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|
# fmt: off
"""ONETEP file parsers.
Implemented:
* Input file
* Output file
* Geometry output file
"""
from io import StringIO
import numpy as np
import pytest
from pytest import approx
from ase.io import read, write
from ase.io.onetep import get_onetep_keywords
eV2au = 27.2116529
angtobohr = 1.889726134583
# Very complex solvation input file with
# many custom defined species
# and constraints
onetep_input = """
task : SINGLEPOINT
ppd_npoints 7 5 5
is_implicit_solvent = T
is_smeared_ion_rep : t
is_sepaRate_restArt_fiLes T
%block lattice_cart
ang
120.00000000 0.00000000 0.00000000
0.00000000 90.00000000 0.00000000
0.00000000 0.00000000 90.00000000
%endblock lattice_cart
#==== ring-resolved PDOS
%block species_ldos_groups
H2 O2 Al2
H3 O3 Al3
H4 O4 Si4
H5 O5 Al5
H6 O6 Al6
H7 O7 Si7
H8 O8 Al8
H9 O9 Al9
H10 O10 Si10
H11 O11 Al11
H12 O12 Al12
H13 O13 Si13
H14 O14 Al14
H15 O15 Al15
H16 O16 Si16
H17 O17 Al17
H18 O18 Al18
H19 O19 Si19
H20 O20 Al20
H21 O21 Al21
H22 O22 Si22
H23 O23 Al23
H24 O24 Al24
HOH OOH
%endblock species_ldos_groups
%block species_cond
H2 H 1 1 13.0
O2 O 8 4 13.0
Al2 Al 13 9 13.0
H3 H 1 1 13.0
O3 O 8 4 13.0
Al3 Al 13 9 13.0
H4 H 1 1 13.0
O4 O 8 4 13.0
Si4 Si 14 9 13.0
H5 H 1 1 13.0
O5 O 8 4 13.0
Al5 Al 13 9 13.0
H6 H 1 1 13.0
O6 O 8 4 13.0
Al6 Al 13 9 13.0
H7 H 1 1 13.0
O7 O 8 4 13.0
Si7 Si 14 9 13.0
H8 H 1 1 13.0
O8 O 8 4 13.0
Al8 Al 13 9 13.0
H9 H 1 1 13.0
O9 O 8 4 13.0
Al9 Al 13 9 13.0
H10 H 1 1 13.0
O10 O 8 4 13.0
Si10 Si 14 9 13.0
H11 H 1 1 13.0
O11 O 8 4 13.0
Al11 Al 13 9 13.0
H12 H 1 1 13.0
O12 O 8 4 13.0
Al12 Al 13 9 13.0
H13 H 1 1 13.0
O13 O 8 4 13.0
Si13 Si 14 9 13.0
H14 H 1 1 13.0
O14 O 8 4 13.0
Al14 Al 13 9 13.0
H15 H 1 1 13.0
O15 O 8 4 13.0
Al15 Al 13 9 13.0
H16 H 1 1 13.0
O16 O 8 4 13.0
Si16 Si 14 9 13.0
H17 H 1 1 13.0
O17 O 8 4 13.0
Al17 Al 13 9 13.0
H18 H 1 1 13.0
O18 O 8 4 13.0
Al18 Al 13 9 13.0
H19 H 1 1 13.0
O19 O 8 4 13.0
Si19 Si 14 9 13.0
H20 H 1 1 13.0
O20 O 8 4 13.0
Al20 Al 13 9 13.0
H21 H 1 1 13.0
O21 O 8 4 13.0
Al21 Al 13 9 13.0
H22 H 1 1 13.0
O22 O 8 4 13.0
Si22 Si 14 9 13.0
H23 H 1 1 13.0
O23 O 8 4 13.0
Al23 Al 13 9 13.0
H24 H 1 1 13.0
O24 O 8 4 13.0
Al24 Al 13 9 13.0
HOH H 1 1 13.0
OOH O 8 4 13.0
%endblock species_cond
%block species_atomic_set
H2 SOLVE
O2 SOLVE
Al2 SOLVE
H3 SOLVE
O3 SOLVE
Al3 SOLVE
H4 SOLVE
O4 SOLVE
Si4 SOLVE
H5 SOLVE
O5 SOLVE
Al5 SOLVE
H6 SOLVE
O6 SOLVE
Al6 SOLVE
H7 SOLVE
O7 SOLVE
Si7 SOLVE
H8 SOLVE
O8 SOLVE
Al8 SOLVE
H9 SOLVE
O9 SOLVE
Al9 SOLVE
H10 SOLVE
O10 SOLVE
Si10 SOLVE
H11 SOLVE
O11 SOLVE
Al11 SOLVE
H12 SOLVE
O12 SOLVE
Al12 SOLVE
H13 SOLVE
O13 SOLVE
Si13 SOLVE
H14 SOLVE
O14 SOLVE
Al14 SOLVE
H15 SOLVE
O15 SOLVE
Al15 SOLVE
H16 SOLVE
O16 SOLVE
Si16 SOLVE
H17 SOLVE
O17 SOLVE
Al17 SOLVE
H18 SOLVE
O18 SOLVE
Al18 SOLVE
H19 SOLVE
O19 SOLVE
Si19 SOLVE
H20 SOLVE
O20 SOLVE
Al20 SOLVE
H21 SOLVE
O21 SOLVE
Al21 SOLVE
H22 SOLVE
O22 SOLVE
Si22 SOLVE
H23 SOLVE
O23 SOLVE
Al23 SOLVE
H24 SOLVE
O24 SOLVE
Al24 SOLVE
HOH SOLVE
OOH SOLVE
%endblock species_atomic_set
%block species_pot
H2 h-optgga1.recpot
O2 o-optgga1.recpot
Al2 al-optgga1.recpot
H3 h-optgga1.recpot
O3 o-optgga1.recpot
Al3 al-optgga1.recpot
H4 h-optgga1.recpot
O4 o-optgga1.recpot
Si4 Si_op_07_nopcc.recpot
H5 h-optgga1.recpot
O5 o-optgga1.recpot
Al5 al-optgga1.recpot
H6 h-optgga1.recpot
O6 o-optgga1.recpot
Al6 al-optgga1.recpot
H7 h-optgga1.recpot
O7 o-optgga1.recpot
Si7 Si_op_07_nopcc.recpot
H8 h-optgga1.recpot
O8 o-optgga1.recpot
Al8 al-optgga1.recpot
H9 h-optgga1.recpot
O9 o-optgga1.recpot
Al9 al-optgga1.recpot
H10 h-optgga1.recpot
O10 o-optgga1.recpot
Si10 Si_op_07_nopcc.recpot
H11 h-optgga1.recpot
O11 o-optgga1.recpot
Al11 al-optgga1.recpot
H12 h-optgga1.recpot
O12 o-optgga1.recpot
Al12 al-optgga1.recpot
H13 h-optgga1.recpot
O13 o-optgga1.recpot
Si13 Si_op_07_nopcc.recpot
H14 h-optgga1.recpot
O14 o-optgga1.recpot
Al14 al-optgga1.recpot
H15 h-optgga1.recpot
O15 o-optgga1.recpot
Al15 al-optgga1.recpot
H16 h-optgga1.recpot
O16 o-optgga1.recpot
Si16 Si_op_07_nopcc.recpot
H17 h-optgga1.recpot
O17 o-optgga1.recpot
Al17 al-optgga1.recpot
H18 h-optgga1.recpot
O18 o-optgga1.recpot
Al18 al-optgga1.recpot
H19 h-optgga1.recpot
O19 o-optgga1.recpot
Si19 Si_op_07_nopcc.recpot
H20 h-optgga1.recpot
O20 o-optgga1.recpot
Al20 al-optgga1.recpot
H21 h-optgga1.recpot
O21 o-optgga1.recpot
Al21 al-optgga1.recpot
H22 h-optgga1.recpot
O22 o-optgga1.recpot
Si22 Si_op_07_nopcc.recpot
H23 h-optgga1.recpot
O23 o-optgga1.recpot
Al23 al-optgga1.recpot
H24 h-optgga1.recpot
O24 o-optgga1.recpot
Al24 al-optgga1.recpot
HOH h-optgga1.recpot
OOH o-optgga1.recpot
%endblock species_pot
%block species
H2 H 1 1 8.0
O2 O 8 4 8.0
Al2 Al 13 9 8.0
H3 H 1 1 8.0
O3 O 8 4 8.0
Al3 Al 13 9 8.0
H4 H 1 1 8.0
O4 O 8 4 8.0
Si4 Si 14 9 8.0
H5 H 1 1 8.0
O5 O 8 4 8.0
Al5 Al 13 9 8.0
H6 H 1 1 8.0
O6 O 8 4 8.0
Al6 Al 13 9 8.0
H7 H 1 1 8.0
O7 O 8 4 8.0
Si7 Si 14 9 8.0
H8 H 1 1 8.0
O8 O 8 4 8.0
Al8 Al 13 9 8.0
H9 H 1 1 8.0
O9 O 8 4 8.0
Al9 Al 13 9 8.0
H10 H 1 1 8.0
O10 O 8 4 8.0
Si10 Si 14 9 8.0
H11 H 1 1 8.0
O11 O 8 4 8.0
Al11 Al 13 9 8.0
H12 H 1 1 8.0
O12 O 8 4 8.0
Al12 Al 13 9 8.0
H13 H 1 1 8.0
O13 O 8 4 8.0
Si13 Si 14 9 8.0
H14 H 1 1 8.0
O14 O 8 4 8.0
Al14 Al 13 9 8.0
H15 H 1 1 8.0
O15 O 8 4 8.0
Al15 Al 13 9 8.0
H16 H 1 1 8.0
O16 O 8 4 8.0
Si16 Si 14 9 8.0
H17 H 1 1 8.0
O17 O 8 4 8.0
Al17 Al 13 9 8.0
H18 H 1 1 8.0
O18 O 8 4 8.0
Al18 Al 13 9 8.0
H19 H 1 1 8.0
O19 O 8 4 8.0
Si19 Si 14 9 8.0
H20 H 1 1 8.0
O20 O 8 4 8.0
Al20 Al 13 9 8.0
H21 H 1 1 8.0
O21 O 8 4 8.0
Al21 Al 13 9 8.0
H22 H 1 1 8.0
O22 O 8 4 8.0
Si22 Si 14 9 8.0
H23 H 1 1 8.0
O23 O 8 4 8.0
Al23 Al 13 9 8.0
H24 H 1 1 8.0
O24 O 8 4 8.0
Al24 Al 13 9 8.0
HOH H 1 1 8.0
OOH O 8 4 8.0
%endblock species
%block species_constraints
H2 NONE
O2 NONE
Al2 NONE
H3 NONE
O3 NONE
Al3 NONE
H4 NONE
O4 NONE
Si4 NONE
H5 NONE
O5 NONE
Al5 NONE
H6 NONE
O6 NONE
Al6 NONE
H7 NONE
O7 NONE
Si7 NONE
H8 NONE
O8 NONE
Al8 NONE
H9 NONE
O9 NONE
Al9 NONE
H10 NONE
O10 NONE
Si10 NONE
H11 NONE
O11 NONE
Al11 NONE
H12 NONE
O12 No:N
Al12 NONE
H13 NONE
O13 N=NE
Si13 NONE
H14 NONE
O14 NONE
Al14 NONE
H15 NONE
O15 NONE
Al15 NONE
H16 NONE
O16 NONE
Si16 NONE
H17 NONE
O17 NONE
Al17 NONE
H18 NONE
O18 NONE
Al18 NONE
H19 NONE
O19 NONE
Si19 NONE
H20 NONE
O20 NONE
Al20 NONE
H21 NONE
O21 NONE
Al21 NONE
H22 NONE
O22 NONE
Si22 NONE
H23 NONE
O23 NONE
Al23 NoNe
H24 NONE
O24 NONE
Al24 NONE
HOH NONE
OOH NONE
%endblock species_constraints
dos_smear : 0.1 eV
kernel_cutoff : 1000.0
cutoff_energy : 1000 eV
odd_psinc_grid : T
xc_functional : B3LYP
timings_level : 3
output_detail : VERBOSE
check_atoms : T
do_properties : T
dx_format T
cube_format F
read_denskern : T
read_tightbox_ngwfs : T
write_denskern : T
write_tightbox_ngwfs : T
initial_dens_realspace : T
# Construct initial density in real space from atomsolver density
# problems with kernel degeneracy: diagonalise it if broken
maxit_palser_mano = -1
maxit_pen : 0
minit_lnv : 8
maxit_lnv : 8
maxit_ngwf_cg : 20
lnv_check_trial_steps : T
tHREADS_NUM_FFTBOXES 8
! hfx_memory_limit 95000 ! przy populate swop OOM
! hfx_memory_limit 85000 ! po prodach
! hfx_memory_limit 75000 ! po prodach na 64
! hfx_memory_limit 60000 ! takze oom na 64
! hfx_memory_limit 50000 ! takze oom na 64
! hfx_memory_limit 50000 ! takze oom na 128
! hfx_memory_limit 40000 ! oom na 128
! hfx_memory_limit 35000 ! oom na 128 w drugim grad
hfx_memory_limit 32000
hfx_memory_weights 1 0 0
%block swri
for_hfx 3 12 V 12 12 RE2
%endblock swri
hfx_use_ri for_hfx
hfx_max_l 3
hfx_max_q 12
hfx_metric ELECTROSTATIC
hfx_cutoff 20.0 bohr
%block species_swri-for_hfx
H2
O2
Al2
H3
O3
Al3
H4
O4
Si4
H5
O5
Al5
H6
O6
Al6
H7
O7
Si7
H8
O8
Al8
H9
O9
Al9
H10
O10
Si10
H11
O11
Al11
H12
O12
Al12
H13
O13
Si13
H14
O14
Al14
H15
O15
Al15
H16
O16
Si16
H17
O17
Al17
H18
O18
Al18
H19
O19
Si19
H20
O20
Al20
H21
O21
Al21
H22
O22
Si22
H23
O23
Al23
H24
O24
Al24
HOH
OOH
%endblock species_swri-for_hfx
%block positions_abs
Al2 89.96156402 49.81122736 62.56876970
O2 92.92087542 49.47107662 65.41280780
H2 92.07238831 48.22763671 66.46727508
H2 94.38352359 48.67739157 64.65313782
O2 92.50135618 50.76742887 60.40125362
H2 92.82638911 49.48619443 59.14458562
Al2 89.96345374 57.94460941 57.80287994
O2 92.91709597 59.06899656 60.44849677
H2 92.06104995 58.52475539 61.98106481
H2 94.38730304 58.00697038 60.20472208
O2 92.50135618 57.68382718 55.45017068
H2 92.81694048 55.94527897 54.99663636
Al2 89.96912292 62.60467450 49.61658555
O2 92.93221378 64.89313306 51.34946458
H2 92.06293968 65.19737900 52.94061413
H2 94.38730304 63.83488633 51.68772559
O2 92.50324591 61.19682839 47.70607224
H2 92.81883020 59.46583909 48.18039355
Al2 89.96156402 40.18874097 27.43119863
O2 92.92087542 40.52889171 24.58716053
H2 92.07238831 41.77233162 23.53269325
H2 94.38352359 41.32257676 25.34683051
O2 92.50135618 39.23253946 29.59871471
H2 92.82638911 40.51377390 30.85538271
Al2 89.96345374 32.05535892 32.19708839
O2 92.91709597 30.93097176 29.55147156
H2 92.06104995 31.47521294 28.01890352
H2 94.38730304 31.99299795 29.79524625
O2 92.50135618 32.31614115 34.54979765
H2 92.81694048 34.05468936 35.00333197
Al2 89.96912292 27.39529383 40.38338278
O2 92.93221378 25.10683527 38.65050375
H2 92.06293968 24.80258933 37.05935420
H2 94.38730304 26.16508200 38.31224274
O2 92.50324591 28.80313994 42.29389608
H2 92.81883020 30.53412924 41.81957478
Al2 89.96156402 62.56876970 40.18874097
O2 92.92087542 65.41280780 40.52889171
H2 92.07238831 66.46727508 41.77233162
H2 94.38352359 64.65313782 41.32257676
O2 92.50135618 60.40125362 39.23253946
H2 92.82638911 59.14458562 40.51377390
Al2 89.96345374 57.80287994 32.05535892
O2 92.91709597 60.44849677 30.93097176
H2 92.06104995 61.98106481 31.47521294
H2 94.38730304 60.20472208 31.99299795
O2 92.50135618 55.45017068 32.31614115
H2 92.81694048 54.99663636 34.05468936
