Generalize CIF file reader (#2843)

cp2k · Jun 30, 2023 · a20b57f · a20b57f
1 parent bd8365e
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Showing 4 changed files with 76 additions and 1 deletion.
diff --git a/src/topology_cif.F b/src/topology_cif.F
@@ -163,8 +163,13 @@ SUBROUTINE read_coordinate_cif(topology, para_env, subsys_section)
       ifield = 0
       ii = 1
       ifield(ii) = 0
-      CALL parser_get_next_line(parser, 1)
+      CALL parser_search_string(parser, "_atom_site_", ignore_case=.FALSE., found=found, &
+                                begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
       DO WHILE (INDEX(parser%input_line, "_atom_site_") /= 0)
+         IF (INDEX(parser%input_line, "_atom_site_label") /= 0) THEN
+            CALL parser_get_next_line(parser, 1)
+            CYCLE
+         END IF
          ii = ii + 1
          CPASSERT(ii <= 20)
 

diff --git a/tests/xTB/regtest-1/3mppa-ase.cif b/tests/xTB/regtest-1/3mppa-ase.cif
@@ -0,0 +1,43 @@
+data_image0
+_chemical_formula_structural       HOHOPOH2C2HSHCH3
+_chemical_formula_sum              "H9 O3 P1 C3 S1"
+_cell_length_a       14.1406
+_cell_length_b       16.8139
+_cell_length_c       15.3143
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  H   H1        1.0  0.57589  0.38395  0.32649  1.0000
+  O   O1        1.0  0.56043  0.42448  0.36966  1.0000
+  H   H2        1.0  0.35359  0.37510  0.42040  1.0000
+  O   O2        1.0  0.39597  0.41781  0.43809  1.0000
+  P   P1        1.0  0.50243  0.38506  0.44926  1.0000
+  O   O3        1.0  0.50948  0.29737  0.45290  1.0000
+  H   H3        1.0  0.57283  0.55133  0.47263  1.0000
+  H   H4        1.0  0.45927  0.54690  0.52055  1.0000
+  C   C1        1.0  0.53401  0.53128  0.53085  1.0000
+  C   C2        1.0  0.54379  0.44141  0.54076  1.0000
+  H   H5        1.0  0.61810  0.42395  0.55022  1.0000
+  S   S1        1.0  0.55889  0.68038  0.59528  1.0000
+  H   H6        1.0  0.50396  0.41959  0.59768  1.0000
+  C   C3        1.0  0.57147  0.57364  0.61129  1.0000
+  H   H7        1.0  0.64641  0.55897  0.62155  1.0000
+  H   H8        1.0  0.53135  0.55537  0.66936  1.0000
+  H   H9        1.0  0.59449  0.70263  0.67351  1.0000
+
diff --git a/tests/xTB/regtest-1/TEST_FILES b/tests/xTB/regtest-1/TEST_FILES
@@ -19,4 +19,5 @@ si_geo.inp                                 1    1.0E-11             -14.51194886
 si_kp.inp                                  1    1.0E-12             -14.73191413260763
 h2o_dimer.inp                              1    1.0E-12             -11.54506384130837
 ghost.inp                                  1    1.0E-12              -1.03458221876736
+tcif.inp                                   1    1.0E-12             -27.71649842836537
 #EOF
diff --git a/tests/xTB/regtest-1/tcif.inp b/tests/xTB/regtest-1/tcif.inp
@@ -0,0 +1,26 @@
+&GLOBAL
+  PROJECT TTcif
+  RUN_TYPE ENERGY
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+  &DFT
+    &QS
+      METHOD xTB
+    &END QS
+    &SCF
+      SCF_GUESS MOPAC
+      MAX_SCF  1
+    &END SCF
+  &END DFT
+  &SUBSYS
+    &CELL
+      CELL_FILE_FORMAT CIF
+      CELL_FILE_NAME ./3mppa-ase.cif
+    &END CELL
+    &TOPOLOGY
+        COORD_FILE_FORMAT CIF
+        COORD_FILE_NAME ./3mppa-ase.cif
+    &END TOPOLOGY
+  &END SUBSYS
+&END FORCE_EVAL