Davide, a follow up question. Will that not affect the resulting thermodynamics? I mean translational or rotational (I can never remember) thermodynamics is dependent on symmetry and I am calculating thermodynamic quantities here

Hi,

job314 said in SCANMODE io error Read_int_1d:

So it turns out having fort.13 and fort.20 is not optional for restart.

Yes, the lack of these two files was the origin of the I/O error.

job314 said in SCANMODE io error Read_int_1d:

PS. I would also like to ask developers to allow uploading compressed files to this forum

Now also .zip, .tar, .tgz, .tar.gz files can be uploaded.

Cheers,

Dear Jonas,

I tried using pymatgen to extract the point-symmetry information from your .xyz file (see the Python script below):

from pymatgen.core import Molecule from pymatgen.symmetry import analyzer bigstructure = Molecule.from_file("yourfile.xyz") PGstructure = analyzer.PointGroupAnalyzer(bigstructure) sym_mol = PGstructure.get_equivalent_atoms() print(sym_mol["eq_sets"])

This returns a Python data structure containing the symmetry-irreducible sets of atoms (only 6 for this system, which is indeed of Ih point group!).
When preparing the CRYSTAL input, be careful with the orientation of your asymmetric unit. In my case, for example, I had to change the sign of the x and y coordinates to make the symmetry consistent with CRYSTAL’s conventions.
Icosahedral point groups are available in CRYSTAL (Ih is point group number 47 in CRYSTAL), so the input fort this molecular cage reads:

Symm. structure MOLECULE 47 6 8 2.605032231 -11.914271806 11.762689798 6 4.344538598 15.664236912 4.366798884 6 3.427479683 14.428996321 8.326818862 6 -8.906580884 1.370529673 14.411150640 1 2.632960331 14.962480562 7.832453804 5 -8.776255231 -2.916256114 14.200279302 COORPRT TESTGEOM END

aerba Christmas is already in the air indeed!

Either way, seems you got your geometry for further optimization 🙂
Cheers,
A

Hi Giu, it worked!

wonderful, thank you both

Hi Jonas,

Would you mind adding the INPUT file as well, for easier checks?

It generally doesn't look too bad, I would wait until the calculations finishes and see how the results look like. There is nothing obviously "wrong", but you can always try tightening the convergence criteria. See earlier post for a great overview of options (especially if you notice in the end that you have negative frequencies appearing!):
Earlier post on "Imaginary frequencies", see comment by Prof. Erba
I personally wouldn't run a geometry optimization together with a frequency calculation, I would split them in too, but I guess that is a matter of taste as the code can handle it : )

Cheers,
Aleks

Dear Jonas,

A good option just for visualization is using the CRYSPLOT webpage, which includes a tool for this based on JSMol and only requires your output file. Another option would be to use JMol, which requires a local installation of Java. Using JSMol locally is not an easy task, as its developed for its usage on web servers. If you really need to do so, you can find some guidance in the the following sites (it will depend on which browser you want to use, and probably also on your OS):

Recent thread on usage of JSMol locally JSMol Wiki post

Hope this helps.

Marcos

Dear Jonas,

first of all, 450 atoms is impressive indeed!
Now moving on to a few comments/thoughts that might be of use to you.

i) From your input file, it appears you still have a few symmetry operators in your simulation cell. Worth checking whether/if that applies to the atoms in the Fe-centred octahedra as that might force a particular solution to the electronic configurations.

ii) Given that your octahedra are not aligned with any particular crystallographic axis in your system, it is not always straightforward to extract the (d-)orbital occupations. You can have a look at the ROTREF keyword in the manual by which you can rotate the eigenvectors in the properties calculation to orient the frame along a principal axis.

iii) In Scenario 1 you are right - you removed 1 H atom, from which indeed the symmetry of the octahedron has been reduced/broken. You could test the case without "neutralization", to see whether the extra electron would stay on the site or delocalize...formation energies might be a good guide...?

iv) Scenario 2 is a bit more complicated. Given that you removed a whole NH4+ tetrahedron, I would expect significant structural distortions occurring in the surrounding of the defect. From there, a conducting state might be not so unrealistic - did you optimize the atomic positions and/or cell parameters following the inclusion of that defect? If so, could be worth seeing where the metallic states originate from (e.g., in the DOS or a charge density difference plot would be sufficient...don't forget SMEAR). The question is where is the extra electron from the anticipated Fe3+ ending if you remove the whole tetrahedron?

v) Finally, I guess it really depends on what you see experimentally and what would be the most representative simulation cell matching the measurements to be able to extract meaningful data for the oxidation state. What could be potentially useful is to take simple bulk structures for which you know the oxidation state of Fe (e.g., Fe2O3, Fe3O4, ...), analyse the corresponding charge densities (e.g., Mulliken) and have a reference state for comparing the charge on the Fe-ion in your Struvite structure.

Hope any of this is useful.

Cheers,
Aleks

job314 said in No space left on device:

those are huge HPC nodes… they can’t be possibly out of disk…

On our cluster, although the total disk space is huge, there are limited disk quotas for each user. Maybe it is the same there for you?

job314 said in No space left on device:

will it affect my convergence or calculation speed?

