Related with Problem with pressure fluctuations

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1

Hi all:
Also I can some problems in NPT and NPH ensemble; I’m trying to study the
oxygen-vacancy diffusion in doped BaTiO3 system. Respect to the Pdamp/Tdamp
parameters I believe that these amounts are related with the relaxation time in the
material, not exactly the relaxation time, but it is proportional to that. Also
these parameters are related by the time step used. In my study’s case, the
temperature and pressure are ok, but the msd remains constant. I did some changes in
the input file and the result are the same. I am a beginner, so please help..!!!!!
This is the input file:

read_restart restartntp.bulk
# the unit used is metal unther PBC conditions after minimization
kspace_style ewald 1.0e-4

velocity all create 773.0 12345 dist gaussian #rot yes mom yes

fix desplaz_store_coord all store/coord

#compute vec all cna/atom 4.37873
#compute coord all coord/atom 2.005
compute desplaz all displace/atom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)/10000
#compute ecatm all ke/atom
compute dcmoxi o msd com yes
compute dcmti Ti msd com yes
compute dcmba Ba msd com yes
#compute epatm all pe/atom
#compute fdrtodas all rdf 10 1 1 1 2 1 3 2 1 2 2 2 3 3 1 3 2 3 3
#compute tensatm all stress/atom
#compute myRDF all rdf 200 1 1 1 2 1 3 2 1 2 2 2 3 3 1 3 2 3 3
#fix 1 all ave/time 100 1 10000 c_myRDF[1] c_myRDF[2] c_myRDF[3] c_myRDF[4]
c_myRDF[5] c_myRDF[6] c_myRDF[7] c_myRDF[8] c_myRDF[9] c_myRDF[10] c_myRDF[11] file
tmp.rdf mode vector

2

I think your problem comes from having the “com yes” option active within the msd calculation. The manual states that in such a case the effects of any drift in the com will be taken out.
Carlos

3

Hi all:
Also I can some problems in NPT and NPH ensemble; I’m trying to study the
oxygen-vacancy diffusion in doped BaTiO3 system. Respect to the Pdamp/Tdamp
parameters I believe that these amounts are related with the relaxation time in the
material, not exactly the relaxation time, but it is proportional to that. Also
these parameters are related by the time step used. In my study’s case, the
temperature and pressure are ok, but the msd remains constant. I did some changes in

well, do atoms actually move around? do you see it using a visualization?
i suspect that most will just stay in place and just vibrate on their
lattice position. also, the motion of the vacancy will likely follow
the grotthuss mechanism and thus be much faster than the diffusion of
any type of individual atom. thus your way of measuring it can't work.
you'll have to write some postprocessing program to identify the
vacancy or vacancies and then generate a trajectory of those in order
to compute their diffusion.

axel.