[Pw_forum] Help about vc-relax
You Lin
ylin at shell.cas.usf.edu
Wed Nov 23 22:48:09 CET 2005
To whom it may concern:
I'm trying to do a variable cell relaxation.
There's no example that I can follow directly, therefore, I have to read
the document to make a sample input file for Si-fcc structure.
The code stops at the second step. The input and output files are listed
below. The error message gives no hint. What did I do wrong?
--------------------- Start here -----------------------------
#!/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/'
/
&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-pr'
press=0.
wmass=10.
/
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 here -----------------------------
The result file is:
--------------------- Start here -----------------------------
Program PWSCF v.3.0 starts ...
Today is 23Nov2005 at 16: 7:42
Ultrasoft (Vanderbilt) Pseudopotentials
Current dimensions of program pwscf are:
ntypx = 10 npk = 40000 lmax = 3
nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8
from setup : info # -1
Dynamics, you should have no symmetries
bravais-lattice index = 0
lattice parameter (a_0) = 9.8000 a.u.
unit-cell volume = 235.2980 (a.u.)^3
number of atoms/cell = 2
number of atomic types = 1
kinetic-energy cutoff = 18.0000 Ry
charge density cutoff = 72.0000 Ry
convergence threshold = 1.0E-08
beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = SLA PZ NOGX NOGC (1100)
nstep = 50
celldm(1)= 9.800000 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of a_0)
a(1) = ( -0.500000 0.000000 0.500000 )
a(2) = ( 0.000000 0.500000 0.500000 )
a(3) = ( -0.500000 0.500000 0.000000 )
reciprocal axes: (cart. coord. in units 2 pi/a_0)
b(1) = ( -1.000000 -1.000000 1.000000 )
b(2) = ( 1.000000 1.000000 1.000000 )
b(3) = ( -1.000000 1.000000 -1.000000 )
PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0
(in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000)
atomic species valence mass pseudopotential
Si 4.00 28.08600 Si( 1.00)
cell mass = 10.00000 AMU
48 Sym.Ops. (with inversion)
Cartesian axes
site n. atom positions (a_0 units)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000
)
2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000
)
number of k points= 10
cart. coord. in units 2pi/a_0
k( 1) = ( 0.1250000 0.1250000 0.1250000), wk =
0.0625000
k( 2) = ( 0.1250000 0.1250000 0.3750000), wk =
0.1875000
k( 3) = ( 0.1250000 0.1250000 0.6250000), wk =
0.1875000
k( 4) = ( 0.1250000 0.1250000 0.8750000), wk =
0.1875000
k( 5) = ( 0.1250000 0.3750000 0.3750000), wk =
0.1875000
k( 6) = ( 0.1250000 0.3750000 0.6250000), wk =
0.3750000
k( 7) = ( 0.1250000 0.3750000 0.8750000), wk =
0.3750000
k( 8) = ( 0.1250000 0.6250000 0.6250000), wk =
0.1875000
k( 9) = ( 0.3750000 0.3750000 0.3750000), wk =
0.0625000
k( 10) = ( 0.3750000 0.3750000 0.6250000), wk =
0.1875000
G cutoff = 175.1560 ( 2421 G-vectors) FFT grid: ( 20, 20, 20)
nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 310
nelec = 8.00 nkb = 8 ngl = 2421
Initial potential from superposition of free atoms
starting charge 7.99901, renormalised to 8.00000
Starting wfc are atomic
total cpu time spent up to now is 0.26 secs
Self-consistent Calculation
iteration # 1 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 1.00E-02, avg # of iterations = 2.0
Threshold (ethr) on eigenvalues was too large:
Diagonalizing with lowered threshold
Davidson diagonalization with overlap
ethr = 9.49E-03, avg # of iterations = 1.0
total cpu time spent up to now is 0.58 secs
total energy = -15.82522609 ryd
estimated scf accuracy < 0.07514793 ryd
iteration # 2 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 9.39E-04, avg # of iterations = 1.1
total cpu time spent up to now is 0.72 secs
total energy = -15.82983341 ryd
estimated scf accuracy < 0.00214100 ryd
iteration # 3 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 2.68E-05, avg # of iterations = 2.3
total cpu time spent up to now is 0.89 secs
total energy = -15.83038757 ryd
estimated scf accuracy < 0.00007807 ryd
iteration # 4 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 9.76E-07, avg # of iterations = 1.9
total cpu time spent up to now is 1.07 secs
total energy = -15.83040504 ryd
estimated scf accuracy < 0.00000597 ryd
iteration # 5 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 7.46E-08, avg # of iterations = 1.8
total cpu time spent up to now is 1.23 secs
total energy = -15.83040678 ryd
estimated scf accuracy < 0.00000003 ryd
iteration # 6 ecut= 18.00 ryd beta=0.70
Davidson diagonalization with overlap
ethr = 3.36E-10, avg # of iterations = 2.4
total cpu time spent up to now is 1.42 secs
End of self-consistent calculation
! total energy = -15.83040721 ryd
estimated scf accuracy < 4.6E-09 ryd
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
Total force = 0.000000 Total SCF correction = 0.000000
entering subroutine stress ...
total stress (ryd/bohr**3) (kbar) P=
134.49
0.00091422 0.00000000 0.00000000 134.49 0.00 0.00
0.00000000 0.00091422 0.00000000 0.00 134.49 0.00
0.00000000 0.00000000 0.00091422 0.00 0.00 134.49
Parrinello-Rahman Damped Cell-Dynamics Minimization
convergence thresholds: EPSE = 0.10E-03 EPSF = 0.10E-02 EPSP =
0.50E+00
Entering Dynamics; it = 1 time = 0.00000 pico-seconds
new lattice vectors (alat unit) :
-0.500065538 -0.000065538 0.500065538
0.000065538 0.500065538 0.500065538
-0.500065538 0.500065538 -0.000065538
new unit-cell volume = 235.4368 (a.u.)^3
new positions in cryst coord
Si 0.000000000 0.000000000 0.000000000
Si -0.250000000 0.750000000 -0.250000000
new positions in cart coord (alat unit)
Si 0.000000000 0.000000000 0.000000000
Si 0.250081922 0.250049153 0.250049153
Ekin = 0.00000000 Ryd T = 0.0 K Etot = -15.83040721
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from checkallsym : error # 2
not orthogonal operation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
--------------------- End here -----------------------------
________________________________________
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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