1
Siesta Version: siesta-trunk-479
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Architecture : atto-intel12-openmpi
3
Compiler flags: /share/apps/openmpi-1.6.5-intel/bin/mpif90 -w -O2 -mp
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Siesta Version : siesta-4.1-1033
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Architecture : x86_64-linux-n-62-18-18
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Compiler version: GNU Fortran (GCC) 7.3.0
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Compiler flags : mpifort -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizatioons -funroll-loops -fprefetch-loop-arrays -fno-second-underscore -flto
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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
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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
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NetCDF-4 MPI-IO support
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METIS ordering support
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* Running on 4 nodes in parallel
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>> Start of run: 29-SEP-2015 15:46:19
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* Running on 8 nodes in parallel
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>> Start of run: 5-NOV-2018 11:11:57
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***********************
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* WELCOME TO SIESTA *
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***********************
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reinit: Reading from standard input
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************************** Dump of input data file ****************************
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# -----------------------------------------------------------------------------
20
SystemName bulk silicon with test of various types of WFS output
21
SystemLabel si_fatbands
24
%block ChemicalSpeciesLabel
26
%endblock ChemicalSpeciesLabel
28
PAO.EnergyShift 300 meV
29
LatticeConstant 5.43 Ang
34
%endblock LatticeVectors
42
ElectronicTemperature 25 meV
44
WFS.Write.For.Bands T # For fat-bands analysis
47
%block BandLines # These are comments
48
1 0.000 0.000 0.000 \Gamma # Begin at Gamma
49
25 2.000 0.000 0.000 X # 25 points from Gamma to X
50
10 2.000 1.000 0.000 W # 10 points from X to W
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15 1.000 1.000 1.000 L # 15 points from W to L
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20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma
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25 1.500 1.500 1.500 K # 25 points from Gamma to K
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WaveFuncKPointsScale pi/a
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%block WaveFuncKPoints # These are comments
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0.000 0.000 0.000 from 1 to 10 # eigenstates 1-10 of Gamma
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2.000 0.000 0.000 1 3 5 # eigenstates 1,3,5 of X
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1.500 1.500 1.500 # all eigenstates of K
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%endblock WaveFuncKPoints
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AtomicCoordinatesFormat Fractional
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%block AtomicCoordinatesAndAtomicSpecies
66
%endblock AtomicCoordinatesAndAtomicSpecies
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************************** End of input data file *****************************
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reinit: Reading from ../si_fatbands.fdf
69
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reinit: -----------------------------------------------------------------------
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reinit: System Name: bulk silicon with test of various types of WFS output
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reinit: -----------------------------------------------------------------------
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reinit: System Label: si_fatbands
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reinit: System Label: si_fatbands
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reinit: -----------------------------------------------------------------------
75
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initatom: Reading input for the pseudopotentials and atomic orbitals ----------
76
Species number: 1 Label: Si Atomic number: 14
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Species number: 1 Atomic number: 14 Label: Si
77
