Failed using new 'structure' variable

Running Abinit Ground state
1

I want to use the variable ‘structure’ to read in my geometry and I get a very strange error in the log file. I am using:

structure “abivars:my_text_file”

my_text_file with the content:

natom   40                                      
acell   7.82000 7.82000 7.82000 angstrom        
angdeg  90 90 90                                
xred_symbols                                   
      0.25000    0.25000    0.00000 O #   1
      0.25000    0.25000    0.50000 O #   2
      0.25000    0.75000    0.00000 O #   3
      0.25000    0.75000    0.50000 O #   4 
      0.75000    0.25000    0.00000 O #   5 
      0.75000    0.25000    0.50000 O #   6
      0.75000    0.75000    0.00000 O #   7
      0.75000    0.75000    0.50000 O #   8
      0.00000    0.25000    0.25000 O #   9
      0.00000    0.25000    0.75000 O #  10
      0.00000    0.75000    0.25000 O #  11
      0.00000    0.75000    0.75000 O #  12
      0.50000    0.25000    0.25000 O #  13
      0.50000    0.25000    0.75000 O #  14
      0.50000    0.75000    0.25000 O #  15
      0.50000    0.75000    0.75000 O #  16
      0.25000    0.00000    0.25000 O #  17
      0.25000    0.00000    0.75000 O #  18
      0.25000    0.50000    0.25000 O #  19
      0.25000    0.50000    0.75000 O #  20
      0.75000    0.00000    0.25000 O #  21
      0.75000    0.00000    0.75000 O #  22
      0.75000    0.50000    0.25000 O #  23
      0.75000    0.50000    0.75000 O #  24

      0.00000    0.00000    0.00000 La #  25
      0.00000    0.00000    0.50000 La #  26
      0.00000    0.50000    0.00000 La #  27
      0.00000    0.50000    0.50000 La #  28
      0.50000    0.00000    0.00000 La #  29
      0.50000    0.00000    0.50000 La #  30
      0.50000    0.50000    0.00000 La #  31
      0.50000    0.50000    0.50000 La #  32

      0.25000    0.25000    0.25000 V #  33
      0.25000    0.25000    0.75000 V #  34
      0.25000    0.75000    0.25000 V #  35
      0.25000    0.75000    0.75000 V #  36
      0.75000    0.25000    0.25000 V #  37
      0.75000    0.25000    0.75000 V #  38
      0.75000    0.75000    0.25000 V #  39
      0.75000    0.75000    0.75000 V #  40

Error in log-file:

--- !ERROR
src_file: m_invars1.F90
src_line: 517
mpi_rank: 0
message: |
    Not enough pseudopotentials in input `pseudos` string, expecting npsp: 17                    
    Perhaps the separator (=a comma) is missing between pseudopotentials in input `pseudos` string.
...

Especially the number 17 is inexplicable to me here.

Do you have any ideas?

2

This looks like you are trying to run a supercell of the cubic perovskite LaVO3, right? Do you have the various symmetry checks turned off so that it is not trying to reduce the input cell to something equivalent but smaller?

3

Yes, that’s correct. I haven’t explicitly disabled symmetry checks, but the calculation works fine if I manually write the data into the .abi input file as follows:

natom   40                     
znucl 8 57 23
ntypat 3
typat 24*1 8*2 8*3                 
acell   7.82000 7.82000 7.82000 angstrom        
angdeg  90 90 90                                
xred                            
      0.25000    0.25000    0.00000 #   1
      0.25000    0.25000    0.50000 #   2
      0.25000    0.75000    0.00000 #   3
      0.25000    0.75000    0.50000 #   4 
      0.75000    0.25000    0.00000 #   5 
      0.75000    0.25000    0.50000 #   6
      0.75000    0.75000    0.00000 #   7
      0.75000    0.75000    0.50000 #   8
      0.00000    0.25000    0.25000 #   9
      0.00000    0.25000    0.75000 #  10
      0.00000    0.75000    0.25000 #  11
      0.00000    0.75000    0.75000 #  12
      0.50000    0.25000    0.25000 #  13
      0.50000    0.25000    0.75000 #  14
      0.50000    0.75000    0.25000 #  15
      0.50000    0.75000    0.75000 #  16
      0.25000    0.00000    0.25000 #  17
      0.25000    0.00000    0.75000 #  18
      0.25000    0.50000    0.25000 #  19
      0.25000    0.50000    0.75000 #  20
      0.75000    0.00000    0.25000 #  21
      0.75000    0.00000    0.75000 #  22
      0.75000    0.50000    0.25000 #  23
      0.75000    0.50000    0.75000 #  24

      0.00000    0.00000    0.00000 #  25
      0.00000    0.00000    0.50000 #  26
      0.00000    0.50000    0.00000 #  27
      0.00000    0.50000    0.50000 #  28
      0.50000    0.00000    0.00000 #  29
      0.50000    0.00000    0.50000 #  30
      0.50000    0.50000    0.00000 #  31
      0.50000    0.50000    0.50000 #  32

      0.25000    0.25000    0.25000 #  33
      0.25000    0.25000    0.75000 #  34
      0.25000    0.75000    0.25000 #  35
      0.25000    0.75000    0.75000 #  36
      0.75000    0.25000    0.25000 #  37
      0.75000    0.25000    0.75000 #  38
      0.75000    0.75000    0.25000 #  39
      0.75000    0.75000    0.75000 #  40

Additionally, the error occurs even before the symmetry finder kicks in. The log file consists almost entirely of the following lines:


- input  file    -> LVO_bulk_2x2x2.abi
- output file    -> LVO_bulk_2x2x2.abo
- root for input  files -> LVO_bulk_2x2x2i
- root for output files -> LVO_bulk_2x2x2o
 
HOME  found in environment, with value /beegfs/home/
-instrng: 58 lines of input have been read from file LVO_bulk_2x2x2.abi
 
-instrng: 44 lines of input have been read from file LVO_bulk_2x2x2
 
 
--- !ERROR
src_file: m_invars1.F90
src_line: 517
mpi_rank: 0
message: |
    Not enough pseudopotentials in input `pseudos` string, expecting npsp: 17                    
    Perhaps the separator (=a comma) is missing between pseudopotentials in input `pseudos` string.
...