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
9
* Running on 8 nodes in parallel
10
>> Start of run: 10-JUN-2018 21:52:14
12
***********************
14
***********************
16
reinit: Reading from standard input
17
************************** Dump of input data file ****************************
22
%block ChemicalSpeciesLabel
24
%endblock ChemicalSpeciesLabel
28
LatticeConstant 4.89 Ang
33
%endblock LatticeVectors
34
AtomicCoordinatesFormat ScaledCartesian
35
%block AtomicCoordinatesAndAtomicSpecies
36
0.000000 0.000000 0.000000 1
37
%endblock AtomicCoordinatesAndAtomicSpecies
38
%block kgrid_Monkhorst_Pack
42
%endblock kgrid_Monkhorst_Pack
49
n=6 0 2 E 3.76509 2.94865
52
n=6 1 2 E 2.50435 0.86601
55
n=6 2 1 E 135.64896 4.82387
59
************************** End of input data file *****************************
61
reinit: -----------------------------------------------------------------------
62
reinit: System Name: bulk Lead
63
reinit: -----------------------------------------------------------------------
64
reinit: System Label: pb_bulk
65
reinit: -----------------------------------------------------------------------
67
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
68
Species number: 1 Label: Pb Atomic number: 82
69
Ground state valence configuration: 6s02 6p02
70
Reading pseudopotential information in formatted form from Pb.psf
72
Pseudopotential generated from a relativistic atomic calculation
73
There are spin-orbit pseudopotentials available
74
Spin-orbit interaction is not included in this calculation
76
Valence configuration for pseudopotential generation:
81
relmxkb: Read Max KB Ang. Momentum= 3 for species Pb
84
===============================================================================
85
Pb Z= 82 Mass= 207.20 Charge=-0.30296
86
Lmxo=2 Lmxkb= 3 BasisType=split Semic=F
87
L=0 Nsemic=0 Cnfigmx=6
96
lambdas: 1.0000 1.0000
97
L=1 Nsemic=0 Cnfigmx=6
106
lambdas: 1.0000 1.0000
107
L=2 Nsemic=0 Cnfigmx=6
117
-------------------------------------------------------------------------------
118
L=0 Nkbl=1 erefs: 0.17977+309
119
L=1 Nkbl=1 erefs: 0.17977+309
120
L=2 Nkbl=1 erefs: 0.17977+309
121
L=3 Nkbl=1 erefs: 0.17977+309
122
===============================================================================
125
atom: Called for Pb (Z = 82)
127
read_vps: Pseudopotential generation method:
128
read_vps: ATM3 Troullier-Martins
129
Total valence charge: 4.00000
131
read_vps: Pseudopotential includes a core correction:
132
read_vps: Pseudo-core for xc-correction
134
xc_check: Exchange-correlation functional:
135
xc_check: Ceperley-Alder
136
V l=0 = -2*Zval/r beyond r= 4.3417
137
V l=1 = -2*Zval/r beyond r= 4.3417
138
V l=2 = -2*Zval/r beyond r= 4.3417
139
V l=3 = -2*Zval/r beyond r= 4.3417
140
All V_l potentials equal beyond r= 2.9469
141
This should be close to max(r_c) in ps generation
142
All pots = -2*Zval/r beyond r= 4.3417
143
Using large-core scheme for Vlocal
145
atom: Estimated core radius 4.34173
146
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 4.73875
147
atom: Maximum radius for r*vlocal+2*Zval: 4.39635
148
GHOST: No ghost state for L = 0
149
GHOST: No ghost state for L = 1
150
GHOST: No ghost state for L = 2
151
GHOST: No ghost state for L = 3
153
KBgen: Kleinman-Bylander projectors:
154
l= 0 rc= 3.021552 el= -0.897425 Ekb= 7.460315 kbcos= 0.182446
155
l= 1 rc= 3.059559 el= -0.274092 Ekb= 2.458119 kbcos= 0.255536
156
l= 2 rc= 3.059559 el= 0.002395 Ekb= 3.554855 kbcos= 0.076826
157
l= 3 rc= 3.059559 el= 0.003524 Ekb= -1.662449 kbcos= -0.034384
159
KBgen: Total number of Kleinman-Bylander projectors: 16
160
atom: -------------------------------------------------------------------------
162
atom: SANKEY-TYPE ORBITALS:
163
atom: Selected multiple-zeta basis: split
165
atom: basis set generated (by rescaling the valence charge)
166
atom: for an anion of charge -0.3030
168
SPLIT: Orbitals with angular momentum L= 0
170
SPLIT: Basis orbitals for state 6s
177
potential(screened) = -1.486593
178
potential(ionic) = -3.374130
185
potential(screened) = -1.638636
186
potential(ionic) = -3.544488
188
SPLIT: Orbitals with angular momentum L= 1
190
SPLIT: Basis orbitals for state 6p
197
potential(screened) = -0.969851
198
potential(ionic) = -2.823604
204
* WARNING: effective split_norm is quite small. Orbitals will be very similar.
