10
10
reinit: -----------------------------------------------------------------------
11
11
reinit: System Label: si001
12
12
reinit: -----------------------------------------------------------------------
13
Siesta Version: trunk-554
14
Architecture : x86_64-linux-gcc
15
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
16
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
17
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
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
21
21
NetCDF-4 MPI-IO support
22
22
METIS ordering support
24
* Running on 4 nodes in parallel
25
>> Start of run: 18-AUG-2016 8:47:03
24
* Running on 8 nodes in parallel
25
>> Start of run: 2-JUL-2017 11:58:28
27
27
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
28
28
Species number: 1 Atomic number: 14 Label: Si
368
367
redata: Require Harris convergence for SCF = F
369
368
redata: Harris energy tolerance for SCF = 0.000100 eV
370
369
redata: Require DM convergence for SCF = T
371
redata: DM tolerance for SCF = 0.000100
370
redata: DM tolerance for SCF = 0.0001
371
redata: Require EDM convergence for SCF = F
372
redata: EDM tolerance for SCF = 0.001000 eV
372
373
redata: Require H convergence for SCF = T
373
374
redata: Hamiltonian tolerance for SCF = 0.001000 eV
374
375
redata: Require (free) Energy convergence for SCF = F
414
411
Total number of electrons: 28.000000
415
412
Total ionic charge: 28.000000
417
* ProcessorY, Blocksize: 2 24
420
* Orbital distribution balance (max,min): 26 24
414
* ProcessorY, Blocksize: 2 13
417
* Orbital distribution balance (max,min): 13 7
422
419
Kpoints in: 3 . Kpoints trimmed: 3
464
461
outcell: Cell volume (Ang**3) : 334.0377
465
462
<dSpData1D:S at geom step 0
466
463
<sparsity:sparsity for geom step 0
467
nrows_g=98 nrows=26 sparsity=1.1352 nnzs=10902, refcount: 7>
468
<dData1D:(new from dSpData1D) n=10902, refcount: 1>
464
nrows_g=98 nrows=13 sparsity=.6013 nnzs=5775, refcount: 7>
465
<dData1D:(new from dSpData1D) n=5775, refcount: 1>
471
468
Initializing Density Matrix...
472
470
Attempting to read DM from file... Failed...
473
DM after filling with atomic data:
474
<dSpData2D:(DM initialized from atoms)
471
DM filled with atomic data:
472
<dSpData2D:DM initialized from atoms
475
473
<sparsity:sparsity for geom step 0
476
nrows_g=98 nrows=26 sparsity=1.1352 nnzs=10902, refcount: 8>
477
<dData2D:(DMatomic) n=10902 m=1, refcount: 1>
474
nrows_g=98 nrows=13 sparsity=.6013 nnzs=5775, refcount: 8>
475
<dData2D:DM n=5775 m=1, refcount: 1>
478
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 158
479
479
New grid distribution: 1
485
489
InitMesh: MESH = 8 x 16 x 24 = 3072
486
490
InitMesh: (bp) = 4 x 8 x 12 = 384
487
491
InitMesh: Mesh cutoff (required, used) = 10.000 12.132 Ry
488
ExtMesh (bp) on 0 = 20 x 20 x 22 = 8800
492
ExtMesh (bp) on 0 = 20 x 20 x 19 = 7600
489
493
New grid distribution: 2
494
502
New grid distribution: 3
499
511
Setting up quadratic distribution...
