<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
Dear all,<br>
<br>
A few months ago, I posted a question regarding a problem with
optimizing the
molecules in a monoclinic unit cell (original message below). After
some helpfull comments (for which I am very grateful, btw), I did some
further testing on this matter. I now suspect that there is a bug in
the CPMD code (both in 3.7.2 and in 3.9.1)! The problem apparently lies
in the treatment of the CELL keyword, as I will try to discuss.<br>
<br>
I first started out with the definition for my molecular system using
the keywords SYMMETRY and CELL:<br>
&SYSTEM
<br>
ANGSTROM
<br>
SYMMETRY
<br>
12
<br>
CELL
<br>
5.0872 2.314338 1.073321 0.0 -0.374493314 0.0<br>
<br>
As Bala Sundaram pointed out to me, this specific format (as given in
the manual) was incorrect and should be replaced by:<br>
&SYSTEM
<br>
ANGSTROM
<br>
SYMMETRY
<br>
12
<br>
CELL
<br>
5.0872 2.314338 1.073321 -0.374493314 0.0 0.0 <br>
That is, the format of the CELL keyword for a monoclinic system is:<br>
a b/a c/a cos(beta) 0 0<br>
A notification of this format is also implemented in version 3.9.1 of
cpmd, although I think some mention in the manual would be helpfull.<br>
Anyhow, the calculation still failed and the reason is quite apparent
in the output:<br>
************************** SUPERCELL ***************************<br>
SYMMETRY: MONOCLINIC<br>
LATTICE CONSTANT(a.u.): 9.61341<br>
CELL DIMENSION: 9.6134 2.3143 1.0733 -0.3745 0.0000 0.0000<br>
VOLUME(OMEGA IN BOHR^3): 2046.33461<br>
LATTICE VECTOR A1(BOHR): 9.6134 0.0000 0.0000<br>
LATTICE VECTOR A2(BOHR): -8.3320 20.6296 0.0000<br>
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 10.3183<br>
As the lattice vectors point out, the a and c axis are perpendicular!!
This is obviously not in accordance with the monoclinic symmetry!<br>
<br>
As this did not solve my problem, I redid my calculation, this time
with the CELL VECTORS keyword:<br>
&SYSTEM
<br>
ANGSTROM
<br>
CELL VECTORS<br>
5.087 0.0 0.0<br>
0.0 11.773 0.0<br>
-2.04447 0.0 5.062781<br>
This calculation was succesfull, but now in the output it appears that
my molecular symmetry is TRICLINIC!!<br>
************************** SUPERCELL ***************************<br>
SYMMETRY: TRICLINIC<br>
LATTICE CONSTANT(a.u.): 9.61304<br>
CELL DIMENSION: 9.6130 2.3143 1.0733 0.0000 -0.3744 0.0000<br>
VOLUME(OMEGA IN BOHR^3): 2046.13616<br>
LATTICE VECTOR A1(BOHR): 9.6130 0.0000 0.0000<br>
LATTICE VECTOR A2(BOHR): 0.0000 22.2477 0.0000<br>
LATTICE VECTOR A3(BOHR): -3.8635 0.0000 9.5673<br>
<br>
Eventually, my calculations succeeded but I hope you agree that there
are certain issues with regard to the SYMMETRY and CELL keywords that
need to be looked at.<br>
<br>
<br>
Sincerely,<br>
Ewald Pauwels.<br>
<br>
<br>
<br>
<br>
Ewald Pauwels wrote:<br>
<blockquote cite="mid41401A0B.4050302@UGent.be" type="cite">Dear all, <br>
<br>
Does anybody have any experience with applying CPMD on monoclinic
crystals? <br>
The system I am studying contains four (organic) molecules in the unit
cell. When I optimize these molecules (only the atomic coordinates -
not the cell constants), I find that the unit cell no longer satisfies
the original symmetry. I.e. all four molecules have a substantially
different conformation! <br>
<br>
I suspect that I must be doing something wrong here. Below is my
inputfile. <br>
