Merge branch 'master' into materials-cli

hexrd/constants.py

@@ -82,7 +82,8 @@
 zeros_3x1 = np.zeros((3, 1))
 zeros_6x1 = np.zeros((6, 1))
 
-# reference beam direction and eta=0 ref in LAB FRAME for standard geometry
+'''reference beam direction and
+eta=0 ref in LAB FRAME for standard geometry'''
 beam_vec = -lab_z
 eta_vec = lab_x
 
@@ -162,7 +163,9 @@
 3628800.]).astype(np.complex128)
 
 """
->> @AUTHOR:     Saransh Singh, Lawrence Livermore National Lab, [email protected]
+>> @AUTHOR:     Saransh Singh,
+                Lawrence Livermore National Lab,
+                [email protected]
 >> @DATE:       11/28/2022 SS 1.0 original
 >> @DETAILS:    constants for rodrigues FZ
 """
@@ -177,7 +180,9 @@
 )
 
 '''
->> @AUTHOR:     Saransh Singh, Lawrence Livermore National Lab, [email protected]
+>> @AUTHOR:     Saransh Singh,
+                Lawrence Livermore National Lab,
+                [email protected]
 >> @DATE:       10/28/2020 SS 1.0 original
 >> @DETAILS:    constants for sphere sectors used for IPF coloring
 '''
@@ -263,7 +268,8 @@ def set_numba_cache():
     4. The NUMBA_CACHE_DIR environment variable is not defined
 
     If all of these are true, then numba will try to write to a
-    directory where it doesn't have permission, and cause the application to
+    directory where it doesn't have permission,
+    and cause the application to
     freeze. Avoid that by setting the cache dir ourselves.
     """
 
@@ -316,8 +322,10 @@ def is_writable_file(path):
 cRestmass = 9.1093837090E-31
 
 '''
-adding another parametrization of the scattering factors. these are more recent
-and more accurate. also used in Vesta (copied from there). see:
+adding another parametrization of the
+scattering factors. these are more recent
+and more accurate. also used in Vesta
+(copied from there). see:
 
 New Analytical coherent Scattering-Factor Functions for Free Atoms and Ions
 BY D. WAASMAIER AND A. KIRFEL
@@ -638,7 +646,9 @@ def is_writable_file(path):
     'Cf': ['0']
 }
 '''
-this dictionary tabulates the small nuclear Thomson term fNT for all elements up to Z=92
+this dictionary tabulates the small
+nuclear Thomson term fNT for all
+elements up to Z=92
 '''
 fNT = {
 'H':-0.00054423,'He':-0.00054817,'Li':-0.00071131,'Be':-0.00097394,'B':-0.0012687,'C':-0.0016442,'N':-0.0019191,'O':-0.0021944,
@@ -737,8 +747,10 @@ def is_writable_file(path):
     229
 ])
 
-''' this variable encodes all the generators (including translations) for all 230 space groups
-    will be used to compute the full space group symmetry operators
+''' this variable encodes all the generators
+(including translations) for all 230 space groups
+will be used to compute the full space group symmetry
+operators
 '''
 SYM_GL = [
     "000                                     ", "100                                     ", "01cOOO0                                 ",
@@ -996,8 +1008,10 @@ def is_writable_file(path):
 }
 
 '''
-this dictionary contains the generators encoded in each letter of the generator string
-the full symmetry is generated by the repeated action of the generator matrix
+this dictionary contains the generators encoded
+in each letter of the generator string
+the full symmetry is generated by the repeated
+action of the generator matrix
 '''
 
 ''' rotational, inversions, mirrors etc. components
@@ -1100,17 +1114,21 @@ def is_writable_file(path):
 SYM_GENERATORS['Y'] = -1./4.
 SYM_GENERATORS['Z'] = -1./8.
 
-
 '''
-    @AUTHOR  Saransh Singh, Lawrence Livermore National Lab, [email protected]
+    @AUTHOR  Saransh Singh,
+    Lawrence Livermore National Lab,
+    [email protected]
     @DATE    11/23/2020 SS 1.0 original
-    @DETAIL. this list of symbols will help us to genrate the point group symmetries
-             in the cartesian space for any point group. this is needed for the
-             supergroup symmetry usd in the coloring scheme used in the package. this
-             needs to be a separate set of routines because the supergroup can be a
-             point group which is not the laue group of the crystal (e.g. m-3 --> m-3m)
-             the notation used will be the same as the one used for the space group
-             without any translations.
+    @DETAIL. this list of symbols will help us to genrate
+             the point group symmetries in the cartesian
+             space for any point group. this is needed for
+             the supergroup symmetry usd in the coloring
+             scheme used in the package. this needs to be a
+             separate set of routines because the supergroup
+             can be a point group which is not the laue group
+             of the crystal (e.g. m-3 --> m-3m) the notation
+             used will be the same as the one used for the
+             space group without any translations.
 '''
 SYM_GL_PG = {
     'c1': '1a',  # only identity rotation

hexrd/material/material.py

@@ -36,8 +36,11 @@
 
 from hexrd.material.crystallography import PlaneData as PData
 from hexrd.material import symmetry, unitcell
+from hexrd.material.symbols import two_origin_choice
 from hexrd.valunits import valWUnit
-from hexrd.constants import ptable, ptableinverse, chargestate
+from hexrd.constants import (ptable,
+                             ptableinverse,
+                             chargestate)
 
 from os import path
 from pathlib import Path
@@ -77,6 +80,12 @@ def _key(x):
     return x.name
 
