[CP2K-user] [CP2K:19034] Terrible lattice constant of FCC copper from cell optimization

Jürg Hutter hutter at chem.uzh.ch
Thu Jun 29 11:39:16 UTC 2023


Hi

where are these numbers from? To me 41 Ry for a 11 electron Cu PP seems very low.
According to the manual units for PW_CUTOFF and GK_CUTOFF are [a.u.^-1]

JH

________________________________________
From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Jibiao Li <science.sweden at gmail.com>
Sent: Thursday, June 29, 2023 1:32 PM
To: cp2k at googlegroups.com
Subject: Re: [CP2K:19033] Terrible lattice constant of FCC copper from cell optimization

Hi Jürg,

For cell optimization for lattice constants, 500 eV or 41 Ry is sufficient. The problem is how should  I convert eV or Ry to the unit of PW_CUTOFF.

May I get  an answer for it?

Best

Jibiao Li


On Thu, 29 Jun 2023 at 19:12, Jürg Hutter <hutter at chem.uzh.ch<mailto:hutter at chem.uzh.ch>> wrote:
Hi

removing the basis doesn't change the calculation (in this case).
The SIRIUS output is in Bohr (6.82) the input was in Angstrom (3.61).

Have you investigated if these parameters are adequate for your system/pseudopotential?

       GK_CUTOFF 5
       PW_CUTOFF 20
       NGRIDK 10 10 10

regards
JH

________________________________________
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Jibiao Li <science.sweden at gmail.com<mailto:science.sweden at gmail.com>>
Sent: Thursday, June 29, 2023 12:36 PM
To: cp2k
Subject: Re: [CP2K:19031] Terrible lattice constant of FCC copper from cell optimization

Hi  Jürg,

I have removed basis set and found that the problem remains. A difficult thing hard to understand : Why a different value (6.8219113397) was taken in the very beginning of the calculations? There must be somthing hard to understand.

The lattice prior to the optimization:
lattice vectors
  a1 :       6.8219113397       0.0000000000       0.0000000000
  a2 :       0.0000000000       6.8219113397       0.0000000000
  a3 :       0.0000000000       0.0000000000       6.8219113397



The head of The output file:

 DBCSR| CPU Multiplication driver                                           XSMM (U)
 DBCSR| Multrec recursion limit                                              512 (U)
 DBCSR| Multiplication stack size                                           1000 (D)
 DBCSR| Maximum elements for images                                    UNLIMITED (U)
 DBCSR| Multiplicative factor virtual images                                   1 (U)
 DBCSR| Use multiplication densification                                       T (D)
 DBCSR| Multiplication size stacks                                             3 (U)
 DBCSR| Use memory pool for CPU allocation                                     F (U)
 DBCSR| Number of 3D layers                                               SINGLE (U)
 DBCSR| Use MPI memory allocation                                              F (U)
 DBCSR| Use RMA algorithm                                                      F (U)
 DBCSR| Use Communication thread                                               T (U)
 DBCSR| Communication thread load                                             42 (D)
 DBCSR| MPI: My process id                                                     0
 DBCSR| MPI: Number of processes                                               8
 DBCSR| OMP: Current number of threads                                        13
 DBCSR| OMP: Max number of threads                                            13
 DBCSR| Split modifier for TAS multiplication algorithm                  1.0E+00 (U)

SIRIUS 7.3.2, git hash: https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2

  **** **** ******  **  PROGRAM STARTED AT               2023-06-29 18:25:42.062
 ***** ** ***  *** **   PROGRAM STARTED ON                               ubuntua
 **    ****   ******    PROGRAM STARTED BY                              jibiaoli
 ***** **    ** ** **   PROGRAM PROCESS ID                                333548
  **** **  *******  **  PROGRAM STARTED IN              /home/jibiaoli/calc/test

 CP2K| version string:                                       CP2K version 2023.1
 CP2K| source code revision number:                                  git:b888bd8
 CP2K| cp2kflags: omp fftw3 libxc pexsi elpa parallel scalapack cosma xsmm max_c
 CP2K|            ontr=4 plumed2 spglib mkl sirius libvori libbqb libvdwxc
 CP2K| is freely available from                            https://www.cp2k.org/
 CP2K| Program compiled at            2023年 06月 28日 星期三 23:59:21 CST
 CP2K| Program compiled on                                               ubuntua
 CP2K| Program compiled for                                   Linux-intel-x86_64
 CP2K| Data directory path                 /home/jibiaoli/codes/cp2k-2023.1/data
 CP2K| Input file name                                                copper.inp