Al2 89.96912292 49.61658555 27.39529383
O2 92.93221378 51.34946458 25.10683527
H2 92.06293968 52.94061413 24.80258933
H2 94.38730304 51.68772559 26.16508200
O2 92.50324591 47.70607224 28.80313994
H2 92.81883020 48.18039355 30.53412924
Al2 89.96156402 27.43119863 49.81122736
O2 92.92087542 24.58716053 49.47107662
H2 92.07238831 23.53269325 48.22763671
H2 94.38352359 25.34683051 48.67739157
O2 92.50135618 29.59871471 50.76742887
H2 92.82638911 30.85538271 49.48619443
Al2 89.96345374 32.19708839 57.94460941
O2 92.91709597 29.55147156 59.06899656
H2 92.06104995 28.01890352 58.52475539
H2 94.38730304 29.79524625 58.00697038
O2 92.50135618 34.54979765 57.68382718
H2 92.81694048 35.00333197 55.94527897
Al2 89.96912292 40.38338278 62.60467450
O2 92.93221378 38.65050375 64.89502279
H2 92.06293968 37.05935420 65.19737900
H2 94.38730304 38.31224274 63.83488633
O2 92.50324591 42.29389608 61.19682839
H2 92.81883020 41.81957478 59.46583909
Al3 87.29704991 45.07368349 63.63646506
O3 89.84440098 46.44373507 61.59934010
H3 91.14264296 45.12848555 61.20060785
O3 88.21545690 48.15960656 65.40335917
H3 87.02114987 49.02321148 66.46538535
O3 89.50236052 42.68884888 65.34855710
H3 91.01225185 43.22364143 66.20271340
Al3 87.29327046 54.38625476 61.10045235
O3 89.83873181 54.54310205 58.64947732
H3 91.13886351 53.20895527 58.97262052
O3 89.48724271 53.18060937 63.78764317
H3 90.99146486 54.07067047 64.27897201
O3 88.21356718 57.94271968 61.08155509
H3 87.01737042 59.22395412 61.56154557
Al3 87.29327046 61.17415168 54.24830474
O3 89.84062153 60.08377959 52.04677359
H3 91.13886351 59.08600410 52.99541619
O3 89.49102216 61.47083871 57.17171135
H3 90.99335458 62.49129092 57.14336545
O3 88.22301581 64.24495694 52.46062365
H3 87.02870878 65.59611125 52.22629759
Al3 87.29704991 44.92628484 26.36350327
O3 89.84440098 43.55623326 28.40062823
H3 91.14264296 44.87148278 28.79936048
O3 88.21545690 41.84036177 24.59660916
H3 87.02114987 40.97675684 23.53458298
O3 89.50236052 47.31111945 24.65141123
H3 91.01225185 46.77632690 23.79725493
Al3 87.29327046 35.61371357 28.89951598
O3 89.83873181 35.45686628 31.35049101
H3 91.13886351 36.79101306 31.02734781
O3 89.48724271 36.81935896 26.21232516
H3 90.99146486 35.92929786 25.72099632
O3 88.21356718 32.05724865 28.91841324
H3 87.01737042 30.77601421 28.43842276
Al3 87.29327046 28.82581665 35.75166359
O3 89.84062153 29.91618873 37.95319474
H3 91.13886351 30.91396423 37.00455213
O3 89.49102216 28.52912962 32.82825698
H3 90.99335458 27.50867741 32.85660288
O3 88.22301581 25.75501139 37.53934468
H3 87.02870878 24.40385708 37.77367074
Al3 87.29704991 63.63646506 44.92628484
O3 89.50236052 65.34855710 47.31111945
H3 91.01225185 66.20271340 46.77632690
O3 89.84440098 61.59934010 43.55623326
H3 91.14264296 61.20060785 44.87148278
O3 88.21545690 65.40335917 41.84036177
H3 87.02114987 66.46538535 40.97675684
Al3 87.29327046 61.10045235 35.61371357
O3 89.83873181 58.64947732 35.45686628
H3 91.13886351 58.97262052 36.79101306
O3 89.48724271 63.78764317 36.81935896
H3 90.99146486 64.27897201 35.92929786
O3 88.21356718 61.08155509 32.05724865
H3 87.01737042 61.56154557 30.77601421
Al3 87.29327046 54.24830474 28.82581665
O3 89.84062153 52.04677359 29.91618873
H3 91.13886351 52.99541619 30.91396423
O3 89.49102216 57.17171135 28.52912962
H3 90.99335458 57.14336545 27.50867741
O3 88.22301581 52.46062365 25.75501139
H3 87.02870878 52.22629759 24.40385708
Al3 87.29704991 26.36350327 45.07368349
O3 89.50236052 24.65141123 42.68884888
H3 91.01225185 23.79725493 43.22364143
O3 89.84440098 28.40062823 46.44373507
H3 91.14264296 28.79936048 45.12848555
O3 88.21545690 24.59660916 48.15960656
H3 87.02114987 23.53458298 49.02321148
Al3 87.29327046 28.89951598 54.38625476
O3 89.83873181 31.35238073 54.54310205
H3 91.13886351 31.02734781 53.20895527
O3 89.48724271 26.21232516 53.18060937
H3 90.99146486 25.72099632 54.07067047
O3 88.21356718 28.91841324 57.94271968
H3 87.01737042 28.43842276 59.22395412
Al3 87.29327046 35.75166359 61.17415168
O3 89.84062153 37.95319474 60.08377959
H3 91.13886351 37.00455213 59.08600410
O3 89.49102216 32.82825698 61.47083871
H3 90.99335458 32.85660288 62.49129092
O3 88.22301581 37.53934468 64.24495694
H3 87.02870878 37.77367074 65.59611125
Si4 84.40765838 49.15927178 60.08755905
O4 84.39254057 48.54322100 57.03565105
H4 84.32828988 46.76120909 56.61046263
O4 86.95311973 50.77876723 60.84533930
Si4 84.40576866 56.13992078 55.97929404
O4 84.38309194 54.08011910 53.64548205
H4 84.33395906 52.32456335 54.17082596
O4 86.95123000 57.92193269 55.82622621
Si4 84.40576866 60.14425084 48.93628407
O4 84.37931249 57.19438806 47.94039831
H4 84.32451042 55.93205089 49.26887591
O4 86.95311973 61.60878873 47.91583187
Si4 84.40765838 40.84069655 29.91240928
O4 84.39254057 41.45674733 32.96431728
H4 84.32828988 43.23875924 33.38950570
O4 86.95311973 39.22120110 29.15462903
Si4 84.40576866 33.86004755 34.02067429
O4 84.38309194 35.91984923 36.35448628
H4 84.33395906 37.67540498 35.82914237
O4 86.95123000 32.07803564 34.17374212
Si4 84.40576866 29.85571749 41.06368425
O4 84.37931249 32.80558027 42.05957002
H4 84.32451042 34.06791744 40.73109242
O4 86.95311973 28.39117960 42.08413646
Si4 84.40765838 60.08755905 40.84069655
O4 84.39254057 57.03565105 41.45674733
H4 84.32828988 56.61046263 43.23875924
O4 86.95311973 60.84533930 39.22120110
Si4 84.40576866 55.97929404 33.86004755
O4 84.38309194 53.64548205 35.91984923
H4 84.33395906 54.17082596 37.67540498
O4 86.95123000 55.82622621 32.07803564
Si4 84.40576866 48.93628407 29.85571749
O4 84.37931249 47.94039831 32.80558027
H4 84.32451042 49.26887591 34.06791744
O4 86.95311973 47.91583187 28.39117960
Si4 84.40765838 29.91240928 49.15927178
O4 84.39254057 32.96431728 48.54322100
H4 84.32828988 33.38950570 46.76120909
O4 86.95311973 29.15462903 50.77876723
Si4 84.40576866 34.02067429 56.13992078
O4 84.38309194 36.35448628 54.08011910
H4 84.33395906 35.82914237 52.32456335
O4 86.95123000 34.17374212 57.92193269
Si4 84.40576866 41.06368425 60.14425084
O4 86.95311973 42.08413646 61.60878873
O4 84.37931249 42.05957002 57.19438806
H4 84.32451042 40.73109242 55.93205089
Al5 81.73558538 45.10202939 63.73095138
O5 84.43600428 46.55711865 61.78831273
O5 84.59474129 44.43117654 65.82854759
H5 84.58151320 42.97986674 66.91325049
Al5 81.73558538 54.45239518 61.16659277
O5 84.59096183 54.92860621 63.31899104
H5 84.58529266 54.21239994 64.98383992
O5 84.43411455 54.73774386 58.75341227
Al5 81.73558538 61.26863799 54.27287118
O5 84.59285156 62.75585260 55.89992554
H5 84.58907211 62.97128140 57.69894499
O5 84.43411455 60.31432621 52.03921468
Al5 81.73558538 44.89793894 26.26901695
O5 84.43600428 43.44284968 28.21165560
O5 84.59474129 45.56879178 24.17142074
H5 84.58151320 47.02010159 23.08671784
Al5 81.73558538 35.54757315 28.83337556
O5 84.59096183 35.07136212 26.68097729
H5 84.58529266 35.78756839 25.01612840
O5 84.43411455 35.26222447 31.24655606
Al5 81.73558538 28.73322006 35.72709715
O5 84.59285156 27.24411573 34.10004279
H5 84.58907211 27.02868693 32.30102334
O5 84.43411455 29.68564212 37.96075365
Al5 81.73558538 63.73095138 44.89793894
O5 84.59474129 65.82854759 45.56879178
H5 84.58151320 66.91325049 47.02010159
O5 84.43600428 61.78831273 43.44284968
Al5 81.73558538 61.16659277 35.54757315
O5 84.59096183 63.31899104 35.07136212
H5 84.58529266 64.98383992 35.78756839
O5 84.43411455 58.75341227 35.26222447
Al5 81.73558538 54.27287118 28.73133034
O5 84.59285156 55.89992554 27.24411573
H5 84.58907211 57.69894499 27.02868693
O5 84.43411455 52.03921468 29.68564212
Al5 81.73558538 26.26901695 45.10202939
O5 84.59474129 24.17142074 44.43117654
H5 84.58151320 23.08671784 42.97986674
O5 84.43600428 28.21165560 46.55711865
Al5 81.73558538 28.83337556 54.45239518
O5 84.59096183 26.68097729 54.92860621
H5 84.58529266 25.01612840 54.21239994
O5 84.43411455 31.24655606 54.73774386
Al5 81.73558538 35.72709715 61.26674827
O5 84.59285156 34.10004279 62.75585260
H5 84.58907211 32.30102334 62.97128140
O5 84.43411455 37.96075365 60.31432621
Al6 79.10886580 49.93972875 63.05064991
O6 81.87542512 50.81656176 60.86801601
O6 81.06284281 48.16338601 65.50540439
H6 82.42722521 48.91360736 66.43326001
O6 79.81751317 53.36013337 63.98417470
H6 78.56840408 54.35223969 64.84211045
Al6 79.10886580 58.29987796 58.16003821
O6 81.87542512 57.96917585 55.82811594
O6 81.06284281 57.98996284 61.17226195
H6 82.42533548 59.10679109 61.59934010
O6 79.82129262 61.72784149 57.26241821
H6 78.57029380 63.01474511 57.50619290
Al6 79.10697607 63.09978279 49.74697666
O6 81.87542512 61.65414216 47.89315515
O6 81.06284281 64.33377407 52.51353598
H6 82.43100466 65.50729411 52.32078390
O6 79.81751317 65.62256742 47.25631738
H6 78.56084517 66.85466897 46.82545978
Al6 79.10886580 40.06023958 26.94931842
O6 81.87542512 39.18340657 29.13195231
O6 81.06284281 41.83658232 24.49456394
H6 82.42722521 41.08636097 23.56670832
O6 79.81751317 36.63983496 26.01579362
H6 78.56840408 35.64772864 25.15785788
Al6 79.10886580 31.70009037 31.84181985
O6 81.87542512 32.03079248 34.17185239
O6 81.06284281 32.01000549 28.82770638
H6 82.42533548 30.89317724 28.40062823
O6 79.82129262 28.27212684 32.73755012
H6 78.57029380 26.98522322 32.49377543
Al6 79.10697607 26.90018554 40.25299167
O6 81.87542512 28.34582617 42.10681318
O6 81.06284281 25.66619426 37.48643234
H6 82.43100466 24.49267422 37.67918443
O6 79.81751317 24.37740091 42.74365095
H6 78.56084517 23.14529935 43.17450855
Al6 79.10886580 63.05064991 40.06023958
O6 81.87542512 60.86801601 39.18340657
O6 81.06284281 65.50540439 41.83658232
H6 82.42722521 66.43326001 41.08636097
O6 79.81751317 63.98417470 36.63983496
H6 78.56840408 64.84211045 35.64772864
Al6 79.10886580 58.15814848 31.70009037
O6 81.87542512 55.82811594 32.03079248
O6 81.06284281 61.17226195 32.01000549
