From 4e970e8fa95a295f92cd7f732944a6ba564a3c36 Mon Sep 17 00:00:00 2001 From: Thomas Kittelmann Date: Wed, 28 Aug 2024 12:24:06 +0200 Subject: [PATCH] import from dgcode ncrystaldev git: candidate for version 3.9.5 --- CHANGELOG | 7 + CMakeLists.txt | 2 +- NCrystal/__init__.py | 2 +- NCrystal/_cli_hfg2ncmat.py | 132 ++++ NCrystal/_hfgdata.py | 545 ++++++++++++++ NCrystal/_msg.py | 4 +- NCrystal/_ncmatimpl.py | 74 +- NCrystal/hfg2ncmat.py | 272 +++++++ NCrystal/ncmat.py | 38 +- README | 15 +- VERSION | 2 +- ncrystal_core/include/NCrystal/NCVersion.hh | 6 +- ncrystal_core/include/NCrystal/ncrystal.h | 6 +- scripts/ncrystal_hfg2ncmat | 755 +------------------- 14 files changed, 1071 insertions(+), 789 deletions(-) create mode 100644 NCrystal/_cli_hfg2ncmat.py create mode 100644 NCrystal/_hfgdata.py create mode 100644 NCrystal/hfg2ncmat.py diff --git a/CHANGELOG b/CHANGELOG index 4c4b0307..76e8ccbe 100644 --- a/CHANGELOG +++ b/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). diff --git a/CMakeLists.txt b/CMakeLists.txt index e21599d4..fc6d84d7 100644 --- a/CMakeLists.txt +++ b/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 ) diff --git a/NCrystal/__init__.py b/NCrystal/__init__.py index 91a6b399..1b72a119 100644 --- a/NCrystal/__init__.py +++ b/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__ diff --git a/NCrystal/_cli_hfg2ncmat.py b/NCrystal/_cli_hfg2ncmat.py new file mode 100644 index 00000000..453b8e32 --- /dev/null +++ b/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}") diff --git a/NCrystal/_hfgdata.py b/NCrystal/_hfgdata.py new file mode 100644 index 00000000..4efeee5f --- /dev/null +++ b/NCrystal/_hfgdata.py @@ -0,0 +1,545 @@ +""" + +Data for hfg2ncmat + +""" + +################################################################################ +## ## +## 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. ## +## ## +################################################################################ + +__all__ = [] + +_cached_data = [None] +def get_data(): + """Hydrogen VDOS for various functional groups (supplementary material of doi:10.1088/1361-648X/abfc13)""" + if _cached_data[0] is None: + _cached_data[0] = _get_data() + return _cached_data[0] + +def _get_data(): + import io + from ._numpy import _np, _ensure_numpy + _ensure_numpy() + thedata=""" +#Energy CHali CHaro CH2 CH3 NH NH2 NH3 OH SH + 0.00000E+00 2.13554E-05 1.33447E-04 4.19945E-05 6.16412E-05 9.87755E-05 1.58844E-04 1.66414E-05 1.10565E-05 9.18572E-06 + 9.01804E-04 4.25611E-05 2.14471E-04 9.06037E-05 1.44290E-04 1.63593E-04 2.14715E-04 3.58153E-05 2.55964E-05 2.65186E-05 + 1.80361E-03 7.85363E-05 3.05676E-04 1.74811E-04 2.98485E-04 2.36042E-04 2.64685E-04 6.78767E-05 5.03742E-05 6.49416E-05 + 2.70541E-03 1.35340E-04 3.94305E-04 3.06398E-04 5.49869E-04 3.07172E-04 3.15534E-04 1.14922E-04 8.57807E-05 1.36052E-04 + 3.60721E-03 2.17858E-04 4.72909E-04 4.94518E-04 9.07625E-04 3.75427E-04 3.81898E-04 1.76387E-04 1.29767E-04 2.46917E-04 + 4.50902E-03 3.25605E-04 5.45649E-04 7.41915E-04 1.35003E-03 4.46001E-04 4.74550E-04 2.48511E-04 1.80479E-04 3.95660E-04 + 5.41082E-03 4.48735E-04 6.27004E-04 1.03959E-03 1.82126E-03 5.24448E-04 5.93392E-04 3.24323E-04 2.39079E-04 5.75327E-04 + 6.31263E-03 5.68995E-04 7.31566E-04 1.36181E-03 2.24894E-03 6.13562E-04 7.28691E-04 3.94879E-04 3.09468E-04 7.85659E-04 + 7.21443E-03 6.68072E-04 8.62561E-04 1.66718E-03 2.58112E-03 7.15253E-04 8.63823E-04 4.52960E-04 3.95789E-04 1.04112E-03 + 8.11623E-03 7.38792E-04 1.01083E-03 1.91299E-03 2.82301E-03 8.31824E-04 9.77799E-04 4.97925E-04 5.01333E-04 1.36244E-03 + 9.01804E-03 7.89848E-04 1.16526E-03 2.08157E-03 3.04246E-03 9.64004E-04 1.05469E-03 5.37190E-04 6.28608E-04 1.75127E-03 + 9.91984E-03 8.38334E-04 1.32013E-03 2.19762E-03 3.32835E-03 1.10625E-03 1.09889E-03 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3.29421E-03 4.05910E-04 1.17954E-07 9.15830E-09 + 3.94088E-01 1.03068E-06 8.86766E-03 4.86110E-04 7.73431E-07 7.51618E-03 3.06723E-03 5.03038E-04 2.34686E-08 1.34885E-09 + 3.94990E-01 6.49723E-07 9.12371E-03 3.38412E-04 3.62843E-07 1.17614E-02 2.73182E-03 7.48432E-04 5.87365E-09 1.67907E-10 + 3.95892E-01 5.00021E-07 8.72659E-03 2.10296E-04 2.05938E-07 1.52914E-02 2.63404E-03 1.07676E-03 1.61645E-08 6.22312E-11 + 3.96794E-01 4.54133E-07 7.39448E-03 1.16834E-04 1.70453E-07 1.63303E-02 2.91455E-03 1.35491E-03 9.67075E-08 2.98012E-10 + 3.97695E-01 4.42227E-07 5.40522E-03 5.86824E-05 1.75751E-07 1.42752E-02 3.40823E-03 1.45199E-03 4.90284E-07 1.56067E-09 + 3.98597E-01 4.34558E-07 3.35586E-03 2.73112E-05 1.77546E-07 1.02040E-02 3.81783E-03 1.33248E-03 2.04229E-06 6.74854E-09 + 3.99499E-01 4.22195E-07 1.75131E-03 1.22546E-05 1.57873E-07 5.96630E-03 3.95854E-03 1.10083E-03 6.98306E-06 2.40180E-08 + 4.00401E-01 4.12125E-07 7.62499E-04 5.50742E-06 1.19114E-07 2.86051E-03 3.81920E-03 9.60349E-04 1.95898E-05 7.04106E-08 + 4.01303E-01 4.22946E-07 2.75707E-04 2.48144E-06 7.51000E-08 1.13332E-03 3.44270E-03 1.10944E-03 4.50685E-05 1.70152E-07 + 4.02204E-01 4.66635E-07 8.30791E-05 1.07054E-06 3.92370E-08 3.79270E-04 2.84946E-03 1.62327E-03 8.49918E-05 3.39148E-07 + 4.03106E-01 5.26676E-07 2.17677E-05 4.16559E-07 1.68973E-08 1.13196E-04 2.09987E-03 2.37517E-03 1.31325E-04 5.57773E-07 + 4.04008E-01 5.59101E-07 6.10158E-06 1.39774E-07 5.97702E-09 3.32956E-05 1.35081E-03 3.07012E-03 1.66191E-04 7.57018E-07 + 4.04910E-01 5.24245E-07 2.74079E-06 3.94005E-08 