[Pw_forum] Re: Pw_forum digest, Vol 1 #103 - 2 msgs
Raghani Pushpa
pushpa at jncasr.ac.in
Thu Jun 12 17:23:37 CEST 2003
Dear sir,
HOMO is non degenerate, the difference in energy between HOMO and LUMO is
around 0.3 ryd.
I did the calculation by starting from the random wave functions instead
of atomic ones, but it didn't solve the problem of missing eigenvalue.
I also wrote the eigenvalues at every iteration and found that there is
no band crossing i.e. from the first iteration itself, the HOMO and LUMO
are interchanged.
Pushpa
>
> Today's Topics:
>
> 1. Re: 'missing eigenvalue' (Stefano de Gironcoli)
> 2. I am with problems to calculate a molecule: adenine (C5H5N5) (Wyllian)
>
> --__--__--
>
> Message: 1
> Date: Thu, 05 Jun 2003 12:43:04 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] 'missing eigenvalue'
> Reply-To: pw_forum at pwscf.org
>
> Are you sure that the HOMO is non degenerate ?
> If the HOMO orbital is degenerate but the number of electrons
> in the cluster does not fill it completely this may induce instability
> in the case you provide more bands than electrons because from one
> iteration to the next the occupied bands could be different.
> Another possible problem, related to the fact that the HOMO orbital is
> missing, could be related to the fact that the code performs iterative
> diagonalization and if the HOMO has different symmetry from the
> current approximate wavefunctions the diagonalization will not find it.
>
> possible actions:
> 1) try to start from random wavefunctions instead of atomic ones. This could
> help if the missing eigenvalue is due to symmetry of the initial guess for
> the wfcs.
> 2) try to do calculations with a small smearing using gaussian or
> Fermi-Dirac
> broadening (avoid Methfessel-Paxton in this case since the fact that it is
> not positive definite could lead to spurious effects when using very few
> k-points).
> This should clarify what is the level structure for your cluster and should
> tell you if there are problem of degeneracy at the Fermi level.
> 3) Usually increasing the number of bands should helps in NOT missing
> eigenvalues;
> the fact that you get problems is an hint that there might be problem of
> degeneracy.
> Write eigenvalues at every iteration (including more bands than Nelec/2)
> to see
> how things evolves and see if there are levels that keep changing.
>
> All the best
>
> Stefano de Gironcoli
>
>
> Raghani Pushpa wrote:
>
> >Dear all,
> >I am doing the calculations on clusters. When I do the calculations at
> >zero temperature (no smearing), I have to restrict the number of bands to
> >the number of filled bands. If I give more number of bands, the program
> >does not converge; I don't understand why is it happening?
> >
> >At degauss=0, the eigenvalues are not same as eigenvalues I get from band
> >structure calculations, I find that in self consistent calculation, the
> >eigenvalue of HOMO is missing and program gives the eigenvalue of LUMO.
> >Could you please tell me why does it happen?
> >
> >regards,
> >Pushpa
> >
> >
> >
> >
>
>
>
>
> --__--__--
>
> Message: 2
> From: "Wyllian" <fisicabiomolecular at yahoo.com.br>
> To: <pw_forum at pwscf.org>
> Date: Thu, 5 Jun 2003 08:06:57 -0300
> Subject: [Pw_forum] I am with problems to calculate a molecule: adenine (C5H5N5)
> Reply-To: pw_forum at pwscf.org
>
> This is a multi-part message in MIME format.
>
> ------=_NextPart_000_0044_01C32B39.6F14F300
> Content-Type: text/plain;
> charset="iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
>
> Please, I am trying to calculate an adenine molecule (C5H5N5). I do not =
> obtain to get resulted. Input could verify this. Thaks.