H6 82.42533548 61.59934010 30.89317724
O6 79.82129262 57.26241821 28.27212684
H6 78.57029380 57.50619290 26.98522322
Al6 79.10697607 49.74697666 26.90018554
O6 81.87542512 47.89315515 28.34582617
O6 81.06284281 52.51353598 25.66619426
H6 82.43100466 52.32078390 24.49267422
O6 79.81751317 47.25631738 24.37740091
H6 78.56084517 46.82545978 23.14529935
Al6 79.10886580 26.94931842 49.93972875
O6 81.87542512 29.13195231 50.81656176
O6 81.06284281 24.49456394 48.16338601
H6 82.42722521 23.56670832 48.91360736
O6 79.81751317 26.01579362 53.36013337
H6 78.56840408 25.15785788 54.35223969
Al6 79.10886580 31.84181985 58.29987796
O6 81.87542512 34.17185239 57.96917585
O6 81.06284281 28.82770638 57.98996284
H6 82.42533548 28.40062823 59.10679109
O6 79.82129262 32.73755012 61.72784149
H6 78.57029380 32.49377543 63.01474511
Al6 79.10697607 40.25299167 63.09978279
O6 81.87542512 42.10681318 61.65414216
O6 81.06284281 37.48643234 64.33377407
H6 82.43100466 37.67918443 65.50729411
O6 79.81751317 42.74365095 65.62256742
H6 78.56084517 43.17450855 66.85466897
Si7 76.35931402 52.95195249 58.48318141
O7 76.39521882 51.59890845 55.68260701
H7 76.37254210 49.76398420 55.72040154
O7 78.90855481 54.73207468 58.84600886
Si7 76.36120374 58.62491088 52.69494971
O7 76.40844690 56.04732419 50.95073232
H7 76.37632155 54.47885135 51.90126466
O7 78.90855481 60.35023100 52.12047291
Si7 76.35931402 45.14927254 60.65447694
O7 78.90666509 46.50798576 61.86579151
O7 76.40466745 45.37792943 57.55154634
H7 76.37821128 43.77355179 56.66337497
Si7 76.35931402 44.85069579 29.34549139
O7 76.40466745 44.62203890 32.44842199
H7 76.37821128 46.22641654 33.33659336
O7 78.90666509 43.49198257 28.13417682
Si7 76.35931402 37.04801584 31.51678692
O7 76.39521882 38.40105988 34.31736132
H7 76.37254210 40.23598413 34.27956679
O7 78.90855481 35.26789365 31.15395947
Si7 76.36120374 31.37505745 37.30501862
O7 76.40844690 33.95264414 39.04923600
H7 76.37632155 35.52111698 38.09870367
O7 78.90855481 29.64973732 37.87949542
Si7 76.35931402 60.65447694 44.85069579
O7 76.40466745 57.55154634 44.62203890
H7 76.37821128 56.66337497 46.22641654
O7 78.90666509 61.86579151 43.49198257
Si7 76.35931402 58.48318141 37.04801584
O7 76.39521882 55.68260701 38.40105988
H7 76.37254210 55.72040154 40.23598413
O7 78.90855481 58.84600886 35.26789365
Si7 76.36120374 52.69494971 31.37505745
O7 76.40844690 50.95073232 33.95264414
H7 76.37632155 51.90126466 35.52111698
O7 78.90855481 52.12047291 29.64973732
Si7 76.35931402 29.34549139 45.14927254
O7 76.40466745 32.44842199 45.37792943
H7 76.37821128 33.33659336 43.77355179
O7 78.90666509 28.13417682 46.50798576
Si7 76.35931402 31.51678692 52.95195249
O7 76.39521882 34.31736132 51.59890845
H7 76.37254210 34.27956679 49.76398420
O7 78.90855481 31.15395947 54.73207468
Si7 76.36120374 37.30501862 58.62491088
O7 76.40844690 39.04923600 56.04732419
H7 76.37632155 38.09870367 54.47885135
O7 78.90855481 37.87949542 60.35023100
Al8 73.56818825 49.93216984 62.99773757
O8 76.32907839 49.84902188 65.25029133
H8 76.31396058 48.67928130 66.63546072
O8 76.34986538 50.83734875 60.76597079
Al8 73.57007798 58.26586288 58.11657450
O8 76.33285785 59.32033016 60.11023576
H8 76.31585031 59.00285614 61.89413740
O8 76.35175511 57.93894023 55.73173990
Al8 73.56818825 63.04498073 49.72996913
O8 76.32907839 64.95549403 50.92994533
H8 76.31585031 65.56965508 52.63447847
O8 76.34797566 61.57477366 47.82323528
Al8 73.56818825 40.06779849 27.00412049
O8 76.32907839 40.15094645 24.74967699
H8 76.31396058 41.32068703 23.36450761
O8 76.34986538 39.16261958 29.23399754
Al8 73.57007798 31.73410545 31.88339383
O8 76.33285785 30.67963816 29.88973257
H8 76.31585031 30.99711219 28.10583093
O8 76.35175511 32.06102810 34.26822843
Al8 73.56818825 26.95498760 40.26999920
O8 76.32907839 25.04447430 39.07002299
H8 76.31585031 24.43031325 37.36548986
O8 76.34797566 28.42519467 42.17673305
Al8 73.56818825 62.99584784 40.06779849
O8 76.32907839 65.25029133 40.15094645
H8 76.31396058 66.63546072 41.32068703
O8 76.34986538 60.76597079 39.16261958
Al8 73.57007798 58.11657450 31.73410545
O8 76.33285785 60.11023576 30.67963816
H8 76.31585031 61.89413740 30.99711219
O8 76.35175511 55.73173990 32.06102810
Al8 73.56818825 49.72996913 26.95498760
O8 76.32907839 50.92994533 25.04447430
H8 76.31585031 52.63447847 24.43031325
O8 76.34797566 47.82323528 28.42519467
Al8 73.56818825 27.00412049 49.93216984
O8 76.32907839 24.74967699 49.84902188
H8 76.31396058 23.36450761 48.67928130
O8 76.34986538 29.23399754 50.83734875
Al8 73.57007798 31.88339383 58.26586288
O8 76.33285785 29.88973257 59.32033016
H8 76.31585031 28.10583093 59.00285614
O8 76.35175511 34.26822843 57.93894023
Al8 73.56818825 40.26999920 63.04498073
O8 76.32907839 39.07002299 64.95549403
H8 76.31585031 37.36548986 65.56965508
O8 76.34797566 42.17673305 61.57477366
Al9 70.94902758 45.10013966 63.64213424
O9 73.77416842 46.50609604 61.79020246
O9 71.61988042 48.15204765 65.42225643
H9 70.32163845 48.87203338 66.45971617
O9 72.88221760 42.75498930 65.54886809
H9 74.21258492 43.21041335 66.69026279
Al9 70.95280703 54.41460066 61.09667290
O9 73.77794787 54.69994933 58.79309652
O9 72.89166623 53.34123611 63.91425483
H9 74.21825410 54.30877598 64.67581454
O9 71.62177015 57.94649913 61.10423180
H9 70.32541790 59.09356301 61.63713462
Al9 70.95091731 61.19115921 54.23318693
O9 73.77605815 60.28598031 52.08834756
O9 72.88977650 61.67303942 57.20950587
H9 74.21825410 62.89191290 57.37958124
O9 71.62177015 64.25818502 52.48330036
H9 70.32352817 65.51485302 52.37180651
Al9 70.94902758 44.89982867 26.35783409
O9 73.77416842 43.49387229 28.20976587
O9 71.61988042 41.84792067 24.57771190
H9 70.32163845 41.12793495 23.54025215
O9 72.88221760 47.24497902 24.45110024
H9 74.21258492 46.78955498 23.30970554
Al9 70.95280703 35.58536767 28.90329543
O9 73.77794787 35.30001900 31.20687181
O9 72.89166623 36.65873222 26.08571350
H9 74.21825410 35.69119235 25.32415379
O9 71.62177015 32.05346919 28.89573653
H9 70.32541790 30.90640532 28.36283370
Al9 70.95091731 28.80880911 35.76678140
O9 73.77605815 29.71398802 37.91162076
O9 72.88977650 28.32692890 32.79046246
H9 74.21825410 27.10805543 32.62038709
O9 71.62177015 25.74178331 37.51666797
H9 70.32352817 24.48511531 37.62816182
Al9 70.94902758 63.64213424 44.89982867
O9 72.88221760 65.54886809 47.24497902
H9 74.21258492 66.69026279 46.78955498
O9 73.77416842 61.79020246 43.49387229
O9 71.61988042 65.42225643 41.84792067
H9 70.32163845 66.45971617 41.12793495
Al9 70.95280703 61.09667290 35.58536767
O9 73.77794787 58.79309652 35.30001900
O9 72.89166623 63.91425483 36.65873222
H9 74.21825410 64.67581454 35.69119235
O9 71.62177015 61.10423180 32.05346919
H9 70.32541790 61.63713462 30.90640532
Al9 70.95091731 54.23318693 28.80880911
O9 73.77605815 52.08834756 29.71398802
O9 72.88977650 57.20950587 28.32692890
H9 74.21825410 57.37958124 27.10805543
O9 71.62177015 52.48330036 25.74178331
H9 70.32352817 52.37180651 24.48511531
Al9 70.94902758 26.35783409 45.10013966
O9 72.88221760 24.45110024 42.75498930
H9 74.21258492 23.30970554 43.21041335
O9 73.77416842 28.20976587 46.50609604
O9 71.61988042 24.57771190 48.15204765
H9 70.32163845 23.54025215 48.87203338
Al9 70.95280703 28.90329543 54.41460066
O9 73.77794787 31.20687181 54.69994933
O9 72.89166623 26.08571350 53.34123611
H9 74.21825410 25.32415379 54.30877598
O9 71.62177015 28.89573653 57.94649913
H9 70.32541790 28.36283370 59.09356301
Al9 70.95091731 35.76678140 61.19115921
O9 73.77605815 37.91162076 60.28598031
O9 72.88977650 32.79046246 61.67303942
H9 74.21825410 32.62038709 62.89191290
O9 71.62177015 37.51666797 64.25818502
H9 70.32352817 37.62816182 65.51485302
Si10 68.18057853 49.18950740 60.04031589
O10 68.16924017 48.60936142 56.98273872
H10 68.17490935 46.82923924 56.54432221
O10 70.75438577 50.79388504 60.81888313
Si10 68.18057853 56.13614133 55.93205089
O10 68.16924017 54.09901636 53.58123135
H10 68.17112990 52.33779144 54.09523691
O10 70.75438577 57.91626351 55.79788032
Si10 68.18246826 60.10456658 48.89471010
O10 68.18246826 57.16604217 47.87425789
H10 68.17679908 55.89614609 49.19706631
O10 70.75438577 61.58800174 47.89126542
Si10 68.18057853 40.81046093 29.95965244
O10 68.16924017 41.39060691 33.01722961
H10 68.17490935 43.17072909 33.45564612
O10 70.75438577 39.20608329 29.18108520
Si10 68.18057853 33.86382700 34.06791744
O10 68.16924017 35.90095197 36.41873698
H10 68.17112990 37.66217689 35.90473142
O10 70.75438577 32.08370482 34.20208801
Si10 68.18246826 29.89540174 41.10525823
O10 68.18246826 32.83392616 42.12571044
H10 68.17679908 34.10382224 40.80290202
O10 70.75438577 28.41196659 42.10870291
Si10 68.18057853 60.04031589 40.81046093
O10 68.16924017 56.98273872 41.39060691
H10 68.17490935 56.54432221 43.17072909
O10 70.75438577 60.81888313 39.20608329
Si10 68.18057853 55.93205089 33.86382700
O10 68.16924017 53.57934163 35.90095197
H10 68.17112990 54.09523691 37.66217689
O10 70.75438577 55.79788032 32.08370482
Si10 68.18246826 48.89471010 29.89540174
O10 68.18246826 47.87425789 32.83392616
H10 68.17679908 49.19706631 34.10382224
O10 70.75438577 47.89126542 28.41196659
Si10 68.17868881 29.95965244 49.18950740
O10 68.16924017 33.01722961 48.60936142
H10 68.17490935 33.45564612 46.82923924
O10 70.75438577 29.18108520 50.79388504
Si10 68.18057853 34.06791744 56.13614133
O10 68.16924017 36.41873698 54.09901636
H10 68.17112990 35.90473142 52.33779144
O10 70.75438577 34.20208801 57.91626351
Si10 68.18246826 41.10525823 60.10456658
O10 70.75438577 42.10870291 61.58800174
O10 68.18246826 42.12571044 57.16604217
H10 68.17679908 40.80290202 55.89614609
Al11 65.40835003 45.09636021 63.63835479
O11 68.18057853 46.55144947 61.69004696
O11 68.17868881 44.42550737 65.76240717
H11 68.17868881 42.92884413 66.78474910