206
potential(screened) = -1.058964
207
potential(ionic) = -2.950318
209
SPLIT: Orbitals with angular momentum L= 2
211
SPLIT: Basis orbitals for state 6d
218
potential(screened) = -1.161104
219
potential(ionic) = -2.940924
220
atom: Total number of Sankey-type orbitals: 13
222
atm_pop: Valence configuration (for local Pseudopot. screening):
226
Vna: chval, zval: 4.00000 4.00000
228
Vna: Cut-off radius for the neutral-atom potential: 6.161226
229
comcore: Pseudo-core radius Rcore= 5.574905
231
atom: _________________________________________________________________________
233
prinput: Basis input ----------------------------------------------------------
237
%block ChemicalSpeciesLabel
238
1 82 Pb # Species index, atomic number, species label
239
%endblock ChemicalSpeciesLabel
241
%block PAO.Basis # Define Basis set
242
Pb 3 -0.303 # Label, l-shells, ionic net charge
243
n=6 0 2 # n, l, Nzeta
246
n=6 1 2 # n, l, Nzeta
249
n=6 2 1 # n, l, Nzeta
254
prinput: ----------------------------------------------------------------------
256
Dumping basis to NetCDF file Pb.ion.nc
257
coor: Atomic-coordinates input format = Cartesian coordinates
258
coor: (in units of alat)
260
siesta: Atomic coordinates (Bohr) and species
261
siesta: 0.00000 0.00000 0.00000 1 1
263
siesta: System type = bulk
265
initatomlists: Number of atoms, orbitals, and projectors: 1 13 16
267
siesta: ******************** Simulation parameters ****************************
269
siesta: The following are some of the parameters of the simulation.
