Error with dihedral constraints in optimization #601
Description
Describe the bug
It seems that I cannot run the xtb when numpy is installed at the same time.
To Reproduce
I create the environment with the script
>>> environment.yml
name: test
channels:
- conda-forge
dependencies:
- xtb
- numpy>=1.11
# Testing
- pytest
- pytest-cov
- codecov
Then I create the conda environment with
conda env create -f environment.yml
conda activate test
Then I create the xtb input file
>>> cat input.xyz
4
H -0.9009500 -0.5085100 -0.7673400
O -0.7280500 0.0249600 0.0239800
O 0.7276200 0.0331600 -0.0269600
H 0.9078200 -0.4139400 0.8146500
>>> cat input.inp
$constrain
force constant=15.0
dihedral: 2, 3, 4, 5, 0
$end
and run xtb
xtb input.xyz --opt --chrg 0 --uhf 0 --gfn 2 --parallel 1 --input input.inp
I got
........................................................................
.............................. CYCLE 43 ..............................
........................................................................
xtb(3410,0x204068600) malloc: Heap corruption detected, free list is damaged at 0x6000018cc4e0
*** Incorrect guard value: 4611367869590665140
xtb(3410,0x204068600) malloc: *** set a breakpoint in malloc_error_break to debug
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x10cd6f4dc
#1 0x10cd6e84d
#2 0x7ff812567e2c
#3 0x7ff81251c113
#4 0x7ff812552214
#5 0x7ff81249ed10
#6 0x7ff8123793e2
#7 0x7ff81238d2f2
#8 0x7ff81236c09e
#9 0x7ff81236b619
#10 0x7ff81236b546
#11 0x7ff812387ad6
#12 0x100a70ae1
#13 0x100ba218e
#14 0x100a65478
#15 0x100bbccfb
#16 0x100b44d4b
#17 0x100b481d0
#18 0x100ae9300
#19 0x1008da09e
#20 0x100bdc4ac
zsh: abort xtb input.xyz --opt --chrg 0 --uhf 0 --gfn 2 --parallel 1 --input input.inp
This is not an issue when I remove the numpy from the conda environment list.