1
Siesta Version: siesta-trunk-479
2
Architecture : atto-intel12-openmpi
3
Compiler flags: /share/apps/openmpi-1.6.5-intel/bin/mpif90 -w -O2 -mp
4
PP flags : -DCDF -DMPI -DTRANSIESTA -DTRANSIESTA
1
Siesta Version : siesta-4.0--578
2
Architecture : x86_64-linux-n-62-25-35
3
Compiler version: GNU Fortran (GCC) 7.3.0
4
Compiler flags : mpif90 -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizationns -funroll-loops -fprefetch-loop-arrays -fno-second-underscore
5
PP flags : -I/zdata/groups/common/nicpa/2018-feb/generic/build-tools/1.0/include -I/zdatta/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/zlib/1.2.11/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/libxml2/2.9.7/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/hwloc/1.11.9/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/openmpi/3.0.0/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/szip/2.1.1/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/hdf5-serial/1.8.18/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/netcdf-serial/4.6.0/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/scalapack/204/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/openblas/0.2.20/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2660v3/elpa/2017.05.003/gnu-7.3.0/include -DSIESTA__ELPA -DMPI -D1 -DFC_HAVE_ABORT -DCDF -DSIESTA__MRRR -DTRANSIESTA -DTRANSIESTA
9
* Running on 4 nodes in parallel
10
>> Start of run: 3-OCT-2015 0:27:38
10
* Running on 8 nodes in parallel
11
>> Start of run: 13-JUN-2018 21:34:45
12
13
***********************
13
14
* WELCOME TO SIESTA *
367
369
Total number of electrons: 99.000000
368
370
Total ionic charge: 99.000000
370
* ProcessorY, Blocksize: 2 21
373
* Orbital distribution balance (max,min): 21 18
372
* ProcessorY, Blocksize: 2 10
375
* Orbital distribution balance (max,min): 11 10
375
377
k-point displ. along 1 input, could be: 0.00 0.50
376
378
k-point displ. along 2 input, could be: 0.00 0.50
418
420
NOTICE: Total number of energy points is not divisable by the number of nodes.
419
421
There are no computational costs associated with increasing this.
420
422
Used # of energy points : 43
421
Optimal # of energy points: 44
423
Optimal # of energy points: 48
422
424
************************ End: TS CHECKS AND WARNINGS **************************
424
426
k-point displ. along 1 input, could be: 0.00 0.50
425
427
k-point displ. along 2 input, could be: 0.00 0.50
426
428
Kpoints in: 40 . Kpoints trimmed: 37
444
446
# 1.4615550 0.8438292 16.7069652 # Right electrode
445
447
# 1.4615550 -0.8438292 19.0936746 #
446
448
##############################################
448
450
transiesta: contour integration path:
449
451
Type Re(c)[eV] Im(c)[eV] Re(weight) Im(weight)
451
resi : 0.00000 0.02707 0.000000000 -0.003979496
452
resi : 0.00000 0.08122 0.000000000 -0.003979496
453
resi : 0.00000 0.13536 0.000000000 -0.003979496
453
resi : 0.00000 0.02707 -0.000000000 -0.003979496
454
resi : 0.00000 0.08122 -0.000000000 -0.003979496
455
resi : 0.00000 0.13536 -0.000000000 -0.003979496
454
456
fermi : 0.19107 0.16243 0.000000000 0.000000000
455
457
fermi : 0.12325 0.16243 0.000000003 0.000000000
456
458
fermi : 0.07467 0.16243 0.000000534 0.000000000
608
610
Orbitals available / used orbitals: 27 / 27
609
611
q-points for expanding electrode (Bohr**-1):
610
612
1 0.00000E+00 0.00000E+00 0.10000E+01
611
Fermi level shift in electrode : 0.00000 eV
613
Fermi level shift in electrode : -0.00000 eV
612
614
Done creating 'bulk_au_111.TSGFR'.