270
siesta: A complete list of the parameters used, including default values,
271
siesta: can be found in file out.fdf
273
redata: Non-Collinear-spin run = F
274
redata: SpinPolarized (Up/Down) run = F
275
redata: Number of spin components = 1
276
redata: Long output = F
277
redata: Number of Atomic Species = 1
278
redata: Charge density info will appear in .RHO file
279
redata: Write Mulliken Pop. = NO
280
redata: Matel table size (NRTAB) = 1024
281
redata: Mesh Cutoff = 75.0000 Ry
282
redata: Net charge of the system = 0.0000 |e|
283
redata: Min. number of SCF Iter = 0
284
redata: Max. number of SCF Iter = 50
285
redata: Mix DM or H after convergence = F
286
redata: Recompute H after scf cycle = F
287
redata: Performing Pulay mixing using = 3 iterations
288
redata: Mix DM in first SCF step ? = F
289
redata: Write Pulay info on disk? = F
290
redata: Discard 1st Pulay DM after kick = F
291
redata: New DM Mixing Weight = 0.0500
292
redata: New DM Occupancy tolerance = 0.000000000001
293
redata: No kicks to SCF
294
redata: DM Mixing Weight for Kicks = 0.5000
295
redata: DM Tolerance for SCF = 0.000100
296
redata: Require (free) Energy convergence in SCF = F
297
redata: DM (free)Energy tolerance for SCF = 0.000010 eV
298
redata: Require Harris convergence for SCF = F
299
redata: DM Harris energy tolerance for SCF = 0.000010 eV
300
redata: Using Saved Data (generic) = F
301
redata: Use continuation files for DM = F
302
redata: Neglect nonoverlap interactions = F
303
redata: Method of Calculation = Diagonalization
304
redata: Divide and Conquer = T
305
redata: Electronic Temperature = 0.0019 Ry
306
redata: Fix the spin of the system = F
307
redata: Dynamics option = Single-point calculation
308
redata: ***********************************************************************
309
Total number of electrons: 4.000000
310
Total ionic charge: 4.000000
312
* ProcessorY, Blocksize: 2 1
315
* Orbital distribution balance (max,min): 2 1
317
k-point displ. along 1 input, could be: 0.50 0.00
318
k-point displ. along 2 input, could be: 0.50 0.00
319
k-point displ. along 3 input, could be: 0.50 0.00
320
Kpoints in: 196 . Kpoints trimmed: 196
322
siesta: k-grid: Number of k-points = 196
323
siesta: k-grid: Cutoff (effective) = 12.102 Ang
324
siesta: k-grid: Supercell and displacements
325
siesta: k-grid: 7 0 0 0.500
326
siesta: k-grid: 0 7 0 0.500
327
siesta: k-grid: 0 0 7 0.500
328
Naive supercell factors: 6 6 6
330
superc: Internal auxiliary supercell: 6 x 6 x 6 = 216
331
superc: Number of atoms, orbitals, and projectors: 216 2808 3456
333
====================================
334
Single-point calculation
335
====================================
337
superc: Internal auxiliary supercell: 6 x 6 x 6 = 216
338
superc: Number of atoms, orbitals, and projectors: 216 2808 3456
340
outcell: Unit cell vectors (Ang):
341
2.445000 2.445000 0.000000
342
2.445000 0.000000 2.445000
343
0.000000 2.445000 2.445000
345
outcell: Cell vector modules (Ang) : 3.457752 3.457752 3.457752
346
outcell: Cell angles (23,13,12) (deg): 60.0000 60.0000 60.0000
347
outcell: Cell volume (Ang**3) : 29.2325
349
Initializing Density Matrix...
350
New grid distribution: 1
360
InitMesh: MESH = 16 x 16 x 16 = 4096
361
InitMesh: (bp) = 8 x 8 x 8 = 512
362
InitMesh: Mesh cutoff (required, used) = 75.000 88.766 Ry
363
ExtMesh (bp) on 0 = 48 x 44 x 42 = 88704
364
New grid distribution: 2
373
New grid distribution: 3
382
Setting up quadratic distribution...
