[CP2K-user] [CP2K:18965] Re: Symmetry broken during Cell optimization of FCC copper

Jibiao Li science.sweden at gmail.com
Fri Jun 23 23:05:43 UTC 2023
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Hi Fabian,

I had compiled everything including sirius by running the script
"./install_cp2k_toolchain.sh". You see everything was compiled:

jibiaoli at ubuntua:~/codes/cp2k/tools/toolchain$ ./install_cp2k_toolchain.sh
MPI is detected and it appears to be OpenMPI
Compiling with 104 processes for target native.
==================== Finding GCC from system paths ====================
path to gcc is /usr/bin/gcc
path to g++ is /usr/bin/g++
path to gfortran is /usr/bin/gfortran
Found include directory /usr/include
Step gcc took 0.00 seconds.
Step intel took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools
====================
OpenBLAS detected LIBCORE = skylakex
OpenBLAS detected ARCH    = x86_64
==================== Installing CMake ====================
cmake-3.25.1 is already installed, skipping it.
Step cmake took 0.00 seconds.
==================== Finding OpenMPI from system paths ====================
path to mpirun is /home/jibiaoli/codes/openmpi-4.1.5/bin/mpirun
path to mpicc is /home/jibiaoli/codes/openmpi-4.1.5/bin/mpicc
path to mpic++ is /home/jibiaoli/codes/openmpi-4.1.5/bin/mpic++
path to mpif90 is /home/jibiaoli/codes/openmpi-4.1.5/bin/mpif90
Step openmpi took 0.00 seconds.
WARNING:
(/home/jibiaoli/codes/cp2k/tools/toolchain/scripts/stage2/install_mkl.sh,
line 23) MKL FFTW3 interface is present, but FFTW library is needed for
FFTW-MPI wrappers.
==================== Finding MKL from system paths ====================
MKLROOT is found to be /home/jibiaoli/intel/oneapi/mkl/2022.1.0
libm is found in ld search path
libdl is found in ld search path
Step mkl took 0.00 seconds.
==================== Installing FFTW ====================
fftw-3.3.10 is already installed, skipping it.
Step fftw took 0.00 seconds.
==================== Installing LIBINT ====================
libint-2.6.0 is already installed, skipping it.
Step libint took 1.00 seconds.
==================== Installing LIBXC ====================
libxc-6.0.0 is already installed, skipping it.
Step libxc took 0.00 seconds.
==================== Installing Libxsmm ====================
libxsmm-1.17 is already installed, skipping it.
Step libxsmm took 0.00 seconds.
Step scalapack took 0.00 seconds.
==================== Installing COSMA ====================
COSMA-2.6.2 is already installed, skipping it.
Step cosma took 0.00 seconds.
==================== Installing ELPA ====================
elpa-2022.11.001 is already installed, skipping it.
Step elpa took 0.00 seconds.
Step ptscotch took 0.00 seconds.
Step superlu took 1.00 seconds.
Step pexsi took 0.00 seconds.
Step quip took 0.00 seconds.
==================== Installing gsl ====================
gsl-2.7 is already installed, skipping it.
Step gsl took 0.00 seconds.
Step plumed took 0.00 seconds.
==================== Installing hdf5 ====================
hdf5-1.12.0 is already installed, skipping it.
Step hdf5 took 0.00 seconds.
==================== Installing libvdwxc ====================
libvdwxc-0.4.0 is already installed, skipping it.
Step libvdwxc took 0.00 seconds.
==================== Installing spglib ====================
spglib-1.16.2 is already installed, skipping it.
Step spglib took 0.00 seconds.
==================== Installing libvori ====================
libvori-220621 is already installed, skipping it.
Step libvori took 1.00 seconds.
Step libtorch took 0.00 seconds.
==================== Installing spfft ====================
SpFFT-1.0.6 is already installed, skipping it.
Step spfft took 0.00 seconds.
==================== Installing spla ====================
SpLA-1.5.4 is already installed, skipping it.
Step spla took 0.00 seconds.
==================== Installing SIRIUS ====================
sirius_dist-7.3.2 is already installed, skipping it.
Step sirius took 0.00 seconds.
==================== generating arch files ====================

It seems that subsections of PW_DFT can not be recognized. Need your help
to resolve the problem.

