[CP2K:2449] Optimized atomic coordinates have been changed
Teodoro Laino
teodor... at gmail.com
Mon Dec 7 14:01:47 UTC 2009
Dear ?,
please check:
http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/QMMM.html#desc_NOCENTER
and also:
http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/QMMM.html#desc_NOCENTER0
if you know what you are doing you can entirely disable the centering ....
Teo
Nguyen Ngoc Ha wrote:
> Dear CP2K Users,
> I have a problem that needs help,
> The optimized atomic coordinates after using optimizations in QMMM
> have been changed, so I can not use these for the next calculations
> such as NEB (I think these new coordinates aren't suitable with the
> old coordinate system). This problem does not occour in QM or MM
> calculations.
> Please note that the atomic coordinates change very far from the
> starting coordinates, so it's different by relax calculations. Here is
> an example:
>
> Before
> &COORD
> Nb 0.00000000 0.00000000 1.65025726
> Nb 0.00000000 0.00000000 4.95077177
> Nb 0.00000000 0.00000000 8.25158481
> Nb 0.00000000 0.00000000 11.55209932
> Nb 0.00000000 0.00000000 14.85261383
> Nb 1.65030000 1.65030000 0.00000000
> Nb 1.65030000 1.65030000 3.30051451
> Nb 1.65030000 1.65030000 6.60132755
> Nb 1.65030000 1.65030000 9.90184206
> Nb 1.65030000 1.65030000 13.20235657
> Nb 3.30060000 0.00000000 1.65025726
> Nb 3.30060000 0.00000000 4.95077177
> Nb 3.30060000 0.00000000 8.25158481
> Nb 3.30060000 0.00000000 11.55209932
> Nb 3.30060000 0.00000000 14.85261383
> Nb 4.95090000 1.65030000 0.00000000
> Nb 4.95090000 1.65030000 3.30051451
> Nb 4.95090000 1.65030000 6.60132755
> Nb 4.95090000 1.65030000 9.90184206
> Nb 4.95090000 1.65030000 13.20235657
> Nb 6.60120000 0.00000000 1.65025726
> Nb 6.60120000 0.00000000 4.95077177
> Nb 6.60120000 0.00000000 8.25158481
> Nb 6.60120000 0.00000000 11.55209932
> Nb 6.60120000 0.00000000 14.85261383
> Nb 8.25150000 1.65030000 0.00000000
> Nb 8.25150000 1.65030000 3.30051451
> Nb 8.25150000 1.65030000 6.60132755
> Nb 8.25150000 1.65030000 9.90184206
> Nb 8.25150000 1.65030000 13.20235657
> Nb 0.00000000 3.30060000 1.65025726
> Nb 0.00000000 3.30060000 4.95077177
> Nb 0.00000000 3.30060000 8.25158481
> Nb 0.00000000 3.30060000 11.55209932
> Nb 0.00000000 3.30060000 14.85261383
> Nb 1.65030000 4.95090000 0.00000000
> Nb 1.65030000 4.95090000 3.30051451
> Nb 1.65030000 4.95090000 6.60132755
> Nb 1.65030000 4.95090000 9.90184206
> Nb 1.65030000 4.95090000 13.20235657
> Nb 3.30060000 3.30060000 1.65025726
> Nb 3.30060000 3.30060000 4.95077177
> Nb 3.30060000 3.30060000 8.25158481
> Nb 3.30060000 3.30060000 11.55209932
> Nb 3.30060000 3.30060000 14.85261383
> Nb 4.95090000 4.95090000 0.00000000
> Nb 4.95090000 4.95090000 3.30051451
> Nb 4.95090000 4.95090000 6.60132755
> Nb 4.95090000 4.95090000 9.90184206
> Nb 4.95090000 4.95090000 13.20235657
> Nb 6.60120000 3.30060000 1.65025726
> Nb 6.60120000 3.30060000 4.95077177
