Optimized atomic coordinates have been changed
Nguyen Ngoc Ha
ha... at hnue.edu.vn
Mon Dec 7 13:56:46 UTC 2009
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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