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Hi
I,m testing last version of lammps interface with a .cif produced from material studio, (testing with UFF force field) but I obtain error
lammps-interface TON_1x1x3_METHANE_B.cif
fatal: Not a git repository (or any of the parent directories): .git
Molecules found in the framework, separating.
Traceback (most recent call last):
File "/usr/local/bin/lammps-interface", line 6, in
exec(compile(open(file).read(), file, 'exec'))
File "/opt/lammps_interface-master/lammps-interface", line 14, in
sim.assign_force_fields()
File "/opt/lammps_interface-master/lammps_interface/lammps_main.py", line 462, in assign_force_fields
atoms = ", ".join([rep.node[j]['element'] for j in rep.nodes()])
File "/opt/lammps_interface-master/lammps_interface/lammps_main.py", line 462, in
atoms = ", ".join([rep.node[j]['element'] for j in rep.nodes()])
AttributeError: 'MolecularGraph' object has no attribute 'node'
my cif file is similar to example in directory test.
Is it peraphs a bug
Could I fix it?
my cif file
data_TON_1x1x3_METHANE
_audit_creation_date 2019-12-12
_audit_creation_method 'Materials Studio'
_symmetry_space_group_name_H-M 'P1'
_symmetry_Int_Tables_number 1 symmetry_cell_setting triclinic
loop
_symmetry_equiv_pos_as_xyz
x,y,z
_cell_length_a 13.8590
_cell_length_b 17.4200
_cell_length_c 15.1140
_cell_angle_alpha 90.0000
_cell_angle_beta 90.0000 cell_angle_gamma 90.0000
loop
_atom_site_label
_atom_site_type_symbol atom_site_description atom_site_fract_x atom_site_fract_y atom_site_fract_z atom_site_charge
Si1 Si Si3 0.29510 0.04820 0.07550 0.00000
Si2 Si Si3 0.20550 0.21120 0.04817 0.00000
O3 O O_3_z 0.09230 0.42680 0.23257 0.00000
O4 O O_3_z 0.09420 0.22240 0.06893 0.00000
O5 O O_3_z 0.27120 0.37890 0.22130 0.00000
O6 O O_3_z 0.22880 0.48000 0.00780 0.00000
O7 O O_3_z 0.27050 0.25840 0.11783 0.00000
Si8 Si Si3 0.79510 0.54820 0.07550 0.00000
Si9 Si Si3 0.70550 0.71120 0.04817 0.00000
O10 O O_3_z 0.59230 0.92680 0.23257 0.00000
O11 O O_3_z 0.59420 0.72240 0.06893 0.00000
O12 O O_3_z 0.77120 0.87890 0.22130 0.00000
O13 O O_3_z 0.72880 0.98000 0.00780 0.00000
O14 O O_3_z 0.77050 0.75840 0.11783 0.00000
Si15 Si Si3 0.70490 0.95180 0.24217 0.00000
Si16 Si Si3 0.79450 0.78880 0.21483 0.00000
O17 O O_3_z 0.90770 0.57320 0.06590 0.00000
O18 O O_3_z 0.90580 0.77760 0.23560 0.00000
O19 O O_3_z 0.72880 0.62110 0.05463 0.00000
O20 O O_3_z 0.77120 0.52000 0.17447 0.00000
O21 O O_3_z 0.72950 0.74160 0.28450 0.00000
Si22 Si Si3 0.20490 0.45180 0.24217 0.00000
Si23 Si Si3 0.29450 0.28880 0.21483 0.00000
O24 O O_3_z 0.40770 0.07320 0.06590 0.00000
O25 O O_3_z 0.40580 0.27760 0.23560 0.00000
O26 O O_3_z 0.22880 0.12110 0.05463 0.00000
O27 O O_3_z 0.27120 0.02000 0.17447 0.00000
O28 O O_3_z 0.22950 0.24160 0.28450 0.00000
Si29 Si Si3 0.29510 0.95180 0.24217 0.00000
Si30 Si Si3 0.20550 0.78880 0.21483 0.00000
O31 O O_3_z 0.09230 0.57320 0.06590 0.00000
O32 O O_3_z 0.09420 0.77760 0.23560 0.00000
O33 O O_3_z 0.27120 0.62110 0.05463 0.00000
O34 O O_3_z 0.22880 0.52000 0.17447 0.00000
O35 O O_3_z 0.27050 0.74160 0.28450 0.00000
Si36 Si Si3 0.79510 0.45180 0.24217 0.00000
Si37 Si Si3 0.70550 0.28880 0.21483 0.00000
O38 O O_3_z 0.59230 0.07320 0.06590 0.00000
O39 O O_3_z 0.59420 0.27760 0.23560 0.00000
O40 O O_3_z 0.77120 0.12110 0.05463 0.00000
O41 O O_3_z 0.72880 0.02000 0.17447 0.00000
O42 O O_3_z 0.77050 0.24160 0.28450 0.00000
Si43 Si Si3 0.70490 0.04820 0.07550 0.00000
Si44 Si Si3 0.79450 0.21120 0.04817 0.00000
O45 O O_3_z 0.90770 0.42680 0.23257 0.00000
O46 O O_3_z 0.90580 0.22240 0.06893 0.00000
O47 O O_3_z 0.72880 0.37890 0.22130 0.00000
O48 O O_3_z 0.77120 0.48000 0.00780 0.00000
O49 O O_3_z 0.72950 0.25840 0.11783 0.00000
Si50 Si Si3 0.20490 0.54820 0.07550 0.00000
Si51 Si Si3 0.29450 0.71120 0.04817 0.00000
O52 O O_3_z 0.40770 0.92680 0.23257 0.00000
O53 O O_3_z 0.40580 0.72240 0.06893 0.00000
O54 O O_3_z 0.22880 0.87890 0.22130 0.00000
O55 O O_3_z 0.27120 0.98000 0.00780 0.00000
O56 O O_3_z 0.22950 0.75840 0.11783 0.00000
Si57 Si Si3 0.00000 0.27370 0.08333 0.00000
Si58 Si Si3 0.00000 0.37680 0.24883 0.00000
O59 O O_3_z 0.00000 0.30620 0.18137 0.00000
O60 O O_3_z 0.00000 0.34500 0.01643 0.00000
Si61 Si Si3 0.50000 0.77370 0.08333 0.00000
Si62 Si Si3 0.50000 0.87680 0.24883 0.00000
O63 O O_3_z 0.50000 0.80620 0.18137 0.00000
O64 O O_3_z 0.50000 0.84500 0.01643 0.00000
Si65 Si Si3 0.00000 0.72630 0.25000 0.00000
Si66 Si Si3 0.00000 0.62320 0.08217 0.00000
O67 O O_3_z 0.00000 0.69380 0.01470 0.00000
O68 O O_3_z 0.00000 0.65500 0.18310 0.00000
Si69 Si Si3 0.50000 0.22630 0.25000 0.00000
Si70 Si Si3 0.50000 0.12320 0.08217 0.00000
O71 O O_3_z 0.50000 0.19380 0.01470 0.00000
