[Pw_forum] Re: Segmentation fault with Setting 2 --- follow-up of Re. ATOMIC_POSITIONS
Yong Jiang
yjiang at asu.edu
Wed Jun 29 01:35:39 CEST 2005
Dear All,
Thanks Dr. Axel Kohlmeyer and Dr. Stefano de Gironcoli very much for their
reply to my last question re. Atomic_Positions.
Here is a problem coming out with these two settings when I was doing phonon
clac of FCC pure Ni.
1.
&system
ibrav=2, nat= 1
ATOMIC_POSITIONS
Ni 0.00 0.00 0.00
2.
&system
ibrav=1, nat= 4,
ATOMIC_POSITIONS {alat}
Ni 0.00 0.00 0.00
Ni 0.5 0.5 0.00
Ni 0.00 0.5 0.5
Ni 0.5 0.00 0.5
During phonon calc at G and K vector (by following example02), I used Setting 1
and got reasonable vibrational frequencies. However, a similar calc using
Setting 2 failed. The code always stops with error "Segmentation fault".
To be more clear, I am attaching the input script, running error message and
some parts of output files (Ni.scf.out and Ni.phG.out) for your reference.
Could somebody kindly take a few minutes to exam this case and help me out from
the error? Thanks a lot!
BTW, I use the serial code of PWscf.
Best,
Yong
**********************
[hzhwc8 at linux1 example02]$ more test_RUN_atGnK
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
# check whether ECHO has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
# set the needed environment variables
. ../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x ph.x"
PSEUDO_LIST="Ni.pbe-nd-rrkjus.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO
$ECHO " checking that needed directories and files exist...\c"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running ph.x as: $PH_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation for Ni with US-PP
cat > Ni.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
tprnfor = .true.
prefix='Ni',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=1, celldm(1) =6.6518, nat= 4, ntyp= 1,
nspin=2,
starting_magnetization(1)=0.5,
degauss=0.03,
smearing='mp',
occupations='smearing',
ecutwfc =25.0
ecutrho =400.0
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ni 58.6934 Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {alat}
Ni 0.00 0.00 0.00
Ni 0.5 .5 0
Ni 0 .5 0.5
Ni 0.5 0 0.5
K_POINTS AUTOMATIC
2 2 2 0 0 0
EOF
$ECHO " running the scf calculation for Ni...\c"
$PW_COMMAND < Ni.scf.in > Ni.scf.out
$ECHO " done"
# phonon calculation at Gamma
cat > Ni.phG.in << EOF
phonons of Ni at Gamma
&inputph
tr2_ph=1.0d-12,
prefix='Ni',
amass(1)=58.6934,
outdir='$TMP_DIR/',
fildyn='Ni.dynG',
/
0.0 0.0 0.0
EOF
$ECHO " running the phonon calculation at Gamma...\c"
$PH_COMMAND < Ni.phG.in > Ni.phG.out
$ECHO " done"
# non self-consistent calculation for phonon at K of Ni with US-PP
cat > Ni.nscf_K.in << EOF
&control
calculation='phonon'
restart_mode='from_scratch',
tprnfor = .true.