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Ground state valence configuration: 3s02 3p02
78
32
Reading pseudopotential information in formatted form from Si.psf
261
215
siesta: A complete list of the parameters used, including default values,
262
216
siesta: can be found in file out.fdf
264
redata: Non-Collinear-spin run = F
265
redata: SpinPolarized (Up/Down) run = F
266
redata: Number of spin components = 1
267
redata: Long output = F
268
redata: Number of Atomic Species = 1
218
redata: Spin configuration = none
219
redata: Number of spin components = 1
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redata: Time-Reversal Symmetry = T
221
redata: Spin-spiral = F
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redata: Long output = F
223
redata: Number of Atomic Species = 1
269
224
redata: Charge density info will appear in .RHO file
270
redata: Write Mulliken Pop. = NO
271
redata: Mesh Cutoff = 90.0000 Ry
272
redata: Net charge of the system = 0.0000 |e|
273
redata: Min. number of SCF Iter = 0
274
redata: Max. number of SCF Iter = 50
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redata: Mix DM or H after convergence = F
276
redata: Recompute H after scf cycle = F
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redata: Performing Pulay mixing using = 3 iterations
278
redata: Mix DM in first SCF step ? = F
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redata: Write Pulay info on disk? = F
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redata: Discard 1st Pulay DM after kick = F
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redata: New DM Mixing Weight = 0.3000
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redata: New DM Occupancy tolerance = 0.000000000001
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redata: Write Mulliken Pop. = NO
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redata: Matel table size (NRTAB) = 1024
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redata: Mesh Cutoff = 90.0000 Ry
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redata: Net charge of the system = 0.0000 |e|
229
redata: Min. number of SCF Iter = 0
230
redata: Max. number of SCF Iter = 1000
231
redata: SCF convergence failure will abort job
232
redata: SCF mix quantity = Hamiltonian
233
redata: Mix DM or H after convergence = F
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redata: Recompute H after scf cycle = F
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redata: Mix DM in first SCF step = T
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redata: Write Pulay info on disk = F
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redata: New DM Mixing Weight = 0.3000
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redata: New DM Occupancy tolerance = 0.000000000001
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redata: No kicks to SCF
284
redata: DM Mixing Weight for Kicks = 0.5000
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redata: DM Tolerance for SCF = 0.000100
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redata: Require (free) Energy convergence in SCF = F
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redata: DM (free)Energy tolerance for SCF = 0.000010 eV
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redata: Require Harris convergence for SCF = F
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redata: DM Harris energy tolerance for SCF = 0.000010 eV
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redata: Using Saved Data (generic) = F
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redata: Use continuation files for DM = F
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redata: Neglect nonoverlap interactions = F
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redata: Method of Calculation = Diagonalization
294
redata: Divide and Conquer = T
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redata: Electronic Temperature = 0.0018 Ry
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redata: Fix the spin of the system = F
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redata: Dynamics option = Single-point calculation
240
redata: DM Mixing Weight for Kicks = 0.5000
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redata: Require Harris convergence for SCF = F
242
redata: Harris energy tolerance for SCF = 0.000100 eV
243
redata: Require DM convergence for SCF = T
244
redata: DM tolerance for SCF = 0.000100
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redata: Require EDM convergence for SCF = F
246
redata: EDM tolerance for SCF = 0.001000 eV
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redata: Require H convergence for SCF = T
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redata: Hamiltonian tolerance for SCF = 0.001000 eV
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redata: Require (free) Energy convergence for SCF = F
250
