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Masoud Nahali
masoudnahali@gmail.com

The DLCTOL keyword was not helpful !


On Mon Feb 7 '11 6:21pm, Luca Maidich wrote
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>Dear Masoud,
>as a preamble I have to tell you that I've never worked on adsorption problems so I cannot answer to your question about the physics of connecting atoms by NONVDW.

>Anyway the question about the linear dependence of the coordinates I think could possibly be solved applying more strict criteria on the generation of DLC using DLCTOL=1e-X keyword in $ZMAT group, where X is an integer greater than 5.

>Hope this could be useful,
>Regards
>Luca Maidich

>On Mon Feb 7 '11 5:38pm, Masoud Nahali wrote
>--------------------------------------------
>>Dear Firefly Users

>>I am studying the molecular oxygen adsorption on some surfaces; and in my input file the distance between the oxygen and the surface atoms is about 3.5 angstrom. I get the below error when I run the job :

>>----------
>>ERROR: BAD DELOCALIZED COORDINATES GENERATED!!!
>>        922 PRIMITIVE INTERNAL COORDINATES ARE BEING USED.
>>        361 LINEARLY INDEPENDENT COMBINATIONS OF THESE ARE FOUND.
>>        366 COORDINATES ARE NEEDED TO HAVE A TOTAL OF 3N-6.

>> IF THE NUMBER OF LINEARLY INDEPENDENT COOORDS IS TOO SMALL,
>> ADD SOME COORDINATES BY -NONVDW- TO CONNECT MONOMER PIECES
>> (ESPECIALLY IF YOU ARE SHORT BY A MULTIPLE OF 6), OR ELSE
>> USE -IXZMAT- TO ADD EXTRA PRIMITIVE COORDINATES.

>> IF THE NUMBER OF LINEARLY INDEPENDENT COOORDS IS TOO BIG,
>> TRY USING -IRZMAT- TO REMOVE SOME PRIMITIVE COORDINATES.
>>----------

>> It seems that I should connect the oxygen to the surface by NONVDW command but I could not find any documentation to guide me how to do it. How can I connect two atoms by NONVDW ? what is the physics of this work ?
>>Also, I do not want to enforce the oxygen to be adsorbed on some specified atoms (may be specified by NONVWD). Oxygen should choose any atoms through optimization procedure.

>>This is my input file commands :

>> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE DFTTYP=B3LYP ECP=read MAXIT=350 MULT=1
>> ICHARG=0 COORD=unique d5=.t. NZVAR=366 $END
>> $SYSTEM TIMLIM=600000 MWORDS=200 $END
>> $SCF DIRSCF=.TRUE. NCONV=5 $END
>> $STATPT OPTTOL=0.0001 NSTEP=150 $END
>> $zmat dlc=.true. auto=.true. $end
>>! to activate P2P inteface and DLB:
>> $P2P P2P=.T. DLB=.T. $END
>>! to speed up Huckel guess:
>> $GUESS guess=HUCKEL $END
>> $smp call64=.t. mkl64=8 load=0 ssg32=0 msu32=0 mkllvl=3 $end
>> $BASIS gbasis=LANL2DZ extfil=.t. $END  

>>I appreciate your help in advance.

>> Best Wishes

>> Masoud
>>--------------
>>Masoud Nahali, Sharif University of Technology
>>