<br>
<br>
Thanks in advance, <br>
Ewald. <br>
<br>
<br>
<br>
------------------------------------------------------- <br>
inputfile <br>
------------------------------------------------------- <br>
&CPMD <br>
RESTART LATEST GEOFILE WAVEFUNCTION <br>
OPTIMIZE GEOMETRY <br>
LSD <br>
ODIIS NO_RESET=50 <br>
10 <br>
TIMESTEP <br>
20 <br>
PRINT <br>
10 <br>
STRUCTURE BONDS ANGLES <br>
&END <br>
<br>
&SYSTEM <br>
ANGSTROM <br>
SYMMETRY <br>
12 <br>
CELL <br>
5.0872 2.314338 1.073321 0.0 -0.374493314 0.0 <br>
CUTOFF <br>
25. <br>
MULTIPLICITY <br>
1 <br>
&END <br>
<br>
&ATOMS <br>
*C_VDB_U BINARY NEWF <br>
LMAX=P <br>
8 <br>
0.218182218417937 1.473520453 0.333090471110274 <br>
0.732546560623109 1.717103823 -1.08374897292691 <br>
1.30308357695184 7.360020453 2.1982999039374 <br>
0.788719234746671 7.603603823 3.61513934797459 <br>
-0.218182218417937 -1.473520453 -0.333090471110274 <br>
-0.732546560623109 -1.717103823 1.08374897292691 <br>
1.73944801378772 4.412979547 2.86448084615795 <br>
2.25381235599289 4.169396177 1.44764140212077 <br>
*N_VDB_U BINARY NEWF <br>
LMAX=P <br>
4 <br>
2.03113800324446 1.040509513 -1.31410549705625 <br>
-0.509872207874679 6.927009513 3.84549587210393 <br>
-2.03113800324446 -1.040509513 1.31410549705625 <br>
3.55240379861424 4.845990487 1.21728487799143 <br>
*O_VDB_U BINARY NEWF <br>
LMAX=P <br>
8 <br>
1.05333382374583 1.104201443 1.19695275049904 <br>
-1.00750738194352 1.676251513 0.53944941448416 <br>
0.467931971623952 6.990701443 1.33443762454863 <br>
2.5287731773133 7.562751513 1.99194096056352 <br>
-1.05333382374583 -1.104201443 -1.19695275049904 <br>
1.00750738194352 -1.676251513 -0.53944941448416 <br>
2.57459961911561 4.782298557 3.72834312554672 <br>
0.513758413426261 4.210248487 3.07083978953184 <br>
*H_VDB_U BINARY NEWF <br>
LMAX=S <br>
20 <br>
2.33817143317496 1.18130282 -2.29299415508719 <br>
2.75812420631155 1.37791192 -0.67745575495101 <br>
1.93653355901116 0.03473035 -1.14763114043162 <br>
0.875530385150063 2.77889892 -1.22357285168305 <br>
0.0131007466085907 1.35318862 -1.81758891709173 <br>
-0.816905637805185 7.06780282 4.82438453013487 <br>
-1.23685841094177 7.26441192 3.20884612999869 <br>
-0.415267763641377 5.92123035 3.67902151547929 <br>
0.645735410219716 8.66539892 3.75496322673072 <br>
1.50816504876119 7.23968862 4.34897929213941 <br>
-2.33817143317496 -1.18130282 2.29299415508719 <br>
-2.75812420631155 -1.37791192 0.67745575495101 <br>
-1.93653355901116 -0.03473035 1.14763114043162 <br>
-0.875530385150063 -2.77889892 1.22357285168305 <br>
-0.0131007466085907 -1.35318862 1.81758891709173 <br>
3.85943722854474 4.70519718 0.23839621996049 <br>
4.27939000168133 4.50858808 1.85393462009667 <br>
3.45779935438094 5.85176965 1.38375923461606 <br>
2.39679618051984 3.10760108 1.30781752336463 <br>
1.53436654197837 4.53331138 0.713801457955944 <br>
&END <br>
<br>
&DFT <br>
LDA CORRELATION PZ <br>
FUNCTIONAL BP <br>
GC-CUTOFF <br>
5.D-5 <br>
&END <br>
------------------------------------------------------------------ <br>
<br>
<br>
<br>
<br>
<br>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Ewald Pauwels
Centre for Molecular Modelling
Laboratory of Theoretical Physics
Ghent University
Proeftuinstraat 86
B-9000 Gent
Belgium
<a class="moz-txt-link-abbreviated" href="mailto:ewald.pauwels@UGent.be">ewald.pauwels@UGent.be</a>
+32 9 264 65 76</pre>
</body>
</html>