ABINIT Discussion Forums

Dear ABINIT friends, For the people who like to work with python and ASE, the following script will convert an ABINIT NetCDF History file into an ASE trajectory file: <snip> #! /Users/willem/anaconda3/bin/python3.7 ############################################################################### # # #...

Dear ABINIT friends, For the people who like to work with python. The same script as above, but now in python code: <snip> #! /Users/willem/anaconda3/bin/python3.7 ############################################################################### # # # a quick hack to extract Cartesian atom positions f...

Dear ABINIT friends, It is relatively easy to extract the atom positions of the images of the STRING calculation, stored in the HIST.nc file. I hope you know a bit of bash scripting: <snip> #! /bin/sh ############################################################################### # # # a quick hack ...

Dear ABINIT friends, To answer my questions partially, it is possible to dump the content of the NetCDF file (HIST.nc) into ASCII. ncdump is your friend: m I don't know how to get ncdump. It was installed on my macOS: /Users/willem/anaconda3/bin/ncdump So it came with some package within anaconda. A...

Dear ABINIT friends, I'm currently performing STRING calculations. There is documentation to this topic within the ABINIT documentation set: m However, after reading the above, I'm still left behind with questions: 1) How do I restart a STRING calculation? 2) How do I ensure that the previous WFK fi...

The unreasonable energy values seem to be due to the PAW data set.

Gregory is currently working on/testing it.

I hope to continue this soon.

Dear ABINIT friends, I'm running a String optimisation with 7 images ( 0 5*1 0). The initial and final state were previously optimised. I had to restart the calculation. Setting: restartxf -1 in the input file makes the pdo_HIST.nc being read during startup. The following can be found in the log fil...

Dear Marc, Gregory and ABINIT friends, At the ABINIT 2019 school, I got the advice to converge the TOLerance on WaveFunction squared Residual to less than 1.00E-20 for the SCF calculation. So I tried this as well for the SCF calculation. The following gives the convergence of the SCF calculation: it...

Dear Gregory and ABINIT friends, Finally it seems to work. There was a bug in ABINIT concerning the format of the PAW data sets. The bug already seemed to be corrected. Version 8.8.4 of ABINIT did not have the correction. So the xml format of the PAW data sets needed to be converted to abinit format...

Dear ABINIT friends, There is a nice tutorial about a STRING calculation m Unfortunately, the tutorial does not mention how to visualise the images and even better the evolution of the ``string of images`` during the optimisation. This is a big deficit to my opinion. If I run a STRING calculation, s...

Dear ABINIT friends, During a STRING calculation and right after STRING METHOD - TIME STEP 3, a segmentation fault occurred. See below for snippet. The endings of the output and log files look reasonable. See below for output. From the log file I conclude that the error occurred while or after writi...

Dear ryne60 and ABINIT friends,

Please don't forget to report on your findings. It is of interest of all ABINIT friends, if we can close the thread in some conclusive way.

Dear Eric and ABINIT friends, I like your idea with setting pawovlp to a large value at the start of the investigations and the decrease the value to zero at the end. At least close to zero, when the system and parameters are used to calculate physical/chemical properties. It makes sense and fits in...

Dear Eric and ABINIT friends, I have tried the suggestions/additions/corrections by Eric, but unfortunately without success. $ tail -f pd.txt.save dfpt_looppert : total number of electrons, from k and k+q fully or partially occupied states are 3.720000E+02 and 3.720000E+02. Initialisation of the fir...

Dear Eric and ABINIT friends, After reading your reply once more, I realised that I already tried to run the calculation with an increased pawovlp value. I set it to 9 and got the overlap error message: overlap ratio of 13.12 % So the error message was logical this time. I had to stop the research w...

Dear ryne60 and ABINIT friends,

Is ISMEAR = -5 comparable with occopt 7?

Dear Eric and ABINIT friends, setting nline = 6 did not improve the outcome. Energy values remain unrealistically huge: -ETOT 1 -723764921.44809 -7.237E+08 7.763E+03 2.282E+20 ETOT 2 -1.07565194714471E+14 -1.076E+14 1.053E+09 3.463E+25 ETOT 3 -9911228406409.3 9.765E+13 6.786E+08 3.775E+24 ETOT 4 -10...

Hello ryne60, onion2440 and ABINIT friends, The point is not the values of the parameters. The point is the comparison with VASP calculation. If the VASP input is equivalent to the ABINIT input, then the question remains why calculation speed of VASP and ABINIT is so different. If I understand you c...

Dear ABINIT friends, Once more I have an issue with pawovlp. See the output of `grep pawovlp pd.in` and `tail -n25 pd.log` below: $ grep pawovlp pd.in pawovlp 6 $ tail -n25 pd.log --- !ERROR src_file: m_paw_tools.F90 src_line: 211 mpi_rank: 0 message: | PAW COMPENSATION DENSITIES ARE OVERLAPPING !!!...

Dear Eric and ABINIT friends, A renewed restart of the STRING calculation showed that restartxf flag is not the only parameter to consider. Once more, all files of the previous run were present. I did not change anything, before I resubmitted the job. After the job was started, I got the following i...

Dear Ryne60 and ABINIT friends, If you state that the calculation is slow, then please specify what you mean with slow. Is it the convergence speed? Or do you need approx. the same amount of cycles, but each cycle is taken more time? Or something else? In my case, the convergence speed of ABINIT was...

Dear Eric and ABINIT friends, It is not only strange, it does not make sense. Since even the default value of pawovlp = 5, which enables an overlap of at least 5%, was not passed. So even if the code would neglect the input, then the default value should be applicable. Though I already reported an i...

Dear Eric and ABINIT friends, Please keep in mind that I did not change other parameters than ``rfphon 1`` from ground state calculation (ion relaxation) to phonon response function calculation. The total energies in the former case seem to be reasonable. This is in contrast to the latter case, wher...

Dear ABINIT friends, The STRING method calculation could proceed into a new TIME STEP. See output of $tailf pd.txt > <snip> .... ------------------------------------------------------------ STRING METHOD: Average[Abs(Etotal(t)-Etotal(t-dt))]= 8.062E-02 Hartree Moving images of the cell... ==========...

O.GGA_PBE-JTH.xml.in I got the phonon response function calculation running. However the calculated energies are abnormal: $ tailf pd.txt ETOT 13 -1.10894776896575E+18 -8.517E+17 1.273E+13 3.928E+29 ETOT 14 -1.79594291525765E+17 9.294E+17 4.354E+12 9.097E+28 ETOT 15 -1.34645008754373E+17 4.495E+16 ...