O72 O O_3_z 0.50000 0.15500 0.18310 0.00000
Si73 Si Si3 0.29510 0.04820 0.40883 0.00000
Si74 Si Si3 0.20550 0.21120 0.38150 0.00000
O75 O O_3_z 0.09230 0.42680 0.56590 0.00000
O76 O O_3_z 0.09420 0.22240 0.40227 0.00000
O77 O O_3_z 0.27120 0.37890 0.55463 0.00000
O78 O O_3_z 0.22880 0.48000 0.34113 0.00000
O79 O O_3_z 0.27050 0.25840 0.45117 0.00000
Si80 Si Si3 0.79510 0.54820 0.40883 0.00000
Si81 Si Si3 0.70550 0.71120 0.38150 0.00000
O82 O O_3_z 0.59230 0.92680 0.56590 0.00000
O83 O O_3_z 0.59420 0.72240 0.40227 0.00000
O84 O O_3_z 0.77120 0.87890 0.55463 0.00000
O85 O O_3_z 0.72880 0.98000 0.34113 0.00000
O86 O O_3_z 0.77050 0.75840 0.45117 0.00000
Si87 Si Si3 0.70490 0.95180 0.57550 0.00000
Si88 Si Si3 0.79450 0.78880 0.54817 0.00000
O89 O O_3_z 0.90770 0.57320 0.39923 0.00000
O90 O O_3_z 0.90580 0.77760 0.56893 0.00000
O91 O O_3_z 0.72880 0.62110 0.38797 0.00000
O92 O O_3_z 0.77120 0.52000 0.50780 0.00000
O93 O O_3_z 0.72950 0.74160 0.61783 0.00000
Si94 Si Si3 0.20490 0.45180 0.57550 0.00000
Si95 Si Si3 0.29450 0.28880 0.54817 0.00000
O96 O O_3_z 0.40770 0.07320 0.39923 0.00000
O97 O O_3_z 0.40580 0.27760 0.56893 0.00000
O98 O O_3_z 0.22880 0.12110 0.38797 0.00000
O99 O O_3_z 0.27120 0.02000 0.50780 0.00000
O100 O O_3_z 0.22950 0.24160 0.61783 0.00000
Si101 Si Si3 0.29510 0.95180 0.57550 0.00000
Si102 Si Si3 0.20550 0.78880 0.54817 0.00000
O103 O O_3_z 0.09230 0.57320 0.39923 0.00000
O104 O O_3_z 0.09420 0.77760 0.56893 0.00000
O105 O O_3_z 0.27120 0.62110 0.38797 0.00000
O106 O O_3_z 0.22880 0.52000 0.50780 0.00000
O107 O O_3_z 0.27050 0.74160 0.61783 0.00000
Si108 Si Si3 0.79510 0.45180 0.57550 0.00000
Si109 Si Si3 0.70550 0.28880 0.54817 0.00000
O110 O O_3_z 0.59230 0.07320 0.39923 0.00000
O111 O O_3_z 0.59420 0.27760 0.56893 0.00000
O112 O O_3_z 0.77120 0.12110 0.38797 0.00000
O113 O O_3_z 0.72880 0.02000 0.50780 0.00000
O114 O O_3_z 0.77050 0.24160 0.61783 0.00000
Si115 Si Si3 0.70490 0.04820 0.40883 0.00000
Si116 Si Si3 0.79450 0.21120 0.38150 0.00000
O117 O O_3_z 0.90770 0.42680 0.56590 0.00000
O118 O O_3_z 0.90580 0.22240 0.40227 0.00000
O119 O O_3_z 0.72880 0.37890 0.55463 0.00000
O120 O O_3_z 0.77120 0.48000 0.34113 0.00000
O121 O O_3_z 0.72950 0.25840 0.45117 0.00000
Si122 Si Si3 0.20490 0.54820 0.40883 0.00000
Si123 Si Si3 0.29450 0.71120 0.38150 0.00000
O124 O O_3_z 0.40770 0.92680 0.56590 0.00000
O125 O O_3_z 0.40580 0.72240 0.40227 0.00000
O126 O O_3_z 0.22880 0.87890 0.55463 0.00000
O127 O O_3_z 0.27120 0.98000 0.34113 0.00000
O128 O O_3_z 0.22950 0.75840 0.45117 0.00000
Si129 Si Si3 0.00000 0.27370 0.41667 0.00000
Si130 Si Si3 0.00000 0.37680 0.58217 0.00000
O131 O O_3_z 0.00000 0.30620 0.51470 0.00000
O132 O O_3_z 0.00000 0.34500 0.34977 0.00000
Si133 Si Si3 0.50000 0.77370 0.41667 0.00000
Si134 Si Si3 0.50000 0.87680 0.58217 0.00000
O135 O O_3_z 0.50000 0.80620 0.51470 0.00000
O136 O O_3_z 0.50000 0.84500 0.34977 0.00000
Si137 Si Si3 0.00000 0.72630 0.58333 0.00000
Si138 Si Si3 0.00000 0.62320 0.41550 0.00000
O139 O O_3_z 0.00000 0.69380 0.34803 0.00000
O140 O O_3_z 0.00000 0.65500 0.51643 0.00000
Si141 Si Si3 0.50000 0.22630 0.58333 0.00000
Si142 Si Si3 0.50000 0.12320 0.41550 0.00000
O143 O O_3_z 0.50000 0.19380 0.34803 0.00000
O144 O O_3_z 0.50000 0.15500 0.51643 0.00000
Si145 Si Si3 0.29510 0.04820 0.74217 0.00000
Si146 Si Si3 0.20550 0.21120 0.71483 0.00000
O147 O O_3_z 0.09230 0.42680 0.89923 0.00000
O148 O O_3_z 0.09420 0.22240 0.73560 0.00000
O149 O O_3_z 0.27120 0.37890 0.88797 0.00000
O150 O O_3_z 0.22880 0.48000 0.67447 0.00000
O151 O O_3_z 0.27050 0.25840 0.78450 0.00000
Si152 Si Si3 0.79510 0.54820 0.74217 0.00000
Si153 Si Si3 0.70550 0.71120 0.71483 0.00000
O154 O O_3_z 0.59230 0.92680 0.89923 0.00000
O155 O O_3_z 0.59420 0.72240 0.73560 0.00000
O156 O O_3_z 0.77120 0.87890 0.88797 0.00000
O157 O O_3_z 0.72880 0.98000 0.67447 0.00000
O158 O O_3_z 0.77050 0.75840 0.78450 0.00000
Si159 Si Si3 0.70490 0.95180 0.90883 0.00000
Si160 Si Si3 0.79450 0.78880 0.88150 0.00000
O161 O O_3_z 0.90770 0.57320 0.73257 0.00000
O162 O O_3_z 0.90580 0.77760 0.90227 0.00000
O163 O O_3_z 0.72880 0.62110 0.72130 0.00000
O164 O O_3_z 0.77120 0.52000 0.84113 0.00000
O165 O O_3_z 0.72950 0.74160 0.95117 0.00000
Si166 Si Si3 0.20490 0.45180 0.90883 0.00000
Si167 Si Si3 0.29450 0.28880 0.88150 0.00000
O168 O O_3_z 0.40770 0.07320 0.73257 0.00000
O169 O O_3_z 0.40580 0.27760 0.90227 0.00000
O170 O O_3_z 0.22880 0.12110 0.72130 0.00000
O171 O O_3_z 0.27120 0.02000 0.84113 0.00000
O172 O O_3_z 0.22950 0.24160 0.95117 0.00000
Si173 Si Si3 0.29510 0.95180 0.90883 0.00000
Si174 Si Si3 0.20550 0.78880 0.88150 0.00000
O175 O O_3_z 0.09230 0.57320 0.73257 0.00000
