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new file: TAMOF-1.cif
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	new file:   TAMOF-1_GFN2-xTB/OptimisationxTB.log
	new file:   TAMOF-1_GFN2-xTB/OptimisationxTB.sh
	new file:   TAMOF-1_GFN2-xTB/TAMOF-1.cif
	new file:   TAMOF-1_GFN2-xTB/TAMOF-1_Optimised.cif
	new file:   TAMOF-1_GFN2-xTB/band.out
	new file:   TAMOF-1_GFN2-xTB/charges
	new file:   TAMOF-1_GFN2-xTB/charges.bin
	new file:   TAMOF-1_GFN2-xTB/detailed.out
	new file:   TAMOF-1_GFN2-xTB/dftb_pin.hsd
	new file:   TAMOF-1_GFN2-xTB/geo.gen
	new file:   TAMOF-1_GFN2-xTB/geo_restart.cif
	new file:   TAMOF-1_GFN2-xTB/log
	new file:   force_field_mixing_rules.def
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@salrodgom
salrodgom committed Jun 8, 2022
1 parent 9645c48 commit 1d0ecc1
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76 changes: 76 additions & 0 deletions TAMOF-1.cif
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data_LOL
_audit_creation_method RASPA-1.0
_audit_creation_date 2015-7-21
_audit_author_name 'Salvador Rodriguez-Gomez'

_cell_length_a 20.1809
_cell_length_b 20.1809
_cell_length_c 20.1809
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 65752.4

_symmetry_cell_setting cubic
_symmetry_space_group_name_Hall 'P 4acd 2ab 3'
_symmetry_space_group_name_H-M 'P 43 3 2'
_symmetry_Int_Tables_number 212

loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'-x+1/2,-y,z+1/2'
'-x,y+1/2,-z+1/2'
'x+1/2,-y+1/2,-z'
'z,x,y'
'z+1/2,-x+1/2,-y'
'-z+1/2,-x,y+1/2'
'-z,x+1/2,-y+1/2'
'y,z,x'
'-y,z+1/2,-x+1/2'
'y+1/2,-z+1/2,-x'
'-y+1/2,-z,x+1/2'
'y+1/4,x+3/4,-z+3/4'
'-y+1/4,-x+1/4,-z+1/4'
'y+3/4,-x+3/4,z+1/4'
'-y+3/4,x+1/4,z+3/4'
'x+1/4,z+3/4,-y+3/4'
'-x+3/4,z+1/4,y+3/4'
'-x+1/4,-z+1/4,-y+1/4'
'x+3/4,-z+3/4,y+1/4'
'z+1/4,y+3/4,-x+3/4'
'z+3/4,-y+3/4,x+1/4'
'-z+3/4,y+1/4,x+3/4'
'-z+1/4,-y+1/4,-x+1/4'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Cu01 Cu 0.625000000000 0.091010000000 0.158990000000 1.02908
O1 O 0.389510000000 0.176320000000 0.296450000000 -0.327125
O2 O 0.355100000000 0.147380000000 0.194710000000 -0.351678
N1 N 0.428800000000 0.297860000000 0.256060000000 -0.181806
N2 N 0.507840000000 0.328890000000 0.323010000000 -0.263934
N3 N 0.465430000000 0.382540000000 0.314930000000 -0.146344
N4 N 0.567920000000 0.166500000000 0.136750000000 -0.30208
N5 N 0.535110000000 0.269400000000 0.121590000000 -0.332955
H5 H 0.536600000000 0.312300000000 0.113900000000 0.235042
C1 C 0.386050000000 0.259330000000 0.211190000000 -0.00753068
H1 H 0.341400000000 0.280800000000 0.211700000000 0.0757818
C2 C 0.485260000000 0.279000000000 0.287070000000 0.164079
H2 H 0.505400000000 0.236600000000 0.283500000000 0.00218674
C3 C 0.418900000000 0.361930000000 0.274480000000 0.139876
H3 H 0.382800000000 0.388400000000 0.259900000000 0.0397027
C4 C 0.411660000000 0.263020000000 0.139790000000 -0.288523
H4A H 0.380500000000 0.239600000000 0.110100000000 0.138079
H4B H 0.413600000000 0.310000000000 0.125600000000 0.15669
C5 C 0.478900000000 0.232700000000 0.133580000000 0.192591
C6 C 0.499790000000 0.168760000000 0.143290000000 -0.0622507
H6 H 0.472000000000 0.132000000000 0.152900000000 0.0692037
C7 C 0.587180000000 0.228200000000 0.123730000000 0.19712
H7 H 0.631900000000 0.241300000000 0.116900000000 -0.0335332
C8 C 0.376790000000 0.187590000000 0.237350000000 0.372865
4 changes: 4 additions & 0 deletions TAMOF-1_GFN2-xTB/OptimisationxTB.log
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/home/salvador/anaconda3/envs/dftb/lib/python3.9/site-packages/ase/io/cif.py:401: UserWarning: crystal system 'cubic' is not interpreted for space group Spacegroup(212, setting=1). This may result in wrong setting!
warnings.warn(
Terminated
(standard_in) 2: syntax error
30 changes: 30 additions & 0 deletions TAMOF-1_GFN2-xTB/OptimisationxTB.sh
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#!/bin/bash
export OMP_NUM_THREADS=6,1
export OMP_STACKSIZE=4G
ulimit -s unlimited
if [ -f geo.gen ] ; then rm -rf geo.gen ; fi
ase convert -i cif -o gen $1 geo.gen
echo '
Geometry = GenFormat {
<<< geo.gen
}
Hamiltonian = xTB {
Method = "GFN2-xTB"
kPointsAndWeights = SuperCellFolding {
2 0 0
0 2 0
0 0 2
0.5 0.5 0.5
}
}
Driver = GeometryOptimization {
LatticeOpt = Yes
}' > dftb_in.hsd
dftb+ > log
rm -rf dftb_in.hsd
x=$(grep " total energy " log | tail -n1 | awk '{print $3}' | sed -E 's/([+-]?[0-9.]+)[eE]\+?(-?)([0-9]+)/(\1*10^\2\3)/g' | bc -lq)
echo "scale=20; 315777.090000000 * $x" | bc -lq
rm -rf input.gen
ase convert -i gen -o cif geo_end.gen geo_end.cif
exit 0
76 changes: 76 additions & 0 deletions TAMOF-1_GFN2-xTB/TAMOF-1.cif
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Original file line number Diff line number Diff line change
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data_LOL
_audit_creation_method RASPA-1.0
_audit_creation_date 2015-7-21
_audit_author_name 'Salvador Rodriguez-Gomez'