redata: (free) Energy tolerance for SCF = 0.000100 eV
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redata: Using Saved Data (generic) = F
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redata: Use continuation files for DM = F
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redata: Neglect nonoverlap interactions = F
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redata: Method of Calculation = Diagonalization
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redata: Electronic Temperature = 290.1109 K
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redata: Fix the spin of the system = F
257
redata: Dynamics option = Single-point calculation
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mix.SCF: Pulay mixing = Pulay
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mix.SCF: Variant = stable
260
mix.SCF: History steps = 3
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mix.SCF: Linear mixing weight = 0.300000
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mix.SCF: Mixing weight = 0.300000
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mix.SCF: SVD condition = 0.1000E-07
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redata: Save all siesta data in one NC = F
298
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redata: ***********************************************************************
271
%block SCF.Mixer.Pulay
280
%endblock SCF.Mixer.Pulay
282
DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
283
Size of DM history Fstack: 1
299
284
Total number of electrons: 8.000000
300
285
Total ionic charge: 8.000000
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* ProcessorY, Blocksize: 2 7
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* Orbital distribution balance (max,min): 7 5
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* ProcessorY, Blocksize: 2 3
290
* Orbital distribution balance (max,min): 5 3
307
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Kpoints in: 32 . Kpoints trimmed: 32
312
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siesta: k-grid: 0 4 0 0.500
313
298
siesta: k-grid: 0 0 4 0.500
314
299
siesta: k-grid: 4 0 0 0.500
315
Naive supercell factors: 5 5 5
301
diag: Algorithm = D&C
302
diag: Parallel over k = F
303
diag: Use parallel 2D distribution = T
304
diag: Parallel block-size = 3
305
diag: Parallel distribution = 2 x 4
306
diag: Used triangular part = Lower
307
diag: Absolute tolerance = 0.100E-15
308
diag: Orthogonalization factor = 0.100E-05
309
diag: Memory factor = 1.0000
310
Using LatticeConstant from fdf file for BandLinesScale: 10.261217 Bohr
311
Beware any cell changes by the end of the run
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Using LatticeConstant from fdf file for BandLinesScale: 10.261217 Bohr
313
Beware any cell changes by the end of the run
314
Using LatticeConstant from fdf file for WaveFuncKPointsScale: 10.261217 Bohr
315
Beware any cell changes by the end of the run
317
317
superc: Internal auxiliary supercell: 5 x 5 x 5 = 125
318
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superc: Number of atoms, orbitals, and projectors: 250 3250 4000
321
ts: **************************************************************
322
ts: Save H and S matrices = F
323
ts: Save DM and EDM matrices = F
324
ts: Fix Hartree potential = F
325
ts: Only save the overlap matrix S = F
326
ts: **************************************************************
328
************************ Begin: TS CHECKS AND WARNINGS ************************
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************************ End: TS CHECKS AND WARNINGS **************************
320
332
====================================
321
333
Single-point calculation
322
334
====================================
332
344
outcell: Cell vector modules (Ang) : 3.839590 3.839590 3.839590
333
345
outcell: Cell angles (23,13,12) (deg): 60.0000 60.0000 60.0000
334
346
outcell: Cell volume (Ang**3) : 40.0258
347
<dSpData1D:S at geom step 0
348
<sparsity:sparsity for geom step 0
349
nrows_g=26 nrows=5 sparsity=5.5311 nnzs=3739, refcount: 7>
350
<dData1D:(new from dSpData1D) n=3739, refcount: 1>
336
353
Initializing Density Matrix...
354
DM filled with atomic data:
355
<dSpData2D:DM initialized from atoms
356
<sparsity:sparsity for geom step 0
357
nrows_g=26 nrows=5 sparsity=5.5311 nnzs=3739, refcount: 8>
358
<dData2D:DM n=3739 m=1, refcount: 1>
360
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 26 161
337
361
New grid distribution: 1
343
371
InitMesh: MESH = 18 x 18 x 18 = 5832
344
372
InitMesh: (bp) = 9 x 9 x 9 = 729
345
373
InitMesh: Mesh cutoff (required, used) = 90.000 91.110 Ry
346
ExtMesh (bp) on 0 = 49 x 45 x 45 = 99225
374
ExtMesh (bp) on 0 = 49 x 45 x 43 = 94815
347
375
New grid distribution: 2
352
384
New grid distribution: 3
357
393
Setting up quadratic distribution...
