Posts made by job314

undefined

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

undefined

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?

undefined

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

undefined

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

undefined

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?

undefined

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

undefined

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

undefined

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

undefined

I see, thank you

undefined

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

undefined

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

undefined

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

undefined

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

undefined

very grateful

undefined

So it turns out having fort.13 and fort.20 is not optional for restart. Now I still need help. I optimizing this 600 atom cluster with Ih and can see that it is not minimum, there are negatives - this is why I am scanning. The scan does not return a reasonable local minimum. I only scanned negative branch but I assume they are symmetrical.
I would appreciate any help

https://www.dropbox.com/t/5jgMXmCEPNLGHpAY

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

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -20 ENDING POINT: 20 STEP:   0.20000
(THE STEP IS GIVEN AS TIMES OF THE CLASSICAL AMPLITUDE AT THE QUANTUM GROUND
STATE ENERGY. THE MAX ATOMIC DISPLACEMENT IN THE STEP IS GIVEN IN BOHR
WITHIN SQUARE BRACKETS)

 MODE(CM-1) DISPLAC   TOTAL ENE(DFT)(AU)  CLASSICAL HARM ENE(AU)  NCYC    DE
[MAX DISP -NATOM-]
  1( -11.5)
[   0.016 -  512-]
           -4.0000  -0.2201822589948E+05  -0.2201822692117E+05     15 -0.7E-09
           -3.8000  -0.2201822596504E+05  -0.2201822688013E+05     15 -0.5E-09
           -3.6000  -0.2201822602580E+05  -0.2201822684119E+05     15 -0.5E-09
           -3.4000  -0.2201822608201E+05  -0.2201822680436E+05     16  0.3E-10
           -3.2000  -0.2201822613398E+05  -0.2201822676964E+05     14  0.1E-08
           -3.0000  -0.2201822618174E+05  -0.2201822673702E+05     17  0.1E-10
           -2.8000  -0.2201822622563E+05  -0.2201822670650E+05     17 -0.7E-10
           -2.6000  -0.2201822626589E+05  -0.2201822667809E+05     18  0.2E-10
           -2.4000  -0.2201822630238E+05  -0.2201822665178E+05     16 -0.9E-10
           -2.2000  -0.2201822633530E+05  -0.2201822662758E+05     17  0.0E+00
           -2.0000  -0.2201822636488E+05  -0.2201822660548E+05     16  0.4E-10
           -1.8000  -0.2201822639128E+05  -0.2201822658549E+05     16 -0.4E-10
           -1.6000  -0.2201822641463E+05  -0.2201822656760E+05     15 -0.4E-10
           -1.4000  -0.2201822643453E+05  -0.2201822655181E+05     17  0.4E-10
           -1.2000  -0.2201822645245E+05  -0.2201822653813E+05     14  0.1E-10
           -1.0000  -0.2201822646714E+05  -0.2201822652656E+05     15 -0.5E-10
           -0.8000  -0.2201822647907E+05  -0.2201822651709E+05     14 -0.4E-10
           -0.6000  -0.2201822648831E+05  -0.2201822650972E+05     15 -0.4E-10
           -0.4000  -0.2201822649498E+05  -0.2201822650446E+05     14  0.3E-10
           -0.2000  -0.2201822649893E+05  -0.2201822650130E+05     12 -0.6E-10
            0.0000  -0.2201822650025E+05  -0.2201822650025E+05   CENTRAL POINT

undefined

I lost my patience... I normally do OPT+FREQ, nobody's on this forum (even developers) favorite method... So I just took my optimization, did frequencies, found fort.13 file, included and scanmode proceeded. I will update if anything else happens.

undefined

Oh, no, Aleks. It did not even start, e.g. it was setting up the scan, about to start the first step and stopped. The lines are the end of my output file, no optimization steps, no SCFOUT.LOG

undefined

Dear all, I am getting the IO error when scanning modes and no idea why. I copied HESSFREQ.DAT and FREQINFO.DAT files into the scan directory. I would appreciate your help

Unfortunately, it is a large system and I can't upload the files here, I will move them via Dropbox, see the link below

https://www.dropbox.com/t/uVxYAZdbhCFpM79K

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -10 ENDING POINT: 10 STEP:   0.40000
(THE STEP IS GIVEN AS TIMES OF THE CLASSICAL AMPLITUDE AT THE QUANTUM GROUND
STATE ENERGY. THE MAX ATOMIC DISPLACEMENT IN THE STEP IS GIVEN IN BOHR
WITHIN SQUARE BRACKETS)

 MODE(CM-1) DISPLAC   TOTAL ENE(DFT)(AU)  CLASSICAL HARM ENE(AU)  NCYC    DE
[MAX DISP -NATOM-]
  1(  -8.5)
[   0.030 -  390-]
io error
Read_int_1d
        300          -1
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

undefined

I have this 600 atom Ih symmetry molecular cage. I am seeking help extracting the asymmetric unit from it to enter into CRYSTAL so I can use Ih symmetry. If anybody could help me with it, I would appreciate it.

B60C300H120O120[Ih].txt

JB

undefined

Hi Aleks, I tried but ended up just using LDREMO keyword
Another superstrange thing (that of course was not happening yesterday), that I can't seem to specify initial and final step anymore properly, it divides it by 10... Bizzare. I now have to multiply initial step by 10 (-1.6 start I want I need to specify as 16!) so it startes at -1.6...

My input is:

EXTERNAL
FREQCALC
RESTART
SCANMODE
1 -16 0 0.1
1
END
END

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -16 ENDING POINT:  0 STEP:   0.10000
(THE STEP IS GIVEN AS TIMES OF THE CLASSICAL AMPLITUDE AT THE QUANTUM GROUND
STATE ENERGY. THE MAX ATOMIC DISPLACEMENT IN THE STEP IS GIVEN IN BOHR
WITHIN SQUARE BRACKETS)

 MODE(CM-1) DISPLAC   TOTAL ENE(DFT)(AU)  CLASSICAL HARM ENE(AU)  NCYC    DE
[MAX DISP -NATOM-]
  1( -62.7)
[   0.028 -    3-]
           -1.6000  -0.1610014638959E+04  -0.1610015023766E+04     18 -0.1E-07
           -1.5000  -0.1610014685887E+04  -0.1610014979469E+04     29  0.5E-06
           -1.4000  -0.1610014719434E+04  -0.1610014938029E+04     13 -0.9E-07
           -1.3000  -0.1610014740251E+04  -0.1610014899447E+04     13 -0.2E-06
           -1.2000  -0.1610014750671E+04  -0.1610014863723E+04     21 -0.9E-08
           -1.1000  -0.1610014754239E+04  -0.1610014830856E+04     15 -0.4E-06
           -1.0000  -0.1610014749993E+04  -0.1610014800848E+04     28  0.1E-07
           -0.9000  -0.1610014740870E+04  -0.1610014773698E+04     23  0.1E-05

Jonas Baltrusaitis

Posts