[CP2K:1782] Re: non-orthorhomic variable cell optimization
Teodoro Laino
teodor... at gmail.com
Tue Feb 17 20:07:43 UTC 2009
Hi Rad,
actually, there was a bug when handling triclinic cells (in the
optimization module).
The bug fix is in the CVS.
Thanks,
Teo
Rad wrote:
> Dear Monica,
>
> Thank you for your response and I really appreciate it. I would like
> to clarify further about my earlier posting as it relates to the
> behavior of the variable cell optimization module.
>
> We are getting reasonable results using the variable cell optimization
> module when it comes to non-monoclinic cells. But We have observed
> consistently in the case of triclinic cells is a change in the lattice
> vectors from the given input even before taking an optimization step.
> It is as if the module is starting with a different initial
> configuration.
>
> Our intention is to understand the process the module follows so that
> we can be comfortable with the final output it produces. For example,
> in one of our studies we gave the following input:
>
> In this case we are providing the experimental lattice configuration
> as the input.
>
> CELL| Vector a [ANGSTROM]: 9.814 0.000 0.000 |
> a| = 9.814
> CELL| Vector b [ANGSTROM]: 0.424 9.038 0.000 |b|
> = 9.048
> CELL| Vector c [ANGSTROM]: 1.575 0.001 20.279 |c|
> = 20.340
> CELL| Angle (b,c)
> [degree]: 89.790
> CELL| Angle (a,c)
> [degree]: 85.559
> CELL| Angle (a,b)
> [degree]: 87.314
>
> Then after the initial set up the module prints the following
> configuration at the 0th step: (This 0th step is before any prior
> calculation has happened)
> ANGSTROM**3]: 1795.645
> CELL| Vector a [ANGSTROM]: 9.807 0.000 0.000 |a|
> = 9.807
> CELL| Vector b [ANGSTROM]: 0.424 9.031 0.000 |b|
> = 9.041
> CELL| Vector c [ANGSTROM]: 1.575 -0.001 20.276 |c|
> = 20.337
> CELL| Angle (b,c)
> [degree]: 89.795
> CELL| Angle (a,c)
> [degree]: 85.559
> CELL| Angle (a,b)
> [degree]: 87.312
>
> This strange switch in the initial geometry is happening only in the
> case of triclinic cells. In addition, the final output volume is off
> by more than 10% in some cases. This is what prompted us to go over
> the output in detail and come up with a pattern.
> It would help us understand and be comfortable with the results if we
> know what is happening at the 0th step and what prompts the change in
> the configuration only for monoclinic cells.
>
> If the developers can take a look at the pattern and provide us with
> any suggestions we would appreciate it.
>
> Thanks
> Rad
>
>
>
> On Feb 13, 9:33 am, monica <monic... at phys.chem.ethz.ch> wrote:
>
>> Dear Rad,
>>
>> I was running recently several triclinic cell optimization jobs
>> (although the angles are very close to 90), with variable hydrostatic
>> pressure (0-20 GPa), and it seemed to work: when comparing the volume
>> with similar orthorhombic cell, optimized manually (energy volume
>> curve). See output below for example. In my case, when the cell was
>> already close to the minimum, only minor changes occurred.