 GLOBAL| Force Environment number                                              1
 GLOBAL| Basis set file name                                           BASIS_SET
 GLOBAL| Potential file name                                           POTENTIAL
 GLOBAL| MM Potential file name                                     MM_POTENTIAL
 GLOBAL| Coordinate file name                                      __STD_INPUT__
 GLOBAL| Method name                                                        CP2K
 GLOBAL| Project name                                                 FCC_Copper
 GLOBAL| Run type                                                       CELL_OPT
 GLOBAL| FFT library                                                       FFTW3
 GLOBAL| Diagonalization library                                            ELPA
 GLOBAL| DGEMM library                                                      BLAS
 GLOBAL| Minimum number of eigenvectors for ELPA usage                        16
 GLOBAL| Orthonormality check for eigenvectors                          DISABLED
 GLOBAL| Matrix multiplication library                                     COSMA
 GLOBAL| All-to-all communication in single precision                          F
 GLOBAL| FFTs using library dependent lengths                                  F
 GLOBAL| Grid backend                                                       AUTO
 GLOBAL| Global print level                                                  LOW
 GLOBAL| MPI I/O enabled                                                       T
 GLOBAL| Total number of message passing processes                             8
 GLOBAL| Number of threads for this process                                   13
 GLOBAL| This output is from process                                           0
 GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE)        default
 GLOBAL| CPU model name            Intel(R) Xeon(R) Platinum 8171M CPU @ 2.30GHz
 GLOBAL| CPUID                                                              1003

 MEMORY| system memory details [Kb]
 MEMORY|                        rank 0           min           max       average
 MEMORY| MemTotal             98585440      98585440      98585440      98585440
 MEMORY| MemFree              57901124      57901124      57901124      57901124
 MEMORY| Buffers                521896        521896        521896        521896
 MEMORY| Cached               29522272      29522272      29522272      29522272
 MEMORY| Slab                  2499004       2499004       2499004       2499004
 MEMORY| SReclaimable          1413276       1413276       1413276       1413276
 MEMORY| MemLikelyFree        89358568      89358568      89358568      89358568


 GENERATE|  Preliminary Number of Bonds generated:                             0
 GENERATE|  Achieved consistency in connectivity generation.

 *******************************************************************************
 *******************************************************************************
 **                                                                           **
 **   #### ##   ## ####  ##### #####           #### ## ####  ## ## ##  ####   **
 **   ## ####   ## ## ## ###   #####          ##    ## ##  # ## ## ## ##      **
 **   #### ## # ## ## ## #####  ###           ##### ## ####  ## ## ## #####   **
 **   ##   ####### ## ## ##     ###              ## ## ## #  ## #####    ##   **
 **   ##   ## # ## ####  ##     ###           ####  ## ##  # ## ##### ####    **
 **                                                                           **
 **   SIRIUS: Domain specific library for electronic structure calculations   **
 **                                                                           **
 *******************************************************************************

SIRIUS version : 7.3.2
git hash       : https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2
git branch     : release v7.3.2
build time     : 2023-06-28 23:11:48
start time     : Thu, 29 Jun 2023 18:25:42

number of MPI ranks           : 8
MPI grid                      : 1 1
maximum number of OMP threads : 13
number of MPI ranks per node  : 8
page size (Kb)                : 4
number of pages               : 24646360
available memory (GB)         : 94

FFT context for density and potential
=====================================
  comm size                             : 8
  plane wave cutoff                     : 20.000000
  grid size                             : 48 48 48   total : 110592
  grid limits                           : -23 24   -23 24   -23 24
  number of G-vectors within the cutoff : 21466
  local number of G-vectors             : 2672
  number of G-shells                    : 395

FFT context for coarse grid
=====================================
  comm size                             : 1
  plane wave cutoff                     : 10.000000
  grid size                             : 24 24 24   total : 13824
  grid limits                           : -11 12   -11 12   -11 12
  number of G-vectors within the cutoff : 2689
  local number of G-vectors             : 337
  number of G-shells                    : 100

number of local G-vector blocks: 1

Unit cell
--------------------------------------------------------------------------------
lattice vectors
  a1 :       6.8219113397       0.0000000000       0.0000000000
  a2 :       0.0000000000       6.8219113397       0.0000000000
  a3 :       0.0000000000       0.0000000000       6.8219113397
reciprocal lattice vectors
  b1 :       0.9210300448       0.0000000000       0.0000000000
  b2 :       0.0000000000       0.9210300448       0.0000000000
  b3 :       0.0000000000       0.0000000000       0.9210300448

unit cell volume :       317.48134574 [a.u.^3]
1/sqrt(omega)    :         0.05612300
MT volume        : 0.000000 ( 0.00%)
IT volume        : 317.481346 (100.00%)