prefix='Ni',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 1, celldm(1) =6.6518, nat= 4, ntyp= 1,
nspin=2,
starting_magnetization(1)=0.5,
degauss=0.03,
smearing='mp',
occupations='smearing',
ecutwfc =25.0
ecutrho =400.0
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
&phonon
xqq(1) = .75, xqq(2) = .75, xqq(3) = 0
/
ATOMIC_SPECIES
Ni 58.6934 Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {alat}
Ni 0.00 0.00 0.00
Ni 0.5 .5 0
Ni 0 .5 0.5
Ni 0.5 0 0.5
K_POINTS AUTOMATIC
2 2 2 0 0 0
EOF
$ECHO " running the non-scf calculation for phonon at K of Ni...\c"
$PW_COMMAND < Ni.nscf_K.in > Ni.nscf_K.out
$ECHO " done"
# phonon calculation at K
cat > Ni.phK.in << EOF
phonons of Ni at K
&inputph
tr2_ph=1.0d-12,
prefix='Ni',
amass(1)=58.6934,
fildyn='NiK.dyn',
outdir='$TMP_DIR/'
/
.75 .75 0
EOF
$ECHO " running the phonon calculation at K...\c"
$PH_COMMAND < Ni.phK.in > Ni.phK.out
$ECHO " done"
********************** (RUNNING ERROR MESSAGE)
running pw.x as: /home/hzhwc8/PWscf/espresso-2.1.3/bin/pw.x
running ph.x as: /home/hzhwc8/PWscf/espresso-2.1.3/bin/ph.x
cleaning /home/hzhwc8/PWscf/tmp... done
running the scf calculation for Ni... done
running the phonon calculation at Gamma..../test_RUN_atGnK: line 88: 7992
Segmentation fault $PH_COMMAND <Ni.phG.in >Ni.phG.out
done
running the non-scf calculation for phonon at K of Ni... done
running the phonon calculation at K...forrtl: severe (24): end-of-file during
read, unit 99, file /home/hzhwc8/PWscf/tmp/recover
Image PC Routine Line Source
ph.x 08585C80 Unknown Unknown Unknown
ph.x 085854E4 Unknown Unknown Unknown
ph.x 0854DD91 Unknown Unknown Unknown
**********************
[hzhwc8 at linux1 results]$ more Ni.phG.out
...
Atomic displacements:
There are 4 irreducible representations
Representation 1 3 modes - To be done
Representation 2 3 modes - To be done
Representation 3 3 modes - To be done
Representation 4 3 modes - To be done
PHONON : 1m47.01s CPU time
Alpha used in Ewald sum = 2.8000
Representation # 1 modes # 1 2 3
Self-consistent Calculation
Pert. # 1: Fermi energy shift (Ryd) = 0.0000 0.0000
Pert. # 2: Fermi energy shift (Ryd) = 0.0000 0.0000
Pert. # 3: Fermi energy shift (Ryd) = 0.0000 0.0000
iter # 1 total cpu time : 142.4 secs av.it.: 4.2
thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.164E-05
(ENDS HERE FOR WHAT REASON ?!)
[hzhwc8 at linux1 results]$ more Ni.scf.out
...
the Fermi energy is 14.7679 ev
! total energy = -343.53169412 ryd
estimated scf accuracy < 3.9E-10 ryd
band energy sum = 36.07464219 ryd
one-electron contribution = -9.08238802 ryd
hartree contribution = 62.01012182 ryd
xc contribution = -120.75407837 ryd
ewald contribution = -275.70655005 ryd
correction for metals = 0.00120050 ryd
total magnetization = 1.90 Bohr mag/cell
absolute magnetization = 2.20 Bohr mag/cell
convergence has been achieved
Forces acting on atoms (Ry/au):
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 1 force = 0.00000000 0.00000000 0.00000000
atom 3 type 1 force = 0.00000000 0.00000000 0.00000000
atom 4 type 1 force = 0.00000000 0.00000000 0.00000000
Total force = 0.000000 Total SCF correction = 0.000000
Writing file Ni.save for program phonon
PWSCF : 1m35.34s CPU time
...
Quoting Yong Jiang <yjiang at asu.edu>:
> Dear All,
>
> I am new to PWscf. The manual seems too simple to clerify everything.
> For
> example, I am very confused with Atomic_Positions, expecially the
> difference
> between {alat} and {crystal}.
>
> To be specific, are the following two settings equivalent to generate
> the SAME
> fcc unit cell, EXCEPT that the total energy by setting 2 would be four
> times of
>
> that by setting 1, i.e. Etot(2)=4*Etot(1)?
>
> 1.
> &system
> ibrav=2, nat= 1
> ATOMIC_POSITIONS
> Cu 0.00 0.00 0.00
>
> 2.
> &system
> ibrav=1, nat= 4,
> ATOMIC_POSITIONS {alat}
> Cu 0.00 0.00 0.00
> Cu 0.5 0.5 0.00
> Cu 0.00 0.5 0.5
> Cu 0.5 0.00 0.5
>
> If we want express the same unit cell in ATOMIC_POSITIONS {crystal},
> what would
>
> it be?
>
> Thanks in advance for help
>
> Yong
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