Alessandro, I would like to keep this in this thread as my ultimate goal is finding cohesive energy of this molecular crystal. Byt doing that, I need help with negative frequency. I optimized a flexible molecule from the crystal conformation and no matter what I do I get low negative frequency. I scanned that frequency but nothing stood out, e.g. I did not see any new minima. I was wondering if you could help me why this negative stands and whether my scan was not extreme enough to jump into another conformation (which is why likely I am getting this negative). See attached
crystal.out
INPUT.d12
scan_INPUT.d12
scan.out
scan_fort.f34

By strain I mean conformational energy. I found old Mimo presentation on urea I'm studying to refresh the procedure

So the right cohesive energy is Ecrystal-Emolecule(BSSE at crystal geometry)?
The "strain" energy is Emolecule(noBSSE at crystal geometry)-Emolecule(gas optimized)

I sort of understand. Let me look again at the famous urea cohesive energy tutorial and get back if I still need help

I am sorry, Alessandro, in what case an isolated molecule have access to neighboring functions? If it is isolated, it has no neighbors and we are back to square one and this is why I wrote this post. Can you give an exampe?

I am sorry for the ignorant question:

what is the purpose of MOLEBSSE keyword (I mean I know what is the purpose, I am confused about its usability)? I am running a classical CRYSTAL and MOLECULE calculation (extracted from CRYSTAL at crystalline geometry) and the same MOLECULE extracted from crystal and optimized to calculate the formation energy (E(crystal)-n*E(molecule)) and strain energy (E(molecule in crystalline geometry)-E(optimized molecule)). For the fully optimized molecule (to get lattice or cohesive energy) I extract the unit with the keyword MOLECULE the molecule that composes the crystal, and optimize it. No MOLEBSSE needed here.

BUt then I would also like to see this "strain" energy, e.g. how much that molecule reorganizes from the crystalline geometry during optimization in a gas phase. But for that, I can again do single point with MOLECULE extraction from a crystal, compare that with fully optimized molecule and I am done. MOLECULE keyword generates a single molecule in gas phase. There are no neighboring molecules (that would contribute their basis sets which can be corrected with BSSE) when one uses MOLECULE keyword. So why have MOLEBSSE here? I knew why but I somehow lost it when I was thinking about it, sorry

Jonas

Also, is there a way to restart calculations since I want to run for a series of increasing temperatures?

Sorry, Alessandro, been reading over the weekend the paper and the manual. How do I perform dynamic stability in terms of vibrational frequencies as a function of temperature? There seem to be various procedures involved on page 265 of the manual but it is not apparent to me how to proceed with the optimized molecular fullerene. Can you please provide input example for several temperatures?

Thank you Alessandro. So I compute frequencies at variable temperatures and see at which temperature I start getting negative modes? Something like this - BUT WHAT ARE THE STRAIN SHAPE VECTORS of 0D SYSTEM?

ELASTCON
THERMOELAS
298
1 0 1 0 0 0
END
END

Alessandro, I read your JPhysChem Lett paper from 2020. It discusses the thermo-elastic constant calculation. Can that be used as an argument, e.g., calculations at various temps would result in some decreasing elastic constant value until it approaches zero?
Additionally, any of these tensor calculations applicable to 0D systems? I have molecular cages, such as fullerene, for example

Exellent. Can that be done at finite temperature? in the example I attached, they did MD simulations at increasing temps and at some point the deviation took place suggesting say at 1000 K system undergoes mechanical stability change, perhaps change in phase. Can Elastic tensors be used for that, e.g. can elastic tensors be calculated at various temperatures and see at which point they become negative to judge something about he instability temperature? Cause that woud work for me wel. Can elastic tensors be calculated at various temperatures or that concept does not exist?

I have a paper revisions requested and they asked for stability calculations. I found a similar paper, they used MD calculations. Thier plot are shown below and they talk about atomic vibrations and Dulong-Petit law. I was wondering if that has anything to do with lattice dynamics of any sort I can calculate in CRYSTAL to measure this equilibrium point before phase transition occurs? So not necessarily the method in the paper below, but something similar that show molecular stability with a temperature in a similar fashion?

Thank you

Yes Aleks that's what I meant. But I see now convergence with k points thank you

it helps, thank you. I just do not see entropy (ever) converging in your slide...