1.73259E-09 1.05523E-05 7.98188E-04 3.41779E-03 1.72179E-04 8.47790E-07 + 4.05812E-01 4.20900E-07 1.80383E-06 9.20361E-09 4.10957E-10 3.50851E-06 5.95161E-04 3.32636E-03 1.45987E-04 7.83167E-07 + 4.06713E-01 2.87883E-07 1.17103E-06 1.76909E-09 7.96820E-11 1.10071E-06 8.45664E-04 2.93041E-03 1.01266E-04 5.96434E-07 + 4.07615E-01 1.73017E-07 6.45601E-07 2.78800E-10 1.26216E-11 3.00560E-07 1.61439E-03 2.43255E-03 5.74521E-05 3.74195E-07 + 4.08517E-01 1.01812E-07 2.93338E-07 3.59525E-11 1.63261E-12 6.96600E-08 2.84523E-03 1.94457E-03 2.66517E-05 1.93240E-07 + 4.09419E-01 7.06475E-08 1.09254E-07 3.78951E-12 1.72405E-13 1.92200E-08 4.23195E-03 1.47718E-03 1.01070E-05 8.20671E-08 + 4.10321E-01 6.05839E-08 3.33165E-08 3.26268E-13 1.48610E-14 3.68300E-08 5.24084E-03 1.02736E-03 3.13267E-06 2.86364E-08 + 4.11222E-01 5.43663E-08 8.31423E-09 2.29371E-14 1.04552E-15 1.64590E-07 5.39375E-03 6.29635E-04 7.93450E-07 8.20272E-09 + 4.12124E-01 4.52309E-08 1.69738E-09 1.31636E-15 6.00297E-17 6.56500E-07 4.61211E-03 3.30682E-04 1.64201E-07 1.92720E-09 + 4.13026E-01 3.63670E-08 2.83425E-10 6.16623E-17 2.81279E-18 2.21898E-06 3.28297E-03 1.46213E-04 2.77602E-08 3.71102E-10 + 4.13928E-01 3.57169E-08 3.89563E-11 2.35741E-18 1.07555E-19 6.33637E-06 1.97786E-03 5.38358E-05 3.83368E-09 5.85276E-11 + 4.14830E-01 5.15584E-08 6.88547E-12 7.35519E-20 3.35616E-21 1.52929E-05 1.11697E-03 1.63966E-05 4.32424E-10 7.55563E-12 + 4.15731E-01 9.07424E-08 2.05504E-11 1.87276E-21 8.54601E-23 3.16022E-05 8.67828E-04 4.12154E-06 3.98355E-11 7.97990E-13 + 4.16633E-01 1.56582E-07 1.29180E-10 3.89127E-23 1.77580E-24 5.90683E-05 1.25544E-03 8.84068E-07 2.99685E-12 6.89207E-14 + 4.17535E-01 2.42704E-07 6.75589E-10 6.59802E-25 3.01112E-26 1.15218E-04 2.26255E-03 2.50816E-07 1.84106E-13 4.86593E-15 + 4.18437E-01 3.26346E-07 2.88601E-09 9.12947E-27 4.16647E-28 2.74799E-04 3.78977E-03 2.71810E-07 9.23540E-15 2.80744E-16 + 4.19339E-01 3.72961E-07 1.00727E-08 1.03082E-28 4.70449E-30 7.56321E-04 5.54292E-03 4.82470E-07 3.78277E-16 1.32333E-17 + 4.20240E-01 3.57298E-07 2.87451E-08 9.49791E-31 4.33471E-32 1.99747E-03 7.01339E-03 7.47682E-07 1.26506E-17 5.09505E-19 + 4.21142E-01 2.84543E-07 6.71627E-08 7.14129E-33 3.25920E-34 4.54354E-03 7.67160E-03 9.51702E-07 3.45422E-19 1.60204E-20 + 4.22044E-01 1.88222E-07 1.28762E-07 4.38156E-35 1.99970E-36 8.57705E-03 7.32770E-03 9.93641E-07 7.70031E-21 4.11318E-22 + 4.22946E-01 1.05919E-07 2.03274E-07 2.19373E-37 1.00120E-38 1.33046E-02 6.39554E-03 8.55444E-07 1.40145E-22 8.62207E-24 + 4.23848E-01 5.77595E-08 2.65734E-07 8.96277E-40 4.09052E-41 1.69372E-02 5.75309E-03 6.15031E-07 2.08232E-24 1.47547E-25 + 4.24749E-01 4.43882E-08 2.90083E-07 2.98816E-42 1.36377E-43 1.77325E-02 6.19840E-03 3.80218E-07 2.52586E-26 2.06112E-27 + 4.25651E-01 5.73055E-08 2.67494E-07 8.12956E-45 3.71026E-46 1.53367E-02 7.88439E-03 2.14667E-07 2.50125E-28 2.35017E-29 + 4.26553E-01 8.68866E-08 2.11261E-07 1.80482E-47 8.23704E-49 1.10365E-02 1.01501E-02 1.21077E-07 2.02201E-30 2.18723E-31 + 4.27455E-01 1.22971E-07 1.44791E-07 3.26966E-50 1.49225E-51 6.67620E-03 1.18637E-02 7.22525E-08 1.33438E-32 1.66139E-33 + 4.28357E-01 1.52780E-07 8.67937E-08 4.83364E-53 2.20603E-54 3.43979E-03 1.20690E-02 4.38102E-08 7.18862E-35 1.02995E-35 + 4.29259E-01 1.62965E-07 4.54619E-08 5.83108E-56 2.66125E-57 1.53064E-03 1.05354E-02 2.46713E-08 3.16135E-37 5.21096E-38 + 4.30160E-01 1.47003E-07 2.06150E-08 5.74018E-59 2.61977E-60 5.94492E-04 7.84452E-03 1.20665E-08 1.13489E-39 2.15160E-40 + 4.31062E-01 1.10843E-07 7.98330E-09 4.61111E-62 2.10447E-63 2.02122E-04 4.96178E-03 4.95431E-09 3.32576E-42 7.25010E-43 + 4.31964E-01 6.92780E-08 2.60484E-09 3.02264E-65 1.37951E-66 5.97985E-05 2.65581E-03 1.68208E-09 7.95566E-45 1.99368E-45 + 4.32866E-01 3.56882E-08 7.08340E-10 1.61686E-68 7.37920E-70 1.52137E-05 1.19821E-03 4.69105E-10 1.55348E-47 4.47396E-48 + 4.33768E-01 1.50972E-08 1.59292E-10 7.05762E-72 3.22104E-73 3.28588E-06 4.53821E-04 1.07130E-10 2.47615E-50 8.19312E-51 + 4.34669E-01 5.23235E-09 2.94720E-11 2.51390E-75 1.14732E-76 5.96320E-07 1.43710E-04 2.00031E-11 3.22170E-53 1.22440E-53 + 4.35571E-01 1.48352E-09 4.47188E-12 7.30701E-79 3.33486E-80 9.03900E-08 3.79002E-05 3.05124E-12 3.42159E-56 1.49318E-56 + 4.36473E-01 3.43786E-10 5.55365E-13 1.73314E-82 7.90992E-84 1.14300E-08 8.29417E-06 3.80065E-13 2.96622E-59 1.48598E-59 + 4.37375E-01 6.50786E-11 5.63844E-14 3.35453E-86 1.53098E-87 1.21000E-09 1.50135E-06 3.86483E-14 2.09897E-62 1.20677E-62 + 4.38277E-01 1.00598E-11 4.67653E-15 5.29823E-90 2.41807E-91 1.10000E-10 2.24162E-07 3.20798E-15 1.21236E-65 7.99732E-66 + 4.39178E-01 1.26952E-12 3.16731E-16 6.82863E-94 3.11653E-95 1.00000E-11 2.75430E-08 2.17333E-16 5.71587E-69 4.32486E-69 + 4.40080E-01 1.30777E-13 1.75127E-17 7.18188E-98 3.27775E-99 0.00000E+00 2.77982E-09 1.20170E-17 2.19964E-72 1.90856E-72 + 4.40982E-01 1.09958E-14 7.90403E-19 6.16375E-102 2.81308E-103 0.00000E+00 2.30103E-10 5.42000E-19 6.90932E-76 6.87300E-76 + 4.41884E-01 7.54566E-16 2.91164E-20 4.31673E-106 1.97012E-107 0.00000E+00 1.56035E-11 2.00000E-20 1.77147E-79 2.01972E-79 + 4.42786E-01 4.22599E-17 8.75386E-22 2.46699E-110 1.12591E-111 0.00000E+00 8.65990E-13 1.00000E-21 3.70717E-83 4.84331E-83 + 4.43687E-01 1.93157E-18 2.14794E-23 1.15049E-114 5.25073E-116 0.00000E+00 3.93100E-14 0.00000E+00 6.33227E-87 9.47756E-87 + 4.44589E-01 7.20500E-20 4.30126E-25 4.37824E-119 1.99819E-120 0.00000E+00 