[DFTB-Plus-User] DFTB+NEGF: the Oxide radius
Yuranan Hanlumyuang
yhanlumyuang at uh.edu
Thu Apr 18 18:08:07 CEST 2013
Hi,
I post a sample input files and structure here for testing. If you
recall,
there is a problem with the oxide radius setting in the cylindrical-gate
part
of the code. If you catch anything odd in the input, please let me know.
The testing inputs yielded no oxide thickness, in a regular dftb run.
Furthermore, this set of input could run to completion when I commented
out the line
if(Rmin_ins.lt.Rmin_gate) Rmin_ins=Rmin_gate
in parcheck.F90, and recompiled dftb. However, the gate length was set
to be longer than the length of the Poisson box. When we tried to correct
the gate, length we obtained the error
scfsum: 3 NaN NaN NaN
In principles, one may test both settings using this set of inputs.
Any comments or solutions are welcome.
Sincerely,
Yuranan Hanlumyuang
University of Houston
On Tue, Apr 2, 2013 at 3:38 PM, <dftb-plus-user-request at dftb-plus.info>wrote:
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> Today's Topics:
>
> 1. Compilation Problem (debs at iitk.ac.in)
> 2. Re: DFTB+NEGF: the Oxide radius (Gabriele Penazzi)
> 3. Re: Compilation Problem (Jacek Jakowski)
> 4. cylindrical gate set up (Xiaobao)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 2 Apr 2013 17:13:10 +0530
> From: debs at iitk.ac.in
> To: dftb-plus-user at dftb-plus.info
> Subject: [DFTB-Plus-User] Compilation Problem
> Message-ID:
> <6ac4f145f2e1f387c48945cf66642aab.squirrel at webmail1.iitk.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi,
> I am new with DFTB+ and I am trying to install it in my Ubuntu 12.04 OS.
> I am getting some error which I can not able to sort out. I am using
> make.x86_64-linux-gfortran file. I have modified the make file and it is
> given below.
>
>
> # -*- makefile -*-
>
> ############################################################################
> # System dependent Makefile options for
> # Linux, gfortran (4.4.3) + Atlas (3.6.0)
>
> ############################################################################
>
> # Fortran 90 compiler
> FC90 = gfortran
>
> # Options for the Fortran 90 compiler
> FC90OPT = -O2 -openmp -funroll-all-loops -fall-intrinsics
>
> # Preprocessor (leave empty, if the compiler has a built in preprocessor)
> CPP = cpp -traditional
>
> # Options for preprocessing
> CPPOPT = -DDEBUG=$(DEBUG) #-DEXTERNALERFC
>
> # Postprocessing of the preprocessor output (add-on pipe)
> CPPPOST = $(ROOT)/utils/fpp/fpp.sh general
>
> # Linker
> LN = $(FC90)
>
> # Linker options
> LNOPT = -static
>
> # Override options for different DEBUG modes
> ifeq ($(DEBUG),1)
> FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics -fbounds-check
> endif
> ifeq ($(DEBUG),2)
> FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics -fbounds-check
> endif
> ifeq ($(DEBUG),3)
> FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics -fbounds-check
> endif
>
> # Library options in general
> ATLASDIR = /usr/lib
> LIBOPT = -L$(ATLASDIR)
>
> # How to link specific libraries
> LIB_LAPACK = -llapack
> LIB_BLAS = -lblas
> # Threaded version may work as well
> # LIB_BLAS = -lptf77blas -lptcblas -latlas
>
>
>
> The error is given below.