614
616
Left : GF atoms / Expanded atoms : 3 / 3
615
617
Left : GF orbitals / Expanded orbitals : 27 / 27
616
618
Right: GF atoms / Expanded atoms : 3 / 3
617
619
Right: GF orbitals / Expanded orbitals : 27 / 27
619
621
Naive supercell factors: 7 7 1
621
623
superc: Internal auxiliary supercell: 7 x 7 x 1 = 49
641
643
TRANSIESTA: No TS-DensityMatrix file found
642
644
TRANSIESTA: Initialization runs using diagon
643
645
New grid distribution: 1
647
4 1: 15 9: 15 64: 125
653
8 1: 15 9: 15 95: 125
649
655
InitMesh: MESH = 30 x 30 x 250 = 225000
650
656
InitMesh: (bp) = 15 x 15 x 125 = 28125
651
657
InitMesh: Mesh cutoff (required, used) = 350.000 374.367 Ry
652
ExtMesh (bp) on 0 = 107 x 100 x 155 = 1658500
658
ExtMesh (bp) on 0 = 107 x 100 x 124 = 1326800
653
659
New grid distribution: 2
657
4 1: 15 1: 15 95: 125
664
5 1: 15 1: 15 111: 125
667
8 1: 15 1: 15 95: 110
658
668
New grid distribution: 3
662
4 1: 15 1: 15 95: 125
672
4 1: 15 1: 15 95: 110
676
8 1: 15 1: 15 111: 125
663
677
Setting up quadratic distribution...
664
ExtMesh (bp) on 0 = 107 x 107 x 123 = 1408227
665
PhiOnMesh: Number of (b)points on node 0 = 6975
666
PhiOnMesh: nlist on node 0 = 570754
678
ExtMesh (bp) on 0 = 107 x 107 x 108 = 1236492
679
PhiOnMesh: Number of (b)points on node 0 = 3600
680
PhiOnMesh: nlist on node 0 = 294436
668
682
stepf: Fermi-Dirac step function
670
684
siesta: Program's energy decomposition (eV):
671
siesta: Ebs = -646.221108
685
siesta: Ebs = -646.221059
672
686
siesta: Eions = 10541.024256
673
siesta: Ena = 524.239359
674
siesta: Ekin = 5986.831336
675
siesta: Enl = -2812.095939
687
siesta: Ena = 524.239355
688
siesta: Ekin = 5986.831337
689
siesta: Enl = -2812.095938
676
690
siesta: DEna = 0.000002
677
691
siesta: DUscf = 0.000000
678
692
siesta: DUext = 0.000000
682
696
siesta: Emeta = 0.000000
683
697
siesta: Emolmec = 0.000000
684
698
siesta: Ekinion = 0.000000
685
siesta: Eharris = -8145.893445
686
siesta: Etot = -8143.516170
687
siesta: FreeEng = -8143.517425
699
siesta: Eharris = -8145.893399
700
siesta: Etot = -8143.516172
701
siesta: FreeEng = -8143.517427
689
703
scf: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
690
704
scf: 1 -8145.8934 -8143.5162 -8143.5174 0.22020 -2.4745
691
timer: Routine,Calls,Time,% = IterSCF 1 13.130 62.46
692
scf: 2 -8145.5700 -8143.5826 -8143.5838 0.21668 -2.4925
693
scf: 3 -8142.1993 -8141.8757 -8141.8765 0.10915 -2.8302
694
scf: 4 -8142.1546 -8141.9597 -8141.9605 0.09524 -2.8242
695
scf: 5 -8142.0942 -8141.9182 -8141.9191 0.00190 -2.8062
696
scf: 6 -8142.0942 -8141.9238 -8141.9247 0.00173 -2.8042
705
timer: Routine,Calls,Time,% = IterSCF 1 5.702 58.87
706
scf: 2 -8145.5700 -8143.5826 -8143.5838 0.21667 -2.4925
707
scf: 3 -8142.1993 -8141.8757 -8141.8765 0.10915 -2.8303
708
scf: 4 -8142.1545 -8141.9596 -8141.9605 0.09524 -2.8242
709
scf: 5 -8142.0942 -8141.9182 -8141.9190 0.00190 -2.8062
710
scf: 6 -8142.0942 -8141.9238 -8141.9246 0.00173 -2.8043
697
711
scf: 7 -8142.0942 -8141.9389 -8141.9397 0.00148 -2.8024
698
scf: 8 -8142.0942 -8141.9622 -8141.9630 0.00076 -2.8004
712
scf: 8 -8142.0942 -8141.9621 -8141.9630 0.00076 -2.8004
699
713
scf: 9 -8142.0942 -8142.0788 -8142.0797 0.00022 -2.8013
700
scf: 10 -8142.0942 -8142.0843 -8142.0852 0.00015 -2.8014
714
scf: 10 -8142.0942 -8142.0843 -8142.0851 0.00015 -2.8014
701
715
scf: 11 -8142.0942 -8142.0868 -8142.0876 0.00012 -2.8018
