Commit cc4d7315 authored by Nick R. Papior's avatar Nick R. Papior
Browse files

Updated transiesta-tbtrans tests with the new settings

- Everything seems in order. In fact some of the
  convergence properties are now better due to the
  constraint on the Hamiltonian.

- Fixed the print-out of error on the energy density
  matrix to print in eV.

- Fixed scripts for TS tests to only compile tbtrans
  if it isn't already compiled.

- Removed mentions of old flags in the TS test.
  Also corrected those which have farther than principal
  cell connections.
  In these situations I have added a remark for the flag
  so it should be clear its use is highly discouraged.
parent 8092b66f
......@@ -10771,7 +10771,7 @@ for the electrodes (with \fdf{TS!Elec.<>} taking precedence).
the principal cell.
\note set this to \fdftrue\ with care, non-physical results may
arise.
arise. Use at your own risk!
\end{fdflogicalF}
......
......@@ -1382,7 +1382,7 @@ for the electrodes (with \fdf{TBT.Elec.<>} taking precedence).
the principal cell.
\note set this to \fdftrue\ with care, non-physical results may
arise.
arise. Use at your own risk!
\end{fdflogicalF}
......
......@@ -130,7 +130,8 @@ contains
subroutine weight_DM(N_Elec,Elecs,N_mu, mus, na_u, lasto, &
spDM, spDMneq, spEDM, n_s, sc_off)
use units, only: eV
#ifdef MPI
use mpi_siesta
#endif
......@@ -642,8 +643,8 @@ contains
! Reduce number of updated elements
allocate(DM(3,2))
DM(1,1) = real(n_nzs,dp)
DM(2,1) = m_err ! DM mean-error
DM(3,1) = Em_err ! EDM mean-error
DM(2,1) = m_err ! DM mean-error
DM(3,1) = Em_err ! EDM mean-error
call MPI_Reduce(DM(1,1),DM(1,2),3,MPI_Double_Precision, &
MPI_SUM, 0, MPI_Comm_World, MPIerror)
! Get total number of updated elements
......@@ -725,8 +726,12 @@ contains
call print_error_estimate(IONode,'ts-err-D:', &
eM,ew,eM_i,eM_j,DMe,m_err)
if ( hasEDM ) then
call print_error_estimate(IONode,'ts-err-E:', &
EeM,Eew,EeM_i,EeM_j,EDMe,Em_err)
EeM = EeM / eV
Eew = Eew / eV
EDMe = EDMe / eV
Em_err = Em_err / eV
call print_error_estimate(IONode,'ts-err-E:', &
EeM,Eew,EeM_i,EeM_j,EDMe,Em_err)
end if
#ifdef TRANSIESTA_DEBUG
......
Siesta Version: trunk-507---ts-scf-685
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -Warray-temporaries -fcheck=array-temps -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG -DTRANSIESTA
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
PARALLEL version
TRANSIESTA support
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 2-JUN-2016 17:42:39
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.20250
************************** Dump of input data file ****************************
SystemName elec_au_111_abc
SystemLabel elec_au_111_abc
......@@ -105,8 +92,22 @@ WriteEigenvalues yes
reinit: -----------------------------------------------------------------------
reinit: System Name: elec_au_111_abc
reinit: -----------------------------------------------------------------------
reinit: System Label: elec_au_111_abc
reinit: System Label: elec_au_111_abc
reinit: -----------------------------------------------------------------------
Siesta Version: trunk-557
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG -DTRANSIESTA
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PARALLEL version
TRANSIESTA support
NetCDF support