>
> /usr/lib/libblas.a(xerbla.o): In function `xerbla_':
> (.text+0x0): multiple definition of `xerbla_'
> /usr/lib/liblapack.a(xerbla.o):(.text+0x0): first defined here
> collect2: ld returned 1 exit status
> make[1]: *** [dftb+] Error 1
> rm disp_common.f90 qm.f90 md_integrator.f90 slako_eq_grid.f90
> short_gamma.f90 sk.f90 thirdorder.f90 rep_poly.f90 nhc_thermostat.f90
> geoopt.f90 tokenreader.f90 scc_init.f90 mainio.f90 intrinsicpr.f90
> dftb+.f90 formatout.f90 bisection.f90 inputdata_.f90 fifo.f90 memman.f90
> fact.f90 xmlutils.f90 sort.f90 md_common.f90 disp_uff.f90
> type_geometry.f90 densitymatrix.f90 shift.f90 etemp.f90 hsdutils.f90
> eigensolver.f90 andersen_thermostat.f90 extcharge.f90 dftb_pls_u.f90
> ext_erfc.f90 spinorbit.f90 stressTensor.f90 initprogram.f90
> broyden_mixer.f90 unitconversion.f90 dispersion.f90 orbital_equiv.f90
> angmomentum.f90 wrapped_pointers.f90 forces.f90 linmin.f90 diis_mixer.f90
> repulsive.f90 accuracy.f90 mixer_adt.f90 stringlist.f90 general_list.f90
> hermite.f90 hsdparser.f90 lapackroutines.f90 old_sk_data.f90
> eigenvects.f90 type_geometry_hsd.f90 berendsen_thermostat.f90
> linkedlist.f90 velocity_verlet.f90 charmanip.f90 energies.f90 scc.f90
> disp_slaterkirkwood.f90 potentials.f90 disp_uff_data.f90 message.f90
> taggedout.f90 parser.f90 blasroutines.f90 thermostat.f90 constraints.f90
> nonscc.f90 numericalDerivs.f90 populations.f90 periodic.f90 hsdutils2.f90
> temp_profile.f90 oldcompat.f90 slako_cont.f90 charge_constraints.f90
> simple_algebra.f90 rep_spline.f90 common_types.f90 dummy_thermostat.f90
> conjgrad.f90 sparse2dense.f90 simple_mixer.f90 stepdesc.f90 rep_cont.f90
> allocate.f90 fileid.f90 coulomb.f90 constants.f90 interpolation.f90
> spin.f90 anderson_mixer.f90 ranlux.f90
> make[1]: Leaving directory
> `/home/user/Downloads/dftb+_1.2.2_src/prg_dftb/_obj_x86_64-linux-gfortran'
> make: *** [_obj_x86_64-linux-gfortran] Error 2
>
> Thanking you in anticipation.
> Regards
> Deb Sankar De
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 02 Apr 2013 15:47:08 +0200
> From: Gabriele Penazzi <gabriele.penazzi at bccms.uni-bremen.de>
> To: dftb-plus-user at dftb-plus.info
> Subject: Re: [DFTB-Plus-User] DFTB+NEGF: the Oxide radius
> Message-ID: <515AE15C.1070206 at bccms.uni-bremen.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Yuranan,
>
> that part has not been tested. If you can send your input file
> (structure included) or a sample one in list I can give a look and see
> if I spot a bug, as the input file looks fine to me.
>
> Gabriele
>
>
>
> On 03/28/2013 04:43 PM, Yuranan Hanlumyuang wrote:
> > Hi
> >
> > I am exploring the cylindrical gate option in the DFTB+NEGF code.
> > This implementation is
> > found in the poisson.f90 source code. To set up a cylindrical gate, I
> > assigned the following parameters
> >
> > Gate = Cylindrical{
> > GateLength[Angstrom] = 10.0
> > GateRadius[Angstrom]= 11.0
> > Kappa=3.9
> > InsulatorLength[Angstrom]=20.0
> > InsulatorRadius[Angstrom]=7.0
> > GatePotential [eV] = 0.0001
> > }
> >
> > However, after a number of checks, the inner gate radius and inner
> > oxide radius
> > always overlap, i.e. no oxide exists in the computation. I am
> > wondering if this is a bug in
> > the code, or I have skipped some steps. The following is an example
> > of the main output.
> > The gate radius clearly coincides with the oxide radius...
> >
> > init Poisson ...
> > Atomic density tolerance: 1.0000000000000001E-005
> > Resulting atomic density cutoff: 7.5048399163437232 a.u.
> > Input PoissonBox= 25.0000 25.0000 25.0000 A
> > PoissAcc= 9.9999999999999995E-008
> > Bulk Boundary Potential: No
> > Atomic cutoff radius= 3.9713905411161612 A
> > Gate: Cylindrical
> > Gate bias= 1.0000000000000000E-004 V
> > Gate length= 10.000000000000000 A
> > Oxide length= 20.000000000000000 A
> > Inner gate radius= 11.000000000000000
> > A <======== Problem here!
