[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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