[gpaw-users] Shift in the coordinates

Daniel Torres d.torres.rangel at gmail.com
Wed Apr 14 21:35:52 CEST 2010 

Hi guys,
I noticed that sometimes the atomic coordinates from the imput file (python 
file) and the coordinates in the txt file (output file) are not the same and 
I was wondering why.
As an example. In the attached py file, the first atom Ni has coordinates
Atom('Ni',(-1.0527,2.0821,17.0359),magmom=1.0),
while in the txt file says
  0 Ni   -1.0527    2.0821   13.4510
what is the reason of this shift?
Thanks and best regards
Dani
-------------- next part --------------
#!/usr/bin/env python
from ase import *
from gpaw import*


a=2*5.8776599999999997
b=2*5.6615700000000002
L=26.0000000000000000

bulk = Atoms([
Atom('Ni',(-1.0527,2.0821,17.0359),magmom=1.0),
Atom('Ni',(1.3186,2.3110,16.9651),magmom=1.0),
Atom('Ni',(-0.0903,4.1794,16.8498),magmom=1.0),
Atom('Ni',(-0.0028,2.8824,18.8402),magmom=1.0),
Atom('C',(-0.0376,2.8430,20.4907),magmom=0.0),
Atom('O',(-0.0376,2.8430,22.0000),magmom=0.0),
Atom('Al',(0.6710,0.6214,15.0542),magmom=0.0),
Atom('Al',(6.5853,0.7052,14.9331),magmom=0.0),
Atom('Al',(0.7636,6.4420,14.9321),magmom=0.0),
Atom('Al',(6.5994,6.3540,14.9538),magmom=0.0),
Atom('Al',(3.7044,0.6743,14.9473),magmom=0.0),
Atom('Al',(9.4428,0.5961,14.8628),magmom=0.0),
Atom('Al',(3.6821,6.3860,14.9445),magmom=0.0),
Atom('Al',(9.5147,6.4002,14.9514),magmom=0.0),
Atom('Al',(5.1319,3.5232,14.3507),magmom=0.0),
Atom('Al',(11.0203,3.5247,14.3888),magmom=0.0),
Atom('Al',(5.1405,9.1782,14.3402),magmom=0.0),
Atom('Al',(11.0062,9.1671,14.3236),magmom=0.0),
Atom('Al',(2.1812,3.5655,14.4039),magmom=0.0),
Atom('Al',(8.0790,3.5208,14.3634),magmom=0.0),
Atom('Al',(2.2033,9.2078,14.3440),magmom=0.0),
Atom('Al',(8.0591,9.1593,14.3364),magmom=0.0),
Atom('O',(5.1525,1.9265,15.2082),magmom=0.0),
Atom('O',(10.8533,1.8348,15.0486),magmom=0.0),
Atom('O',(5.1441,7.6044,15.2194),magmom=0.0),
Atom('O',(11.0146,7.6074,15.2073),magmom=0.0),
Atom('O',(2.3303,1.9678,15.2956),magmom=0.0),
Atom('O',(8.0538,1.9127,15.2099),magmom=0.0),
Atom('O',(2.2148,7.6417,15.2309),magmom=0.0),
Atom('O',(8.0674,7.6024,15.2375),magmom=0.0),
Atom('O',(5.1345,5.1277,15.2011),magmom=0.0),
Atom('O',(11.0136,5.1844,15.2321),magmom=0.0),
Atom('O',(5.1371,10.7692,15.1983),magmom=0.0),
Atom('O',(10.9552,10.7337,15.1918),magmom=0.0),
Atom('O',(2.2086,5.1912,15.1984),magmom=0.0),
Atom('O',(8.0800,5.1279,15.2143),magmom=0.0),
Atom('O',(2.1949,10.7986,15.1972),magmom=0.0),
Atom('O',(8.0210,10.7476,15.1848),magmom=0.0),
Atom('O',(0.7302,3.5027,13.3409),magmom=0.0),
Atom('O',(6.6102,3.5122,13.3168),magmom=0.0),
Atom('O',(0.7338,9.1668,13.3078),magmom=0.0),
Atom('O',(6.6023,9.1639,13.2974),magmom=0.0),
Atom('O',(3.6463,3.5173,13.3311),magmom=0.0),
Atom('O',(9.5509,3.5437,13.3271),magmom=0.0),
Atom('O',(3.6700,9.1779,13.3074),magmom=0.0),
Atom('O',(9.5286,9.1600,13.3012),magmom=0.0),
Atom('O',(0.7264,0.7236,13.1544),magmom=0.0),
Atom('O',(6.5996,0.7177,13.0729),magmom=0.0),
Atom('O',(0.7285,6.3957,13.0858),magmom=0.0),
Atom('O',(6.6104,6.3862,13.0964),magmom=0.0),
