SIGSEGV when building solvation cavity

[alexei-matveev]

Some info for a SIGSEGV in more_triangles()

Stack trace:
#0 0x00000000007ee6aa in polyhedron_module::more_triangles (xyz_t=..., ind_t=..., n_ind=, n_xyz_st=22, n_ind_st=32) at solvation/polyhedron_module.f90:876
#1 0x000000000064d100 in solv_cavity_module::tesselation () at solvation/solv_cavity_module.f90:3110
#2 0x0000000000653d90 in solv_cavity_module::points_on_cavity_surface () at solvation/solv_cavity_module.f90:1032
#3 0x00000000007ee1ec in disp_rep_wrap () at solvation/disp_rep_wrap.f90:97
#4 0x00000000007e50a7 in build_mol_surfaces () at build_mol_surfaces.F90:79
#5 0x0000000000594307 in main_master () at main_master.f90:454
#6 0x00000000004abe72 in paragauss::qm_run (world=0) at modules/paragauss.f90:156

Location:

paragauss-gpl/solvation/polyhedron_module.f90

Line 859 in 33771e1

xyz_t_buf=(xyz_t(i1,:)+xyz_t(i2,:))/2.0_r8_kind

was:

https://github.com/alexei-matveev/paragauss-gpl/blob/master/solvation/polyhedron_module.f90#L876

871 ind_buf(next_i,neighbour)=i1
872
873 label_k: do k=1,3
874 if (k==j) cycle label_k
875 i2=ind_t(i,k)
876 xyz_t_buf=(xyz_t(i1,:)+xyz_t(i2,:))/2.0_r8_kind
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
877 xyz_tt=(radius/sqrt(dot_product(xyz_t_buf,xyz_t_buf)))*xyz_t_buf
878
879 label_l: do l=1,n_xyz_st

[alexei-matveev]

Increasing the literal constant from 30 to 100 at
https://github.com/alexei-matveev/paragauss-gpl/blob/master/solvation/solv_cavity_module.f90#L95

# define MAX_POL_VER 100

does not help ...

[alexei-matveev]

Recompiling with bounds cheking gives:

At line 878 of file solvation/polyhedron_module.f90
Fortran runtime error: Index '19' of dimension 1 of array 'xyz_t.0' outside of expected range (1:18)

[alexei-matveev]

SK reported that after removal of two hydrogens the SIGSEGV goes. His input features 41 atom.
There is MAX_ATOMS_QMMM = 40 literal in the code. And this newly introduced ABORT() does fire:

i_poly=0
if ( N_atom_spheres >= MAX_ATOMS_QMMM .and. &
     name_point_group=='C1  ') then
   ABORT('here')
   if(output_cavity_data .and. .not.do_gradients) &
        write (output_unit,*) 'The OCTAHEDRON is inscribed into each sphere'
   call generate_octahedron(N_atom_spheres,do_cavitation,do_gradients)
   i_poly=1

[alexei-matveev]

AS authored a fix: 2305b37

[alexei-matveev]

See ref to the commit above.