NetCDF-4 support
NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 18-AUG-2016 21:56:26
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 79 Label: Au
......@@ -285,7 +286,7 @@ siesta: System type = bulk
initatomlists: Number of atoms, orbitals, and projectors: 3 27 48
coxmol: Writing XMOL coordinates into file elec_au_111_abc.xyz
coxmol: Writing XMOL coordinates into file elec_au_111_abc.xyz
siesta: ******************** Simulation parameters ****************************
siesta:
......@@ -293,9 +294,10 @@ siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin-spiral = F
redata: Long output = F
redata: Number of Atomic Species = 1
redata: Charge density info will appear in .RHO file
......@@ -304,6 +306,7 @@ redata: Mesh Cutoff = 350.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 300
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
......@@ -313,13 +316,16 @@ redata: New DM Mixing Weight = 0.0300
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: DM Tolerance for SCF = 0.000100
redata: Require H convergence for SCF = F
redata: Hamiltonian Tolerance in SCF = 0.000100 Ry
redata: Require (free) Energy convergence in SCF = F
redata: DM (free)Energy tolerance for SCF = 0.000010 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris energy tolerance for SCF = 0.000010 eV
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.0001
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
......@@ -332,10 +338,30 @@ mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 5
mix.SCF: Linear mixing weight = 0.030000
mix.SCF: Damping = 0.030000
mix.SCF: Mixing weight = 0.030000
mix.SCF: SVD condition = 0.1000E-07
redata: Save data in SIESTA.nc = F
redata: ***********************************************************************
%block SCF.Mixers
Pulay
%endblock SCF.Mixers
%block SCF.Mixer.Pulay
# Mixing method
method pulay
variant stable
# Mixing options
weight 0.0300
weight.linear 0.0300
history 5
restart 0
restart.save 1
# Continuation options
%endblock SCF.Mixer.Pulay
DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 33.000000
......@@ -436,40 +462,41 @@ cdiag-debug: Node=0, lwork= 1148>= lworkq= 5535, lrwork= 243>= l
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -215.406896
siesta: Ebs = -264.770512
siesta: Eions = 3513.674752
siesta: Ena = 174.746453
siesta: Ekin = 1995.610445
siesta: Enl = -937.365313
siesta: EldaU = 0.000000
siesta: DEna = 0.000001
siesta: DUscf = 0.000000
siesta: Ekin = 1869.332386
siesta: Enl = -859.638120
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 34.134750
siesta: DUscf = 2.421423
siesta: DUext = 0.000000
siesta: Exc = -433.822196
siesta: Exc = -420.772220
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -2715.297671
siesta: Etot = -2714.505362
siesta: FreeEng = -2714.505804
siesta: Eharris = -2710.535822
siesta: Etot = -2713.450080
siesta: FreeEng = -2713.450522
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)dHmx(Ry)
scf: 1 -2715.2977 -2714.5054 -2714.5058 0.2202 -2.4747 -1.0000
timer: Routine,Calls,Time,% = IterSCF 1 14.036 82.97
scf: 2 -2715.1899 -2714.5275 -2714.5279 0.2166 -2.5188 -1.0000
scf: 3 -2714.0654 -2713.9626 -2713.9628 0.1093 -3.5476 -1.0000
scf: 4 -2714.0551 -2713.9777 -2713.9780 0.0977 -3.5266 -1.0000
