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numat / RASPA2

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https://github.com/iraspa/RASPA2
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Seg fault that depends on number of atoms in .cif #20

Open CorySimon opened 8 years ago

CorySimon commented 8 years ago

Hi. I am simulating a CO2 adsorption isotherm and I'd like RASPA to pull the charges from the .cif, which are different from every atom. So, following the manual, I put in my simulation.input file:

UseChargesFromCIFFile yes
RemoveAtomNumberCodeFromLabel yes

Using the following .cif file, I do not get a seg fault and RASPA reads the charges appropriately.

data_KAXQIL-clean_labeled

_cell_length_a 5.567300
_cell_length_b 11.821400
_cell_length_c 22.760300
_cell_angle_alpha 100.355998
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
_cell_volume 1473.528419

_symmetry_space_group_name_H-M   'P 1'
_symmetry_Int_Tables_number 1

loop_
_symmetry_equiv_pos_as_xyz
 'x, y, z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Ca1 Ca 0.755850 0.636820 0.722870 1.0
H1 H 0.199600 0.194500 0.618900 1.0
C1 C 0.741400 0.004540 0.734890 0.0
S1 S 0.963630 0.398350 0.607680 -1.0
O1 O 0.805000 0.493100 0.630960 -1.0

However, when I use the exact same .cif file, except adding more atoms to the end, I receive a seg fault. Why would the seg fault depend on the number of atoms in the .cif file? Is there a limit to how many different atoms e.g. O12 that we can label differently? Thanks. Below is the .cif file that yields a seg fault.

UPDATE The seg fault goes away when I change the simulation.input to read:

UseChargesFromCIFFile no

and instead put charges in the pseudo_atoms.def file.

data_KAXQIL-clean_labeled

_cell_length_a 5.567300
_cell_length_b 11.821400
_cell_length_c 22.760300
_cell_angle_alpha 100.355998
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
_cell_volume 1473.528419

_symmetry_space_group_name_H-M   'P 1'
_symmetry_Int_Tables_number 1

loop_
_symmetry_equiv_pos_as_xyz
 'x, y, z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Ca1 Ca 0.755850 0.636820 0.722870 1.593783
Ca2 Ca 0.255850 0.863180 0.777130 1.593776
Ca3 Ca 0.244150 0.363180 0.277130 1.593783
Ca4 Ca 0.744150 0.136820 0.222870 1.593776
H1 H 0.199600 0.194500 0.618900 0.099731
H2 H 0.124900 0.231800 0.406100 0.115298
H3 H 0.554100 0.420600 0.537200 0.098276
H4 H 0.562300 0.338800 0.672900 0.102220
H5 H 0.478300 0.183900 0.719700 0.086178
H6 H 0.118600 0.043900 0.669100 0.107920
H7 H 0.206600 0.275100 0.507800 0.099698
H8 H 0.471300 0.373100 0.435800 0.094271
H9 H 0.699600 0.305500 0.881100 0.099731
H10 H 0.624900 0.268200 0.093900 0.115298
H11 H 0.054100 0.079400 0.962800 0.098276
H12 H 0.062300 0.161200 0.827100 0.102220
H13 H 0.978300 0.316100 0.780300 0.086178
H14 H 0.618600 0.456100 0.830900 0.107920
H15 H 0.706600 0.224900 0.992200 0.099698
H16 H 0.971300 0.126900 0.064200 0.094271
H17 H 0.800400 0.805500 0.381100 0.099731
H18 H 0.875100 0.768200 0.593900 0.115298
H19 H 0.445900 0.579400 0.462800 0.098276
H20 H 0.437700 0.661200 0.327100 0.102220
H21 H 0.521700 0.816100 0.280300 0.086178
H22 H 0.881400 0.956100 0.330900 0.107920
H23 H 0.793400 0.724900 0.492200 0.099698
H24 H 0.528700 0.626900 0.564200 0.094271
H25 H 0.300400 0.694500 0.118900 0.099731
H26 H 0.375100 0.731800 0.906100 0.115298
H27 H 0.945900 0.920600 0.037200 0.098276
H28 H 0.937700 0.838800 0.172900 0.102220
H29 H 0.021700 0.683900 0.219700 0.086178
H30 H 0.381400 0.543900 0.169100 0.107920
H31 H 0.293400 0.775100 0.007800 0.099698
H32 H 0.028700 0.873100 0.935800 0.094271
C1 C 0.741400 0.004540 0.734890 0.770321
C2 C 0.739300 0.276740 0.344930 0.753881
C3 C 0.890800 0.355060 0.531360 -0.212544
C4 C 0.889600 0.281060 0.642190 -0.226848
C5 C 0.056700 0.192960 0.639960 -0.035051
C6 C 0.011400 0.270250 0.432280 -0.051244
C7 C 0.792700 0.301280 0.410690 -0.111260
C8 C 0.668700 0.383440 0.510800 -0.030029
C9 C 0.672800 0.279490 0.671900 -0.016710
C10 C 0.624400 0.187240 0.700250 -0.049265
C11 C 0.007100 0.102620 0.669600 -0.058585
C12 C 0.061000 0.296550 0.493050 -0.037486
C13 C 0.791700 0.099820 0.699940 -0.108435
C14 C 0.620400 0.355460 0.450210 -0.036560
C15 C 0.241400 0.495460 0.765110 0.770321
C16 C 0.239300 0.223260 0.155070 0.753880
C17 C 0.390800 0.144940 0.968640 -0.212544
C18 C 0.389600 0.218940 0.857810 -0.226848
C19 C 0.556700 0.307040 0.860040 -0.035051
C20 C 0.511400 0.229750 0.067720 -0.051244
C21 C 0.292700 0.198720 0.089310 -0.111260
C22 C 0.168700 0.116560 0.989200 -0.030029
C23 C 0.172800 0.220510 0.828100 -0.016710
C24 C 0.124400 0.312760 0.799750 -0.049265
C25 C 0.507100 0.397380 0.830400 -0.058585
C26 C 0.561000 0.203450 0.006950 -0.037486
C27 C 0.291700 0.400180 0.800060 -0.108435
C28 C 0.120400 0.144540 0.049790 -0.036560
C29 C 0.258600 0.995460 0.265110 0.770321
C30 C 0.260700 0.723260 0.655070 0.753881
C31 C 0.109200 0.644940 0.468640 -0.212544
C32 C 0.110400 0.718940 0.357810 -0.226848
C33 C 0.943300 0.807040 0.360040 -0.035051
C34 C 0.988600 0.729750 0.567720 -0.051244
C35 C 0.207300 0.698720 0.589310 -0.111260
C36 C 0.331300 0.616560 0.489200 -0.030030
C37 C 0.327200 0.720510 0.328100 -0.016710
C38 C 0.375600 0.812760 0.299750 -0.049265
C39 C 0.992900 0.897380 0.330400 -0.058585
C40 C 0.939000 0.703450 0.506950 -0.037486
C41 C 0.208300 0.900180 0.300060 -0.108435
C42 C 0.379600 0.644540 0.549790 -0.036560
C43 C 0.758600 0.504540 0.234890 0.770321
C44 C 0.760700 0.776740 0.844930 0.753881
C45 C 0.609200 0.855060 0.031360 -0.212544
C46 C 0.610400 0.781060 0.142190 -0.226848
C47 C 0.443300 0.692960 0.139960 -0.035051
C48 C 0.488600 0.770250 0.932280 -0.051244
C49 C 0.707300 0.801280 0.910690 -0.111260
C50 C 0.831300 0.883440 0.010800 -0.030030
C51 C 0.827200 0.779490 0.171900 -0.016710
C52 C 0.875600 0.687240 0.200250 -0.049265
C53 C 0.492900 0.602620 0.169600 -0.058585
C54 C 0.439000 0.796550 0.993050 -0.037486
C55 C 0.708300 0.599820 0.199940 -0.108435
C56 C 0.879600 0.855460 0.950210 -0.036560
S1 S 0.963630 0.398350 0.607680 1.152829
S2 S 0.463630 0.101650 0.892320 1.152829
S3 S 0.036370 0.601650 0.392320 1.152829
S4 S 0.536370 0.898350 0.107680 1.152829
O1 O 0.805000 0.493100 0.630960 -0.623849
O2 O 0.915200 0.262260 0.309360 -0.784012
O3 O 0.218900 0.415340 0.611760 -0.532385
O4 O 0.525700 0.984230 0.743780 -0.735465
O5 O 0.919100 0.956950 0.752850 -0.713610
O6 O 0.525100 0.267580 0.328320 -0.711065
O7 O 0.305000 0.006900 0.869040 -0.623848
O8 O 0.415200 0.237740 0.190640 -0.784011
O9 O 0.718900 0.084660 0.888240 -0.532385
O10 O 0.025700 0.515770 0.756220 -0.735465
O11 O 0.419100 0.543050 0.747150 -0.713610
O12 O 0.025100 0.232420 0.171680 -0.711065
O13 O 0.195000 0.506900 0.369040 -0.623849
O14 O 0.084800 0.737740 0.690640 -0.784012
O15 O 0.781100 0.584660 0.388240 -0.532385
O16 O 0.474300 0.015770 0.256220 -0.735465
O17 O 0.080900 0.043050 0.247150 -0.713610
O18 O 0.474900 0.732420 0.671680 -0.711065
O19 O 0.695000 0.993100 0.130960 -0.623848
O20 O 0.584800 0.762260 0.809360 -0.784012
O21 O 0.281100 0.915340 0.111760 -0.532385
O22 O 0.974300 0.484230 0.243780 -0.735465
O23 O 0.580900 0.456950 0.252850 -0.713611
O24 O 0.974900 0.767580 0.828320 -0.711065
patrickfuller commented 8 years ago

I'd recommend emailing David Dubbeldam, the author of RASPA. This repo is just a mirror of his code.