O176 O O_3_z 0.09420 0.77760 0.90227 0.00000
O177 O O_3_z 0.27120 0.62110 0.72130 0.00000
O178 O O_3_z 0.22880 0.52000 0.84113 0.00000
O179 O O_3_z 0.27050 0.74160 0.95117 0.00000
Si180 Si Si3 0.79510 0.45180 0.90883 0.00000
Si181 Si Si3 0.70550 0.28880 0.88150 0.00000
O182 O O_3_z 0.59230 0.07320 0.73257 0.00000
O183 O O_3_z 0.59420 0.27760 0.90227 0.00000
O184 O O_3_z 0.77120 0.12110 0.72130 0.00000
O185 O O_3_z 0.72880 0.02000 0.84113 0.00000
O186 O O_3_z 0.77050 0.24160 0.95117 0.00000
Si187 Si Si3 0.70490 0.04820 0.74217 0.00000
Si188 Si Si3 0.79450 0.21120 0.71483 0.00000
O189 O O_3_z 0.90770 0.42680 0.89923 0.00000
O190 O O_3_z 0.90580 0.22240 0.73560 0.00000
O191 O O_3_z 0.72880 0.37890 0.88797 0.00000
O192 O O_3_z 0.77120 0.48000 0.67447 0.00000
O193 O O_3_z 0.72950 0.25840 0.78450 0.00000
Si194 Si Si3 0.20490 0.54820 0.74217 0.00000
Si195 Si Si3 0.29450 0.71120 0.71483 0.00000
O196 O O_3_z 0.40770 0.92680 0.89923 0.00000
O197 O O_3_z 0.40580 0.72240 0.73560 0.00000
O198 O O_3_z 0.22880 0.87890 0.88797 0.00000
O199 O O_3_z 0.27120 0.98000 0.67447 0.00000
O200 O O_3_z 0.22950 0.75840 0.78450 0.00000
Si201 Si Si3 0.00000 0.27370 0.75000 0.00000
Si202 Si Si3 0.00000 0.37680 0.91550 0.00000
O203 O O_3_z 0.00000 0.30620 0.84803 0.00000
O204 O O_3_z 0.00000 0.34500 0.68310 0.00000
Si205 Si Si3 0.50000 0.77370 0.75000 0.00000
Si206 Si Si3 0.50000 0.87680 0.91550 0.00000
O207 O O_3_z 0.50000 0.80620 0.84803 0.00000
O208 O O_3_z 0.50000 0.84500 0.68310 0.00000
Si209 Si Si3 0.00000 0.72630 0.91667 0.00000
Si210 Si Si3 0.00000 0.62320 0.74883 0.00000
O211 O O_3_z 0.00000 0.69380 0.68137 0.00000
O212 O O_3_z 0.00000 0.65500 0.84977 0.00000
Si213 Si Si3 0.50000 0.22630 0.91667 0.00000
Si214 Si Si3 0.50000 0.12320 0.74883 0.00000
O215 O O_3_z 0.50000 0.19380 0.68137 0.00000
O216 O O_3_z 0.50000 0.15500 0.84977 0.00000
C217 C C_3 0.48755 0.50164 0.47804 0.00000
H218 H H 0.56691 0.50164 0.47804 0.00000
H219 H H 0.46110 0.55857 0.49807 0.00000
H220 H H 0.46110 0.45812 0.52484 0.00000
H221 H H 0.46110 0.48823 0.41120 0.00000
loop
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_ccdc_geom_bond_type
Si1 O26 1.599 . S
Si1 O27 1.609 . S
Si1 O24 1.627 . S
Si1 O55 1.603 1_545 S
Si2 O4 1.586 . S
Si2 O7 1.611 . S
Si2 O26 1.605 . S
Si2 O172 1.594 1_554 S
O3 Si58 1.567 . S
O3 Si22 1.627 . S
O4 Si57 1.597 . S
O5 Si22 1.599 . S
O5 Si23 1.605 . S
O6 Si50 1.603 . S
O6 Si166 1.609 1_554 S
O7 Si23 1.594 . S
Si8 O19 1.599 . S
Si8 O20 1.609 . S
Si8 O17 1.627 . S
Si8 O48 1.603 . S
Si9 O11 1.586 . S
Si9 O14 1.611 . S
Si9 O19 1.605 . S
Si9 O165 1.594 1_554 S
O10 Si62 1.567 . S
O10 Si15 1.627 . S
O11 Si61 1.597 . S
O12 Si15 1.599 . S
O12 Si16 1.605 . S
O13 Si159 1.609 1_554 S
O13 Si43 1.603 1_565 S
O14 Si16 1.594 . S
Si15 O85 1.609 . S
Si15 O41 1.603 1_565 S
Si16 O18 1.586 . S
Si16 O21 1.611 . S
O17 Si66 1.567 1_655 S
O18 Si65 1.597 1_655 S
O20 Si36 1.603 . S
O21 Si81 1.594 . S
Si22 O78 1.609 . S
Si22 O34 1.603 . S
Si23 O25 1.586 . S
Si23 O28 1.611 . S
O24 Si70 1.567 . S
O25 Si69 1.597 . S
O27 Si29 1.603 1_545 S
O28 Si74 1.594 . S
Si29 O54 1.599 . S
Si29 O127 1.609 . S
Si29 O52 1.627 . S
Si29 O27 1.603 1_565 S
Si30 O32 1.586 . S
Si30 O35 1.611 . S
Si30 O54 1.605 . S
Si30 O56 1.594 . S
O31 Si66 1.567 . S
O31 Si50 1.627 . S
O32 Si65 1.597 . S
O33 Si50 1.599 . S
O33 Si51 1.605 . S
O34 Si50 1.609 . S
O35 Si123 1.594 . S
Si36 O47 1.599 . S
Si36 O120 1.609 . S
Si36 O45 1.627 . S
Si37 O39 1.586 . S
Si37 O42 1.611 . S
Si37 O47 1.605 . S
Si37 O49 1.594 . S
O38 Si70 1.567 . S
O38 Si43 1.627 . S
O39 Si69 1.597 . S
O40 Si43 1.599 . S
O40 Si44 1.605 . S
O41 Si43 1.609 . S
O41 Si15 1.603 1_545 S
O42 Si116 1.594 . S
Si43 O13 1.603 1_545 S
Si44 O46 1.586 . S
Si44 O49 1.611 . S
Si44 O186 1.594 1_554 S
O45 Si58 1.567 1_655 S
O46 Si57 1.597 1_655 S
O48 Si180 1.609 1_554 S
Si51 O53 1.586 . S
Si51 O56 1.611 . S
Si51 O179 1.594 1_554 S
O52 Si62 1.567 . S
O53 Si61 1.597 . S
O55 Si1 1.603 1_565 S
O55 Si173 1.609 1_554 S
Si57 O59 1.586 . S
Si57 O60 1.602 . S
Si57 O46 1.597 1_455 S
Si58 O59 1.598 . S
Si58 O132 1.623 . S
Si58 O45 1.567 1_455 S
O60 Si202 1.623 1_554 S
Si61 O63 1.586 . S
Si61 O64 1.602 . S
Si62 O63 1.598 . S
Si62 O136 1.623 . S
O64 Si206 1.623 1_554 S
Si65 O139 1.586 . S
Si65 O68 1.602 . S
Si65 O18 1.597 1_455 S
Si66 O67 1.598 . S
Si66 O68 1.623 . S
Si66 O17 1.567 1_455 S
O67 Si209 1.586 1_554 S
Si69 O143 1.586 . S
Si69 O72 1.602 . S
Si70 O71 1.598 . S
Si70 O72 1.623 . S
O71 Si213 1.586 1_554 S
Si73 O98 1.599 . S
Si73 O99 1.609 . S
Si73 O96 1.627 . S
Si73 O127 1.603 1_545 S
Si74 O76 1.586 . S
Si74 O79 1.611 . S
Si74 O98 1.605 . S
O75 Si130 1.567 . S
O75 Si94 1.627 . S
O76 Si129 1.597 . S
O77 Si94 1.599 . S
O77 Si95 1.605 . S
