Posts made by job314

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

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

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I see, thank you

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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

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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

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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

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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

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very grateful

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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

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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.

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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

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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

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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

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Oh, I see... somewhere among the files I found this. It is unusual since everything converged optimized/converged otherwise. Now wonder I can't restart, it is not restart problem. Why would i become linearly dependent in SCANMODE but not before?

ERROR **** CHOLSK **** BASIS SET LINEARLY DEPENDENT

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No idea... I just have no idea... I ran a complete run and all of a sudden the same abort. So frustrating since I do not understand the error

output.out INPUT.d12

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT:  -1 ENDING POINT:  0 STEP:  20.00000
(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)
[   5.606 -    3-]
Abort(1) on node 31 (rank 31 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31

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fort.f34 INPUT.d12 job.out Further on this problem - I managed to run this without restart - I am notoriously bad restarting. Tryiong to get rid of this small negative frequenyc. I do not see from the scan any problems, e.g. any local minimum I could restart calculation from. It just decreases monotonically...

MODE(CM-1) DISPLAC   TOTAL ENE(DFT)(AU)  CLASSICAL HARM ENE(AU)  NCYC    DE
 [MAX DISP -NATOM-]
   1( -62.1)
 [   0.113 -    3-]
            -4.0000  -0.1610002871486E+04  -0.1610016919330E+04     43 -0.9E-10
            -3.6000  -0.1610006913204E+04  -0.1610016489435E+04     32 -0.4E-10
            -3.2000  -0.1610009918764E+04  -0.1610016104792E+04     34  0.2E-11
            -2.8000  -0.1610012035843E+04  -0.1610015765400E+04     37 -0.8E-11
            -2.4000  -0.1610013425826E+04  -0.1610015471261E+04     39  0.2E-08
            -2.0000  -0.1610014243529E+04  -0.1610015222375E+04    121  0.4E-09
            -1.6000  -0.1610014634134E+04  -0.1610015018740E+04     39 -0.5E-12
            -1.2000  -0.1610014749019E+04  -0.1610014860357E+04     78  0.4E-10
            -0.8000  -0.1610014729596E+04  -0.1610014747227E+04     54 -0.1E-09
            -0.4000  -0.1610014679529E+04  -0.1610014679349E+04     36  0.1E-11
             0.0000  -0.1610014656723E+04  -0.1610014656723E+04   CENTRAL POINT

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Hi all, trying to eliminate a negative frequency via SCANMODE. Job aborts with no particular message before scanning. I have FREQINFO file for the restart
FREQINFO.DAT INPUT.d12 input.f34 input.out

EXTERNAL
FREQCALC
RESTART
SCANMODE
1 -10 10 0.4
1
END
END

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( -62.1)
[   0.113 -    3-]

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Hi Giu, it worked!

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Hi all, I am not getting the right geometry inputs for 1/3 and 2/3 positions. For example, for the structure below, I am trying to enter for the group 164:

CRYSTAL
0 0 0
164
3.186 4.653
3
27	0.0 0.0 0.0
1 0.333 0.6666 0.4134
8	 0.3333 0.666 0.2128

and it ends up being incorrect stoichiometry, which tells me these fractional positions were not parsed correctly.

 CRYSTAL CALCULATION
 (INPUT ACCORDING TO THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY)
 CRYSTAL FAMILY                       :  HEXAGONAL   
 CRYSTAL CLASS  (GROTH - 1921)        :  DITRIGONAL SCALENOHEDRAL             

 SPACE GROUP (CENTROSYMMETRIC)        :  P -3 M 1        

 LATTICE PARAMETERS  (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
        A           B           C        ALPHA        BETA       GAMMA
     3.18600     3.18600     4.65300    90.00000    90.00000   120.00000


 NUMBER OF IRREDUCIBLE ATOMS IN THE CONVENTIONAL CELL:    3

 INPUT COORDINATES

 ATOM AT. N.              COORDINATES
   1  27     0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
   2   1     3.330000000000E-01  6.666000000000E-01  4.134000000000E-01
   3   8     3.333000000000E-01  6.660000000000E-01  2.128000000000E-01

 *******************************************************************************

 << INFORMATION >>: FROM NOW ON, ALL COORDINATES REFER TO THE PRIMITIVE CELL

 *******************************************************************************

 LATTICE PARAMETERS  (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
       A          B          C        ALPHA      BETA     GAMMA        VOLUME
    3.18600    3.18600    4.65300    90.00000  90.00000 120.00000     40.903006

 COORDINATES OF THE EQUIVALENT ATOMS (FRACTIONAL UNITS)

 N. ATOM EQUIV AT. N.          X                  Y                  Z

   1   1   1   27 CO    0.00000000000E+00  0.00000000000E+00  0.00000000000E+00

   2   2   1    1 H     3.33000000000E-01 -3.33400000000E-01  4.13400000000E-01
   3   2   2    1 H     3.33400000000E-01 -3.33600000000E-01  4.13400000000E-01
   4   2   3    1 H     3.33600000000E-01 -3.33000000000E-01  4.13400000000E-01
   5   2   4    1 H    -3.33600000000E-01  3.33400000000E-01 -4.13400000000E-01
   6   2   5    1 H    -3.33000000000E-01  3.33600000000E-01 -4.13400000000E-01
   7   2   6    1 H    -3.33400000000E-01  3.33000000000E-01 -4.13400000000E-01
   8   2   7    1 H    -3.33000000000E-01  3.33400000000E-01 -4.13400000000E-01
   9   2   8    1 H    -3.33400000000E-01  3.33600000000E-01 -4.13400000000E-01
  10   2   9    1 H    -3.33600000000E-01  3.33000000000E-01 -4.13400000000E-01
  11   2  10    1 H     3.33600000000E-01 -3.33400000000E-01  4.13400000000E-01
  12   2  11    1 H     3.33000000000E-01 -3.33600000000E-01  4.13400000000E-01
  13   2  12    1 H     3.33400000000E-01 -3.33000000000E-01  4.13400000000E-01

  14   3   1    8 O     3.33300000000E-01 -3.34000000000E-01  2.12800000000E-01
  15   3   2    8 O     3.34000000000E-01 -3.32700000000E-01  2.12800000000E-01
  16   3   3    8 O     3.32700000000E-01 -3.33300000000E-01  2.12800000000E-01
  17   3   4    8 O    -3.32700000000E-01  3.34000000000E-01 -2.12800000000E-01
  18   3   5    8 O    -3.33300000000E-01  3.32700000000E-01 -2.12800000000E-01
  19   3   6    8 O    -3.34000000000E-01  3.33300000000E-01 -2.12800000000E-01
  20   3   7    8 O    -3.33300000000E-01  3.34000000000E-01 -2.12800000000E-01
  21   3   8    8 O    -3.34000000000E-01  3.32700000000E-01 -2.12800000000E-01
  22   3   9    8 O    -3.32700000000E-01  3.33300000000E-01 -2.12800000000E-01
  23   3  10    8 O     3.32700000000E-01 -3.34000000000E-01  2.12800000000E-01
  24   3  11    8 O     3.33300000000E-01 -3.32700000000E-01  2.12800000000E-01
  25   3  12    8 O     3.34000000000E-01 -3.33300000000E-01  2.12800000000E-01

Jonas Baltrusaitis

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