 
+def get_default_sgsetting(sgnum):
+    if sgnum in two_origin_choice:
+        return 1
+    else:
+        return 0
+
 #
 # ---------------------------------------------------CLASS:  Material
 #
@@ -148,7 +157,7 @@ def __init__(
         material_file=None,
         dmin=None,
         kev=None,
-        sgsetting=DFLT_SGSETTING,
+        sgsetting=None,
     ):
         """Constructor for Material
 
@@ -165,8 +174,6 @@ def __init__(
 
         self.description = ''
 
-        self.sgsetting = sgsetting
-
         if material_file:
             # >> @ date 08/20/2020 SS removing dependence on hklmax
             if isinstance(material_file, (Path, str)):
@@ -180,6 +187,9 @@ def __init__(
                 self._readCif(material_file)
             elif isinstance(material_file, h5py.Group) or form in h5_suffixes:
                 self._readHDFxtal(fhdf=material_file, xtal=name)
+            if sgsetting is not None:
+                if sgsetting in [0, 1]:
+                    self._sgsetting = sgsetting
         else:
             # default name
             self._name = Material.DFLT_XTAL
@@ -189,8 +199,8 @@ def __init__(
             #
             self.description = ''
             #
-            self.sgnum = Material.DFLT_SGNUM
             self._sgsetting = Material.DFLT_SGSETTING
+            self.sgnum = Material.DFLT_SGNUM
             #
             self._atominfo = Material.DFLT_ATOMINFO
             #
@@ -645,6 +655,7 @@ def _readCif(self, fcif=DFLT_NAME + '.cif'):
                 lparms[i] = _degrees(lparms[i])
 
         self._lparms = lparms
+        self._sgsetting = get_default_sgsetting(sgnum)
         self.sgnum = sgnum
 
         # fractional atomic site, occ and vibration amplitude
@@ -795,7 +806,6 @@ def _readCif(self, fcif=DFLT_NAME + '.cif'):
 
         self._atomtype = np.asarray(atomtype).astype(np.int32)
         self._charge = charge
-        self._sgsetting = 0
 
         self._dmin = Material.DFLT_DMIN
         self._beamEnergy = Material.DFLT_KEV
@@ -864,6 +874,9 @@ def _readHDFxtal(self, fhdf=DFLT_NAME, xtal=DFLT_NAME):
         self._lparms = lparms
 
         # fill space group and lattice parameters
+        self._sgsetting = np.array(
+            gid.get('SpaceGroupSetting'), dtype=np.int32
+        ).item()
         self.sgnum = sgnum
 
         # the U factors are related to B by the relation B = 8pi^2 U
@@ -880,10 +893,6 @@ def _readHDFxtal(self, fhdf=DFLT_NAME, xtal=DFLT_NAME):
             self._charge = ['0'] * self._atomtype.shape[0]
         self._atom_ntype = self._atomtype.shape[0]
 
-        self._sgsetting = np.array(
-            gid.get('SpaceGroupSetting'), dtype=np.int32
-        ).item()
-
         if 'stiffness' in gid:
             # we're assuming the stiffness is in units of GPa
             self.stiffness = np.array(gid.get('stiffness'))
@@ -1428,8 +1437,7 @@ def loadMaterialList(cfgFile):
 
 
 def load_materials_hdf5(
-    f, dmin=None, kev=None, sgsetting=Material.DFLT_SGSETTING
-):
+        f, dmin=None, kev=None):
     """Load materials from an HDF5 file
 
     The file uses the HDF5 file format.
@@ -1452,7 +1460,6 @@ def load_materials_hdf5(
         'material_file': f,
         'dmin': dmin,
         'kev': kev,
-        'sgsetting': sgsetting,
     }
     return {name: Material(name, **kwargs) for name in names}
 

hexrd/material/mksupport.py

@@ -1,6 +1,9 @@
-from hexrd.material.symbols import pstr_Elements, sitesym, \
-    tworig, PrintPossibleSG, TRIG, pstr_spacegroup,\
-    pstr_mkxtal
+from hexrd.material.symbols import (pstr_Elements,
+                                    two_origin_choice,
+                                    PrintPossibleSG,
+                                    TRIG,
+                                    pstr_spacegroup,
+                                    pstr_mkxtal)
 import h5py
 import os
 import numpy as np
@@ -11,6 +14,7 @@
                                      unitcell_volume)
 
 
+
 def mk(filename, xtalname):
 
     # print some initial information for the user
@@ -278,14 +282,15 @@ def GetSpaceGroup(xtal_sys, btrigonal, bhexset):
 def SpaceGroupSetting(sgnum):
 
     iset = 1
-    if(sgnum in tworig):
-        idx = tworig.index(sgnum)
+    if(sgnum in two_origin_choice):
+        sitesym1 = two_origin_choice[sgnum][0]
+        sitesym2 = two_origin_choice[sgnum][1]
         print(' ---------------------------------------------')
         print(' This space group has two origin settings.')
         print(' The first setting has site symmetry    : ' +
-              sitesym[2*idx - 2])
+              sitesym1)
         print(' the second setting has site symmetry   : ' +
-              sitesym[2*idx - 1])
+              sitesym2)
         iset = input(' Which setting do you wish to use (1/2) : ')
         if(not iset.isdigit()):
             raise ValueError("Invalid integer value for atomic number.")
@@ -297,7 +302,6 @@ def SpaceGroupSetting(sgnum):
 
     return iset-1
 
-
 def GetAtomInfo():
 
     print(pstr_Elements)