O78 Si122 1.603 . S
O79 Si95 1.594 . S
Si80 O91 1.599 . S
Si80 O92 1.609 . S
Si80 O89 1.627 . S
Si80 O120 1.603 . S
Si81 O83 1.586 . S
Si81 O86 1.611 . S
Si81 O91 1.605 . S
O82 Si134 1.567 . S
O82 Si87 1.627 . S
O83 Si133 1.597 . S
O84 Si87 1.599 . S
O84 Si88 1.605 . S
O85 Si115 1.603 1_565 S
O86 Si88 1.594 . S
Si87 O157 1.609 . S
Si87 O113 1.603 1_565 S
Si88 O90 1.586 . S
Si88 O93 1.611 . S
O89 Si138 1.567 1_655 S
O90 Si137 1.597 1_655 S
O92 Si108 1.603 . S
O93 Si153 1.594 . S
Si94 O150 1.609 . S
Si94 O106 1.603 . S
Si95 O97 1.586 . S
Si95 O100 1.611 . S
O96 Si142 1.567 . S
O97 Si141 1.597 . S
O99 Si101 1.603 1_545 S
O100 Si146 1.594 . S
Si101 O126 1.599 . S
Si101 O199 1.609 . S
Si101 O124 1.627 . S
Si101 O99 1.603 1_565 S
Si102 O104 1.586 . S
Si102 O107 1.611 . S
Si102 O126 1.605 . S
Si102 O128 1.594 . S
O103 Si138 1.567 . S
O103 Si122 1.627 . S
O104 Si137 1.597 . S
O105 Si122 1.599 . S
O105 Si123 1.605 . S
O106 Si122 1.609 . S
O107 Si195 1.594 . S
Si108 O119 1.599 . S
Si108 O192 1.609 . S
Si108 O117 1.627 . S
Si109 O111 1.586 . S
Si109 O114 1.611 . S
Si109 O119 1.605 . S
Si109 O121 1.594 . S
O110 Si142 1.567 . S
O110 Si115 1.627 . S
O111 Si141 1.597 . S
O112 Si115 1.599 . S
O112 Si116 1.605 . S
O113 Si115 1.609 . S
O113 Si87 1.603 1_545 S
O114 Si188 1.594 . S
Si115 O85 1.603 1_545 S
Si116 O118 1.586 . S
Si116 O121 1.611 . S
O117 Si130 1.567 1_655 S
O118 Si129 1.597 1_655 S
Si123 O125 1.586 . S
Si123 O128 1.611 . S
O124 Si134 1.567 . S
O125 Si133 1.597 . S
O127 Si73 1.603 1_565 S
Si129 O131 1.586 . S
Si129 O132 1.602 . S
Si129 O118 1.597 1_455 S
Si130 O131 1.598 . S
Si130 O204 1.623 . S
Si130 O117 1.567 1_455 S
Si133 O135 1.586 . S
Si133 O136 1.602 . S
Si134 O135 1.598 . S
Si134 O208 1.623 . S
Si137 O211 1.586 . S
Si137 O140 1.602 . S
Si137 O90 1.597 1_455 S
Si138 O139 1.598 . S
Si138 O140 1.623 . S
Si138 O89 1.567 1_455 S
Si141 O215 1.586 . S
Si141 O144 1.602 . S
Si142 O143 1.598 . S
Si142 O144 1.623 . S
Si145 O170 1.599 . S
Si145 O171 1.609 . S
Si145 O168 1.627 . S
Si145 O199 1.603 1_545 S
Si146 O148 1.586 . S
Si146 O151 1.611 . S
Si146 O170 1.605 . S
O147 Si202 1.567 . S
O147 Si166 1.627 . S
O148 Si201 1.597 . S
O149 Si166 1.599 . S
O149 Si167 1.605 . S
O150 Si194 1.603 . S
O151 Si167 1.594 . S
Si152 O163 1.599 . S
Si152 O164 1.609 . S
Si152 O161 1.627 . S
Si152 O192 1.603 . S
Si153 O155 1.586 . S
Si153 O158 1.611 . S
Si153 O163 1.605 . S
O154 Si206 1.567 . S
O154 Si159 1.627 . S
O155 Si205 1.597 . S
O156 Si159 1.599 . S
O156 Si160 1.605 . S
O157 Si187 1.603 1_565 S
O158 Si160 1.594 . S
Si159 O13 1.609 1_556 S
Si159 O185 1.603 1_565 S
Si160 O162 1.586 . S
Si160 O165 1.611 . S
O161 Si210 1.567 1_655 S
O162 Si209 1.597 1_655 S
O164 Si180 1.603 . S
O165 Si9 1.594 1_556 S
Si166 O178 1.603 . S
Si166 O6 1.609 1_556 S
Si167 O169 1.586 . S
Si167 O172 1.611 . S
O168 Si214 1.567 . S
O169 Si213 1.597 . S
O171 Si173 1.603 1_545 S
O172 Si2 1.594 1_556 S
Si173 O198 1.599 . S
Si173 O196 1.627 . S
Si173 O55 1.609 1_556 S
Si173 O171 1.603 1_565 S
Si174 O176 1.586 . S
Si174 O179 1.611 . S
Si174 O198 1.605 . S
Si174 O200 1.594 . S
O175 Si210 1.567 . S
O175 Si194 1.627 . S
O176 Si209 1.597 . S
O177 Si194 1.599 . S
O177 Si195 1.605 . S
O178 Si194 1.609 . S
O179 Si51 1.594 1_556 S
Si180 O191 1.599 . S
Si180 O189 1.627 . S
Si180 O48 1.609 1_556 S
Si181 O183 1.586 . S
Si181 O186 1.611 . S
Si181 O191 1.605 . S
Si181 O193 1.594 . S
O182 Si214 1.567 . S
O182 Si187 1.627 . S
O183 Si213 1.597 . S
O184 Si187 1.599 . S
O184 Si188 1.605 . S
O185 Si187 1.609 . S
O185 Si159 1.603 1_545 S
O186 Si44 1.594 1_556 S
Si187 O157 1.603 1_545 S
Si188 O190 1.586 . S
Si188 O193 1.611 . S
O189 Si202 1.567 1_655 S
O190 Si201 1.597 1_655 S
Si195 O197 1.586 . S
Si195 O200 1.611 . S
O196 Si206 1.567 . S
O197 Si205 1.597 . S
O199 Si145 1.603 1_565 S
Si201 O203 1.586 . S
Si201 O204 1.602 . S
Si201 O190 1.597 1_455 S
Si202 O203 1.598 . S
Si202 O60 1.623 1_556 S
Si202 O189 1.567 1_455 S
Si205 O207 1.586 . S
Si205 O208 1.602 . S
Si206 O207 1.598 . S
Si206 O64 1.623 1_556 S
Si209 O212 1.602 . S
Si209 O67 1.586 1_556 S
Si209 O162 1.597 1_455 S
Si210 O211 1.598 . S
Si210 O212 1.623 . S
Si210 O161 1.567 1_455 S
Si213 O216 1.602 . S
Si213 O71 1.586 1_556 S
Si214 O215 1.598 . S
Si214 O216 1.623 . S
C217 H218 1.100 . S
C217 H219 1.100 . S
C217 H220 1.100 . S
C217 H221 1.100 . S
The text was updated successfully, but these errors were encountered:
Hi
I,m testing last version of lammps interface with a .cif produced from material studio, (testing with UFF force field) but I obtain error
lammps-interface TON_1x1x3_METHANE_B.cif
fatal: Not a git repository (or any of the parent directories): .git
Molecules found in the framework, separating.
