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Add example CIF files that illustrate the usage of the ATOM_ANALYTICAL category #425

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vaitkus opened this issue Jun 19, 2023 · 2 comments
Closed

Add example CIF files that illustrate the usage of the ATOM_ANALYTICAL category #425

vaitkus opened this issue Jun 19, 2023 · 2 comments

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@vaitkus
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vaitkus commented Jun 19, 2023

As discussed in PR #313 it would be useful to have a full example of how the ATOM_ANALYTICAL category could be used in a CIF file (see #313 (review)).
@rowlesmr
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I'm putting one together. I made it in v1.1 with my TOPAS CIF making stuff and manually altered it to v2.0. So it should work with no errors at all ;).

@rowlesmr
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rowlesmr commented Jun 24, 2023 •
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An abridged one:

#\#CIF_2.0

#######	Begin common information	#######
data_global

_diffrn.ambient_temperature	295
_diffrn.ambient_pressure	101.3

_diffrn_radiation.probe	x-ray
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.value
_diffrn_radiation_wavelength.wt
_diffrn_radiation_wavelength.type
	1    1.7889847   0.378
...
	8    1.6207938   0.00147

#######	End common information	#######

#######	Begin powder crystal structure	#######
data_Goethite_0020
_pd_phase.id	Goethite_0020
_pd_phase.name	Goethite

_cell.length_a    4.5991(2)
_cell.length_b    9.9268(5)
_cell.length_c    3.01059(14)
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 90
_cell.volume      137.446(11)

_exptl_crystal_density_diffrn	4.1343(3)
_exptl_absorpt_coefficient_mu	17.7460(14)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	orthorhombic
_space_group.name_H-M_alt
;P b n m
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	  8 'x+1/2, -y+1/2, z+1/2 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Fe1	Fe+3	  4	0.04893	0.853657	0.25	0.9205(8)	0.4642662
Al1	Al+3	  4	0.04893	0.853657	0.25	0.0795(8)	0.4642662
O1	O-2 	  4	0.7057	0.19914 	0.25	1       	0.5661205
O2	O-2 	  4	0.1987	0.05298 	0.25	1       	0.5842806
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Hematite_0020
_pd_phase.id	Hematite_0020
_pd_phase.name	Hematite

_cell.length_a    5.0253(11)
_cell.length_b    5.0253(11)
_cell.length_c    13.744(5)
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 120
_cell.volume      300.59(17)

_exptl_crystal_density_diffrn	5.155(3)
_exptl_absorpt_coefficient_mu	23.448(13)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	trigonal
_space_group.name_H-M_alt
;R -3 c H
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	 36 'x+1/3, x-y-1/3, z+1/6 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Fe1	Fe+3	 12	0    	0	0.35528	0.928(7)	0.35
Al1	Al+3	 12	0    	0	0.35528	0.072(7)	0.35
O1	O-2 	 18	0.3071	0	0.25  	1        	0.74
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Quartz_0020
_pd_phase.id	Quartz_0020
_pd_phase.name	Quartz

_cell.length_a    4.9134
_cell.length_b    4.9134
_cell.length_c    5.4052
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 120
_cell.volume      113.007337

_exptl_crystal_density_diffrn	2.64865267
_exptl_absorpt_coefficient_mu	14.6131524
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	trigonal
_space_group.name_H-M_alt
;P 32 2 1
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	  6 '-x, -x+y, -z-1/3 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Si1	Si+4	  3	0.46987	0   	0.6666667	1	0.466
O1	O-2  	  6	0.4141	0.2681	0.7855  	1	1.026
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Kaolinite_0020
_pd_phase.id	Kaolinite_0020
_pd_phase.name	Kaolinite_C

_cell.length_a    5.14971
_cell.length_b    8.93507
_cell.length_c    7.418(3)
_cell.angle_alpha 91.928
_cell.angle_beta  105.044
_cell.angle_gamma 89.792
_cell.volume      329.41(13)

_exptl_crystal_density_diffrn	2.6027(10)
_exptl_absorpt_coefficient_mu	12.281(5)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	triclinic
_space_group.name_H-M_alt
;P1
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Al1	Al+3	  1	0.352	0.501	0.471	1	0.25
...
H8	H   	  1	0.611	0.292	0.7	1	1
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Nacrite_0020
_pd_phase.id	Nacrite_0020
_pd_phase.name	Nacrite_4M

_cell.length_a    5.173(6)
_cell.length_b    8.978(9)
_cell.length_c    28.66
_cell.angle_alpha 90
_cell.angle_beta  91.72
_cell.angle_gamma 90
_cell.volume      1331(2)