> Nb 6.60120000 3.30060000 8.25158481
> Nb 6.60120000 3.30060000 11.55209932
> Nb 6.60120000 3.30060000 14.85261383
> Nb 8.25150000 4.95090000 0.00000000
> Nb 8.25150000 4.95090000 3.30051451
> Nb 8.25150000 4.95090000 6.60132755
> Nb 8.25150000 4.95090000 9.90184206
> Nb 8.25150000 4.95090000 13.20235657
> Nb 0.00000000 6.60120000 1.65025726
> Nb 0.00000000 6.60120000 4.95077177
> Nb 0.00000000 6.60120000 8.25158481
> Nb 0.00000000 6.60120000 11.55209932
> Nb 0.00000000 6.60120000 14.85261383
> Nb 1.65030000 8.25150000 0.00000000
> Nb 1.65030000 8.25150000 3.30051451
> Nb 1.65030000 8.25150000 6.60132755
> Nb 1.65030000 8.25150000 9.90184206
> Nb 1.65030000 8.25150000 13.20235657
> Nb 3.30060000 6.60120000 1.65025726
> Nb 3.30060000 6.60120000 4.95077177
> Nb 3.30060000 6.60120000 8.25158481
> Nb 3.30060000 6.60120000 11.55209932
> Nb 3.30060000 6.60120000 14.85261383
> Nb 4.95090000 8.25150000 0.00000000
> Nb 4.95090000 8.25150000 3.30051451
> Nb 4.95090000 8.25150000 6.60132755
> Nb 4.95090000 8.25150000 9.90184206
> Nb 4.95090000 8.25150000 13.20235657
> Nb 6.60120000 6.60120000 1.65025726
> Nb 6.60120000 6.60120000 4.95077177
> Nb 6.60120000 6.60120000 8.25158481
> Nb 6.60120000 6.60120000 11.55209932
> Nb 6.60120000 6.60120000 14.85261383
> Nb 8.25150000 8.25150000 0.00000000
> Nb 8.25150000 8.25150000 3.30051451
> Nb 8.25150000 8.25150000 6.60132755
> Nb 8.25150000 8.25150000 9.90184206
> Nb 8.25150000 8.25150000 13.20235657
> N 5.52104564 5.04991800 15.48250580
> N 4.12103014 5.04991800 15.48250580
> &END COORD
>
> after (from optimized xyz output file)
> Nb 0.8251500000 0.8251500000 -5.8670465634
> Nb 0.8251499993 0.8251500015 -2.5665296526
> Nb 0.8251500063 0.8251499973 0.7342836783
> Nb 0.8123579681 0.8353539813 4.2099471157
> Nb 0.8356608250 0.8245097295 7.1673515290
> Nb 2.4754500000 2.4754500000 -7.5175897014
> Nb 2.4754500000 2.4754500000 -4.2167848953
> Nb 2.4754499995 2.4754499998 -0.9159750826
> Nb 2.4754503196 2.4754499612 2.3845651850
> Nb 2.4708986253 2.4615001238 5.6811562694
> Nb 4.1257500000 0.8251500000 -5.8670465634
> Nb 4.1257499996 0.8251499998 -2.5665296519
> Nb 4.1257499978 0.8251499982 0.7342837827
> Nb 4.1213910285 0.8286426378 4.2286067256
> Nb 4.1016477077 0.8285162555 7.1369486254
> Nb 5.7760500000 2.4754500000 -7.5175897014
> Nb 5.7760500000 2.4754500000 -4.2167848953
> Nb 5.7760499995 2.4754500006 -0.9159750835
> Nb 5.7760507186 2.4754479180 2.3845637483
> Nb 5.7654732846 2.4794787037 5.6832360567
> Nb 7.4263500000 0.8251500000 -5.8670465651
> Nb 7.4263499998 0.8251499994 -2.5665296520
> Nb 7.4263500035 0.8251499970 0.7342838223
> Nb 7.4264152165 0.8344101946 4.2366328595
> Nb 7.4515742620 0.8250619517 7.1141506280
> Nb 9.0766500000 2.4754500000 -7.5175897014
> Nb 9.0766500000 2.4754500000 -4.2167848953
> Nb 9.0766500007 2.4754499999 -0.9159750830
> Nb 9.0766490529 2.4754510187 2.3845645571