358
ExtMesh (bp) on 0 = 49 x 45 x 45 = 99225
359
PhiOnMesh: Number of (b)points on node 0 = 225
360
PhiOnMesh: nlist on node 0 = 18321
394
ExtMesh (bp) on 0 = 45 x 45 x 45 = 91125
395
PhiOnMesh: Number of (b)points on node 0 = 125
396
PhiOnMesh: nlist on node 0 = 9760
362
398
stepf: Fermi-Dirac step function
364
400
siesta: Program's energy decomposition (eV):
365
siesta: Ebs = -74.505005
401
siesta: Ebs = -73.640184
366
402
siesta: Eions = 380.802124
367
siesta: Ena = 114.848182
368
siesta: Ekin = 80.404549
369
siesta: Enl = 36.046992
370
siesta: DEna = 0.000000
371
siesta: DUscf = 0.000000
403
siesta: Ena = 114.848340
404
siesta: Ekin = 81.893038
405
siesta: Enl = 29.332741
406
siesta: Eso = 0.000000
407
siesta: Eldau = 0.000000
408
siesta: DEna = 4.187562
409
siesta: DUscf = 0.264534
372
410
siesta: DUext = 0.000000
373
siesta: Exc = -64.706935
411
siesta: Enegf = 0.000000
412
siesta: Exc = -65.159608
374
413
siesta: eta*DQ = 0.000000
375
414
siesta: Emadel = 0.000000
376
415
siesta: Emeta = 0.000000
377
416
siesta: Emolmec = 0.000000
378
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siesta: Ekinion = 0.000000
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siesta: Eharris = -215.470652
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siesta: Etot = -214.209336
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siesta: FreeEng = -214.209336
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scf: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
384
scf: 1 -215.4707 -214.2093 -214.2093 1.81760 -3.8996
385
timer: Routine,Calls,Time,% = IterSCF 1 0.256 10.83
386
scf: 2 -215.4379 -215.4358 -215.4358 0.00974 -3.8091
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scf: 3 -215.4376 -215.4313 -215.4313 0.00480 -3.8162
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scf: 4 -215.4375 -215.4375 -215.4375 0.00037 -3.8267
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scf: 5 -215.4375 -215.4376 -215.4376 0.00026 -3.8268
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scf: 6 -215.4375 -215.4375 -215.4375 0.00013 -3.8266
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scf: 7 -215.4375 -215.4375 -215.4375 0.00008 -3.8266
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SCF Convergence by dMax criterion
394
max |DM_out - DM_in|: 0.00007908
395
SCF cycle converged after 7 iterations
418
siesta: Eharris = -216.624578
419
siesta: Etot = -215.435517
420
siesta: FreeEng = -215.435517
422
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
423
scf: 1 -216.624578 -215.435517 -215.435517 1.817604 -3.900050 0.120725
424
timer: Routine,Calls,Time,% = IterSCF 1 0.312 23.96
425
scf: 2 -215.437482 -215.436522 -215.436522 0.002943 -3.872863 0.074717
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scf: 3 -215.437707 -215.437178 -215.437178 0.004798 -3.826824 0.002658
427
scf: 4 -215.437188 -215.437183 -215.437183 0.000457 -3.826975 0.000508
428
scf: 5 -215.437183 -215.437183 -215.437183 0.000040 -3.826964 0.000312
430
SCF Convergence by DM+H criterion
431
max |DM_out - DM_in| : 0.0000404071
432
max |H_out - H_in| (eV) : 0.0003122125
433
SCF cycle converged after 5 iterations
397
435
Using DM_out to compute the final energy and forces
399
siesta: E_KS(eV) = -215.4375
401
siesta: E_KS - E_eggbox = -215.4375
436
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 26 161
438
siesta: E_KS(eV) = -215.4372
440
siesta: E_KS - E_eggbox = -215.4372
403
442
siesta: Atomic forces (eV/Ang):
404
443
----------------------------------------
405
Tot 0.000219 0.000219 0.000219
406
----------------------------------------
408
Res 0.021130 sqrt( Sum f_i^2 / 3N )
409
----------------------------------------
410
Max 0.021239 constrained
444
Tot 0.000221 0.000221 0.000221
445
----------------------------------------
447
Res 0.021230 sqrt( Sum f_i^2 / 3N )
448
----------------------------------------
449
Max 0.021340 constrained
412
Stress-tensor-Voigt (kbar): 13.88 13.88 13.88 10.73 10.73 10.73
413
(Free)E + p*V (eV/cell) -215.7842
414
Target enthalpy (eV/cell) -215.4375
451
Stress-tensor-Voigt (kbar): 13.69 13.69 13.69 10.72 10.72 10.72
452
(Free)E + p*V (eV/cell) -215.7793
453
Target enthalpy (eV/cell) -215.4372
415
454
Writing WFSX for selected k-points in si_fatbands.selected.WFSX
416
455
Writing WFSX for COOP/COHP in si_fatbands.fullBZ.WFSX
417
456
Computing bands...