I see, thank you

I am used to seeing 3 zero frequency modes in the crystal frequency calculation output. This urea crystal calculation has only two - I was wondering why and can I use this outcome for thermodynamics calculations with this missing mode

MODES         EIGV          FREQUENCIES     IRREP  IR   INTENS    RAMAN
             (HARTREE**2)   (CM**-1)     (THZ)             (KM/MOL)
    1-   2   -0.1181E-19      0.0000    0.0000  (E  )   A (     0.00)   A
    3-   3    0.2094E-19      0.0000    0.0000  (B2 )   A (     0.00)   A
    4-   4    0.1254E-06     77.7189    2.3300  (B1 )   I (     0.00)   A
    5-   5    0.2460E-06    108.8462    3.2631  (A2 )   I (     0.00)   I
    6-   7    0.3349E-06    127.0111    3.8077  (E  )   A (     0.00)   A
    8-   8    0.4355E-06    144.8406    4.3422  (A1 )   I (     0.00)   A
    9-  10    0.6407E-06    175.6769    5.2667  (E  )   A (     0.00)   A
   11-  12    0.1108E-05    230.9837    6.9247  (E  )   A (     0.00)   A
   13-  13    0.4844E-05    483.0526   14.4816  (B1 )   I (     0.00)   A
   14-  14    0.6693E-05    567.8172   17.0227  (A1 )   I (     0.00)   A
   15-  16    0.6926E-05    577.5886   17.3157  (E  )   A (     0.00)   A
   17-  17    0.7310E-05    593.3990   17.7897  (B2 )   A (     0.00)   A
   18-  19    0.7970E-05    619.6054   18.5753  (E  )   A (     0.00)   A
   20-  20    0.8638E-05    645.0548   19.3383  (A2 )   I (     0.00)   I
   21-  21    0.1067E-04    717.0169   21.4956  (B1 )   I (     0.00)   A
   22-  22    0.1286E-04    787.0371   23.5948  (A2 )   I (     0.00)   I
   23-  24    0.1322E-04    798.0946   23.9263  (E  )   A (     0.00)   A
   25-  26    0.1420E-04    826.9504   24.7914  (E  )   A (     0.00)   A
   27-  27    0.2232E-04   1036.9495   31.0870  (B2 )   A (     0.00)   A
   28-  28    0.2251E-04   1041.3084   31.2176  (A1 )   I (     0.00)   A
   29-  30    0.2535E-04   1105.1276   33.1309  (E  )   A (     0.00)   A
   31-  31    0.2780E-04   1157.1639   34.6909  (B2 )   A (     0.00)   A
   32-  32    0.3003E-04   1202.7304   36.0569  (A1 )   I (     0.00)   A
   33-  34    0.4803E-04   1521.0625   45.6003  (E  )   A (     0.00)   A
   35-  35    0.4892E-04   1535.0190   46.0187  (A1 )   I (     0.00)   A
   36-  36    0.5334E-04   1602.8976   48.0537  (B2 )   A (     0.00)   A
   37-  38    0.5717E-04   1659.4784   49.7499  (E  )   A (     0.00)   A
   39-  39    0.5840E-04   1677.2645   50.2831  (A1 )   I (     0.00)   A
   40-  40    0.6098E-04   1713.8726   51.3806  (B2 )   A (     0.00)   A
   41-  42    0.2380E-03   3386.0936  101.5125  (E  )   A (     0.00)   A
   43-  43    0.2424E-03   3416.7391  102.4313  (A1 )   I (     0.00)   A
   44-  44    0.2438E-03   3426.7219  102.7305  (B2 )   A (     0.00)   A
   45-  46    0.2612E-03   3547.0252  106.3371  (E  )   A (     0.00)   A
   47-  47    0.2614E-03   3548.4246  106.3791  (A1 )   I (     0.00)   A
   48-  48    0.2657E-03   3577.3918  107.2475  (B2 )   A (     0.00)   A

urea.out

Dear all, what is the purpose of the phonon dispersion calculations according to the tutorial? What is the effect we are seeing, going beyond the gamma point?

https://tutorials.crystalsolutions.eu/tutorial.html?td=thermo&tf=thermo2#phonon

More importantly, how do I set it up properly? What size SCELPHONO should I be after? Is the point to have all of my crystals about the same atoms in the generated SCELPHONO for appropriate comparison? I was perusing the tutorial but I could not quite understand the purpose or the correct setup of SCELPHONO

thank you

Jonas

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

For the isolated molecule such as CO2 which is D infinity h, what is the symmetry group? I could not find this one in the manual

very grateful