1.46000E-15 0.00000E+00 8.82838E-91 1.51340E-90 + 4.45491E-01 2.19328E-21 7.02937E-27 1.35963E-123 6.20522E-125 0.00000E+00 4.00000E-17 0.00000E+00 1.00463E-94 1.97204E-94 + 4.46393E-01 5.44867E-23 9.37524E-29 3.44542E-128 1.57246E-129 0.00000E+00 0.00000E+00 0.00000E+00 9.33104E-99 2.09692E-98 + 4.47295E-01 1.10463E-24 1.02045E-30 7.12470E-133 3.25165E-134 0.00000E+00 0.00000E+00 0.00000E+00 7.07379E-103 1.81950E-102 + 4.48196E-01 1.82757E-26 9.06445E-33 1.20225E-137 5.48696E-139 0.00000E+00 0.00000E+00 0.00000E+00 4.37692E-107 1.28832E-106 + 4.49098E-01 2.46752E-28 6.57103E-35 1.65548E-142 7.55547E-144 0.00000E+00 0.00000E+00 0.00000E+00 2.21044E-111 7.44385E-111 + 4.50000E-01 2.71877E-30 3.88746E-37 1.86019E-147 8.48974E-149 0.00000E+00 0.00000E+00 0.00000E+00 9.11124E-116 3.50975E-115 +""" + ll = _np.genfromtxt(io.StringIO(thedata),names=True) + fgs=['CHali','CHaro','CH2','CH3','NH','NH2','NH3','OH','SH'] + return ll['Energy'].copy()*1e3, dict((k,ll[k].copy()) for k in fgs) diff --git a/NCrystal/_msg.py b/NCrystal/_msg.py index 0b65c128..196d275b 100644 --- a/NCrystal/_msg.py +++ b/NCrystal/_msg.py @@ -49,8 +49,8 @@ def _default_pymsghandler( msg, msgtype ): def _setMsgHandler( handler ): from ._chooks import _get_raw_cfcts _rawfct = _get_raw_cfcts() - _rawfct['setmsghandler'](_default_pymsghandler) - _was_set = [True] + _rawfct['setmsghandler'](handler) + _was_set[0] = True def _setDefaultPyMsgHandlerIfNotSet(): if not _was_set[0]: diff --git a/NCrystal/_ncmatimpl.py b/NCrystal/_ncmatimpl.py index 6b0324ab..d8328350 100644 --- a/NCrystal/_ncmatimpl.py +++ b/NCrystal/_ncmatimpl.py @@ -199,17 +199,35 @@ def from_info( info_obj ): return _composerimpl_from_info( info_obj ) @staticmethod - def from_ncmat( data ): + def from_ncmat( data, keep_header = False ): from .misc import AnyTextData td = AnyTextData(data) if '\n' not in td.content and not td.content.startswith('NCMAT'): return NCMATComposerImpl.from_cfgstr( td.content ) o = _nc_core.directLoad( td, doScatter = False, doAbsorption = False ) - return NCMATComposerImpl.from_info( o.info ) - - def update_atomdb( self, element_or_isotope, data, *, mass=None, coh_scat_len=None, incoh_xs=None, abs_xs=None ): - label,res=_decode_update_atomdb( element_or_isotope,data=data,mass=mass, - coh_scat_len=coh_scat_len,incoh_xs=incoh_xs,abs_xs=abs_xs ) + c = NCMATComposerImpl.from_info( o.info ) + comments = None + if keep_header: + comments = _extractInitialHeaderCommentsFromNCMATData(td) + if comments: + _hr='---------------------------------------------------------' + comments = [ + '>'*70, + 'Comments found in NCMAT data from which the NCMATComposer', + 'was initialised. Subsequent updates to the NCMATComposer', + 'object might have invalidated some or all of these:' + ]+ list('>>> '+e for e in comments) + ['<'*70] + if comments: + c.add_comments( comments, add_empty_line_divider = True ) + return c + + def update_atomdb( self, element_or_isotope, data, *, mass=None, + coh_scat_len=None, incoh_xs=None, abs_xs=None ): + label,res=_decode_update_atomdb( element_or_isotope, + data=data,mass=mass, + coh_scat_len=coh_scat_len, + incoh_xs=incoh_xs, + abs_xs=abs_xs ) self.__dirty() if 'atomdb' not in self.__params: self.__params['atomdb'] = {} @@ -328,7 +346,9 @@ def add_comments( self, comments, add_empty_line_divider ): if 'top_comments' not in self.__params: self.__params['top_comments'] = [] - elif add_empty_line_divider and self.__params['top_comments'] and self.__params['top_comments'][-1]: + elif ( add_empty_line_divider + and self.__params['top_comments'] + and self.__params['top_comments'][-1] ): self.__params['top_comments'].append('') for e in l: @@ -1072,6 +1092,12 @@ def create_ncmat( self, *, cfg_params='', meta_data = False, #md['chemform_per_unit_cell'] = _chemform_per_cell md['title'] = _title + disable_autotitle = False + if comments and comments[0]=='<>': + #hidden feature (might not actually be used yet) + comments = comments[1:] + disable_autotitle = True + if comments and comments[0]=='<>': #hidden feature for our command-line scripts. comments = comments[1:] @@ -1081,10 +1107,11 @@ def create_ncmat( self, *, cfg_params='', meta_data = False, _ = _[:-4] out.append('# Autogenerated by %s'%_) - out += [ '#',f'# {_title}','#' ] - if is_crystal: - _ = '+'.join(f'{count:g}x{lbl}' for lbl,count in _chem_compos) - out += [ f'# Atoms per unit cell: {_}','#' ] + if not disable_autotitle: + out += [ '#',f'# {_title}','#' ] + if is_crystal: + _ = '+'.join(f'{count:g}x{lbl}' for lbl,count in _chem_compos) + out += [ f'# Atoms per unit cell: {_}','#' ] for tc in comments: out.append(('# %s'%tc).rstrip()) @@ -1914,3 +1941,28 @@ def addline( s ): else: addline(p0) return out[0] + +def _extractInitialHeaderCommentsFromNCMATData( ncmat_data, dedent = True ): + #Extracts initial comments, dedented appropriately. Returns None if data + #does not look like NCMAT data (an empty list returned is not a failure, it + #just means no comments). + from .misc import AnyTextData + td = AnyTextData(ncmat_data) + if '\n' not in td.content and not td.content.startswith('NCMAT'): + return None + comments = [] + first = True + for line in td.content.splitlines(): + if first: + first = False + continue + if line.strip().startswith('@'): + break + line=line.lstrip() + if line.startswith('#'): + comments.append(line[1:].rstrip()) + #dedent and return: + if dedent: + while