I have a problem using the a-TDEP post-processing tool.
I installed abinit on my computer using abiconda (https://github.com/abinit/abiconda). That worked and now I am able to run md calculations with abinit. I was also able to do the TDEP analysis on the "t37_HIST.nc" trajectory as explained in the guide (https://docs.abinit.org/theory/a-TDEP/a-TDEP_Guide.pdf).
My issue is that I am not able to do a TDEP analysis on a new trajectory I got via MD calculations with abinit (or with VASP via the vasprun.xml). I think that the problem is related to the "*_HIST.nc" file created by the MD calculations because I also generated input.in files via the qTDEP-tool.
Input files:
"mdto.in" to generate the "mdto_HIST.nc" file (ran without issues):
Code: Select all
prtden 0 prtwf 0 prteig 0
#Definition of the atoms
acell 6.32 6.32 6.32
rprim 1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
natom 5
ntypat 3
znucl 55 82 53
xred 0.51 0.52 0.53 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5
typat 1 2 3 3 3
#Definition of the planewave basis set
ecut 10
#Definition of the k-point grid
kptopt 1
ngkpt 1 1 1
nshiftk 1
shiftk 0.5 0.5 0.5
#Definition of the SCF procedure
nstep 30
toldfe 1.0d-6
diemac 5.0
#Definition of XC funtional (PBE-D3(BJ))
ixc 11
vdw_xc 7
#vdw_tol 1.0d-10
iomode 1
#Molecular Dynamics parameters
ionmov 8
ntime 120
dtion 100
mdtemp 300 300
optcell 0
## After modifying the following section, one might need to regenerate the pickle database with runtests.py -r
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
#%% [files]
#%% files_to_test =
#%% tbase1_1.out, tolnlines= 0, tolabs= 0.000e+00, tolrel= 0.000e+00
#%% psp_files = 01h.pspgth
#%% [paral_info]
#%% max_nprocs = 1
#%% [extra_info]
#%% authors = Unknown
#%% keywords =
#%% description = H2 molecule in a big box
#%%<END TEST_INFO>
Code: Select all
NormalMode
# Unit cell definition
brav 1 0
angle 9.000000000e+01 9.000000000e+01 9.000000000e+01
natom_unitcell 5
xred_unitcell 5.100000000e-01 5.200000000e-01 5.300000000e-01 0.000000000e+00 0.000000000e+00 0.000000000e+00 5.000000000e-01 0.000000000e+00 0.000000000e+00 0.000000000e+00 5.000000000e-01 0.000000000e+00 0.000000000e+00 0.000000000e+00 5.000000000e-01
typat_unitcell 1 2 3 3 3
# Supercell definition
multiplicity 1.00 0.00 0.00 -0.00 1.00 0.00 -0.00 -0.00 1.00
temperature 1253.25
# Computation details
nstep_max 120
nstep_min 1
Rcut 3.160
# Optional inputs
Slice 1
Ngqpt2 2 2 2
DosDeltae 0.000005
Use_Ideal_Positions 1
TheEnd
output when trying qTDEP-tool (same error if I run "tdep <input.files> log" in a terminal) :
OpenGL might use VBO
Give name for input file
.input.in
Give name for HIST file
.mdto_HIST.nc
Give root name for generic output files:
1253.25K
Succesfully open mdto_HIST.nc for reading
Extracting information from NetCDF file...
At line 340 of file m_tdep_readwrite.F90 (unit = 40, file = 'input.in')
Fortran runtime error: Bad integer for item 2 in list input
Error termination. Backtrace:
#0 0x7f479777d024 in read_integer
at /home/conda/feedstock_root/build_artifacts/ctng-compilers_1598124794965/work/.build/x86_64-conda-linux-gnu/src/gcc/libgfortran/io/list_read.c:1099
#1 0x7f479777f1a1 in list_formatted_read_scalar
at /home/conda/feedstock_root/build_artifacts/ctng-compilers_1598124794965/work/.build/x86_64-conda-linux-gnu/src/gcc/libgfortran/io/list_read.c:2170
#2 0x56375d1212b1 in __m_tdep_readwrite_MOD_tdep_readecho
at /home/gmatteo/miniconda3/conda-bld/abinit_1571600667188/work/src/80_tdep/m_tdep_readwrite.F90:340
#3 0x56375d107393 in tdep
at /home/gmatteo/miniconda3/conda-bld/abinit_1571600667188/work/src/98_main/tdep.F90:112
#4 0x56375d106eae in main
at /home/gmatteo/miniconda3/conda-bld/abinit_1571600667188/work/src/98_main/tdep.F90:51
my questions:
1. In the "t37_HIST.nc" example on github (https://github.com/abinit/abinit/tree/m ... s/v8/Input), how is this trajectory calculated, what are the input files to generate this trajectory?
2. Are there certain criteria that should be taken into account for the trajectory (e.g. NVT ensemble)?
3. To use trajectories generated via other codes, it would be easier to do the TDEP analysis via the ASCII files fcart.dat, xred.dat and etot.dat, as explained in the guide (because "*_HIST.nc" files are not human readable). How do these files look like and how do I need to change the input.files file and input.in file or could you give an example that works?