[Pw_forum] Fwd: Re: Segmentation fault with Setting 2 --- follow-up of Re. ATOMIC_POSITIONS

[Eyvaz Isaev]

Hi, 

I can suggest that errors are due to your system
configuration. 
May be your local network is slow or it configured
improperly.

Bests,
Eyvaz.

--- Yong Jiang <yjiang at asu.edu> wrote:

> (This is a resubmission of my last email) 
> 
> Dear All,
> 
> During phonon calc at G and K vector (by following
> example02), I used Setting 1 
> of ATOMIC_POSITIONS and got reasonable vibrational
> frequencies. Setting 2 is 
> equivalent as Setting 1. However, a similar phonon
> calc using Setting 2 failed. 
> The code always stops with error "Segmentation
> fault". 
> 
> 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 
> 
> 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?
> 
> 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"
> 
> 
=== message truncated ===


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