702
scf: 12 -8142.0942 -8142.0869 -8142.0878 0.00011 -2.8018
703
scf: 13 -8142.0942 -8142.0889 -8142.0897 0.00008 -2.8020
716
scf: 12 -8142.0942 -8142.0869 -8142.0877 0.00011 -2.8018
717
scf: 13 -8142.0942 -8142.0888 -8142.0897 0.00008 -2.8020
705
719
SCF Convergence by dMax criterion
706
max |DM_out - DM_in|: 0.00007728
720
max |DM_out - DM_in|: 0.00007721
707
721
SCF cycle converged after 13 iterations
709
723
************************
715
729
transiesta: Total elements / Updated elements : 96831 / 18309
717
Efermi from SIESTA : -2.80201
731
Efermi from SIESTA : -2.80203
718
732
Total charge [Qt0] : 99.00000
719
733
Charge in update region [Qc] : 32.69499
720
734
Charge outside update region [Qcn] : 66.30501
721
Left electrode [L] : 32.69496
735
Left electrode [L] : 32.69497
722
736
Left electrode/device [L-C] : 0.30500
723
737
Device [C] : 32.69499
724
Device/right electrode [C-R] : 0.30502
738
Device/right electrode [C-R] : 0.30501
725
739
Right electrode [R] : 32.69502
726
740
Other [O] : 0.30502
728
742
Reading GF file, with title:
729
/home/albertog/code/SIESTA/trunk-ag/TS_ParIntel/Tests/TranSiesta-TBTrans/ts_au/work/Scat_bulk_au_111/bulk_au_111.TSGFL
730
744
Title: 'Generated GF file'
732
746
Reading GF file, with title:
733
/home/albertog/code/SIESTA/trunk-ag/TS_ParIntel/Tests/TranSiesta-TBTrans/ts_au/work/Scat_bulk_au_111/bulk_au_111.TSGFR
734
748
Title: 'Generated GF file'
736
750
ts-charge: O L L-C C C-R R Qt
737
751
ts-charge: 0.305 32.695 0.305 32.692 0.305 32.695 98.997
739
753
siesta: Program's energy decomposition (eV):
740
siesta: Ebs = -688.941899
754
siesta: Ebs = -688.940534
741
755
siesta: Eions = 10541.024256
742
siesta: Ena = 524.239359
743
siesta: Ekin = 5727.243645
744
siesta: Enl = -2652.406652
745
siesta: DEna = 70.390661
746
siesta: DUscf = 3.468622
756
siesta: Ena = 524.239355
757
siesta: Ekin = 5727.244179
758
siesta: Enl = -2652.406922
759
siesta: DEna = 70.390522
760
siesta: DUscf = 3.468609
747
761
siesta: DUext = 0.000000
748
siesta: Exc = -1274.005594
762
siesta: Exc = -1274.005665
749
763
siesta: eta*DQ = 0.000000
750
764
siesta: Emadel = 0.000000
751
765
siesta: Emeta = 0.000000
752
766
siesta: Emolmec = 0.000000
753
767
siesta: Ekinion = 0.000000
754
siesta: Eharris = -8142.084100
755
siesta: Etot = -8142.094215
756
siesta: FreeEng = -8142.095067
768
siesta: Eharris = -8142.084035
769
siesta: Etot = -8142.094179
770
siesta: FreeEng = -8142.095032
758
772
transiesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
759
transiesta: 1 -8142.0841 -8142.0942 -8142.0951 0.00057 -2.8020
760
timer: Routine,Calls,Time,% = TS 1 0.695 0.39
761
timer: Routine,Calls,Time,% = TS_calc 2 0.692 0.38
773
transiesta: 1 -8142.0840 -8142.0942 -8142.0950 0.00058 -2.8020
774
timer: Routine,Calls,Time,% = TS 1 0.608 0.77
775
timer: Routine,Calls,Time,% = TS_calc 2 0.606 0.77
762
776
ts-charge: O L L-C C C-R R Qt
763
777
ts-charge: 0.305 32.695 0.305 32.696 0.305 32.695 99.001
764
transiesta: 2 -8142.0981 -8142.0939 -8142.0947 0.00029 -2.8020
778
transiesta: 2 -8142.0980 -8142.0938 -8142.0947 0.00029 -2.8020
765
779
ts-charge: O L L-C C C-R R Qt
766
780
ts-charge: 0.305 32.695 0.305 32.695 0.305 32.695 99.000
767
transiesta: 3 -8142.0938 -8142.0940 -8142.0948 0.00008 -2.8020
781
transiesta: 3 -8142.0938 -8142.0939 -8142.0948 0.00008 -2.8020
769
783
SCF Convergence by dMax criterion
