[CP2K-user] [CP2K:17757] Re: Crystal optimization with periodic boundary conditions
Victor Nazarychev
nazarychev at gmail.com
Mon Sep 26 15:28:49 UTC 2022
Dear Prof. Jürg Hutter,
Thank you very much for your response. I changed the basis sets for the
atom types, and the simulation started.
However, the energy significantly increases during the first step of the
scf field calculation.
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy
Change
------------------------------------------------------------------------------
1 P_Mix/Diag. 0.40E+00 34.1 1.49352991 -3306.5025219983
-3.31E+03
2 P_Mix/Diag. 0.40E+00 52.5 0.97283893 -3337.7996220399
-3.13E+01
3 P_Mix/Diag. 0.40E+00 51.8 0.88366630 -3355.9794833839
-1.82E+01
4 P_Mix/Diag. 0.40E+00 52.4 1.49440081 -3366.3903106073
-1.04E+01
5 P_Mix/Diag. 0.40E+00 52.3 4.78093105 -3357.3113062081
9.08E+00
6 P_Mix/Diag. 0.40E+00 55.6 5.13204666 8949.0258399209
1.23E+04
7 P_Mix/Diag. 0.40E+00 55.7 4.87209898 1382.2558657457
-7.57E+03
8 P_Mix/Diag. 0.40E+00 52.1 4.11402739 5878.6202919895
4.50E+03
9 P_Mix/Diag. 0.40E+00 52.1 3.90597954 3458.6520635220
-2.42E+03
10 P_Mix/Diag. 0.40E+00 52.1 4.44874753 5101.5066833448
1.64E+03
11 P_Mix/Diag. 0.40E+00 52.4 4.40856697 4378.1126110753
-7.23E+02
12 P_Mix/Diag. 0.40E+00 52.1 4.62106313 4808.7707611559
4.31E+02
13 P_Mix/Diag. 0.40E+00 52.3 4.69047378 4716.1178362235
-9.27E+01
Below is my input file.
Could you expect that it is due to the standard PW cut-off or "small" basis
set?
Best wishes,
Victor
####################################################################
&GLOBAL
PROJECT crys_pbc
RUN_TYPE GEO_OPT ! ENERGY
PRINT_LEVEL MEDIUM
EXTENDED_FFT_LENGTHS .TRUE.
&END GLOBAL
&MOTION
&GEO_OPT
TYPE MINIMIZATION
MAX_DR 1.0E-03
MAX_FORCE 1.0E-03
RMS_DR 1.0E-03
RMS_FORCE 1.0E-03
MAX_ITER 200
OPTIMIZER CG
&CG
MAX_STEEP_STEPS 0
RESTART_LIMIT 9.0E-01
&END CG
! KEEP_SYMMETRY .TRUE.
! OPTIMIZER CG !LBFGS
&END
&PRINT
&TRAJECTORY LOW
ADD_LAST NUMERIC
LOG_PRINT_KEY T
FORMAT XMOL
&EACH
GEO_OPT 1
&END EACH
&END TRAJECTORY
&RESTART LOW
ADD_LAST NUMERIC
LOG_PRINT_KEY T
&EACH
GEO_OPT 1
&END EACH
&END RESTART
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Quickstep ! Electronic structure method (DFT,...)
STRESS_TENSOR NUMERICAL
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&POISSON ! Solver requested for non periodic
calculations
PERIODIC XYZ
&END POISSON
&SCF ! Parameters controlling the convergence of
the scf. This section should not be changed.
SCF_GUESS ATOMIC
EPS_SCF 1.0E-6
MAX_SCF 60
&PRINT
&RESTART SILENT
ADD_LAST NUMERIC
COMMON_ITERATION_LEVELS 1
FILENAME =./WFN_restart.wfn
LOG_PRINT_KEY T
&EACH
&END EACH
&END RESTART
&END PRINT
&END SCF
&XC ! Parameters needed to compute the
electronic exchange potential
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
CELL_FILE_FORMAT CIF
ABC 4.6284 140.3208 9.4837
SYMMETRY MONOCLINIC
PERIODIC XYZ
MULTIPLE_UNIT_CELL 3 1 3
&END CELL
&TOPOLOGY ! Section used to center the atomic
coordinates in the given box. Useful for big molecules
COORD_FILE_FORMAT cif
COORD_FILE_NAME ./cell.cif
! &CENTER_COORDINATES
! CENTER_POINT 5. 5. 5.