all( ( e.startswith(' ') or not e) for e in comments ): + comments = [ e[1:] for e in comments ] + return comments diff --git a/NCrystal/hfg2ncmat.py b/NCrystal/hfg2ncmat.py new file mode 100644 index 00000000..b219b7c0 --- /dev/null +++ b/NCrystal/hfg2ncmat.py @@ -0,0 +1,272 @@ + +################################################################################ +## ## +## 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. ## +## ## +################################################################################ + +""" + +Utilities for generating NCMAT files for hydrogen rich amorphous materials +(based on doi:10.1088/1361-648X/abfc13). + +""" + +__all__ = [ 'hfg2ncmat'] + +def _default_debye_temp(): + #Note: keep in synch with value mentioned in docstring of hfg2ncmat + #function, as well as the NCMATComposer.from_hfg method. + return 400.0 + +def _parseChemicalFormula(chemform): + import re + def err(): + from .exceptions import NCBadInput + raise NCBadInput(f'Invalid chemical formula: "{chemform}"') + def is_ascii(s): + #str.isascii requires python 3.7 + return all(ord(c) < 128 for c in s) + if not is_ascii(chemform) or not chemform.isalnum(): + err() + d={} + prev=None + def add(element,count): + d[element] = d.get(element,0) + count + + chemform_unused = chemform.strip() + for e in re.findall('[A-Z][a-z]?|[0-9]+', chemform.strip()): + if chemform_unused.startswith(e): + chemform_unused = chemform_unused[len(e):].strip() + else: + err() + if e.isdigit(): + if prev is None or prev.isdigit(): + err() + v=int(e) + if v<1 or v>1000000000: + err() + add(prev,v) + prev=None + continue + if prev is not None: + add(prev,1) + prev = None + prev = e + if prev is not None: + add(prev,1) + if chemform_unused: + err() + return d + +def _parseHydrogenBindingSpecification(spec): + from .exceptions import NCBadInput + def err(): + raise NCBadInput(f'Invalid hydrogen binding specification: "{spec}"') + def is_ascii(s): + #str.isascii requires python 3.7 + return all(ord(c) < 128 for c in s) + if not is_ascii(spec) or not spec.replace('+','').isalnum(): + err() + + fg2nH=dict(CHali=1,CHaro=1,CH2=2,CH3=3,NH=1,NH2=2,NH3=3,OH=1,SH=1) + d={} + for part in spec.split('+'): + p=part.strip().split('x') + if len(p)!=2: + err() + count,fg=p + if not fg in fg2nH: + raise NCBadInput(f'Unknown functional group in "{spec}": "{fg}"') + if not count.isdigit() or not 1 <= int(count) <= 10000: + raise NCBadInput(f'Invalid count in "{spec}": "{count}"') + d[fg] = d.get(fg,0)+int(count)*fg2nH[fg] + return d + +def hfg2ncmat( spec, + formula, *, + density, + title, + debyetemp = _default_debye_temp(), + verbose = True, + notrim = False ): + """Function which can be used to generate NCMAT data 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, NCMAT data is +generated. In this NCMAT data, non-hydrogen atoms are treated with a simplistic +model (idealised Debye model of phonon vibrations, assuming a Debye temperature +of 400K for all atoms unless the debyetemp parameter is provided. 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 the spec string: + + 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 function 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 (unless verbose=False). + +""" + #NOTE: Keep the description above synchronised with help text of of the + #ncrystal_hfg2ncmat command-line app! + + from ._hfgdata import get_data as hfg_get_data + #FIXME: CHECK ARGS + #FIXME: seems to parse!!!!! --formula CH6s + + if verbose: + from ._common import print + else: + def print(*args,**kwargs): + pass + + spec_parsed = _parseHydrogenBindingSpecification(spec) + chemform = _parseChemicalFormula(formula) + + nH = chemform.get('H',-999) + if sum(v for k,v in spec_parsed.items()) != nH: + from .exceptions import NCBadInput + raise NCBadInput('number of hydrogen items in --formula' + ' and --spec does not match up.') + + egrid,vdos = hfg_get_data() + + #Calculate hydrogen VDOS: + + h_vdos = sum( nh * vdos[fgname] for fgname,nh in sorted(spec_parsed.items())) + h_vdos /= h_vdos.max() + + debye_cut_bin = 4#shave off first few points, to force parabolic behaviour near E=0. + if not notrim: + for i in range(len(h_vdos)): + if egrid[i]<0.05: + continue#don't touch first bins + if h_vdos[i]<1e-7: + h_vdos[i]=0.0 + ntrim=2 + assert debye_cut_bin%ntrim==0 + debye_cut_bin //= ntrim + h_vdos = h_vdos[::ntrim] + egrid = egrid[::ntrim] + + while len(h_vdos)>10 and h_vdos[-2]==0.0 and h_vdos[-1]==0.0: + h_vdos = h_vdos[0:-1] + egrid = egrid[0:-1] + + appname='ncrystal_hfg2ncmat' + + initial_comments='#\n' + for l in title.replace('\\n','\n').splitlines(): + initial_comments+= f'# {l}\n' if l.strip() else '#\n' + initial_comments+='#' + + recordargs=[ f'--spec={spec}', + f'--formula={formula}', + f'--density={density}' ] + if _default_debye_temp() != debyetemp: + recordargs.append('--debyetemp=%.14g'%debyetemp) + if notrim: + recordargs.append('--notrim') + recordargs='\n# '.join(recordargs) + + out = f"""NCMAT v5 +{initial_comments} +# ---------------------------------------------------------------------------- +# +# File generated by {appname} with: +# +# {recordargs} +# +# The hydrogen VDOS curve in this file is constructed using data from: +# +# "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 +# +# Considering only scat. lengths and composition, incoherent scattering on +# hydrogen accounts for <<>> of scattering in this material (a higher