@ccp-nc/crystvis-js 0.4.13

package/test/data/frac.cell

@@ -0,0 +1,8 @@
+%BLOCK LATTICE_ABC
+10.0 14.1421356 10.0
+90   90   45
+%ENDBLOCK LATTICE_ABC
+
+%BLOCK POSITIONS_FRAC
+H   0.5     0.5     0.5
+%ENDBLOCK POSITIONS_FRAC

package/test/data/org.cif

@@ -0,0 +1,427 @@
+#------------------------------------------------------------------------------
+#$Date: 2016-02-18 17:37:37 +0200 (Thu, 18 Feb 2016) $
+#$Revision: 176729 $
+#$URL: svn://www.crystallography.net/cod/cif/1/50/19/1501936.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/
+#
+# All data on this site have been placed in the public domain by the
+# contributors.
+#
+data_1501936
+loop_
+_publ_author_name
+'Stewart, Craig'
+'McDonald, Robert'
+'West, F. G.'
+_publ_section_title
+;
+ Expedient route to the tigliane-daphnane skeleton via oxonium ylide
+ [1,2]-shift.
+;
+_journal_issue                   4
+_journal_name_full               'Organic letters'
+_journal_page_first              720
+_journal_page_last               723
+_journal_paper_doi               10.1021/ol102953s
+_journal_volume                  13
+_journal_year                    2011
+_chemical_formula_moiety         'C21 H26 O4'
+_chemical_formula_sum            'C21 H26 O4'
+_chemical_formula_weight         342.42
+_chemical_name_systematic
+; 
+ ? 
+;
+_space_group_IT_number           2
+_symmetry_cell_setting           triclinic
+_symmetry_space_group_name_Hall  '-P 1'
+_symmetry_space_group_name_H-M   'P -1'
+_atom_sites_solution_hydrogens   geom
+_atom_sites_solution_primary     direct
+_atom_sites_solution_secondary   difmap
+_audit_creation_method           SHELXL-97
+_cell_angle_alpha                79.9846(4)
+_cell_angle_beta                 82.2194(4)
+_cell_angle_gamma                77.7988(4)
+_cell_formula_units_Z            2
+_cell_length_a                   8.2302(3)
+_cell_length_b                   8.2837(3)
+_cell_length_c                   13.1837(4)
+_cell_measurement_reflns_used    7347
+_cell_measurement_temperature    173(2)
+_cell_measurement_theta_max      27.48
+_cell_measurement_theta_min      2.54
+_cell_volume                     860.57(5)
+_computing_cell_refinement       'Bruker SAINT'
+_computing_data_collection       'Bruker APEX2'
+_computing_data_reduction        'Bruker SAINT'
+_computing_molecular_graphics    'Bruker SHELXTL'
+_computing_publication_material  'Bruker SHELXTL'
+_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
+_computing_structure_solution    'SHELXD (Schneider & Sheldrick, 2002)'
+_diffrn_ambient_temperature      173(2)
+_diffrn_measured_fraction_theta_full 0.986
+_diffrn_measured_fraction_theta_max 0.986
+_diffrn_measurement_device_type  'Bruker APEX-II CCD'
+_diffrn_measurement_method       '\f and \w scans'
+_diffrn_radiation_monochromator  graphite
+_diffrn_radiation_source         'fine-focus sealed tube'
+_diffrn_radiation_type           MoK\a
+_diffrn_radiation_wavelength     0.71073
+_diffrn_reflns_av_R_equivalents  0.0099
+_diffrn_reflns_av_sigmaI/netI    0.0146
+_diffrn_reflns_limit_h_max       10
+_diffrn_reflns_limit_h_min       -10
+_diffrn_reflns_limit_k_max       10
+_diffrn_reflns_limit_k_min       -10
+_diffrn_reflns_limit_l_max       17
+_diffrn_reflns_limit_l_min       -17
+_diffrn_reflns_number            7543
+_diffrn_reflns_theta_full        27.48
