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Messages - Julian Schneider

Pages: 1 ... 8 9 [10]
136
Questions and Answers / Re: Presure calculations
« on: April 14, 2015, 09:36 »
For a static system (i.e. obtained from a geometry optimization), the pressure can be calculated from the stress tensor via P = -1/3 (s_xx + s_yy + s_zz) (see attached script).
At finite temperature (i.e. in a molecular dynamics run) there would be an additional contribution of the kinetic energy: P = 2/3 E_kin/V - 1/3 (s_xx + s_yy + s_zz).

If you want to compare the enthalpy of two systems, you have to simulate them at the desired target pressure. In a molecular dynamics simulation, this can easily be achieved by employing one the NPT-methods. If you intend to obtain the structures via a geometry optimization, you have to optimize the cell until the desired target stress is reached. In ATK2015, this can easily be achieved via the target_stress parameter.

137
Questions and Answers / Re: Bond angle distribution plot
« on: April 1, 2015, 09:04 »
There will be an bond angle analysis in the MD-Analyzer plugin in ATK-2015, which makes it possible to obtain such a plot with few clicks.
In ATK-2014, it is unfortunately only possible by writing a python script .

138
Ideally, the snapshots obtained from an equilibrium MD simulation will be sampled from canonical distribution automatically (ergodicity theorem).  Therefore, no additional weighting is necessary. The configurations with high energy and low exp(-E/kT) weight will be correspondingly rare in the MD simulation anyway. Of course, for shorter MD simulations this holds only approximately.

139
Hi Jenny,

Unless you are explicitly interested in thermal or temperature dependent properties (e.g. thermal expansion), performing a geometry optimization at 0K and then calculating the desired properties based on the final structure is in fact the most common approach, in particular when you are interested in electronic-structure-related properties.
I see that your MD temperature is 50 K, and for this low temperature I would expect the difference to the 0K-structure to be very small.
The disadvantage of finite-temperature-structures is that there is no unique structure but rather an ensemble of configurations that you would have to average over.
If you really want to use finite temperature structures, then in your case, you would have to use the the NPTMelchionna-thermostat isntead of the NPTBerendsen-thermostat. The reason is that you have an anisotropic structure that is only periodic in z-direction, and NPTBerendsen treats everything as isotropic (cf. MD-tutorial), which probably causes your error message.
So you'd have to use something like:

method = NPTMelchionna(
    time_step=1*femtoSecond,
    reservoir_temperature=50*Kelvin,
    external_stress=1*bar,
    thermostat_timescale=100*femtoSecond,
    barostat_timescale=100*femtoSecond,
    bulk_modulus=1e+06*bar,
    initial_velocity=initial_velocity,
    mask=[[False, False, False], [False, False, False], [False, False, True]]
)

140
Questions and Answers / Re: al2o3 cif file
« on: January 30, 2015, 09:48 »
Sorry, the file was indeed missing. It is attached to the tutorial now.

141
Questions and Answers / Re: vacancy formation energy
« on: November 19, 2014, 16:19 »
It's essentially all in the tutorial (cf. "Summarizing the calculations").
The total energy corresponds to LaMnO3, but the contributions (in energy, forces and stress) arising from the difference, e.g. between O being simulated inside the basis set of LaMnO3-x and as a single atom, are removed. Vice versa for LaMnO3-x .
Now, you have to optimize LaMnO3 with BSSE correction and get the total energy E(LaMnO3). Then you optimize and calculate  E (LaMnO3-x) and E(O) with the same settings but without BSSE.
Then you do the same thing for O2 (with BSSE) and O (without). and get the BSSE-corrected O2 binding energy from E(O2-binding) = E(O2)-2E(O).

Finally, you combine everything as shown in Ref. 4 in the tutorial to get the vacancy formation energy:
E(vac)= E(LaMnO3-x) - E(LaMnO3) + E(O) + 1/2 E(O2 - binding) 


142
Questions and Answers / Re: vacancy formation energy
« on: November 19, 2014, 13:19 »
You can for example calculate the vacancy formation energy as described in Ref. 4 in the BSSE-tutorial (J. Theor. Comput. Chem. 11, 1261 (2012)) using a single oxygen atom as intermediate step.
Following the tutorial, when calculating the LaMnO3 system, the LaMnO3-x part of the system would then correspond to "layer1" in the tutorial, and the oxygen atom would correspond to "layer2".
Similarly, the two oxygen atoms in the O2-molecule atom would be "layer1" and "layer2", respectively.

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