scf: 5 -2714.0314 -2713.9721 -2713.9724 0.0013 -3.4191 -1.0000
scf: 6 -2714.0314 -2713.9749 -2713.9752 0.0014 -3.4190 -1.0000
scf: 7 -2714.0314 -2714.0323 -2714.0326 0.0002 -3.4177 -1.0000
scf: 8 -2714.0314 -2714.0303 -2714.0307 0.0001 -3.4178 -1.0000
scf: 9 -2714.0314 -2714.0314 -2714.0317 0.0000 -3.4178 -1.0000
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -2710.535822 -2713.450080 -2713.450522 0.220190 -2.474736 1.770049
timer: Routine,Calls,Time,% = IterSCF 1 13.720 82.95
scf: 2 -2713.552048 -2713.501250 -2713.501669 0.003041 -2.518453 1.692743
scf: 3 -2714.399726 -2714.031333 -2714.031651 0.058907 -3.404162 0.023979
scf: 4 -2714.031060 -2714.031235 -2714.031556 0.001172 -3.422817 0.021486
scf: 5 -2714.031458 -2714.031365 -2714.031686 0.001288 -3.418100 0.001858
scf: 6 -2714.031364 -2714.031365 -2714.031685 0.000080 -3.417042 0.002725
scf: 7 -2714.031368 -2714.031367 -2714.031687 0.000361 -3.417816 0.000195
scf: 8 -2714.031367 -2714.031367 -2714.031687 0.000022 -3.417765 0.000003
SCF Convergence by dDmax criteria
max |DM_out - DM_in|: 0.00000114
SCF cycle converged after 9 iterations
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000218475
max |H_out - H_in| (eV) : 0.0000026756
SCF cycle converged after 8 iterations
Using DM_out to compute the final energy and forces
......@@ -486,7 +513,7 @@ siesta: Atomic forces (eV/Ang):
----------------------------------------
Max 0.000000 constrained
Stress-tensor-Voigt (kbar): 26.44 26.44 52.94 -0.00 0.00 0.00
Stress-tensor-Voigt (kbar): 26.44 26.44 52.94 -0.00 -0.00 -0.00
(Free)E + p*V (eV/cell) -2715.1982
Target enthalpy (eV/cell) -2714.0317
......@@ -505,7 +532,7 @@ Atom Qatom Qorb
mulliken: Qtot = 33.000
coxmol: Writing XMOL coordinates into file elec_au_111_abc.xyz
coxmol: Writing XMOL coordinates into file elec_au_111_abc.xyz
siesta: Eigenvalues (eV):
ik is eps
......@@ -6389,19 +6416,20 @@ siesta: Eigenvalues (eV):
1960 1 -10.58 -9.89 -9.89 -9.48 -9.48 -8.07 -8.06 -6.78 -6.78 -6.19
-6.19 -5.42 -5.41 -5.27 -5.27 -3.93 -2.17 -2.17 -0.58 4.46
4.46 8.20 8.20 11.32 11.32 19.01 19.02
siesta: Fermi energy = -3.417764 eV
siesta: Fermi energy = -3.417765 eV
siesta: Program's energy decomposition (eV):
siesta: Ebs = -250.027541
siesta: Ebs = -250.027565
siesta: Eions = 3513.674752
siesta: Ena = 174.746453
siesta: Ekin = 1909.084379
siesta: Enl = -884.137746
siesta: EldaU = 0.000000
siesta: DEna = 23.462927
siesta: Ekin = 1909.084400
siesta: Enl = -884.137759
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 23.462921
siesta: DUscf = 1.156166
siesta: DUext = 0.000000
siesta: Exc = -424.668794
siesta: Exc = -424.668796
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
......@@ -6412,21 +6440,23 @@ siesta: Etot = -2714.031367
siesta: FreeEng = -2714.031687
siesta: Final energy (eV):
siesta: Band Struct. = -250.027541
siesta: Kinetic = 1909.084379
siesta: Hartree = 308.792170
siesta: Band Struct. = -250.027565
siesta: Kinetic = 1909.084400
siesta: Hartree = 308.792180
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -424.668794
siesta: Ion-electron = -2220.937003
siesta: Exch.-corr. = -424.668796
siesta: Ion-electron = -2220.937032
siesta: Ion-ion = -2286.302119
siesta: Ekinion = 0.000000
siesta: Total = -2714.031367
siesta: Fermi = -3.417765
siesta: Stress tensor (static) (eV/Ang**3):