+_diffrn_reflns_theta_max         27.48
+_diffrn_reflns_theta_min         1.58
+_exptl_absorpt_coefficient_mu    0.090
+_exptl_absorpt_correction_T_max  0.9723
+_exptl_absorpt_correction_T_min  0.9471
+_exptl_absorpt_correction_type   integration
+_exptl_absorpt_process_details   'SADABS (Sheldrick, 2008)'
+_exptl_crystal_colour            colourless
+_exptl_crystal_density_diffrn    1.321
+_exptl_crystal_density_method    'not measured'
+_exptl_crystal_description       prism
+_exptl_crystal_F_000             368
+_exptl_crystal_size_max          0.61
+_exptl_crystal_size_mid          0.35
+_exptl_crystal_size_min          0.31
+_refine_diff_density_max         0.347
+_refine_diff_density_min         -0.262
+_refine_diff_density_rms         0.054
+_refine_ls_extinction_method     none
+_refine_ls_goodness_of_fit_ref   1.029
+_refine_ls_hydrogen_treatment    constr
+_refine_ls_matrix_type           full
+_refine_ls_number_parameters     227
+_refine_ls_number_reflns         3894
+_refine_ls_number_restraints     0
+_refine_ls_restrained_S_all      1.029
+_refine_ls_R_factor_all          0.0447
+_refine_ls_R_factor_gt           0.0418
+_refine_ls_shift/su_max          0.000
+_refine_ls_shift/su_mean         0.000
+_refine_ls_structure_factor_coef Fsqd
+_refine_ls_weighting_details
+'calc w=1/[\s^2^(Fo^2^)+(0.0666P)^2^+0.2631P] where P=(Fo^2^+2Fc^2^)/3'
+_refine_ls_weighting_scheme      calc
+_refine_ls_wR_factor_gt          0.1105
+_refine_ls_wR_factor_ref         0.1138
+_reflns_number_gt                3564
+_reflns_number_total             3894
+_reflns_threshold_expression     I>2\s(I)
+_cod_data_source_file            ol102953s_si_002.cif
+_cod_data_source_block           16
+_cod_depositor_comments
+;
+The following automatic conversions were performed:
+
+'_symmetry_cell_setting' value 'Triclinic' changed to 'triclinic'
+according to /home/saulius/struct/CIF-dictionaries/cif_core.dic
+dictionary named 'cif_core.dic' version 2.4.1 from 2010-06-29.
+
+Automatic conversion script
+Id: cif_fix_values 1715 2011-07-08 13:25:40Z adriana 
+;
+_cod_database_code               1501936
+loop_
+_symmetry_equiv_pos_as_xyz
+'x, y, z'
+'-x, -y, -z'
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_U_iso_or_equiv
+_atom_site_adp_type
+_atom_site_occupancy
+_atom_site_symmetry_multiplicity
+_atom_site_calc_flag
+_atom_site_refinement_flags
+O1 O 0.43325(9) 0.00289(10) 0.22205(6) 0.02475(18) Uani 1 1 d .
+O2 O 0.25690(11) 0.06668(12) 0.48190(6) 0.0318(2) Uani 1 1 d .
+H2O H 0.1572 0.0969 0.4682 0.048 Uiso 1 1 calc R
+O3 O 0.03180(9) 0.07400(10) 0.35068(6) 0.02243(18) Uani 1 1 d .
+O4 O -0.05742(9) 0.12277(10) 0.18848(6) 0.02204(18) Uani 1 1 d .
+C1 C 0.23130(16) 0.31699(15) 0.05350(9) 0.0292(3) Uani 1 1 d .
+H1A H 0.1668 0.2801 0.0066 0.035 Uiso 1 1 calc R
+H1B H 0.1966 0.4394 0.0512 0.035 Uiso 1 1 calc R
+C2 C 0.41826(17) 0.26953(18) 0.02240(10) 0.0362(3) Uani 1 1 d .
+H2A H 0.4570 0.3551 -0.0324 0.043 Uiso 1 1 calc R
+H2B H 0.4466 0.1600 -0.0026 0.043 Uiso 1 1 calc R
+C3 C 0.49496(16) 0.26142(18) 0.12251(10) 0.0346(3) Uani 1 1 d .
+H3A H 0.5020 0.3746 0.1340 0.041 Uiso 1 1 calc R
+H3B H 0.6086 0.1915 0.1204 0.041 Uiso 1 1 calc R
+C4 C 0.37765(13) 0.18364(14) 0.20769(9) 0.0236(2) Uani 1 1 d .
+C5 C 0.37169(15) 0.22671(15) 0.31723(9) 0.0278(2) Uani 1 1 d .
+H5A H 0.2716 0.3123 0.3326 0.033 Uiso 1 1 calc R
+H5B H 0.4728 0.2685 0.3250 0.033 Uiso 1 1 calc R
+C6 C 0.36401(14) 0.05939(14) 0.38863(9) 0.0249(2) Uani 1 1 d .
+H6 H 0.4795 0.0130 0.4087 0.030 Uiso 1 1 calc R
+C7 C 0.33164(13) -0.05107(13) 0.31315(8) 0.0221(2) Uani 1 1 d .
+H7 H 0.3766 -0.1709 0.3390 0.026 Uiso 1 1 calc R
+C8 C 0.14955(13) -0.03284(13) 0.28705(8) 0.0200(2) Uani 1 1 d .
+C9 C 0.09823(15) -0.20349(14) 0.30165(9) 0.0274(2) Uani 1 1 d .
+H9A H 0.1342 -0.2692 0.3677 0.033 Uiso 1 1 calc R
+H9B H -0.0251 -0.1870 0.3061 0.033 Uiso 1 1 calc R
+C10 C 0.17450(18) -0.30157(15) 0.21329(10) 0.0335(3) Uani 1 1 d .
+H10A H 0.2980 -0.3217 0.2093 0.040 Uiso 1 1 calc R
+H10B H 0.1393 -0.4111 0.2257 0.040 Uiso 1 1 calc R
+C11 C 0.11557(18) -0.20110(15) 0.11223(10) 0.0320(3) Uani 1 1 d .
+H11A H -0.0079 -0.1821 0.1166 0.038 Uiso 1 1 calc R
+H11B H 0.1615 -0.2652 0.0546 0.038 Uiso 1 1 calc R
+C12 C 0.17208(14) -0.03337(14) 0.09030(8) 0.0243(2) Uani 1 1 d .
+H12A H 0.2952 -0.0536 0.0750 0.029 Uiso 1 1 calc R
+H12B H 0.1235 0.0326 0.0277 0.029 Uiso 1 1 calc R
+C13 C 0.12298(12) 0.06918(12) 0.17872(8) 0.0190(2) Uani 1 1 d .
+C14 C 0.20338(13) 0.22587(13) 0.16509(8) 0.0210(2) Uani 1 1 d .
+H14 H 0.1286 0.3076 0.2067 0.025 Uiso 1 1 calc R
+C15 C -0.11096(13) 0.13931(14) 0.29369(8) 0.0222(2) Uani 1 1 d .
+H15 H -0.1989 0.0710 0.3197 0.027 Uiso 1 1 calc R
+C16 C -0.17827(13) 0.31719(14) 0.31250(9) 0.0246(2) Uani 1 1 d .
+C17 C -0.21011(15) 0.44865(15) 0.23268(10) 0.0285(2) Uani 1 1 d .
+H17 H -0.1901 0.4287 0.1628 0.034 Uiso 1 1 calc R
+C18 C -0.27164(16) 0.61039(16) 0.25492(11) 0.0356(3) Uani 1 1 d .
+H18 H -0.2950 0.7001 0.2001 0.043 Uiso 1 1 calc R
+C19 C -0.29871(16) 0.64062(17) 0.35582(12) 0.0402(3) Uani 1 1 d .
+H19 H -0.3359 0.7515 0.3706 0.048 Uiso 1 1 calc R
+C20 C -0.2715(2) 0.5084(2) 0.43574(13) 0.0532(4) Uani 1 1 d .
+H20 H -0.2928 0.5283 0.5056 0.064 Uiso 1 1 calc R
+C21 C -0.2133(2) 0.34710(19) 0.41411(11) 0.0450(4) Uani 1 1 d .
+H21 H -0.1973 0.2566 0.4692 0.054 Uiso 1 1 calc R
+loop_
+_atom_site_aniso_label
+_atom_site_aniso_U_11
+_atom_site_aniso_U_22
+_atom_site_aniso_U_33
+_atom_site_aniso_U_23
+_atom_site_aniso_U_13
+_atom_site_aniso_U_12
+O1 0.0204(4) 0.0269(4) 0.0259(4) -0.0057(3) -0.0017(3) -0.0012(3)
+O2 0.0315(4) 0.0438(5) 0.0215(4) -0.0075(4) -0.0049(3) -0.0067(4)
+O3 0.0201(4) 0.0270(4) 0.0189(4) -0.0043(3) -0.0034(3) 0.0000(3)
+O4 0.0195(4) 0.0265(4) 0.0204(4) -0.0038(3) -0.0048(3) -0.0031(3)
+C1 0.0362(6) 0.0255(5) 0.0262(6) 0.0017(4) -0.0051(5) -0.0101(5)
+C2 0.0391(7) 0.0386(7) 0.0290(6) 0.0001(5) 0.0050(5) -0.0127(5)
+C3 0.0282(6) 0.0416(7) 0.0349(6) -0.0006(5) 0.0006(5) -0.0155(5)
+C4 0.0217(5) 0.0248(5) 0.0253(5) -0.0034(4) -0.0030(4) -0.0068(4)
+C5 0.0307(6) 0.0285(6) 0.0277(6) -0.0061(4) -0.0078(4) -0.0092(4)
+C6 0.0234(5) 0.0292(6) 0.0230(5) -0.0055(4) -0.0074(4) -0.0028(4)
+C7 0.0214(5) 0.0223(5) 0.0218(5) -0.0028(4) -0.0056(4) -0.0008(4)
+C8 0.0213(5) 0.0196(5) 0.0191(5) -0.0029(4) -0.0035(4) -0.0031(4)
+C9 0.0341(6) 0.0219(5) 0.0272(6) 0.0021(4) -0.0083(5) -0.0093(4)
+C10 0.0480(7) 0.0194(5) 0.0349(6) -0.0034(5) -0.0132(5) -0.0058(5)
+C11 0.0472(7) 0.0235(6) 0.0294(6) -0.0073(4) -0.0117(5) -0.0083(5)
+C12 0.0299(5) 0.0235(5) 0.0205(5) -0.0059(4) -0.0041(4) -0.0040(4)
+C13 0.0188(5) 0.0189(5) 0.0196(5) -0.0026(4) -0.0039(4) -0.0027(4)
+C14 0.0219(5) 0.0200(5) 0.0217(5) -0.0024(4) -0.0034(4) -0.0051(4)
+C15 0.0188(5) 0.0261(5) 0.0212(5) -0.0015(4) -0.0033(4) -0.0038(4)
+C16 0.0187(5) 0.0278(5) 0.0268(5) -0.0059(4) -0.0028(4) -0.0020(4)
+C17 0.0250(5) 0.0286(6) 0.0312(6) -0.0035(5) -0.0044(4) -0.0032(4)
+C18 0.0289(6) 0.0276(6) 0.0484(8) -0.0032(5) -0.0076(5) -0.0008(5)
+C19 0.0284(6) 0.0338(7) 0.0599(9) -0.0201(6) -0.0106(6) 0.0049(5)
+C20 0.0639(10) 0.0522(9) 0.0397(8) -0.0233(7) -0.0113(7) 0.0147(8)
+C21 0.0585(9) 0.0408(8) 0.0282(7) -0.0085(6) -0.0068(6) 0.0113(6)
+loop_
+_atom_type_symbol
+_atom_type_description
+_atom_type_scat_dispersion_real
+_atom_type_scat_dispersion_imag
+_atom_type_scat_source
+C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+loop_
+_geom_angle_atom_site_label_1
+_geom_angle_atom_site_label_2
+_geom_angle_atom_site_label_3
+_geom_angle
+C7 O1 C4 102.79(8)
+C15 O3 C8 106.30(7)
+C15 O4 C13 107.90(7)
+C2 C1 C14 105.14(9)
+C1 C2 C3 103.37(10)
+C2 C3 C4 105.12(10)
+O1 C4 C3 108.63(9)
+O1 C4 C5 103.13(9)
+C3 C4 C5 117.53(10)
+O1 C4 C14 108.27(8)
+C3 C4 C14 105.59(9)
+C5 C4 C14 113.35(9)
+C4 C5 C6 103.88(9)
+O2 C6 C5 116.61(10)
+O2 C6 C7 117.45(10)
+C5 C6 C7 102.19(9)
+O1 C7 C6 100.99(9)
+O1 C7 C8 109.50(8)
+C6 C7 C8 118.01(9)
+O3 C8 C9 108.90(9)
+O3 C8 C13 99.92(8)
+C9 C8 C13 113.17(9)
+O3 C8 C7 111.63(8)
+C9 C8 C7 111.12(9)
+C13 C8 C7 111.61(8)
+C10 C9 C8 112.28(10)
+C11 C10 C9 108.77(10)
+C10 C11 C12 110.83(10)
+C13 C12 C11 114.11(9)
+O4 C13 C12 108.21(8)
+O4 C13 C8 100.85(8)
+C12 C13 C8 114.25(8)
+O4 C13 C14 108.43(8)
