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

PeterRemoto At the moment I am afraid I do not have an explanation for the difference you experienced between CRYSTAL17 and CRYSTAL23 as I am unable to reproduce the erratic behavior with CRYSTAL23.

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)

you're the best, thank you for going extra mile

thank you

very grateful, I will run it again but not sure what to do here if it aborts again

Dear Jonas,

Thanks for reaching out and being one of the most active users of these early days of the forum. Your question gives us the chance to clarify some aspects of the output file that might not be obvious to non expert users. Below, I will refer to your output file.

Harmonic Frequencies and IR intensities

To compute harmonic frequencies and IR intensities (with the default approach of the Berry phase) the input looks like:

FREQCALC INTENS ENDFREQ

In the output file, the following table is printed:

HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH EIGENVALUES (EIGV) OF THE MASS WEIGHTED HESSIAN MATRIX AND HARMONIC TRANSVERSE OPTICAL (TO) FREQUENCIES. IRREP LABELS REFER TO SYMMETRY REPRESENTATION ANALYSIS; A AND I INDICATE WHETHER THE MODE IS ACTIVE OR INACTIVE, RESPECTIVELY, FOR IR AND RAMAN; INTEGRATED IR INTENSITIES IN BRACKETS. CONVERSION FACTORS FOR FREQUENCIES: 1 CM**(-1) = 0.4556335E-05 HARTREE 1 THZ = 0.3335641E+02 CM**(-1) HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH MODES EIGV FREQUENCIES IRREP IR INTENS RAMAN (HARTREE**2) (CM**-1) (THZ) (KM/MOL) 1- 1 0.3488E-07 40.9894 1.2288 (A ) A ( 0.40) A 2- 2 0.6077E-07 54.1037 1.6220 (A ) A ( 0.96) A 3- 3 0.6801E-07 57.2344 1.7158 (A ) A ( 2.45) A 4- 4 0.2238E-06 103.8371 3.1130 (A ) A ( 11.47) A [...]

For each mode (or set of degenerate modes) its eigenvalue (in Ha\(^2\)), harmonic frequency (in cm\(^{-1}\) and THz) and irreducible representation get printed. In addition, labels specifying whether the mode is IR/Raman active are also displayed (A and I indicate whether the mode is active or inactive, respectively).

Raman intensities

Raman intensities can be computed via a coupled-perturbed approach by inserting the INTRAMAN keyword followed by the INTCPHF block in the input deck:

FREQCALC INTRAMAN INTCPHF END ENDFREQ

Raman intensities are computed for each independent component of the polarizability tensor (xx, xy, xz, yy, yz, zz, labeled as "Single Crystal" in the output file) and are also averaged to mimic polycrystalline powder samples (total, parallel polarisation, perpendicular polarisation averages are printed in the output).

POLYCRYSTALLINE ISOTROPIC INTENSITIES (ARBITRARY UNITS) MODES FREQUENCIES I_tot I_par I_perp ---------------------------------------------------------------- 1- 1 40.9894 (A ) 0.46 0.27 0.19 2- 2 54.1037 (A ) 7.35 4.23 3.12 3- 3 57.2344 (A ) 12.79 8.82 3.96 4- 4 103.8371 (A ) 13.66 7.89 5.77 SINGLE CRYSTAL DIRECTIONAL INTENSITIES (ARBITRARY UNITS) MODES FREQUENCIES I_xx I_xy I_xz I_yy I_yz I_zz ---------------------------------------------------------------------------- 1- 1 40.9894 (A ) 0.00 0.37 0.02 0.63 0.00 0.21 2- 2 54.1037 (A ) 3.17 0.69 0.00 4.35 3.66 10.05 3- 3 57.2344 (A ) 3.82 3.54 0.02 3.50 0.03 27.53 4- 4 103.8371 (A ) 2.57 1.81 0.01 16.25 3.34 19.62

For more details on such polycrystalline averages, please refer to sections 8.4 and 8.7 of the CRYSTAL23 manual.

Raman spectrum

A continuous Raman spectrum can be simulated by use of the RAMSPEC block, as in:

FREQCALC INTRAMAN INTCPHF END RAMSPEC END ENDFREQ

The simulated spectrum is printed in an external file named RAMSPEC.DAT that contains several columns: column 1 with frequencies in cm\(^{-1}\), columns 2-4 with polycrystalline intensities (total, parallel, perpendicular), columns 5-10 with single crystal intensities (xx, xy, xz, yy, yz, zz).

Effect of Temperature and Laser wavelength

The effect of temperature and laser wavelength on computed Raman intensities can be accounted for by use of the RAMANEXP keyword, as in:

FREQCALC INTRAMAN INTCPHF END RAMANEXP 298 532 RAMSPEC END ENDFREQ

Here we set 298 K for the temperature and 532 nm for the laser wavelength. This option modifies the values of all computed Raman intensities (in the output and in the RAMSPEC.DAT file accordingly).

Please, note that other properties (harmonic frequencies and IR intensities) are not affected by this option and thus remain unchanged in the output.

Plots

When CRYSPLOT reads the CRYSTAL output file it only plots the total intensity of the polycrystalline powder model.

When CRYSPLOT reads the RAMSPEC.DAT file it plots all components:

Screenshot 2025-03-13 at 12.47.37.png

Other plotting tools can be used to plot specific columns of the RAMSPEC.DAT file (e.g., CRYSTALClear, gnuplot).