2
***********************
4
***********************
6
reinit: Reading from ../si001.fdf
8
reinit: -----------------------------------------------------------------------
9
reinit: System Name: Si(100)-2x1 3 layers (H-saturated
10
reinit: -----------------------------------------------------------------------
11
reinit: System Label: si001
12
reinit: -----------------------------------------------------------------------
13
Siesta Version: siesta-4.1--731
14
Architecture : x86_64-linux-n-62-18-14
15
Compiler flags: mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto -fuse-linker-plugin
16
PP flags : -I/zdata/groups/common/nicpa/2016-oct/generic/build-tools/1.0/include -I/zdatta/groups/common/nicpa/2016-oct/generic/gmp/6.1.0/include -I/zdata/groups/common/nicpa/2016-oct/generic/mpfr/3.1.4/include -I/zdata/groups/common/nicpa/2016-oct/generic/mpc/1.0.3/include -I/zdata/groups/common/nicpa/2016-oct/generic/isl/0.16.1/include -I/zdata/groups/common/nicpa/2016-oct/generic/gcc/6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/generic/numactl/2.0.11/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/zlib/1.2.8/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/libxml2/2.9.4/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/hwloc/1.11.4/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/openmpi/2.0.1/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/hdf5/1.8.17/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/pnetcdf/1.7.0/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/netcdf/4.4.1/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/flook/0.7.0/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/parmetis/4.0.3/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/scalapack/204/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/openblas/0.2.19/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/mumps/5.0.2/gnu-6.2.0/include -I/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/fftw/3.3.5/gnu-6.2.0/include -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__METIS -DSIESTA__MUMPS -DTS_NOCHECKS -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DSIESTA__FLOOK
17
Libraries : -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmumps -lmumps_common -llpord -lparmetis -lmetis -lscalapack -lopenblas -lmetis -flto -fuse-linker-plugin -L/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/flook/0.7.0/gnu-6.2.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2016-oct/XeonE5-2665/flook/0.7.0/gnu-6.2.0/lib -lflookall -ldl
1
Siesta Version : siesta-4.1-1033
2
Architecture : x86_64-linux-n-62-18-18
3
Compiler version: GNU Fortran (GCC) 7.3.0
4
Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
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/XeonE5-2665/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/XeonE5-2665/libxml2/2.9.7/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/hwloc/1.11.9/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/openmpi/3.0.0/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/szip/2.1.1/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/hdf5/1.8.18/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/pnetcdf/1.8.1/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/netcdf/4.6.0/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/flook/0.7.0/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/parmetis/4.0.3/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/scalapack/204/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/openblas/0.2.20/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/scotch/6.0.4/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/mumps/5.1.2/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/fftw/3.3.7/gnu-7.3.0/include -I/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/elpa/2017.05.003/gnu-7.3.0/include/elpa -DSIESTA__ELPA -DMPI -D1 -DFC_HAVE_ABORT -DCDF -DCDF4 -DSIESTA__FLOOK -DNCDF -DNCDF_4 -DNCDF_PARALLEL -DSIESTA__METIS -DSIESTA__MUMPS -DTS_NOCHECKS -DSIESTA__MRRR