+C12 C13 C14 114.66(9)
+C8 C13 C14 109.39(8)
+C1 C14 C13 116.60(9)
+C1 C14 C4 105.76(9)
+C13 C14 C4 111.64(8)
+O4 C15 O3 107.05(8)
+O4 C15 C16 114.21(9)
+O3 C15 C16 108.24(8)
+C17 C16 C21 119.43(11)
+C17 C16 C15 122.58(10)
+C21 C16 C15 117.97(11)
+C16 C17 C18 119.94(12)
+C19 C18 C17 120.39(12)
+C18 C19 C20 119.60(13)
+C19 C20 C21 120.19(14)
+C16 C21 C20 120.35(13)
+loop_
+_geom_bond_atom_site_label_1
+_geom_bond_atom_site_label_2
+_geom_bond_distance
+O1 C7 1.4286(13)
+O1 C4 1.4568(13)
+O2 C6 1.4152(14)
+O3 C15 1.4376(12)
+O3 C8 1.4498(12)
+O4 C15 1.4184(13)
+O4 C13 1.4518(12)
+C1 C2 1.5232(18)
+C1 C14 1.5436(15)
+C2 C3 1.5236(19)
+C3 C4 1.5252(16)
+C4 C5 1.5387(15)
+C4 C14 1.5597(14)
+C5 C6 1.5422(16)
+C6 C7 1.5459(15)
+C7 C8 1.5534(14)
+C8 C9 1.5328(15)
+C8 C13 1.5454(14)
+C9 C10 1.5254(17)
+C10 C11 1.5237(17)
+C11 C12 1.5256(16)
+C12 C13 1.5217(14)
+C13 C14 1.5507(14)
+C15 C16 1.5115(15)
+C16 C17 1.3847(16)
+C16 C21 1.3854(17)
+C17 C18 1.3954(17)
+C18 C19 1.376(2)
+C19 C20 1.385(2)
+C20 C21 1.386(2)
+loop_
+_geom_hbond_atom_site_label_D
+_geom_hbond_atom_site_label_H
+_geom_hbond_atom_site_label_A
+_geom_hbond_distance_DH
+_geom_hbond_distance_HA
+_geom_hbond_distance_DA
+_geom_hbond_angle_DHA
+O2 H2O O3 0.84 2.03 2.6856(11) 134.4
+loop_
+_geom_torsion_atom_site_label_1
+_geom_torsion_atom_site_label_2
+_geom_torsion_atom_site_label_3
+_geom_torsion_atom_site_label_4
+_geom_torsion
+C14 C1 C2 C3 -36.03(12)
+C1 C2 C3 C4 38.59(13)
+C7 O1 C4 C3 171.08(9)
+C7 O1 C4 C5 45.66(10)
+C7 O1 C4 C14 -74.71(10)
+C2 C3 C4 O1 90.00(11)
+C2 C3 C4 C5 -153.50(11)
+C2 C3 C4 C14 -25.95(13)
+O1 C4 C5 C6 -19.76(11)
+C3 C4 C5 C6 -139.21(10)
+C14 C4 C5 C6 97.07(10)
+C4 C5 C6 O2 -140.12(9)
+C4 C5 C6 C7 -10.64(11)
+C4 O1 C7 C6 -52.55(9)
+C4 O1 C7 C8 72.65(10)
+O2 C6 C7 O1 167.08(9)
+C5 C6 C7 O1 38.13(10)
+O2 C6 C7 C8 47.83(13)
+C5 C6 C7 C8 -81.11(11)
+C15 O3 C8 C9 -81.23(10)
+C15 O3 C8 C13 37.59(9)
+C15 O3 C8 C7 155.72(8)
+O1 C7 C8 O3 -122.30(9)
+C6 C7 C8 O3 -7.63(13)
+O1 C7 C8 C9 115.92(10)
+C6 C7 C8 C9 -129.40(10)
+O1 C7 C8 C13 -11.42(12)
+C6 C7 C8 C13 103.25(11)
+O3 C8 C9 C10 160.32(9)
+C13 C8 C9 C10 50.17(12)
+C7 C8 C9 C10 -76.32(11)
+C8 C9 C10 C11 -59.99(13)
+C9 C10 C11 C12 60.93(14)
+C10 C11 C12 C13 -53.49(14)
+C15 O4 C13 C12 150.64(9)
+C15 O4 C13 C8 30.42(9)
+C15 O4 C13 C14 -84.43(9)
+C11 C12 C13 O4 -68.27(11)
+C11 C12 C13 C8 43.17(13)
+C11 C12 C13 C14 170.58(9)
+O3 C8 C13 O4 -40.93(9)
+C9 C8 C13 O4 74.70(10)
+C7 C8 C13 O4 -159.07(8)
+O3 C8 C13 C12 -156.73(8)
+C9 C8 C13 C12 -41.11(12)
+C7 C8 C13 C12 85.12(11)
+O3 C8 C13 C14 73.20(9)
+C9 C8 C13 C14 -171.18(9)
+C7 C8 C13 C14 -44.95(11)
+C2 C1 C14 C13 -104.72(11)
+C2 C1 C14 C4 20.01(12)
+O4 C13 C14 C1 -86.70(11)
+C12 C13 C14 C1 34.33(13)
+C8 C13 C14 C1 164.18(9)
+O4 C13 C14 C4 151.61(8)
+C12 C13 C14 C4 -87.37(11)
+C8 C13 C14 C4 42.48(11)
+O1 C4 C14 C1 -112.58(9)
+C3 C4 C14 C1 3.62(12)
+C5 C4 C14 C1 133.64(10)
