command line interface to make a new material

hexrd/cli/main.py

@@ -16,7 +16,7 @@
 from hexrd.cli import find_orientations
 from hexrd.cli import fit_grains
 from hexrd.cli import pickle23
-
+from hexrd.cli import make_material
 
 try:
     _version = version("hexrd")
@@ -66,6 +66,7 @@ def main():
     find_orientations.configure_parser(sub_parsers)
     fit_grains.configure_parser(sub_parsers)
     pickle23.configure_parser(sub_parsers)
+    make_material.configure_parser(sub_parsers)
 
     try:
         import argcomplete

hexrd/cli/make_material.py

@@ -0,0 +1,39 @@
+import sys
+from hexrd.cli import help
+
+descr = (f'make a new material file in the '
+         f'hdf5 format using the command line. '
+         f'user specifies the file and crystal '
+         f'names')
+example = """
+examples:
+    hexrd make_material --file material.h5 --xtal diamond
+"""
+
+
+def configure_parser(sub_parsers):
+
+    p = sub_parsers.add_parser('make-material',
+                               description=descr, help=descr)
+
+    p.add_argument(
+        '-f', '--file', type=str,
+        default='test.h5',
+        help='name of h5 file, default = test.h5'
+    )
+
+    p.add_argument(
+        '-x', '--xtal', type=str,
+        default='xtal',
+        help='name of crystal, default = xtal'
+    )
+
+    p.set_defaults(func=execute)
+
+
+def execute(args, parser):
+    from hexrd.material.mksupport import mk
+
+    file = args.file
+    xtal = args.xtal
+    mk(file, xtal)

hexrd/material/mksupport.py

@@ -9,7 +9,10 @@
 import numpy as np
 import datetime
 import getpass
-from hexrd.material.unitcell import _StiffnessDict, _pgDict
+from hexrd.material.unitcell import (_StiffnessDict,
+                                     _pgDict,
+                                     unitcell_volume)
+
 
 
 def mk(filename, xtalname):
@@ -330,8 +333,8 @@ def GetAtomInfo():
 def GetAsymmetricPositions(aniU):
 
     asym = input(
-        "Enter asymmetric position of atom in unit cell \
-         separated by comma (fractional coordinates) :  ")
+        f'Enter asymmetric position of atom in unit cell '
+        f'separated by comma (fractional coordinates) :  ')
     asym = [x.strip() for x in asym.split(',')]
 
     for i, x in enumerate(asym):
@@ -483,7 +486,6 @@ def WriteH5Data(fid, AtomInfo, lat_param, path=None):
     material.h5 file output
     @Date 01/14/2022 SS added tThWidth to materials file
     """
-
     # Add the path prefix if we have been given one
     if path is not None:
         path = f"{path}/{AtomInfo['xtalname']}"
@@ -519,32 +521,41 @@ def WriteH5Data(fid, AtomInfo, lat_param, path=None):
     did = gid.create_dataset("stiffness", (6, 6), dtype=np.float64)
     did.write_direct(np.array(AtomInfo['stiffness'], dtype=np.float64))
 
+    P = AtomInfo['pressure'] if 'pressure' in AtomInfo else 1.01325E-4  # 1 atm
     did = gid.create_dataset("pressure", (1,), dtype=np.float64)
-    did.write_direct(np.array(AtomInfo['pressure'], dtype=np.float64))
+    did.write_direct(np.array(P, dtype=np.float64))
 
+    T = AtomInfo['temperature'] if 'temperature' in AtomInfo else 293  # R.T.
     did = gid.create_dataset("temperature", (1,), dtype=np.float64)
-    did.write_direct(np.array(AtomInfo['temperature'], dtype=np.float64))
+    did.write_direct(np.array(T, dtype=np.float64))
 
+    k0 = AtomInfo['k0'] if 'k0' in AtomInfo else 100.0
     did = gid.create_dataset("k0", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['k0']], dtype=np.float64))
+    did.write_direct(np.array([k0], dtype=np.float64))
 
+    k0p = AtomInfo['k0p'] if 'k0p' in AtomInfo else 0.0
     did = gid.create_dataset("k0p", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['k0p']], dtype=np.float64))
+    did.write_direct(np.array([k0p], dtype=np.float64))
 
+    dk0dt = AtomInfo['dk0dt'] if 'dk0dt' in AtomInfo else 0.0
     did = gid.create_dataset("dk0dt", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['dk0dt']], dtype=np.float64))
+    did.write_direct(np.array([dk0dt], dtype=np.float64))
 
+    dk0pdt = AtomInfo['dk0pdt'] if 'dk0pdt' in AtomInfo else 0.0
     did = gid.create_dataset("dk0pdt", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['dk0pdt']], dtype=np.float64))
+    did.write_direct(np.array([dk0pdt], dtype=np.float64))
 
+    alpha_t = AtomInfo['alpha_t'] if 'alpha_t' in AtomInfo else 0.0
     did = gid.create_dataset("alpha_t", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['alpha_t']], dtype=np.float64))
+    did.write_direct(np.array([alpha_t], dtype=np.float64))
 
+    dalpha_t_dt = AtomInfo['dalpha_t_dt'] if 'dalpha_t_dt' in AtomInfo else 0.0
     did = gid.create_dataset("dalpha_t_dt", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['dalpha_t_dt']], dtype=np.float64))
+    did.write_direct(np.array([dalpha_t_dt], dtype=np.float64))
 
