Posts

• ---

  extract asymmetric fragment
  undefined dmitoli

  Dear Jonas,

  I tried using pymatgen to extract the point-symmetry information from your .xyz file (see the Python script below):

  from pymatgen.core import Molecule
  from pymatgen.symmetry import analyzer
  
  bigstructure = Molecule.from_file("yourfile.xyz")
  PGstructure = analyzer.PointGroupAnalyzer(bigstructure)
  sym_mol = PGstructure.get_equivalent_atoms()
  
  print(sym_mol["eq_sets"])
  

  This returns a Python data structure containing the symmetry-irreducible sets of atoms (only 6 for this system, which is indeed of Ih point group!).
  When preparing the CRYSTAL input, be careful with the orientation of your asymmetric unit. In my case, for example, I had to change the sign of the x and y coordinates to make the symmetry consistent with CRYSTAL’s conventions.
  Icosahedral point groups are available in CRYSTAL (Ih is point group number 47 in CRYSTAL), so the input fort this molecular cage reads:

  Symm. structure 
  MOLECULE
  47
  6
  8       2.605032231   -11.914271806    11.762689798
  6       4.344538598    15.664236912     4.366798884
  6       3.427479683    14.428996321     8.326818862
  6      -8.906580884     1.370529673    14.411150640             
  1       2.632960331    14.962480562     7.832453804    
  5      -8.776255231    -2.916256114    14.200279302     
  COORPRT
  TESTGEOM
  END
  

  aerba Christmas is already in the air indeed!

• ---

  SCF convergence ferromagnetic MIL-127
  undefined GiacomoAmbrogio

  As a general suggestion, I would recommend adding SMEAR, and possibly enabling DIIS, which can also be helpful. However, when using SPINLOCK, be careful, you should only turn DIIS on after SPINLOCK is disabled, so make sure to use THREDIIS instead.

  You can also try increasing FMIXING to around 90 or 95, and using slightly higher TOLINTEG values.

  Additionally, increasing SHRINK to 2 2 could be helpful. If the system goes through a metallic state, this adjustment can improve the Fermi surface (computational cost should not increase significantly).

  The input file should be similar to this: INPUT.d12

  As an additional note, targeting a high-spin state with all Fe atoms having +5 spin may not be physically reasonable for this type of MOF. Such a configuration could lead to severe instability in the electronic structure, which often manifests as SCF convergence issues. It might be worth checking whether a lower or mixed-spin configuration is more appropriate for the system.

• ---

  SCF convergence ferromagnetic MIL-127
  undefined GiacomoAmbrogio

  Hi Wim,

  Could you please provide the geometry of your system? An output file would also be very helpful.

  In the meantime, please have a look at this thread.

• ---

  extract asymmetric fragment
  undefined aerba

  Hi,

  Jefferson Maul has managed to generate this .cif file with 4 symmetry operators. As you suggest, there are probably more but this is what he could extract so far.

  Beautiful system by the way: looks like a Christmas tree bauble!

  

• ---

  SCANMODE io error Read_int_1d
  undefined aerba

  Hi,

  job314 said in SCANMODE io error Read_int_1d:

  So it turns out having fort.13 and fort.20 is not optional for restart.

  Yes, the lack of these two files was the origin of the I/O error.

  job314 said in SCANMODE io error Read_int_1d:

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

  Now also .zip, .tar, .tgz, .tar.gz files can be uploaded.

  Cheers,

• ---

  Double Walled Naontubes X(n1,0)@Y(n2>>n1,0)
  undefined SilviaCasassa

  hello
  about VLAB I'll ask to the developer...
  As for the MULTIWALL nanotubes.. there is another procedure you can follow, which use the keyword MULTIWALL. These are the steps, using as a test system a graphene sheet:
  1) build a two-wall nanotube ---> see 2wall.jpg

  Title
  SLAB
  77
  2.47
  1
  6 0.33333333 0.6666666667 0.000000
  NANOMULTI
  2
  WALL
  1
  ROLLINGV
  6 6
  WALL
  2
  ROLLINGV
  12 12
  NANOJMOL
  ENDWALL
  [Basis Set]
  

  2. use the MULTIWALL.DAT file as a fort.34 and restart with the EXTERNAL keyword substituting one of the two wall with different atom(s). In this case, the inner wall becomes a nitrogen wall, see ---> ext2wall.jpg

  Title
  EXTERNAL
  ATOMSUBS
  24
  1 7
  2 7
  3 7
  4 7
  5 7
  6 7
  7 7
  8 7
  9 7
  10 7
  11 7
  12 7
  13 7
  14 7
  15 7
  16 7
  17 7
  18 7
  19 7
  20 7
  21 7
  22 7
  23 7
  24 7
  END
  [Basis Set]
  

  
  

• ---

  Double Walled Naontubes X(n1,0)@Y(n2>>n1,0)
  undefined SilviaCasassa

  the ZnO@GaN were done exactly in this way... if you roll up a two-layers slab you end with a double wall nanotube

• ---

  Double Walled Naontubes X(n1,0)@Y(n2>>n1,0)
  undefined SilviaCasassa

  goodmorning,

  ok... now I understand better. This is an example. I chose the space group 73 because the 78 has a mirror plane... I don't know which kind of lattice do you want to simulate ...neither if the two lattice (BeO and MgO) are commensurable ...but the idea is to build a two-layers slab, one layer of MgO and the other layer of BeO and then roll the slab
  The lattice parameter is chosen randomly ...

