2017-03-04 11:26 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> 1) Angles
>
> I realized I was not using the development version. Sorry about this. This
> issue seems to have been corrected in the development version. I'm still
> not exactly what the change was to fix this, but it is correct in the
> development version.
>
> 2) Dihedrals
>
> I found two issues
>
> a) In potential_to_lammps.sh, there was a scaling to degrees for the "scale"
> step. This seems to be the cause of it dropping points in the smoothing
> step. If you remove this being applied to the $bondtype="dihedral", this
> issue goes away.
The issue is that the table beginning and ending should be converted
to degrees as well in the case of dihedral potentials. For the "angle"
type this issue doesn't appear as the table always goes from 0 to 180
(both in degrees already.)
>
> However, there was a second issue related to the units LAMMPS expects for
> the dihedral. I originally thought the default was radians, but it appears
> it is degrees. We need to add this to table_to_tab.pl so that LAMMPS knows
> the table is in radians. Then remove the previous check for dihedrals when
> it is scaling.
>
> } elsif ($type eq "dihedral" ) {
> printf(OUTFILE "VOTCA"\n");
> printf(OUTFILE "N %i RADIANS\n\n",$#r+1);
> .
> .
> .
>
> LAMMPS seems to be finicky for the derivative for the dihedrals, and I think
> the amount of noise in the distribution is causing an issue for short runs
> and LAMMPS is complaining that the dihedral table has inconsistent forces.
> I'm assuming VOTCA is generating these from a spline? The issue seems to be
> alleviated with longer runs. However, LAMMPS has an option to leave off the
> forces for the dihedral table and let LAMMPS calculate them. I'll look into
> this some more to see if this helps.
>
> I'll work on a pull request if you agree.
Thanks Josh! Your pull request at
<https://github.com/votca/csg/pull/202> seems to fix the two issues
above.
Christoph
>
> Thanks.
>
> Josh
>
>
>
>
>
> On Friday, March 3, 2017 at 9:34:52 PM UTC-5, Joshua Moore wrote:
>>
>> Hello,
>>
>> I am seeing some issues with angle and dihedral translation issues.
>>
>> 1) Angles
>>
>> In the attached ANGLE_ISSUE.PNG, I illustrate the issue.
>>
>> On step000, the initial angle potential is inverted correctly from the
>> angle distribution. The unit conversion appears to be correct. On step001,
>> it also is translated corrected during the scale, smoothing, extrapolation,
>> interpolation, and shifting steps. However, it appears when the LAMMPS
>> table file is written for the angle, something goes wrong. Here I compare
>> to the initial inversion by hand which is shifted in step000, which accounts
>> for the difference. The smoothing, extrapolation, interpolation steps fall
>> on top of one another, and the shifting step is shifted of course.
>>
>> Again here the issue appears to be the lammps table writing step, although
>> I haven't been able to find the issue in the code. Any ideas?
>>
>> 2) Dihedrals
>>
>> See attached DIHEDRAL_ISSUE.PNG
>>
>> Here, there may very well be a LAMMPS table writing issue as with the
>> angles, but on step001 the first issue that occurs is on the smoothing
>> steps, where it drops most of the data points and fits only 11 points. This
>> is the cause for the difference. This is then populated through to the next
>> steps including writing the LAMMPS table file. Although the smooth,
>> extrapolation, interpolation, and shifting steps are in radians, the scaling
>> step writes the file in degrees, although it appears this is not
>> subsequently used. This scaling step is correct in the translation of the
>> potential and the number of points. The next step I think after this is the
>> smoothing step which again drops most of the points and appears to be the
>> major issue here.
>>
>> I think the dihedral issue might be a general issue in VOTCA and not
>> necessarily a problem with interfacing with LAMMPS?
>>
>>
>> Thanks in advance.
>>
>> Josh
>>
>>
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