Atom('O',(3.6630,0.7290,13.0998),magmom=0.0),
Atom('O',(9.4967,0.6785,13.0305),magmom=0.0),
Atom('O',(3.6647,6.3992,13.0880),magmom=0.0),
Atom('O',(9.5481,6.3935,13.0988),magmom=0.0),
Atom('Al',(5.1230,0.6882,12.0931),magmom=0.0),
Atom('Al',(11.0200,0.6892,12.1242),magmom=0.0),
Atom('Al',(5.1384,6.3554,12.1026),magmom=0.0),
Atom('Al',(11.0117,6.3589,12.0934),magmom=0.0),
Atom('Al',(2.1801,0.6900,12.1279),magmom=0.0),
Atom('Al',(8.0396,0.6781,12.0318),magmom=0.0),
Atom('Al',(2.1994,6.3555,12.0887),magmom=0.0),
Atom('Al',(8.0777,6.3528,12.0998),magmom=0.0),
Atom('Al',(0.7291,3.5775,11.3959),magmom=0.0),
Atom('Al',(6.6054,3.5861,11.3863),magmom=0.0),
Atom('Al',(0.7334,9.2455,11.3730),magmom=0.0),
Atom('Al',(6.5982,9.2289,11.3653),magmom=0.0),
Atom('Al',(3.6633,3.5796,11.3972),magmom=0.0),
Atom('Al',(9.5467,3.5869,11.3924),magmom=0.0),
Atom('Al',(3.6681,9.2449,11.3719),magmom=0.0),
Atom('Al',(9.5427,9.2474,11.3698),magmom=0.0),
Atom('O',(5.1359,4.7789,11.3032),magmom=0.0),
Atom('O',(11.0206,4.7823,11.2970),magmom=0.0),
Atom('O',(5.1364,10.4400,11.2802),magmom=0.0),
Atom('O',(11.0249,10.4389,11.3033),magmom=0.0),
Atom('O',(2.1963,4.7790,11.2919),magmom=0.0),
Atom('O',(8.0809,4.7837,11.2888),magmom=0.0),
Atom('O',(2.2023,10.4469,11.2938),magmom=0.0),
Atom('O',(8.0581,10.4210,11.2475),magmom=0.0),
Atom('O',(5.1419,2.2496,11.1818),magmom=0.0),
Atom('O',(11.0304,2.2481,11.1991),magmom=0.0),
Atom('O',(5.1440,7.9049,11.1729),magmom=0.0),
Atom('O',(11.0203,7.9101,11.1743),magmom=0.0),
Atom('O',(2.2007,2.2434,11.1913),magmom=0.0),
Atom('O',(8.0776,2.2604,11.1699),magmom=0.0),
Atom('O',(2.2071,7.9110,11.1726),magmom=0.0),
Atom('O',(8.0810,7.8998,11.1705),magmom=0.0)
#Atom('O',(0.7353,3.4131,9.3660),magmom=0.0),
#Atom('O',(6.6107,3.4167,9.3607),magmom=0.0),
#Atom('O',(0.7371,9.0808,9.3642),magmom=0.0),
#Atom('O',(6.6092,9.0686,9.3536),magmom=0.0),
#Atom('O',(3.6757,3.4132,9.3662),magmom=0.0),
#Atom('O',(9.5594,3.4145,9.3666),magmom=0.0),
#Atom('O',(3.6755,9.0761,9.3604),magmom=0.0),
#Atom('O',(9.5597,9.0791,9.3633),magmom=0.0),
#Atom('O',(0.7375,0.8824,9.2691),magmom=0.0),
#Atom('O',(6.6158,0.8825,9.2839),magmom=0.0),
#Atom('O',(0.7372,6.5448,9.2731),magmom=0.0),
#Atom('O',(6.6136,6.5411,9.2727),magmom=0.0),
#Atom('O',(3.6790,0.8834,9.2719),magmom=0.0),
#Atom('O',(9.5521,0.8826,9.2763),magmom=0.0),
#Atom('O',(3.6767,6.5428,9.2732),magmom=0.0),
#Atom('O',(9.5566,6.5445,9.2721),magmom=0.0),
#Atom('Al',(5.1466,2.0800,9.1563),magmom=0.0),
#Atom('Al',(11.0268,2.0753,9.1582),magmom=0.0),
#Atom('Al',(5.1471,7.7343,9.1510),magmom=0.0),
#Atom('Al',(11.0256,7.7389,9.1551),magmom=0.0),
#Atom('Al',(2.2089,2.0741,9.1557),magmom=0.0),
#Atom('Al',(8.0855,2.0832,9.1494),magmom=0.0),
#Atom('Al',(2.2087,7.7356,9.1536),magmom=0.0),
#Atom('Al',(8.0862,7.7325,9.1554),magmom=0.0),
#Atom('Al',(0.7380,4.9749,8.4467),magmom=0.0),
#Atom('Al',(6.6156,4.9771,8.4441),magmom=0.0),
#Atom('Al',(0.7389,10.6393,8.4412),magmom=0.0),
#Atom('Al',(6.6159,10.6393,8.4494),magmom=0.0),
#Atom('Al',(3.6767,4.9744,8.4475),magmom=0.0),
#Atom('Al',(9.5565,4.9760,8.4471),magmom=0.0),
