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,



More information about the CP2K-user mailing list