[DFTB-Plus-User] waveplot
Jacek Jakowski
jjakowski at gmail.com
Mon Aug 17 06:11:53 CEST 2015
Dear Balint and All:
I have difficulties with getting waveplot to work. Neither precompiled
nor my own build (ifort) can produce correct results for this small
system:
*17 CSi H P 1 3 0.00000 0.00000 0.00000 2 1 -1.35774
-1.35774 -1.35774 3 1 1.35774 1.35774 -1.35774 4 1
-1.35774 1.35774 1.35774 5 1 1.35774 -1.35774 1.35774 6
2 -1.93509 -1.93509 -0.78038 7 2 -0.78038 -1.93509
-1.93509 8 2 -1.93509 -0.78038 -1.93509 9 2 1.93509
1.93509 -0.7803810 2 1.93509 0.78038 -1.9350911 2
0.78038 1.93509 -1.9350912 2 -0.78038 1.93509 1.9350913
2 -1.93509 0.78038 1.9350914 2 -1.93509 1.93509
0.7803815 2 1.93509 -0.78038 1.9350916 2 0.78038
-1.93509 1.9350917 2 1.93509 -1.93509 0.78038*
Both versions of waveplot (precompilied and my own build) crash with the
following error:
=====================
================================================================================
WAVEPLOT 0.3
================================================================================
Interpreting input file 'waveplot_in.hsd'
--------------------------------------------------------------------------------
WARNING!
-> The following 8 node(s) had been ignored by the parser:
(1)
Path: waveplot/Basis/C
Line: 1-41 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(2)
Path: waveplot/Basis/B
Line: 63-103 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(3)
Path: waveplot/Basis/N
Line: 105-145 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(4)
Path: waveplot/Basis/O
Line: 147-187 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(5)
Path: waveplot/Basis/Na
Line: 189-229 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(6)
Path: waveplot/Basis/Al
Line: 231-290 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(7)
Path: waveplot/Basis/Ti
Line: 414-482 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
(8)
Path: waveplot/Basis/Cu
Line: 484-552 (File:
/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd)
Processed input written as HSD to 'waveplot_pin.hsd'
Processed input written as XML to 'waveplot_pin.xml'
--------------------------------------------------------------------------------
Doing initialisation
Starting main program
Origin
-3.77945 -3.77945 -3.77945
Box
7.55890 .00000 .00000
.00000 7.55890 .00000
.00000 .00000 7.55890
Spatial resolution [1/Bohr]:
6.61472 6.61472 6.61472
*** glibc detected ***
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot:
malloc(): memory corruption: 0x0000000002fd5f20 ***
*** glibc detected ***
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot:
malloc(): memory corruption: 0x0000000002fd5f20 ***
.============
Here is the traceback from intel debugger (idbc where):=====
===========================
(idb) where
#0 0x0000000001214094 in __lll_lock_wait () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#1 0x000000000120f688 in _L_lock_854 () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#2 0x000000000000fdcf in ?? ()
#3 0x0000000001359eba in _Unwind_Find_FDE () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#4 0x0000000001356349 in uw_frame_state_for () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#5 0x00000000013577b5 in uw_init_context_1 () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#6 0x0000000001358398 in _Unwind_Backtrace () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#7 0x00000000013115b0 in __backtrace () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#8 0x00000000012e908b in __libc_message () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#9 0x00000000012ef362 in malloc_printerr () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#10 0x00000000012f2d23 in _int_malloc () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#11 0x00000000012f3a6e in __malloc () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#12 0x0000000001359648 in search_object () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#13 0x0000000001359fa2 in _Unwind_Find_FDE () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#14 0x0000000001356349 in uw_frame_state_for () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#15 0x00000000013577b5 in uw_init_context_1 () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#16 0x0000000001358398 in _Unwind_Backtrace () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#17 0x00000000013115b0 in __backtrace () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#18 0x00000000012e908b in __libc_message () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#19 0x00000000012ef362 in malloc_printerr () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#20 0x00000000012f2d23 in _int_malloc () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#21 0x00000000012f3a6e in __malloc () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#22 0x00000000012531d9 in for_alloc_allocatable () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#23 0x000000000040cd0a in inlined local_getvalue (origin=Info: symbol
origin is defined but not allocated (optimized away)
<no value>, gridvecs=Info: symbol gridvecs is defined but not allocated
(optimized away)
<no value>, eigvecsreal=Info: symbol eigvecsreal is defined but not
allocated (optimized away)
<no value>, eigvecscmpl=Info: symbol eigvecscmpl is defined but not
allocated (optimized away)
<no value>, natom=Info: symbol natom is defined but not allocated
(optimized away)
<no value>, norb=Info: symbol norb is defined but not allocated (optimized
away)
<no value>, coords=Info: symbol coords is defined but not allocated
(optimized away)
<no value>, specie=Info: symbol specie is defined but not allocated
(optimized away)
<no value>, cutoffs=Info: symbol cutoffs is defined but not allocated
(optimized away)
<no value>, istos=Info: symbol istos is defined but not allocated
(optimized away)
<no value>, angmoms=Info: symbol angmoms is defined but not allocated
(optimized away)
<no value>, stos=Info: symbol stos is defined but not allocated (optimized
away)
<no value>, tperiodic=Info: symbol tperiodic is defined but not allocated
(optimized away)
<no value>, treal=Info: symbol treal is defined but not allocated
(optimized away)
<no value>, latvecs=Info: symbol latvecs is defined but not allocated
(optimized away)
<no value>, recvecs2p=Info: symbol recvecs2p is defined but not allocated
(optimized away)
<no value>, kpoints=Info: symbol kpoints is defined but not allocated
(optimized away)
<no value>, kindexes=Info: symbol kindexes is defined but not allocated
(optimized away)
<no value>, ncell=Info: symbol ncell is defined but not allocated
(optimized away)
<no value>, cellvec=Info: symbol cellvec is defined but not allocated
(optimized away)
<no value>, tadddensities=Info: symbol tadddensities is defined but not
allocated (optimized away)
<no value>, valuereal=Info: symbol valuereal is defined but not allocated
(optimized away)
<no value>, valuecmpl=Info: symbol valuecmpl is defined but not allocated
(optimized away)
<no value>) at
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/molorb.F90:320
#24 in MOLECULARORBITAL::molecularorbital_getvalue_real (self=
(...), origin=(...), gridvecs=(...), eigvecsreal=(...), value=(...),
adddensities=<no value>) at molorb.f90:196
#25 0x0000000000401b38 in waveplot () at
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/waveplot.F90:116
#26 0x00000000004005d6 in main () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#27 0x00000000012c6edb in __libc_start_main () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
#28 0x0000000000400429 in _start () in
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/_obj_x86_64-comet-linux-ifort/waveplot
=======
and result of " backtrace full"
====
no value>) at
/home/jjakowsk/Development/DFTB+/dftb+_1.2.2_src_cpu/waveplot/src/molorb.F90:320
adddensities=<no value>Info: symbol allzero is defined but not
allocated (optimized away)
Info: symbol angmoms is defined but not allocated (optimized away)