Al11 65.41401921 54.41460066 61.10990098
O11 68.18624771 54.89648087 63.27930679
H11 68.19002716 54.10846499 64.91014060
O11 68.18246826 54.68672124 58.68538212
Al11 65.41023976 61.18926949 54.24074584
O11 68.18246826 62.68971218 55.88102827
H11 68.18246826 62.82199302 57.68949636
O11 68.18246826 60.22739879 52.00330988
Al11 65.40835003 44.90360812 26.36161354
O11 68.18057853 43.44851886 28.30992137
O11 68.17868881 45.57446096 24.23756116
H11 68.17868881 47.07112420 23.21521923
Al11 65.41401921 35.58536767 28.89006735
O11 68.18624771 35.10348746 26.72066154
H11 68.19002716 35.89150334 25.08982773
O11 68.18246826 35.31324708 31.31458621
Al11 65.41023976 28.81069884 35.75922249
O11 68.18246826 27.31025615 34.11894005
H11 68.18246826 27.17797531 32.31047197
O11 68.18246826 29.77256953 37.99665845
Al11 65.40835003 63.63835479 44.90360812
O11 68.17868881 65.76240717 45.57446096
H11 68.17868881 66.78474910 47.07112420
O11 68.18057853 61.69004696 43.44851886
Al11 65.41401921 61.10990098 35.58536767
O11 68.18624771 63.27930679 35.10348746
H11 68.19002716 64.91014060 35.89150334
O11 68.18246826 58.68538212 35.31324708
Al11 65.41023976 54.24074584 28.81069884
O11 68.18246826 55.88102827 27.31025615
H11 68.18246826 57.68949636 27.17797531
O11 68.18246826 52.00330988 29.77256953
Al11 65.40835003 26.36161354 45.09636021
O11 68.17868881 24.23756116 44.42550737
H11 68.17868881 23.21521923 42.92884413
O11 68.18057853 28.30992137 46.55144947
Al11 65.41401921 28.89006735 54.41460066
O11 68.18624771 26.72066154 54.89648087
H11 68.19002716 25.08982773 54.10846499
O11 68.18246826 31.31458621 54.68672124
Al11 65.41023976 35.75922249 61.18926949
O11 68.18246826 34.11894005 62.68971218
H11 68.18246826 32.31047197 62.82199302
O11 68.18246826 37.99665845 60.22739879
Al12 62.79485854 49.92461094 62.99584784
O12 65.61055075 50.79577477 60.82833176
O12 64.73560746 48.14259902 65.42414616
H12 66.03573917 48.86258475 66.45593672
O12 63.47516001 53.32989775 63.92559319
H12 62.17880776 54.29743762 64.74195496
Al12 62.79485854 58.26208343 58.12980259
O12 65.61055075 57.92193269 55.80921867
O12 64.74505610 57.94649913 61.12123934
H12 66.04329807 59.09356301 61.64658326
O12 63.47327029 61.66925997 57.22273396
H12 62.17502831 62.91458961 57.43627303
Al12 62.79107909 63.02230401 49.73374858
O12 65.61055075 61.58422229 47.89315515
O12 64.73560746 64.25062612 52.48896954
H12 66.04140835 65.49784548 52.35479897
O12 63.47138056 65.53375028 47.25442766
H12 62.16746940 66.71293950 46.82168033
Al12 62.79485854 40.07535739 27.00412049
O12 65.61055075 39.20419356 29.17163657
O12 64.73560746 41.85736931 24.57582217
H12 66.03573917 41.13738358 23.54403161
O12 63.47516001 36.67007058 26.07437514
H12 62.17880776 35.70253070 25.25801337
Al12 62.79485854 31.73788490 31.87016574
O12 65.61055075 32.07803564 34.19074965
O12 64.74505610 32.05346919 28.87872899
H12 66.04329807 30.90640532 28.35338507
O12 63.47327029 28.33070836 32.77723437
H12 62.17502831 27.08537872 32.56369530
Al12 62.79107909 26.97766432 40.26621975
O12 65.61055075 28.41574604 42.10681318
O12 64.73560746 25.74934221 37.51099879
H12 66.04140835 24.50212285 37.64516935
O12 63.47138056 24.46621805 42.74554067
H12 62.16746940 23.28702883 43.17828800
Al12 62.79485854 62.99584784 40.07535739
O12 65.61055075 60.82833176 39.20419356
O12 64.73560746 65.42414616 41.85736931
H12 66.03573917 66.45593672 41.13738358
O12 63.47516001 63.92559319 36.67007058
H12 62.17880776 64.74195496 35.70253070
Al12 62.79485854 58.12980259 31.73788490
O12 65.61055075 55.80921867 32.07803564
O12 64.74505610 61.12123934 32.05346919
H12 66.04329807 61.64658326 30.90640532
O12 63.47327029 57.22273396 28.33070836
H12 62.17502831 57.43627303 27.08537872
Al12 62.79107909 49.73374858 26.97766432
O12 65.61055075 47.89315515 28.41574604
O12 64.73560746 52.48707982 25.74934221
H12 66.04140835 52.35479897 24.50212285
O12 63.47138056 47.25442766 24.46621805
H12 62.16746940 46.82168033 23.28702883
Al12 62.79485854 27.00412049 49.92461094
O12 65.61055075 29.17163657 50.79577477
O12 64.73560746 24.57582217 48.14259902
H12 66.03573917 23.54403161 48.86258475
O12 63.47516001 26.07437514 53.32989775
H12 62.17880776 25.25801337 54.29743762
Al12 62.79485854 31.87016574 58.26208343
O12 65.61055075 34.19074965 57.92193269
O12 64.74505610 28.87872899 57.94649913
H12 66.04329807 28.35338507 59.09356301
O12 63.47327029 32.77723437 61.66925997
H12 62.17502831 32.56369530 62.91458961
Al12 62.79107909 40.26621975 63.02230401
O12 65.61055075 42.10681318 61.58422229
O12 64.73560746 37.51288851 64.25062612
H12 66.04140835 37.64516935 65.49784548
O12 63.47138056 42.74554067 65.53375028
H12 62.16746940 43.17828800 66.71293950
Si13 60.03018894 52.94061413 58.46428414
O13 57.45827143 54.69428015 58.79687598
O13 60.02640949 50.82223093 60.73951463
O13 60.03585812 51.57812146 55.65993030
H13 60.02829922 49.74130748 55.70906318
O13 62.59643728 54.69805960 58.80065543
Si13 60.02263004 58.57955745 52.69494971
O13 57.45638171 60.26708305 52.09401674
O13 60.02451977 57.90492516 55.72796044
O13 60.01885059 55.98874267 50.96396041
H13 60.02829922 54.42782874 51.93150028
O13 62.59076810 60.26708305 52.09590647
Si13 60.02263004 45.15305200 60.59967488
O13 57.45449198 46.50609604 61.77508465
O13 62.59265782 46.50420631 61.77319492
O13 60.01885059 45.38170888 57.49296482
H13 60.02074031 43.77166206 56.61046263
O13 60.02263004 42.18051251 61.51619214
Si13 60.02263004 44.84691633 29.40029345
O13 57.45449198 43.49387229 28.22488368
O13 60.01885059 44.61825945 32.50700351
H13 60.02074031 46.22830627 33.38950570
O13 62.59265782 43.49576202 28.22677341
O13 60.02263004 47.81945582 28.48377619
Si13 60.03018894 37.05935420 31.53568418
O13 57.45827143 35.30568818 31.20309235
O13 60.02640949 39.17773739 29.26045370
O13 60.03585812 38.42184687 34.34003803
H13 60.02829922 40.25866085 34.29090515
O13 62.59643728 35.30190873 31.19931290
Si13 60.02263004 31.42041088 37.30501862
O13 57.45638171 29.73288528 37.90595159
O13 60.02451977 32.09504317 34.27200789
O13 60.01885059 34.01122565 39.03600792
H13 60.02829922 35.57213959 38.06846805
O13 62.59076810 29.73288528 37.90406186
Si13 60.02263004 60.59967488 44.84691633
O13 60.02263004 61.51619214 47.81945582
O13 57.45449198 61.77508465 43.49387229
O13 60.01885059 57.49296482 44.61825945
H13 60.02074031 56.61046263 46.22830627
O13 62.59265782 61.77319492 43.49576202
Si13 60.03018894 58.46428414 37.05935420
O13 57.45827143 58.79687598 35.30568818
O13 60.02640949 60.73951463 39.17773739
O13 60.03585812 55.65993030 38.42184687
H13 60.02829922 55.70906318 40.25866085
O13 62.59643728 58.80065543 35.30190873
Si13 60.02263004 52.69494971 31.42041088
O13 57.45638171 52.09401674 29.73288528
O13 60.02451977 55.72796044 32.09504317
O13 60.01885059 50.96396041 34.01122565
H13 60.02829922 51.93150028 35.57213959
O13 62.59076810 52.09590647 29.73288528
Si13 60.02263004 29.40029345 45.15305200
O13 60.02263004 28.48377619 42.18051251
O13 57.45449198 28.22488368 46.50609604
O13 60.01885059 32.50700351 45.38170888
H13 60.02074031 33.38950570 43.77166206
O13 62.59265782 28.22677341 46.50420631
Si13 60.03018894 31.53568418 52.94061413
O13 57.45827143 31.20309235 54.69428015
O13 60.02640949 29.26045370 50.82223093
O13 60.03585812 34.34003803 51.57812146
H13 60.02829922 34.29090515 49.74130748
O13 62.59643728 31.19931290 54.69805960
Si13 60.02263004 37.30501862 58.57955745
O13 57.45638171 37.90595159 60.26708305
O13 60.02451977 34.27200789 57.90492516
O13 60.01885059 39.03600792 55.98874267
H13 60.02829922 38.06846805 54.42782874
O13 62.59076810 37.90406186 60.26708305
Al14 57.25229126 49.92461094 62.99395812
O14 55.30776289 48.14637848 65.42225643
H14 53.99629283 48.87014365 66.43892919
O14 56.57576924 53.33178748 63.91992401
H14 57.87401122 54.30121708 64.72683715
O14 54.43659906 50.79577477 60.82455231
Al14 57.25229126 58.25830398 58.12602313
O14 55.30209371 57.94460941 61.11368044
H14 53.99440310 59.08600410 61.62957572
O14 56.57576924 61.66737025 57.22084423
H14 57.87590095 62.90892043 57.43060385
O14 54.43659906 57.91815324 55.80732895
Al14 57.25418099 63.02230401 49.73185885
O14 55.31154234 64.25062612 52.48707982
H14 54.00196201 65.49406603 52.35479897
O14 56.57576924 65.53186056 47.25253793
H14 57.87590095 66.71482923 46.82168033
O14 54.43659906 61.58233256 47.89315515
Al14 57.25229126 40.07535739 27.00601021
O14 55.30776289 41.85358985 24.57771190
H14 53.99629283 41.12982468 23.56103914
O14 56.57576924 36.66818085 26.08004432
H14 57.87401122 35.69875125 25.27313118
O14 54.43659906 39.20419356 29.17541602
Al14 57.25229126 31.74166435 31.87394519
O14 55.30209371 32.05535892 28.88628789
H14 53.99440310 30.91396423 28.37039261
O14 56.57576924 28.33259808 32.78101382
H14 57.87590095 27.09104790 32.56936448
O14 54.43659906 32.08181509 34.19263938
Al14 57.25418099 26.97766432 40.26810948
O14 55.31154234 25.74934221 37.51288851
H14 54.00196201 24.50590230 37.64516935
O14 56.57576924 24.46810777 42.74743040
H14 57.87590095 23.28513910 43.17828800
O14 54.43659906 28.41763577 42.10681318
Al14 57.25229126 62.99395812 40.07535739
O14 55.30776289 65.42225643 41.85358985
H14 53.99629283 66.43892919 41.12982468
O14 56.57576924 63.91992401 36.66818085
H14 57.87401122 64.72683715 35.69875125
O14 54.43659906 60.82455231 39.20419356
Al14 57.25229126 58.12602313 31.74166435
O14 55.30209371 61.11368044 32.05535892
H14 53.99440310 61.62957572 30.91396423
O14 56.57576924 57.21895450 28.33448781
H14 57.87590095 57.43060385 27.09104790
O14 54.43659906 55.80732895 32.08181509
Al14 57.25418099 49.73185885 26.97766432
O14 55.31154234 52.48707982 25.74934221
H14 54.00196201 52.35479897 24.50590230
O14 56.57576924 47.25253793 24.46810777
H14 57.87590095 46.82168033 23.28513910
O14 54.43659906 47.89315515 28.41763577
Al14 57.25229126 27.00601021 49.92461094