Traceback (most recent call last):
File "/usr/local/bin/lammps-interface", line 6, in
exec(compile(open(file).read(), file, 'exec'))
File "/opt/lammps_interface-master/lammps-interface", line 14, in
sim.assign_force_fields()
File "/opt/lammps_interface-master/lammps_interface/lammps_main.py", line 462, in assign_force_fields
atoms = ", ".join([rep.node[j]['element'] for j in rep.nodes()])
File "/opt/lammps_interface-master/lammps_interface/lammps_main.py", line 462, in
atoms = ", ".join([rep.node[j]['element'] for j in rep.nodes()])
AttributeError: 'MolecularGraph' object has no attribute 'node'
my cif file is similar to example in directory test.
Is it peraphs a bug
Could I fix it?
my cif file
data_TON_1x1x3_METHANE
_audit_creation_date 2019-12-12
_audit_creation_method 'Materials Studio'
_symmetry_space_group_name_H-M 'P1'
_symmetry_Int_Tables_number 1
symmetry_cell_setting triclinic
loop
_symmetry_equiv_pos_as_xyz
x,y,z
_cell_length_a 13.8590
_cell_length_b 17.4200
_cell_length_c 15.1140
_cell_angle_alpha 90.0000
_cell_angle_beta 90.0000
cell_angle_gamma 90.0000
loop
_atom_site_label
_atom_site_type_symbol
atom_site_description
atom_site_fract_x
atom_site_fract_y
atom_site_fract_z
atom_site_charge
Si1 Si Si3 0.29510 0.04820 0.07550 0.00000
Si2 Si Si3 0.20550 0.21120 0.04817 0.00000
O3 O O_3_z 0.09230 0.42680 0.23257 0.00000
O4 O O_3_z 0.09420 0.22240 0.06893 0.00000
O5 O O_3_z 0.27120 0.37890 0.22130 0.00000
O6 O O_3_z 0.22880 0.48000 0.00780 0.00000
O7 O O_3_z 0.27050 0.25840 0.11783 0.00000
Si8 Si Si3 0.79510 0.54820 0.07550 0.00000
Si9 Si Si3 0.70550 0.71120 0.04817 0.00000
O10 O O_3_z 0.59230 0.92680 0.23257 0.00000
O11 O O_3_z 0.59420 0.72240 0.06893 0.00000
O12 O O_3_z 0.77120 0.87890 0.22130 0.00000
O13 O O_3_z 0.72880 0.98000 0.00780 0.00000
O14 O O_3_z 0.77050 0.75840 0.11783 0.00000
Si15 Si Si3 0.70490 0.95180 0.24217 0.00000
Si16 Si Si3 0.79450 0.78880 0.21483 0.00000
O17 O O_3_z 0.90770 0.57320 0.06590 0.00000
O18 O O_3_z 0.90580 0.77760 0.23560 0.00000
O19 O O_3_z 0.72880 0.62110 0.05463 0.00000
O20 O O_3_z 0.77120 0.52000 0.17447 0.00000
O21 O O_3_z 0.72950 0.74160 0.28450 0.00000
Si22 Si Si3 0.20490 0.45180 0.24217 0.00000
Si23 Si Si3 0.29450 0.28880 0.21483 0.00000
O24 O O_3_z 0.40770 0.07320 0.06590 0.00000
O25 O O_3_z 0.40580 0.27760 0.23560 0.00000
O26 O O_3_z 0.22880 0.12110 0.05463 0.00000
O27 O O_3_z 0.27120 0.02000 0.17447 0.00000
O28 O O_3_z 0.22950 0.24160 0.28450 0.00000
Si29 Si Si3 0.29510 0.95180 0.24217 0.00000
Si30 Si Si3 0.20550 0.78880 0.21483 0.00000
O31 O O_3_z 0.09230 0.57320 0.06590 0.00000
O32 O O_3_z 0.09420 0.77760 0.23560 0.00000
O33 O O_3_z 0.27120 0.62110 0.05463 0.00000
O34 O O_3_z 0.22880 0.52000 0.17447 0.00000
O35 O O_3_z 0.27050 0.74160 0.28450 0.00000
Si36 Si Si3 0.79510 0.45180 0.24217 0.00000
Si37 Si Si3 0.70550 0.28880 0.21483 0.00000
O38 O O_3_z 0.59230 0.07320 0.06590 0.00000
O39 O O_3_z 0.59420 0.27760 0.23560 0.00000
O40 O O_3_z 0.77120 0.12110 0.05463 0.00000
O41 O O_3_z 0.72880 0.02000 0.17447 0.00000
O42 O O_3_z 0.77050 0.24160 0.28450 0.00000
Si43 Si Si3 0.70490 0.04820 0.07550 0.00000
Si44 Si Si3 0.79450 0.21120 0.04817 0.00000
O45 O O_3_z 0.90770 0.42680 0.23257 0.00000
O46 O O_3_z 0.90580 0.22240 0.06893 0.00000
O47 O O_3_z 0.72880 0.37890 0.22130 0.00000
O48 O O_3_z 0.77120 0.48000 0.00780 0.00000
O49 O O_3_z 0.72950 0.25840 0.11783 0.00000
Si50 Si Si3 0.20490 0.54820 0.07550 0.00000
Si51 Si Si3 0.29450 0.71120 0.04817 0.00000
O52 O O_3_z 0.40770 0.92680 0.23257 0.00000
O53 O O_3_z 0.40580 0.72240 0.06893 0.00000
O54 O O_3_z 0.22880 0.87890 0.22130 0.00000
O55 O O_3_z 0.27120 0.98000 0.00780 0.00000
O56 O O_3_z 0.22950 0.75840 0.11783 0.00000
Si57 Si Si3 0.00000 0.27370 0.08333 0.00000
Si58 Si Si3 0.00000 0.37680 0.24883 0.00000
O59 O O_3_z 0.00000 0.30620 0.18137 0.00000
O60 O O_3_z 0.00000 0.34500 0.01643 0.00000
Si61 Si Si3 0.50000 0.77370 0.08333 0.00000
Si62 Si Si3 0.50000 0.87680 0.24883 0.00000
O63 O O_3_z 0.50000 0.80620 0.18137 0.00000
O64 O O_3_z 0.50000 0.84500 0.01643 0.00000
Si65 Si Si3 0.00000 0.72630 0.25000 0.00000
Si66 Si Si3 0.00000 0.62320 0.08217 0.00000
O67 O O_3_z 0.00000 0.69380 0.01470 0.00000
O68 O O_3_z 0.00000 0.65500 0.18310 0.00000
Si69 Si Si3 0.50000 0.22630 0.25000 0.00000
Si70 Si Si3 0.50000 0.12320 0.08217 0.00000
O71 O O_3_z 0.50000 0.19380 0.01470 0.00000
O72 O O_3_z 0.50000 0.15500 0.18310 0.00000
Si73 Si Si3 0.29510 0.04820 0.40883 0.00000
Si74 Si Si3 0.20550 0.21120 0.38150 0.00000
O75 O O_3_z 0.09230 0.42680 0.56590 0.00000
O76 O O_3_z 0.09420 0.22240 0.40227 0.00000
O77 O O_3_z 0.27120 0.37890 0.55463 0.00000
O78 O O_3_z 0.22880 0.48000 0.34113 0.00000
O79 O O_3_z 0.27050 0.25840 0.45117 0.00000
Si80 Si Si3 0.79510 0.54820 0.40883 0.00000
Si81 Si Si3 0.70550 0.71120 0.38150 0.00000
O82 O O_3_z 0.59230 0.92680 0.56590 0.00000
O83 O O_3_z 0.59420 0.72240 0.40227 0.00000
O84 O O_3_z 0.77120 0.87890 0.55463 0.00000
O85 O O_3_z 0.72880 0.98000 0.34113 0.00000
O86 O O_3_z 0.77050 0.75840 0.45117 0.00000
Si87 Si Si3 0.70490 0.95180 0.57550 0.00000
Si88 Si Si3 0.79450 0.78880 0.54817 0.00000
O89 O O_3_z 0.90770 0.57320 0.39923 0.00000
O90 O O_3_z 0.90580 0.77760 0.56893 0.00000
O91 O O_3_z 0.72880 0.62110 0.38797 0.00000
O92 O O_3_z 0.77120 0.52000 0.50780 0.00000
O93 O O_3_z 0.72950 0.74160 0.61783 0.00000
Si94 Si Si3 0.20490 0.45180 0.57550 0.00000
Si95 Si Si3 0.29450 0.28880 0.54817 0.00000
O96 O O_3_z 0.40770 0.07320 0.39923 0.00000
O97 O O_3_z 0.40580 0.27760 0.56893 0.00000
O98 O O_3_z 0.22880 0.12110 0.38797 0.00000
O99 O O_3_z 0.27120 0.02000 0.50780 0.00000
O100 O O_3_z 0.22950 0.24160 0.61783 0.00000
Si101 Si Si3 0.29510 0.95180 0.57550 0.00000
Si102 Si Si3 0.20550 0.78880 0.54817 0.00000
O103 O O_3_z 0.09230 0.57320 0.39923 0.00000
O104 O O_3_z 0.09420 0.77760 0.56893 0.00000
O105 O O_3_z 0.27120 0.62110 0.38797 0.00000
O106 O O_3_z 0.22880 0.52000 0.50780 0.00000
O107 O O_3_z 0.27050 0.74160 0.61783 0.00000
Si108 Si Si3 0.79510 0.45180 0.57550 0.00000
Si109 Si Si3 0.70550 0.28880 0.54817 0.00000
O110 O O_3_z 0.59230 0.07320 0.39923 0.00000
O111 O O_3_z 0.59420 0.27760 0.56893 0.00000
O112 O O_3_z 0.77120 0.12110 0.38797 0.00000
O113 O O_3_z 0.72880 0.02000 0.50780 0.00000
O114 O O_3_z 0.77050 0.24160 0.61783 0.00000
Si115 Si Si3 0.70490 0.04820 0.40883 0.00000
Si116 Si Si3 0.79450 0.21120 0.38150 0.00000
O117 O O_3_z 0.90770 0.42680 0.56590 0.00000
O118 O O_3_z 0.90580 0.22240 0.40227 0.00000
O119 O O_3_z 0.72880 0.37890 0.55463 0.00000
O120 O O_3_z 0.77120 0.48000 0.34113 0.00000
O121 O O_3_z 0.72950 0.25840 0.45117 0.00000
Si122 Si Si3 0.20490 0.54820 0.40883 0.00000
Si123 Si Si3 0.29450 0.71120 0.38150 0.00000
O124 O O_3_z 0.40770 0.92680 0.56590 0.00000
O125 O O_3_z 0.40580 0.72240 0.40227 0.00000
O126 O O_3_z 0.22880 0.87890 0.55463 0.00000
O127 O O_3_z 0.27120 0.98000 0.34113 0.00000
O128 O O_3_z 0.22950 0.75840 0.45117 0.00000
Si129 Si Si3 0.00000 0.27370 0.41667 0.00000
Si130 Si Si3 0.00000 0.37680 0.58217 0.00000
O131 O O_3_z 0.00000 0.30620 0.51470 0.00000
O132 O O_3_z 0.00000 0.34500 0.34977 0.00000
Si133 Si Si3 0.50000 0.77370 0.41667 0.00000
Si134 Si Si3 0.50000 0.87680 0.58217 0.00000
O135 O O_3_z 0.50000 0.80620 0.51470 0.00000
O136 O O_3_z 0.50000 0.84500 0.34977 0.00000
Si137 Si Si3 0.00000 0.72630 0.58333 0.00000
Si138 Si Si3 0.00000 0.62320 0.41550 0.00000
O139 O O_3_z 0.00000 0.69380 0.34803 0.00000
O140 O O_3_z 0.00000 0.65500 0.51643 0.00000
Si141 Si Si3 0.50000 0.22630 0.58333 0.00000
Si142 Si Si3 0.50000 0.12320 0.41550 0.00000
O143 O O_3_z 0.50000 0.19380 0.34803 0.00000
O144 O O_3_z 0.50000 0.15500 0.51643 0.00000
Si145 Si Si3 0.29510 0.04820 0.74217 0.00000
Si146 Si Si3 0.20550 0.21120 0.71483 0.00000
O147 O O_3_z 0.09230 0.42680 0.89923 0.00000
O148 O O_3_z 0.09420 0.22240 0.73560 0.00000
O149 O O_3_z 0.27120 0.37890 0.88797 0.00000
O150 O O_3_z 0.22880 0.48000 0.67447 0.00000
O151 O O_3_z 0.27050 0.25840 0.78450 0.00000
Si152 Si Si3 0.79510 0.54820 0.74217 0.00000
Si153 Si Si3 0.70550 0.71120 0.71483 0.00000
O154 O O_3_z 0.59230 0.92680 0.89923 0.00000
O155 O O_3_z 0.59420 0.72240 0.73560 0.00000
O156 O O_3_z 0.77120 0.87890 0.88797 0.00000
O157 O O_3_z 0.72880 0.98000 0.67447 0.00000
O158 O O_3_z 0.77050 0.75840 0.78450 0.00000
Si159 Si Si3 0.70490 0.95180 0.90883 0.00000
Si160 Si Si3 0.79450 0.78880 0.88150 0.00000
O161 O O_3_z 0.90770 0.57320 0.73257 0.00000
O162 O O_3_z 0.90580 0.77760 0.90227 0.00000
O163 O O_3_z 0.72880 0.62110 0.72130 0.00000
O164 O O_3_z 0.77120 0.52000 0.84113 0.00000
O165 O O_3_z 0.72950 0.74160 0.95117 0.00000
Si166 Si Si3 0.20490 0.45180 0.90883 0.00000
Si167 Si Si3 0.29450 0.28880 0.88150 0.00000
O168 O O_3_z 0.40770 0.07320 0.73257 0.00000
O169 O O_3_z 0.40580 0.27760 0.90227 0.00000
O170 O O_3_z 0.22880 0.12110 0.72130 0.00000
O171 O O_3_z 0.27120 0.02000 0.84113 0.00000
O172 O O_3_z 0.22950 0.24160 0.95117 0.00000
Si173 Si Si3 0.29510 0.95180 0.90883 0.00000
Si174 Si Si3 0.20550 0.78880 0.88150 0.00000
O175 O O_3_z 0.09230 0.57320 0.73257 0.00000
