Thanks, Andres. It is really helpful! I get *.MDE file now after setting
"WriteMDhistory" as true, so simple and so useful!
However, I am still puzzled by the data structure in MDE file. The iomd.f
in SIESTA package, which takes care of this output, shows that
------------------------ iomd.f ----------------------------------------
write(iuene,"(6a)") '#Step', 'T(K)', 'E_KS', 'E_tot', 'Vol', 'P(kBar)'
write(iuene,'(i6,1x,f9.2,2(1x,f13.5),1x,f11.3,1x,f11.3)')
. istep, temp, eks*eV, getot*eV, volume, Psol
------------------------------------------------------------------------
with
--------------------------- iomd.f ------------------------------------
c real*8 temp : Temperature of ions
c real*8 eks : Kohn-Sham energy
c real*8 getot : Total energy
c integer istep : Present time step
c real*8 volume : cell volume in Ang**3
c real*8 Psol : total pressure (static plus kinetik) in kBar
---------------------------------------------------------------------
For the "Total energy getot", the "write_md_record.F" code tells that,
------------------------ write_md_record.F -----------------------------
getot = Etot_output + Ekinion + kn + kpr + vn + vpr
------------------------------------------------------------------------
The "dynamics.f' shows that
-------------------------- dynamics.f --------------------------------
C real*8 kn : Kinetic energy of Nose variable
C real*8 kpr : Kinetic energy of Parrinello-Rahman variable
C real*8 vn : Potential energyy of Nose variable
C real*8 vpr : Potential energyy of P-R variables
----------------------------------------------------------------------
From above, we can see that the 1st four columes(istep,temp,eks*eV,getot*eV) in
MDE file are,
MD steps, ionic temperature(ionic kinetic energy), electronic KS energy, and
Total energy,
respectively.
But (Total energy - KS energy)/ionic temperature is not a constant, as you
suggested!
So here my consequent questions are:
(1) Is E_KS is the potential energy of the system, as you said?
(2) Why doesn't Total energy include ion-ion interaction?
Looking forward to having your or other's reply, thanks!
Best regards!
H.H.Guo
-----原始邮件-----
发件人: aguado <[email protected]>
发送时间: 2011年2月18日 星期五
收件人: siesta-l <[email protected]>
抄送:
主题: Re: [SIESTA-L] Potential energy saving in MD run
Dear guohuaihong,
I'm not sure that I understand what you are precisely meaning, but the
potential energy at each step of an MD run is given in the file *.MDE,
under the column E_KS. This means that E_KS is the potential energy of the
system, understood as the total energy (given in the E_tot column) minus
the kinetic energy (which is given in the form of a temperature in column
T).
I hope this answers your question. I don't know either what kind of system
are you simulating, but in case it is a finite system like a molecule or
cluster, keep in mind that the temperature definition depends on the
statistical ensemble. The T given in the *.MDE file is just one possible
definition, extracted from equipartition as applied to the kinetic energy.
Best wishes,
Andres Aguado
On Fri, 18 Feb 2011, guohuaihong wrote:
Dear SIESTA users:
I intend to get system potential energy (including electronic, ionic and
pseudopotential) for each MD step
as doing Nose molecular dynamics (MD) simulation in SIESTA.
I have a few questions to ask:
1. How to obtain system potential? As we know, in each MD step, code only
gives out
E_KS and Free Energy
of electrons. The total energy or the total potential won't be given until the
last MD
step.
2. The clue may lie in the following setting.
SaveNeutralAtomPotential True
SaveTotalPotential True
However, according to the SIESTA-3.0-b manual, "SaveTotalPotential" is "to
write the
valence total effective
local potential (local pseudopotential + Hartree + Vxc), at the mesh...". Does
it
include both electronic and
ionic contributions?
3. If "SaveTotalPotential" only refers to the electronic part, I guess we have
to use
"SaveNeutralAtomPotential"
to calculate ionic part. Is it correct? "SaveNeutralAtomPotential" is a new
command in
3.0-b version compared
with stable version 2.0.2 and defines "the sum of the hartree potential of a
pseudo
atomic valence charge plus
the local pseudopotential". Then, both have local pseudopotential part, how can
we avoid
the double-counting?
4. How to save those potential in one file (such as *.VT or VH) in sequence
like *.ANI
during the MD runs.
Any suggestion will be appriciated! Thank you very much!
Best wishes,
HH GUO
--
Magnetism and Magnetic Materials Division
Shenyang Materials Science National Laboratory
Institute of Metal Research
Chinese Academy of Sciences
72 Wenhua Road,Shenyang 110016, China
+86-15140243901 (mobile)
work: [email protected]