O14 55.30776289 24.57771190 48.14637848
H14 53.99629283 23.56103914 48.87014365
O14 56.57576924 26.08004432 53.33178748
H14 57.87401122 25.27313118 54.30121708
O14 54.43659906 29.17541602 50.79577477
Al14 57.25229126 31.87394519 58.25830398
O14 55.30209371 28.88628789 57.94460941
H14 53.99440310 28.37039261 59.08600410
O14 56.57576924 32.78101382 61.66737025
H14 57.87590095 32.56936448 62.90892043
O14 54.43659906 34.19263938 57.91815324
Al14 57.25418099 40.26810948 63.02230401
O14 56.57576924 42.74743040 65.53186056
H14 57.87590095 43.17828800 66.71482923
O14 54.43659906 42.10681318 61.58233256
O14 55.31154234 37.51288851 64.25062612
H14 54.00196201 37.64516935 65.49406603
Al15 54.63691005 45.09824993 63.63835479
O15 51.86468155 46.55144947 61.69004696
O15 51.86657127 44.42739709 65.76429689
H15 51.86657127 42.93262358 66.78852855
Al15 54.63313059 54.41271093 61.10423180
O15 51.86279182 54.89648087 63.27552734
H15 51.85901237 54.11224445 64.90825087
O15 51.86468155 54.68483152 58.68160267
Al15 54.63691005 61.18926949 54.23885611
O15 51.86657127 62.69349163 55.88102827
H15 51.86657127 62.82388275 57.68949636
O15 51.86657127 60.22550907 52.00330988
Al15 54.63691005 44.90171840 26.36161354
O15 51.86468155 43.44851886 28.30992137
O15 51.86657127 45.57257124 24.23567144
H15 51.86657127 47.06734475 23.21332950
Al15 54.63313059 35.58725740 28.89573653
O15 51.86279182 35.10348746 26.72444099
H15 51.85901237 35.88772388 25.09171746
O15 51.86468155 35.31513681 31.31836566
Al15 54.63691005 28.81069884 35.76111222
O15 51.86657127 27.30836642 34.11894005
H15 51.86657127 27.17608558 32.31047197
O15 51.86657127 29.77445926 37.99665845
Al15 54.63691005 63.63835479 44.90171840
O15 51.86657127 65.76429689 45.57257124
H15 51.86657127 66.78852855 47.06734475
O15 51.86468155 61.69004696 43.44851886
Al15 54.63313059 61.10423180 35.58725740
O15 51.86279182 63.27552734 35.10348746
H15 51.85901237 64.90825087 35.88772388
O15 51.86468155 58.68160267 35.31513681
Al15 54.63691005 54.23885611 28.81069884
O15 51.86657127 55.88102827 27.30836642
H15 51.86657127 57.68949636 27.17608558
O15 51.86657127 52.00330988 29.77445926
Al15 54.63691005 26.36161354 45.09824993
O15 51.86657127 24.23567144 44.42739709
H15 51.86657127 23.21332950 42.93262358
O15 51.86468155 28.30992137 46.55144947
Al15 54.63313059 28.89573653 54.41271093
O15 51.86279182 26.72444099 54.89648087
H15 51.85901237 25.09171746 54.11224445
O15 51.86468155 31.31836566 54.68483152
Al15 54.63691005 35.76111222 61.18926949
O15 51.86657127 34.11894005 62.69349163
H15 51.86657127 32.31047197 62.82388275
O15 51.86657127 37.99665845 60.22550907
Si16 51.86468155 49.18950740 60.03842616
O16 51.86657127 48.60936142 56.98273872
H16 51.86846100 46.82923924 56.54243248
O16 49.29276403 50.79577477 60.82077286
Si16 51.86468155 56.13614133 55.93016116
O16 51.86279182 54.10090609 53.57745190
H16 51.87035073 52.33968116 54.09145746
O16 49.29276403 57.92004297 55.79977004
Si16 51.86279182 60.10456658 48.89471010
O16 51.85523291 57.16604217 47.87425789
H16 51.86657127 55.89614609 49.19706631
O16 49.29465376 61.58989147 47.89126542
Si16 51.86468155 40.81046093 29.96154217
O16 51.86657127 41.39060691 33.01722961
H16 51.86846100 43.17072909 33.45753584
O16 49.29276403 39.20419356 29.17919547
Si16 51.86468155 33.86382700 34.06980717
O16 51.86279182 35.89906224 36.42251643
H16 51.87035073 37.66028716 35.90851087
O16 49.29276403 32.07992536 34.20019829
Si16 51.86279182 29.89540174 41.10525823
O16 51.85523291 32.83203644 42.12571044
H16 51.86657127 34.10382224 40.80290202
O16 49.29465376 28.41007686 42.10870291
Si16 51.86468155 60.03842616 40.81046093
O16 51.86657127 56.98273872 41.39060691
H16 51.86846100 56.54243248 43.17072909
O16 49.29276403 60.82077286 39.20419356
Si16 51.86468155 55.93016116 33.86382700
O16 51.86279182 53.57745190 35.89906224
H16 51.87035073 54.09145746 37.66028716
O16 49.29276403 55.79977004 32.07992536
Si16 51.86279182 48.89471010 29.89540174
O16 51.85523291 47.87425789 32.83203644
H16 51.86657127 49.19706631 34.10382224
O16 49.29465376 47.89126542 28.41007686
Si16 51.86468155 29.96154217 49.18950740
O16 51.86657127 33.01722961 48.60936142
H16 51.86846100 33.45753584 46.82923924
O16 49.29276403 29.17919547 50.79577477
Si16 51.86468155 34.06980717 56.13614133
O16 51.86279182 36.42251643 54.10090609
H16 51.87035073 35.90851087 52.33968116
O16 49.29276403 34.20019829 57.92004297
Si16 51.86279182 41.10525823 60.10456658
O16 51.85523291 42.12571044 57.16604217
H16 51.86657127 40.80290202 55.89614609
O16 49.29465376 42.10870291 61.58989147
Al17 49.09623250 45.10202939 63.64402397
O17 48.42537966 48.15204765 65.42225643
H17 49.71039355 48.87014365 66.47672371
O17 46.27487111 46.50609604 61.79020246
O17 47.16115275 42.75687903 65.54886809
H17 45.83078543 43.21419280 66.69026279
Al17 49.09434277 54.41460066 61.09667290
O17 47.15548357 53.34123611 63.91614456
H17 45.83078543 54.30877598 64.68148371
O17 48.42537966 57.94649913 61.10423180
H17 49.71417300 59.09923219 61.64469353
O17 46.27298139 54.69805960 58.79120680
Al17 49.09812222 61.19304894 54.23318693
O17 47.15737330 61.67492915 57.20950587
H17 45.83078543 62.89569235 57.38525042
O17 48.42726938 64.25818502 52.48330036
H17 49.72173191 65.52052220 52.37180651
O17 46.27487111 60.28787004 52.08834756
Al17 49.09623250 44.89793894 26.35594436
O17 48.42537966 41.84792067 24.57771190
H17 49.71039355 41.12982468 23.52324462
O17 46.27487111 43.49387229 28.20976587
O17 47.16115275 47.24308930 24.45110024
H17 45.83078543 46.78577553 23.30970554
Al17 49.09434277 35.58347795 28.90329543
O17 47.15548357 36.65873222 26.08382377
H17 45.83078543 35.69119235 25.31848461
O17 48.42537966 32.05346919 28.89573653
H17 49.71417300 30.90073614 28.35527480
O17 46.27298139 35.30190873 31.20876153
Al17 49.09812222 28.80691939 35.76678140
O17 47.15737330 28.32503918 32.79046246
H17 45.83078543 27.10427598 32.61471791
O17 48.42726938 25.74178331 37.51666797
H17 49.72173191 24.47944613 37.62816182
O17 46.27487111 29.71209829 37.91162076
Al17 49.09623250 63.64402397 44.89793894
O17 47.16115275 65.54886809 47.24308930
H17 45.83078543 66.69026279 46.78577553
O17 48.42537966 65.42225643 41.84792067
H17 49.71039355 66.47672371 41.12982468
O17 46.27487111 61.79020246 43.49387229
Al17 49.09434277 61.09667290 35.58536767
O17 47.15548357 63.91614456 36.65873222
H17 45.83078543 64.68148371 35.69119235
O17 48.42537966 61.10423180 32.05346919
H17 49.71417300 61.64469353 30.90073614
O17 46.27298139 58.79120680 35.30190873
Al17 49.09812222 54.23318693 28.80691939
O17 47.15737330 57.20950587 28.32503918
H17 45.83078543 57.38525042 27.10427598
O17 48.42726938 52.48330036 25.74178331
H17 49.72173191 52.37180651 24.47944613
O17 46.27487111 52.08834756 29.71209829
Al17 49.09623250 26.35594436 45.10202939
O17 47.16115275 24.45110024 42.75687903
H17 45.83078543 23.30970554 43.21419280
O17 48.42537966 24.57771190 48.15204765
H17 49.71039355 23.52324462 48.87014365
O17 46.27487111 28.20976587 46.50609604
Al17 49.09434277 28.90329543 54.41460066
O17 47.15548357 26.08382377 53.34123611
H17 45.83078543 25.31848461 54.30877598
O17 48.42537966 28.89573653 57.94649913
H17 49.71417300 28.35527480 59.09923219
O17 46.27298139 31.20876153 54.69805960
Al17 49.09812222 35.76678140 61.19304894
O17 47.15737330 32.79046246 61.67492915
H17 45.83078543 32.61471791 62.89569235
O17 48.42726938 37.51666797 64.25818502
H17 49.72173191 37.62816182 65.52052220
O17 46.27487111 37.91162076 60.28787004
Al18 46.47896155 49.93216984 62.99773757
O18 43.71807141 49.85091161 65.24840161
H18 43.72752004 48.68117102 66.63357100
O18 43.70106387 50.83545902 60.76408107
Al18 46.47518210 58.26586288 58.11657450
O18 43.71429196 59.31655071 60.11023576
H18 43.72374059 58.99718696 61.89413740
O18 43.69917415 57.93516078 55.72985017
Al18 46.48085128 63.04687045 49.72996913
O18 43.71807141 64.95171458 50.93183506
H18 43.72752004 65.56776536 52.63447847
O18 43.70295360 61.57099420 47.82323528
Al18 46.47896155 40.06779849 27.00223076
O18 43.71807141 40.14905672 24.75156672
H18 43.72752004 41.31879731 23.36639733
O18 43.70106387 39.16450931 29.23588726
Al18 46.47518210 31.73410545 31.88339383
O18 43.71429196 30.68341762 29.88973257
H18 43.72374059 31.00278136 28.10583093
O18 43.69917415 32.06480755 34.27011816
Al18 46.48085128 26.95309788 40.26999920
O18 43.71807141 25.04825375 39.06813327
H18 43.72752004 24.43220297 37.36548986
O18 43.70295360 28.42897413 42.17673305
Al18 46.47896155 62.99773757 40.06779849
O18 43.71807141 65.24840161 40.14905672
H18 43.72752004 66.63357100 41.31879731
O18 43.70106387 60.76408107 39.16450931
Al18 46.47518210 58.11657450 31.73410545
O18 43.71429196 60.11023576 30.68341762
H18 43.72374059 61.89413740 31.00278136
O18 43.69917415 55.72985017 32.06480755
Al18 46.48085128 49.72996913 26.95309788
O18 43.71807141 50.93183506 25.04825375
H18 43.72752004 52.63447847 24.43220297
O18 43.70295360 47.82323528 28.42897413
Al18 46.47896155 27.00223076 49.93216984
O18 43.71807141 24.75156672 49.85091161
H18 43.72752004 23.36639733 48.68117102
O18 43.70106387 29.23588726 50.83545902
Al18 46.47518210 31.88339383 58.26586288
O18 43.71429196 29.88973257 59.31655071
H18 43.72374059 28.10583093 58.99718696
O18 43.69917415 34.27011816 57.93516078
Al18 46.48085128 40.26999920 63.04687045
O18 43.71807141 39.06813327 64.95171458
H18 43.72752004 37.36548986 65.56776536
O18 43.70295360 42.17673305 61.57099420
Si19 43.69161524 52.95006276 58.48129168
O19 41.14237445 54.72829522 58.84222941
O19 43.65760017 51.59701872 55.67882756
H19 43.68405634 49.76398420 55.71662209
Si19 43.69161524 58.62302115 52.69305998
O19 41.14426417 60.34456183 52.11858319
O19 43.65193099 56.04543446 50.94884260
H19 43.68216661 54.47696162 51.89937493
Si19 43.69350497 45.14927254 60.65069749
O19 41.14426417 46.50609604 61.86012233