value +# implies more accurate modelling). +# +@STATEOFMATTER + solid +@DENSITY + {density} g_per_cm3 +""" + + ntot = sum(n for elem,n in chemform.items()) + for elem,n in chemform.items(): + if elem=='H': + continue + out+=f"""@DYNINFO + element {elem} + fraction {n}/{ntot} + type vdosdebye + debye_temp {debyetemp} +""" + out+=f"""@DYNINFO + element H + fraction {nH}/{ntot} + type vdos + vdos_egrid {0.001*egrid[debye_cut_bin]:.8g} {0.001*egrid[-1]:.8g} +""" + from .ncmat import formatVectorForNCMAT + out += formatVectorForNCMAT('vdos_density',h_vdos[debye_cut_bin:]) + print ("Generated NCMAT data...") + print ("Verifying that it can be loaded with NCrystal...") + from .core import load as nc_load + loaded_mat = nc_load(out) + print ("Succesfully loaded...") + + breakdown = [] + for di in loaded_mat.info.dyninfos: + for cohtype in 'incoherent','coherent': + key='%s (%s)'%(di.atomData.displayLabel(),cohtype) + sigma = di.atomData.coherentXS() if cohtype=='coherent' else di.atomData.incoherentXS() + breakdown+=[(di.fraction*sigma,key)] + sigma_tot = sum(s for s,k in breakdown) + print("Contribution breakdown based on composition:") + for s,key in reversed(sorted(breakdown)): + print (" Contribution to bound scattering XS from %s is %5.2f %%"%(key.ljust(14),s*100.0/sigma_tot)) + if key=='H (incoherent)': + contrib_incH = s/sigma_tot + + return out.replace('<<>>','%.3g%%'%(100.0*contrib_incH)) diff --git a/NCrystal/ncmat.py b/NCrystal/ncmat.py index c41f8212..0993b888 100644 --- a/NCrystal/ncmat.py +++ b/NCrystal/ncmat.py @@ -89,15 +89,16 @@ def __init__(self, data = None, fmt = None, quiet = False, plotlabel = None ): explicitly. Supported fmt's are "cif", "cfgstr", "ncmat", (for NCMAT data), "info" (for NCrystal.Info or LoadedMaterial objects), ase (for ASE structures). Finally, the format "via_ase" is special, since it will - always for the input to be processed with ASE, even if another more - obvious format exists (i.e. CIF files will be processed via ASE first, - not passed along directly to the NCrystal.CIFLoader). As an alternative - to the "fmt" parameter, one can also invoke the various .from_xxx(..) - static methods. This has the potential advantage of allowing the - specification of parameters dedicated only to that input data type. + always process the input with ASE, even if another more obvious format + exists (i.e. CIF files will be processed via ASE first, not passed along + directly to the NCrystal.CIFLoader). As an alternative to the "fmt" + parameter, one can also invoke the various .from_xxx(..) static + methods. This has the potential advantage of allowing the specification + of parameters dedicated only to that input data type. If quiet=True, no informative messages will be emitted, and the plotlabel will be passed along to .set_plotlabel(). + """ from ._ncmatimpl import NCMATComposerImpl as Impl self.__impl = ( data if isinstance( data, Impl ) @@ -170,6 +171,31 @@ def from_ncmat( data ): from ._ncmatimpl import NCMATComposerImpl as Impl return NCMATComposer( Impl.from_ncmat( data ) ) + @staticmethod + def from_hfg( spec, + formula, *, + density, + title, + debyetemp = 400.0, + verbose = True, + notrim = False ): + """Constructs an amorphous hydrogen-rich material via the hfg2ncmat + function from the NCrystal.hfg2ncmat module. Refer to that function for + usage instructions. + """ + from .hfg2ncmat import _default_debye_temp, hfg2ncmat + from ._ncmatimpl import NCMATComposerImpl as Impl + assert _default_debye_temp()==400.0, "from_hfg default must be updated" + ncmat = hfg2ncmat( spec = spec, + formula = formula, + density = density, + title = title, + debyetemp = debyetemp, + verbose = verbose, + notrim = notrim ) + return NCMATComposer( Impl.from_ncmat( ncmat, + keep_header=True ) ) + def __call__( self, cfg_params = None, **kwargs ): """Convenience short-cut for the .create_ncmat() method""" return self.create_ncmat( cfg_params = cfg_params, **kwargs ) diff --git a/README b/README index 7ed0196d..95274ff1 100644 --- a/README +++ b/README @@ -242,14 +242,13 @@ OK for v3.2 though). You can use NCrystal in two ways in McStas. You can either use it for advanced studies with the McStas Union sub-system through the NCrystal_process component, -or it can be used via the dedicated (and simpler+less feature-rich) -NCrystal_sample.comp. In any case, the McStas instrument file compilation will -need to build against NCrystal, and it uses the ncrystal-config command to -figure out the correct settings for doing so. Thus, you can always invoke -"ncrystal-config -s" to find out if you have the right NCrystal installation -available and active. Depending on how you installed McStas, NCrystal is most -likely already available. If not, you can try one of the following ways of -enabling it: +or it can be used via the dedicated NCrystal_sample.comp which is simpler but +less feature rich. In any case, the McStas instrument file compilation will need +to build against NCrystal, and it uses the ncrystal-config command to figure out +the correct settings for doing so. Thus, you can always invoke "ncrystal-config +-s" to find out if you have the right NCrystal installation available and +active. Depending on how you installed McStas, NCrystal is most likely already +available. If not, you can try one of the following ways of enabling it: $> conda install -c conda-forge ncrystal [if you are in a conda-forge env] $> python3 -mpip install ncrystal [for non-conda users] diff --git a/VERSION b/VERSION index e0d61b5b..11aaa068 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -3.9.4 +3.9.5 diff --git a/ncrystal_core/include/NCrystal/NCVersion.hh b/ncrystal_core/include/NCrystal/NCVersion.hh index f1816154..f3251168 100644 --- a/ncrystal_core/include/NCrystal/NCVersion.hh +++ b/ncrystal_core/include/NCrystal/NCVersion.hh @@ -39,9 +39,9 @@ #define NCRYSTAL_VERSION_MAJOR 3 #define NCRYSTAL_VERSION_MINOR 9 -#define NCRYSTAL_VERSION_PATCH 4 -#define NCRYSTAL_VERSION 3009004 /* (1000000*MAJOR+1000*MINOR+PATCH) */ -#define NCRYSTAL_VERSION_STR "3.9.4" +#define NCRYSTAL_VERSION_PATCH 5 +#define NCRYSTAL_VERSION 3009005 /* (1000000*MAJOR+1000*MINOR+PATCH) */ +#define NCRYSTAL_VERSION_STR "3.9.5" #include "NCrystal/ncapi.h" #include diff --git a/ncrystal_core/include/NCrystal/ncrystal.h b/ncrystal_core/include/NCrystal/ncrystal.h index e7357f0e..6355d44a 100644 --- a/ncrystal_core/include/NCrystal/ncrystal.h +++ b/ncrystal_core/include/NCrystal/ncrystal.h @@ -1201,9 +1201,9 @@ extern "C" { #endif #define NCRYSTAL_VERSION_MAJOR 3 #define NCRYSTAL_VERSION_MINOR 9 -#define NCRYSTAL_VERSION_PATCH 4 -#define NCRYSTAL_VERSION 3009004 /* (1000000*MAJOR+1000*MINOR+PATCH) */ -#define NCRYSTAL_VERSION_STR "3.9.4" +#define NCRYSTAL_VERSION_PATCH 5 +#define NCRYSTAL_VERSION 3009005 /* (1000000*MAJOR+1000*MINOR+PATCH) */ +#define NCRYSTAL_VERSION_STR "3.9.5" NCRYSTAL_API int ncrystal_version(void); /* returns NCRYSTAL_VERSION */ NCRYSTAL_API const char * ncrystal_version_str(void); /* returns NCRYSTAL_VERSION_STR */ diff --git a/scripts/ncrystal_hfg2ncmat b/scripts/ncrystal_hfg2ncmat index 49d2d398..50fc09fd 100755 --- a/scripts/ncrystal_hfg2ncmat +++ b/scripts/ncrystal_hfg2ncmat @@ -77,756 +77,5 @@ def ncImportSubModule( mainmodule, submodulename ): return getattr(_,submodulename) ################################################################################################ NC = fixSysPathAndImportNCrystal() - -import re -import argparse -import io -import numpy as np - -def get_data(): - """Hydrogen VDOS for various functional groups (supplementary material of doi:10.1088/1361-648X/abfc13)""" - thedata=""" -#Energy CHali CHaro CH2 CH3 NH NH2 NH3 OH SH - 0.00000E+00 2.13554E-05 1.33447E-04 4.19945E-05 6.16412E-05 9.87755E-05 1.58844E-04 1.66414E-05 1.10565E-05 9.18572E-06 - 9.01804E-04 4.25611E-05 2.14471E-04 9.06037E-05 1.44290E-04 1.63593E-04 2.14715E-04 3.58153E-05 2.55964E-05 2.65186E-05 - 1.80361E-03 7.85363E-05 3.05676E-04 1.74811E-04 2.98485E-04 2.36042E-04 2.64685E-04 6.78767E-05 5.03742E-05 6.49416E-05 - 2.70541E-03 1.35340E-04 3.94305E-04 3.06398E-04 5.49869E-04 3.07172E-04 3.15534E-04 1.14922E-04 8.57807E-05 1.36052E-04 - 3.60721E-03 2.17858E-04 4.72909E-04 4.94518E-04 9.07625E-04 3.75427E-04 3.81898E-04 1.76387E-04 1.29767E-04 2.46917E-04 - 4.50902E-03 3.25605E-04 5.45649E-04 7.41915E-04 1.35003E-03 4.46001E-04 4.74550E-04 2.48511E-04 1.80479E-04 3.95660E-04 - 5.41082E-03 4.48735E-04 6.27004E-04 1.03959E-03 1.82126E-03 5.24448E-04 5.93392E-04 3.24323E-04 2.39079E-04 5.75327E-04 - 6.31263E-03 5.68995E-04 7.31566E-04 1.36181E-03 2.24894E-03 6.13562E-04 7.28691E-04 3.94879E-04 3.09468E-04 7.85659E-04 - 7.21443E-03 6.68072E-04 8.62561E-04 1.66718E-03 2.58112E-03 7.15253E-04 8.63823E-04 4.52960E-04 3.95789E-04 1.04112E-03 - 8.11623E-03 7.38792E-04 1.01083E-03 1.91299E-03 2.82301E-03 8.31824E-04 9.77799E-04 4.97925E-04 5.01333E-04 1.36244E-03 - 9.01804E-03 7.89848E-04 1.16526E-03 2.08157E-03 3.04246E-03 9.64004E-04 1.05469E-03 5.37190E-04 6.28608E-04 1.75127E-03 - 9.91984E-03 8.38334E-04 1.32013E-03 2.19762E-03 3.32835E-03 1.10625E-03 1.09889E-03 5.80584E-04 7.75871E-04 2.16194E-03 - 1.08216E-02 8.94610E-04 1.46840E-03 2.30773E-03 3.71962E-03 1.24042E-03 1.13848E-03 6.30132E-04 9.29796E-04 2.49355E-03 - 1.17234E-02 9.52165E-04 1.59183E-03 2.42918E-03 4.15102E-03 1.33632E-03 1.20438E-03 6.74345E-04 1.06380E-03 2.62439E-03 - 1.26253E-02 9.92401E-04 1.66731E-03 2.52363E-03 4.46588E-03 1.36908E-03 1.30279E-03 6.94751E-04 1.15067E-03 2.48124E-03 - 1.35271E-02 1.00056E-03 1.68600E-03 2.53463E-03 4.50492E-03 1.34115E-03 1.41275E-03 6.80982E-04 1.18161E-03 2.09326E-03 - 1.44289E-02 9.77866E-04 1.66055E-03 2.44867E-03 4.20991E-03 1.27929E-03 1.51185E-03 6.40946E-04 1.17339E-03 1.58157E-03 - 1.53307E-02 9.39376E-04 1.61225E-03 2.30892E-03 3.65939E-03 1.20412E-03 1.59661E-03 5.97357E-04 1.15725E-03 1.09459E-03 - 1.62325E-02 9.01295E-04 1.55825E-03 2.17637E-03 3.01643E-03 1.11074E-03 1.67237E-03 5.75495E-04 1.15906E-03 7.44844E-04 - 1.71343E-02 8.69515E-04 1.51159E-03 2.09365E-03 2.43893E-03 9.87278E-04 1.72917E-03 5.92606E-04 1.18137E-03 5.84810E-04 - 1.80361E-02 8.38573E-04 1.47991E-03 2.08070E-03 2.01605E-03 8.43933E-04 1.73756E-03 6.53383E-04 1.19666E-03 6.14449E-04 - 1.89379E-02 8.00728E-04 1.45323E-03 2.13783E-03 1.76553E-03 7.11190E-04 1.67048E-03 7.49362E-04 1.16275E-03 7.93397E-04 - 1.98397E-02 7.55884E-04 1.39954E-03 2.23602E-03 1.68583E-03 6.11496E-04 1.52619E-03 8.60650E-04 1.05581E-03 1.04638E-03 - 2.07415E-02 7.13469E-04 1.28590E-03 2.31545E-03 1.82084E-03 5.43303E-04 1.33199E-03 9.62313E-04 8.91678E-04 1.27519E-03 - 2.16433E-02 6.86955E-04 1.10959E-03 2.31413E-03 2.28323E-03 4.93518E-04 1.13214E-03 1.03645E-03 7.12840E-04 1.39276E-03 - 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4.12124E-01 4.52309E-08 