Dipole correction & number of cores - bug ?
ashish dabral
ashishd... at gmail.com
Thu Aug 24 16:42:31 UTC 2017
Dear all,
I have been facing some strange issues with CP2K version 4.1 and I'm
looking forward having your advice.
I would like to apply the self-consistent dipole correction for a slab
calculation and I noticed an inconsistent behavior of cp2k with respect to
the number of cores used:
Whenever I'm running a simple exercise of a water molecule in a box (see
the attached test.inp file) using 1 core, the dipole correction is working
smoothly and I'm reaching convergence without any issue. On the other hand
if I'm using more than 1 core, cp2k returns the following error message:
" Dipole correction needs more vacuum space above the surface ".
I hence hacked a bit the code to understand what I did wrong and printed
some information from the surface_dipole.F routine.
I monitored the "height_min" and "rhoav_min" internal variables that are
used to detect the position of the vacuum section in the supercell.
If I'm correct, line 183 of the routine is basically checking whether the
average of the electronic density (rhoav_min - if I got it well) is low
enough (IF (rhoav_min >= 1.E-5_dp) -> stop) to provide the index of the
numerical grid that corresponds to vacuum.
The strange thing is that whenever I'm using 1 core, cp2k detects a
rhoav_min value of 2.776668424252914E-007 within the first scf cycle and
goes on without any issue until convergence.
On the other hand, while whenever I'm using 2 and 4 cores, it returns a
value of :2.327421985372404E-004 and 6.156728744828596E-005, respectively.
In both cases, this is larger than the threshold used to detect the vacuum
part at line 183 (IF (rhoav_min >= 1.E-5_dp)) - I attached the log files
for your inconvenience.
I was naively expecting that rhoav_min should be the same, independently of
the number of the grid used but obviously either there is an issue with the
averaged value or the system is probing another point of the grid. Unless
if I'm mistaken, it looks to me that there is an issue with the collection
by mpi of the grid values or something like that but unfortunately, I could
not trace further the issue.
I'm hence wondering if someone else has met the issue and if so, I'd really
appreciate if you could help me figuring out what is on-going and what I
missed.
Thank you very much for your help,
Regards,
Ashish
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DBCSR| Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Randmat seed 12341313
DBCSR| Multiplication size stacks 3
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation T
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2017-08-24 18:25:24.364
***** ** *** *** ** PROGRAM STARTED ON clust069
** **** ****** PROGRAM STARTED BY dabral58
***** ** ** ** ** PROGRAM PROCESS ID 8675
**** ** ******* ** PROGRAM STARTED IN /tmp/scratch/dabral58/tmp
CP2K| version string: CP2K version 4.1
CP2K| source code revision number: svn:17462
CP2K| cp2kflags: libint fftw3 libxc elpa3 parallel mpi3 scalapack libxsmm libde
CP2K| riv_max_am1=5 libint_max_am=6
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Thu Aug 24 17:56:33 CEST 2017
CP2K| Program compiled on clust069
CP2K| Program compiled for new_imec
CP2K| Data directory path /imec/other/abinitio/source/cp2k/tar/cp2k-4.1/data
CP2K| Input file name H2O.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| Potential file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name H2O
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. ELPA
GLOBAL| Run type ENERGY_FORCE
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| Total number of message passing processes 1
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 198083204 198083204 198083204 198083204
MEMORY| MemFree 148986076 148986076 148986076 148986076
MEMORY| Buffers 390276 390276 390276 390276
MEMORY| Cached 46145820 46145820 46145820 46145820
MEMORY| Slab 896716 896716 896716 896716
MEMORY| SReclaimable 800844 800844 800844 800844
MEMORY| MemLikelyFree 196323016 196323016 196323016 196323016
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
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** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000 - 2016) **
** **
*******************************************************************************
SCF PARAMETERS Density guess: ATOMIC
--------------------------------------------------------
max_scf: 100
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 5.00E-04
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
No outer SCF
DISTRIBUTION OF THE PARTICLES (ROWS)
Process row Number of particles Number of matrix rows
0 3 -1
Sum 3 -1
DISTRIBUTION OF THE PARTICLES (COLUMNS)
Process col Number of particles Number of matrix columns
0 3 -1
Sum 3 -1
DISTRIBUTION OF THE NEIGHBOR LISTS
Total number of particle pairs: 342
Total number of matrix elements: 14406
Average number of particle pairs: 342
Maximum number of particle pairs: 342
Average number of matrix element: 14406
Maximum number of matrix elements: 14406
DISTRIBUTION OF THE OVERLAP MATRIX
Number of non-zero blocks: 6
Percentage non-zero blocks: 100.00
Average number of blocks per CPU: 6
Maximum number of blocks per CPU: 6
Average number of matrix elements per CPU: 384
Maximum number of matrix elements per CPU: 384
Number of electrons: 8
Number of occupied orbitals: 4
Number of molecular orbitals: 4
Number of orbital functions: 23
Number of independent orbital functions: 23
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : CG : conjugate gradient
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
Line search : 2PNT : 2 energies, one gradient
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
Min. height: 9.86856980506947 rhoav_min : 2.776668424252914E-007
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -1.791727633430895E-004 a.u.