6
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lz -lzmuumps -lmumps_common -lesmumps -lscotch -lscotcherr -lpord -lparmetis -lmetis -lelpa -lscalapack -lopenblas -L/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/flook/0.7.0/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonE5-2665/flook/0.7.0/gnu-7.3.0/lib -lflookall -ldl -flto -fuse-linker-plugin -lmetis
516
538
stepf: Fermi-Dirac step function
518
540
siesta: Program's energy decomposition (eV):
519
siesta: Ebs = -266.692378
541
siesta: Ebs = -266.691691
520
542
siesta: Eions = 1221.235657
521
siesta: Ena = 369.290948
522
siesta: Ekin = 313.032744
523
siesta: Enl = 67.385181
543
siesta: Ena = 369.291243
544
siesta: Ekin = 313.032682
545
siesta: Enl = 67.385399
524
546
siesta: Eso = 0.000000
525
547
siesta: Eldau = 0.000000
526
siesta: DEna = -2.627881
527
siesta: DUscf = 4.805819
548
siesta: DEna = -2.627694
549
siesta: DUscf = 4.805817
528
550
siesta: DUext = 0.000000
529
siesta: Exc = -233.067388
551
siesta: Enegf = 0.000000
552
siesta: Exc = -233.067408
530
553
siesta: eta*DQ = 0.000000
531
554
siesta: Emadel = 0.000000
532
555
siesta: Emeta = 0.000000
533
556
siesta: Emolmec = 0.000000
534
557
siesta: Ekinion = 0.000000
535
siesta: Eharris = -700.149933
536
siesta: Etot = -702.416235
537
siesta: FreeEng = -702.416235
558
siesta: Eharris = -700.149098
559
siesta: Etot = -702.415618
560
siesta: FreeEng = -702.415618
539
562
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
540
scf: 1 -700.149933 -702.416235 -702.416235 1.772601 -4.550128 5.195629
541
timer: Routine,Calls,Time,% = IterSCF 1 0.099 7.50
542
scf: 2 -703.699341 -703.109589 -703.109589 0.017783 -4.544368 3.818628
543
scf: 3 -703.902145 -703.688866 -703.688866 0.036569 -4.524277 1.123502
544
scf: 4 -703.813441 -703.767856 -703.767856 0.027096 -4.392198 0.524221
545
scf: 5 -703.793405 -703.782611 -703.782611 0.009864 -4.338378 0.319891
546
scf: 6 -703.790471 -703.787149 -703.787149 0.007294 -4.292852 0.227083
547
scf: 7 -703.792426 -703.790843 -703.790843 0.005374 -4.235145 0.063861
548
scf: 8 -703.792110 -703.791515 -703.791515 0.000856 -4.233642 0.044477
549
scf: 9 -703.792320 -703.792044 -703.792044 0.001582 -4.242441 0.013837
550
scf: 10 -703.792084 -703.792065 -703.792065 0.000249 -4.242138 0.012700
551
scf: 11 -703.792126 -703.792098 -703.792098 0.000472 -4.240589 0.007495
552
scf: 12 -703.792118 -703.792109 -703.792109 0.000387 -4.238592 0.003802
553
scf: 13 -703.792112 -703.792110 -703.792110 0.000083 -4.238097 0.002554
554
scf: 14 -703.792113 -703.792112 -703.792112 0.000072 -4.237727 0.001367
555
scf: 15 -703.792112 -703.792112 -703.792112 0.000035 -4.237770 0.000981
563
scf: 1 -700.149098 -702.415618 -702.415618 1.772562 -4.549606 5.195636
564
timer: Routine,Calls,Time,% = IterSCF 1 0.106 4.16
565
scf: 2 -703.698721 -703.108971 -703.108971 0.017782 -4.543845 3.818639
566
scf: 3 -703.901524 -703.688248 -703.688248 0.036569 -4.523752 1.123505
567
scf: 4 -703.812821 -703.767237 -703.767237 0.027100 -4.391671 0.524217
568
scf: 5 -703.792786 -703.781993 -703.781993 0.009862 -4.337853 0.319888
569
scf: 6 -703.789853 -703.786531 -703.786531 0.007293 -4.292325 0.227081
570
scf: 7 -703.791808 -703.790224 -703.790224 0.005374 -4.234615 0.063862
571
scf: 8 -703.791492 -703.790897 -703.790897 0.000856 -4.238209 0.044478
572
scf: 9 -703.791702 -703.791426 -703.791426 0.001582 -4.241914 0.013839
573