1.69738E-09 1.31636E-15 6.00297E-17 6.56500E-07 4.61211E-03 3.30682E-04 1.64201E-07 1.92720E-09 - 4.13026E-01 3.63670E-08 2.83425E-10 6.16623E-17 2.81279E-18 2.21898E-06 3.28297E-03 1.46213E-04 2.77602E-08 3.71102E-10 - 4.13928E-01 3.57169E-08 3.89563E-11 2.35741E-18 1.07555E-19 6.33637E-06 1.97786E-03 5.38358E-05 3.83368E-09 5.85276E-11 - 4.14830E-01 5.15584E-08 6.88547E-12 7.35519E-20 3.35616E-21 1.52929E-05 1.11697E-03 1.63966E-05 4.32424E-10 7.55563E-12 - 4.15731E-01 9.07424E-08 2.05504E-11 1.87276E-21 8.54601E-23 3.16022E-05 8.67828E-04 4.12154E-06 3.98355E-11 7.97990E-13 - 4.16633E-01 1.56582E-07 1.29180E-10 3.89127E-23 1.77580E-24 5.90683E-05 1.25544E-03 8.84068E-07 2.99685E-12 6.89207E-14 - 4.17535E-01 2.42704E-07 6.75589E-10 6.59802E-25 3.01112E-26 1.15218E-04 2.26255E-03 2.50816E-07 1.84106E-13 4.86593E-15 - 4.18437E-01 3.26346E-07 2.88601E-09 9.12947E-27 4.16647E-28 2.74799E-04 3.78977E-03 2.71810E-07 9.23540E-15 2.80744E-16 - 4.19339E-01 3.72961E-07 1.00727E-08 1.03082E-28 4.70449E-30 7.56321E-04 5.54292E-03 4.82470E-07 3.78277E-16 1.32333E-17 - 4.20240E-01 3.57298E-07 2.87451E-08 9.49791E-31 4.33471E-32 1.99747E-03 7.01339E-03 7.47682E-07 1.26506E-17 5.09505E-19 - 4.21142E-01 2.84543E-07 6.71627E-08 7.14129E-33 3.25920E-34 4.54354E-03 7.67160E-03 9.51702E-07 3.45422E-19 1.60204E-20 - 4.22044E-01 1.88222E-07 1.28762E-07 4.38156E-35 1.99970E-36 8.57705E-03 7.32770E-03 9.93641E-07 7.70031E-21 4.11318E-22 - 4.22946E-01 1.05919E-07 2.03274E-07 2.19373E-37 1.00120E-38 1.33046E-02 6.39554E-03 8.55444E-07 1.40145E-22 8.62207E-24 - 4.23848E-01 5.77595E-08 2.65734E-07 8.96277E-40 4.09052E-41 1.69372E-02 5.75309E-03 6.15031E-07 2.08232E-24 1.47547E-25 - 4.24749E-01 4.43882E-08 2.90083E-07 2.98816E-42 1.36377E-43 1.77325E-02 6.19840E-03 3.80218E-07 2.52586E-26 2.06112E-27 - 4.25651E-01 5.73055E-08 2.67494E-07 8.12956E-45 3.71026E-46 1.53367E-02 7.88439E-03 2.14667E-07 2.50125E-28 2.35017E-29 - 4.26553E-01 8.68866E-08 2.11261E-07 1.80482E-47 8.23704E-49 1.10365E-02 1.01501E-02 1.21077E-07 2.02201E-30 2.18723E-31 - 4.27455E-01 1.22971E-07 1.44791E-07 3.26966E-50 1.49225E-51 6.67620E-03 1.18637E-02 7.22525E-08 1.33438E-32 1.66139E-33 - 4.28357E-01 1.52780E-07 8.67937E-08 4.83364E-53 2.20603E-54 3.43979E-03 1.20690E-02 4.38102E-08 7.18862E-35 1.02995E-35 - 4.29259E-01 1.62965E-07 4.54619E-08 5.83108E-56 2.66125E-57 1.53064E-03 1.05354E-02 2.46713E-08 3.16135E-37 5.21096E-38 - 4.30160E-01 1.47003E-07 2.06150E-08 5.74018E-59 2.61977E-60 5.94492E-04 7.84452E-03 1.20665E-08 1.13489E-39 2.15160E-40 - 4.31062E-01 1.10843E-07 7.98330E-09 4.61111E-62 2.10447E-63 2.02122E-04 4.96178E-03 4.95431E-09 3.32576E-42 7.25010E-43 - 4.31964E-01 6.92780E-08 2.60484E-09 3.02264E-65 1.37951E-66 5.97985E-05 2.65581E-03 1.68208E-09 7.95566E-45 1.99368E-45 - 4.32866E-01 3.56882E-08 7.08340E-10 1.61686E-68 7.37920E-70 1.52137E-05 1.19821E-03 4.69105E-10 1.55348E-47 4.47396E-48 - 4.33768E-01 1.50972E-08 1.59292E-10 7.05762E-72 3.22104E-73 3.28588E-06 4.53821E-04 1.07130E-10 2.47615E-50 8.19312E-51 - 4.34669E-01 5.23235E-09 2.94720E-11 2.51390E-75 1.14732E-76 5.96320E-07 1.43710E-04 2.00031E-11 3.22170E-53 1.22440E-53 - 4.35571E-01 1.48352E-09 4.47188E-12 7.30701E-79 3.33486E-80 9.03900E-08 3.79002E-05 3.05124E-12 3.42159E-56 1.49318E-56 - 4.36473E-01 3.43786E-10 5.55365E-13 1.73314E-82 7.90992E-84 1.14300E-08 8.29417E-06 3.80065E-13 2.96622E-59 1.48598E-59 - 4.37375E-01 6.50786E-11 5.63844E-14 3.35453E-86 1.53098E-87 1.21000E-09 1.50135E-06 3.86483E-14 2.09897E-62 1.20677E-62 - 4.38277E-01 1.00598E-11 4.67653E-15 5.29823E-90 2.41807E-91 1.10000E-10 2.24162E-07 3.20798E-15 1.21236E-65 7.99732E-66 - 4.39178E-01 1.26952E-12 3.16731E-16 6.82863E-94 3.11653E-95 1.00000E-11 2.75430E-08 2.17333E-16 5.71587E-69 4.32486E-69 - 4.40080E-01 1.30777E-13 1.75127E-17 7.18188E-98 3.27775E-99 0.00000E+00 2.77982E-09 1.20170E-17 2.19964E-72 1.90856E-72 - 4.40982E-01 1.09958E-14 7.90403E-19 6.16375E-102 2.81308E-103 0.00000E+00 2.30103E-10 5.42000E-19 6.90932E-76 6.87300E-76 - 4.41884E-01 7.54566E-16 2.91164E-20 4.31673E-106 1.97012E-107 0.00000E+00 1.56035E-11 2.00000E-20 1.77147E-79 2.01972E-79 - 4.42786E-01 4.22599E-17 8.75386E-22 2.46699E-110 1.12591E-111 0.00000E+00 8.65990E-13 1.00000E-21 3.70717E-83 4.84331E-83 - 4.43687E-01 1.93157E-18 2.14794E-23 1.15049E-114 5.25073E-116 0.00000E+00 3.93100E-14 0.00000E+00 6.33227E-87 9.47756E-87 - 4.44589E-01 7.20500E-20 4.30126E-25 4.37824E-119 1.99819E-120 0.00000E+00 1.46000E-15 0.00000E+00 8.82838E-91 1.51340E-90 - 4.45491E-01 2.19328E-21 7.02937E-27 1.35963E-123 6.20522E-125 0.00000E+00 4.00000E-17 0.00000E+00 1.00463E-94 1.97204E-94 - 4.46393E-01 5.44867E-23 9.37524E-29 3.44542E-128 1.57246E-129 0.00000E+00 0.00000E+00 0.00000E+00 9.33104E-99 2.09692E-98 - 4.47295E-01 1.10463E-24 1.02045E-30 7.12470E-133 3.25165E-134 0.00000E+00 0.00000E+00 0.00000E+00 7.07379E-103 1.81950E-102 - 4.48196E-01 1.82757E-26 9.06445E-33 1.20225E-137 5.48696E-139 0.00000E+00 0.00000E+00 0.00000E+00 4.37692E-107 1.28832E-106 - 4.49098E-01 2.46752E-28 6.57103E-35 1.65548E-142 7.55547E-144 0.00000E+00 0.00000E+00 0.00000E+00 2.21044E-111 7.44385E-111 - 4.50000E-01 2.71877E-30 3.88746E-37 1.86019E-147 8.48974E-149 0.00000E+00 0.00000E+00 0.00000E+00 9.11124E-116 3.50975E-115 -""" - l = np.genfromtxt(io.StringIO(thedata),names=True) - return l['Energy'].copy()*1e3, dict((k,l[k].copy()) for k in ['CHali','CHaro','CH2','CH3','NH','NH2','NH3','OH','SH']) - -def parseChemicalFormula(chemform): - def err(): - raise RuntimeError(f'Invalid chemical formula: "{chemform}"') - def is_ascii(s): - #str.isascii requires python 3.7 - return all(ord(c) < 128 for c in s) - if not is_ascii(chemform) or not chemform.isalnum(): - err() - d={} - prev=None - def add(element,count): - d[element] = d.get(element,0) + count - for e in re.findall('[A-Z][a-z]?