_cell_length_a 20.1809
_cell_length_b 20.1809
_cell_length_c 20.1809
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 65752.4

_symmetry_cell_setting cubic
_symmetry_space_group_name_Hall 'P 4acd 2ab 3'
_symmetry_space_group_name_H-M 'P 43 3 2'
_symmetry_Int_Tables_number 212

loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'-x+1/2,-y,z+1/2'
'-x,y+1/2,-z+1/2'
'x+1/2,-y+1/2,-z'
'z,x,y'
'z+1/2,-x+1/2,-y'
'-z+1/2,-x,y+1/2'
'-z,x+1/2,-y+1/2'
'y,z,x'
'-y,z+1/2,-x+1/2'
'y+1/2,-z+1/2,-x'
'-y+1/2,-z,x+1/2'
'y+1/4,x+3/4,-z+3/4'
'-y+1/4,-x+1/4,-z+1/4'
'y+3/4,-x+3/4,z+1/4'
'-y+3/4,x+1/4,z+3/4'
'x+1/4,z+3/4,-y+3/4'
'-x+3/4,z+1/4,y+3/4'
'-x+1/4,-z+1/4,-y+1/4'
'x+3/4,-z+3/4,y+1/4'
'z+1/4,y+3/4,-x+3/4'
'z+3/4,-y+3/4,x+1/4'
'-z+3/4,y+1/4,x+3/4'
'-z+1/4,-y+1/4,-x+1/4'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Cu01 Cu 0.625000000000 0.091010000000 0.158990000000 1.02908
O1 O 0.389510000000 0.176320000000 0.296450000000 -0.327125
O2 O 0.355100000000 0.147380000000 0.194710000000 -0.351678
N1 N 0.428800000000 0.297860000000 0.256060000000 -0.181806
N2 N 0.507840000000 0.328890000000 0.323010000000 -0.263934
N3 N 0.465430000000 0.382540000000 0.314930000000 -0.146344
N4 N 0.567920000000 0.166500000000 0.136750000000 -0.30208
N5 N 0.535110000000 0.269400000000 0.121590000000 -0.332955
H5 H 0.536600000000 0.312300000000 0.113900000000 0.235042
C1 C 0.386050000000 0.259330000000 0.211190000000 -0.00753068
H1 H 0.341400000000 0.280800000000 0.211700000000 0.0757818
C2 C 0.485260000000 0.279000000000 0.287070000000 0.164079
H2 H 0.505400000000 0.236600000000 0.283500000000 0.00218674
C3 C 0.418900000000 0.361930000000 0.274480000000 0.139876
H3 H 0.382800000000 0.388400000000 0.259900000000 0.0397027
C4 C 0.411660000000 0.263020000000 0.139790000000 -0.288523
H4A H 0.380500000000 0.239600000000 0.110100000000 0.138079
H4B H 0.413600000000 0.310000000000 0.125600000000 0.15669
C5 C 0.478900000000 0.232700000000 0.133580000000 0.192591
C6 C 0.499790000000 0.168760000000 0.143290000000 -0.0622507
H6 H 0.472000000000 0.132000000000 0.152900000000 0.0692037
C7 C 0.587180000000 0.228200000000 0.123730000000 0.19712
H7 H 0.631900000000 0.241300000000 0.116900000000 -0.0335332
C8 C 0.376790000000 0.187590000000 0.237350000000 0.372865
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