Re: [Phonopy-users] ERROR Creating supercell by Phonop3y
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From: Atsushi T. <atz...@gm...> - 2023-07-13 00:52:16
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Hi, Please read https://phonopy.github.io/phonopy/symmetry.html. Togo On Wed, Jul 12, 2023 at 6:50 PM Seyed Vahid Hosseini <vah...@gm...> wrote: > > Hello dear phono3py users: > I have problem creating supercell for my structure. > this is my input file: > ############################################### > &control > calculation='scf', > verbosity = 'low', > restart_mode = 'from_scratch', > prefix = 'input-kappa', > tstress = .true., > tprnfor = .true., > forc_conv_thr = 1.0D-4 > pseudo_dir ='./', > outdir= './', > nstep=3000, > wf_collect=.true. > / > > &SYSTEM > ibrav=0, > nat=10, > ntyp=2, > ecutwfc=40, > ecutrho=400, > occupations='smearing', > degauss=0.002, > smearing='mv', > / > &electrons > diagonalization='cg', > mixing_mode = 'plain', > mixing_beta = 0.4, > conv_thr = 1.0d-6, > electron_maxstep=600 > / > &IONS > ion_dynamics = 'bfgs', > / > &CELL > cell_dynamics = 'bfgs', > / > > ATOMIC_SPECIES > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.9994 O.pbe-van_ak.UPF > > K_POINTS {automatic} > 4 4 4 0 0 0 > > CELL_PARAMETERS (bohr) > 8.777485583 -3.914331818 -0.006161821 > 8.777485583 3.914331818 -0.006161821 > -3.276301914 0.000000000 10.503396064 > > ATOMIC_POSITIONS (crystal) > Ti 0.3514812176 0.3514812176 0.6762452335 > Ti 0.6485187824 0.6485187824 0.3237547665 > Ti 0.3370406879 0.3370406879 0.1732195302 > Ti 0.6629593121 0.6629593121 0.8267804698 > Ti -0.0000000000 -0.0000000000 0.5000000000 > O 0.5000000000 0.5000000000 0.0000000000 > O 0.1715541780 0.1715541780 0.8319048573 > O 0.8284458220 0.8284458220 0.1680951427 > O 0.1711642338 0.1711642338 0.3451210511 > O 0.8288357662 0.8288357662 0.6548789489 > > ########################################################## > > > phono3py --qe -d --dim="2 2 2" --pa="F" -c input.in > _ _____ > _ __ | |__ ___ _ __ ___|___ / _ __ _ _ > | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | | > | |_) | | | | (_) | | | | (_) |__) | |_) | |_| | > | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, | > |_| |_| |___/ > 2.7.0 > > -------------------------[time 2023-07-12 13:14:32]------------------------- > Compiled with OpenMP support (max 4 threads). > Python version 3.9.17 > Spglib version 2.0.2 > Traceback (most recent call last): > File "/home/cpg/.local/bin/phono3py", line 45, in <module> > main(**argparse_control) > File "/home/cpg/dev/phono3py/phono3py/cui/phono3py_script.py", line 1164, in main > phono3py = create_phono3py_supercells( > File "/home/cpg/dev/phono3py/phono3py/cui/create_supercells.py", line 73, in create_phono3py_supercells > phono3py = Phono3py( > File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 279, in __init__ > self._build_primitive_cell() > File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 2442, in _build_primitive_cell > self._primitive = self._get_primitive_cell( > File "/home/cpg/dev/phono3py/phono3py/api_phono3py.py", line 2547, in _get_primitive_cell > return get_primitive( > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 849, in get_primitive > return Primitive( > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 389, in __init__ > self._run(supercell, positions_to_reorder=positions_to_reorder) > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 526, in _run > self._p2s_map = self._create_primitive_cell( > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 538, in _create_primitive_cell > trimmed_cell, p2s_map, _ = _trim_cell( > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 1008, in _trim_cell > tcell = TrimmedCell( > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 669, in __init__ > self._run(cell, relative_axes, positions_to_reorder, check_overlap, symprec) > File "/home/cpg/dev/phonopy/phonopy/structure/cells.py", line 754, in _run > raise RuntimeError("Remapping of atoms by TrimmedCell failed.") > RuntimeError: Remapping of atoms by TrimmedCell failed. > cpg@cpg-MS-7693:~/Desktop/Vahid/kappa/m-TiO/scf$ > > Any help would be appreciated. > > Best regards > Vahid > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |