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Alex Granovsky

Dear Dawid,

I have examined your output and found that what was constrained
in your input file and during Firefly execution was not a torsion
(coordinate type 3) but rather the out of plane bend (coordinate type 4).
Note, these two coordinate types are not the same!

There is a trivial typo in your input. Instead of


there should be


If you look into output, you'll see that this out of plane bend
stays perfectly constrained at 22.3313384 degrees during optimization.
Search output file for strings like:

     1 PLA.BEND    3    2    6    7                 0.3897554      22.3313384

Hope this helps.

All the best,
Alex Granovsky

On Wed Mar 29 '17 10:38am, Dawid wrote
>Dear Prof. Granovsky,

>Thank you for your kind answer and explaining precisely how to
>use multithreading in my case.

>Nevertheless, I have double checked the actual geometries during
>optimization and even though I have constrained my torsion, it
>slightly varies during optimization, however by up to ca. 0.5 degree.
>So I have figured out that this is a something like a numerical
>echo from my optimization. I am attaching the output from
>calculations that I have concerned to be correct in terms of
>constraints even though the dihedral somehow varies. I had to
>however delete some output with MCHF natural orbitals. Otherwise,
>the file size was too large.

>Best wishes,
>Dawid Grabarek

>On Tue Mar 28 '17 9:34pm, Alex Granovsky wrote
>>Dear Dawid,

>>I'm sorry for delay with my reply. Indeed, the use of DLCs for
>>geometry optimization (with or without constrains, this does not
>>matter) is the recommended way with Firefly. It is good you have
>>already figured this out.

>>As to torsion angle variations you observed, I'm sure that
>>there are no variations in frozen torsion at the geometries
>>along the energy optimization path itself. Please double check this.
>>At the same time, at distorted intermediate geometries used to
>>compute numerical gradients, violation of constrains is indeed
>>possible and is even required.

>>On a separate note, I have a comment concerning your use of XP mode
>>with Firefly. Upon examination of your previously posted input and
>>output (from system-blows-up.tar.gz archive) it seems to me you do
>>not use XP mode optimally. Indeed, the job was running in parallel
>>using 12 processes on a single host wn0361. There is nothing wrong
>>with this so far. However, np variable in $smp group was set to 24
>>and you requested plain XP mode.

>>As you can find in the output:


     Switching to XP mode with    12 groups of processes.
     Maximum size of group is      1 process(es).

>>This means that there were 12 XP groups and hence 12 XP master
>>processes. As requested, each XP master used 24 threads during
>>summation of XMCQDPT2 series, i.e., 288 threads in aggregate.
>>At the same time, there were only 56 cores available (again, this
>>number can be found in output). Use of 256 threads simultaneously
>>caused severe resource oversubscription resulting in serious
>>performance degradation. It would be much better to run this job
>>in parallel using e.g., 14 processes and requesting plain XP mode
>>with np=4 in $smp group. This would lead to 14*4 = 56 threads in
>>aggregate hence avoiding oversubscription and resulting in better
>>overall performance.

>>Hope this helps.

>>Kind regards,
>>Alex Granovsky
>>On Wed Mar 22 '17 11:15am, Dawid wrote
>>>Dear All,

>>>I have figured out how to do it.
>>>I attach my input file, so that others who struggle with this
>>>have a working example.

>>>By the way, I noticed that while the constraints generally work,
>>>the constrained dihedral somehow varies during optimization
>>>by less than 0.5 degrees. Is that related to the way the Z-matrix
>>>was automatically generated?

>>>Best wishes,
>>>Dawid Grabarek

>>>On Mon Mar 13 '17 11:49am, Dawid wrote
>>>>Dear Alex,

>>>>Thank you for helping me out with this.

>>>>Nevertheless, after all I have decided to do my constrained
>>>>optimization somehow different.
>>>>I'd like to provide the coordinates in XYZ format and constrain
>>>>one dihedral angle (torsion). My system blows up and I get
>>>>warnings on the singularity (if I understand it correctly) of the
>>>>G matrix.
>>>>Could you have one more look at my input and output, please?

>>>>Best wishes,
>>>>Dawid Grabarek
>>>>On Sat Mar 11 '17 8:30pm, Alex Granovsky wrote
>>>>>Dear Dawid,

>>>>>there are two errors in your original input file, the first is an
>>>>>extra line in the $DATA group and the second is too long input line
>>>>>in the $ZMT group (current limit is 80 symbols per line).

>>>>>I have attached fixed input file for your reference.

>>>>>Kind regards,
>>>>>Alex Granovsky
>>>>>On Thu Mar 9 '17 10:31pm, Dawid wrote
>>>>>>Dear Firefly Users,

>>>>>>I encounter issues with z-matrix definition in Firefly. I attach
>>>>>>my input and output files. Could you explain why I get this error,

>>>>>>Best wishes,

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