|[0-9]+', chemform): - if e.isdigit(): - if prev is None or prev.isdigit(): - err() - v=int(e) - if v<1 or v>1000000000: - err() - add(prev,v) - prev=None - continue - if prev is not None: - add(prev,1) - prev = None - prev = e - if prev is not None: - add(prev,1) - return d - -def parseHydrogenBindingSpecification(spec): - def err(): - raise RuntimeError(f'Invalid hydrogen binding specification: "{spec}"') - def is_ascii(s): - #str.isascii requires python 3.7 - return all(ord(c) < 128 for c in s) - if not is_ascii(spec) or not spec.replace('+','').isalnum(): - err() - - fg2nH=dict(CHali=1,CHaro=1,CH2=2,CH3=3,NH=1,NH2=2,NH3=3,OH=1,SH=1) - d={} - for part in spec.split('+'): - p=part.strip().split('x') - if len(p)!=2: - err() - count,fg=p - if not fg in fg2nH: - raise RuntimeError(f'Unknown functional group in "{spec}": "{fg}"') - if not count.isdigit() or not 1 <= int(count) <= 10000: - raise RuntimeError(f'Invalid count in "{spec}": "{count}"') - d[fg] = d.get(fg,0)+int(count)*fg2nH[fg] - return d - - -default_debye_temp = 400.0 - -def parseArgs(): - fdt = default_debye_temp - 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. - -""" - 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)") - 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=f"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=f"Debye temperature (kelvin) of non-hydrogen 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 - -args = parseArgs() - -spec = parseHydrogenBindingSpecification(args.spec) -chemform = parseChemicalFormula(args.formula) -density = args.density - -nH = chemform.get('H',-999) -if sum(v for k,v in spec.items()) != nH: - raise SystemExit('Error: number of hydrogen items in --formula and --spec does not match up.') - -egrid,vdos=get_data() - -#Calculate hydrogen VDOS: - -h_vdos = sum( nh * vdos[fgname] for fgname,nh in sorted(spec.items())) -h_vdos /= h_vdos.max() - -debye_cut_bin = 4#shave off first few points, to force parabolic behaviour near E=0. -if not args.notrim: - for i in range(len(h_vdos)): - if egrid[i]<0.05: - continue#don't touch first bins - if h_vdos[i]<1e-7: - h_vdos[i]=0.0 - ntrim=2 - assert debye_cut_bin%ntrim==0 - debye_cut_bin //= ntrim - h_vdos = h_vdos[::ntrim] - egrid = egrid[::ntrim] - -while len(h_vdos)>10 and h_vdos[-2]==0.0 and h_vdos[-1]==0.0: - h_vdos = h_vdos[0:-1] - egrid = egrid[0:-1] - -appname='ncrystal_hfg2ncmat' - -initial_comments='#\n' -for l in args.title.replace('\\n','\n').splitlines(): - initial_comments+= f'# {l}\n' if l.strip() else '#\n' -initial_comments+='#' - -recordargs=[ f'--spec={args.spec}', - f'--formula={args.formula}', - f'--density={args.density}' ] -if default_debye_temp != args.debyetemp: - recordargs.append('--debyetemp=%.14g'%args.debyetemp) -if args.notrim: - recordargs.append('--notrim') -recordargs='\n# '.join(recordargs) - -out = f"""NCMAT v5 -{initial_comments} -# ---------------------------------------------------------------------------- -# -# File generated by {appname} with: -# -# {recordargs} -# -# The hydrogen VDOS curve in this file is constructed using data from: -# -# "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 -# -# Considering only scat. lengths and composition, incoherent scattering on -# hydrogen accounts for <<>> of scattering in this material (a higher value -# implies more accurate modelling). -# -@STATEOFMATTER - solid -@DENSITY - {density} g_per_cm3 -""" - -ntot = sum(n for elem,n in chemform.items()) -for elem,n in chemform.items(): - if elem=='H': - continue - out+=f"""@DYNINFO - element {elem} - fraction {n}/{ntot} - type vdosdebye - debye_temp {args.debyetemp} -""" -out+=f"""@DYNINFO - element H - fraction {nH}/{ntot} - type vdos - vdos_egrid {0.001*egrid[debye_cut_bin]:.8g} {0.001*egrid[-1]:.8g} -""" -out += NC.formatVectorForNCMAT('vdos_density',h_vdos[debye_cut_bin:]) -print ("Generated NCMAT data...") -print ("Verifying that it can be loaded with NCrystal...") -NC.registerInMemoryFileData('test.ncmat',out) -info = NC.createInfo("virtual::test.ncmat") -sc = NC.createScatter("virtual::test.ncmat") -print ("Succesfully loaded...") - -breakdown = [] -for di in info.dyninfos: - for cohtype in 'incoherent','coherent': - key='%s (%s)'%(di.atomData.displayLabel(),cohtype) - sigma = di.atomData.coherentXS() if cohtype=='coherent' else di.atomData.incoherentXS() - breakdown+=[(di.fraction*sigma,key)] -sigma_tot = sum(s for s,k in breakdown) -print("Contribution breakdown based on composition:") -for s,key in reversed(sorted(breakdown)): - print (" Contribution to bound scattering XS from %s is %5.2f %%"%(key.ljust(14),s*100.0/sigma_tot)) - if key=='H (incoherent)': - contrib_incH = s/sigma_tot - -outfile = pathlib.Path(args.output) -if outfile.exists() and not args.force: - raise SystemExit('Error: output file already exists (run with --force to overwrite)') -outfile.write_text(out.replace('<<>>','%.3g%%'%(100.0*contrib_incH))) -print(f"Wrote: {outfile}") +cli = ncImportSubModule( NC, '_cli_hfg2ncmat' ) +cli.main()