>>
>> Monica
>>
>> output for example
>> CELL| Volume
>> [ANGSTROM**3]: 1798.737
>> CELL| Vector a [ANGSTROM]: 9.814 0.000 0.000 |a|
>> = 9.814
>> CELL| Vector b [ANGSTROM]: 0.424 9.038 0.000 |b|
>> = 9.048
>> CELL| Vector c [ANGSTROM]: 1.575 0.001 20.279 |c|
>> = 20.340
>> CELL| Angle (b,c)
>> [degree]: 89.790
>> CELL| Angle (a,c)
>> [degree]: 85.559
>> CELL| Angle (a,b)
>> [degree]: 87.314
>> CELL| Grid size for subcell
>> generation 2.000
>> CELL| Volume
>> [ANGSTROM**3]: 1795.645
>> CELL| Vector a [ANGSTROM]: 9.807 0.000 0.000 |a|
>> = 9.807
>> CELL| Vector b [ANGSTROM]: 0.424 9.031 0.000 |b|
>> = 9.041
>> CELL| Vector c [ANGSTROM]: 1.575 -0.001 20.276 |c|
>> = 20.337
>> CELL| Angle (b,c)
>> [degree]: 89.795
>> CELL| Angle (a,c)
>> [degree]: 85.559
>> CELL| Angle (a,b)
>> [degree]: 87.312
>> CELL| Grid size for subcell
>> generation 2.000
>> CELL| Volume
>> [ANGSTROM**3]: 1785.878
>> CELL| Vector a [ANGSTROM]: 9.783 0.000 0.000 |a|
>> = 9.783
>> CELL| Vector b [ANGSTROM]: 0.424 9.008 0.000 |b|
>> = 9.018
>> CELL| Vector c [ANGSTROM]: 1.574 -0.006 20.266 |c|
>> = 20.327
>> CELL| Angle (b,c)
>> [degree]: 89.810
>> CELL| Angle (a,c)
>> [degree]: 85.560
>> CELL| Angle (a,b)
>> [degree]: 87.307
>>
>> On Feb 11, 10:47 pm, Rad <rad.... at arl.army.mil> wrote:
>>
>>
>>
>>
>>> Hello everybody,
>>>
>>> We seem to be having an issue with non-orthorhombic cell optimization
>>> when the lattice has all the three angles other than 90 degrees. Here
>>> is what appears to be happening: After the initial set up, the module
>>> Changes the lattice vectors by keeping the lengths the same but the
>>> angles are slightly different. This happens only when all the angles
>>> are not 90-degrees. The regtest for non-orthorhombic includes only one
>>> angle 120 and the rest are 90s. So the scenario I described might be
>>> missed out. This issue we have observed in several executables we have
>>> built over the last several months and on multiple architectures.
>>>
>>> ==================================================================================
>>> Here is the output just after the set up which is the same as the
>>> input:
>>> CELL| Volume
>>> [ANGSTROM**3]: 442.524
>>> CELL| Vector a [ANGSTROM]: 9.010 0.000 0.000 |a|
>>> = 9.010
>>> CELL| Vector b [ANGSTROM]: -4.510 7.821 0.000 |b|
>>> = 9.028
>>> CELL| Vector c [ANGSTROM]: -0.216 -2.630 6.280 |c|
>>> = 6.812
>>> CELL| Angle (b,c)
>>> [degree]: 108.580
>>> CELL| Angle (a,c)
>>> [degree]: 91.820
>>> CELL| Angle (a,b)
>>> [degree]: 119.970
>>>
>>> Here is when it got changed just before the first step of the
>>> optimization:
>>>
>>> CELL| Volume
>>> [ANGSTROM**3]: 449.960
>>> CELL| Vector a [ANGSTROM]: 9.010 0.000 0.000 |a|
>>> = 9.010
>>> CELL| Vector b [ANGSTROM]: -4.510 7.821 0.000 |b|
>>> = 9.028
>>> CELL| Vector c [ANGSTROM]: -0.216 -2.363 6.386 |c|
>>> = 6.812
>>> CELL| Angle (b,c)
>>> [degree]: 106.534
>>> CELL| Angle (a,c)
>>> [degree]: 91.820
>>> CELL| Angle (a,b)
>>> [degree]: 119.970
>>> CELL| Grid size for subcell
>>> generation 2.000
>>>
>>> -------- Informations at step = 0 ------------
>>> Optimization Method = SD
>>> Total Energy = -386.4717739715
>>> Internal Pressure [bar] = 18296.7247113471
>>> ---------------------------------------------------
>>>
>>> --------------------------
>>> OPTIMIZATION STEP: 1
>>> =================================================================================
>>> Could someone please take a look at this issue and let me know what
>>> might be the issue.
>>>
>>> Thanks
>>> Rad- Hide quoted text -
>>>
>> - Show quoted text -
>>
> >
>
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