siesta: 0.016503 -0.000000 0.000000
siesta: -0.000000 0.016503 0.000000
siesta: 0.000000 0.000000 0.033043
siesta: 0.016503 -0.000000 -0.000000
siesta: -0.000000 0.016503 -0.000000
siesta: -0.000000 -0.000000 0.033043
siesta: Cell volume = 52.983633 Ang**3
......@@ -6434,7 +6464,7 @@ siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: -0.00023979 -0.00023979 Ry/Bohr**3
siesta: -0.02201655 -0.02201655 eV/Ang**3
siesta: -35.27477532 -35.27477646 kBar
siesta: -35.27479099 -35.27479058 kBar
(Free)E+ p_basis*V_orbitals = -2711.952916
(Free)Eharris+ p_basis*V_orbitals = -2711.952916
>> End of run: 2-JUN-2016 17:44:59
>> End of run: 18-AUG-2016 21:58:17
TBtrans Version: trunk-507---ts-scf-685
TBtrans Version: trunk-557
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -Warray-temporaries -fcheck=array-temps -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG -DTBTRANS
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PARALLEL version
NetCDF support
NetCDF-4 support
......@@ -10,7 +10,7 @@ NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 2-JUN-2016 18:07:45
>> Start of run: 18-AUG-2016 22:27:45
************************
* WELCOME TO TBtrans *
......@@ -132,7 +132,8 @@ TS.Voltage 1.00000 eV
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.DM.Update none
TS.Elecs.Neglect.Principal true
TS.Elecs.GF.ReUse true
%block TS.Elecs
Left
......@@ -153,7 +154,7 @@ TS.Elecs.GF.ReUse true
TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
part circle
from -30.00000 eV + V/2 to -10. kT + V/2
from -40.00000 eV + V/2 to -10. kT + V/2
points 30
method g-legendre
%endblock TS.Contour.c-Left
......@@ -165,7 +166,7 @@ TS.Contours.Eq.Pole 2.50000 eV
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
part circle
from -30.00000 eV - V/2 to -10. kT - V/2
from -40.00000 eV - V/2 to -10. kT - V/2
points 30
method g-legendre
%endblock TS.Contour.c-Right
......@@ -175,7 +176,7 @@ TS.Contours.Eq.Pole 2.50000 eV
points 10
method g-fermi
%endblock TS.Contour.t-Right
TS.Elecs.Eta 0.0001000000 eV
TS.Elecs.Eta 0.0001 eV
%block TS.Contours.nEq
neq
%endblock TS.Contours.nEq
......@@ -204,9 +205,6 @@ reinit: System Name: au_111_capacitor
reinit: -----------------------------------------------------------------------
reinit: System Label: au_111_capacitor
reinit: -----------------------------------------------------------------------
redata: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
......@@ -239,6 +237,7 @@ tbt: Saving down-folded self-energies = F
tbt: No delta-Hamiltonian
tbt: Data files stored in current folder
tbt: No compression of TBT.nc files
tbt: Default NetCDF precision = single
tbt: Use parallel MPI-IO for NetCDF file = F
tbt: >> Electrodes <<
tbt: >> Left
......@@ -254,6 +253,7 @@ tbt: Electronic temperature = 99.999269 K
tbt: Bulk values in electrode = T
tbt: Hamiltonian E-C Ef fractional shift = 0.0000
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 2.3867 Ang
tbt: >> Right
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
......@@ -268,6 +268,7 @@ tbt: Electronic temperature = 99.999269 K
tbt: Bulk values in electrode = T
tbt: Hamiltonian E-C Ef fractional shift = 0.0000
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 2.3867 Ang
ts: >> TBtrans contour <<
ts: Device Green function imaginary Eta = 0.000 eV
