<div dir="ltr"><div dir="ltr">Hi all, <div> </div><div>if Jürg is right, then there must be something wrong with the manual units for PW_CUTOFF and GK_CUTOFF are [a.u.^-1]. Why is it in the inverse proportion? How should I convert the conventional cutoff of 80Ry to the PW_CUTOFF value here in CP2K. Do other people have a clear answer? I would be very appreciated if you could provide a definite answer.</div><div> </div><div>Regards</div><div>Jibiao Li</div><div> </div></div> <div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 30 Jun 2023 at 22:33, Jürg Hutter <<a href="mailto:hutter@chem.uzh.ch">hutter@chem.uzh.ch</a>> wrote: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi looks to me you got something wrong in your input. approximate number of G vectors : 0 So your definition of cutoff is wrong. I don't know how the input value is defined (e.g. as an energy or as the length of a reciprocal vector or ...) but at this point I would either start looking into the code or make some experiments. Change the input value and calculate the expected number of G-vectors and compare to the output. My guess 100 Ry energy cutoff is either 50 or 7 in the SIRIUS input units. regards JH ________________________________________ From: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> on behalf of Jibiao Li <<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a>> Sent: Friday, June 30, 2023 3:06 PM To: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> Subject: Re: [CP2K:19040] Terrible lattice constant of FCC copper from cell optimization Hi Jürg, This time I used a larger one, say 80Ry. That is 0.025 for PW_CUTOFF here in CP2K. However, as I tried to run it, it stopped with the error below, What should I do to remove this error? ... ... XC functionals ============== 1) XC_GGA_X_PBE: Perdew, Burke & Ernzerhof J. P. Perdew, K. Burke, and M. Ernzerhof., Phys. Rev. Lett. 77, 3865 (1996) (10.1103/PhysRevLett.77.3865) J. P. Perdew, K. Burke, and M. Ernzerhof., Phys. Rev. Lett. 78, 1396 (1997) (10.1103/PhysRevLett.78.1396) 2) XC_GGA_C_PBE: Perdew, Burke & Ernzerhof J. P. Perdew, K. Burke, and M. Ernzerhof., Phys. Rev. Lett. 77, 3865 (1996) (10.1103/PhysRevLett.77.3865) J. P. Perdew, K. Burke, and M. Ernzerhof., Phys. Rev. Lett. 78, 1396 (1997) (10.1103/PhysRevLett.78.1396) memory consumption ================== approximate number of G+k vectors : 0 approximate number of G vectors : 0 approximate number of coarse G vectors : 0 approximate size of wave-functions for each k-point: 0 Mb, 0 Mb/rank approximate memory consumption of Davidson solver: 0 Mb/rank approximate memory consumption of FFT transforms: 0 Mb/rank =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 334186 RUNNING AT ubuntua = KILLED BY SIGNAL: 9 (Killed) =================================================================================== &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 0.012 PW_CUTOFF 0.025 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 Regards Jibiao Li On Thu, 29 Jun 2023 at 19:39, Jürg Hutter <<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a><mailto:<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a>>> wrote: 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: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>>> on behalf of Jibiao Li <<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a><mailto:<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a>>> Sent: Thursday, June 29, 2023 1:32 PM To: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> 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 <<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a><mailto:<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a>><mailto:<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a><mailto:<a href="mailto:hutter@chem.uzh.ch" target="_blank">hutter@chem.uzh.ch</a>>>> 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: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>>> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a><mailto:<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>>>> on behalf of Jibiao Li <<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a><mailto:<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a>><mailto:<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a><mailto:<a href="mailto:science.sweden@gmail.com" target="_blank">science.sweden@gmail.com</a>>>> 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: <a href="https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2" rel="noreferrer" target="_blank">https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2</a> **** **** ****** ** 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 <a href="https://www.cp2k.org/" rel="noreferrer" target="_blank">https://www.cp2k.org/</a> 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 : <a href="https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2" rel="noreferrer" target="_blank">https://api.github.com/repos/electronic-structure/SIRIUS/git/ref/tags/v7.3.2</a> 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: <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>>> on behalf of Jibiao Li <<a href="mailto:science...@gmail.com" target="_blank">science...@gmail.com</a><mailto:<a href="mailto:science...@gmail.com" target="_blank">science...@gmail.com</a>><mailto:<a href="mailto:science...@gmail.com" target="_blank">science...@gmail.com</a><mailto:<a href="mailto:science...@gmail.com" target="_blank">science...@gmail.com</a>>>> Sent: Thursday, June 29, 2023 3:23 AM To: <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>> 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 -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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