770
max |DM_out - DM_in|: 0.00008117
784
max |DM_out - DM_in|: 0.00008210
771
785
SCF cycle converged after 3 iterations
773
787
Using DM_out to compute the final energy and forces
780
794
----------------------------------------
781
795
Tot -0.000000 -0.000000 0.000001
782
796
----------------------------------------
784
798
Res 0.000394 sqrt( Sum f_i^2 / 3N )
785
799
----------------------------------------
786
Max 0.001429 constrained
800
Max 0.001430 constrained
788
Stress-tensor-Voigt (kbar): 26.39 26.39 53.15 0.00 -0.00 -0.00
789
(Free)E + p*V (eV/cell) -8145.5978
802
Stress-tensor-Voigt (kbar): 26.17 26.17 52.93 -0.00 -0.00 -0.00
803
(Free)E + p*V (eV/cell) -8145.5759
790
804
Target enthalpy (eV/cell) -8142.0946
792
806
mulliken: Atomic and Orbital Populations:
819
833
coxmol: Writing XMOL coordinates into file bulk_au_111.xyz
821
835
siesta: Program's energy decomposition (eV):
822
siesta: Ebs = -689.075315
836
siesta: Ebs = -689.074319
823
837
siesta: Eions = 10541.024256
824
siesta: Ena = 524.239359
825
siesta: Ekin = 5727.239574
826
siesta: Enl = -2652.406537
827
siesta: DEna = 70.392631
828
siesta: DUscf = 3.468654
838
siesta: Ena = 524.239355
839
siesta: Ekin = 5727.240046
840
siesta: Enl = -2652.406792
841
siesta: DEna = 70.392515
842
siesta: DUscf = 3.468642
829
843
siesta: DUext = 0.000000
830
siesta: Exc = -1274.003163
844
siesta: Exc = -1274.003210
831
845
siesta: eta*DQ = 0.000000
832
846
siesta: Emadel = 0.000000
833
847
siesta: Emeta = 0.000000
834
848
siesta: Emolmec = 0.000000
835
849
siesta: Ekinion = 0.000000
836
siesta: Eharris = -8142.093808
837
siesta: Etot = -8142.093738
838
siesta: FreeEng = -8142.094590
850
siesta: Eharris = -8142.093771
851
siesta: Etot = -8142.093700
852
siesta: FreeEng = -8142.094553
840
854
siesta: Final energy (eV):
841
siesta: Band Struct. = -689.075315
842
siesta: Kinetic = 5727.239574
843
siesta: Hartree = 987.292039
855
siesta: Band Struct. = -689.074319
856
siesta: Kinetic = 5727.240046
857
siesta: Hartree = 987.291845
844
858
siesta: Ext. field = 0.000000
845
siesta: Exch.-corr. = -1274.003163
846
siesta: Ion-electron = -6723.715845
847
siesta: Ion-ion = -6858.906344
859
siesta: Exch.-corr. = -1274.003210
860
siesta: Ion-electron = -6723.716033
861
siesta: Ion-ion = -6858.906348
848
862
siesta: Ekinion = 0.000000
849
siesta: Total = -8142.093738
863
siesta: Total = -8142.093700
851
865
siesta: Stress tensor (static) (eV/Ang**3):
852
siesta: 0.016472 0.000000 -0.000000
853
siesta: 0.000000 0.016472 -0.000000
854
siesta: -0.000000 -0.000000 0.033175
866
siesta: 0.016334 -0.000000 -0.000000
867
siesta: -0.000000 0.016334 -0.000000
868
siesta: -0.000000 -0.000000 0.033037
856
870
siesta: Cell volume = 158.950899 Ang**3
858
872
siesta: Pressure (static):
859
873
siesta: Solid Molecule Units
860
siesta: -0.00024004 -0.00024050 Ry/Bohr**3
861
siesta: -0.02203980 -0.02208226 eV/Ang**3
862
siesta: -35.31203260 -35.38006732 kBar
863
(Free)E+ p_basis*V_orbitals = -8135.858278
864
(Free)Eharris+ p_basis*V_orbitals = -8135.858348
865
>> End of run: 3-OCT-2015 0:30:49
874
siesta: -0.00023854 -0.00023900 Ry/Bohr**3
875
siesta: -0.02190196 -0.02194442 eV/Ang**3
876
siesta: -35.09119035 -35.15922136 kBar
877
(Free)E+ p_basis*V_orbitals = -8135.858240
878
(Free)Eharris+ p_basis*V_orbitals = -8135.858311
879
>> End of run: 13-JUN-2018 21:36:09