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

Hi Othmen!

I think that you have a problem in the geometry sections of your input files. When dealing with monoclinic structures, only one angle (beta) has to be specified as alfa and gamma are 90 by default, see page 22 of Crystal User's Manual. Furthermore, in input1 the atomic coordinates are missing, while in input2 94 atoms coordinates are written but you specified that 95 atoms are present.

Let me know if you have other problems 🙂

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).

Hi aimipa!

Yes there is an option to set an anisotropic grid from NEWK, you can find it at page 346 of the CRYSTAL User's Manual, see also the screenshot I attach below. You have to set IS=0 and then you can choose three different shrinking factors along B1, B2 and B3.

For example:

NEWK 0 12 12 8 4

sets a shrinking factor of 12, 8 and 4 along the three reciprocal lattice vectors.

I have never tested this anisotropic option in a BOLTZTRA calculation, would you mind let me know if it works? 🙂

newk.png

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.

Yes sure. No problem.
I'm copying it here below.
Thank you for the help

Daria

Furfural CRYSTAL 0 0 0 19 7.83542762 10.92181175 14.94182734 90.000000 90.000000 90.000000 33 8 1.907561246186E-01 3.035506248522E-01 4.408415126674E-01 8 -4.953260939445E-01 3.221701934644E-01 3.435788389827E-01 6 2.036695655476E-01 3.000622663369E-01 3.482645168957E-01 6 4.363374159111E-02 2.908170991680E-01 3.122160878064E-01 1 1.581732742072E-02 2.880586476013E-01 2.419150131741E-01 6 -7.402527715589E-02 2.893444053747E-01 3.842913887226E-01 1 -2.109486401803E-01 2.822752418693E-01 3.798189138779E-01 6 2.099722211847E-02 2.968688203007E-01 4.606664256414E-01 1 -9.310483322231E-03 2.937832972654E-01 -4.691825366176E-01 6 3.647591498990E-01 3.132132214593E-01 3.052219591009E-01 1 3.550467304924E-01 3.168499490771E-01 2.320173417360E-01 8 2.803460822693E-01 -3.091160241316E-01 4.442088720927E-01 8 -4.110526913885E-01 -3.641439806750E-01 3.516630126321E-01 6 2.872037985115E-01 -3.695128622796E-01 3.626185432797E-01 6 1.245767077225E-01 -3.991101749711E-01 3.362778399038E-01 1 9.163169834882E-02 -4.467733390550E-01 2.755816936910E-01 6 1.226510841197E-02 -3.550438914407E-01 4.034527830796E-01 1 -1.250093786328E-01 -3.609739865930E-01 4.033488316714E-01 6 1.122081912874E-01 -3.009269785992E-01 4.671425614917E-01 1 8.596288473646E-02 -2.539158941058E-01 -4.709004162095E-01 6 4.474098992917E-01 -3.907868742186E-01 3.203804132925E-01 1 4.349587971852E-01 -4.336723578587E-01 2.540887571847E-01 8 1.068738713332E-01 -3.851604875541E-02 3.194441316968E-01 8 -2.354778627755E-01 -1.170305051641E-02 3.709929081706E-01 6 5.921416878240E-02 -5.109842318475E-03 4.052174692072E-01 6 2.027905991547E-01 1.001107546720E-02 4.563966208009E-01 1 2.038099671676E-01 3.508046669402E-02 -4.738476409789E-01 6 3.453540637796E-01 -1.523126326522E-02 4.003413693017E-01 1 4.790458182320E-01 -1.335338648893E-02 4.173410231626E-01 6 2.808235437569E-01 -4.461452496729E-02 3.184022003331E-01 1 3.367732131084E-01 -7.306049141011E-02 2.558072164743E-01 6 -1.187612609562E-01 6.696688015001E-03 4.250681762815E-01 1 -1.454796120848E-01 3.516201574611E-02 4.940534466886E-01 FREQCALC NUMDERIV 2 INTENS INTRAMAN INTCPHF END END BASISSET POB-TZVP-REV2 DFT B3LYP-D3 XLGRID ENDdft SHRINK 4 4 TOLDEE 10 SCFDIR LEVSHIFT 6 1 FMIXING 30 TOLINTEG 7 7 7 7 14 EXCHSIZE 13220300 BIPOSIZE 13220300 ENDscf

Hi,

Hmmm...even though the SI file of the paper you have shared does point to using HSE06, it remains not entirely clear whether its parameters were kept default or altered (for all systems together or individually for instance).

There are also differences between what different codes consider as "default" settings. For example, within the code used in the paper (VASP, nice code, no doubt), the defaults for HSE06 read (taken from https://www.vasp.at/wiki/index.php/List_of_hybrid_functionals) :
$$ \omega= 0.2\ \mathring{A} , \quad c = 0.25, \quad \text{correlation}=\text{PBE}, $$ with the first number reading the range separation parameter (omega) and the second the fraction of exact exchange used (c).