DIP. CORR. : ENERGY CORR. : 6.399944371034874E-004 a.u.
---
1 OT CG 0.80E-01 1.0 0.38243266 -16.5161045336 -1.65E+01
Min. height: 9.86856980506947 rhoav_min : 1.458486387896576E-007
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -3.549792648118965E-004 a.u.
DIP. CORR. : ENERGY CORR. : 2.512596926675403E-003 a.u.
---
2 OT LS 0.55E-01 0.9 -16.8112132542
Min. height: 10.0785393753901 rhoav_min : 8.894601344569855E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -3.982426961010405E-004 a.u.
DIP. CORR. : ENERGY CORR. : 3.162450273472157E-003 a.u.
---
3 OT CG 0.55E-01 1.5 0.31961035 -16.8652175179 -3.49E-01
Min. height: 10.0785393753901 rhoav_min : 1.143422251163904E-007
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -1.045936655097399E-004 a.u.
DIP. CORR. : ENERGY CORR. : 2.180370832142000E-004 a.u.
---
4 OT LS 0.57E-01 0.9 -17.1306877518
Min. height: 10.0785393753901 rhoav_min : 1.197164143954366E-007
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -9.082663892354682E-005 a.u.
DIP. CORR. : ENERGY CORR. : 1.644006816441490E-004 a.u.
---
5 OT CG 0.57E-01 1.5 0.15790115 -17.1282577852 -2.63E-01
Min. height: 10.0785393753901 rhoav_min : 6.858293910207531E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -1.620988045698050E-004 a.u.
DIP. CORR. : ENERGY CORR. : 5.238107610659199E-004 a.u.
---
6 OT LS 0.48E-01 0.9 -17.1758152988
Min. height: 10.0785393753901 rhoav_min : 7.048632428513973E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -1.543339630102247E-004 a.u.
DIP. CORR. : ENERGY CORR. : 4.748207393164167E-004 a.u.
---
7 OT CG 0.48E-01 1.5 0.09637456 -17.1774857647 -4.92E-02
Min. height: 10.0785393753901 rhoav_min : 3.538917871551732E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.332155651243405E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.084396722138596E-003 a.u.
---
8 OT LS 0.50E-01 0.9 -17.1987144563
Min. height: 10.0785393753901 rhoav_min : 3.461296242312211E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.357728683234345E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.108312421872916E-003 a.u.
---
9 OT CG 0.50E-01 1.5 0.03689518 -17.1987482822 -2.13E-02
Min. height: 10.0785393753901 rhoav_min : 3.227297238286387E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.334715912880112E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.086784834939196E-003 a.u.
---
10 OT LS 0.12E+00 0.9 -17.2037024879
Min. height: 10.0785393753901 rhoav_min : 3.259499279150189E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.290955442611722E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.046428152483357E-003 a.u.
---
11 OT CG 0.12E+00 1.5 0.01763843 -17.2060406584 -7.29E-03
Min. height: 10.0785393753901 rhoav_min : 3.538531965213110E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.194395342185409E-004 a.u.
