non-orthorhomic variable cell optimization
Rad
rad.... at arl.army.mil
Wed Feb 25 16:37:10 UTC 2009
Dear Teo,
Thank you for your response and the fix has partially worked in the
sense
that it prints the correct lattice parameters in the 0th step as the
input.
However, it looks like the fix has broken other parts of the code. One
of
the systems I tried had volume going from 400 A3 to 1000 A3 during the
second step
Of the optimization and then the calculation stalled. The same
calculation
used to run smoothly before the fix except for the problem I reported
earlier. I am attaching here with the input I tested along with the
associated POTENTIAL and BASIS_SET files. You can run the input using
an
executable before the fix as well as after the fix and compare the
behavior.
Please take a look at this issue or someone from the team to resolve
this at
your convenience. I really appreciate the prompt response we get from
the
cp2k team and please feel free to ask if you need more information
about the
input.
I have uploaded three files with the prefix "RAD_TEST" and please let
me know if you trouble accessing them.
Thanks
Rad
On Feb 17, 3:07 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> 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 -- Hide quoted text -
>
> - Show quoted text -
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