......@@ -374,30 +375,64 @@ tbtrans: Sum of electrode and sparse memory: 1.461 MB
tbtrans: Initializing data file: au_111_capacitor.TBT.nc
tbtrans: LHS Green function size / memory: 8748 / 0.13 MB
tbtrans: RHS Green function size / memory: 1620 / 0.02 MB
tbt: Initial ETA in 20.388 s
tbt: Calculated 5.000 %, ETA in 13.148 s
tbt: Calculated 10.000 %, ETA in 12.024 s
tbt: Calculated 15.000 %, ETA in 10.291 s
tbt: Calculated 20.000 %, ETA in 9.760 s
tbt: Calculated 25.000 %, ETA in 9.396 s
tbt: Calculated 30.000 %, ETA in 8.932 s
tbt: Calculated 35.000 %, ETA in 8.387 s
tbt: Calculated 40.000 %, ETA in 7.458 s
tbt: Calculated 45.000 %, ETA in 6.693 s
tbt: Calculated 50.000 %, ETA in 6.184 s
tbt: Calculated 55.000 %, ETA in 5.626 s
tbt: Calculated 60.000 %, ETA in 5.024 s
tbt: Calculated 65.000 %, ETA in 4.258 s
tbt: Calculated 70.000 %, ETA in 3.552 s
tbt: Calculated 75.000 %, ETA in 2.997 s
tbt: Calculated 80.000 %, ETA in 2.423 s
tbt: Calculated 85.000 %, ETA in 1.816 s
tbt: Calculated 90.000 %, ETA in 1.202 s
tbt: Calculated 95.000 %, ETA in 0.598 s
tbt: Completed in 11.964 s
tbt: Initial ETA in 61.164 s
tbt: Calculated 5.000 %, ETA in 13.756 s
tbt: Calculated 10.000 %, ETA in 11.808 s
tbt: Calculated 15.000 %, ETA in 9.973 s
tbt: Calculated 20.000 %, ETA in 9.296 s
tbt: Calculated 25.000 %, ETA in 8.904 s
tbt: Calculated 30.000 %, ETA in 8.428 s
tbt: Calculated 35.000 %, ETA in 7.911 s
tbt: Calculated 40.000 %, ETA in 7.026 s
tbt: Calculated 45.000 %, ETA in 6.292 s
tbt: Calculated 50.000 %, ETA in 5.804 s
tbt: Calculated 55.000 %, ETA in 5.282 s
tbt: Calculated 60.000 %, ETA in 4.707 s
tbt: Calculated 65.000 %, ETA in 3.985 s
tbt: Calculated 70.000 %, ETA in 3.321 s
tbt: Calculated 75.000 %, ETA in 2.799 s
tbt: Calculated 80.000 %, ETA in 2.262 s
tbt: Calculated 85.000 %, ETA in 1.696 s
tbt: Calculated 90.000 %, ETA in 1.123 s
tbt: Calculated 95.000 %, ETA in 0.558 s
tbt: Completed in 11.152 s
Currents (ensure entire Fermi function window):
Left -> Right, V [V] / I [A]: 0.999999 V / 0.00000 A
Left -> Right, V [V] / P [W]: 0.999999 V / 0.00000 W
>> End of run: 2-JUN-2016 18:07:57
Section Calls Walltime %
global_section 1 12.006 100.00
tbtrans 1 12.006 100.00
MPI_COMM_RANK 1 0.000 0.00
MPI_COMM_SIZE 1 0.000 0.00
MPI_BCAST 110 0.002 0.01
MPI_BARRIER 3 0.001 0.00
tri-init 1 0.005 0.04
tri-init-elec 1 0.002 0.02
TS-rgn2tri 1 0.000 0.00
MPI_BCAST 6 0.000 0.00
TS-rgn2tri 1 0.001 0.01
MPI_BCAST 4 0.001 0.01
TBT 1 11.882 98.96
MPI_BCAST 39 0.002 0.02
setup-HS 34 0.132 1.10
MPI_ALLGATHER 3400 0.009 0.07
read-GS 1700 10.197 84.94
MPI_ALLREDUCE 1700 0.003 0.03
SE-dwn 1700 0.271 2.25
ts_expand 3400 0.005 0.05
insert-SE 10200 0.009 0.08
Gf-prep 1700 0.165 1.38
insert-SED 3400 0.018 0.15
V_TM_Pinv 1700 0.117 0.98
DOS-Gf-A-T 1700 0.100 0.83
dGFGGF 1700 0.063 0.53
A-Block-Gamma 1700 0.014 0.12
TT-eig 1700 0.019 0.16
cdf-w-T 1700 0.270 2.25
MPI_RECV 3400 0.021 0.18
MPI_BARRIER 1 0.000 0.00
cdf2ascii 1 0.058 0.48
>> End of run: 18-AUG-2016 22:27:57
TBtrans Version: trunk-507---ts-scf-685
TBtrans Version: trunk-557
Architecture : x86_64-linux-gcc
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -Warray-temporaries -fcheck=array-temps -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