DIP. CORR. : ENERGY CORR. : 9.600698342610922E-004 a.u.
---
12 OT LS 0.79E-01 0.9 -17.2068713460
Min. height: 10.0785393753901 rhoav_min : 3.435005830208955E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.228357351315230E-004 a.u.
DIP. CORR. : ENERGY CORR. : 9.900199245361163E-004 a.u.
---
13 OT CG 0.79E-01 1.5 0.01211285 -17.2071290807 -1.09E-03
Min. height: 10.0785393753901 rhoav_min : 3.813475584458790E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.196888399715649E-004 a.u.
DIP. CORR. : ENERGY CORR. : 9.622507554609639E-004 a.u.
---
14 OT LS 0.55E-01 0.9 -17.2074334546
Min. height: 10.0785393753901 rhoav_min : 3.692239271200973E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.206702502552345E-004 a.u.
DIP. CORR. : ENERGY CORR. : 9.708686308787321E-004 a.u.
---
15 OT CG 0.55E-01 1.5 0.00540470 -17.2075016836 -3.73E-04
Min. height: 10.0785393753901 rhoav_min : 3.662584729873376E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.252730710617480E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.011798400858714E-003 a.u.
---
16 OT LS 0.78E-01 0.9 -17.2075972642
Min. height: 10.0785393753901 rhoav_min : 3.651207726074519E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.271413464299494E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.028652818369307E-003 a.u.
---
17 OT CG 0.78E-01 1.5 0.00276250 -17.2076060371 -1.04E-04
Min. height: 10.0785393753901 rhoav_min : 3.675930893441705E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.272462856652694E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.029603895363984E-003 a.u.
---
18 OT LS 0.85E-01 0.9 -17.2076356978
Min. height: 10.0785393753901 rhoav_min : 3.678549336206129E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.272549810279191E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.029682725452204E-003 a.u.
---
19 OT CG 0.85E-01 1.5 0.00175973 -17.2076359219 -2.99E-05
Min. height: 10.0785393753901 rhoav_min : 3.665238452081181E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.268373931111135E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.025901943544845E-003 a.u.
---
20 OT LS 0.62E-01 0.9 -17.2076436145
Min. height: 10.0785393753901 rhoav_min : 3.668428549499970E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.269508029138694E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.026928054152994E-003 a.u.
---
21 OT CG 0.62E-01 1.5 0.00100543 -17.2076447943 -8.87E-06
Min. height: 10.0785393753901 rhoav_min : 3.680370432116368E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.263194810716890E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.021221863546503E-003 a.u.
---
22 OT LS 0.66E-01 0.9 -17.2076478703
Min. height: 10.0785393753901 rhoav_min : 3.681165402971098E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.262782162186246E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.020849445468026E-003 a.u.
---
23 OT CG 0.66E-01 1.6 0.00039085 -17.2076478819 -3.09E-06
*** SCF run converged in 23 steps ***
Electronic density on regular grids: -7.9999696498 0.0000303502
Core density on regular grids: 8.0000000301 0.0000000301
Total charge density on r-space grids: 0.0000303802
Total charge density g-space grids: 0.0000303802
Overlap energy of the core charge distribution: 0.00000004675667
Self energy of the core charge distribution: -44.34715499673765
Core Hamiltonian energy: 12.85669158945410
Hartree energy: 18.49396668377177
Exchange-correlation energy: -4.21115120511165
Total energy: -17.20764788186677
ELECTRIC/MAGNETIC MOMENTS
Reference Point [Bohr] 0.00000000 0.00000000 0.00000000
Charges
Electronic= 8.00000000 Core= -8.00000000 Total= 0.00000000
Dipole vectors are based on the periodic (Berry phase) operator.
They are defined modulo integer multiples of the cell matrix [Debye].