! &END
&END
&KIND H
ELEMENT H
BASIS_SET SZV-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND O
ELEMENT O
BASIS_SET SZV-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND C
ELEMENT C
BASIS_SET SZV-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND N
ELEMENT N
BASIS_SET SZV-MOLOPT-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&END SUBSYS
&END FORCE_EVAL
####################################################################
пт, 9 сент. 2022 г. в 18:44, Jürg Hutter <hutter at chem.uzh.ch>:
> Hi
>
> probably there is not enough memory? You can try a smaller basis set and a
> lower
> PW cutoff to see if it runs through.
> Another possibility is to monitor your memory usage during the run.
>
> regards
> JH
>
> ________________________________________
> From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Victor
> Nazarychev <nazarychev at gmail.com>
> Sent: Friday, September 9, 2022 8:55 AM
> To: cp2k
> Subject: [CP2K:17639] Re: Crystal optimization with periodic boundary
> conditions
>
> Dear users and developers of CP2K,
>
> I tried starting the simulation of the crystal structure using cp2k. To do
> that, I used an input file:
>
> &GLOBAL
> PROJECT crys_pbc_opt
> RUN_TYPE GEO_OPT
> PRINT_LEVEL MEDIUM
> EXTENDED_FFT_LENGTHS .TRUE.
> &END GLOBAL
>
> &MOTION
> &GEO_OPT
>
> ! KEEP_SPACE_GROUP .TRUE.
> OPTIMIZER LBFGS
>
> &END GEO_OPT
> &END MOTION
>
> &FORCE_EVAL
> METHOD Quickstep ! Electronic structure method (DFT,...)
> &DFT
> BASIS_SET_FILE_NAME BASIS_MOLOPT
> POTENTIAL_FILE_NAME POTENTIAL
>
> &POISSON ! Solver requested for non periodic
> calculations
> PERIODIC XYZ
> &END POISSON
> &SCF ! Parameters controlling the convergence
> of the scf. This section should not be changed.
> SCF_GUESS ATOMIC
> EPS_SCF 1.0E-6
> MAX_SCF 300
> &END SCF
> &XC ! Parameters needed to compute the
> electronic exchange potential
> &XC_FUNCTIONAL PBE
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
>
> &SUBSYS
> &CELL
> CELL_FILE_FORMAT CIF
> ABC 9.2568 140.3208 18.9674
> PERIODIC XYZ
> &END CELL
> &TOPOLOGY ! Section used to center the atomic
> coordinates in the given box. Useful for big molecules
> COORD_FILE_FORMAT cif
> COORD_FILE_NAME ./cell.cif
> ! &CENTER_COORDINATES
> ! CENTER_POINT 5. 5. 5.
> ! &END
> &END
> &KIND H
> ELEMENT H
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q1
> &END KIND
> &KIND O
> ELEMENT O
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q6
> &END KIND
> &KIND C
> ELEMENT C
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q4
> &END KIND
> &KIND N
> ELEMENT N
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q5
> &END KIND
> &END SUBSYS
> &END FORCE_EVAL
>
> ##############################################
>
> The simulation starts, but only one step of SCF wavefunction optimization
> is passed, and then the calculation stops without errors.
>
> Re-scaling the density matrix to get the right number of electrons
> # Electrons Trace(P) Scaling
> factor
> 8576 8575.456
> 1.000
>
>
> SCF WAVEFUNCTION OPTIMIZATION
>
> Step Update method Time Convergence Total energy
> Change
>
> ------------------------------------------------------------------------------
> 1 P_Mix/Diag. 0.40E+00 ****** 1.37713667 -13502.7304100109
> -1.35E+04
>
> How do you think, what happens? How could I change the input file to solve
> this problem?
>
> Best regards,
> Victor
>
> суббота, 20 августа 2022 г. в 17:41:05 UTC+3, Victor Nazarychev:
>
> Dear users and developers of CP2K,
>
> I am a new user of CP2K. I want to use CP2K to simulate the DFT of a
> polymer crystal, which contains ~2500 atoms (C, N, O, H). This initial
> crystal conformation was suggested by the experimenters, and I need to
> optimize this structure to find the minimal energy state.
>
> I'm considering using CP2K due to its ability to do periodic DFT
> calculations. My question is related to what DFT functional and basis sets
> can be used to optimize a periodic crystal structure if such a massive
> system is considered? Maybe some there exists some examples of an input
> file for the problem of optimizing crystal systems using periodic boundary
> conditions?
>
> For these calculations, I have a workstation with an AMD Ryzen 5950x and
> 64 GB of memory. Also, is it possible to speed up the calculation with the
> GPU?
>
> Best wishes,
>
> Victor
>
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