500
ExtMesh (bp) on 0 = 20 x 19 x 19 = 7220
501
PhiOnMesh: Number of (b)points on node 0 = 36
502
PhiOnMesh: nlist on node 0 = 3428
503
cdiag-debug: Node=1, lwork= 4128>= lworkq= 3074, lrwork= 8181>= lrworkq= 8083, liwork= 720>= liworkq= 704
504
cdiag-debug: Node=2, lwork= 4080>= lworkq= 3026, lrwork= 8181>= lrworkq= 8083, liwork= 720>= liworkq= 704
505
cdiag-debug: Node=3, lwork= 4032>= lworkq= 3026, lrwork= 7893>= lrworkq= 7795, liwork= 720>= liworkq= 704
506
cdiag-debug: Node=0, lwork= 4176>= lworkq= 3074, lrwork= 8481>= lrworkq= 8383, liwork= 720>= liworkq= 704
512
ExtMesh (bp) on 0 = 20 x 19 x 18 = 6840
513
PhiOnMesh: Number of (b)points on node 0 = 24
514
PhiOnMesh: nlist on node 0 = 2168
508
516
stepf: Fermi-Dirac step function
510
518
siesta: Program's energy decomposition (eV):
511
siesta: Ebs = -266.692379
519
siesta: Ebs = -266.692378
512
520
siesta: Eions = 1221.235657
513
521
siesta: Ena = 369.290948
514
522
siesta: Ekin = 313.032744
515
siesta: Enl = 67.385180
523
siesta: Enl = 67.385181
516
524
siesta: Eso = 0.000000
517
525
siesta: Eldau = 0.000000
518
siesta: DEna = -2.627880
526
siesta: DEna = -2.627881
519
527
siesta: DUscf = 4.805819
520
528
siesta: DUext = 0.000000
521
529
siesta: Exc = -233.067388
531
539
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
532
540
scf: 1 -700.149933 -702.416235 -702.416235 1.772601 -4.550128 5.195629
533
timer: Routine,Calls,Time,% = IterSCF 1 0.208 8.14
534
scf: 2 -703.699340 -703.109589 -703.109589 0.017783 -4.544368 3.818628
535
scf: 3 -703.902144 -703.688866 -703.688866 0.036569 -4.524277 1.123502
536
scf: 4 -703.813441 -703.767855 -703.767855 0.027096 -4.392198 0.524221
537
scf: 5 -703.793405 -703.782611 -703.782611 0.009863 -4.338378 0.319891
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
538
546
scf: 6 -703.790471 -703.787149 -703.787149 0.007294 -4.292852 0.227083
539
547
scf: 7 -703.792426 -703.790843 -703.790843 0.005374 -4.235145 0.063861
540
548
scf: 8 -703.792110 -703.791515 -703.791515 0.000856 -4.233642 0.044477
547
555
scf: 15 -703.792112 -703.792112 -703.792112 0.000035 -4.237770 0.000981
549
557
SCF Convergence by DM+H criterion
550
max |DM_out - DM_in| : 0.0000347459
551
max |H_out - H_in| (eV): 0.0009805584
558
max |DM_out - DM_in| : 0.0000347458
559
max |H_out - H_in| (eV) : 0.0009805585
552
560
SCF cycle converged after 15 iterations
554
562
Using DM_out to compute the final energy and forces
563
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 158
556
565
siesta: E_KS(eV) = -703.7921
558
567
siesta: E_KS - E_eggbox = -703.7921
560
569
siesta: Atomic forces (eV/Ang):
561
1 -0.000508 0.010182 -0.006748
562
2 0.000226 -0.034550 0.008252
570
1 -0.000508 0.010182 -0.006749
571
2 0.000226 -0.034550 0.008251
563
572
3 -0.000529 -0.014660 0.009445
564
4 0.000231 0.001599 0.003672
565
5 -0.000064 0.066200 0.371350
566
6 -0.000024 -0.367474 -0.940828
573
4 0.000231 0.001599 0.003673
574
5 -0.000064 0.066201 0.371351
575
6 -0.000024 -0.367474 -0.940827
567
576
7 2.227197 -0.102766 0.973876
568
8 -2.227175 -0.102797 0.973832
577
8 -2.227175 -0.102798 0.973832
569
578
9 2.316500 0.075793 0.677013
570
10 -2.316488 0.075874 0.676989
579
10 -2.316488 0.075874 0.676990
571
580
----------------------------------------
572
Tot -0.000635 -0.392599 2.746853
581
Tot -0.000635 -0.392600 2.746856
573
582
----------------------------------------
575
Res 0.906702 sqrt( Sum f_i^2 / 3N )