  Title
  SLAB
  73
  3.47
  4
  8 0.5 0.0 0.000000
  4  0.0 0.0 0.0000
  12 0.5 0.0 2.200000
  8  0.0 0.0 2.2000
  SWCNT
  10 10
  TESTGEOM
  END
  END
  

• ---

  Double Walled Naontubes X(n1,0)@Y(n2>>n1,0)
  undefined SilviaCasassa

  Hello,
  thank you for your question. Could you be more precise? I don't understand exactly what you mean but this is the input file for a double wall nanotube created starting from a graphene layer:

  title
  SLAB
  77 
  2.47
  1
  6 0.33333333 0.6666666667 0.000000
  NANOMULTI
  2
  WALL
  1
  ROLLINGV
  6  6
  WALL
  2
  ROLLINGV
  12    12
  NANOJMOL
  ENDWALL
  END
  END
  

  you can have a look at the Tutorial, on the Crystal web page:
  https://tutorials.crystalsolutions.eu/tutorial.html?td=mwnanotube&tf=MW_tutorial

  I hope it helps...

• ---

  OPTGEOM for RUNCONFS
  undefined aerba

  Hi,

  Before running the actual single-point or geometry optimization calculations on the configurations with RUNCONFS, a list of configurations needs to be generated by use of the CONFRAND option. The list of generated configurations is saved into a file CONFIGURATIONS.DAT that is then read by the next RUNCONFS calculation.

  Let us go through this step-by-step. I take your system as an example.

  • First, you would setup an input for the CONFRAND calculation. For instance:

  Title
  CRYSTAL
  0 0 0
  194
  3.065 17.656
  4
  22 0 0 0.5
  14 0 0 0.75
  22 0.666666 0.333333 0.364919
  6 0.333333 0.666666 0.427507
  SCELCONF
  1 0 0
  0 1 0
  0 0 1
  CONFRAND
  1
  5
  2
  END
  

  Here I am selecting just one crystallographic site for substitution, specified by atom number 5, which is a Ti atom. Given the symmetry of this system, that atom has a multiplicity of 4 (i.e. there are other 3 Ti atoms symmetry-related to it). This can be inspected from here (in bold the selected atoms, in italic its symmetry-equivalents):

   N. ATOM EQUIV AT. N.          X                  Y                  Z
  
     1   1   1   22 TI    0.00000000000E+00  0.00000000000E+00 -5.00000000000E-01
     2   1   2   22 TI    0.00000000000E+00  0.00000000000E+00  0.00000000000E+00
  
     3   2   1   14 SI    0.00000000000E+00  0.00000000000E+00 -2.50000000000E-01
     4   2   2   14 SI    0.00000000000E+00  0.00000000000E+00  2.50000000000E-01
  
   **5   3   1   22 TI   -3.33334000000E-01  3.33333000000E-01  3.64919000000E-01**
    *6   3   2   22 TI    3.33334000000E-01 -3.33333000000E-01 -1.35081000000E-01
     7   3   3   22 TI    3.33333000000E-01 -3.33333000000E-01 -3.64919000000E-01
     8   3   4   22 TI   -3.33333000000E-01  3.33334000000E-01  1.35081000000E-01*
  
     9   4   1    6 C     3.33333000000E-01 -3.33334000000E-01  4.27507000000E-01
    10   4   2    6 C    -3.33333000000E-01  3.33334000000E-01 -7.24930000000E-02
    11   4   3    6 C    -3.33333000000E-01  3.33334000000E-01 -4.27507000000E-01
    12   4   4    6 C     3.33334000000E-01 -3.33333000000E-01  7.24930000000E-02
  

  The last input parameter of CONFRAND, which I set to 2, determines how many of these 4 Ti atoms will be substituted.

  • By running it you get the following output:

  *******************************************************************************
    SUBSTITUTIONS AT SITES (LABELS) : 
      5    7    6    8
    **********************************            COMPOSITION :          2 /   4
    **********************************          NUMBER OF SIC :                3
   *******************************************************************************
   --->              1      SIC  FOUND AT TRY              1   -   CONFIGURATION 
     0   0   1   1
     MULTIPLICITY      2   -   RANK           1   -   CANONICAL RANK           1
   --->              2      SIC  FOUND AT TRY              2   -   CONFIGURATION 
     1   0   1   0
     MULTIPLICITY      2   -   RANK           5   -   CANONICAL RANK           2
   --->              3      SIC  FOUND AT TRY              4   -   CONFIGURATION 
     1   0   0   1
     MULTIPLICITY      2   -   RANK           3   -   CANONICAL RANK           4
   *******************************************************************************
                     3      SIC  FOUND  AFTER              4       TRIES
   *******************************************************************************
  

  that is 3 symmetry-independent configurations (SICs) are found and stored in the external file CONFIGURATIONS.DAT.

  • At this point you are ready to run a RUNCONFS calculation (note that the CONFIGURATIONS.DAT file generated at the previous step needs to be placed inside the scratch folder of the new job). For instance with:

  Title
  CRYSTAL
  0 0 0
  194
  3.065 17.656
  4
  22 0 0 0.5
  14 0 0 0.75
  22 0.666666 0.333333 0.364919
  6 0.333333 0.666666 0.427507
  SCELCONF
  1 0 0
  0 1 0
  0 0 1
  RUNCONFS
  ATOMSUBS
  22 273
  END
  

  In this case I ask to substitute Ti with Ta.

  Hope this helps,