[Pw_forum] Help about vc-relax
You Lin
ylin at shell.cas.usf.edu
Mon Dec 5 18:21:56 CET 2005
I don't know how to post as a follow up.
But here's the test job:
---- Start of the script ----
#!/bin/sh
EXAMPLE_DIR=`pwd`
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use pw.x to calculate the total energy
and"
$ECHO "the band structure of four simple systems: Si, Al, Cu, Ni."
# set the needed environment variables
. ../environment_variables
rm -rf $EXAMPLE_DIR/results
# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST="Si.vbc.UPF Al.vbc.UPF Cu.pz-d-rrkjus.UPF NiUS.RRKJ3.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO " checking that needed directories and files exist...\c"
# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
if test ! -d $DIR ; then
$ECHO
$ECHO "ERROR: $DIR not existent or not a directory"
$ECHO "Aborting"
exit 1
fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
cd $EXAMPLE_DIR/results
# check for executables
for FILE in $BIN_LIST ; do
if test ! -x $BIN_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
$ECHO "Aborting"
exit 1
fi
done
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
if test ! -r $PSEUDO_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
$ECHO "Aborting"
exit 1
fi
done
$ECHO " done"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
ecut=18.
#UPF=SiPBE_nc.UPF
#UPF=Si.vbc.UPF
#UPF=Si.pbe-n-van.UPF
#UPF=Si.pw91-n-van.UPF
#UPF=Si.pbe-rrkj.UPF
UPF=Si.pz-vbc.UPF
for diago in david ; do
#for celldm in 6.08 6.18 6.28 6.38 6.48 6.58 6.68 6.78 6.88 ; do
for celldm in 09.80 ; do
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
#rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > si.scf.$diago.in << EOF
&control
calculation = 'vc-relax'
restart_mode='from_scratch',
prefix='silicon',
tstress = .true.
tprnfor = .true.
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/', nstep = 100
/
&system
ibrav= 0, celldm(1) =$celldm, nat= 2, ntyp= 1,
ecutwfc =$ecut
/
&electrons
diagonalization='$diago'
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-8
/
&ions
upscale=10
/
&cell
cell_dynamics='damp-w'
press=0.
wmass=.1
/
ATOMIC_SPECIES
Si 28.086 $UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
CELL_PARAMETERS
-0.500000 0.000000 0.500000
0.000000 0.500000 0.500000
-0.500000 0.500000 0.000000
K_POINTS
10
0.1250000 0.1250000 0.1250000 1.00
0.1250000 0.1250000 0.3750000 3.00
0.1250000 0.1250000 0.6250000 3.00
0.1250000 0.1250000 0.8750000 3.00
0.1250000 0.3750000 0.3750000 3.00
0.1250000 0.3750000 0.6250000 6.00
0.1250000 0.3750000 0.8750000 6.00
0.1250000 0.6250000 0.6250000 3.00
0.3750000 0.3750000 0.3750000 1.00
0.3750000 0.3750000 0.6250000 3.00
EOF
$ECHO " running the scf calculation for Si...\c"
$PW_COMMAND < si.scf.$diago.in > si.scf.$diago.$celldm.out
$ECHO " done"
done
done
$ECHO
$ECHO "$EXAMPLE_DIR : done"
---- End of the script ----
This is a script for relaxing Si fcc structure for 100 steps using
Wentzcovitch algorithm from scratch.
I can run this script from scratch for 100 steps (nstep=100) with no
error. But if I run it for 50 steps(set nstep=50) and continue from there
by changing the line
restart_mode='from_scratch',
to
restart_mode='restart',
Then it reports:
---- Start of output ----
Program PWSCF v.3.0 starts ...
Today is 5Dec2005 at 12:19:12
Ultrasoft (Vanderbilt) Pseudopotentials
Current dimensions of program pwscf are:
ntypx = 10 npk = 40000 lmax = 3
nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8
Starting configuration read from file silicon.save
Reading file silicon.save
warning: symmetry operation # 6 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
warning: symmetry operation # 10 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
warning: symmetry operation # 14 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
warning: symmetry operation # 25 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
warning: symmetry operation # 41 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
warning: symmetry operation # 45 not allowed. fractional
translation:
0.2454073 0.2637782 0.2454073 in crystal coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from checkallsym : error # 1
not orthogonal operation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
---- End of output ----
So I AM using Wentzcovitch algorithm in both cases. (M=50 and N=50)
But it seems the "restart" mode changed the symmetry??
Thanks for the help.
> Still got a question: After my first run, I wish to start a from the
> silicon.save by changing the control option:
>
> restart_mode='restart'
>
> Then the the code reported:
> [....]
> from checkallsym : error # 1
> not orthogonal operation
> The symmetry is wrong again? I was using symmetry-conserving
> algorithm: the Wentzcovitch algorithm (cell_dynamics='damp-w').
> And it runs fine if I start from scratch.
if the SAME job gives different results when
- started for N steps and then restarted for M more steps
- started for N+M steps
please provide a test job
P.
--
Paolo Giannozzi e-mail: giannozz at nest.sns.it
Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513
Piazza dei Cavalieri 7 I-56126 Pisa, Italy
________________________________________
You Lin
Department of Physics
University of South Florida
4202 East Fowler Avenue
Tampa, FL 33620
________________________________________
Tel: (813)396-9220 [Office]
Homepage: http://shell.cas.usf.edu/~ylin
________________________________________
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