_exptl_crystal_density_diffrn	2.537(4)
_exptl_absorpt_coefficient_mu	12.160(19)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	monoclinic
_space_group.name_H-M_alt
;C 1 c 1
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	  4 'x+1/2, -y+1/2, z+1/2 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Al1	Al+3	  4	-0.25	0.3333333	0   	1	1
...
O18	O-2 	  4	0.0778	0.3333333	0.4618	1	1
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Anatase_0020
_pd_phase.id	Anatase_0020
_pd_phase.name	Anatase

_cell.length_a    3.7850(8)
_cell.length_b    3.7850(8)
_cell.length_c    9.522(6)
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 90
_cell.volume      136.42(10)

_exptl_crystal_density_diffrn	3.889(3)
_exptl_absorpt_coefficient_mu	70.49(5)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	tetragonal
_space_group.name_H-M_alt
;I 41/a m d S
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	 32 'x, y+1/2, -z+1/4 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Ti1	Ti+4	  4	0	0	0   	1	0.458
O1	O-2 	  8	0	0	0.20806	1	0.568
#######	End powder crystal structure	#######


#######	Begin powder crystal structure	#######
data_Rutile_0020
_pd_phase.id	Rutile_0020
_pd_phase.name	Rutile

_cell.length_a    4.600(3)
_cell.length_b    4.600(3)
_cell.length_c    3.001(9)
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 90
_cell.volume      63.5(2)

_exptl_crystal_density_diffrn	4.178(14)
_exptl_absorpt_coefficient_mu	75.7(3)
_cell_measurement.theta_min	2.50394
_cell_measurement.theta_max	47.504047
_space_group.crystal_system	tetragonal
_space_group.name_H-M_alt
;P 42/m n m
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	 16 'x+1/2, -y+1/2, z+1/2 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Ti1	Ti+4	  2	0    	0    	0	1	1
O1	O-2 	  4	0.30392	0.30392	0	1	1
#######	End powder crystal structure	#######


#######	Begin powder diffraction data	#######
data_DIFFRACTOGRAM_0020
_pd_diffractogram.id	DIFFRACTOGRAM_0020

_pd_meas.datetime_initiated	2023-06-19T21:00:34+08:00
_pd_meas.scan_method	scan

_refine_ls.goodness_of_fit_all	1.33237
_pd_proc_ls.prof_R_factor	0.06355
_pd_proc_ls.prof_wR_factor	0.08219
_pd_proc_ls.prof_wR_expected	0.06168
_pd_calc.method	Rietveld

loop_
_pd_phase_mass.phase_id
_pd_phase_mass.percent
Goethite_0020	70.6(2)
Hematite_0020	8.11(17)
Quartz_0020 	6.48(6)
Kaolinite_0020	1.88(18)
Nacrite_0020	1.21(12)
Anatase_0020	0.35(3)
Rutile_0020 	0.44(4)
#amor 10.9(4)

_pd_qpa_external_std.diffractogram_id   SRM676A
_pd_char.mass_atten_coef_mu_calc        4.52708878
_pd_qpa_overall.method                  external_standard

loop_
_pd_pref_orient_March_Dollase.id
_pd_pref_orient_March_Dollase.phase_id
_pd_pref_orient_March_Dollase.hkl
_pd_pref_orient_March_Dollase.fract
_pd_pref_orient_March_Dollase.fract_su
1   Kaolinite_0020   [0 0 1]   0.75   0.23
2   Nacrite_0020     [0 0 1]   2.0    .

loop_
_atom_analytical.id
_atom_analytical.analyte
_atom_analytical.meas_id
_atom_analytical.chemical_species
_atom_analytical.chemical_species_mass_percent
 1 Fe  a   'Fe'	    49.09
 2 Si  a   'Si O2' 	10.48
 3 Al  a   'Al2 O3'	 6.02
 4 Ti  a   'Ti O2'   0.75
 5 Mn  a   'Mn'	     0.15
 6 Ca  a   'Ca O'    0.14
 7 P   a   'P'       0.454
 8 S   a   'S'       0.007
 9 Mg  a   'Mg O'    0.27
10 K   a   'K2 O'    0.014
11 Na  a   'Na'	     0.01

loop_
_atom_analytical_mass_loss.id
_atom_analytical_mass_loss.meas_id
_atom_analytical_mass_loss.percent
_atom_analytical_mass_loss.temperature
LOI1 a   9.6   698
LOI2 a  10.71  923
LOI3 a  10.99 1273

loop_
_atom_analytical_source.id
_atom_analytical_source.technique
_atom_analytical_source.equipment_make
a  XRF 'Panalytical Axios'

loop_
	_refln.index_h
	_refln.index_k
	_refln.index_l
	_pd_refln.phase_id
	_refln.d_spacing
	_refln.wavelength_id
	_refln.F_squared_calc
	_refln.F_squared_meas
   0	   0	   2	Goethite_0020	   1.505293    1	   69.552141	   70.767265
...
   3	   2	   0	Rutile_0020 	   1.275743    1	    0.017815	    0.017914