[X] [ 36.02403204 0.00000000 0.00000000 ] [i]
[Y]=[ 0.00000000 36.02403204 0.00000000 ]*[j]
[Z] [ 0.00000000 0.00000000 38.42563418 ] [k]
Dipole moment [Debye]
X= 0.00158071 Y= -0.00031208 Z= 1.88781449 Total= 1.88781518
Min. height: 10.0785393753901 rhoav_min : 3.675929195958831E-008
---
DIP. CORR. : DIR. OF THE CORRECTION : Z
DIP. CORR. : CORR. POT. APP. : -2.263235505134872E-004 a.u.
DIP. CORR. : ENERGY CORR. : 1.021258531767185E-003 a.u.
---
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -17.207648511124667
-------------------------------------------------------------------------------
- -
- DBCSR STATISTICS -
- -
-------------------------------------------------------------------------------
COUNTER TOTAL BLAS SMM ACC
flops 5 x 4 x 4 320 0.0% 100.0% 0.0%
flops 13 x 4 x 4 416 0.0% 100.0% 0.0%
flops 13 x 5 x 4 13520 0.0% 100.0% 0.0%
flops 5 x 13 x 4 13520 0.0% 100.0% 0.0%
flops 5 x 5 x 4 15600 0.0% 100.0% 0.0%
flops 4 x 4 x 4 15872 0.0% 100.0% 0.0%
flops 13 x 13 x 4 35152 0.0% 100.0% 0.0%
flops 5 x 4 x 5 38400 0.0% 100.0% 0.0%
flops 4 x 4 x 23 43424 0.0% 100.0% 0.0%
flops 13 x 4 x 5 49920 0.0% 100.0% 0.0%
flops 5 x 4 x 13 49920 0.0% 100.0% 0.0%
flops 23 x 4 x 23 55016 0.0% 100.0% 0.0%
flops 23 x 4 x 4 59616 0.0% 100.0% 0.0%
flops 13 x 4 x 13 64896 0.0% 100.0% 0.0%
flops total 455.592000E+03 0.0% 100.0% 0.0%
flops max/rank 455.592000E+03 0.0% 100.0% 0.0%
matmuls inhomo. stacks 0 0.0% 0.0% 0.0%
matmuls total 868 0.0% 100.0% 0.0%
number of processed stacks 575 0.0% 100.0% 0.0%
average stack size 0.0 1.5 0.0
marketing flops 488.568000E+03
-------------------------------------------------------------------------------
# multiplications 353
max memory usage/rank 168.222720E+06
# max total images/rank 1
# MPI messages exchanged 0
# MPI messages filtered 0
MPI messages size (elements):
total size 0.000000E+00
min size 0.000000E+00
max size 0.000000E+00
average size 0.000000E+00
MPI breakdown and total messages size (bytes):
size <= 128 0 0
128 < size <= 8192 0 0
8192 < size <= 32768 0 0
32768 < size <= 131072 0 0
131072 < size <= 4194304 0 0
4194304 < size <= 16777216 0 0
16777216 < size 0 0
-------------------------------------------------------------------------------
MEMORY| Estimated peak process memory [MiB] 161
-------------------------------------------------------------------------------
- -
- MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 6 0.000
MP_Bcast 351 0.000 640. 861.17
MP_Allreduce 1728 0.001 52. 74.11
MP_Sync 1029 0.000
MP_Alltoall 1545 0.003 163. 74.11
MP_Wait 8472 0.002
MP_comm_split 46 0.000
MP_ISend 1408 0.001 52. 55.54
MP_IRecv 1408 0.001 52. 119.66
MP_Memory 14284 0.003
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- R E F E R E N C E S -
- -
-------------------------------------------------------------------------------
CP2K version 4.1, the CP2K developers group (2016).
CP2K is freely available from https://www.cp2k.org/ .
Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost.
Electronic Structure Calculations on Graphics Processing Units, John Wiley & Sons, Ltd, 173-190 (2016).
GPU-Accelerated Sparse Matrix-Matrix Multiplication for Linear Scaling Density Functional Theory.
http://dx.doi.org/10.1002/9781118670712.ch8
Borstnik, U; VandeVondele, J; Weber, V; Hutter, J.
PARALLEL COMPUTING, 40 (5-6), 47-58 (2014).
