[DFTB-Plus-User] Help on melting quartz to obtain amorphous silica
Jan M. Knaup
Jan.Knaup at bccms.uni-bremen.de
Wed May 22 16:47:17 CEST 2013
Dear Su,
I try to steer clear of NPT ensembles. You would probably need to
significantly increase the k-point sampling. Even then, pressures are known
to oscillate wildly. Since for generating an amorphous model, the pressure
is not very important, I would advise you not to bother with a barostat.
It's more important to ensure that you really achieve melting and that you
thermalize your melt long enough to be uncorrelated with the initial
crystalline structure.
Incidentally, maybe it would be better for you to start with a random
distribution of atoms rather than a crystal structure. I understand you are
interested in getting an amorphous model, not the dynamics of melting or
amorphization. Starting from a stable crystal structure might not be
helpful at all.
Best,
Jan
Jan M. Knaup | Fon +49-(0)421-218-62351
Dipl. Phys. Dr. rer. nat. | Fax +49-(0)421-218-62770
Universität Bremen - BCCMS |
Am Fallturm 1 | Jan.Knaup at bccms.uni-bremen.de
28359 Bremen | JanKnaup at gmail.com
Germany | www.bccms.uni-bremen.de
2013/5/22 苏锐 <su_rui at outlook.com>
> Hello Jan,
>
> Thanks for you advices.
> Just as you pointed out, I start from the beta cristobalite phase which
> owns a similar density (2.2 g/cm3) as the glassy state. In fact, i also
> gave a try for the npt essemble at first and found the pressure is very
> hard to be equilibrated. The pressure oscillated from about -10 GPa to
> 10GPa. Is there some advice on that problem?
>
> Key part of the npt input:
> Driver = VelocityVerlet {
> MovedAtoms = 1:-1
> TimeStep [fs] = 0.5
>
> Thermostat = NoseHoover {
> Temperature [Kelvin] = TemperatureProfile {
> constant 1 300
> constant 1000 300
> linear 2000 4000
> constant 2000 4000
> exponential 5000 300
> }
> CouplingStrength [cm^-1] = 3000
> }
> Barostat = {
> Pressure [Pa] = 1.0e5
> Timescale [fs] = 10
> }
> OutputPrefix = "amorphous_md"
> }
> The number of timesteps is set very small for test purpose.
>
> Regards
> Su
>
> *发件人:* Jan M. Knaup
> *发送时间:* 2013年5月22日, 星期三 21:28
>
> *收件人:* User list for DFTB+ related questions
>
> Dear Su,
>
> you have keep in mind two important factors:
> First, the melting temperature depends strongly on the pressure, which is
> connected to the supercell volume. Since people mostly simulate at
> optimized or experimental 0K cell volumes, the melting point is shifted
> upwards considerably. 4000K is not necessarily high enough for an oxide
> material at 0K volume. The 1800K melting temperature you mention is the
> isobaric melting temperature at 1 atmosphere pressure. I'm sure you will
> find a much higher pressure in your simulation box.
> Second, in most cases, amorphous phases of a material have a lower density
> than the crystalline ones. Depending on the specific behavior of SiO2, at
> the relatively high equilibrium density of your starting material, the
> crystalline phase may just be very favorable over the amorphous.
> From both these consideration folows, that you might want to reconsider
> your simulation cell volume and rescale to either the density of your
> amorhpous target phase or the density at the melting temperature.
>
> Additionally, you don't have to think your material is melted, you can
> know quite precisely. To decide, you can analyze the radial pair
> distribution function, the self diffusion or the Lindemann index of your
> simulated cell.
>
> Best,
>
> Jan
>
> Jan M. Knaup | Fon +49-(0)421-218-62351
> Dipl. Phys. Dr. rer. nat. | Fax +49-(0)421-218-62770
> Universität Bremen - BCCMS |
> Am Fallturm 1 | Jan.Knaup at bccms.uni-bremen.de
> 28359 Bremen | JanKnaup at gmail.com
> Germany | www.bccms.uni-bremen.de
>
>
> 2013/5/22 苏锐 <su_rui at outlook.com>
>
>> Hello,
>> I have looked the structure evolution, I think the system got melted
>> at 4000K. But the structure seems to be re-crystalized during cooling
>> procedure. Considering that the melting point of quartz is about 1800K, I
>> think 4000K should be sufficiently large to push the system out of FE
>> minima. So maybe 4000K is too low for generating bulk defects?
>> Thanks
>> Su
>>
>> *发件人:* Ben Hourahine
>> *发送时间:* 2013年5月22日, 星期三 15:43
>> *收件人:* User list for DFTB+ related questions
>>
>> Hello,
>>
>> melting tends to proceed from defects, so its quite possible that your
>> annealing never left the free energy
>> minima of the perfect crystal (just ending up super-heating the
>> crystobalite structure above its melting
>> point and then cooling down again). Did you look at the structure at high
>> temperatures?
>>
>> Regards
>>
>> Ben
>>
>> On 22/05/13 02:51, 苏锐 wrote:
>>
>> Hi!
>> I am now trying to obtain amorphous silica through the melting and
>> quenching procedure. The initial system is built using a 2x2x2 supercell of
>> beta-cristobalit containing 192 atoms. I meet a problem that the quenched
>> structure is “defect free”. That means no non-bridging oxygen atoms or
>> 5-member rings etc. that might exist in amrphous structure. I think there
>> might be some error in my md input. Would someone have a look at my input
>> and give some advices?
>>
>> Here is my input:
>>
>> Geometry = GenFormat {
>> <<< silica222.gen
>> }
>>
>> Driver = VelocityVerlet {
>> MovedAtoms = 1:-1
>> TimeStep [fs] = 1.0
>> Thermostat = NoseHoover {
>> Temperature [Kelvin] = TemperatureProfile {
>> # initial temperature = 4000K
>> constant 1 4000
>> # melt at 4000K for 5ps = 5000 step
>> constant 5000 4000
>> # reduce to 3000 in 20ps
>> exponential 20000 300
>> # equilibrium at 300K
>> constant 5000 300
>> }
>> CouplingStrength [cm^-1] = 3000
>> }
>> MDRestartFrequency = 100
>> OutputPrefix = "amorphous_md"
>> }
>>
>> Hamiltonian = DFTB {
>> SCC = Yes
>> SlaterKosterFiles = {
>> Si-O = "./skf/Si-O.skf"
>> O-Si = "./skf/O-Si.skf"
>> Si-Si = "./skf/Si-Si.skf"
>> O-O = "./skf/O-O.skf"
>> }
>> MaxAngularMomentum = {
>> O = "p"
>> Si = "d"
>> }
>> Filling = Fermi {
>> Temperature [Kelvin] = 300.0
>> }
>> KPointsAndWeights = {
>> 0.0 0.0 0.0 1.0
>> }
>> }
>>
>> Options {}
>>
>> ParserOptions {
>> ParserVersion = 4
>> }
>>
>>
>> --
>> Dr. B. Hourahine, SUPA, Department of Physics,
>> University of Strathclyde, John Anderson Building,
>> 107 Rottenrow, Glasgow G4 0NG, UK.
>> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>>
>> Strathclyde 2012 THE Awards UK University of the Year
>>
>> The University of Strathclyde is a charitable body,
>> registered in Scotland, number SC015263
>>
>>
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>>
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