Info: symbol atomallorbval is defined but not allocated (optimized away)
atomorbvalcmpl=
atomorbvalreal=Info: symbol cellvec is defined but not allocated
(optimized away)
Info: symbol coords is defined but not allocated (optimized away)
curcoords={{1.003402267916671e-316, 1.9762625833649862e-322,
1.0034113587245545e-316}, {4.9406564584124654e-324, 0, 0},
{4.9406564584124654e-324, 0, 0}}Info: symbol cutoffs is defined but not
allocated (optimized away)
diff={1.8280428896126122e-322, 1.171896834764303e-316,
1.2951683872905358e-318}
eigvecscmpl=Info: symbol eigvecscmpl is defined but not allocated
(optimized away)
eigvecsreal=Info: symbol eigvecsreal is defined but not allocated
(optimized away)
---Type <return> to continue, or q <return> to quit---
frac={0, 2.4521292223285412e-316, 1.1718373492605438e-316}
gridvecs=Info: symbol gridvecs is defined but not allocated (optimized
away)
Info: symbol i1 is defined but not allocated (optimized away)
Info: symbol i2 is defined but not allocated (optimized away)
Info: symbol i3 is defined but not allocated (optimized away)
Info: symbol iatom is defined but not allocated (optimized away)
Info: symbol icell is defined but not allocated (optimized away)
Info: symbol ieig is defined but not allocated (optimized away)
il=19214809
im=0Info: symbol ind is defined but not allocated (optimized away)
Info: symbol iorb is defined but not allocated (optimized away)
Info: symbol ispecie is defined but not allocated (optimized away)
Info: symbol istos is defined but not allocated (optimized away)
kindexes=Info: symbol kindexes is defined but not allocated (optimized
away)
kpoints=Info: symbol kpoints is defined but not allocated (optimized
away)
Info: symbol latvecs is defined but not allocated (optimized away)
Info: symbol natom is defined but not allocated (optimized away)
Info: symbol ncell is defined but not allocated (optimized away)
Info: symbol nnonzero is defined but not allocated (optimized away)
Info: symbol nonzeroindcontainer is defined but not allocated (optimized
away)
nonzeroindices=Info: symbol nonzeromask is defined but not allocated
(optimized away)
Info: symbol norb is defined but not allocated (optimized away)
npoints={134217728, 0, 0, 0}
origin=Info: symbol origin is defined but not allocated (optimized away)
Info: symbol phases is defined but not allocated (optimized away)
Info: symbol recvecs2p is defined but not allocated (optimized away)
=====
And my input file waveplot_in.hsd:
===
# General options
Options = {
TotalChargeDensity = Yes # Total density be plotted?
TotalChargeDifference = Yes # Total density difference plotted?
ChargeDensity = Yes # Charge density for each state?
RealComponent = Yes # Real component of the
wavefunction?
PlottedSpins = { 1 -1 }
#PlottedLevels = Range{ 4} #1: -1 } # Range {1 -1 } # Levels to
plot
#PlottedLevels = Range {1 -1 } # Levels to plot
#PlottedLevels = 4 # Range{ 4} #1: -1 } # Range {1 -1 } #
Levels to plot
PlottedLevels = 1:-1 # Range{ 4} #1: -1 } # Range {1 -1 } #
Levels to plot
PlottedRegion = { # Region to plot
Origin [Angstrom] = { -2.0 -2.0 -2.0 }
Box [Angstrom] = {
4.0 0.0 0.0
0.0 4.0 0.0
0.0 0.0 4.0
}
}
NrOfPoints = { 50 50 50 } # Number of grid points in each
direction
NrOfCachedGrids = -1 # Nr of cached grids (speeds up
things)
Verbose = Yes # Wanna see a lot of messages?
}
DetailedXML = "detailed.xml" # File containing the detailed xml
output
# of DFTB+
EigenvecBin = "eigenvec.bin" # File cointaining the binary
eigenvecs
# Definition of the basis
Basis = {
Resolution = 0.01
# Including mio-0-1.hsd. (If you use a set, which depends on other sets,
# the wfc.*.hsd files for each required set must be included in a similar
# way.
#<<+ "wfc.mio-1-1.hsd"
<<+ "/home/jjakowsk/Development/DFTB+/SlaKo/matsci-0-3/wfc.matsci-0-3.hsd"
}
======
I would appreciate any suggestion.
Jacek
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20150817/e96f7316/attachment-0001.html>
More information about the DFTB-Plus-User
mailing list