

To execute the tutorials, create a working directory (Work*) and copy there the input files and the files file of the lesson. This will be explicitly mentioned in the first lessons, that will tell you more about the files file (see also section 1.1). The files file ending with _x (e.g. tbase1_x.files) must be edited every time you start to use a new input file.

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, see the topic on parallelism.

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_the_absolute_path_to_the_abinit_top_level_dir
export PATH=$ABI_HOME/src/98_main/:$PATH
export ABI_TESTS=$ABI_HOME/tests/ export ABI_PSPDIR=$ABI_TESTS/Psps_for_tests/  # Pseudopotentials used in examples.


Examples in this tutorial use these shell variables: copy and paste the code snippets into the terminal (remember to set ABI_HOME first!). 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.

## Summary of the previous tutorial¶

We studied the H$_2$ molecule in a big box. We used 10 Ha as cut-off energy, a 10x10x10 Bohr$^3$ supercell, the local-density approximation (as well as the local-spin-density approximation) in the Teter parametrization (ixc = 1, the default), and a pseudopotential from the Goedecker-Hutter-Teter table.

At this stage, we compared our results:

• bond length: 1.522 Bohr
• atomisation energy at that bond length: 0.1656 Ha = 4.506 eV

with the experimental data (as well as theoretical data using a much more accurate technique than DFT)

• bond length: 1.401 Bohr
• atomisation energy: 4.747 eV

The bond length is awful (nearly 10% off), and the atomisation energy is a bit too low, 5% off.

## 2 The convergence in ecut (I)¶

2.1.a Computing the bond length and corresponding atomisation energy in one run.

Before beginning, you might consider to work in a different subdirectory as for tutorial 1. Why not Work2?

Because we will compute many times the bond length and atomisation energy, it is worth to make a single input file that will do all the associated operations. You should try to use 2 datasets (try to combine $ABI_TESTS/tutorial/Input/tbase1_3.in with tbase1_5.in). Do not try to have the same position of the H atom as one of the H$_2$ atoms in the optimized geometry. cd$ABI_TESTS/tutorial/Input
mkdir Work2
cd Work2
cp ../tbase2_x.files .   # You will need to edit this file.
cp ../tbase2_1.in .


The input file tbase2_1.in is an example of file that will do the job,

while tbase2_1.out is an example of output file:

You might use $ABI_TESTS/tutorial/Input/tbase2_x.files as files file (do not forget to modify it, like in tutorial 1, although it does not differ from tbase1_x.files. Execute the code with: abinit < tbase2_x.files > log 2> err &  The run should take less than one minute. You should obtain the values:  etotal1 -1.1058360644E+00 etotal2 -4.7010531489E-01  and  xcart1 -7.6091015760E-01 0.0000000000E+00 0.0000000000E+00 7.6091015760E-01 0.0000000000E+00 0.0000000000E+00  These are similar to those determined in tutorial 1, although they have been obtained in one run. You can also check that the residual forces are lower than 5.0d-4. Convergence issues are discussed in section 7 of the abinit help file. You should read it. By the way, you have read many parts of the abinit help file! You are missing the sections 2, 5, 7. You are also missing the description of many input variables. We suggest that you finish reading entirely the abinit help file now, while the knowledge of the input variables will come in the long run. 2.1.b Many convergence parameters have already been identified. We will focus only on ecut and acell. This is because • the convergence of the SCF cycle and geometry determination are well under control thanks to toldfe, toldff and tolmxf (this might not be the case for other physical properties) • there is no k point convergence study to be done for an isolated system in a big box: no additional information is gained by adding a k-point beyond one • the boxcut value is automatically chosen larger than 2 by ABINIT, see the determination of the input variable ngfft by preprocessing • we are using ionmov = 2 for the determination of the geometry. ## 3 The convergence in ecut (II)¶ For the check of convergence with respect to ecut, you have the choice between doing different runs of the tbase2_1.in file with different values of ecut, or doing a double loop of datasets, as proposed in$ABI_TESTS/tutorial/Input/tbase2_2.in. The values of ecut have been chosen between 10 Ha and 35 Ha, by step of 5 Ha. If you want to make a double loop, you might benefit of reading again the double-loop section of the abinit_help file.