+    v0 = AtomInfo['v0'] if 'v0' in AtomInfo else unitcell_volume(lat_param)
     did = gid.create_dataset("v0", (1,), dtype=np.float64)
-    did.write_direct(np.array([AtomInfo['v0']], dtype=np.float64))
+    did.write_direct(np.array([v0], dtype=np.float64))
 
     if "tThWidth" in AtomInfo:
         did = gid.create_dataset("tThWidth", (1,), dtype=np.float64)

hexrd/material/symbols.py

@@ -1,27 +1,28 @@
-
-pstr_mkxtal = "\n\n    This is a program to create a HDF5 file for storing crystallographic information.\n "
-pstr_mkxtal = pstr_mkxtal + " The following inputs are required:\n "
-pstr_mkxtal = pstr_mkxtal + "         Crystal System:\n"
-pstr_mkxtal = pstr_mkxtal + "                 1. Cubic\n"
-pstr_mkxtal = pstr_mkxtal + "                 2. Tetragonal\n"
-pstr_mkxtal = pstr_mkxtal + "                 3. Orthorhombic\n"
-pstr_mkxtal = pstr_mkxtal + "                 4. Hexagonal\n"
-pstr_mkxtal = pstr_mkxtal + "                 5. Trigonal\n"
-pstr_mkxtal = pstr_mkxtal + "                 6. Monoclinic\n"
-pstr_mkxtal = pstr_mkxtal + "                 7. Triclinic\n\n"
-pstr_mkxtal = pstr_mkxtal + "         Space group number\n"
-pstr_mkxtal = pstr_mkxtal + "         Atomic number (Z) for all species in unit cell\n"
-pstr_mkxtal = pstr_mkxtal + "         Asymmetric positions for all atoms in unit cell\n"
-pstr_mkxtal = pstr_mkxtal + "         Debye-Waller factors for all atoms in the unit cell\n"
-pstr_mkxtal = pstr_mkxtal + "         You'll be prompted for these values now\n\n"
-pstr_mkxtal = pstr_mkxtal + "\n Note about the trigonal system:\n"
-pstr_mkxtal = pstr_mkxtal + " -------------------------------\n"
-pstr_mkxtal = pstr_mkxtal + " Primitive trigonal crystals are defined with respect to a HEXAGONAL\n"
-pstr_mkxtal = pstr_mkxtal + " reference frame.  Rhombohedral crystals can be referenced with\n"
-pstr_mkxtal = pstr_mkxtal + " respect to a HEXAGONAL basis (first setting), or with respect to\n"
-pstr_mkxtal = pstr_mkxtal + " a RHOMBOHEDRAL basis (second setting).  The default setting for\n"
-pstr_mkxtal = pstr_mkxtal + " trigonal symmetry is the hexagonal setting.  When you select\n"
-pstr_mkxtal = pstr_mkxtal + " crystal system 5 above, you will be prompted for the setting. \n"
+pstr_mkxtal = (
+    f'\n\n This is a program to create a HDF5 file for storing '
+    f'crystallographic information.\n'
+    f' The following inputs are required:\n '
+    f'         Crystal System:\n'
+    f'                 1. Cubic\n'
+    f'                 2. Tetragonal\n'
+    f'                 3. Orthorhombic\n'
+    f'                 4. Hexagonal\n'
+    f'                 5. Trigonal\n'
+    f'                 6. Monoclinic\n'
+    f'                 7. Triclinic\n\n'
+    f'         Space group number\n'
+    f'         Atomic number (Z) for all species in unit cell\n'
+    f'         Asymmetric positions for all atoms in unit cell\n'
+    f'         Debye-Waller factors for all atoms in the unit cell\n'
+    f'         You\'ll be prompted for these values now \n\n'
+    f'\n Note about the trigonal system:\n'
+    f' -------------------------------\n'
+    f' Primitive trigonal crystals are defined with respect to a HEXAGONAL\n'
+    f' reference frame.  Rhombohedral crystals can be referenced with\n'
+    f' respect to a HEXAGONAL basis (first setting), or with respect to\n'
+    f' a RHOMBOHEDRAL basis (second setting).  The default setting for\n'
+    f' trigonal symmetry is the hexagonal setting.  When you select\n'
+    f' crystal system 5 above, you will be prompted for the setting. \n')
 
 pstr_spacegroup = [
     " P  1      ", " P -1      ", \

hexrd/material/unitcell.py

@@ -49,6 +49,19 @@ def _calcstar(v, sym, mat):
     return vsym
 
 
+def unitcell_volume(lp):
+    '''helper function to explicitly compute unitcell
+    volume (in A^3) using the forula. the unitcell class
+    value is set using the determinant of the metric tensor
+    '''
+    ca = np.cos(np.radians(lp['alpha']))
+    cb = np.cos(np.radians(lp['beta']))
+    cg = np.cos(np.radians(lp['gamma']))
+
+    fact = np.sqrt(1 - ca**2 - cb**2 - cg**2 + 2*ca*cb*cg)
+    # 1E3 factor to go from nm to A
+    return lp['a']*lp['b']*lp['c']*fact*1E3
+
 class unitcell:
 
     '''