> > Inner oxide radius= 11.000000000000000 A
> > <======== Problem here!
> > Dielectric constant of gate insulator= 3.8999999999999999
> > Smoothing of eps_r= 5.4802053668788773
> > Local Boundary Conditions= Squared
> > dR_cont( 1)= 2.000A
> > Local Boundary Conditions= Squared
> > dR_cont( 2)= 2.000A
> >
> > There is a following line in the code parcheck.F90:
> >
> > if(Rmin_ins.lt.Rmin_gate) Rmin_ins=Rmin_gate
> >
> >
> >
> > As another check, I plotted the voltage drop across cross-section
> > of the cylindrical gate. I observed
> > no change in the slopes of the voltage as spatial distance ran across
> > the supposed interface between
> > the oxide and vacuum region. To me, this indicates that the oxide has
> > never been taken into account when the poisson
> > equation is solved. ...
> >
> > If someone would like to test my input file, I would be happy to
> > post it here.
> > In the mean time, any comments will be greatly appreciated.
> >
> > Best,
> > Yuranan Hanlumyuang
> > University of Houston
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at dftb-plus.info
> > http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
> --
> Dr. Gabriele Penazzi
> BCCMS - University of Bremen
>
> http://www.bccms.uni-bremen.de/
> http://sites.google.com/site/gabrielepenazzi/
>
> phone: +49 (0) 421 218 62337
> fax: +49 (0) 421 218 62770
>
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 2 Apr 2013 12:04:50 -0400
> From: Jacek Jakowski <jjakowski at gmail.com>
> To: "User list for DFTB+ related questions"
> <dftb-plus-user at dftb-plus.info>
> Subject: Re: [DFTB-Plus-User] Compilation Problem
> Message-ID:
> <CAM2nsyTws8BAcFyvnXC3PCokt2N=
> 4a92VoHFs-D9Cw4B-hw2tg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> You should replace line:
> LIBOPT = -L$(ATLASDIR)
> with
> LIBOPT =
> ---
>
> Jacek
>
>
>
> On Tue, Apr 2, 2013 at 7:43 AM, <debs at iitk.ac.in> wrote:
>
> > Hi,
> > I am new with DFTB+ and I am trying to install it in my Ubuntu 12.04 OS.
> > I am getting some error which I can not able to sort out. I am using
> > make.x86_64-linux-gfortran file. I have modified the make file and it is
> > given below.
> >
> >
> > # -*- makefile -*-
> >
> >
> ############################################################################
> > # System dependent Makefile options for
> > # Linux, gfortran (4.4.3) + Atlas (3.6.0)
> >
> >
> ############################################################################
> >
> > # Fortran 90 compiler
> > FC90 = gfortran
> >
> > # Options for the Fortran 90 compiler
> > FC90OPT = -O2 -openmp -funroll-all-loops -fall-intrinsics
> >
> > # Preprocessor (leave empty, if the compiler has a built in preprocessor)
> > CPP = cpp -traditional
> >
> > # Options for preprocessing
> > CPPOPT = -DDEBUG=$(DEBUG) #-DEXTERNALERFC
> >
> > # Postprocessing of the preprocessor output (add-on pipe)
> > CPPPOST = $(ROOT)/utils/fpp/fpp.sh general
> >
> > # Linker
> > LN = $(FC90)
> >
> > # Linker options
> > LNOPT = -static
> >
> > # Override options for different DEBUG modes
> > ifeq ($(DEBUG),1)
> > FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics
> -fbounds-check
> > endif
> > ifeq ($(DEBUG),2)
> > FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics
> -fbounds-check
> > endif
> > ifeq ($(DEBUG),3)
> > FC90OPT = -g -Wall -std=f2003 -pedantic -fall-intrinsics
> -fbounds-check
> > endif
> >
> > # Library options in general
> > ATLASDIR = /usr/lib
> > LIBOPT = -L$(ATLASDIR)
> >
> > # How to link specific libraries
> > LIB_LAPACK = -llapack
> > LIB_BLAS = -lblas
> > # Threaded version may work as well
> > # LIB_BLAS = -lptf77blas -lptcblas -latlas
> >
> >
> >
> > The error is given below.