>
> Wyllian
> http://www.biophysics.hpg.com.br =20
>
>
>
> #/bin/sh
> ####################################################################
> #
> # set the needed environment variables
> #
> . ../../../environment_variables
> #
> # check whether echo needs the -e option
> if [ "`echo -e`" =3D "-e" ]; then
> echo=3D'echo'
> else
> echo=3D'echo -e'
> fi
> #
> $echo ' '=20
> $echo ' running '$0':'
> $echo ' pw.x to compute the equilibrium'
> $echo ' geometry of a molecule, C5H5N5 - Adenina. '
> $echo ' '=20
> #
> # check that needed directories and files exist
> #
> $echo ' PW_ROOT is defined as '$PW_ROOT' '
> $echo ' PSEUDO_DIR is defined as '$PSEUDO_DIR' '
> $echo ' TMP_DIR is defined as '$TMP_DIR' '
> $echo ' '
> $echo ' checking that needed directories and files exist; \c'
> if [ ! -d $PW_ROOT ]; then=20
> $echo;$echo ' STOPPING: directory '$PW_ROOT' does not exist'; exit
> else
> if [ ! -f $PW_ROOT/main/pw.x ]; then=20
> echo;echo ' STOPPING: executable '$PW_ROOT/main/pw.x' does not =
> exist'; exit
> fi
> fi
> if [ ! -d $PSEUDO_DIR ]; then=20
> $echo;$echo ' STOPPING: directory '$PSEUDO_DIR' does not exist'; exit
> else
> if [ ! -f $PSEUDO_DIR/H.vbc ]; then=20
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not =
> exist';=20
> exit
> fi
> if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then=20
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUS.RRKJ3' does =
> not exis
> t'; exit
> fi
> if [ ! -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' =
> does not e
> xist'; exit
> fi
> if [ ! -f $PSEUDO_DIR/C.vbc ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not =
> exist';=20
> exit
> fi
> if [ ! -f $PSEUDO_DIR/CUS.RRKJ3 ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not =
> exist';=20
> exit
> fi
> if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/CUSPBE.RRKJ3' =
> does not e
> xist'; exit
> fi
> if [ ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' =
> does not e
> xist'; exit
> fi
> if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 ]; then
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUS.RRKJ3' does =
> not exis
> t'; exit
> fi
> fi
> if [ i! -d $TMP_DIR ]; then=20
> $echo;$echo ' STOPPING: directory '$TMP_DIR' does not exist'; exit
> fi
>
> $echo ' done'
> #
> # clean TMP_DIR
> #
> $echo ' cleaning '$TMP_DIR' ; \c'
> rm -f $TMP_DIR/*
> $echo ' done'
> #
> # self-consistent calculation
> #
> cat > adenina1.in << EOF
> C5H5N5 molecule + relax
> C5H5N5
> &input
> ibrav=3D0, celldm(1)=3D1.d0, nat=3D15,ntyp=3D3,
> pseudop(1) =3D 'CUS.RRKJ3', =20
> pseudop(2) =3D 'HUS.RRKJ3',
> pseudop(3) =3D 'NUS.RRKJ3',
> pseudo_dir =3D '$PSEUDO_DIR/',=20
> tmp_dir=3D'$TMP_DIR/',
> ecut(1)=3D24.0, dual=3D6,
> beta(1)=3D0.3, upscale=3D10,
> tr2 =3D 1.0d-14, iswitch=3D1,
> niter=3D100, nstep=3D100,
> output_pot=3D'c5h5n5pot',
> &end
> 14.0 0.0 0.0
> 0.0 14.0 0.0
> 0.0 0.0 14.0
> cubic
> -4.279664 -2.380489 0.676900 1
> 0.015307 -2.366316 0.844708 1
> 0.010016 0.051590 -0.222799 1
> -2.329655 1.250432 -0.851322 1
> 3.897562 -0.881558 0.346576 1
> -6.079629 -3.364659 1.041240 2
> 3.257511 -4.583532 1.953033 2
> 5.965679 -8.416466 0.418008 2
> -0.491329 4.467314 -2.209657 2
> -3.950852 4.517203 -2.374064 2
> 2.453432 0.933336 -0.511738 3
> -2.252932 3.610512 -1.899176 3