O19 43.65382072 45.37981915 57.54776688
H19 43.68027688 43.77544151 56.65959552
Si19 43.69350497 44.85069579 29.34927084
O19 41.14426417 43.49387229 28.13984600
O19 43.65382072 44.62014918 32.45220145
H19 43.68027688 46.22452682 33.34037281
Si19 43.69161524 37.04990557 31.51867665
O19 41.14237445 35.27167311 31.15773892
O19 43.65760017 38.40294961 34.32114077
H19 43.68405634 40.23598413 34.28334624
Si19 43.69161524 31.37694717 37.30690834
O19 41.14426417 29.65540650 37.88138514
O19 43.65193099 33.95453387 39.05112573
H19 43.68216661 35.52300670 38.10059340
Si19 43.69350497 60.65069749 44.85069579
O19 41.14426417 61.86012233 43.49387229
O19 43.65382072 57.54776688 44.62203890
H19 43.68027688 56.65959552 46.22452682
Si19 43.69161524 58.48129168 37.04990557
O19 41.14237445 58.84222941 35.27167311
O19 43.65760017 55.67882756 38.40294961
H19 43.68405634 55.71473236 40.23598413
Si19 43.69161524 52.69305998 31.37694717
O19 41.14426417 52.11858319 29.65540650
O19 43.65193099 50.94884260 33.95453387
H19 43.68216661 51.89937493 35.52300670
Si19 43.69350497 29.34927084 45.14927254
O19 41.14426417 28.13984600 46.50609604
O19 43.65382072 32.45220145 45.37981915
H19 43.68027688 33.34037281 43.77544151
Si19 43.69161524 31.52056637 52.95006276
O19 41.14237445 31.15773892 54.72829522
O19 43.65760017 34.32114077 51.59701872
H19 43.68405634 34.28334624 49.76209447
Si19 43.69161524 37.30690834 58.62302115
O19 41.14426417 37.88138514 60.34456183
O19 43.65193099 39.05112573 56.04543446
H19 43.68216661 38.10059340 54.47696162
Al20 40.94017373 49.93783902 63.04498073
O20 38.98808645 48.16338601 65.50162493
H20 37.61425542 48.91171763 66.41625247
O20 40.23530582 53.35824365 63.97661580
H20 41.48819436 54.35034996 64.82888237
O20 38.17550413 50.81467203 60.86045711
Al20 40.94017373 58.29420878 58.15436903
O20 38.98430700 57.98807311 61.16659277
H20 37.61425542 59.09734246 61.58422229
O20 40.23341609 61.72217231 57.25674903
H20 41.48819436 63.00529647 57.49863400
O20 38.17550413 57.96161695 55.82055703
Al20 40.94206346 63.09411361 49.74697666
O20 38.98997618 64.33188435 52.51164626
H20 37.61425542 65.49595576 52.31889417
O20 40.23719554 65.61689824 47.25631738
H20 41.49386354 66.84899980 46.82734951
O20 38.17739386 61.64658326 47.89315515
Al20 40.94017373 40.06212931 26.95498760
O20 38.98808645 41.83658232 24.49834339
H20 37.61425542 41.08825070 23.58371586
O20 40.23530582 36.64172468 26.02335253
H20 41.48819436 35.64961837 25.17108596
O20 38.17550413 39.18529630 29.13951122
Al20 40.93828400 31.70575955 31.84559930
O20 38.98430700 32.01189522 28.83337556
H20 37.61425542 30.90262587 28.41574604
O20 40.23341609 28.27779602 32.74321930
H20 41.48819436 26.99467185 32.50133433
O20 38.17550413 32.03835138 34.17941130
Al20 40.94206346 26.90585472 40.25299167
O20 38.98997618 25.66808398 37.48832207
H20 37.61425542 24.50401257 37.68107415
O20 40.23719554 24.38307009 42.74365095
H20 41.49386354 23.15096853 43.17261882
O20 38.17739386 28.35338507 42.10681318
Al20 40.94017373 63.04498073 40.06212931
O20 38.98808645 65.50162493 41.83658232
H20 37.61425542 66.41625247 41.08825070
O20 40.23530582 63.97661580 36.64172468
H20 41.48819436 64.82888237 35.64961837
O20 38.17550413 60.86045711 39.18529630
Al20 40.93828400 58.15436903 31.70575955
O20 38.98430700 61.16659277 32.01189522
H20 37.61425542 61.58422229 30.90262587
O20 40.23341609 57.25674903 28.27779602
H20 41.48819436 57.49863400 26.99467185
O20 38.17550413 55.82055703 32.03835138
Al20 40.94206346 49.74697666 26.90585472
O20 38.98997618 52.51164626 25.66808398
H20 37.61425542 52.31889417 24.50401257
O20 40.23719554 47.25631738 24.38307009
H20 41.49386354 46.82734951 23.15096853
O20 38.17739386 47.89315515 28.35338507
Al20 40.94017373 26.95498760 49.93783902
O20 38.98808645 24.49834339 48.16338601
H20 37.61425542 23.58371586 48.91171763
O20 40.23530582 26.02335253 53.35824365
H20 41.48819436 25.17108596 54.35034996
O20 38.17550413 29.13951122 50.81467203
Al20 40.93828400 31.84559930 58.29420878
O20 38.98430700 28.83337556 57.98807311
H20 37.61425542 28.41574604 59.09734246
O20 40.23341609 32.74321930 61.72217231
H20 41.48819436 32.50133433 63.00529647
O20 38.17550413 34.17941130 57.96161695
Al20 40.94206346 40.25299167 63.09411361
O20 40.23719554 42.74365095 65.61689824
H20 41.49197381 43.17261882 66.84899980
O20 38.17739386 42.10681318 61.64658326
O20 38.98997618 37.48832207 64.33188435
H20 37.61425542 37.68107415 65.49595576
Al21 38.31723361 45.10202939 63.72717193
O21 35.61492498 46.55711865 61.78831273
O21 35.46752633 44.43495600 65.83232704
H21 35.48075441 42.97797701 66.90947104
Al21 38.31534388 54.45050546 61.16092359
O21 35.46752633 54.93049594 63.31710132
H21 35.47697496 54.20673076 64.98006047
O21 35.61492498 54.73774386 58.74963282
Al21 38.31723361 61.26485854 54.27098146
O21 35.46941605 62.76152178 55.90181526
H21 35.47697496 62.96372250 57.70272444
O21 35.61492498 60.31999538 52.03921468
Al21 38.31723361 44.89793894 26.27279640
O21 35.61492498 43.44284968 28.21165560
O21 35.46752633 45.56501233 24.16764129
H21 35.48075441 47.02199132 23.09049729
Al21 38.31534388 35.54946287 28.83904474
O21 35.46752633 35.06947239 26.68286701
H21 35.47697496 35.79323757 25.01990786
O21 35.61492498 35.26222447 31.25033551
Al21 38.31723361 28.73510979 35.72898687
O21 35.46941605 27.23844655 34.09815306
H21 35.47697496 27.03624583 32.29724389
O21 35.61492498 29.67997295 37.96075365
Al21 38.31723361 63.72717193 44.89793894
O21 35.46752633 65.83232704 45.56501233
H21 35.48075441 66.90947104 47.02199132
O21 35.61492498 61.78831273 43.44284968
Al21 38.31534388 61.16092359 35.54946287
O21 35.46752633 63.31710132 35.06947239
H21 35.47697496 64.98006047 35.79323757
O21 35.61492498 58.74963282 35.26222447
Al21 38.31723361 54.27098146 28.73510979
O21 35.46941605 55.90181526 27.23844655
H21 35.47697496 57.70272444 27.03624583
O21 35.61492498 52.03921468 29.67997295
Al21 38.31723361 26.27279640 45.10202939
O21 35.46752633 24.16764129 44.43495600
H21 35.48075441 23.09049729 42.97797701
O21 35.61492498 28.21165560 46.55711865
Al21 38.31534388 28.83904474 54.45050546
O21 35.46752633 26.68286701 54.93049594
H21 35.47697496 25.01990786 54.20673076
O21 35.61492498 31.25033551 54.73774386
Al21 38.31723361 35.72898687 61.26485854
O21 35.46941605 34.09815306 62.76152178
H21 35.47697496 32.29724389 62.96372250
O21 35.61492498 37.96075365 60.31999538
Si22 35.63949142 49.15738205 60.08566932
O22 35.64516060 48.53944155 57.03565105
H22 35.70941130 46.75742964 56.61046263
O22 33.09969926 50.78254668 60.84911875
Si22 35.63949142 56.14181051 55.97740432
O22 35.63760170 54.08200882 53.63981287
H22 35.70563184 52.32645308 54.16326706
O22 33.10158898 57.93327105 55.83000566
Si22 35.64138115 60.14614056 48.93628407
O22 35.64705033 57.19627779 47.94228803
H22 35.71130102 55.93394061 49.27265536
O22 33.10158898 61.62012709 47.91583187
Si22 35.63949142 40.84258628 29.91429901
O22 35.64516060 41.46052678 32.96431728
H22 35.70941130 43.24253869 33.38950570
O22 33.09969926 39.21742165 29.15084958
Si22 35.63949142 33.85815782 34.02256401
O22 35.63760170 35.91795950 36.36015546
H22 35.70563184 37.67351525 35.83670127
O22 33.10158898 32.06669728 34.16996266
Si22 35.64138115 29.85382777 41.06368425
O22 35.64705033 32.80369054 42.05768030
H22 35.71130102 34.06602772 40.72731297
O22 33.10158898 28.37984124 42.08413646
Si22 35.63949142 60.08566932 40.84258628
O22 35.64516060 57.03565105 41.46052678
H22 35.70941130 56.61046263 43.24253869
O22 33.09969926 60.84911875 39.21742165
Si22 35.63949142 55.97740432 33.85815782
O22 35.63760170 53.63981287 35.91795950
H22 35.70563184 54.16326706 37.67351525
O22 33.10158898 55.83000566 32.06669728
Si22 35.64138115 48.93628407 29.85382777
O22 35.64705033 47.94228803 32.80369054
H22 35.71130102 49.27265536 34.06602772
O22 33.10158898 47.91583187 28.37984124
Si22 35.63949142 29.91429901 49.15738205
O22 35.64516060 32.96431728 48.53944155
H22 35.70941130 33.38950570 46.75742964
O22 33.09969926 29.15084958 50.78254668
Si22 35.63949142 34.02256401 56.14181051
O22 35.63760170 36.36015546 54.08200882
H22 35.70563184 35.83670127 52.32645308
O22 33.10158898 34.16996266 57.93327105
Si22 35.64138115 41.06368425 60.14614056
O22 35.64705033 42.05768030 57.19627779
H22 35.71130102 40.72731297 55.93394061
O22 33.10158898 42.08413646 61.62012709
Al23 32.75954852 45.07935267 63.64780342
O23 31.83547235 48.16149629 65.41091807
H23 33.01277185 49.02699094 66.48995180
O23 30.21219745 46.44751452 61.60878873
H23 28.91395547 45.13226501 61.21194620
O23 30.57691463 42.68884888 65.37123382
H23 29.07836166 43.20474417 66.25562573
Al23 32.76143825 54.39192394 61.10423180
O23 30.58825299 53.18816828 63.80465071
H23 29.09158975 54.07822937 64.32054599
O23 31.83547235 57.94460941 61.08722427
H23 33.01655130 59.23340275 61.58422229
O23 30.21597690 54.55255068 58.65136705
H23 28.91395547 53.22407308 58.97828970
Al23 32.76332797 61.18926949 54.25208419
O23 30.58825299 61.49162570 57.18493943
H23 29.09725893 62.52530599 57.18493943
O23 31.82980318 64.25629529 52.46629283
H23 33.01088212 65.61878797 52.24141540
O23 30.21597690 60.09889741 52.04866331
H23 28.91773493 59.10490136 52.99541619
Al23 32.75954852 44.92061566 26.35216491
O23 31.83358263 41.83847204 24.58905026
H23 33.01277185 40.97297739 23.51001653
O23 30.21219745 43.55245381 28.39117960
H23 28.91395547 44.86770332 28.78802213
O23 30.57691463 47.31111945 24.62873451
H23 29.07836166 46.79522416 23.74434260
Al23 32.76143825 35.60804439 28.89573653
O23 30.58825299 36.81180005 26.19531762
H23 29.09158975 35.92173896 25.67942234
O23 31.83547235 32.05535892 28.91274406
H23 33.01655130 30.76656557 28.41574604
O23 30.21597690 35.44741765 31.34860128
H23 28.91395547 36.77589525 31.02167863
Al23 32.76332797 28.81069884 35.74788414