> Nb 9.1026727428 2.4693423063 5.6778675657
> Nb 0.8251500000 4.1257500000 -5.8670465634
> Nb 0.8251500010 4.1257499986 -2.5665296534
> Nb 0.8251499970 4.1257499962 0.7342837290
> Nb 0.8283255384 4.1273166509 4.2249050298
> Nb 0.8113190443 4.0934660592 7.1430749593
> Nb 2.4754500000 5.7760500000 -7.5175897014
> Nb 2.4754500000 5.7760500000 -4.2167848952
> Nb 2.4754500000 5.7760500007 -0.9159750830
> Nb 2.4754505444 5.7760488745 2.3845649344
> Nb 2.4578659359 5.7638915779 5.6677733476
> Nb 4.1257500000 4.1257500000 -5.8670465634
> Nb 4.1257499992 4.1257499985 -2.5665296532
> Nb 4.1257499926 4.1257500031 0.7342836836
> Nb 4.1416937252 4.1106849618 4.2228586826
> Nb 4.0656317369 4.1130240314 7.2010521301
> Nb 5.7760500000 5.7760500000 -7.5175897014
> Nb 5.7760500000 5.7760500000 -4.2167848953
> Nb 5.7760500002 5.7760500004 -0.9159750826
> Nb 5.7760492288 5.7760507802 2.3845648495
> Nb 5.7939227293 5.7912040647 5.6996966668
> Nb 7.4263500000 4.1257500000 -5.8670465634
> Nb 7.4263500000 4.1257500001 -2.5665296518
> Nb 7.4263500013 4.1257500029 0.7342837053
> Nb 7.4202243288 4.1224963845 4.2228097985
> Nb 7.4179769805 4.1822175808 7.2374981397
> Nb 9.0766500000 5.7760500000 -7.5175897014
> Nb 9.0766500000 5.7760500000 -4.2167848952
> Nb 9.0766499995 5.7760500005 -0.9159750824
> Nb 9.0766517495 5.7760488817 2.3845640475
> Nb 9.0801281845 5.7738951645 5.6835237529
> Nb 0.8251500000 7.4263500000 -5.8670465651
> Nb 0.8251500000 7.4263499998 -2.5665296517
> Nb 0.8251499983 7.4263500016 0.7342838042
> Nb 0.8280100427 7.4304570507 4.2313037776
> Nb 0.8285053370 7.4409238024 7.1384715752
> Nb 2.4754500000 9.0766500000 -7.5175897014
> Nb 2.4754500000 9.0766500000 -4.2167848953
> Nb 2.4754500003 9.0766499999 -0.9159750813
> Nb 2.4754477665 9.0766520816 2.3845637554
> Nb 2.4505990800 9.1089171043 5.6700465122
> Nb 4.1257500000 7.4263500000 -5.8670465634
> Nb 4.1257500014 7.4263499994 -2.5665296526
> Nb 4.1257500034 7.4263499976 0.7342835766
> Nb 4.1115065181 7.4433918907 4.2167382010
> Nb 3.9303675378 7.6032411590 7.1899251620
> Nb 5.7760500000 9.0766500000 -7.5175897014
> Nb 5.7760500000 9.0766500000 -4.2167848952
> Nb 5.7760499993 9.0766499993 -0.9159750830
> Nb 5.7760511963 9.0766514810 2.3845650320
> Nb 5.7697189770 9.0921834619 5.6653522883
> Nb 7.4263500000 7.4263500000 -5.8670465634
> Nb 7.4263499989 7.4263500009 -2.5665296531
> Nb 7.4263499942 7.4263500002 0.7342835642
> Nb 7.4378835622 7.4237753897 4.2139845010
> Nb 7.4900855107 7.4349359208 7.2348039994
> Nb 9.0766500000 9.0766500000 -7.5175897014
> Nb 9.0766500000 9.0766500000 -4.2167848953
> Nb 9.0766500002 9.0766499999 -0.9159750828
> Nb 9.0766505309 9.0766508448 2.3845649991
> Nb 9.0953603997 9.0977769622 5.6816232514
> N 6.1540341268 5.9617179215 8.1146201413
> N 4.8786820062 5.9623145044 8.1356065389
>
> PS: I have turned on or off NOCENTER but the same result.
>
> Best regards,
>
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