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Re^6: A VALUE WAS GIVEN FOR A VARIABLE H NOT FOUND IN THE Z-MATRIX

Alex Granovsky
gran@classic.chem.msu.su


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

 $zmat
  ifzmat(1)=4,3,2,6,7
 $end

there should be

 $zmat
  ifzmat(1)=3,3,2,6,7
 $end

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,
>>>>>>please?

>>>>>>Best wishes,
>>>>>>Dawid


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