[CPMD-list] classical MD velocity incorporation in CPMD input file

[Axel Kohlmeyer]

On Tue, 3 May 2005, sanjeev narooka wrote:

SN> Hello All cpmd user


hello sanjeev,

 
SN> I have one more question, in Axel web page it is
SN> indicated that
SN>   
SN> "Archive the coordinates and velocities of the last 
SN> 50 
SN>             -----------------------------
SN> ps of the trajectory at 2 fs distance for late"

this is just so you can analyze the data (e.g. calculate
velocity autocorrelation functions) and compare to the 
equivalent results from CPMD runs.

 
SN> i can have the coordinates of all atoms from moldy to
SN> be used in cpmd run, but it is not possible to get the
SN> velocity of every atoms separately by using moldy
SN> utility "dumpext" as it is providing only centre of
SN> mass velocity  not the velocity of all 32 oxygen atom,
SN> or the velocity of 64 Hydrogen atom.

well, you _can_ get the angular velocites of the molecules
from the quaternion velocities and compute from that the
velocities of the individual atoms. that is a bit of not
so obvious vector algebra, but doable (i have some code
to do that for water, if you really, really want to do that).

SN> and i think in order to have cpmd read the old
SN> velocity, we first have to generate a Gemetry file in
SN> the cpmd format using these velocities obtained from
SN> previous classical md run. And then start cpmd
SN> specifying Restart,if i am right

no. since the classical water geometry is a bit different 
from the one obtained by the cpmd you will have to do
some additional equilibration anyways and for that using
a new velocity distribution (as generated by the 
TEMPERATURE keyword) is just as good. 

SN> so how it is possible to label the velocity of all
SN> atoms in the supercell of cpmd. or we have to make
SN> cpmd read only the velocity of centre of mass and that
SN> will be the incorporation of old velocity from
SN> classical run in cpmd input file

in the given example you just use the xyz2cpmd script
to create the &ATOMS and &SYSTEM section to complete
the given cpmd input template. for other systems, you
can also take an old input and just adjust/rewrite
the &SYSTEM/&ATOMS sections to match your new system
with a text editor. please see the manual for a more
detailed description of the input syntax and 
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-tutor/part3.html
for a simpler example with more detailed commentary.

in fact, i'd recommend to start with the tutorial - however
incomplete it currently is - before you work through water example
(it has been integrated into the tutorial, but without the classical
pre-equilibration).

regards,
	axel.

SN> thanks
SN> your truly
SN> sanjeev
SN> 
SN> 
SN> 
SN> 
SN> 
SN> 
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-- 

=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.