scf: 10 -703.791465 -703.791446 -703.791446 0.000249 -4.241610 0.012701
574
scf: 11 -703.791508 -703.791480 -703.791480 0.000472 -4.240061 0.007492
575
scf: 12 -703.791500 -703.791491 -703.791491 0.000387 -4.238064 0.003802
576
scf: 13 -703.791494 -703.791492 -703.791492 0.000083 -4.237569 0.002554
577
scf: 14 -703.791494 -703.791493 -703.791493 0.000072 -4.237199 0.001367
578
scf: 15 -703.791494 -703.791494 -703.791494 0.000035 -4.237242 0.000981
557
580
SCF Convergence by DM+H criterion
558
max |DM_out - DM_in| : 0.0000347458
559
max |H_out - H_in| (eV) : 0.0009805585
581
max |DM_out - DM_in| : 0.0000347465
582
max |H_out - H_in| (eV) : 0.0009805868
560
583
SCF cycle converged after 15 iterations
562
585
Using DM_out to compute the final energy and forces
563
586
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 158
565
siesta: E_KS(eV) = -703.7921
588
siesta: E_KS(eV) = -703.7915
567
siesta: E_KS - E_eggbox = -703.7921
590
siesta: E_KS - E_eggbox = -703.7915
569
592
siesta: Atomic forces (eV/Ang):
570
1 -0.000508 0.010182 -0.006749
571
2 0.000226 -0.034550 0.008251
572
3 -0.000529 -0.014660 0.009445
573
4 0.000231 0.001599 0.003673
574
5 -0.000064 0.066201 0.371351
575
6 -0.000024 -0.367474 -0.940827
576
7 2.227197 -0.102766 0.973876
577
8 -2.227175 -0.102798 0.973832
578
9 2.316500 0.075793 0.677013
579
10 -2.316488 0.075874 0.676990
580
----------------------------------------
581
Tot -0.000635 -0.392600 2.746856
582
----------------------------------------
584
Res 0.906703 sqrt( Sum f_i^2 / 3N )
585
----------------------------------------
586
Max 0.034550 constrained
593
1 -0.000510 0.004140 -0.004492
594
2 0.000227 -0.031237 0.007980
595
3 -0.000530 -0.008707 0.007576
596
4 0.000229 0.001316 0.005676
597
5 -0.000063 0.066902 0.372279
598
6 -0.000024 -0.371098 -0.937560
599
7 2.229204 -0.102746 0.972294
600
8 -2.229182 -0.102777 0.972250
601
9 2.318454 0.075790 0.675448
602
10 -2.318442 0.075871 0.675424
603
----------------------------------------
604
Tot -0.000635 -0.392546 2.746875
605
----------------------------------------
607
Res 0.907115 sqrt( Sum f_i^2 / 3N )
608
----------------------------------------
609
Max 0.031237 constrained
588
Stress-tensor-Voigt (kbar): -63.37 -2.74 17.77 0.00 2.87 0.00
589
(Free)E + p*V (eV/cell) -700.4322
590
Target enthalpy (eV/cell) -703.7921
611
Stress-tensor-Voigt (kbar): -63.27 -2.73 17.82 0.00 2.89 0.00
612
(Free)E + p*V (eV/cell) -700.4425
613
Target enthalpy (eV/cell) -703.7915
592
615
mulliken: Atomic and Orbital Populations:
621
644
coxmol: Writing XMOL coordinates into file si001.xyz
623
646
siesta: Program's energy decomposition (eV):
624
siesta: Ebs = -268.372591
647
siesta: Ebs = -268.372168
625
648
siesta: Eions = 1221.235657
626
siesta: Ena = 369.290948
627
siesta: Ekin = 305.186202
628
siesta: Enl = 70.732598
649
siesta: Ena = 369.291243
650
siesta: Ekin = 305.186124
651
siesta: Enl = 70.732793
629
652
siesta: Eso = 0.000000
630
653
siesta: Eldau = 0.000000
631
siesta: DEna = 0.689822
654
siesta: DEna = 0.690034
632
655
siesta: DUscf = 2.237207
633
656
siesta: DUext = 0.000000
634
siesta: Exc = -230.693231
657
siesta: Enegf = 0.000000
658
siesta: Exc = -230.693237
635
659
siesta: eta*DQ = 0.000000
636
660
siesta: Emadel = 0.000000
637
661
siesta: Emeta = 0.000000
638
662
siesta: Emolmec = 0.000000
639
663
siesta: Ekinion = 0.000000
640
siesta: Eharris = -703.792112
641
siesta: Etot = -703.792112
642
siesta: FreeEng = -703.792112
664
siesta: Eharris = -703.791494
665
siesta: Etot = -703.791494
666
siesta: FreeEng = -703.791494
644
668
siesta: Final energy (eV):
645
siesta: Band Struct. = -268.372591
646
siesta: Kinetic = 305.186202
647
siesta: Hartree = 896.012029
669
siesta: Band Struct. = -268.372168
