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GAMESS computing and quantum chemistry

  1. Sep 29, 2015 #1
    Hi everyone, this isn't homework problem but something i would like to study and i am currently interested into. So how to start, this problem belongs more to quantum chemistry but i haven't found the topic in chemistry part of this site. I am learning to compute with program GAMESS but since its more like off-school work i dont have as much time as i would like to have, i ecountered a problem when i tried to freez a dihedral angle of my molecule which i am trying to optimize. If someone uses this program, could you tell me, should i use function ifzmat or ifreeze?
    With ifzmat i had problem cause the function has to be set with a number in brackets for example: ifzmat(1): 1, 1, 3. I dont really understand the number in brackets, what does it mean? and if the numbers after it should be coordinates to freez, why is there twice 1 (i know it doesn't have to be but i found this in example on the internet)
    When i discussed this with my lector, we couldn't find answer and decided to use function ifreeze which we wrote down as ifreeze: 33 since the coordinate we needed to freeze was 33rd, i will try to copy the input,


    $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT $END
    $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
    $STATPT IFREEZ=33 NSTEP=200 $END
    $DATA
    PHENYLTIOPHENE
    C1
    H1
    C1 1 1.0752332
    C2 2 1.3856673 1 120.2300232
    C3 2 1.3850981 1 120.2390998 3 -179.8082788
    C4 3 1.3837972 2 120.2531929 1 -179.6736029
    C5 4 1.3843858 2 120.2888343 1 -179.8985509
    C6 5 1.3932995 3 120.6779238 2 -0.6189671
    H2 3 1.0754326 2 120.0994626 1 -0.3675182
    H3 4 1.0753420 2 120.1081738 1 -0.3449202
    H4 5 1.0746626 3 119.7871759 2 178.2742561
    H5 6 1.0749846 4 119.5814726 2 178.7535613
    C7 7 1.4791299 5 120.0810730 3 -179.0096901
    C8 12 1.3509983 7 127.8399432 5 20.0000000
    C9 13 1.4342716 12 113.4248345 7 -179.7625624
    C10 14 1.3442719 13 112.5947283 12 -0.0544747
    S1 12 1.7399634 13 110.4766327 14 -0.2157713
    H6 13 1.0737231 12 123.0822795 16 -178.6611354
    H7 14 1.0735350 13 123.6537119 12 -179.5677157
    H8 15 1.0709858 14 127.9105249 13 -179.8643985
    $END
    ~
    okay so this is it, this input was working and program was running, i thought the output was just what i needed but when I tried to compute energy of this molecule i found that final Z matrix didn't have that coordinate frozen as i was expecting, we are taliking exactly about this line C8 12 1.3509983 7 127.8399432 5 20.0000000
    and the number that needs to be set is those 20°, it represents the dihedral angle of my molecule, Phenyltoiophene. In the final Z matrix in output it gets to something around 39° (as when optimizing without that freeze function). So the final question is, how do I set the input so i can have that angle frozen, are the numbers behind ifzmat exact coordinates of molecules that are influenced with this dihedral angle and finally, what does that number in the brackets mean? This is it, i hope i haven't forgotten to add anything and thanks in advance, its my first time on this site.
     
  2. jcsd
  3. Sep 30, 2015 #2

    DrDu

    User Avatar
    Science Advisor

    It has been eons since I used gamess, so I can't answer your questions in depth. ifzmat(1): 1, 1, 3 Here, the first one means that the internal coordinate is a bond length between atoms 1 and 3. 2 would be a bond angle between the following 3 atoms and 3 a torsion between the following 4 atoms. The (1) is, I guess, fortran style, to start to write to the array ifzmat in the 1st cell. To use ifreez, I would guess that you have to define a z-matrix explicitly. So the ifzmat command is probably the easiest way to go: ifzmat(1) 3 8 12 7 5
     
    Last edited: Sep 30, 2015
  4. Oct 5, 2015 #3
    Hi! I know i am answering bit late, but i think it needs to be said how it did work out in the end. I have tried to use ifzmat as you adviced me and i believe there was no mistake in input, but it just wouldn't work! It always came up with an error, for example:

    ERROR *** ATTEMPTING A BOGUS READ OF A DAF RECORD.
    RECORD NUMBER 39 OF LENGTH 0 HAS NO LENGTH.

    THIS ERROR IS LIKELY TO BE A BUG IN THE PROGRAM, BUT
    PLEASE CONSIDER INPUT ERRORS AS A POSSIBLE CAUSE, TOO.
    MANUAL CHAPTER -PROG.DOC- HAS A LIST OF ALL DIRECT ACCESS FILE RECORD NUMBERS,
    WHICH WILL HELP YOU UNDERSTAND WHAT THE INCORRECT DATA IS SUPPOSED TO BE.

    EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed Sep 30 23:59:40 2015
    440000 WORDS OF DYNAMIC MEMORY USED
    STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
    TOTAL WALL CLOCK TIME= 0.3 SECONDS, CPU UTILIZATION IS 14.29%
    A fatal error occurred on DDI Process 0.
    ddikick.x: application process 0 quit unexpectedly.
    ddikick.x: Fatal error detected.

    etc.

    or this one:
    ...COORD TYPE I J K L M N
    INTERNAL COORD. 1 AT SUBSCRIPT 1 IS OF ILLEGAL TYPE 0
    EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Fri Oct 2 10:33:44 2015
    440000 WORDS OF DYNAMIC MEMORY USED
    STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
    TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 25.00%
    A fatal error occurred on DDI Process 0.
    ddikick.x: application process 0 quit unexpectedly....


    In this case i have used izmat alongside ifzmat and we can see that in line COORD TYPE I J K L M N the gamess recognised (or it looks like it did) that there is something more to do with these coordinates, but failed to do so.

    I don't know what causes this and what does it mean at all, but i have managed to go by other way around, again by using ifreeze which was really easy to use in the end.
    All i had to do was to set NZVAR=51 (the number of coordinates) and then use ifreeze(1)=33. Which for gamess probably meant, "you have 51 coordinates, freeze 33rd one".

    So this problem is most likely solved and I am gonna write new post about using ifreeze for others to save time from endless googling that leads only to people with similiar problems but with no answers. But anyway, could you please send me any inputs where you have used ifzmat function if you still have any? I don't really like the idea of leaving this problem unanswered completely so I am gonna give it some more research.
     
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