[Wien] compilation problems in the new pes module
Peter Blaha
pblaha at theochem.tuwien.ac.at
Tue Jul 10 21:59:04 CEST 2018
I guess your case.int (and thus the dos files) is wrong.
The output says:
Valence orbitals according to periodic table data:
Ti4s3d
O 2s2p
so we need the Ti 4s and 3d PDOS and O 2s,2p PDOS (and the total DOS)
You always have to define the "chemical valence orbitals", but not all
possible PDOS.
Am 10.07.2018 um 16:54 schrieb Pavel Ondračka:
> So after applying the suggested compilation fixes (+ the one
> uninitialized variable fix suggested later) I started to test the pes
> program. My testcase was simple anatase TiO2. The program finishes
> fine, however the spectrum is strange (looks like the Ti3p peak is
> almost invisible). So I run with valgrind to see if there are some
> obvious errors.
>
> --------------------
>
> ==16577== Conditional jump or move depends on uninitialised value(s)
> ==16577== at 0x40DD43: read_database2_ (read_database2.f:26)
> ==16577== by 0x402CE3: MAIN__ (pes.f:151)
> ==16577== by 0x40176C: main (pes.f:3)
> ==16577== Uninitialised value was created by a stack allocation
> ==16577== at 0x40DC5A: read_database2_ (read_database2.f:1)
>
> ios is used uninitialized at
> read_database2.f:26 do while (ios == 0)
>
> -------------------
>
> ==22496== Conditional jump or move depends on uninitialised value(s)
> ==22496== at 0x41054E: abs_smooth (SPLINE.f:170)
> ==22496== by 0x41054E: setup_ (SPLINE.f:88)
> ==22496== by 0x41099C: spline_ (SPLINE.f:15)
> ==22496== by 0x40E791: read_database2_ (read_database2.f:111)
> ==22496== by 0x402CE3: MAIN__ (pes.f:151)
> ==22496== by 0x40176C: main (pes.f:3)
> ==22496== Uninitialised value was created by a stack allocation
> ==22496== at 0x410980: spline_ (SPLINE.f:1)
>
> this is the delta_x variable first defined in SPLINE and passed down to
> setup in
> SPLINE.f:15 call setup(delta_x,X,F,N,strt,stp,J,interpolation)
> further down to abs_smooth at:
> SPLINE.f:88 call abs_smooth(m4 - m3, delta_x, w1)
> where it is finally used in:
> SPLINE.f:170 if (x >= delta_x) then
> without initialization
>
> -------------------
>
> ==29640== Conditional jump or move depends on uninitialised value(s)
> ==29640== at 0x40E3EA: unpolarized (read_database2.f:153)
> ==29640== by 0x40E3EA: read_database2_ (read_database2.f:79)
> ==29640== by 0x402CE3: MAIN__ (pes.f:151)
> ==29640== by 0x40176C: main (pes.f:3)
> ==29640== Uninitialised value was created by a stack allocation
> ==29640== at 0x40DC5A: read_database2_ (read_database2.f:1)
>
> This is the counter variable at
> read_database2.f:153 do I=1,counter
> even though is should initialized at
> read_database2.f:40 counter = 0
> the line was not reached at this point, since it is guarded by several
> ifs so it is possible that in some cases the variable can stay
> uninitialized. Should ever the counter be 0 at the read_database2.f:153
> line?
>
> --------------------------
>
> ==22325== Conditional jump or move depends on uninitialised value(s)
> ==22325== at 0x4801F7A0: __multf3 (in /usr/lib64/libgcc_s-8-
> 20180502.so.1)
> ==22325== by 0x41251F: unpolarized_ (read_database2.f:155)
> ==22325== by 0x412E4A: read_database2_ (read_database2.f:79)
> ==22325== by 0x403414: MAIN__ (pes.f:151)
> ==22325== by 0x40560A: main (pes.f:3)
> ==22325== Uninitialised value was created by a stack allocation
> ==22325== at 0x4125C9: read_database2_ (read_database2.f:1)
>
> This is the unitialized beta variable. Obviously similar to the above
> warning we somehow missed the initialization block starting at
> read_database2.f:46 and ending at read_database2.f:56 and there are
> more troubles ahead (another 1000+ valgrind warnings).
>
> At this moment I stopped since I suspect something went wrong earlier
> and there is no reason to debug codepaths which should probably never
> be reached. It is possible that I messed something in the
> initialization or my input files are not in order...
>
>
> The complete output looks like this:
>
> ================================================
> Please enter the excitation energy (ev):
> 1486.6
> nat: 2
> mult: 2 4
> aname :Ti O
> _______
> Valence orbitals according to periodic table data:
> Ti4s3d
> O 2s2p
> ___________
> opening 9 100k_7Rk_PBE.dos2ev
> opening 10 100k_7Rk_PBE.dos3ev
> ________________
> Valence Partial orbital found in case.DOS file:
> Ti4s 1
> Ti3d 1
> O 2s 2
> O 2p 2
> ____________________
> Enter database (default: 1)
> 1 Total cross section & Asymmetry & Non-dipole parameters 100-10000
> eV
> (Trzhaskovskaya etal., Unpolarized & linearly polarized X-ray
> source)
> Recommended option !
> 2 Total cross section 10-1500eV
> (Yeh & Lindau 1985; Unpolarized X-ray source)
> 3 No cross sections (for testing renormalization)
> 1
> ________________
> Enter Calulation Scheme (default: 1)
> 1 Unpolarized X-ray source (general)
>
> Linearlly polarized X-ray source
> 2 Dipole & NON Dipole - parallel
> 3 Dipole - perpendicular
> 4 Dipole & NON Dipole - perpendicular
> 5 LDAD
> 1
> __________________________________
> Partial Orbital Cross section
> Ti4s 0.54346D-01
> Ti3d 0.54346D-01
> O 2s 0.54346D-01
> O 2p 0.54346D-01
> ________________
> Continue with q_sphere?(Recommended)(Y/n)
> y
> Partial Orbital Average q_sphere
> Ti4s 0.73799998D-01
> Ti3d 0.72439998D+00
> O 2s 0.87150002D+00
> O 2p 0.79375005D+00
> _____________________
> Optimize q_sphere?(Y/n)
> n
>
> 100k_7Rk_PBE.pes1-3 is ready!
>
> Note: The following floating-point exceptions are signalling:
> IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
> STOP pes end
>
>
> The int file looks like this:
> Title
> -5.50 0.002 1.500 0.03 # EMIN, DE, EMAX, Gauss-broadening(>de)
> 17 N 0.000 # NUMBER OF DOS-CASES below, G/L/B
> broadening (Ry)
> 0 1 total # atom, case=column in qtl-header, label
> 1 1 Atom1 tot
> 1 2 Atom1 s
> 1 3 Atom1
> 1 4 Atom1
> 1 5 Atom1
> 1 6 Atom1
> 1 7 Atom1
> 1 8 Atom1
> 1 9 Atom1
> 1 10 Atom1
> 2 1 Atom2
> 2 2 Atom2
> 2 3 Atom2
> 2 4 Atom2
> 2 5 Atom2
> 2 6 Atom2
>
> With the corresponding lines from qtl file:
> JATOM 1 MULT= 2 ISPLIT= 3 tot,s,p,pxy,pz,d,dz2,d(x2-
> y2),d(yz+xz),dxy,
>
> JATOM 2 MULT= 4 ISPLIT= 2 tot,s,p,px,py,pz,
>
> So hopefully my input should be fine...
> Any help will be appreciated.
>
> Best regards
> Pavel
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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
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