Siesta

Unable to generate DMHS.nc file

Asked by sukhito teh

Hi all. I am a new user of siesta(version 4.1) and I am trying to get the density matrix in NDF4 format, i.e. DM.nc file. I had specified the following parameters in my input files:
CDF.Compress 9
CDF.Save True
SaveHS True
Write.DMHS.Netcdf True
Write.H True
WriteDMHS.History.NetCDF False
SCFMustConverge True

After the calculation had finished, I did obtain the SystemLabel.nc file but not the DMHS.nc file. When I take a look at the OUTVARS.yml file, the netcdf and netcdf4_mpi flags are off, can this be the reason for the mentioned problem?
siesta:
  version: "master-post-4.1-264"
  arch: "unknown"
  compiler: "ifort (IFORT) 19.0.5.281 20190815"
  fflags: "mpifort -O2 -fPIC -fp-model source -mkl=sequential -I/cluster/intel-2019u5/neetcdf-4-4.6.3/include -I/cluster/intel-2019u5/hdf5-1.8.21/include"
  fppflags: "-DFC_HAVE_ABORT -DMPI -DNCDF -DNCDF_4"
  libs: "libncdf.a libfdict.a -L/cluster/intel/compilers_and_libraries_2019.5.281/linuux/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -L/cluster/intel-2019u5/netcdf-4-4.6.3/lib -lnetcdff -lnetcdf -L/cluster/intel-2019u5/hdf5-1.8.21/lib -lhdf5_fortran -lhdf5 -lz"
  build: "mpi"
  openmp: "no"
  gemm3m: "no"
  netcdf: "no"
  netcdf4: "yes"
  netcdf4_mpi: "no"
  metis: "no"
  chess: "no"
  elpa: "no"
  flook: "no"
  pexsi: "no"

Please let me know if you find out what are the causes for this problem. Thank you for your time.

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Nick Papior
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Best Nick Papior (nickpapior) said : 		#1

Yes.

You should also use the flag -DCDF.

However, the SystemLabel.nc also contains the DM, so it should be there?

What do you want?

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sukhito teh (sukhitoteh) said : 		#2

Thank you for the reply. I am using a Python package named TB2J, and it required Hamiltonian and matrices of Overlap Wavefunction .
Honestly, I don't know how to read information from these files, so I am basically following the instruction of TB2J which had stated DMHS.nc and SystemLabel.nc as required input files. Are all information in DMHS.nc included in SystemLabel.nc file as well?

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Nick Papior (nickpapior) said : 		#3

Yes, they are :)

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sukhito teh (sukhitoteh) said : 		#4

Thank you for all the reply. The problem was solved after NETCFD3 flag (DCDF) was used in compilation.

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sukhito teh (sukhitoteh) said : 		#5

Thanks Nick Papior, that solved my question.