[CPMD-list] problems with surface
Ari.P.Seitsonen at iki.fi
Ari.P.Seitsonen at iki.fi
Thu Mar 13 11:01:06 CET 2003
Hello ?,
Two or more atoms are on top of each other as you have set also the
periodic replicas. Please remove them (e.g. atoms R_1, which is
obtained with the translation R_1 + A_1; A_1 = first basis vector, R_1
= atomic coordinates), for example the fifth and sixth copper atoms.
Also you have a metallic system, so it might be easier to use the free
energy functional.
Greetings,
apsi
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> Hello CPMD friends:
>
>
> I was trying to do some calculations for a bimetallic model cluster Cu-Rh (36 atoms of Cu and 1 atom of Rh) containing just 2 layers. First I tried to do wavefunction optimization and later, I wanted to put couple of organic molecules over the layer. The input file I used for the calculation is given below this. When I tried to do the wavefunction optimization without using the option "SURFACE", I get an energy value around -116000 AU and this value was oscillating between -113000 to -117000. The following are three steps of the calculation.
>
>
> 1738 1.859E+00 5.473E-01 -115750.395940 -1.567E+03 10.96
> 1739 1.263E+00 3.452E-01 -116693.538377 -9.431E+02 11.09
> 1740 1.837E+00 5.569E-01 -115997.858927 6.957E+02 11.07
>
>
>
> When I used the option "SURFACE" in &SYSTEM section, I got an error as:
>
>
> ATOM TYPE= 2 NUM= 5 6.789029586568773E-002
> 6.83085362150138 11.3015480061868
> ATOM TYPE= 2 NUM= 6 19.6300540501884
> 6.83085362150138 11.3015480061868
>
>
>
> PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY CLOSE
>
>
>
> Could anyone give some suggestions where I am wrong? I feel that, probably my problem is with cell parameters. I am not sure how to use periodic condition for just 2 layers. Also I want to know if I use the option "SURFACE", is it possible to put molecules like CH2=CH-Cl on top of the surface to study the adsorption?
>
>
> I would be grateful for any suggestions from any one.
>
>
> Thanks in advance,
>
>
> Regards,
>
>
> Arvi.
>
>
> My input file I used for calculation is given below.
>
>
> &CPMD
> OPTIMIZE WAVEFUNCTION
> ISOLATED MOLECULE
> &END
> &DFT
> FUNCTIONAL BLYP
> &END
> &SYSTEM
> SYMMETRY
> 0
> CELL ABSOLUTE
> 10.42370400 7.229252 10.42370400 0.0 0.0 0.0
> POINT GROUP
> AUTO
> CUTOFF
> 30.
> ANGSTROM
> &END
> &ATOMS
> *Rh.fpp KLEINMAN-BYLANDER
> LMAX=D
> 1
> 0.000000 0.000000 0.000000
> *Cu.fpp KLEINMAN-BYLANDER
> LMAX=D
> 36
> 2.620000 0.000000 0.000000
> -2.620000 0.000000 0.000000
> 0.000000 2.620000 0.000000
> 0.000000 -2.620000 0.000000
> -5.175926 0.000000 0.000000
> 5.175926 0.000000 0.000000
> 0.000000 5.175926 0.000000
> 0.000000 -5.175926 0.000000
> 2.555926 -2.555926 0.000000
> 2.555926 2.555926 0.000000
> -2.555926 2.555926 0.000000
> -2.555926 -2.555926 0.000000
> -5.111852 -2.555926 0.000000
> -5.111852 2.555926 0.000000
> 5.111852 2.555926 0.000000
> 5.111852 -2.555926 0.000000
> 2.555926 -5.111852 0.000000
> 2.555926 5.111852 0.000000
> -2.555926 5.111852 0.000000
> -2.555926 -5.111852 0.000000
> 1.277963 -1.278963 -1.807313
> 1.277963 1.276963 -1.807313
> -1.277963 1.276963 -1.807313
> -1.277963 -1.278963 -1.807313
> 1.277963 -3.833889 -1.807313
> 1.277963 3.833889 -1.807313
> -1.277963 3.833889 -1.807313
> -1.277963 -3.833889 -1.807313
> 3.833889 -3.833889 -1.807313
> 3.833889 3.833889 -1.807313
> -3.833889 3.833889 -1.807313
> -3.833889 -3.833889 -1.807313
> 3.833889 -1.277963 -1.807313
> 3.833889 1.277963 -1.807313
> -3.833889 1.277963 -1.807313
> -3.833889 -1.277963 -1.807313
> CONSTRAINTS
> FIX ATOMS
> 37
> 1
> 2
> ...