O23 30.58825299 28.50834263 32.81502890
H23 29.09536920 27.47466234 32.81502890
O23 31.82980318 25.74367304 37.53367550
H23 33.01088212 24.38118036 37.75855293
O23 30.21597690 29.90107092 37.95130502
H23 28.91773493 30.89506696 37.00455213
Al23 32.75954852 63.64780342 44.92061566
O23 30.57691463 65.37123382 47.31111945
H23 29.07836166 66.25562573 46.79522416
O23 31.83358263 65.41091807 41.83847204
H23 33.01277185 66.48995180 40.97297739
O23 30.21219745 61.60878873 43.55245381
H23 28.91395547 61.21194620 44.86770332
Al23 32.76143825 61.10423180 35.60804439
O23 30.58636326 63.80465071 36.81180005
H23 29.09158975 64.32054599 35.92173896
O23 31.83547235 61.08722427 32.05535892
H23 33.01655130 61.58422229 30.76656557
O23 30.21597690 58.65136705 35.44741765
H23 28.91395547 58.97828970 36.77589525
Al23 32.76332797 54.25208419 28.81069884
O23 30.58825299 57.18493943 28.50834263
H23 29.09536920 57.18493943 27.47466234
O23 31.82980318 52.46629283 25.74367304
H23 33.01088212 52.24141540 24.38118036
O23 30.21597690 52.04866331 29.90107092
H23 28.91773493 52.99541619 30.89506696
Al23 32.75954852 26.35216491 45.07935267
O23 30.57691463 24.62873451 42.68884888
H23 29.07836166 23.74434260 43.20474417
O23 31.83358263 24.58905026 48.16149629
H23 33.01277185 23.51001653 49.02699094
O23 30.21219745 28.39117960 46.44751452
H23 28.91395547 28.78802213 45.13226501
Al23 32.76143825 28.89573653 54.39192394
O23 30.58636326 26.19531762 53.18816828
H23 29.09158975 25.67942234 54.07822937
O23 31.83547235 28.91274406 57.94460941
H23 33.01655130 28.41574604 59.23340275
O23 30.21597690 31.34860128 54.55255068
H23 28.91395547 31.02167863 53.22407308
Al23 32.76332797 35.74788414 61.18926949
O23 30.58825299 32.81502890 61.49162570
H23 29.09536920 32.81502890 62.52530599
O23 31.82980318 37.53367550 64.25629529
H23 33.01088212 37.75855293 65.61878797
O23 30.21597690 37.95130502 60.09889741
H23 28.91773493 37.00455213 59.10490136
Al24 30.10448305 49.81689654 62.59333614
O24 27.09225931 49.52398896 65.37690300
H24 27.75933270 48.18606273 66.44270864
H24 25.62016251 48.88148201 64.50006999
O24 27.55146280 50.77498778 60.42959951
H24 27.24154769 49.49186361 59.16915206
Al24 30.10637278 57.96539640 57.82366692
O24 27.09792849 59.11435000 60.38046663
H24 27.76878133 58.50018894 61.97350591
H24 25.61638306 58.12413341 59.95716793
O24 27.55335253 57.70839362 55.47284739
H24 27.25288605 55.96606596 55.02309253
Al24 30.10070360 62.63302039 49.62414445
O24 27.09036958 64.89691251 51.26442689
H24 27.76878133 65.17281256 52.94628331
H24 25.61260361 63.82543769 51.40615637
O24 27.55524226 61.22706401 47.71174142
H24 27.24910659 59.49607471 48.19929081
Al24 30.10448305 40.18307179 27.40663219
O24 27.09225931 40.47597937 24.62306533
H24 27.75933270 41.81390560 23.55725969
H24 25.62016251 41.11848632 25.49989834
O24 27.55146280 39.22498055 29.57036882
H24 27.24154769 40.50810472 30.83081627
Al24 30.10637278 32.03457193 32.17630140
O24 27.09792849 30.88561833 29.61950170
H24 27.76878133 31.49977938 28.02646242
H24 25.61638306 31.87583492 30.04091067
O24 27.55335253 32.29157471 34.52712094
H24 27.25288605 34.03390237 34.97687580
Al24 30.10070360 27.36694794 40.37582388
O24 27.09036958 25.10305581 38.73554144
H24 27.76878133 24.82715577 37.05368502
H24 25.61260361 26.17453063 38.59381196
O24 27.55524226 28.77290431 42.28822691
H24 27.24910659 30.50389362 41.80067752
Al24 30.10448305 62.59333614 40.18307179
O24 27.09225931 65.37690300 40.47597937
H24 27.75933270 66.44270864 41.81390560
H24 25.62016251 64.50006999 41.11848632
O24 27.55146280 60.42959951 39.22498055
H24 27.24154769 59.16915206 40.50810472
Al24 30.10637278 57.82366692 32.03457193
O24 27.09792849 60.38046663 30.88561833
H24 27.76878133 61.97350591 31.49977938
H24 25.61638306 59.95716793 31.87583492
O24 27.55335253 55.47284739 32.29157471
H24 27.25288605 55.02309253 34.03390237
Al24 30.10070360 49.62414445 27.36694794
O24 27.09036958 51.26442689 25.10305581
H24 27.76878133 52.94628331 24.82715577
H24 25.61260361 51.40615637 26.17453063
O24 27.55524226 47.71174142 28.77290431
H24 27.24910659 48.19929081 30.50389362
Al24 30.10448305 27.40663219 49.81689654
O24 27.09225931 24.62306533 49.52398896
H24 27.75933270 23.55725969 48.18606273
H24 25.62016251 25.49989834 48.88148201
O24 27.55146280 29.57036882 50.77498778
H24 27.24154769 30.83081627 49.49186361
Al24 30.10637278 32.17630140 57.96539640
O24 27.09792849 29.61950170 59.11435000
H24 27.76878133 28.02646242 58.50018894
H24 25.61638306 30.04280040 58.12413341
O24 27.55335253 34.52712094 57.70839362
H24 27.25288605 34.97687580 55.96606596
Al24 30.10070360 40.37582388 62.63302039
O24 27.09036958 38.73554144 64.89691251
H24 27.76878133 37.05368502 65.17281256
H24 25.61260361 38.59381196 63.82543769
O24 27.55524226 42.28822691 61.22706401
H24 27.24910659 41.80067752 59.49607471
OOH 60.02263004 49.82634517 65.22383517
HOH 60.02074031 48.64904567 66.60144565
OOH 60.02263004 59.29198427 60.10834604
HOH 60.02074031 58.96695134 61.89035795
OOH 60.02263004 64.90258169 50.93183506
HOH 60.02074031 65.50351466 52.64203737
OOH 60.02263004 40.17362316 24.77613316
HOH 60.02074031 41.35092265 23.39852268
OOH 60.02263004 30.70798406 29.89162229
HOH 60.02074031 31.03301699 28.10961038
OOH 60.02263004 25.09738664 39.06813327
HOH 60.02074031 24.49645367 37.35793095
OOH 60.02263004 65.22383517 40.17362316
HOH 60.02074031 66.60144565 41.35092265
OOH 60.02263004 60.10834604 30.70798406
HOH 60.02074031 61.89035795 31.03301699
OOH 60.02263004 50.93183506 25.09738664
HOH 60.02074031 52.64203737 24.49645367
OOH 60.02263004 24.77613316 49.82634517
HOH 60.02074031 23.39852268 48.64904567
OOH 60.02263004 29.89162229 59.29198427
HOH 60.02074031 28.10961038 58.96695134
OOH 60.02263004 39.06813327 64.90258169
HOH 60.02074031 37.35793095 65.50351466
%endblock positions_abs"""
def test_onetep_input():
"""Read onetep input file."""
# For tests we use a StringIO object.
# in-memory text-file like object.
fd = StringIO(onetep_input)
atoms = read(fd, format='onetep-in')
fd.seek(0)
original_cell = atoms.get_cell()
original_tags = atoms.get_tags()
original_species = atoms.info['onetep_species']
original_keywords = get_onetep_keywords(fd)
fd.seek(0)
original_keywords = dict(sorted(original_keywords.items()))
# We test for the correct number of tags and species
assert len(set(original_species)) == 71
assert len(set(original_tags)) == 24
assert len(atoms) == 1_416
assert original_cell.cellpar() == approx(
[120.0, 90.0, 90.0, 90.0, 90.0, 90.0])
fdbis = StringIO()
# We pass the pseudopotentials manually as well,
# Â To test if it is working correctly.
write(fdbis, atoms, format='onetep-in',
keywords=original_keywords,
pseudopotentials=original_keywords['species_pot'])
fdbis.seek(0)
cycled_atoms = read(fdbis, format='onetep-in')
fdbis.seek(0)
cycled_keywords = get_onetep_keywords(fdbis)
# The dictionary should be similar, cycled dictionary
# Might have additional keywords (the defaults), which
# is normal
for key in original_keywords:
keyl = key.lower()
assert keyl in cycled_keywords
assert cycled_keywords[keyl] == original_keywords[key]
# Is everything well written ?
assert cycled_atoms.positions == approx(atoms.positions)
assert cycled_atoms.info['onetep_species'] == original_species
assert np.all(cycled_atoms.get_tags() == original_tags)
assert cycled_atoms.get_cell().cellpar() == approx(original_cell.cellpar())
@pytest.fixture()
def test_onetep_recursive_include_input(datadir):
testfile_path = datadir / "onetep_include.dat"
with pytest.raises(ValueError):
read(testfile_path, format='onetep-in')
@pytest.fixture()
def test_onetep_nested_include_input(datadir):
testfile_path = datadir / "onetep_include_nested.dat"
with pytest.raises(ValueError):
read(testfile_path, format='onetep-in')
test_output = """
|Linear-Scaling Ab Initio Total Energy Program|
--------------------------------------------------------------------------------
---------------------------------- INPUT FILE ----------------------------------
--------------------------------------------------------------------------------
cutoff_energy : 25
edft : F
forces_output_detail : verbose
output_detail : verbose
paw : F
do_properties = T
read_denskern : F
read_hamiltonian : F
read_tightbox_ngwfs : F
task : singlepoint
write_forces : T
xc_functional : pbe
zero_total_force: : T
%BLOCK LATTICE_CART
ang
14.00000000 0.00000000 0.00000000
0.00000000 15.52647800 0.00000000
0.00000000 0.00000000 14.59630900
%ENDBLOCK LATTICE_CART
%BLOCK POSITIONS_ABS
ang
O 7.000000 7.763239 7.596309
HKO 7.000000 8.526478 7.000000
H1 7.000000 7.000000 7.000000
%ENDBLOCK POSITIONS_ABS
%BLOCK SPECIES
H1 H 1 -1 9.0
HKO H 1 -1 9.0
O O 8 -1 9.0
%ENDBLOCK SPECIES
%BLOCK SPECIES_POT
H1 H_NCP19_PBE.usp
HKO H_NCP19_PBE.usp
O O_NCP19_PBE.usp
%ENDBLOCK SPECIES_POT
...
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000049392392 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.15138690746626 |
| Pseudopotential (local) : -45.29591161192612 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.33142854358881 |
| Hartree : 17.94293053457817 |
| Exchange-correlation : -4.25961784082707 |
| Ewald : 3.64621627669446 |
| Total : -17.14642427760311 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.29591161192528 |
| Hartree : 17.94293053457780 |
--------------------------------------------------------
Integrated density : 7.99999999999942
Integrated density tr(KS) : 8.00000000000000
================================================================================
...
Mulliken Atomic Populations
---------------------------
Species Ion Total Charge (e) Spin (hbar)
=================================================
O 1 7.011 -1.011 0.00
H 2 0.494 0.506 0.00
H 3 0.494 0.506 -0.00
=================================================
...