2.2.a You have likely seen a big increase of the CPU time needed to do the calculation. You should also look at the increase of the memory needed to do the calculation (go back to the beginning of the output file). The output data are as follows:

    etotal11 -1.1058360644E+00
etotal12 -4.7010531489E-01
etotal21 -1.1218716100E+00
etotal22 -4.7529731401E-01
etotal31 -1.1291943792E+00
etotal32 -4.7773586424E-01
etotal41 -1.1326879404E+00
etotal42 -4.7899908214E-01
etotal51 -1.1346739190E+00
etotal52 -4.7972721653E-01
etotal61 -1.1359660026E+00
etotal62 -4.8022016459E-01

xcart11 -7.6091015760E-01  0.0000000000E+00  0.0000000000E+00
7.6091015760E-01  0.0000000000E+00  0.0000000000E+00
xcart12  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart21 -7.5104912643E-01  0.0000000000E+00  0.0000000000E+00
7.5104912643E-01  0.0000000000E+00  0.0000000000E+00
xcart22  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart31 -7.3977108831E-01  0.0000000000E+00  0.0000000000E+00
7.3977108831E-01  0.0000000000E+00  0.0000000000E+00
xcart32  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart41 -7.3304273322E-01  0.0000000000E+00  0.0000000000E+00
7.3304273322E-01  0.0000000000E+00  0.0000000000E+00
xcart42  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart51 -7.3001570260E-01  0.0000000000E+00  0.0000000000E+00
7.3001570260E-01  0.0000000000E+00  0.0000000000E+00
xcart52  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart61 -7.2955902118E-01  0.0000000000E+00  0.0000000000E+00
7.2955902118E-01  0.0000000000E+00  0.0000000000E+00
xcart62  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00


The corresponding atomisation energies and interatomic distances are:

ecut (Ha) atomisation energy (Ha) interatomic distance (Bohr)
10 .1656 1.522
15 .1713 1.502
20 .1737 1.480
25 .1747 1.466
30 .1753 1.460
35 .1756 1.459

In order to obtain 0.2% relative accuracy on the bond length or atomisation energy, one should use a kinetic cut-off energy of 30 Ha. We will keep in mind this value for the final run.

## 4 The convergence in acell¶

The same technique as for ecut should be now used for the convergence in acell. We will explore acell starting from 8 8 8 to 18 18 18, by step of 2 2 2. We keep ecut 10 for this study. Indeed, it is a rather general rule that there is little cross-influence between the convergence of ecut and the convergence of acell.

The file $ABI_TESTS/tutorial/Input/tbase2_3.in can be used as an example. The output results in$ABI_TESTS/tutorial/Refs/tbase2_3.out are as follows:

    etotal11   -1.1188124709E+00
etotal12   -4.8074164402E-01
etotal21   -1.1058360838E+00
etotal22   -4.7010531489E-01
etotal31   -1.1039109527E+00
etotal32   -4.6767804802E-01
etotal41   -1.1039012868E+00
etotal42   -4.6743724199E-01
etotal51   -1.1041439411E+00
etotal52   -4.6735895176E-01
etotal61   -1.1042058281E+00
etotal62   -4.6736729718E-01

xcart11   -7.8330751426E-01  0.0000000000E+00  0.0000000000E+00
7.8330751426E-01  0.0000000000E+00  0.0000000000E+00
xcart12    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart21   -7.6024281092E-01  0.0000000000E+00  0.0000000000E+00
7.6024281092E-01  0.0000000000E+00  0.0000000000E+00
xcart22    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart31   -7.5428234893E-01  0.0000000000E+00  0.0000000000E+00
7.5428234893E-01  0.0000000000E+00  0.0000000000E+00
xcart32    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart41   -7.5446921004E-01  0.0000000000E+00  0.0000000000E+00
7.5446921004E-01  0.0000000000E+00  0.0000000000E+00
xcart42    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart51   -7.5384974520E-01  0.0000000000E+00  0.0000000000E+00
7.5384974520E-01  0.0000000000E+00  0.0000000000E+00
xcart52    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
xcart61   -7.5373336127E-01  0.0000000000E+00  0.0000000000E+00
7.5373336127E-01  0.0000000000E+00  0.0000000000E+00
xcart62    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00


