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Alex Granovsky
gran@classic.chem.msu.su

>For my case, why did you suggest these two extra coordinate: IXZMAT(1)=4,4,2,3,1, 2,1,4,2? Are there any rules and rationales for designing them?

As I suggested these two extra coordinates I need to explain
my reasons.

Both of these coordinates was used to correct the deficiencies
of the automatically generated set of primitives i.e. to make
the set of primitives a well-defined one at all possible scan
geometries.
The first one is especially suitable to describe the out of
plane deformations of this molecule, in particular at geometries
where angular and torsion variables become ill-defined (i.e.
when angles become close to 0 or 180 degrees and/or when torsions
are formed by three or four atoms lying on a straight line).

The second one is needed because closer to the end of the
geometry scan one of automatically generated angles becomes
ill defined. This affects the completeness of the coordinate
set i.e. the Cartesian coordinates of atoms 4 and 2 cannot
be longer recovered using the information on internals.
To solve this problem, I added the well defined angle 1 - 4 - 2.

Hope this helps

Kind regards,
Alex Granovsky


On Mon Apr 15 '13 7:28pm, Patrick SK Pang wrote
-----------------------------------------------
>Dear Thomas,

>For my case, why did you suggest these two extra coordinate: IXZMAT(1)=4,4,2,3,1, 2,1,4,2? Are there any rules and rationales for designing them?

>Regards,

>Patrick

>On Sun Apr 14 '13 9:47pm, Thomas wrote
>--------------------------------------
>>Dear Patrick,

>>SCAN=.T. triggers the use of a specific scan engine that is designed to be used for scans in DLCs, and that is generally the most suitable for most types of scans. In other words, if you're performing a PES scan in DLCs, it is recommended to specify this keyword as .T.

>>IXZMAT can be used to specify an extra array of simple internal coordinates which you want to have added to the list generated by AUTO. Unlike NONVDW, IXZMAT will add only the coordinate(s) you specify. Its format is identical to that of IZMAT.
>>
>>
>>Kind regards,
>>Thom
>>
>>
>>
>>On Sat Apr 13 '13 8:25pm, Patrick SK Pang wrote
>>-----------------------------------------------
>>>Dear Alex,

>>>How to use the the keyword "scan"? I could not find this keyword in the manual "Firefly_input_rev002[1]".
>>>For IXZMAT, are there any rules for designing extra internal coordinates?

>>>Regards,

>>>Patrick

>>>On Sat Apr 13 '13 4:16pm, Alex Granovsky wrote
>>>----------------------------------------------
>>>>Dear Patrick,

>>>>another comment is that your input file is too complicated
>>>>in its part related to scan. One could use:

>>>>

 $ZMAT DLC=.T. AUTO=.T. $END
 $ZMAT IFZMAT(1)=1,1,3 SCAN=.T. $END
 $ZMAT NONVDW(1)=1,3 $END
 $ZMAT IXZMAT(1)=4,4,2,3,1, 2,1,4,2 $END

>>>>where two last lines are added to help Firefly creating good DLCs.

>>>>Kind regards,
>>>>Alex Granovsky
>>>>
>>>>
>>>>
>>>>On Thu Apr 11 '13 4:03pm, Patrick SK Pang wrote
>>>>-----------------------------------------------
>>>>>Dear all,

>>>>>During the PES calculation, an error occurred:
>>>>>*** ERROR ***
>>>>> THERE ARE NOT ENOUGH PRIMITIVE INTERNAL COORDINATES �= � �6
>>>>> SO THAT SUBTRACTING THE DESIRED NUMBER OF CONSTRAINTS= � �1
>>>>> LEAVES AT LEAST 3N-6= � �6 COORDINATES.
>>>>> THIS CONDITION IS LIKELY ONLY FOR VERY SMALL MOLECULES.
>>>>> A POSSIBLE CURE IS TO USE -NONVDW- INPUT TO ADD ANOTHER
>>>>> COORDINATE TO THE PRIMITIVE SET.

>>>>>How can I solve the problem? My input file is as follows.
>>>>> $CONTRL RUNTYP=RSURFACE $END
>>>>> $CONTRL SCFTYP=ROHF $END
>>>>> $CONTRL ICHARG=0 MULT=2 $END
>>>>> $CONTRL NZVAR=6 $END
>>>>> $ZMAT DLC=.T. AUTO=.T. $END
>>>>> $ZMAT NONVDW(1)=1,3 $END
>>>>> $ZMAT AUTOFV=.T. $END
>>>>> $ZMAT IFZMAT(1)=1,1,3 $END
>>>>> $SURF NDISP1=10 DISP1=0.1 IVEC1(1)=3,1 $END
>>>>> $SURF IGRP1(1)=1 ORIG1=0 $END
>>>>> $SURF REUSE=.T. $END
>>>>> $BASIS GBASIS=N31 NGAUSS=6 $END
>>>>> $BASIS NDFUNC=1 NPFUNC=1 $END
>>>>> $BASIS DIFFSP=.TRUE. DIFFS=.TRUE. $END
>>>>> $SYSTEM TIMLIM=10000 MWORDS=100 $END
>>>>> $P2P P2P=.T. DLB=.T. $END
>>>>> $STATPT NSTEP=200 METHOD=GDIIS $END
>>>>> $STATPT NOREG=5 $END
>>>>> $DATA
>>>>>Molecule specification
>>>>>C1
>>>>> H � � � � � 1.0 �-2.3435327563 �-1.4295899817 �-0.0238032723
>>>>> C � � � � � 6.0 �-0.9795164645 �-0.1539031417 �-0.0767996305
>>>>> O � � � � � 8.0 �-1.4047028866 �-1.3858686815 �-0.1806826770
>>>>> O � � � � � 8.0 �-1.5522821736 � 0.8327670425 � 0.1654033876
>>>>> $END

>>>>>Best regards,

>>>>>Patrick