Within CRYSTAL (also nice code, no doubt), these read (taken from the manual, page 138):
$$ \omega= 0.11\ a_0^{-1}, \quad c = 0.25, \quad \text{correlation}=\text{PBE}, $$ adopting the same labels.

Not sure about the exact definition of units (perhaps a developer can comment if this is indeed Bohr radius as assumed?), but you can already see the subtle differences having to be taken into account when comparing between codes.

A few other thoughts worth considering:

In the paper, the structure was optimized with PBEsol and on top of that geometry HSE06 was applied as a single-point calculation. Not sure about the exact composition of those ZIFs, but the structural differences could play a significant role as well (planewave codes are very costly when optimizing a structure with hybrid functionals). Here is also a good read on this topic: doi.org/10.1088/2516-1075/aafc4b

One final small comment. Within the PAW formalism implemented in VASP, scalar relativistic effects are included in the pseudopotentials by default. No problem, cool feature, but should be taken into account when comparing results, especially for heavier elements (longer discussion found here https://blog.vasp.at/forum/viewtopic.php?t=902)

Hope this helps!

Cheers,
Aleks

Thanks Jacques! These are very informative.
The information for specific basis sets is helpful, I will try them.

Hello Prof. Erba,

Thank you for providing the reference and relevant pages. This is very useful.

Best,
Danny

Thank you so much
this helped a lot

Thank you very much for the detailed explanation—this really helped clarify things for me! The plot and your explanation made it all very clear.

Your response is incredibly valuable—thank you so much.I suspect that the DIIS/Anderson extrapolation might have 'hit' a local minimum, so the density guess in iteration 8 happened to yield a total energy extremely close to that of the previous step, resulting in a very small ΔE.
CYC 0 ETOT(AU) -8.456120523718E+03 DETOT -8.46E+03 tst 0.00E+00 PX 1.00E+00
CYC 1 ETOT(AU) -8.390242659622E+03 DETOT 6.59E+01 tst 0.00E+00 PX 1.00E+00
CYC 2 ETOT(AU) -8.391027170997E+03 DETOT -7.85E-01 tst 3.34E-03 PX 1.13E-01
CYC 3 ETOT(AU) -8.391734802465E+03 DETOT -7.08E-01 tst 2.44E-03 PX 1.02E-01
CYC 4 ETOT(AU) -8.392064543836E+03 DETOT -3.30E-01 tst 8.38E-04 PX 4.49E-02
CYC 5 ETOT(AU) -8.392086825687E+03 DETOT -2.23E-02 tst 1.24E-04 PX 1.72E-02
CYC 6 ETOT(AU) -8.392095974656E+03 DETOT -9.15E-03 tst 2.86E-05 PX 9.66E-03
CYC 7 ETOT(AU) -8.392097542826E+03 DETOT -1.57E-03 tst 3.85E-06 PX 4.81E-03
CYC 8 ETOT(AU) -8.392097541980E+03 DETOT 8.46E-07 tst 5.41E-06 PX 3.18E-03
CYC 9 ETOT(AU) -8.392098065539E+03 DETOT -5.24E-04 tst 4.69E-06 PX 3.18E-03
While this DETOT value satisfies the default energy convergence criterion, the corresponding values suggest that the electron density had not yet fully stabilized. This aligns well with your suggestion that tightening the convergence threshold would lead to a more reliable result.
Thank you again for your guidance.

Many thanks for your detailed explanation and for checking the code — that definitely clarifies things. I really appreciate your help!

Oh yes, right. My apologies. I did not notice this. Thank you Giacomo!

Hi,

Can you try to re-run the COHP calculation by using:

COHP 16 500 200 360 2 12 0

instead of

COHP 16 500 200 360 1 12 0

This should generate a file COHP.DAT
Let me know how this goes.

Hi Alessandro and Giacomo,

Thank you for the clear and helpful explanations!

I tried running the calculation with 32 cores, and it indeed helped with memory management. I’ll continue experimenting to optimize performance. Really appreciate your guidance and the references!

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

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

Dear Eleonora and Aleks,

Thank you so much for the detailed explanation and for sharing the corrected input/output file. That really clarified the issue. I tried your suggested settings with FMIXING and SPINLOCK adjustments, and the geometry optimization is running well with no errors. Have a nice day!

Best,
Aparajita

Hi,

I think that the best way to proceed in this case would be to restart the calculation one or more times. To do this, you just have to make sure that the scratch folder is not deleted when the calculation stops. Basically, you would run a first job with:

FREQCALC END

Then, after the first calculation stops (maybe because you reached a wall clock time limit) you would run a second job restarting from the first as:

FREQCALC RESTART END

In order to make this restart work, you need a few files from the previous job to be placed in the scratch folder of the new job: FREQINFO.DAT, fort.13 and fort.9 (to be renamed fort.20 in the new folder).

If needed, you can repeat this restart process multiple times until completion of the frequency calculation.

Hope this helps,