_pd_calc_overall.component_presentation_order
[
Goethite_0020
Hematite_0020
Quartz_0020
Kaolinite_0020
Nacrite_0020
Anatase_0020
Rutile_0020
]

loop_
	_pd_meas.2theta_scan
	_pd_meas.counts_total
	_pd_proc.ls_weight
	_pd_calc.intensity_total
	_pd_proc.intensity_bkg_calc
	_pd_calc.component_intensities_total
   1	 5.023636	791	0.001264	799.014950	798.748050	[	798.959975	798.770338	 0.000000	798.780417	798.748384	 0.000000	 0.000000	]
...
5712	95.008094	 77	0.012987	 76.586601	6 3.972674	[	 70.915388	 67.711360	64.027401	 65.137999	 64.414912	63.974624	64.240963	]

#######	End powder diffraction data	#######


#######	Begin powder crystal structure	#######
data_STD_Aluminium_oxide_alpha
_pd_phase.id	STD_Aluminium_oxide_alpha
_pd_phase.name	Alumina

_cell.length_a    4.75935(3)
_cell.length_b    4.75935(3)
_cell.length_c    12.99295(11)
_cell.angle_alpha 90
_cell.angle_beta  90
_cell.angle_gamma 120
_cell.volume      254.879(4)

_exptl_crystal_density_diffrn	3.98568(6)
_exptl_absorpt_coefficient_mu	19.4470(3)
_cell_measurement.theta_min	4.0007923
_cell_measurement.theta_max	47.504047
_space_group.name_H-M_alt
;R -3 c H
;
loop_
	_space_group_symop.id
	_space_group_symop.operation_xyz
	  1 'x, y, z '
...
	 36 'x+1/3, x-y-1/3, z+1/6 '

loop_
	_atom_site.label
	_atom_site.type_symbol
	_atom_site.site_symmetry_multiplicity
	_atom_site.fract_x
	_atom_site.fract_y
	_atom_site.fract_z
	_atom_site.occupancy
	_atom_site.B_iso_or_equiv
Al1	Al+3	 12	0   	0	0.14772	1	0.318
O1	O-2  	 18	0.3064	0	0.25	1	0.334
#######	End powder crystal structure	#######


#######	Begin powder diffraction data	#######
data_SRM676A
_pd_diffractogram.id	SRM676A

_pd_meas.datetime_initiated	2023-06-19T20:01:53+08:00
_pd_meas.scan_method	scan

_refine_ls.goodness_of_fit_all	1.32287
_pd_proc_ls.prof_R_factor	0.07675
_pd_proc_ls.prof_wR_factor	0.11393
_pd_proc_ls.prof_wR_expected	0.08613
_pd_calc.method	Rietveld

loop_
	_pd_phase_mass.phase_id
	_pd_phase_mass.percent
	_pd_phase_mass.percent_su
STD_Aluminium_oxide_alpha	99.02   1.11

_pd_qpa_external_std.k_factor           321.82
_pd_char.mass_atten_coef_mu_calc        4.87922752
_pd_qpa_overall.method                  external_standard

loop_
	_refln.index_h
	_refln.index_k
	_refln.index_l
	_pd_refln.phase_id
	_refln.d_spacing
	_refln.wavelength_id
	_refln.F_squared_calc
	_refln.F_squared_meas
   0	   0	   6	99	   2.165492    1	    1.074481	    1.322490
...
   3	   0	   0	99	   1.373906    1	  291.868903	  285.389678

loop_
	_pd_meas.2theta_scan
	_pd_meas.counts_total
	_pd_proc.ls_weight
	_pd_calc.intensity_total
	_pd_proc.intensity_bkg_calc
 190	 8.001585	66	0.015152	62.572173	62.572174
...
5712	95.008094	26	0.038462	25.050297	23.441636

#######	End powder diffraction data	#######

@rowlesmr rowlesmr mentioned this issue Jun 24, 2023
Merged
@vaitkus vaitkus closed this as completed Jun 28, 2023
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@vaitkus @rowlesmr