[gpaw-users] Vibration analysis with GPAW
Jens Jørgen Mortensen
jjmo at dtu.dk
Wed Aug 22 08:58:03 CEST 2018
On 08/21/2018 01:47 PM, Chang Liu via gpaw-users wrote:
>
> Hi,
>
>
> I am trying to run vibration analysis on a few trajectories obtained
> from NEB calculations. Below is one of the input files:
>
>
> from gpaw import *
> from ase.vibrations import Vibrations
> from ase.io import *
> from ase.units import Pascal, m, Bohr
> from gpaw.utilities import h2gpts
> import numpy as np
>
> name = '2co'
> state = 0
> xc = 'BEEF-vdW'
>
> mixer = Mixer(0.1, 5, weight = 100.0)
> calc = GPAW(#gpts = h2gpts(0.2, slab.get_cell(), idiv=8),
> poissonsolver = {'dipolelayer':'xy','eps':1e-12},
> kpts = {'density':2},
> xc = xc,
> symmetry = {'point_group':False},
> mixer = mixer,
> eigensolver=Davidson(3),
> spinpol = False,
> occupations = FermiDirac(0.1),
> maxiter = 1000,
> )
> neb_states = read('%s_neb.traj@:'%name)
> slab = neb_states[state]
> slab.center(vacuum=5.,axis=2)
> slab.cell[2][2]+=10.
> slab.pbc = (1,1,0)
>
> calc.set(gpts = h2gpts(0.2, slab.get_cell(), idiv=8),txt =
> '%s_%d_gpaw.out' % (name,state))
> slab.set_calculator(calc)
> e_f = slab.get_potential_energy()
> rho = slab.calc.get_all_electron_density(gridrefinement=4)
> write('%s_%d.cube'% (name,state), slab, data=rho * Bohr**3)
> f = open('Energy_%s_%d.txt' % (name,state), 'w')
> f.write('%.3f\n' % e_f)
> f.close()
>
> vib = Vibrations(slab,range(45,49),'vib_%s_%d'%(name,state))
> vib.run()
> vib.summary(log='vib_%s_%d.log'%(name,state))
> vib.write_mode()
> vib_energies = vib.get_energies()
>
> With GPAW-1.3.0, the calculation was finished without any problem.
> However, with both 1.4.0 and 1.4.1b1, all the calculations crash with
> such an error:
>
>
>
> ___ ___ ___ _ _ _
> | | |_ | | | |
> | | | | | . | | | |
> |__ | _|___|_____| 1.4.1b1
> |___|_|
>
> User: chliu at b-cn0521.hpc2n.umu.se
> Date: Mon Aug 20 21:55:05 2018
> Arch: x86_64
> Pid: 68732
> Python: 2.7.14
> gpaw:
> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw
> _gpaw: /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/bin/gpaw-python
> ase:
> /home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase
> (version 3.16.3b1)
> numpy:
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg/numpy
> (version 1.13.1)
> scipy:
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy
> (version 0.19.1)
> units: Angstrom and eV
> cores: 84
>
> Input parameters:
> eigensolver: {name: dav,
> niter: 3}
> kpts: {density: 2}
> maxiter: 1000
> mixer: {backend: pulay,
> beta: 0.1,
> method: separate,
> nmaxold: 5,
> weight: 100.0}
> occupations: {name: fermi-dirac,
> width: 0.1}
> poissonsolver: {dipolelayer: xy,
> eps: 1e-12}
> spinpol: False
> symmetry: {point_group: False}
> xc: BEEF-vdW
>
> Writing vib_2co_0.eq.pckl
> rank=00 L00: Traceback (most recent call last):
> rank=00 L01: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/__init__.py",
> line 200, in main
> rank=00 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
> rank=00 L03: File
> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
> line 252, in run_path
> rank=00 L04: return _run_module_code(code, init_globals, run_name,
> path_name)
> rank=00 L05: File
> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
> line 82, in _run_module_code
> rank=00 L06: mod_name, mod_fname, mod_loader, pkg_name)
> rank=00 L07: File
> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
> line 72, in _run_code
> rank=00 L08: exec code in run_globals
> rank=00 L09: File "2co_0.py", line 40, in <module>
> rank=00 L10: vib.run()
> rank=00 L11: File
> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/vibrations/vibrations.py",
> line 131, in run
> rank=00 L12: self.calculate(atoms, filename, fd)
> rank=00 L13: File
> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/vibrations/vibrations.py",
> line 168, in calculate
> rank=00 L14: forces = self.calc.get_forces(atoms)
> rank=00 L15: File
> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/calculators/calculator.py",
> line 515, in get_forces
> rank=00 L16: return self.get_property('forces', atoms)
> rank=00 L17: File
> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/calculators/calculator.py",
> line 548, in get_property
> rank=00 L18: self.calculate(atoms, [name], system_changes)
> rank=00 L19: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/calculator.py",
> line 297, in calculate
> rank=00 L20: self.log, self.call_observers)
> rank=00 L21: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/scf.py",
> line 62, in run
> rank=00 L22: wfs.eigensolver.iterate(ham, wfs)
> rank=00 L23: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py",
> line 84, in iterate
> rank=00 L24: wfs.orthonormalize(kpt)
> rank=00 L25: File
> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/utils/timing.py",
> line 173, in new_method
> rank=00 L26: x = method(slf, *args, **kwargs)
> rank=00 L27: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py",
> line 396, in orthonormalize
> rank=00 L28: S.invcholesky()
> rank=00 L29: File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/matrix.py",
> line 248, in invcholesky
> rank=00 L30: check_finite=debug)
> rank=00 L31: File
> "/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/linalg/decomp_cholesky.py",
> line 81, in
> cholesky
> rank=00 L32: check_finite=check_finite)
> rank=00 L33: File
> "/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/linalg/decomp_cholesky.py",
> line 30, in
> _cholesky
> rank=00 L34: raise LinAlgError("%d-th leading minor not positive
> definite" % info)
> rank=00 L35: LinAlgError: 21-th leading minor not positive definite
> GPAW CLEANUP (node 0): <class 'numpy.linalg.linalg.LinAlgError'>
> occurred. Calling MPI_Abort!
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 42.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> The GPAW versions 1.3.0, 1.4.0 and 1.4.1b1 were all installed with the
> same modules (OpenMPI, Scipy, Numpy, etc.). It seems to be related
> with the change from 1.3.0 to 1.4.0... Could you please help me?
> Thanks a lot!
>
Could you try to run the GPAW tests in parallel and show us the output?
$ gpaw -P 4 test
Jens Jørgen
>
> Best wishes,
> Chang Liu
> ----------------------------------------------------------
> Chang Liu
> PhD student
> Fysikum, Albanova, Stockholm University
> S-106 91 Stockholm, Sweden
> +46 767159891
> http://xsolasgroup.fysik.su.se/
>
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20180822/21531b30/attachment-0001.html>
More information about the gpaw-users
mailing list