Sparse matrix multiplication: The distributed block-compressed sparse
row library.
http://dx.doi.org/10.1016/j.parco.2014.03.012
Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 4 (1), 15-25 (2014).
CP2K: atomistic simulations of condensed matter systems.
http://dx.doi.org/10.1002/wcms.1159
VandeVondele, J; Hutter, J.
JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007).
Gaussian basis sets for accurate calculations on molecular systems in
gas and condensed phases.
http://dx.doi.org/10.1063/1.2770708
Krack, M.
THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005).
Pseudopotentials for H to Kr optimized for gradient-corrected
exchange-correlation functionals.
http://dx.doi.org/10.1007/s00214-005-0655-y
VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T;
Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005).
QUICKSTEP: Fast and accurate density functional calculations using a
mixed Gaussian and plane waves approach.
http://dx.doi.org/10.1016/j.cpc.2004.12.014
Frigo, M; Johnson, SG.
PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005).
The design and implementation of FFTW3.
http://dx.doi.org/10.1109/JPROC.2004.840301
VandeVondele, J; Hutter, J.
JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003).
An efficient orbital transformation method for electronic structure
calculations.
http://dx.doi.org/10.1063/1.1543154
Hartwigsen, C; Goedecker, S; Hutter, J.
PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998).
Relativistic separable dual-space Gaussian pseudopotentials from H to Rn.
http://dx.doi.org/10.1103/PhysRevB.58.3641
Lippert, G; Hutter, J; Parrinello, M.
MOLECULAR PHYSICS, 92 (3), 477-487 (1997).
A hybrid Gaussian and plane wave density functional scheme.
http://dx.doi.org/10.1080/002689797170220
Perdew, JP; Burke, K; Ernzerhof, M.
PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996).
Generalized gradient approximation made simple.
http://dx.doi.org/10.1103/PhysRevLett.77.3865
Goedecker, S; Teter, M; Hutter, J.
PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996).
Separable dual-space Gaussian pseudopotentials.
http://dx.doi.org/10.1103/PhysRevB.54.1703
-------------------------------------------------------------------------------
- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.014 0.014 30.027 30.027
qs_forces 1 2.0 0.000 0.000 29.741 29.741
qs_energies 1 3.0 0.000 0.000 28.651 28.651
scf_env_do_scf 1 4.0 0.000 0.000 27.907 27.907
scf_env_do_scf_inner_loop 23 5.0 0.001 0.001 26.960 26.960
rebuild_ks_matrix 24 6.9 0.000 0.000 15.033 15.033
qs_ks_build_kohn_sham_matrix 24 7.9 0.003 0.003 15.032 15.032
qs_rho_update_rho 24 6.0 0.000 0.000 14.123 14.123
calculate_rho_elec 24 7.0 13.291 13.291 14.123 14.123
qs_ks_update_qs_env 24 6.0 0.000 0.000 14.035 14.035
sum_up_and_integrate 13 8.8 0.226 0.226 7.370 7.370
integrate_v_rspace 13 9.8 6.839 6.839 7.144 7.144
qs_vxc_create 24 8.9 0.001 0.001 6.233 6.233
xc_rho_set_and_dset_create 24 10.9 0.228 0.228 5.213 5.213
xc_functional_eval 24 11.9 0.000 0.000 3.858 3.858
pbe_lda_eval 24 12.9 3.858 3.858 3.858 3.858
xc_vxc_pw_create 13 9.8 0.445 0.445 3.846 3.846
xc_exc_calc 11 10.0 0.030 0.030 2.386 2.386
pw_nn_compose_r 148 11.5 1.472 1.472 1.472 1.472
pw_transfer 295 9.8 0.007 0.007 1.386 1.386
fft_wrap_pw1pw2 247 10.8 0.001 0.001 1.306 1.306
fft_wrap_pw1pw2_100 99 11.5 0.228 0.228 1.182 1.182
qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 0.999 0.999
init_scf_loop 1 5.0 0.000 0.000 0.947 0.947
calc_dipsurf_potential 24 8.9 0.408 0.408 0.828 0.828
density_rs2pw 24 8.0 0.000 0.000 0.767 0.767
init_scf_run 1 4.0 0.000 0.000 0.608 0.608
scf_env_initial_rho_setup 1 5.0 0.000 0.000 0.608 0.608
-------------------------------------------------------------------------------
The number of warnings for this run is : 0
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2017-08-24 18:25:54.496
***** ** *** *** ** PROGRAM RAN ON clust069
** **** ****** PROGRAM RAN BY dabral58
***** ** ** ** ** PROGRAM PROCESS ID 8675
**** ** ******* ** PROGRAM STOPPED IN /tmp/scratch/dabral58/tmp
-------------- next part --------------