+O1 C4 C14 C13 15.19(11)
+C3 C4 C14 C13 131.38(10)
+C5 C4 C14 C13 -98.59(10)
+C13 O4 C15 O3 -7.90(10)
+C13 O4 C15 C16 111.90(9)
+C8 O3 C15 O4 -20.10(10)
+C8 O3 C15 C16 -143.65(9)
+O4 C15 C16 C17 9.96(15)
+O3 C15 C16 C17 129.09(11)
+O4 C15 C16 C21 -171.89(11)
+O3 C15 C16 C21 -52.76(14)
+C21 C16 C17 C18 2.13(19)
+C15 C16 C17 C18 -179.75(10)
+C16 C17 C18 C19 0.94(19)
+C17 C18 C19 C20 -2.8(2)
+C18 C19 C20 C21 1.6(3)
+C17 C16 C21 C20 -3.3(2)
+C15 C16 C21 C20 178.47(14)
+C19 C20 C21 C16 1.5(3)

package/test/data/pyridine.xyz

@@ -0,0 +1,13 @@
+11
+Pyridine molecule (source: Wikipedia)
+C       -0.180226841      0.360945118     -1.120304970
+C       -0.180226841      1.559292118     -0.407860970
+C       -0.180226841      1.503191118      0.986935030
+N       -0.180226841      0.360945118      1.685965030
+C       -0.180226841     -0.781300882      0.986935030
+C       -0.180226841     -0.837401882     -0.407860970
+H       -0.180226841      0.360945118     -2.206546970
+H       -0.180226841      2.517950118     -0.917077970
+H       -0.180226841      2.421289118      1.572099030
+H       -0.180226841     -1.699398882      1.572099030
+H       -0.180226841     -1.796059882     -0.917077970

package/test/data/si8.xyz

@@ -0,0 +1,10 @@
+8
+Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.0 5.44" Properties=species:S:1:pos:R:3:spin:R:1 Time=0.0
+Si        0.00000000      0.00000000      0.00000000    1.0
+Si        1.36000000      1.36000000      1.36000000    0.0
+Si        2.72000000      2.72000000      0.00000000    0.0
+Si        4.08000000      4.08000000      1.36000000    0.0
+Si        2.72000000      0.00000000      2.72000000    0.0
+Si        4.08000000      1.36000000      4.08000000    0.0
+Si        0.00000000      2.72000000      2.72000000    0.0
+Si        1.36000000      4.08000000      4.08000000    0.0

package/test/loader.js

@@ -0,0 +1,107 @@
+'use strict';
+
+import chai from 'chai'
+import chaiAlmost from 'chai-almost'
+
+import fs from 'fs'
+import path from 'path'
+import { fileURLToPath } from 'url';
+
+import { Loader } from '../lib/loader.js'
+
+const expect = chai.expect
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+
+
+chai.use(chaiAlmost(1e-3));
+
+describe('#loading', function() {
+    it('should load properly an XYZ file', function() {
+
+        var loader = new Loader();
+
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'pyridine.xyz'), "utf8");
+        var a = loader.load(xyz, 'xyz')['xyz'];
+
+        expect(a.get_chemical_symbols()).to.deep.equal(['C', 'C', 'C', 'N', 'C', 'C',
+            'H', 'H', 'H', 'H', 'H'
+        ]);
+    });
+    it('should load properly an extended XYZ file', function() {
+
+        var loader = new Loader();
+
+        var xyz = fs.readFileSync(path.join(__dirname, 'data', 'si8.xyz'), "utf8");
+        var a = loader.load(xyz, 'xyz')['xyz'];
+
+        expect(a.get_cell()).to.deep.almost.equal([