> 37
> END CONSTRAINTS
> &END
>
>
>
>
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>
> <P><FONT face="Times New Roman">Hello CPMD friends:</FONT></P>
> <P><FONT face="Times New Roman">I was trying to do some calculations for a bimetallic model cluster Cu-Rh (36 atoms of Cu and 1 atom of Rh) containing just 2 layers. First I tried to do wavefunction optimization and later, I wanted to put couple of organic molecules over the layer. The input file I used for the calculation is given below this. When I tried to do the wavefunction optimization without using the option "SURFACE", I get an energy value around -116000 AU and this value was oscillating between -113000 to -117000. The following are three steps of the calculation.</FONT></P>
> <P>1738 1.859E+00 5.473E-01 -115750.395940 -1.567E+03 10.96<BR>1739 1.263E+00 3.452E-01 -116693.538377 -9.431E+02 11.09<BR>1740 1.837E+00 5.569E-01 -115997.858927 6.957E+02 11.07<BR></P>
> <P><FONT face="Times New Roman">When I used the option "SURFACE" in &SYSTEM section, I got an error as: </FONT></P>
> <P> ATOM TYPE= 2 NUM= 5 6.789029586568773E-002<BR> 6.83085362150138 11.3015480061868<BR> ATOM TYPE= 2 NUM= 6 19.6300540501884<BR> 6.83085362150138 11.3015480061868</P>
> <P><BR> PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY CLOSE<BR></P>
> <P><FONT face="Times New Roman">Could anyone give some suggestions where I am wrong? I feel that, probably my problem is with cell parameters. I am not sure how to use periodic condition for just 2 layers. Also I want to know if I use the option "SURFACE", is it possible to put molecules like CH2=CH-Cl on top of the surface to study the adsorption?</FONT></P>
> <P><FONT face="Times New Roman">I would be grateful for any suggestions from any one.</FONT></P>
> <P><FONT face="Times New Roman">Thanks in advance,</FONT></P>
> <P><FONT face="Times New Roman">Regards,</FONT></P>
> <P><FONT face="Times New Roman">Arvi.</FONT></P>
> <P><FONT face="Times New Roman">My input file I used for calculation is given below.</FONT></P>
> <P> &CPMD<BR> OPTIMIZE WAVEFUNCTION<BR> ISOLATED MOLECULE<BR> &END<BR> &DFT<BR> FUNCTIONAL BLYP<BR> &END<BR> &SYSTEM<BR> SYMMETRY<BR> 0<BR> CELL ABSOLUTE<BR> 10.42370400 7.229252 10.42370400 0.0 0.0 0.0<BR> POINT GROUP<BR> AUTO<BR> CUTOFF<BR> 30.<BR> ANGSTROM<BR> &END<BR> &ATOMS<BR>*Rh.fpp KLEINMAN-BYLANDER<BR> LMAX=D<BR> 1<BR> 0.000000 0.000000 0.000000<BR>*Cu.fpp KLEINMAN-BYLANDER<BR> LMAX=D<BR> 36<BR> 2.620000 0.000000 0.000000<BR> &n!
bs!
> p;!
> !
> -2.620000 0.000000 0.000000<BR> 0.000000 2.620000 0.000000<BR> 0.000000 -2.620000 0.000000<BR> -5.175926 0.000000 0.000000<BR> 5.175926 0.000000 0.000000<BR> 0.000000 5.175926 0.000000<BR> !
&n!
> bs!
> !
> p; 0.000000 -5.175926 0.000000<BR> 2.555926 -2.555926 0.000000<BR> 2.555926 2.555926 0.000000<BR> -2.555926 2.555926 0.000000<BR> -2.555926 -2.555926 0.000000<BR> -5.111852 -2.555926 0.000000<BR> !
&n!
> bs!
> !
> p; -5.111852 2.555926 0.000000<BR> 5.111852 2.555926 0.000000<BR> 5.111852 -2.555926 0.000000<BR> 2.555926 -5.111852 0.000000<BR> 2.555926 5.111852 0.000000<BR> -2.555926 5.111852 0.000000<BR> &nb!
sp!
> ;&!
> !
> nbsp; -2.555926 -5.111852 0.000000<BR> 1.277963 -1.278963 -1.807313<BR> 1.277963 1.276963 -1.807313<BR> -1.277963 1.276963 -1.807313<BR> -1.277963 -1.278963 -1.807313<BR> 1.277963 -3.833889 -1.807313<BR> &nbs!
p;!
> &n!
> !
> bsp; 1.277963 3.833889 -1.807313<BR> -1.277963 3.833889 -1.807313<BR> -1.277963 -3.833889 -1.807313<BR> 3.833889 -3.833889 -1.807313<BR> 3.833889 3.833889 -1.807313<BR> -3.833889 3.833889 -1.807313<BR> !
&n!
> bs!
> !
> p; -3.833889 -3.833889 -1.807313<BR> 3.833889 -1.277963 -1.807313<BR> 3.833889 1.277963 -1.807313<BR> -3.833889 1.277963 -1.807313<BR> -3.833889 -1.277963 -1.807313<BR> CONSTRAINTS<BR> FIX ATOMS<BR> 37<BR> 1<BR> 2<BR> ...<BR> 37<BR> END CONSTRAINTS<BR> &END<BR></P>
> <P> </P>
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