DBCSR| Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Randmat seed 12341313
DBCSR| Multiplication size stacks 3
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation T
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2017-08-24 18:26:55.221
***** ** *** *** ** PROGRAM STARTED ON clust069
** **** ****** PROGRAM STARTED BY dabral58
***** ** ** ** ** PROGRAM PROCESS ID 11004
**** ** ******* ** PROGRAM STARTED IN /tmp/scratch/dabral58/tmp
CP2K| version string: CP2K version 4.1
CP2K| source code revision number: svn:17462
CP2K| cp2kflags: libint fftw3 libxc elpa3 parallel mpi3 scalapack libxsmm libde
CP2K| riv_max_am1=5 libint_max_am=6
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Thu Aug 24 17:56:33 CEST 2017
CP2K| Program compiled on clust069
CP2K| Program compiled for new_imec
CP2K| Data directory path /imec/other/abinitio/source/cp2k/tar/cp2k-4.1/data
CP2K| Input file name H2O.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| Potential file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name H2O
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. ELPA
GLOBAL| Run type ENERGY_FORCE
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| Total number of message passing processes 2
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 198083204 198083204 198083204 198083204
MEMORY| MemFree 148947448 148947448 148947448 148947448
MEMORY| Buffers 390276 390276 390276 390276
MEMORY| Cached 46148196 46148196 46148196 46148196
MEMORY| Slab 896420 896420 896420 896420
MEMORY| SReclaimable 800840 800840 800840 800840
MEMORY| MemLikelyFree 196286760 196286760 196286760 196286760
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000 - 2016) **
** **
*******************************************************************************
SCF PARAMETERS Density guess: ATOMIC
--------------------------------------------------------
max_scf: 100
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 5.00E-04
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
No outer SCF
DISTRIBUTION OF THE PARTICLES (ROWS)
Process row Number of particles Number of matrix rows
0 1 -1
1 2 -1
Sum 3 -1
DISTRIBUTION OF THE PARTICLES (COLUMNS)
Process col Number of particles Number of matrix columns
0 3 -1
Sum 3 -1
DISTRIBUTION OF THE NEIGHBOR LISTS
Total number of particle pairs: 342
Total number of matrix elements: 14406
Average number of particle pairs: 171
Maximum number of particle pairs: 284
Average number of matrix element: 7203
Maximum number of matrix elements: 8660
DISTRIBUTION OF THE OVERLAP MATRIX
Number of non-zero blocks: 6
Percentage non-zero blocks: 100.00
Average number of blocks per CPU: 3
Maximum number of blocks per CPU: 4
Average number of matrix elements per CPU: 197
Maximum number of matrix elements per CPU: 244
Number of electrons: 8
Number of occupied orbitals: 4
Number of molecular orbitals: 4
Number of orbital functions: 23
Number of independent orbital functions: 23
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : CG : conjugate gradient
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
Line search : 2PNT : 2 energies, one gradient
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
Min. height: 14.6978699224439 rhoav_min : 2.327421985372404E-004
Min. height: 14.6978699224439 rhoav_min : 2.327421985372404E-004
*******************************************************************************
* ___ *
* / \ *
* [ABORT] *
* \___/ Dipole correction needs more vacuum space above the surface *
* | *
Min. height: 14.6978699224439 rhoav_min : 2.327421985372404E-004
Min. height: 14.6978699224439 rhoav_min : 2.327421985372404E-004
* O/| *
* /| | *
* / \ surface_dipole.F:188 *
*******************************************************************************
===== Routine Calling Stack =====
9 calc_dipsurf_potential
8 qs_ks_build_kohn_sham_matrix
7 rebuild_ks_matrix
6 qs_ks_update_qs_env
5 init_scf_loop