+            [5.44, 0, 0],
+            [0, 5.44, 0],
+            [0, 0, 5.44]
+        ]);
+        expect(a.get_array('spin')).to.deep.equal([1, 0, 0, 0, 0, 0, 0, 0]);
+    });
+    it('should load properly a CIF file', function() {
+
+        var loader = new Loader();
+
+        var cif = fs.readFileSync(path.join(__dirname, 'data', 'org.cif'), "utf8");
+        var a = loader.load(cif)['1501936'];
+
+
+        chai.expect(a.get_cell()).to.deep.almost.equal([
+            [8.2302, 0.0, 0.0],
+            [1.7507207912272031, 8.096583378263006, 0.0],
+            [1.7848106706548383, 1.959874486240255, 12.914460443940394]
+        ]);
+    });
+    it('should load properly a Magres file', function() {
+
+        var loader = new Loader();
+
+        var magres = fs.readFileSync(path.join(__dirname, 'data', 'ethanol.magres'), "utf8");
+        var a = loader.load(magres, 'magres')['magres'];
+
+        expect(loader.status).to.equal(Loader.STATUS_SUCCESS);
+        expect(a.length()).to.equal(9);
+        // Parsing positions
+        expect(a.get_positions()[0]).to.deep.equal([2.129659, 2.823711, 2.349943]);
+        // Susceptibility
+        expect(a.info.sus.data).to.deep.equal([[1,0,0],[0,1,0],[0,0,1]]);
+        // Shielding
+        expect(a.get_array('ms')[4].data).to.deep.equal([
+            [25.946849893, -2.77588906551, 3.75442739434],
+            [-1.77463107727, 29.7225814726, -0.398037457666],
+            [3.04599241075, -1.46601607492, 26.5018075671]
+        ]);
+        // Version
+        expect(a.info['magres-version']).to.equal('1.0');
+
+        // Test for failure
+        loader.load('Something', 'magres');
+        expect(loader.error_message).to.equal('Invalid Magres file format: no version line');
+
+        loader.load('#$magres-abinitio-v1.0\n[block]\n[another]', 'magres');
+        expect(loader.error_message).to.equal('Invalid Magres file format: block opened without closing');
+
+    });
+    it('should load properly a CELL file', function() {
+
+        var loader = new Loader();
+
+        var cell = fs.readFileSync(path.join(__dirname, 'data', 'ethanol.cell'), "utf8");
+        var a = loader.load(cell, 'cell')['cell'];
+
+        expect(a.get_cell()).to.almost.deep.equal([[6,0,0],[0,6,0],[0,0,6]]);
+        expect(a.get_chemical_symbols()).to.deep.equal(['H', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'O']);
+        expect(a.get_positions()[0]).to.almost.deep.equal([2.129659, 2.823711, 2.349943]);
+        
+        // Test an example with ABC lattice and FRAC positions
+        cell = fs.readFileSync(path.join(__dirname, 'data', 'frac.cell'), "utf8");
+        a = loader.load(cell, 'cell')['cell'];
+
+        expect(a.get_cell()).to.almost.deep.equal([[10.0, 0, 0], [10.0, 10.0, 0], [0, 0, 10.0]]);
+        expect(a.get_positions()[0]).to.almost.deep.equal([10.0, 5.0, 5.0]);
+
+    });
+});