584
Res 0.906703 sqrt( Sum f_i^2 / 3N )
576
585
----------------------------------------
577
586
Max 0.034550 constrained
612
621
coxmol: Writing XMOL coordinates into file si001.xyz
614
623
siesta: Program's energy decomposition (eV):
615
siesta: Ebs = -268.372592
624
siesta: Ebs = -268.372591
616
625
siesta: Eions = 1221.235657
617
626
siesta: Ena = 369.290948
618
siesta: Ekin = 305.186203
619
siesta: Enl = 70.732597
627
siesta: Ekin = 305.186202
628
siesta: Enl = 70.732598
620
629
siesta: Eso = 0.000000
621
630
siesta: Eldau = 0.000000
622
631
siesta: DEna = 0.689822
623
632
siesta: DUscf = 2.237207
624
633
siesta: DUext = 0.000000
625
siesta: Exc = -230.693232
634
siesta: Exc = -230.693231
626
635
siesta: eta*DQ = 0.000000
627
636
siesta: Emadel = 0.000000
628
637
siesta: Emeta = 0.000000
633
642
siesta: FreeEng = -703.792112
635
644
siesta: Final energy (eV):
636
siesta: Band Struct. = -268.372592
637
siesta: Kinetic = 305.186203
645
siesta: Band Struct. = -268.372591
646
siesta: Kinetic = 305.186202
638
647
siesta: Hartree = 896.012029
639
648
siesta: Eldau = 0.000000
640
649
siesta: Eso = 0.000000
641
650
siesta: Ext. field = 0.000000
642
siesta: Exch.-corr. = -230.693232
651
siesta: Exch.-corr. = -230.693231
643
652
siesta: Ion-electron = -2064.723754
644
653
siesta: Ion-ion = 390.426642
645
654
siesta: Ekinion = 0.000000
647
656
siesta: Fermi = -4.237770
649
658
siesta: Atomic forces (eV/Ang):
650
siesta: 1 -0.000508 0.010182 -0.006748
651
siesta: 2 0.000226 -0.034550 0.008252
659
siesta: 1 -0.000508 0.010182 -0.006749
660
siesta: 2 0.000226 -0.034550 0.008251
652
661
siesta: 3 -0.000529 -0.014660 0.009445
653
siesta: 4 0.000231 0.001599 0.003672
654
siesta: 5 -0.000064 0.066200 0.371350
655
siesta: 6 -0.000024 -0.367474 -0.940828
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
656
665
siesta: 7 2.227197 -0.102766 0.973876
657
siesta: 8 -2.227175 -0.102797 0.973832
666
siesta: 8 -2.227175 -0.102798 0.973832
658
667
siesta: 9 2.316500 0.075793 0.677013
659
siesta: 10 -2.316488 0.075874 0.676989
668
siesta: 10 -2.316488 0.075874 0.676990
660
669
siesta: ----------------------------------------
661
siesta: Tot -0.000635 -0.392599 2.746853
670
siesta: Tot -0.000635 -0.392600 2.746856
663
672
siesta: Constrained forces (eV/Ang):
664
siesta: 1 -0.000508 0.010182 -0.006748
665
siesta: 2 0.000226 -0.034550 0.008252
673
siesta: 1 -0.000508 0.010182 -0.006749
674
siesta: 2 0.000226 -0.034550 0.008251
666
675
siesta: 3 -0.000529 -0.014660 0.009445
667
siesta: 4 0.000231 0.001599 0.003672
676
siesta: 4 0.000231 0.001599 0.003673
668
677
siesta: 5 0.000000 0.000000 0.000000
669
678
siesta: 6 0.000000 0.000000 0.000000
670
679
siesta: 7 0.000000 0.000000 0.000000
685
694
siesta: Solid Molecule Units
686
695
siesta: 0.00010955 0.00018157 Ry/Bohr**3
687
696
siesta: 0.01005847 0.01667136 eV/Ang**3
688
siesta: 16.11561852 26.71075147 kBar
697
siesta: 16.11562007 26.71075289 kBar
689
698
(Free)E+ p_basis*V_orbitals = -699.082881
690
699
(Free)Eharris+ p_basis*V_orbitals = -699.082881
692
701
siesta: Electric dipole (a.u.) = -0.000000 0.000000 -0.019421
693
siesta: Electric dipole (Debye) = -0.000000 0.000000 -0.049362
702
siesta: Electric dipole (Debye) = -0.000000 0.000000 -0.049363
695
704
dhscf: Vacuum level (max, mean) = -0.031773 -0.167737 eV
696
>> End of run: 18-AUG-2016 8:47:08
705
>> End of run: 2-JUL-2017 11:58:31