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000017 0.00000001 0.00168584 *
* H 2 0.00000005 0.00468666 -0.00084292 *
* H 3 -0.00000021 -0.00468667 -0.00084292 *
* *
**********************************************************
* TOTAL: 0.00000000 0.00000000 -0.00000000 *
**********************************************************
"""
def test_onetep_output():
fd = StringIO(test_output)
atoms = read(fd, format='onetep-out')
rpositions = np.loadtxt(test_output.splitlines()[27:30],
usecols=(1, 2, 3))
rcell = np.loadtxt(test_output.splitlines()[21:24])
assert len(atoms) == 3
assert atoms.get_chemical_symbols() == ['O', 'H', 'H']
assert list(atoms.get_tags()) == [0, 0, 1]
assert atoms.info['onetep_species'] == ['O', 'HKO', 'H1']
assert atoms.get_cell() == approx(rcell)
assert atoms.positions == approx(rpositions)
assert atoms.get_total_energy() == approx(-17.14642427760311 * 27.2116529)
assert atoms.get_magnetic_moments() == approx([0, 0, 0])
assert atoms.get_charges() == approx([-1.011, 0.506, 0.506])
fdi = StringIO()
write(fdi, atoms, format='onetep-in', keywords={'species_pot': []})
fdi.seek(0)
cycled_atoms = read(fdi, format='onetep-in')
assert cycled_atoms.positions == approx(atoms.positions)
assert cycled_atoms.get_cell().array \
== approx(atoms.get_cell().array)
assert cycled_atoms.get_chemical_symbols() == ['O', 'H', 'H']
assert list(cycled_atoms.get_tags()) == [0, 0, 1]
assert cycled_atoms.info['onetep_species'] == ['O', 'HKO', 'H1']
test_geom = """
|Linear-Scaling Ab Initio Total Energy Program|
--------------------------------------------------------------------------------
---------------------------------- INPUT FILE ----------------------------------
--------------------------------------------------------------------------------
cutoff_energy : 25
edft : F
forces_output_detail : verbose
output_detail : verbose
paw : F
do_properties = T
pseudo_path : /home/td5g20/PseudoPotentials/CASTEP
read_denskern : F
read_hamiltonian : F
read_tightbox_ngwfs : F
task : geometryoptimization
write_forces : T
xc_functional : pbe
zero_total_force: : T
spin_polarized : T
%BLOCK LATTICE_CART
ang
14.00000000 0.00000000 0.00000000
0.00000000 15.52647800 0.00000000
0.00000000 0.00000000 14.59630900
%ENDBLOCK LATTICE_CART
%BLOCK POSITIONS_ABS
ang
O 7.000000 7.763239 7.596309
H 7.000000 8.526478 7.000000
H 7.000000 7.000000 7.000000
%ENDBLOCK POSITIONS_ABS
%BLOCK SPECIES
H H 1 -1 9.0
O O 8 -1 9.0
%ENDBLOCK SPECIES
%BLOCK SPECIES_POT
H H_NCP19_PBE.usp
O O_NCP19_PBE.usp
%ENDBLOCK SPECIES_POT
--------------------------------------------------------------------------------
-------------------------------- END INPUT FILE --------------------------------
--------------------------------------------------------------------------------
================================================================================
<<<<<<<<<<<<<<<<<<<< Starting ONETEP Geometry Optimisation >>>>>>>>>>>>>>>>>>>>>
================================================================================
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228083 14.670396 14.354944 x
x H 2 13.228083 16.112708 13.228083 x
x H 3 13.228083 13.228083 13.228083 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000049365477 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.15138700581343 |
| Pseudopotential (local) : -45.29591196181978 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.33142848578819 |
| Hartree : 17.94293076819679 |
| Exchange-correlation : -4.25961788057561 |
| Ewald : 3.64621627669446 |
| Total : -17.14642427747891 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.29591196181885 |
| Hartree : 17.94293076819639 |
--------------------------------------------------------
Integrated density : 7.99999999999935
Integrated spin density : 0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : 0.00000000000000
================================================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000017 0.00000001 0.00168584 *
* H 2 0.00000005 0.00468665 -0.00084292 *
* H 3 -0.00000021 -0.00468666 -0.00084292 *
* *
**********************************************************
* TOTAL: -0.00000000 0.00000000 0.00000000 *
**********************************************************
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228083 14.670396 14.354944 x
x H 2 13.228083 16.112708 13.228083 x
x H 3 13.228083 13.228083 13.228083 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
================================================================================
Starting BFGS iteration 1 ...
================================================================================
--------------------------------------------------------------------------------
BFGS: starting iteration 1 with trial guess (lambda= 1.000000)
--------------------------------------------------------------------------------
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228083 14.670396 14.357610 x
x H 2 13.228083 16.120121 13.226750 x
x H 3 13.228083 13.220671 13.226750 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000171727103 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.13481223219661 |
| Pseudopotential (local) : -45.23291246538913 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.32646093297728 |
| Hartree : 17.91882908342904 |
| Exchange-correlation : -4.25560090215423 |
| Ewald : 3.61486999206686 |
| Total : -17.14646299282811 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.23291246538828 |
| Hartree : 17.91882908342841 |
--------------------------------------------------------
Integrated density : 7.99999999999959
Integrated spin density : 0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : 0.00000000000000
================================================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000016 -0.00000002 -0.00307940 *
* H 2 0.00000004 0.00097257 0.00153970 *
* H 3 -0.00000020 -0.00097256 0.00153971 *
* *
**********************************************************
* TOTAL: 0.00000000 0.00000000 0.00000000 *
**********************************************************
================================================================================
Starting BFGS iteration 2 ...
================================================================================
--------------------------------------------------------------------------------
BFGS: starting iteration 2 with trial guess (lambda= 1.000000)
--------------------------------------------------------------------------------
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228084 14.670396 14.353542 x
x H 2 13.228083 16.124318 13.228784 x
x H 3 13.228082 13.216473 13.228784 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000192244606 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.13593475185653 |
| Pseudopotential (local) : -45.23397489927260 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.32747190453635 |
| Hartree : 17.91926583391236 |
| Exchange-correlation : -4.25563115178118 |
| Ewald : 3.61539396585219 |
| Total : -17.14648340396906 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.23397489927187 |
| Hartree : 17.91926583391191 |
--------------------------------------------------------
Integrated density : 7.99999999999975
Integrated spin density : 0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : 0.00000000000000
================================================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000009 0.00000001 -0.00166320 *
* H 2 0.00000007 0.00050115 0.00083161 *
* H 3 -0.00000016 -0.00050116 0.00083160 *
* *
**********************************************************
* TOTAL: 0.00000000 0.00000000 -0.00000000 *
**********************************************************
--------------------------------------------------------------------------------
BFGS: improving iteration 2 with line minimization (lambda= 2.139448)
--------------------------------------------------------------------------------
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228084 14.670396 14.348907 x
x H 2 13.228083 16.129100 13.231101 x
x H 3 13.228082 13.211691 13.231101 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000062544500 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.13744677158684 |
| Pseudopotential (local) : -45.23541018986488 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.32868109575617 |
| Hartree : 17.92001657331161 |
| Exchange-correlation : -4.25573633839171 |
| Ewald : 3.61587019993617 |
| Total : -17.14649407917814 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.23541018986398 |
| Hartree : 17.92001657331134 |
--------------------------------------------------------
Integrated density : 7.99999999999966
Integrated spin density : -0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : -0.00000000000000
================================================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000005 0.00000004 -0.00041890 *
* H 2 0.00000008 0.00005458 0.00020947 *
* H 3 -0.00000013 -0.00005462 0.00020943 *
* *
**********************************************************
* TOTAL: 0.00000000 -0.00000000 -0.00000000 *
**********************************************************
================================================================================
Starting BFGS iteration 3 ...
================================================================================
--------------------------------------------------------------------------------
BFGS: starting iteration 3 with trial guess (lambda= 1.000000)
--------------------------------------------------------------------------------
-------------------------------
Cell Contents
-------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228084 14.670396 14.347758 x
x H 2 13.228083 16.130115 13.231676 x
x H 3 13.228081 13.210676 13.231676 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000195824432 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.13806089541814 |
| Pseudopotential (local) : -45.23657364189620 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.32907290394940 |
| Hartree : 17.92040456637980 |
| Exchange-correlation : -4.25580224655208 |
| Ewald : 3.61648868205110 |
| Total : -17.14649464854864 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.23657364189524 |
| Hartree : 17.92040456637923 |
--------------------------------------------------------
Integrated density : 7.99999999999938
Integrated spin density : 0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : 0.00000000000000
================================================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000002 -0.00000005 0.00005977 *
* H 2 0.00000009 -0.00001746 -0.00002990 *
* H 3 -0.00000011 0.00001751 -0.00002987 *
* *
**********************************************************
* TOTAL: -0.00000000 0.00000000 0.00000000 *
**********************************************************
================================================================================
BFGS : Final Configuration:
================================================================================
-------------------------------
Cell Contents
-------------------------------
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x Element Atom Absolute co-ordinates of atoms x
x Number x y z x
x----------------------------------------------------------x
x O 1 13.228084 14.670396 14.347758 x
x H 2 13.228083 16.130115 13.231676 x
x H 3 13.228081 13.210676 13.231676 x
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........................................................
| *** NGWF optimisation converged *** |
| RMS NGWF gradient = 0.00000195826989 |
| Criteria satisfied: |
| -> RMS NGWF gradient lower than set threshold. |
========================================================
================================================================================
---------------- ENERGY COMPONENTS (Eh) ----------------
| Kinetic : 12.13806088831265 |
| Pseudopotential (local) : -45.23657354211792 |
| Pseudo (non-coul chg cor) : 0.00000000000000
| Pseudopotential (non-local): -1.32907295131071 |
| Hartree : 17.92040450997095 |
| Exchange-correlation : -4.25580223545482 |
| Ewald : 3.61648868205110 |
| Total : -17.14649464854874 |
--------------------------------------------------------
------ LOCAL ENERGY COMPONENTS FROM MATRIX TRACES ------
| Pseudopotential (local) : -45.23657354211692 |
| Hartree : 17.92040450997042 |
--------------------------------------------------------
Integrated density : 7.99999999999944
Integrated spin density : 0.00000000000000
Integrated |spin density| : 0.00000000000000
Local density approx. <S^2> : 0.00000000000000
Integrated density tr(KS) : 8.00000000000000
Integrated spin tr(KS) : -0.00000000000000
================================================================================
Mulliken Atomic Populations
---------------------------
Species Ion Total Charge (e) Spin (hbar)
=================================================
O 1 7.009 -1.009 -0.00
H 2 0.495 0.505 0.00
H 3 0.495 0.505 0.00
=================================================
********************* Unconstrained **********************
************************* Forces *************************
* *
* Element Atom Cartesian components (Eh/a) *
* ------------------------------------------------------ *
* x y z *
* *
* O 1 0.00000002 -0.00000005 0.00005976 *
* H 2 0.00000009 -0.00001747 -0.00002990 *
* H 3 -0.00000011 0.00001751 -0.00002986 *
* *
**********************************************************
* TOTAL: 0.00000000 0.00000000 0.00000000 *
**********************************************************
"""
def test_geom_output():
positions_to_test = [14.354944, 14.357610, 14.353542, 14.347758]
forces_to_test = [0.00168584, -0.00307940, -0.00166320, 0.00005977]
energy_to_test = [-17.14642427747891, -17.14646299282811,
-17.14648340396906, -17.14649464854864]
fd = StringIO(test_geom)
atoms = read(fd, format='onetep-out', index="::")
# Last configuration should have the properties:
last_charges = atoms[-1].get_charges()
last_magnetic_moments = atoms[-1].get_magnetic_moments()
assert last_charges == approx([-1.009, 0.505, 0.505])
assert last_magnetic_moments == approx([0, 0, 0])
# We test the z positions of the oxygen atom
# and we test if the forces correspond to the correct
# positions
for i, x in enumerate(atoms):
tmp = x.positions[0][-1] * angtobohr
assert tmp == approx(positions_to_test[i])
assert x.get_forces()[
0][-1] == approx(forces_to_test[i] * eV2au * angtobohr)
assert x.get_total_energy() == approx(energy_to_test[i] * eV2au)
# We test an output that has different ONETEP
# outputs in it. (multi-calculation output)
weird_output = '\n'.join([test_output,
test_geom,
test_output])
def test_weird_output():
energy_to_test = [-17.14642427760311, -17.14642427747891,
-17.14646299282811, -17.14648340396906,
-17.14649464854864, -17.14642427760311]
fd = StringIO(weird_output)
atoms_list = read(fd, format='onetep-out', index="::")
# Should be 1 + 4 + 1
assert len(atoms_list) == 6
# The before last configuration should be the same as the
# last configuration of the previous test
last_charges = atoms_list[-2].get_charges()
last_magnetic_moments = atoms_list[-2].get_magnetic_moments()
assert last_charges == approx([-1.009, 0.505, 0.505])
assert last_magnetic_moments == approx([0, 0, 0])
# The first and last energy should be equal
first_energy = atoms_list[0].get_total_energy()
last_energy = atoms_list[-1].get_total_energy()
# The most important: we test all the
# energy to make sure configurations
# didn't get mixed up...
assert first_energy == approx(last_energy)
for ref_energy, test_atoms in zip(energy_to_test, atoms_list):
test_energy = test_atoms.get_potential_energy()
assert test_energy == approx(ref_energy * eV2au)
|