The corresponding atomisation energies and interatomic distances are:

acell (Bohr) atomisation energy (Ha) interatomic distance (Bohr)
8 .1574 1.568
10 .1656 1.522
12 .1686 1.509
14 .1691 1.510
16 .1694 1.508
18 .1695 1.508

In order to reach 0.2% convergence on the interatomic distance, one needs acell 12 12 12. The atomisation energy needs acell 14 14 14 to be converged at that level. At 12 12 12, the difference is .0009 Ha = 0.024 eV, which is sufficiently small for practical purposes. We will use acell 12 12 12 for the final run.

For most solids the size of the unit cell will be smaller than that. We are treating a lot of vacuum in this supercell! So, the H$_2$ study, with this pseudopotential, turns out to be not really easy. Of course, the number of states to be treated is minimal! This allows to have reasonable CPU time still.

## 5 The final calculation in Local (Spin) Density Approximation¶

We now use the correct values of both ecut and acell. Well, you should modify the tbase2_3.in file to make a calculation with acell 12 12 12 and ecut 30. You can still use the double loop feature with udtset 1 2 (which reduces to a single loop), to minimize the modifications to the file.

The file $ABI_TESTS/tutorial/Input/tbase2_4.in can be taken as an example of input file: while$ABI_TESTS/tutorial/Refs/tbase2_4.out is as an example of output file:

Since we are doing the calculation at a single (ecut, acell) pair, the total CPU time is not as much as for the previous determinations of optimal values through series calculations. However, the memory needs have still increased a bit.

The output data are:

    etotal11 -1.1329369190E+00
etotal12 -4.7765320721E-01

xcart11 -7.2594741339E-01  0.0000000000E+00  0.0000000000E+00
7.2594741339E-01  0.0000000000E+00  0.0000000000E+00
xcart12  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00

• The corresponding atomisation energy is 0.1776 Ha = 4.833 eV
• The interatomic distance is 1.452 Bohr.
• These are our final data for the local (spin) density approximation.

We have used ixc = 1. Other expressions for the local (spin) density approximation [2, 3 … 7] are possible. The values 1, 2, 3 and 7 should give about the same results, since they all start from the XC energy of the homogeneous electron gas, as determined by Quantum Monte Carlo calculations. Other possibilities (ixc = 4, 5, 6) are older local density functionals, that could not rely on these data.

## 6 The use of the Generalized Gradient Approximation¶

We will use the Perdew-Burke-Ernzerhof functional proposed in [Perdew1996]

In principle, for GGA, one should use another pseudopotential than for LDA. However, for the special case of Hydrogen, and in general pseudopotentials with a very small core (including only the 1s orbital), pseudopotentials issued from the LDA and from the GGA are very similar. So, we will not change our pseudopotential. This will save us lot of time, as we should not redo an ecut convergence test

Important

ecut is often characteristic of the pseudopotentials that are used in a calculation.

Independently of the pseudopotential, an acell convergence test should not be done again, since the vacuum is treated similarly in LDA or GGA.

So, our final values within GGA will be easily obtained by setting ixc to 11 in tbase2_4.in.

    etotal11 -1.1621428376E+00
etotal12 -4.9869631917E-01

xcart11 -7.1190611804E-01  0.0000000000E+00  0.0000000000E+00
7.1190611804E-01  0.0000000000E+00  0.0000000000E+00
xcart12  0.0000000000E+00  0.0000000000E+00  0.0000000000E+00

• The corresponding atomisation energy is 0.1648 Ha = 4.483 eV
• The interatomic distance is 1.424 Bohr.
• These are our final data for the generalized gradient approximation.

Once more, here are the experimental data:

• bond length: 1.401 Bohr
• atomisation energy: 4.747 eV

In GGA, we are within 2% of the experimental bond length, but 5% of the experimental atomisation energy. In LDA, we were within 4% of the experimental bond length, and within 2% of the experimental atomisation energy.

Important

Do not forget that the typical accuracy of LDA and GGA varies with the class of materials studied.