418
457
Writing WFSX for bands in si_fatbands.bands.WFSX
420
459
siesta: Program's energy decomposition (eV):
421
siesta: Ebs = -73.796701
460
siesta: Ebs = -73.797139
422
461
siesta: Eions = 380.802124
423
siesta: Ena = 114.848182
424
siesta: Ekin = 81.648692
425
siesta: Enl = 29.319489
426
siesta: DEna = 4.386113
427
siesta: DUscf = 0.252715
462
siesta: Ena = 114.848340
463
siesta: Ekin = 81.648391
464
siesta: Enl = 29.318772
465
siesta: Eso = 0.000000
466
siesta: Eldau = 0.000000
467
siesta: DEna = 4.387143
468
siesta: DUscf = 0.252748
428
469
siesta: DUext = 0.000000
429
siesta: Exc = -65.090528
470
siesta: Enegf = 0.000000
471
siesta: Exc = -65.090454
430
472
siesta: eta*DQ = 0.000000
431
473
siesta: Emadel = 0.000000
432
474
siesta: Emeta = 0.000000
433
475
siesta: Emolmec = 0.000000
434
476
siesta: Ekinion = 0.000000
435
siesta: Eharris = -215.437459
436
siesta: Etot = -215.437459
437
siesta: FreeEng = -215.437459
477
siesta: Eharris = -215.437183
478
siesta: Etot = -215.437183
479
siesta: FreeEng = -215.437183
439
481
siesta: Final energy (eV):
440
siesta: Band Struct. = -73.796701
441
siesta: Kinetic = 81.648692
442
siesta: Hartree = 14.748890
482
siesta: Band Struct. = -73.797139
483
siesta: Kinetic = 81.648391
484
siesta: Hartree = 14.748504
485
siesta: Eldau = 0.000000
486
siesta: Eso = 0.000000
443
487
siesta: Ext. field = 0.000000
444
siesta: Exch.-corr. = -65.090528
445
siesta: Ion-electron = -100.071586
446
siesta: Ion-ion = -146.672928
488
siesta: Enegf = 0.000000
489
siesta: Exch.-corr. = -65.090454
490
siesta: Ion-electron = -100.070855
491
siesta: Ion-ion = -146.672770
447
492
siesta: Ekinion = 0.000000
448
siesta: Total = -215.437459
493
siesta: Total = -215.437183
494
siesta: Fermi = -3.826964
450
496
siesta: Stress tensor (static) (eV/Ang**3):
451
siesta: 0.008663 0.006697 0.006697
452
siesta: 0.006697 0.008663 0.006697
453
siesta: 0.006697 0.006697 0.008663
497
siesta: 0.008546 0.006690 0.006690
498
siesta: 0.006690 0.008546 0.006690
499
siesta: 0.006690 0.006690 0.008546
455
501
siesta: Cell volume = 40.025752 Ang**3
457
503
siesta: Pressure (static):
458
504
siesta: Solid Molecule Units
459
siesta: -0.00009436 -0.00010216 Ry/Bohr**3
460
siesta: -0.00866344 -0.00938007 eV/Ang**3
461
siesta: -13.88051217 -15.02869848 kBar
462
(Free)E+ p_basis*V_orbitals = -214.226785
463
(Free)Eharris+ p_basis*V_orbitals = -214.226785
464
>> End of run: 29-SEP-2015 15:46:24
505
siesta: -0.00009308 -0.00010092 Ry/Bohr**3
506
siesta: -0.00854635 -0.00926637 eV/Ang**3
507
siesta: -13.69290630 -14.84652658 kBar
508
(Free)E+ p_basis*V_orbitals = -214.226509
509
(Free)Eharris+ p_basis*V_orbitals = -214.226509
510
>> End of run: 5-NOV-2018 11:12:01
added
removed
Tests/Reference/si_fatbands.out
