[gpaw-users] Vibration analysis with GPAW

Chang Liu chang.liu at fysik.su.se
Tue Aug 21 13:47:29 CEST 2018 

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!


Best wishes,
Chang Liu
----------------------------------------------------------
                        Chang Liu
                       PhD student
Fysikum, Albanova, Stockholm University
       S-106 91 Stockholm, Sweden
                 +46 767159891
    http://xsolasgroup.fysik.su.se/
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