Possibly, but not much I think.

Alessandro, the setback is temporary. What I really appreciate is that you gave CRYSTAL more life via user support than it ever had. I am very grateful for it

Hi,

In CRYSTAL, the most general syntax to specify exchange-correlation (xc) functionals is, within the DFT input block through the EXCHANGE and CORRELAT keywords as:

DFT EXCHANGE label of exchange functional (e.g. VBH, BECKE, PBE, ...) CORRELAT label of correlation functional (e.g. VWN, LYP, PBE, ...) ENDDFT

For certain standard combinations of exchange and correlation functionals, we have implemented single keywords. For instance:

DFT BLYP ENDDFT

is equivalent to

DFT EXCHANGE BECKE CORRELAT LYP ENDDFT

Another example (here the "XC" letters are appended at the end of the name to reflect that the functional is used for both the exchange and correlation part):

DFT PBESOLXC ENDDFT

is equivalent to

DFT EXCHANGE PBESOL CORRELAT PBESOL ENDDFT

For PBE, there are three equivalent ways to define it in CRYSTAL:

DFT PBEXC ENDDFT

or

DFT PBE ENDDFT

or

DFT EXCHANGE PBE CORRELAT PBE ENDDFT

There isn't a general rule, I'm afraid. This syntax aspects are discussed at page 134 of CRYSTAL23 User's Manual.

Hope this clarifies things a little,

I tried rerunning it with fewer nodes - thought it is some parallel issue. A problem again

ANGULAR INTEGRATION - INTERVALS (ACCURACY LEVEL [N. POINTS] UPPER LIMIT):
1( 4[ 86] 0.2) 2( 8[ 194] 0.5) 3( 12[ 350] 0.9) 4( 16[ 974] 3.5)
5( 12[ 350]9999.0)
CYCLE 0 ALPHA 227.814788 EPSILON 1.894274 DELTA 2.2781E+02
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 1902.88 TCPU 1885.42
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 1904.27 TCPU 1886.79
DIIS TEST: 0.61205E+01 AT CPHF CYCLE 1 - MIX 60 %
CYCLE 1 ALPHA 257.133404 EPSILON 2.009363 DELTA 2.9319E+01
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2002.77 TCPU 1984.78
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2004.16 TCPU 1986.16
DIIS TEST: 0.71887E+01 AT CPHF CYCLE 2 - DIIS ACTIVE - HISTORY: 2 CYCLES
CYCLE 2 ALPHA 268.265588 EPSILON 2.053062 DELTA 1.1132E+01
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2102.04 TCPU 2083.54
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2103.42 TCPU 2084.92
DIIS TEST: 0.36370E+00 AT CPHF CYCLE 3 - DIIS ACTIVE - HISTORY: 3 CYCLES
CYCLE 3 ALPHA 276.769385 EPSILON 2.086443 DELTA 8.5038E+00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2202.03 TCPU 2183.04
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2203.42 TCPU 2184.42
DIIS TEST: 0.54051E-01 AT CPHF CYCLE 4 - DIIS ACTIVE - HISTORY: 4 CYCLES
CYCLE 4 ALPHA 278.095061 EPSILON 2.091647 DELTA 1.3257E+00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2302.12 TCPU 2282.64
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2303.51 TCPU 2284.02
DIIS TEST: 0.85023E-02 AT CPHF CYCLE 5 - DIIS ACTIVE - HISTORY: 5 CYCLES
CYCLE 5 ALPHA 278.435921 EPSILON 2.092985 DELTA 3.4086E-01
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2402.16 TCPU 2382.20
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2403.54 TCPU 2383.57
DIIS TEST: 0.38480E-03 AT CPHF CYCLE 6 - DIIS ACTIVE - HISTORY: 6 CYCLES
CYCLE 6 ALPHA 278.461661 EPSILON 2.093086 DELTA 2.5739E-02
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2502.06 TCPU 2481.62
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2503.45 TCPU 2482.99
DIIS TEST: 0.44991E-03 AT CPHF CYCLE 7 - DIIS ACTIVE - HISTORY: 7 CYCLES
CYCLE 7 ALPHA 278.460154 EPSILON 2.093080 DELTA -1.5071E-03
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2601.70 TCPU 2580.74
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2603.08 TCPU 2582.11
DIIS TEST: 0.36243E-03 AT CPHF CYCLE 8 - DIIS ACTIVE - HISTORY: 8 CYCLES
CYCLE 8 ALPHA 278.473843 EPSILON 2.093134 DELTA 1.3689E-02
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2701.77 TCPU 2680.26
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2703.15 TCPU 2681.62
DIIS TEST: 0.85073E-04 AT CPHF CYCLE 9 - DIIS ACTIVE - HISTORY: 9 CYCLES
CYCLE 9 ALPHA 278.474328 EPSILON 2.093136 DELTA 4.8487E-04
forrtl: severe (256): unformatted I/O to unit open for formatted transfers, unit 85, file /dev/null
Image PC Routine Line Source
Pcrystal 0000000007374206 Unknown Unknown Unknown
Pcrystal 0000000001BA179E Unknown Unknown Unknown
Pcrystal 0000000000A8038B Unknown Unknown Unknown
Pcrystal 0000000000A63D97 Unknown Unknown Unknown
Pcrystal 0000000000D4DAD1 Unknown Unknown Unknown
Pcrystal 000000000074B942 Unknown Unknown Unknown
Pcrystal 000000000040591E Unknown Unknown Unknown
Pcrystal 00000000004053FD Unknown Unknown Unknown
libc.so.6 000014B7C14295D0 Unknown Unknown Unknown
libc.so.6 000014B7C1429680 __libc_start_main Unknown Unknown
Pcrystal 0000000000405315 Unknown Unknown Unknown

