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Re^5: A VALUE WAS GIVEN FOR A VARIABLE H NOT FOUND IN THE Z-MATRIX

Dawid
dawid.grabarek@pwr.edu.pl


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

This message contains the 28330 kb attachment
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