O176 O O_3_z 0.09420 0.77760 0.90227 0.00000
O177 O O_3_z 0.27120 0.62110 0.72130 0.00000
O178 O O_3_z 0.22880 0.52000 0.84113 0.00000
O179 O O_3_z 0.27050 0.74160 0.95117 0.00000
Si180 Si Si3 0.79510 0.45180 0.90883 0.00000
Si181 Si Si3 0.70550 0.28880 0.88150 0.00000
O182 O O_3_z 0.59230 0.07320 0.73257 0.00000
O183 O O_3_z 0.59420 0.27760 0.90227 0.00000
O184 O O_3_z 0.77120 0.12110 0.72130 0.00000
O185 O O_3_z 0.72880 0.02000 0.84113 0.00000
O186 O O_3_z 0.77050 0.24160 0.95117 0.00000
Si187 Si Si3 0.70490 0.04820 0.74217 0.00000
Si188 Si Si3 0.79450 0.21120 0.71483 0.00000
O189 O O_3_z 0.90770 0.42680 0.89923 0.00000
O190 O O_3_z 0.90580 0.22240 0.73560 0.00000
O191 O O_3_z 0.72880 0.37890 0.88797 0.00000
O192 O O_3_z 0.77120 0.48000 0.67447 0.00000
O193 O O_3_z 0.72950 0.25840 0.78450 0.00000
Si194 Si Si3 0.20490 0.54820 0.74217 0.00000
Si195 Si Si3 0.29450 0.71120 0.71483 0.00000
O196 O O_3_z 0.40770 0.92680 0.89923 0.00000
O197 O O_3_z 0.40580 0.72240 0.73560 0.00000
O198 O O_3_z 0.22880 0.87890 0.88797 0.00000
O199 O O_3_z 0.27120 0.98000 0.67447 0.00000
O200 O O_3_z 0.22950 0.75840 0.78450 0.00000
Si201 Si Si3 0.00000 0.27370 0.75000 0.00000
Si202 Si Si3 0.00000 0.37680 0.91550 0.00000
O203 O O_3_z 0.00000 0.30620 0.84803 0.00000
O204 O O_3_z 0.00000 0.34500 0.68310 0.00000
Si205 Si Si3 0.50000 0.77370 0.75000 0.00000
Si206 Si Si3 0.50000 0.87680 0.91550 0.00000
O207 O O_3_z 0.50000 0.80620 0.84803 0.00000
O208 O O_3_z 0.50000 0.84500 0.68310 0.00000
Si209 Si Si3 0.00000 0.72630 0.91667 0.00000
Si210 Si Si3 0.00000 0.62320 0.74883 0.00000
O211 O O_3_z 0.00000 0.69380 0.68137 0.00000
O212 O O_3_z 0.00000 0.65500 0.84977 0.00000
Si213 Si Si3 0.50000 0.22630 0.91667 0.00000
Si214 Si Si3 0.50000 0.12320 0.74883 0.00000
O215 O O_3_z 0.50000 0.19380 0.68137 0.00000
O216 O O_3_z 0.50000 0.15500 0.84977 0.00000
C217 C C_3 0.48755 0.50164 0.47804 0.00000
H218 H H 0.56691 0.50164 0.47804 0.00000
H219 H H 0.46110 0.55857 0.49807 0.00000
H220 H H 0.46110 0.45812 0.52484 0.00000
H221 H H 0.46110 0.48823 0.41120 0.00000
loop
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_ccdc_geom_bond_type
Si1 O26 1.599 . S
Si1 O27 1.609 . S
Si1 O24 1.627 . S
Si1 O55 1.603 1_545 S
Si2 O4 1.586 . S
Si2 O7 1.611 . S
Si2 O26 1.605 . S
Si2 O172 1.594 1_554 S
O3 Si58 1.567 . S
O3 Si22 1.627 . S
O4 Si57 1.597 . S
O5 Si22 1.599 . S
O5 Si23 1.605 . S
O6 Si50 1.603 . S
O6 Si166 1.609 1_554 S
O7 Si23 1.594 . S
Si8 O19 1.599 . S
Si8 O20 1.609 . S
Si8 O17 1.627 . S
Si8 O48 1.603 . S
Si9 O11 1.586 . S
Si9 O14 1.611 . S
Si9 O19 1.605 . S
Si9 O165 1.594 1_554 S
O10 Si62 1.567 . S
O10 Si15 1.627 . S
O11 Si61 1.597 . S
O12 Si15 1.599 . S
O12 Si16 1.605 . S
O13 Si159 1.609 1_554 S
O13 Si43 1.603 1_565 S
O14 Si16 1.594 . S
Si15 O85 1.609 . S
Si15 O41 1.603 1_565 S
Si16 O18 1.586 . S
Si16 O21 1.611 . S
O17 Si66 1.567 1_655 S
O18 Si65 1.597 1_655 S
O20 Si36 1.603 . S
O21 Si81 1.594 . S
Si22 O78 1.609 . S
Si22 O34 1.603 . S
Si23 O25 1.586 . S
Si23 O28 1.611 . S
O24 Si70 1.567 . S
O25 Si69 1.597 . S
O27 Si29 1.603 1_545 S
O28 Si74 1.594 . S
Si29 O54 1.599 . S
Si29 O127 1.609 . S
Si29 O52 1.627 . S
Si29 O27 1.603 1_565 S
Si30 O32 1.586 . S
Si30 O35 1.611 . S
Si30 O54 1.605 . S
Si30 O56 1.594 . S
O31 Si66 1.567 . S
O31 Si50 1.627 . S
O32 Si65 1.597 . S
O33 Si50 1.599 . S
O33 Si51 1.605 . S
O34 Si50 1.609 . S
O35 Si123 1.594 . S
Si36 O47 1.599 . S
Si36 O120 1.609 . S
Si36 O45 1.627 . S
Si37 O39 1.586 . S
Si37 O42 1.611 . S
Si37 O47 1.605 . S
Si37 O49 1.594 . S
O38 Si70 1.567 . S
O38 Si43 1.627 . S
O39 Si69 1.597 . S
O40 Si43 1.599 . S
O40 Si44 1.605 . S
O41 Si43 1.609 . S
O41 Si15 1.603 1_545 S
O42 Si116 1.594 . S
Si43 O13 1.603 1_545 S
Si44 O46 1.586 . S
Si44 O49 1.611 . S
Si44 O186 1.594 1_554 S
O45 Si58 1.567 1_655 S
O46 Si57 1.597 1_655 S
O48 Si180 1.609 1_554 S
Si51 O53 1.586 . S
Si51 O56 1.611 . S
Si51 O179 1.594 1_554 S
O52 Si62 1.567 . S
O53 Si61 1.597 . S
O55 Si1 1.603 1_565 S
O55 Si173 1.609 1_554 S
Si57 O59 1.586 . S
Si57 O60 1.602 . S
Si57 O46 1.597 1_455 S
Si58 O59 1.598 . S
Si58 O132 1.623 . S
Si58 O45 1.567 1_455 S
O60 Si202 1.623 1_554 S
Si61 O63 1.586 . S
Si61 O64 1.602 . S
Si62 O63 1.598 . S
Si62 O136 1.623 . S
O64 Si206 1.623 1_554 S
Si65 O139 1.586 . S
Si65 O68 1.602 . S
Si65 O18 1.597 1_455 S
Si66 O67 1.598 . S
Si66 O68 1.623 . S
Si66 O17 1.567 1_455 S
O67 Si209 1.586 1_554 S
Si69 O143 1.586 . S
Si69 O72 1.602 . S
Si70 O71 1.598 . S
Si70 O72 1.623 . S
O71 Si213 1.586 1_554 S
Si73 O98 1.599 . S
Si73 O99 1.609 . S
Si73 O96 1.627 . S
Si73 O127 1.603 1_545 S