383
ExtMesh (bp) on 0 = 44 x 44 x 44 = 85184
384
PhiOnMesh: Number of (b)points on node 0 = 64
385
PhiOnMesh: nlist on node 0 = 3606
387
stepf: Fermi-Dirac step function
389
siesta: Program's energy decomposition (eV):
390
siesta: Ebs = -29.862827
391
siesta: Eions = 122.930792
392
siesta: Ena = 18.410263
393
siesta: Ekin = 36.550578
394
siesta: Enl = 13.411994
395
siesta: DEna = -0.000000
396
siesta: DUscf = 0.000000
397
siesta: DUext = 0.000000
398
siesta: Exc = -291.677632
399
siesta: eta*DQ = 0.000000
400
siesta: Emadel = 0.000000
401
siesta: Emeta = 0.000000
402
siesta: Emolmec = 0.000000
403
siesta: Ekinion = 0.000000
404
siesta: Eharris = -349.891412
405
siesta: Etot = -346.235590
406
siesta: FreeEng = -346.236932
408
scf: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
409
scf: 1 -349.8914 -346.2356 -346.2369 0.24264 -2.1271
410
timer: Routine,Calls,Time,% = IterSCF 1 0.823 53.58
411
scf: 2 -349.8462 -349.8421 -349.8437 0.04052 -2.2852
412
scf: 3 -349.8458 -349.6262 -349.6278 0.05032 -2.2748
413
scf: 4 -349.8458 -349.8550 -349.8566 0.00169 -2.2742
414
scf: 5 -349.8458 -349.8464 -349.8480 0.00014 -2.2732
415
scf: 6 -349.8458 -349.8464 -349.8479 0.00013 -2.2732
416
scf: 7 -349.8458 -349.8457 -349.8473 0.00001 -2.2731
418
SCF Convergence by dMax criterion
419
max |DM_out - DM_in|: 0.00001030
420
SCF cycle converged after 7 iterations
422
Using DM_out to compute the final energy and forces
424
siesta: E_KS(eV) = -349.8458
426
siesta: E_KS - E_eggbox = -349.8458
428
siesta: Atomic forces (eV/Ang):
429
----------------------------------------
430
Tot -0.000000 -0.000000 -0.000000
431
----------------------------------------
433
Res 0.000000 sqrt( Sum f_i^2 / 3N )
434
----------------------------------------
435
Max 0.000000 constrained
437
Stress-tensor-Voigt (kbar): 98.97 98.97 98.97 -8.74 -8.74 -8.74
438
(Free)E + p*V (eV/cell) -351.6531
439
Target enthalpy (eV/cell) -349.8474
441
siesta: Program's energy decomposition (eV):
442
siesta: Ebs = -30.652433
443
siesta: Eions = 122.930792
444
siesta: Ena = 18.410263
445
siesta: Ekin = 31.119526
446
siesta: Enl = 11.602286
447
siesta: DEna = 1.961502
448
siesta: DUscf = 0.091472
449
siesta: DUext = 0.000000
450
siesta: Exc = -290.100087
451
siesta: eta*DQ = 0.000000
452
siesta: Emadel = 0.000000
453
siesta: Emeta = 0.000000
454
siesta: Emolmec = 0.000000
455
siesta: Ekinion = 0.000000
456
siesta: Eharris = -349.845829
457
siesta: Etot = -349.845829
458
siesta: FreeEng = -349.847407
460
siesta: Final energy (eV):
461
siesta: Band Struct. = -30.652433
462
siesta: Kinetic = 31.119526
463
siesta: Hartree = 1.221843
464
siesta: Ext. field = 0.000000
465
siesta: Exch.-corr. = -290.100087
466
siesta: Ion-electron = -16.950554
467
siesta: Ion-ion = -75.136558
468
siesta: Ekinion = 0.000000
469
siesta: Total = -349.845829
471
siesta: Stress tensor (static) (eV/Ang**3):
472
siesta: 0.061768 -0.005456 -0.005456
473
siesta: -0.005456 0.061768 -0.005456
474
siesta: -0.005456 -0.005456 0.061768
476
siesta: Cell volume = 29.232542 Ang**3
478
siesta: Pressure (static):
479
siesta: Solid Molecule Units
480
siesta: -0.00067274 -0.00067274 Ry/Bohr**3
481
siesta: -0.06176846 -0.06176846 eV/Ang**3
482
siesta: -98.96505569 -98.96505569 kBar
483
(Free)E+ p_basis*V_orbitals = -349.197457
484
(Free)Eharris+ p_basis*V_orbitals = -349.197457
485
>> End of run: 10-JUN-2018 21:52:21
added
removed
Tests/Reference/pb_bulk.out