4 scf_env_do_scf
3 qs_energies
2 qs_forces
1 CP2K
-------------- next part --------------
DBCSR| Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Randmat seed 12341313
DBCSR| Multiplication size stacks 3
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation T
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2017-08-24 18:29:39.471
***** ** *** *** ** PROGRAM STARTED ON clust069
** **** ****** PROGRAM STARTED BY dabral58
***** ** ** ** ** PROGRAM PROCESS ID 14931
**** ** ******* ** PROGRAM STARTED IN /tmp/scratch/dabral58/tmp
CP2K| version string: CP2K version 4.1
CP2K| source code revision number: svn:17462
CP2K| cp2kflags: libint fftw3 libxc elpa3 parallel mpi3 scalapack libxsmm libde
CP2K| riv_max_am1=5 libint_max_am=6
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Thu Aug 24 17:56:33 CEST 2017
CP2K| Program compiled on clust069
CP2K| Program compiled for new_imec
CP2K| Data directory path /imec/other/abinitio/source/cp2k/tar/cp2k-4.1/data
CP2K| Input file name H2O.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| Potential file name /imec/scratch/abinitio/dejamb18/CP2K/cp2
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name H2O
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. ELPA
GLOBAL| Run type ENERGY_FORCE
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| Total number of message passing processes 4
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 198083204 198083204 198083204 198083204
MEMORY| MemFree 148862892 148862892 148862892 148862892
MEMORY| Buffers 390276 390276 390276 390276
MEMORY| Cached 46151028 46151028 46151028 46151028
MEMORY| Slab 896540 896540 896540 896540
MEMORY| SReclaimable 800892 800892 800892 800892
MEMORY| MemLikelyFree 196205088 196205088 196205088 196205088
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000 - 2016) **
** **
*******************************************************************************
SCF PARAMETERS Density guess: ATOMIC
--------------------------------------------------------
max_scf: 100
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 5.00E-04
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
No outer SCF
DISTRIBUTION OF THE PARTICLES (ROWS)
Process row Number of particles Number of matrix rows
0 1 -1
1 2 -1
Sum 3 -1
DISTRIBUTION OF THE PARTICLES (COLUMNS)
Process col Number of particles Number of matrix columns
0 1 -1
1 2 -1
Sum 3 -1
DISTRIBUTION OF THE NEIGHBOR LISTS
Total number of particle pairs: 342
Total number of matrix elements: 14406
Average number of particle pairs: 86
Maximum number of particle pairs: 245
Average number of matrix element: 3602
Maximum number of matrix elements: 6125
DISTRIBUTION OF THE OVERLAP MATRIX
Number of non-zero blocks: 6
Percentage non-zero blocks: 100.00
Average number of blocks per CPU: 2
Maximum number of blocks per CPU: 3
Average number of matrix elements per CPU: 104
Maximum number of matrix elements per CPU: 179
Number of electrons: 8
Number of occupied orbitals: 4
Number of molecular orbitals: 4
Number of orbital functions: 23
Number of independent orbital functions: 23
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : CG : conjugate gradient
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
Line search : 2PNT : 2 energies, one gradient
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
*******************************************************************************
* ___ *
* / \ *
* [ABORT] *
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
Min. height: 14.6978699224439 rhoav_min : 6.156728744828596E-005
* \___/ Dipole correction needs more vacuum space above the surface *
* | *
* O/| *
* /| | *
* / \ surface_dipole.F:188 *
*******************************************************************************
===== Routine Calling Stack =====
9 calc_dipsurf_potential
8 qs_ks_build_kohn_sham_matrix
7 rebuild_ks_matrix
6 qs_ks_update_qs_env
5 init_scf_loop
4 scf_env_do_scf
3 qs_energies
2 qs_forces
1 CP2K
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