Si74 O76 1.586 . S
Si74 O79 1.611 . S
Si74 O98 1.605 . S
O75 Si130 1.567 . S
O75 Si94 1.627 . S
O76 Si129 1.597 . S
O77 Si94 1.599 . S
O77 Si95 1.605 . S
O78 Si122 1.603 . S
O79 Si95 1.594 . S
Si80 O91 1.599 . S
Si80 O92 1.609 . S
Si80 O89 1.627 . S
Si80 O120 1.603 . S
Si81 O83 1.586 . S
Si81 O86 1.611 . S
Si81 O91 1.605 . S
O82 Si134 1.567 . S
O82 Si87 1.627 . S
O83 Si133 1.597 . S
O84 Si87 1.599 . S
O84 Si88 1.605 . S
O85 Si115 1.603 1_565 S
O86 Si88 1.594 . S
Si87 O157 1.609 . S
Si87 O113 1.603 1_565 S
Si88 O90 1.586 . S
Si88 O93 1.611 . S
O89 Si138 1.567 1_655 S
O90 Si137 1.597 1_655 S
O92 Si108 1.603 . S
O93 Si153 1.594 . S
Si94 O150 1.609 . S
Si94 O106 1.603 . S
Si95 O97 1.586 . S
Si95 O100 1.611 . S
O96 Si142 1.567 . S
O97 Si141 1.597 . S
O99 Si101 1.603 1_545 S
O100 Si146 1.594 . S
Si101 O126 1.599 . S
Si101 O199 1.609 . S
Si101 O124 1.627 . S
Si101 O99 1.603 1_565 S
Si102 O104 1.586 . S
Si102 O107 1.611 . S
Si102 O126 1.605 . S
Si102 O128 1.594 . S
O103 Si138 1.567 . S
O103 Si122 1.627 . S
O104 Si137 1.597 . S
O105 Si122 1.599 . S
O105 Si123 1.605 . S
O106 Si122 1.609 . S
O107 Si195 1.594 . S
Si108 O119 1.599 . S
Si108 O192 1.609 . S
Si108 O117 1.627 . S
Si109 O111 1.586 . S
Si109 O114 1.611 . S
Si109 O119 1.605 . S
Si109 O121 1.594 . S
O110 Si142 1.567 . S
O110 Si115 1.627 . S
O111 Si141 1.597 . S
O112 Si115 1.599 . S
O112 Si116 1.605 . S
O113 Si115 1.609 . S
O113 Si87 1.603 1_545 S
O114 Si188 1.594 . S
Si115 O85 1.603 1_545 S
Si116 O118 1.586 . S
Si116 O121 1.611 . S
O117 Si130 1.567 1_655 S
O118 Si129 1.597 1_655 S
Si123 O125 1.586 . S
Si123 O128 1.611 . S
O124 Si134 1.567 . S
O125 Si133 1.597 . S
O127 Si73 1.603 1_565 S
Si129 O131 1.586 . S
Si129 O132 1.602 . S
Si129 O118 1.597 1_455 S
Si130 O131 1.598 . S
Si130 O204 1.623 . S
Si130 O117 1.567 1_455 S
Si133 O135 1.586 . S
Si133 O136 1.602 . S
Si134 O135 1.598 . S
Si134 O208 1.623 . S
Si137 O211 1.586 . S
Si137 O140 1.602 . S
Si137 O90 1.597 1_455 S
Si138 O139 1.598 . S
Si138 O140 1.623 . S
Si138 O89 1.567 1_455 S
Si141 O215 1.586 . S
Si141 O144 1.602 . S
Si142 O143 1.598 . S
Si142 O144 1.623 . S
Si145 O170 1.599 . S
Si145 O171 1.609 . S
Si145 O168 1.627 . S
Si145 O199 1.603 1_545 S
Si146 O148 1.586 . S
Si146 O151 1.611 . S
Si146 O170 1.605 . S
O147 Si202 1.567 . S
O147 Si166 1.627 . S
O148 Si201 1.597 . S
O149 Si166 1.599 . S
O149 Si167 1.605 . S
O150 Si194 1.603 . S
O151 Si167 1.594 . S
Si152 O163 1.599 . S
Si152 O164 1.609 . S
Si152 O161 1.627 . S
Si152 O192 1.603 . S
Si153 O155 1.586 . S
Si153 O158 1.611 . S
Si153 O163 1.605 . S
O154 Si206 1.567 . S
O154 Si159 1.627 . S
O155 Si205 1.597 . S
O156 Si159 1.599 . S
O156 Si160 1.605 . S
O157 Si187 1.603 1_565 S
O158 Si160 1.594 . S
Si159 O13 1.609 1_556 S
Si159 O185 1.603 1_565 S
Si160 O162 1.586 . S
Si160 O165 1.611 . S
O161 Si210 1.567 1_655 S
O162 Si209 1.597 1_655 S
O164 Si180 1.603 . S
O165 Si9 1.594 1_556 S
Si166 O178 1.603 . S
Si166 O6 1.609 1_556 S
Si167 O169 1.586 . S
Si167 O172 1.611 . S
O168 Si214 1.567 . S
O169 Si213 1.597 . S
O171 Si173 1.603 1_545 S
O172 Si2 1.594 1_556 S
Si173 O198 1.599 . S
Si173 O196 1.627 . S
Si173 O55 1.609 1_556 S
Si173 O171 1.603 1_565 S
Si174 O176 1.586 . S
Si174 O179 1.611 . S
Si174 O198 1.605 . S
Si174 O200 1.594 . S
O175 Si210 1.567 . S
O175 Si194 1.627 . S
O176 Si209 1.597 . S
O177 Si194 1.599 . S
O177 Si195 1.605 . S
O178 Si194 1.609 . S
O179 Si51 1.594 1_556 S
Si180 O191 1.599 . S
Si180 O189 1.627 . S
Si180 O48 1.609 1_556 S
Si181 O183 1.586 . S
Si181 O186 1.611 . S
Si181 O191 1.605 . S
Si181 O193 1.594 . S
O182 Si214 1.567 . S
O182 Si187 1.627 . S
O183 Si213 1.597 . S
O184 Si187 1.599 . S
O184 Si188 1.605 . S
O185 Si187 1.609 . S
O185 Si159 1.603 1_545 S
O186 Si44 1.594 1_556 S
Si187 O157 1.603 1_545 S
Si188 O190 1.586 . S
Si188 O193 1.611 . S
O189 Si202 1.567 1_655 S
O190 Si201 1.597 1_655 S
Si195 O197 1.586 . S
Si195 O200 1.611 . S
O196 Si206 1.567 . S
O197 Si205 1.597 . S
O199 Si145 1.603 1_565 S
Si201 O203 1.586 . S
Si201 O204 1.602 . S
Si201 O190 1.597 1_455 S
Si202 O203 1.598 . S
Si202 O60 1.623 1_556 S
Si202 O189 1.567 1_455 S
Si205 O207 1.586 . S
Si205 O208 1.602 . S
Si206 O207 1.598 . S
Si206 O64 1.623 1_556 S
Si209 O212 1.602 . S
Si209 O67 1.586 1_556 S
Si209 O162 1.597 1_455 S
Si210 O211 1.598 . S
Si210 O212 1.623 . S
Si210 O161 1.567 1_455 S
Si213 O216 1.602 . S
Si213 O71 1.586 1_556 S
Si214 O215 1.598 . S
Si214 O216 1.623 . S
C217 H218 1.100 . S
C217 H219 1.100 . S
C217 H220 1.100 . S
C217 H221 1.100 . S
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