Made to read unit cell and supercell matrix as computed from basis vectors of unit cell and supercell instead of reading supercell in automatic mode

phonopy/interface/__init__.py

@@ -33,6 +33,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import os
+import numpy as np
 from phonopy.interface.phonopy_yaml import PhonopyYaml
 from phonopy.file_IO import parse_disp_yaml, write_FORCE_SETS
 
@@ -111,13 +112,9 @@ def write_supercells_with_displacements(interface_mode,
 
 def read_crystal_structure(filename=None,
                            interface_mode=None,
-                           chemical_symbols=None,
-                           read_supercell=False):
+                           chemical_symbols=None):
     if filename is None:
-        if read_supercell:
-            cell_filename = get_default_supercell_filename(interface_mode)
-        else:
-            cell_filename = get_default_cell_filename(interface_mode)
+        cell_filename = get_default_cell_filename(interface_mode)
     else:
         cell_filename = filename
 
@@ -145,18 +142,19 @@ def read_crystal_structure(filename=None,
     if interface_mode == 'phonopy_yaml':
         phpy = PhonopyYaml()
         phpy.read(cell_filename)
-        if phpy.supercell is None:  # supposed "disp.yaml"
-            return phpy.unitcell, (cell_filename, None)
-        else:  # supposed "phonopy_disp.yaml" or "phonopy.yaml"
-            if read_supercell:
-                cell = phpy.supercell
-            else:
-                cell = phpy.unitcell
-            if 'phonopy' in phpy.yaml and 'calculator' in phpy.yaml['phonopy']:
+        cell = phpy.unitcell
+        if 'phonopy' in phpy.yaml:
+            if 'calculator' in phpy.yaml['phonopy']:
                 calculator = phpy.yaml['phonopy']['calculator']
             else:
                 calculator = None
-            return cell, (cell_filename, calculator)
+            tmat = np.dot(np.linalg.inv(cell.get_cell().T),
+                          phpy.supercell.get_cell().T)
+            tmat = np.rint(tmat).astype('intc')
+        else:
+            calculator = None
+            tmat = np.eye(3, dtype='intc')
+        return cell, (cell_filename, calculator, tmat)
     elif interface_mode is None or interface_mode == 'vasp':
         from phonopy.interface.vasp import read_vasp
         if chemical_symbols is None:

scripts/phonopy

@@ -420,23 +420,58 @@ else:
     phonopy_conf = PhonopyConfParser(args=args)
     settings = phonopy_conf.get_settings()
 
-##########################################
-# Set calculator interface and read cell #
-##########################################
-_interface_mode = get_interface_mode(args)
-if settings.get_supercell_matrix() is None and _interface_mode is None:
+is_band_auto = (type(settings.get_band_paths()) is str and
+                settings.get_band_paths() == 'auto')
+
+##################################################
+# Set calculator interface and crystal structure #
+##################################################
+_supercell_matrix = settings.get_supercell_matrix()
+
+# 1. When DIM is not set, PRIMITIVE_AXES = AUTO is set.
+# 2. If BAND == AUTO, PRIMITIVE_AXES = AUTO is set.
+if _supercell_matrix is None or is_band_auto:
+    is_primitive_axes_auto = True
+else:
+    is_primitive_axes_auto = (type(settings.get_primitive_matrix()) is str and
+                              settings.get_primitive_matrix() == 'auto')
+
+if _supercell_matrix is None:
     _interface_mode = "phonopy_yaml"
+else:
+    _interface_mode = get_interface_mode(args)
+
 unitcell, optional_structure_info = read_crystal_structure(
     filename=settings.get_cell_filename(),
     interface_mode=_interface_mode,
-    chemical_symbols=settings.get_chemical_symbols(),
-    read_supercell=(settings.get_supercell_matrix() is None))
+    chemical_symbols=settings.get_chemical_symbols())
+
 unitcell_filename = optional_structure_info[0]
+
 if _interface_mode == 'phonopy_yaml':
+    # interface_mode and supercell_matrix are overwritten.
     interface_mode = optional_structure_info[1]
+    _supercell_matrix = optional_structure_info[2]
 else:
     interface_mode = _interface_mode
 
+if _supercell_matrix is None:
+    if is_primitive_axes_auto:
+        supercell_matrix = np.eye(3, dtype='intc')
+    else:
+        msg = "Supercell matrix (DIM or --dim) is not found."
+        print_error_message(msg)
+        if log_level > 0:
+            print_error()
+        sys.exit(1)
+else:
+    supercell_matrix = _supercell_matrix
+
+if is_primitive_axes_auto:
+    primitive_matrix = guess_primitive_matrix(unitcell, symprec=args.symprec)
+else:
+    primitive_matrix = settings.get_primitive_matrix()
+
 if unitcell is None:
     print_error_message("Crystal structure file of %s could not be found." %
                         unitcell_filename)
@@ -463,44 +498,14 @@ if magmoms is not None:
             print_error()
         sys.exit(1)
 
-    if settings.get_primitive_matrix() == 'auto':
-        error_text = "'PRIMITIVE_AXES = auto' can not be used with MAGMOM"
+    if is_primitive_axes_auto == 'auto':
+        error_text = ("'PRIMITIVE_AXES = auto', 'BAND = auto', or no DIM "
+                      "setting can not be used with MAGMOM.")
         print_error_message(error_text)
         if log_level > 0:
             print_error()
         sys.exit(1)
 
-######################################
-# Set supercell and primitive matrix #
-######################################
-# When BAND = AUTO, automatic choice of primitive matrix is activated.
-is_band_auto = (type(settings.get_band_paths()) is str and
-                settings.get_band_paths() == 'auto')
-is_primitive_axes_auto = (type(settings.get_primitive_matrix()) is str and
-                          settings.get_primitive_matrix() == 'auto')
-
-# When DIM is not set, PRIMITIVE_AXES = AUTO is set.
-if settings.get_supercell_matrix() is None:
-    is_primitive_axes_auto = True
-    supercell_matrix = np.eye(3, dtype='intc')
-else:
-    supercell_matrix = settings.get_supercell_matrix()
-
-if is_primitive_axes_auto or is_band_auto:
-    primitive_matrix = guess_primitive_matrix(unitcell, symprec=args.symprec)
-else:
-    primitive_matrix = settings.get_primitive_matrix()
-
-if settings.get_supercell_matrix() is None:
-    if is_primitive_axes_auto or is_band_auto:
-        supercell_matrix = np.eye(3, dtype='intc')
-    else:
-        msg = "Supercell matrix (DIM or --dim) is not found."
-        print_error_message(msg)
-        if log_level > 0:
-            print_error()
-        sys.exit(1)
-
 ######################
 # Set physical units #
 ######################