> 2.527699 -2.915659 1.188827 3
> -2.199264 -3.629598 1.310904 3
> -4.478275 -0.033070 -0.369631 3
> 'C ' 1 1 1.0
> 'H ' 1 2 1.0
> 'N ' 1 3 1.0 =20
> 0
> 1 1 1
> 0 0 0=20
> EOF
> $echo ' running the geometry relaxation for adenina; \c'
> $PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in > =
> adenina1.out
> $echo ' Adenina done'
>
>
>
>
> ---
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> ------=_NextPart_000_0044_01C32B39.6F14F300
> Content-Type: text/html;
> charset="iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
>
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
> <HTML><HEAD>
> <META http-equiv=3DContent-Type content=3D"text/html; =
> charset=3Diso-8859-1">
> <META content=3D"MSHTML 6.00.2800.1106" name=3DGENERATOR>
> <STYLE></STYLE>
> </HEAD>
> <BODY bgColor=3D#ffffff>
> <DIV><FONT face=3DArial size=3D2>
> <DIV lang=3Den=20
> style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; =
> PADDING-TOP: 10px"><FONT=20
> size=3D4>Please, I am trying to calculate an adenine molecule (C5H5N5). =
> I do not=20
> obtain to get resulted. Input could verify this. Thaks.</FONT></DIV>
> <DIV lang=3Den=20
> style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; =
> PADDING-TOP: 10px"> </DIV>
> <DIV lang=3Den=20
> style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; =
> PADDING-TOP: 10px"><FONT=20
> size=3D4>Wyllian</FONT></DIV>
> <DIV lang=3Den=20
> style=3D"PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; =
> PADDING-TOP: 10px"><FONT=20
> size=3D4><A=20
> href=3D"http://www.biophysics.hpg.com.br">http://www.biophysics.hpg.com.b=
> r</A>=20
> </FONT> </DIV></FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial color=3D#0000ff=20
> size=3D2>#/bin/sh<BR>####################################################=
> ################<BR>#<BR>#=20
> set the needed environment variables<BR>#<BR>.=20
> ../../../environment_variables<BR>#<BR># check whether echo needs the -e =
>
> option<BR>if [ "`echo -e`" =3D "-e" ]; then<BR> =20
> echo=3D'echo'<BR>else<BR> echo=3D'echo =
> -e'<BR>fi<BR>#<BR>$echo ' '=20
> <BR>$echo ' running '$0':'<BR>$echo ' pw.x to compute the =
> equilibrium'<BR>$echo=20
> ' geometry of a molecule, C5H5N5 - Adenina. '<BR>$echo ' ' <BR>#<BR># =
> check that=20
> needed directories and files exist<BR>#<BR>$echo ' =
> PW_ROOT =20
> is defined as '$PW_ROOT' '<BR>$echo ' PSEUDO_DIR is defined =
> as=20
> '$PSEUDO_DIR' '<BR>$echo ' TMP_DIR is defined as =
>
> '$TMP_DIR' '<BR>$echo ' '<BR>$echo ' checking that needed directories =
> and files=20
> exist; \c'<BR>if [ ! -d $PW_ROOT ]; then <BR> $echo;$echo '=20
> STOPPING: directory '$PW_ROOT' does not exist'; exit<BR>else<BR> =
> if [ ! -f=20
> $PW_ROOT/main/pw.x ]; then <BR> echo;echo ' =
> STOPPING:=20
> executable '$PW_ROOT/main/pw.x' does not exist'; exit<BR> =
> fi<BR>fi<BR>if [=20
> ! -d $PSEUDO_DIR ]; then <BR> $echo;$echo ' STOPPING: =
> directory=20
> '$PSEUDO_DIR' does not exist'; exit<BR>else<BR> if [ ! -f=20
> $PSEUDO_DIR/H.vbc ]; then <BR> $echo;$echo =
> '=20
> STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not exist'; =
> <BR>exit<BR> =20
> fi<BR> if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then=20
> <BR> $echo;$echo ' STOPPING: pseudop file=20
> '$PSEUDO_DIR/HUS.RRKJ3' does not exis<BR>t'; exit<BR> fi<BR> =
