import from dgcode ncrystaldev git: candidate for version 3.9.5

CHANGELOG

@@ -1,3 +1,10 @@
+v3.9.5 2024-08-28
+     * Make ncrystal_hfg2ncmat functionality available in Python API as well in
+       the new NCrystal.hfg2ncmat module. Also add NCMATComposer.from_hfg(..)
+       factory function to access the functionality.
+     * Fix bug in Python-C++ message handler infrastructure which potentially
+       caused message handler to be set more than once.
+
 v3.9.4 2024-08-22
      * Fix PhononDOSAnalyser (github issue #187).
 

CMakeLists.txt

@@ -86,7 +86,7 @@ endif()
 
 cmake_policy( SET CMP0048 NEW )#Not sure if this is really needed
 
-project( NCrystal VERSION 3.9.4 ${_project_metadata} )
+project( NCrystal VERSION 3.9.5 ${_project_metadata} )
 
 unset( _project_metadata )
 

NCrystal/__init__.py

@@ -54,7 +54,7 @@
 
 #NB: Synchronize meta-data below with fields in setup.py+template_setup.py.in meta data:
 __license__ = "Apache 2.0, http://www.apache.org/licenses/LICENSE-2.0"
-__version__ = '3.9.4'
+__version__ = '3.9.5'
 __status__ = "Production"
 __author__ = "NCrystal developers (Thomas Kittelmann, Xiao Xiao Cai)"
 __copyright__ = "Copyright 2015-2024 %s"%__author__

NCrystal/_cli_hfg2ncmat.py

@@ -0,0 +1,132 @@
+
+################################################################################
+##                                                                            ##
+##  This file is part of NCrystal (see https://mctools.github.io/ncrystal/)   ##
+##                                                                            ##
+##  Copyright 2015-2024 NCrystal developers                                   ##
+##                                                                            ##
+##  Licensed under the Apache License, Version 2.0 (the "License");           ##
+##  you may not use this file except in compliance with the License.          ##
+##  You may obtain a copy of the License at                                   ##
+##                                                                            ##
+##      http://www.apache.org/licenses/LICENSE-2.0                            ##
+##                                                                            ##
+##  Unless required by applicable law or agreed to in writing, software       ##
+##  distributed under the License is distributed on an "AS IS" BASIS,         ##
+##  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  ##
+##  See the License for the specific language governing permissions and       ##
+##  limitations under the License.                                            ##
+##                                                                            ##
+################################################################################
+
+def _parseArgs( default_debye_temp ):
+    fdt = default_debye_temp
+    #NOTE: Keep the description below synchronised with doc-string of the
+    #hfg2ncmat python API function:
+    descr=f"""
+
+Script which can be used to generate NCMAT files for hydrogen-rich amorphous
+materials, in which the hydrogen atoms are bound to certain standard functional
+groups (e.g. carbohydrates, polyimides, polymers, ...). Based on the material's
+density, (empirical) chemical formula, and the specification of hydrogen
+bindings in terms of standard functional groups, an NCMAT file is generated. In
+this NCMAT file, non-hydrogen atoms are treated with a simplistic model
+(idealised Debye model of phonon vibrations, assuming a Debye temperature of
+{fdt}K for all atoms unless --debyetemp is specified), and the hydrogen atoms
+are treated with a proper phonon density of state (VDOS) curve, which is
+constructed based on the provided binding specifications. This is done using an
+idea (and VDOS curves from) the following publication:
+
+  "Thermal neutron cross sections of amino acids from average contributions
+  of functional groups", G. Romanelli, et. al., J. Phys.: Condens. Matter,
+  (2021). doi:10.1088/1361-648X/abfc13
+
+Example of valid spec strings for the --spec parameter. Note only the hydrogen
+bindings are important here:
+
+     "1xCHali+2xCH2+8xCHaro+2xCH3+1xOH" (20 hydrogen atoms)
+     "1xNH+3xSH+2xCH2" (8 hydrogen atoms).
+
+List of valid bindings which can be used in --spec:
+
+      CHali (1 hydrogen atom, aliphatic binding)
+      CHaro (1 hydrogen atom, aromatic binding, e.g. on phenyl group).
+      CH2 (2 hydrogen atoms)
+      CH3 (3 hydrogen atoms)
+      NH (1 hydrogen atom)
+      NH2 (2 hydrogen atoms)
+      NH3 (3 hydrogen atoms)
+      OH (1 hydrogen atom)
+      SH (1 hydrogen atom)
+
+Note that as only hydrogen atoms will have a realistic VDOS curve, and as the
+incoherent approximation is employed, the realism of the resulting material
+modelling will be higher for materials with more hydrogen atoms. As a metric of
+this, the script prints out how much of the total scattering cross section (sum
+of sigma_coh+sigma_incoh for all atoms), is due to the sigma_incoh contribution
+from hydrogen atoms.
+
+"""
+    import argparse
+    from argparse import RawTextHelpFormatter
+    parser = argparse.ArgumentParser(description=descr,
+                                     formatter_class=RawTextHelpFormatter)
+    parser.add_argument("--output",'-o',default='autogen.ncmat',type=str,
+                        help=(f"Output file name (defaults to autogen.ncmat)."
+                              " Can be stdout."))
+    parser.add_argument('--force',action='store_true',
+                        help=(f"Will overwrite existing file "
+                              "if it already exists."))
+    parser.add_argument("--spec",'-s',metavar='SPEC',type=str,required=True,
+                        help=f"Hydrogen binding specification (see above).")
+    parser.add_argument("--formula",'-f',metavar='FORMULA',
+                        type=str,
+                        required=True,
+                        help=("Chemical formula such as C20H18O3 (only"
+                              " the relative ratios matter)."))
+    parser.add_argument("--density",'-d',metavar='DENSITY',
+                        type=float,
+                        required=True,
+                        help=f"Material density in g/cm3.")
+    parser.add_argument("--debyetemp",metavar='VALUE',
+                        type=float,
+                        default=default_debye_temp,
+                        help=("Debye temperature (kelvin) of non-hydrogen"
+                              f" atoms (default is {default_debye_temp})."))
+    parser.add_argument("--title",type=str,required=True,
+                        help=('Title string of material (will be placed as'
+                              ' comment near top of output file). Use \\n '
+                              'for line-breaks.'))
+    parser.add_argument('--notrim',action='store_true',
+                        help=f"No trimming of resulting VDOS curve.")
+    args=parser.parse_args()
+    return args
+
+def main():
+    import pathlib
+    from ._common import print
+    from .hfg2ncmat import _default_debye_temp, hfg2ncmat
+    args = _parseArgs( _default_debye_temp() )
+    do_stdout = args.output=='stdout'
+    try:
+        ncmat =  hfg2ncmat( spec = args.spec,
+                            formula = args.formula,
+                            density = args.density,
+                            title = args.title,
+                            debyetemp = args.debyetemp,
+                            verbose = not do_stdout,
+                            notrim = args.notrim )
+    except RuntimeError as e:
+        raise SystemExit('Error: %s'%str(e))
+    if do_stdout:
+        print(ncmat)
+        return
+    outfile = pathlib.Path(args.output)
+    if outfile.exists() and not args.force:
+        raise SystemExit('Error: output file already exists'
+                         ' (run with --force to overwrite)')
+    if not outfile.parent.is_dir():
+        raise SystemExit('Error: output directory does not exist:'
+                         f' { outfile.parent }')
+    outfile.write_text(ncmat)
+    print(f"Wrote: {outfile}")