a-TDEP input error

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tbraecke
Posts: 1
Joined: Tue Sep 22, 2020 3:52 pm

a-TDEP input error

Post by tbraecke » Wed Sep 23, 2020 2:40 pm

Dear developers

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>
With the resulting "mdto_HIST.nc" and following input.in file (generated via qTDEP), I had an error doing the a-TDEP post analysis:

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
The error:

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?

ebousquet
Posts: 449
Joined: Tue Apr 19, 2011 11:13 am
Location: University of Liege, Belgium

Re: a-TDEP input error

Post by ebousquet » Tue Oct 13, 2020 4:01 pm

Dear tbraecke,
Sounds like you got a response from private contact with the developer. Could tell us what was the problem and solution?
Best wishes,
Eric

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