&GLOBAL
  PROJECT FCC_Copper
  RUN_TYPE CELL_OPT
  PRINT_LEVEL LOW
&END GLOBAL

&FORCE_EVAL
  METHOD SIRIUS
  STRESS_TENSOR ANALYTICAL
  &SUBSYS
    &CELL
      A 3.61 0.00 0.00
      B 0.00 3.61 0.00
      C 0.00 0.00 3.61
      SYMMETRY CUBIC
      PERIODIC XYZ
    &END CELL
    &COORD
      Cu   0.000 0.000 0.000
      Cu   0.000 1.805 1.805
      Cu   1.805 0.000 1.805
      Cu   1.805 1.805 0.000
    &END COORD
    &KIND Cu
       POTENTIAL GTH-PBE-q11
    &END KIND
  &END SUBSYS
  &PW_DFT
    &CONTROL
       VERBOSITY 2
    &END CONTROL
    &PARAMETERS
       ELECTRONIC_STRUCTURE_METHOD  pseudopotential
       GK_CUTOFF 5
       PW_CUTOFF 20
       NUM_DFT_ITER 399
       NGRIDK 10 10 10
    &END PARAMETERS
    &ITERATIVE_SOLVER
       ENERGY_TOLERANCE 1e-5
       NUM_STEPS 20
       SUBSPACE_SIZE 4
    &END ITERATIVE_SOLVER
    &MIXER
       BETA 0.3
       TYPE BROYDEN2
    &END MIXER
  &END PW_DFT
  &DFT
    &XC
      &XC_FUNCTIONAL
        &GGA_X_PBE
        &END GGA_X_PBE
        &GGA_C_PBE
        &END GGA_C_PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
&END FORCE_EVAL

&MOTION
  &CELL_OPT
    MAX_ITER 200
    OPTIMIZER BFGS
    KEEP_SYMMETRY .TRUE.
  &END CELL_OPT
&END MOTION

Best

Jibiao Li
On Thursday, 29 June 2023 at 16:24:04 UTC+8 Jürg Hutter wrote:
Hi

you are doing a plane wave calculation, so you don't have to specify a Gaussian basis set.
However, the crucial parameter is now the PW cutoff. Make sure you have a reasonable value,
either by testing or by comparing to literature.

regards
JH

________________________________________
From: cp... at googlegroups.com<mailto:cp... at googlegroups.com> <cp... at googlegroups.com<mailto:cp... at googlegroups.com>> on behalf of Jibiao Li <science... at gmail.com<mailto:science... at gmail.com>>
Sent: Thursday, June 29, 2023 3:23 AM
To: cp... at googlegroups.com<mailto:cp... at googlegroups.com>
Subject: [CP2K:19024] Terrible lattice constant of FCC copper from cell optimization

Hi all,

I got a terrible lattice constant (2.71) that is in significant disagreement with the experimental value (3.61). Something wrong with my input file ?

*******************************************************************************
*** GEOMETRY OPTIMIZATION COMPLETED ***
*******************************************************************************

Reevaluating energy at the minimum

CELL| Volume [angstrom^3]: 19.962031
CELL| Vector a [angstrom]: 2.713 0.000 0.000 |a| = 2.712699
CELL| Vector b [angstrom]: 0.000 2.713 0.000 |b| = 2.712699
CELL| Vector c [angstrom]: 0.000 0.000 2.713 |c| = 2.712699
CELL| Angle (b,c), alpha [degree]: 90.000000
CELL| Angle (a,c), beta [degree]: 90.000000
CELL| Angle (a,b), gamma [degree]: 90.000000
CELL| Requested initial symmetry: CUBIC
CELL| Numerically orthorhombic: YES
CELL| Periodicity XYZ


&GLOBAL
PROJECT FCC_Copper
RUN_TYPE CELL_OPT
PRINT_LEVEL LOW
&END GLOBAL

&FORCE_EVAL
METHOD SIRIUS
STRESS_TENSOR ANALYTICAL
&SUBSYS
&CELL
A 3.61 0.00 0.00
B 0.00 3.61 0.00
C 0.00 0.00 3.61
SYMMETRY CUBIC
PERIODIC XYZ
&END CELL
&COORD
Cu 0.000 0.000 0.000
Cu 0.000 1.805 1.805
Cu 1.805 0.000 1.805
Cu 1.805 1.805 0.000
&END COORD
&KIND Cu
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q11
&END KIND
&END SUBSYS
&PW_DFT
&CONTROL
VERBOSITY 2
&END CONTROL
&PARAMETERS
ELECTRONIC_STRUCTURE_METHOD pseudopotential
GK_CUTOFF 5.0
PW_CUTOFF 20.00
NUM_DFT_ITER 399
NGRIDK 10 10 10
&END PARAMETERS
&ITERATIVE_SOLVER
ENERGY_TOLERANCE 1e-5
NUM_STEPS 20
SUBSPACE_SIZE 4
&END ITERATIVE_SOLVER
&MIXER
BETA 0.3
TYPE BROYDEN2
&END MIXER
&END PW_DFT
&DFT
&XC
&XC_FUNCTIONAL
&GGA_X_PBE
&END GGA_X_PBE
&GGA_C_PBE
&END GGA_C_PBE
&END XC_FUNCTIONAL
&END XC
&END DFT
&END FORCE_EVAL

&MOTION
&CELL_OPT
MAX_ITER 200
OPTIMIZER BFGS
KEEP_SYMMETRY .TRUE.
&END CELL_OPT
&END MOTION

Best Regards

Jibiao Li

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