> >
> > /usr/lib/libblas.a(xerbla.o): In function `xerbla_':
> > (.text+0x0): multiple definition of `xerbla_'
> > /usr/lib/liblapack.a(xerbla.o):(.text+0x0): first defined here
> > collect2: ld returned 1 exit status
> > make[1]: *** [dftb+] Error 1
> > rm disp_common.f90 qm.f90 md_integrator.f90 slako_eq_grid.f90
> > short_gamma.f90 sk.f90 thirdorder.f90 rep_poly.f90 nhc_thermostat.f90
> > geoopt.f90 tokenreader.f90 scc_init.f90 mainio.f90 intrinsicpr.f90
> > dftb+.f90 formatout.f90 bisection.f90 inputdata_.f90 fifo.f90 memman.f90
> > fact.f90 xmlutils.f90 sort.f90 md_common.f90 disp_uff.f90
> > type_geometry.f90 densitymatrix.f90 shift.f90 etemp.f90 hsdutils.f90
> > eigensolver.f90 andersen_thermostat.f90 extcharge.f90 dftb_pls_u.f90
> > ext_erfc.f90 spinorbit.f90 stressTensor.f90 initprogram.f90
> > broyden_mixer.f90 unitconversion.f90 dispersion.f90 orbital_equiv.f90
> > angmomentum.f90 wrapped_pointers.f90 forces.f90 linmin.f90 diis_mixer.f90
> > repulsive.f90 accuracy.f90 mixer_adt.f90 stringlist.f90 general_list.f90
> > hermite.f90 hsdparser.f90 lapackroutines.f90 old_sk_data.f90
> > eigenvects.f90 type_geometry_hsd.f90 berendsen_thermostat.f90
> > linkedlist.f90 velocity_verlet.f90 charmanip.f90 energies.f90 scc.f90
> > disp_slaterkirkwood.f90 potentials.f90 disp_uff_data.f90 message.f90
> > taggedout.f90 parser.f90 blasroutines.f90 thermostat.f90 constraints.f90
> > nonscc.f90 numericalDerivs.f90 populations.f90 periodic.f90 hsdutils2.f90
> > temp_profile.f90 oldcompat.f90 slako_cont.f90 charge_constraints.f90
> > simple_algebra.f90 rep_spline.f90 common_types.f90 dummy_thermostat.f90
> > conjgrad.f90 sparse2dense.f90 simple_mixer.f90 stepdesc.f90 rep_cont.f90
> > allocate.f90 fileid.f90 coulomb.f90 constants.f90 interpolation.f90
> > spin.f90 anderson_mixer.f90 ranlux.f90
> > make[1]: Leaving directory
> >
> `/home/user/Downloads/dftb+_1.2.2_src/prg_dftb/_obj_x86_64-linux-gfortran'
> > make: *** [_obj_x86_64-linux-gfortran] Error 2
> >
> > Thanking you in anticipation.
> > Regards
> > Deb Sankar De
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at dftb-plus.info
> > http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
> >
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> ------------------------------
>
> Message: 4
> Date: Wed, 3 Apr 2013 04:23:22 +0800 (CST)
> From: Xiaobao <xiaobaojsyz at 163.com>
> To: dftb-plus-user at dftb-plus.info
> Subject: [DFTB-Plus-User] cylindrical gate set up
> Message-ID: <2c9f7398.485.13dcc6b1305.Coremail.xiaobaojsyz at 163.com>
> Content-Type: text/plain; charset="gbk"
>
> Hi,
>
> Anyone know how to set up a cylindrical gate? I referred the manual, it
> says now Planar gate is allowed, however, when we check the source code,
> seems there is some way to set up a cylindrical gate and also there are
> already some work used cylindrical gate. I would be very appreciated if you
> can give some idea. My current try is:
> Gate = Cylindrical{
> GateLength [Angstrom] = 10.0
> GateRadius [Angstrom] = 18.0
> kappa = 3.9
> InsulatorLength [Angstrom] = 20.0
> InsulatorRadius[Angstrom]=12.0
> GatePotential [eV]= 0.001
> }
> but the runs are not converge. If I remove this part, then it converges
> well. I have tried to vary the radius and length, but it did not help. I am
> guessing there is something wrong with gate setup. Thank you for your help!
> xiaobao,
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>
> _______________________________________________
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> DFTB-Plus-User at dftb-plus.info
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