Compiler flags: mpif90 -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PP flags : -DSIESTA__FLOOK -DSIESTA__METIS -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DGRID_DP -DMPI_TIMING -DTRANSIESTA_TIMING -DTBTRANS_TIMING -DSIESTA__MUMPS -DNCDF_PARALLEL -DNCDF -DNCDF_4 -DSCALAPACK_DEBUG -DTBTRANS
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz
Libraries : -lzmumps -lmumps_common -lpord -lparmetis -lmetis -L/opt/scalapack/204/gnu-6.1.0/lib -Wl,-rpath=/opt/scalapack/204/gnu-6.1.0/lib -lscalapack -L/opt/openblas/0.2.17/gnu-6.1.0/lib -Wl,-rpath=/opt/openblas/0.2.17/gnu-6.1.0/lib -lopenblas -L/home/nicpa/phd/esl/flook -lflookall -ldl -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -m64 -fPIC -O3 -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fgraphite -fipa-icf -fipa-pure-const -march=native -fschedule-fusion -fselective-scheduling -fipa-sra -fipa-cp -fno-second-underscore -I/opt/zlib/1.2.8/gnu-6.1.0/include -I/opt/hdf5/1.8.16/gnu-6.1.0/include -I/opt/pnetcdf/1.7.0/gnu-6.1.0/include -I/opt/netcdf/4.4.0/gnu-6.1.0/include -I/opt/openmpi/1.10.2/gnu-6.1.0/include -I/opt/mumps/5.0.1/gnu-6.1.0/include
PARALLEL version
NetCDF support
NetCDF-4 support
......@@ -10,7 +10,7 @@ NetCDF-4 MPI-IO support
METIS ordering support
* Running on 2 nodes in parallel
>> Start of run: 2-JUN-2016 17:54:52
>> Start of run: 18-AUG-2016 22:05:54
************************
* WELCOME TO TBtrans *
......@@ -126,7 +126,8 @@ TS.Voltage 0.00000 eV
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update cross-terms
TS.Elecs.DM.Update none
TS.Elecs.Neglect.Principal true
TS.Elecs.GF.ReUse true
%block TS.Elecs
Left
......@@ -147,7 +148,7 @@ TS.Elecs.GF.ReUse true
TS.Contours.Eq.Pole 2.50000 eV
%block TS.Contour.c-Left
part circle
from -30.00000 eV + V/2 to -10. kT + V/2
from -40.00000 eV + V/2 to -10. kT + V/2
points 30
method g-legendre
%endblock TS.Contour.c-Left
......@@ -159,7 +160,7 @@ TS.Contours.Eq.Pole 2.50000 eV
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
part circle
from -30.00000 eV - V/2 to -10. kT - V/2
from -40.00000 eV - V/2 to -10. kT - V/2
points 30
method g-legendre
%endblock TS.Contour.c-Right
......@@ -197,9 +198,6 @@ reinit: System Name: bulk_au_111
reinit: -----------------------------------------------------------------------
reinit: System Label: bulk_au_111
reinit: -----------------------------------------------------------------------
redata: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
......@@ -232,6 +230,7 @@ tbt: Saving down-folded self-energies = F
tbt: No delta-Hamiltonian
tbt: Data files stored in current folder
tbt: No compression of TBT.nc files
tbt: Default NetCDF precision = single
tbt: Use parallel MPI-IO for NetCDF file = F
tbt: >> Electrodes <<
tbt: >> Left
......@@ -246,6 +245,7 @@ tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 99.999269 K
tbt: Bulk values in electrode = T
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 2.3867 Ang
tbt: >> Right
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
......@@ -259,6 +259,7 @@ tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 99.999269 K
tbt: Bulk values in electrode = T
tbt: Electrode self-energy imaginary Eta = 0.1000E-03 eV
tbt: Electrode self-energy accuracy = 0.1000E-13 eV
tbt: Electrode inter-layer distance (semi-inf) = 2.3867 Ang