> if [ !=20
> -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then<BR> =20
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' does not =
>
> e<BR>xist'; exit<BR> fi<BR> if [ ! -f $PSEUDO_DIR/C.vbc ];=20
> then<BR> $echo;$echo ' STOPPING: pseudop =
> file=20
> '$PSEUDO_DIR/C.vbc' does not exist'; <BR>exit<BR> fi<BR> if =
> [ ! -f=20
> $PSEUDO_DIR/CUS.RRKJ3 ]; then<BR> =
> $echo;$echo '=20
> STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; =
> <BR>exit<BR> =20
> fi<BR> if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ];=20
> then<BR> $echo;$echo ' STOPPING: pseudop =
> file=20
> '$PSEUDO_DIR/CUSPBE.RRKJ3' does not e<BR>xist'; exit<BR> =
> fi<BR> if [=20
> ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then<BR> =20
> $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' does not =
>
> e<BR>xist'; exit<BR> fi<BR> if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 =
> ];=20
> then<BR> $echo;$echo ' STOPPING: pseudop =
> file=20
> '$PSEUDO_DIR/NUS.RRKJ3' does not exis<BR>t'; exit<BR> =
> fi<BR>fi<BR>if=20
> [ i! -d $TMP_DIR ]; then <BR> $echo;$echo ' =
> STOPPING:=20
> directory '$TMP_DIR' does not exist'; exit<BR>fi</FONT></DIV>
> <DIV><FONT color=3D#0000ff></FONT> </DIV>
> <DIV><FONT face=3DArial color=3D#0000ff size=3D2>$echo ' done'<BR>#<BR># =
> clean=20
> TMP_DIR<BR>#<BR> $echo ' cleaning '$TMP_DIR' ; \c'<BR>rm -f=20
> $TMP_DIR/*<BR>$echo ' done'<BR>#<BR># self-consistent =
> calculation<BR>#<BR>cat=20
> > adenina1.in << EOF<BR>C5H5N5 molecule +=20
> relax<BR>C5H5N5<BR> &input<BR> ibrav=3D0,=20
> celldm(1)=3D1.d0, nat=3D15,ntyp=3D3,<BR> pseudop(1) =
> =3D=20
> 'CUS.RRKJ3', <BR> pseudop(2) =3D=20
> 'HUS.RRKJ3',<BR> pseudop(3) =3D=20
> 'NUS.RRKJ3',<BR> pseudo_dir =3D '$PSEUDO_DIR/',=20
> <BR> tmp_dir=3D'$TMP_DIR/',<BR> =
> ecut(1)=3D24.0,=20
> dual=3D6,<BR> beta(1)=3D0.3, =
> upscale=3D10,<BR> tr2=20
> =3D 1.0d-14, iswitch=3D1,<BR> niter=3D100,=20
> nstep=3D100,<BR> =20
> output_pot=3D'c5h5n5pot',<BR> &end<BR>14.0 =
> 0.0 =20
> 0.0<BR> 0.0 14.0 0.0<BR> 0.0 =
> 0.0 =20
> 14.0<BR>cubic<BR>-4.279664 -2.380489 0.676900 1<BR> 0.015307=20
> -2.366316 0.844708 1<BR> 0.010016 0.051590 -0.222799=20
> 1<BR>-2.329655 1.250432 -0.851322 1<BR> 3.897562 =
> -0.881558 =20
> 0.346576 1<BR>-6.079629 -3.364659 1.041240 2<BR> 3.257511=20
> -4.583532 1.953033 2<BR> 5.965679 -8.416466 0.418008=20
> 2<BR>-0.491329 4.467314 -2.209657 2<BR>-3.950852 4.517203 =
> -2.374064=20
> 2<BR> 2.453432 0.933336 -0.511738 3<BR>-2.252932 =
> 3.610512=20
> -1.899176 3<BR> 2.527699 -2.915659 1.188827 3<BR>-2.199264=20
> -3.629598 1.310904 3<BR>-4.478275 -0.033070 -0.369631 3<BR>'C ' 1 =
> 1=20
> 1.0<BR>'H ' 1 2 1.0<BR>'N ' 1 3 1.0 <BR> 0<BR> 1 1 =
> 1<BR> 0=20
> 0 0 <BR>EOF<BR>$echo ' running the geometry relaxation for adenina;=20
> \c'<BR>$PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in =
> >=20
> adenina1.out<BR>$echo ' Adenina done'<BR></DIV>
> <DIV> </DIV>
> <DIV> </DIV>
> <DIV><BR>---<BR>Outgoing mail is certified Virus Free.<BR>Checked by AVG =
>
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>
> ------=_NextPart_000_0044_01C32B39.6F14F300--
>
>
>
> --__--__--
>
> _______________________________________________
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