#Atom('Al',(3.6789,10.6400,8.4441),magmom=0.0),
#Atom('Al',(9.5538,10.6400,8.4423),magmom=0.0),
#Atom('O',(5.1453,4.9504,7.4510),magmom=0.0),
#Atom('O',(11.0242,4.9512,7.4497),magmom=0.0),
#Atom('O',(5.1487,10.6130,7.4506),magmom=0.0),
#Atom('O',(11.0235,10.6131,7.4488),magmom=0.0),
#Atom('O',(2.2077,4.9510,7.4512),magmom=0.0),
#Atom('O',(8.0865,4.9500,7.4519),magmom=0.0),
#Atom('O',(2.2092,10.6129,7.4494),magmom=0.0),
#Atom('O',(8.0829,10.6137,7.4507),magmom=0.0),
#Atom('O',(5.1468,2.1505,7.2289),magmom=0.0),
#Atom('O',(11.0227,2.1503,7.2295),magmom=0.0),
#Atom('O',(5.1452,7.8118,7.2284),magmom=0.0),
#Atom('O',(11.0239,7.8133,7.2289),magmom=0.0),
#Atom('O',(2.2076,2.1504,7.2278),magmom=0.0),
#Atom('O',(8.0841,2.1508,7.2280),magmom=0.0),
#Atom('O',(2.2064,7.8121,7.2290),magmom=0.0),
#Atom('O',(8.0855,7.8115,7.2300),magmom=0.0),
#Atom('Al',(0.7382,2.1351,6.1886),magmom=0.0),
#Atom('Al',(6.6155,2.1350,6.1865),magmom=0.0),
#Atom('Al',(0.7384,7.7964,6.1873),magmom=0.0),
#Atom('Al',(6.6167,7.7965,6.1897),magmom=0.0),
#Atom('Al',(3.6783,2.1348,6.1878),magmom=0.0),
#Atom('Al',(9.5558,2.1351,6.1876),magmom=0.0),
#Atom('Al',(3.6773,7.7961,6.1885),magmom=0.0),
#Atom('Al',(9.5553,7.7962,6.1885),magmom=0.0),
#Atom('Al',(5.1480,4.9612,5.5882),magmom=0.0),
#Atom('Al',(11.0258,4.9608,5.5862),magmom=0.0),
#Atom('Al',(5.1486,10.6218,5.5874),magmom=0.0),
#Atom('Al',(11.0259,10.6224,5.5862),magmom=0.0),
#Atom('Al',(2.2099,4.9608,5.5868),magmom=0.0),
#Atom('Al',(8.0871,4.9611,5.5876),magmom=0.0),
#Atom('Al',(2.2099,10.6226,5.5862),magmom=0.0),
#Atom('Al',(8.0864,10.6220,5.5863),magmom=0.0),
#Atom('O',(0.7358,0.5383,5.3387),magmom=0.0),
#Atom('O',(6.6136,0.5381,5.3381),magmom=0.0),
#Atom('O',(0.7362,6.1998,5.3373),magmom=0.0),
#Atom('O',(6.6138,6.2000,5.3395),magmom=0.0),
#Atom('O',(3.6754,0.5379,5.3384),magmom=0.0),
#Atom('O',(9.5518,0.5381,5.3389),magmom=0.0),
#Atom('O',(3.6750,6.1999,5.3378),magmom=0.0),
#Atom('O',(9.5521,6.2000,5.3374),magmom=0.0),
#Atom('O',(0.7449,3.7276,5.3279),magmom=0.0),
#Atom('O',(6.6227,3.7281,5.3282),magmom=0.0),
#Atom('O',(0.7451,9.3895,5.3272),magmom=0.0),
#Atom('O',(6.6230,9.3886,5.3284),magmom=0.0),
#Atom('O',(3.6842,3.7276,5.3276),magmom=0.0),
#Atom('O',(9.5608,3.7276,5.3276),magmom=0.0),
#Atom('O',(3.6838,9.3889,5.3284),magmom=0.0),
#Atom('O',(9.5608,9.3892,5.3280),magmom=0.0)
] ,
            cell=(a,b,L),
            pbc=(True, True, True),
            constraint=FixAtoms(range(-32))   )
#           constraint=FixAtoms(range(-64))   )
bulk.center(axis=2)
#calc = GPAW(nbands= 900 ,
calc = GPAW(nbands= -10 ,
               xc='RPBE',
               spinpol=True,
               mixer=MixerSum(0.1, 5,  100.0),
               maxiter=120,
               kpts=(1,1,1),
               h=0.20,
               width=0.1,
               txt='slab.txt')
bulk.set_calculator(calc)
traj = PickleTrajectory('cell.traj', 'w', bulk)
relax = QuasiNewton(bulk)
relax.attach(traj)
relax.run(fmax=0.01)
energy = bulk.get_potential_energy()

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