Best

Jibiao Li

On Fri, 23 Jun 2023 at 22:03, fabia... at gmail.com <fabianducry at gmail.com>
wrote:

> Hi Jibiao,
>
> You did not give the initial symmetry in the input (should go to the &CELL
> section). That is why the KEEP_SYMMETRY does have no effect.
>
> As for your second issue, did you compile cp2k with sirirus?
>
> Cheers,
> Fabian
> On Friday, 23 June 2023 at 09:24:24 UTC+2 Jibiao Li wrote:
>
>> Hi, all
>>
>> I tried to perform Cell optimization using cp2k 2023.1 (see the input
>> below), but it stopped and complained with the following error message.
>>
>>
>>  *******************************************************************************
>>  *   ___
>>       *
>>  *  /   \
>>      *
>>  * [ABORT]
>>       *
>>  *  \___/             unknown subsection PARAMETERS of section PW_DFT
>>      *
>>  *    |
>>      *
>>  *  O/|
>>      *
>>  * /| |
>>      *
>>  * / \
>> input/input_parsing.F:185 *
>>
>>  *******************************************************************************
>> What's wrong with my input file?
>>
>> Best
>>
>> Jibiao Li
>>
>>
>> &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
>>     &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 PBE
>>       &END XC_FUNCTIONAL
>>     &END XC
>>   &END DFT
>> &END FORCE_EVAL
>> &MOTION
>>   &CELL_OPT
>>     MAX_ITER 200
>>     OPTIMIZER CG
>>     KEEP_SYMMETRY .TRUE.
>>   &END CELL_OPT
>> &END MOTION
>> On Friday, 23 June 2023 at 10:27:18 UTC+8 Jibiao Li wrote:
>>
>>> Hi, all
>>>
>>> I tried to test cp2k by optimizing FCC Cu with the setting
>>> "KEEP_SYMMETRY .TRUE.", but KEEP_SYMMETRY does not work at all. You see the
>>> lattice constants during the optimization, the calculation breaks the
>>> initial symmetry.
>>>
>>> Something wrong with my input file？ What's the correct way to optimzie
>>> FCC Cu with the original space symmetry kept?
>>>
>>> ... ...
>>>
>>>  CELL| Volume [angstrom^3]:
>>>  46.639032
>>>  CELL| Vector a [angstrom]:       3.607     0.000     0.000   |a| =
>>> 3.607475
>>>  CELL| Vector b [angstrom]:      -0.001     3.607     0.000   |b| =
>>> 3.607475
>>>  CELL| Vector c [angstrom]:       0.000     0.000     3.584   |c| =
>>> 3.583792
>>>  CELL| Angle (b,c), alpha [degree]:
>>>  90.000000
>>>  CELL| Angle (a,c), beta  [degree]:
>>>  90.000000
>>>  CELL| Angle (a,b), gamma [degree]:
>>>  90.010923
>>>  CELL| Numerically orthorhombic:                                     NO
>>>  CELL| Periodicity
>>>          XYZ
>>> ... ...
>>>
>>> &GLOBAL
>>>   PROJECT FCC_Cu
>>>   RUN_TYPE CELL_OPT
>>>   PRINT_LEVEL LOW
>>> &END GLOBAL
>>> &FORCE_EVAL
>>>   METHOD QS
>>>   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
>>>       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
>>>   &DFT
>>>     BASIS_SET_FILE_NAME BASIS_MOLOPT
>>>     POTENTIAL_FILE_NAME POTENTIAL
>>>     &QS
>>>       METHOD GPW
>>>       EPS_DEFAULT 1.0E-10
>>>     &END QS
>>>     &MGRID
>>>       CUTOFF 320
>>>       REL_CUTOFF 30
>>>     &END MGRID
>>>     &SCF
>>>       MAX_SCF 279
>>>       &DIAGONALIZATION .TRUE.
>>>         ALGORITHM STANDARD
>>>       &END DIAGONALIZATION
>>>       &MIXING .TRUE.
>>>         ALPHA 0.5
>>>         METHOD DIRECT_P_MIXING
>>>       &END MIXING
>>>     &END SCF
>>>     &XC
>>>       &XC_FUNCTIONAL PBE
>>>       &END XC_FUNCTIONAL
>>>     &END XC
>>>   &END DFT
>>> &END FORCE_EVAL
>>>
>>> &MOTION
>>>   &CELL_OPT
>>>     MAX_ITER 200
>>>     OPTIMIZER CG
>>>     KEEP_SYMMETRY .TRUE.
>>>   &END CELL_OPT
>>> &END MOTION
>>>
>>> Jibiao Li
>>> Chongqing, China
>>>
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