aerba I've noticed for my systems, these SCF convergence issues appear when I try to compute for intensities in a restart job. Then when removing intensities, they converge fine and progress forward.

Is it possible to finish the frequency calculations first and then compute for the Raman intensities afterwards? Would that be a work around? Maybe with RAMANREA - because I have the TENS_RAMAN.DAT, but it just gets stuck at some point during HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
FORCE CONSTANT MATRIX - NUMERICAL ESTIMATE
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
and doesn't progress with restarts

It makes sense, thank you.

OK, here we go. It just is stuck, always the same position in the output

(ceres20-compute-46:0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95)
(ceres24-compute-18:96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191)

export TMPDIR=/local/bgfs/jonas.baltrusaitis/15383115
export TMOUT=5400
export SINGULARITY_TMPDIR=/local/bgfs/jonas.baltrusaitis/15383115

MAX NUMBER OF SCF CYCLES 200 CONVERGENCE ON DELTAP 10**-20
WEIGHT OF F(I) IN F(I+1) 30% CONVERGENCE ON ENERGY 10**-10
SHRINK. FACT.(MONKH.) 6 6 6 NUMBER OF K POINTS IN THE IBZ 64
SHRINKING FACTOR(GILAT NET) 6 NUMBER OF K POINTS(GILAT NET) 64

*** K POINTS COORDINATES (OBLIQUE COORDINATES IN UNITS OF IS = 6)
1-R( 0 0 0) 2-C( 1 0 0) 3-C( 2 0 0) 4-R( 3 0 0)
5-C( 0 1 0) 6-C( 1 1 0) 7-C( 2 1 0) 8-C( 3 1 0)
9-C( 0 2 0) 10-C( 1 2 0) 11-C( 2 2 0) 12-C( 3 2 0)
13-R( 0 3 0) 14-C( 1 3 0) 15-C( 2 3 0) 16-R( 3 3 0)
17-C( 0 0 1) 18-C( 1 0 1) 19-C( 2 0 1) 20-C( 3 0 1)
21-C( 0 1 1) 22-C( 1 1 1) 23-C( 2 1 1) 24-C( 3 1 1)
25-C( 0 2 1) 26-C( 1 2 1) 27-C( 2 2 1) 28-C( 3 2 1)
29-C( 0 3 1) 30-C( 1 3 1) 31-C( 2 3 1) 32-C( 3 3 1)
33-C( 0 0 2) 34-C( 1 0 2) 35-C( 2 0 2) 36-C( 3 0 2)
37-C( 0 1 2) 38-C( 1 1 2) 39-C( 2 1 2) 40-C( 3 1 2)
41-C( 0 2 2) 42-C( 1 2 2) 43-C( 2 2 2) 44-C( 3 2 2)
45-C( 0 3 2) 46-C( 1 3 2) 47-C( 2 3 2) 48-C( 3 3 2)
49-R( 0 0 3) 50-C( 1 0 3) 51-C( 2 0 3) 52-R( 3 0 3)
53-C( 0 1 3) 54-C( 1 1 3) 55-C( 2 1 3) 56-C( 3 1 3)
57-C( 0 2 3) 58-C( 1 2 3) 59-C( 2 2 3) 60-C( 3 2 3)
61-R( 0 3 3) 62-C( 1 3 3) 63-C( 2 3 3) 64-R( 3 3 3)

DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
X Y Z X Y Z
13.1430453 0.0000000 0.0000000 0.4780616 0.0000000 0.0000000
0.0000000 11.6066979 0.0000000 0.0000000 0.5413413 0.0000000
0.0000000 0.0000000 21.1989478 0.0000000 0.0000000 0.2963914

DISK SPACE FOR EIGENVECTORS (FTN 10) 53868000 REALS

SYMMETRY ADAPTION OF THE BLOCH FUNCTIONS ENABLED
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT gordsh1 TELAPSE 186.18 TCPU 45.44

Good! The clean way is:

CRYSTAL
1 0 0
P 21/A

I guess the extra "1"s you put are safe as they correspond to the identity operator.

For the purpose of finding the minimum energy structure to then do Raman calculations, it is.

EOS gives you much more than that of course: the p(V) or, equivalently, V(p) relation (i.e. structure as a function of pressure), the bulk modulus K(p), and allows to compute the enthalpy H(p).

Thank you very much, that worked (but not restart)