670
siesta: Kinetic = 305.186124
671
siesta: Hartree = 896.012131
648
672
siesta: Eldau = 0.000000
649
673
siesta: Eso = 0.000000
650
674
siesta: Ext. field = 0.000000
651
siesta: Exch.-corr. = -230.693231
652
siesta: Ion-electron = -2064.723754
653
siesta: Ion-ion = 390.426642
675
siesta: Enegf = 0.000000
676
siesta: Exch.-corr. = -230.693237
677
siesta: Ion-electron = -2064.723448
678
siesta: Ion-ion = 390.426937
654
679
siesta: Ekinion = 0.000000
655
siesta: Total = -703.792112
656
siesta: Fermi = -4.237770
680
siesta: Total = -703.791494
681
siesta: Fermi = -4.237242
658
683
siesta: Atomic forces (eV/Ang):
659
siesta: 1 -0.000508 0.010182 -0.006749
660
siesta: 2 0.000226 -0.034550 0.008251
661
siesta: 3 -0.000529 -0.014660 0.009445
662
siesta: 4 0.000231 0.001599 0.003673
663
siesta: 5 -0.000064 0.066201 0.371351
664
siesta: 6 -0.000024 -0.367474 -0.940827
665
siesta: 7 2.227197 -0.102766 0.973876
666
siesta: 8 -2.227175 -0.102798 0.973832
667
siesta: 9 2.316500 0.075793 0.677013
668
siesta: 10 -2.316488 0.075874 0.676990
684
siesta: 1 -0.000510 0.004140 -0.004492
685
siesta: 2 0.000227 -0.031237 0.007980
686
siesta: 3 -0.000530 -0.008707 0.007576
687
siesta: 4 0.000229 0.001316 0.005676
688
siesta: 5 -0.000063 0.066902 0.372279
689
siesta: 6 -0.000024 -0.371098 -0.937560
690
siesta: 7 2.229204 -0.102746 0.972294
691
siesta: 8 -2.229182 -0.102777 0.972250
692
siesta: 9 2.318454 0.075790 0.675448
693
siesta: 10 -2.318442 0.075871 0.675424
669
694
siesta: ----------------------------------------
670
siesta: Tot -0.000635 -0.392600 2.746856
695
siesta: Tot -0.000635 -0.392546 2.746875
672
697
siesta: Constrained forces (eV/Ang):
673
siesta: 1 -0.000508 0.010182 -0.006749
674
siesta: 2 0.000226 -0.034550 0.008251
675
siesta: 3 -0.000529 -0.014660 0.009445
676
siesta: 4 0.000231 0.001599 0.003673
698
siesta: 1 -0.000510 0.004140 -0.004492
699
siesta: 2 0.000227 -0.031237 0.007980
700
siesta: 3 -0.000530 -0.008707 0.007576
701
siesta: 4 0.000229 0.001316 0.005676
677
702
siesta: 5 0.000000 0.000000 0.000000
678
703
siesta: 6 0.000000 0.000000 0.000000
679
704
siesta: 7 0.000000 0.000000 0.000000
681
706
siesta: 9 0.000000 0.000000 0.000000
682
707
siesta: 10 0.000000 0.000000 0.000000
683
708
siesta: ----------------------------------------
684
siesta: Tot -0.000581 -0.037430 0.014621
709
siesta: Tot -0.000583 -0.034488 0.016739
686
711
siesta: Stress tensor (static) (eV/Ang**3):
687
siesta: -0.039553 0.000001 0.000000
688
siesta: 0.000001 -0.001713 0.001792
689
siesta: 0.000000 0.001791 0.011091
712
siesta: -0.039491 0.000001 0.000000
713
siesta: 0.000001 -0.001707 0.001806
714
siesta: 0.000000 0.001805 0.011121
691
716
siesta: Cell volume = 334.037723 Ang**3
693
718
siesta: Pressure (static):
694
719
siesta: Solid Molecule Units
695
siesta: 0.00010955 0.00018157 Ry/Bohr**3
696
siesta: 0.01005847 0.01667136 eV/Ang**3
697
siesta: 16.11562007 26.71075289 kBar
698
(Free)E+ p_basis*V_orbitals = -699.082881
699
(Free)Eharris+ p_basis*V_orbitals = -699.082881
701
siesta: Electric dipole (a.u.) = -0.000000 0.000000 -0.019421
702
siesta: Electric dipole (Debye) = -0.000000 0.000000 -0.049363
704
dhscf: Vacuum level (max, mean) = -0.031773 -0.167737 eV
705
>> End of run: 2-JUL-2017 11:58:31
720
siesta: 0.00010919 0.00018160 Ry/Bohr**3
721
siesta: 0.01002576 0.01667404 eV/Ang**3
722
siesta: 16.06320683 26.71503941 kBar
723
(Free)E+ p_basis*V_orbitals = -699.082263
724
(Free)Eharris+ p_basis*V_orbitals = -699.082263
726
siesta: Electric dipole (a.u.) = -0.000000 0.000000 -0.019394
727
siesta: Electric dipole (Debye) = -0.000000 0.000000 -0.049296
729
dhscf: Vacuum level (max, mean) = -0.031787 -0.167749 eV
730
>> End of run: 5-NOV-2018 11:05:56