Electrostatic predictor causing segfaults

Alloy Theoretic Automated Toolkit (ATAT)
1

I didn’t see any information on how to enable the electrostatics predictor for the binary MAPS code; I assume the process is to set

PLUGINMAPS=predrs.o predcs.o tlambda.o ridge.o predes.o

in src/makefile?

In any case, I am encountering segfaults when using this predictor with MMAPS as well. The error occurs after the second "touch" command, i.e. during the second "Finding best structure…" step. With debug flags enabled, the error is:

Array out of range: -1/0

I get this with the latest beta (with and without -DSLOWENUMALGO) and with the stable version.

2

First of all, in your example, your incorrectly copied the rocksalt structure.
the 3rd line of:

5.64 5.64 5.64 90 90 90
0   0.5 0.5
0.5 0   [b]0[/b]
0.5 0.5 0
0 0 0 Na_pv,K_pv
0.5 0.5 0.5 Cl

has one 0.5 missing at the boldfaced character.
If your want the rocksalt structure (sorry I incorrectly guessed what you wanted) then your lat.in should be


5.64 5.64 5.64 90 90 90
0.000000 0.500000 0.500000
0.500000 0.000000 0.500000
0.500000 0.500000 0.000000
0.000000 0.000000 0.000000 Na_pv,K_pv
0.500000 0.500000 0.500000 Cl

That does not crash, as far as I can tell.

3

Sorry I lost track of this request.
I’ve fixed the problem. in mrefine.c++ change

  Array<Array<Real> > concentration;
  calc_regression_matrices(&corr_matrix,&energy);
  if (corr_matrix.get_size()(0)<corr_matrix.get_size()(1)) { // enough structures?;
    if (pfitinfo) {pfitinfo->status=CEFitInfo::fit_impossible;}
    return;
  }
  if (pfitinfo) {pfitinfo->status=CEFitInfo::fit_ok;}
  calc_concentration(&concentration,corr_matrix);
  init_predictors();

to

  Array<Array<Real> > concentration;
  init_predictors();
  calc_regression_matrices(&corr_matrix,&energy);
  if (corr_matrix.get_size()(0)<corr_matrix.get_size()(1)) { // enough structures?;
    if (pfitinfo) {pfitinfo->status=CEFitInfo::fit_impossible;}
    return;
  }
  if (pfitinfo) {pfitinfo->status=CEFitInfo::fit_ok;}
  calc_concentration(&concentration,corr_matrix);

(note that the only change is re-ordering the init_predictors(); call )
This will be corrected in version 3.43.

4

Hi, thanks for the reply.

That lat.in file was directly based on the rocksalt_lat.in file in the examples folder. Still, I tried converting it with cellcvrt -rr &lt; lat.in
as suggested. The output of this program looks the same to me, and gets the same segfault when used as lat.in:

5.640000 0.000000 0.000000
0.000000 5.640000 0.000000
0.000000 0.000000 5.640000
0.000000 0.500000 0.500000
0.500000 0.000000 0.500000
0.500000 0.500000 0.000000
0.000000 0.000000 0.000000 Na_pv,K_pv
0.500000 0.500000 0.500000 Cl

I tried the cubic unit cell from your post but unfortunately I still get the segfault when generating structures after reading output.

5

Sorry for the delay (busy time)!
The problem is that your lat.in has atoms that overlap (so the code is confused about which kind atom should be on some site).
Your lat.in should be:

5.64 5.64 5.64 90 90 90
1 0 0
0 1 0
0 0 1
0 0 0 Na_pv,K_pv
0.5 0.5 0.5 Cl

You can double-check for overlaps with
cellcvrt -rr < lat.in
(-rr means remove redundant) and you will see that your 2 sites get reduced to 1.
The above lat.in does not have that problem.

6

Minimal input to reproduce error, using VASP and based on rocksalt example:

lat.in:

5.64 5.64 5.64 90 90 90
0   0.5 0.5
0.5 0   0
0.5 0.5 0
0 0 0 Na_pv,K_pv
0.5 0.5 0.5 Cl

es.in:


Na_pv=1.0
K_pv=1.0
Cl=-1.0

vasp.wrap: copied from examples directory

mmaps -d -ks=es &
pollmach runstruct_vasp &

or just

mmaps -d -ks=es &
touch ready
echo "1" > 0/energy
touch ready
7

Hi Axel,

thank you for looking into this and spotting the error in my earlier structure. This error was mine and is not in the examples folder. However, I experience the same segfault with the lat.in you supply, and indeed every other lat.in that I have tried with the electrostatic predictor.

Can you confirm that you were able to

  • Initialise MAPS or MMAPS using the -ks=es argument
  • Generate the first structure and write an energy file
  • Touch "ready" and generate a second structure?

This is where it always falls down for me. I can generate multiple structures before any energies are written. The problem comes when generating structures after energy has been read.

8

The error seems to be caused in predes.c++ when "inlat" is set to -1 and this is used as an index for str.atom_type. This is in the ElectroStaticPredictor::get_energy function definition.

I notice that in predrs.c++ which_atom values of -1 are skipped over as spectator atoms, which is equivalent to "inlat". However, with the electrostatics predictor I get the -1 value of inlat even in a system with no "spectator" atoms.

As best as I can follow the chain backwards:

  • "inlat" = -1, used as array index in str.atom_type :arrow: ERROR
  • -1 was default return value of which_atom (xtalutil.c++) given an atom_pos of size zero
  • atom_pos of size zero means the lattice is empty
  • lattice is obtained when ElectroStaticPredictor is initiated from the ClusterExpansion object

It’s not clear to me why the ClusterExpansion object is getting screwed up on the second step but it only seems to be a problem when using -p=es. In any case, it now looks more like a bug or user error than a compilation error.