import from dgcode git: version 2.6.0

CHANGELOG

@@ -1,3 +1,56 @@
+v2.6.0 2020-04-05
+      * Introduce NCMAT v4 which introduces a few new features, as described in
+        detail in the ncmat_doc.md file. The most important new feature relies
+        on the fact that it is possible to estimate atomic
+        mean-squared-displacements directly from a phonon density of state
+        distribution (VDOS), meaning that it is now allowed (and actually
+        recommended) to skip @DEBYETEMPERATURE's for crystalline materials where
+        atoms have VDOS curves available). This is not only useful, but improves
+        low-temperature reliability of the Debye-Waller factors used in the
+        elastic scattering components. This development was helped by Kemal
+        Ramic and Jose Ignacio Marquez Damian from the ESS Spallation Physics
+        group, and more details are available in the ncrystal GitHub issue
+        #58. The other new feature in NCMAT v4 is a new optional syntax for the
+        @CELL section, which allows more compact specification for certain
+        crystal systems (in particular cubic systems).
+      * The vast majority of crystalline materials in the NCrystal data library
+        were updated to take advantage of the new features, and in addition the
+        number of VDOS curves was increased dramatically, meaning that the
+        dynamics in almost all crystalline materials are now described using
+        actual VDOS curves rather than just Debye temperatures.
+      * Missing VDOS curves for all elements in beryllium-fluoride (BeF2),
+        aragonite (CaCO3), cuprite (Cu2O), periclase (MgO), and quartz (SiO2)
+        were provided by Kemal Ramic from the ESS Spallation Physics group,
+        based on modelling with Phonopy, VASP and OCLIMAX software.
+      * Missing VDOS curves for 14 mono-atomic materials were added (fixing
+        github issue #39): Au, Ba, Cr, Mg, Mo, Na, Nb, Pd, Pt, Rb, Sc, Sn, Y,
+        and Zn. Refer to comments in the individual NCMAT files for references
+        concerning the origin of these curves.
+      * Missing VDOS curves were added to uranium oxide (UO2), taken from
+        DOI:10.1103/PhysRevB.102.134312. Note that UO2 NCMAT files with VDOS
+        tuned for specific temperatures are available (refer to comments in the
+        UO2 NCMAT file for details).
+      * All existing files with VDOS have been update to NCMAT v4, and had
+        @DEBYETEMPERATURE sections removed in order to benefit from the better
+        performance of getting the atomic displacements from the VDOS.
+      * Added new material: gamma-Iron (Fe_sg225_Iron-gamma.ncmat) with VDOS
+        curve. At the same time, the not particularly useful beta-Iron file was
+        removed, so the NCrystal data library now contains both alpha- and
+        gamma-iron, both with VDOS curves.
+      * Expose debyeIsotropicMSD and debyeTempFromIsotropicMSD functions from
+        NCDebyeMSD.hh header to C and Python, allowing conversions between
+        atomic mean-squared-displacement and Debye temperature.
+      * Improve robustness of the function debyeTempFromIsotropicMSD. Previously
+        the internally deployed root-finding algorithm could fail under some
+        scenarios (e.g. non-ultra cold rubidium).
+      * Various improvements for ncrystal_vdos2ncmat.
+      * Compilation fix for pre-Catalina OSX where the aligned_alloc function is
+        apparently missing.
+      * Fix bug where early calls to removeAllDataSources could get reverted by
+        subsequent plugin loading.
+      * Before defining macros in public headers, check if present already and
+        if so undefine.
+
 v2.5.81 2020-04-01
       * RC2 for incoming release v2.6.0.
 

CMakeLists.txt

@@ -69,7 +69,7 @@ if(NOT DEFINED NCRYSTAL_NOTOUCH_CMAKE_BUILD_TYPE)
 endif()
 
 #Setup project:
-project(NCrystal VERSION 2.5.81 LANGUAGES CXX C)
+project(NCrystal VERSION 2.6.0 LANGUAGES CXX C)
 
 if(NOT DEFINED NCRYSTAL_NOTOUCH_CMAKE_BUILD_TYPE)
   if ("${CMAKE_BUILD_TYPE}" STREQUAL "")

VERSION

@@ -1 +1 @@
-2.5.81
+2.6.0

data/UO2_sg225_Uraninite.ncmat

@@ -13,6 +13,7 @@ NCMAT v4
 #     G. Noguere, J. P. Scotta, S. Xu, A. Filhol, J. Ollivier, E. Farhi,
 #     Y. Calzavarra, S. Rols, B. Fak, J.-M. Zanotti, and Q. Berrod
 #     Phys. Rev. B 102, 134312 - Published 30 October 2020
+#     https://doi.org/10.1103/PhysRevB.102.134312
 #
 # The paper above provided VDOS curves at 300K, 350K, 420K, 600K, 900K, 1200K,
 # and 1675K. Most users will likely get decent performance for materials at most

ncrystal_core/include/NCrystal/NCVersion.hh

@@ -38,10 +38,10 @@
 #endif
 
 #define NCRYSTAL_VERSION_MAJOR 2
-#define NCRYSTAL_VERSION_MINOR 5
-#define NCRYSTAL_VERSION_PATCH 81
-#define NCRYSTAL_VERSION   2005081 /* (1000000*MAJOR+1000*MINOR+PATCH)   */
-#define NCRYSTAL_VERSION_STR "2.5.81"
+#define NCRYSTAL_VERSION_MINOR 6
+#define NCRYSTAL_VERSION_PATCH 0
+#define NCRYSTAL_VERSION   2006000 /* (1000000*MAJOR+1000*MINOR+PATCH)   */
+#define NCRYSTAL_VERSION_STR "2.6.0"
 
 #include "NCrystal/ncapi.h"
 #include <stdexcept>

ncrystal_core/include/NCrystal/internal/NCElIncScatter.hh

@@ -42,8 +42,17 @@ namespace NCrystal {
     const char * name() const noexcept final { return "ElIncScatter"; }
     virtual ~ElIncScatter();
 
-    //Construct from Info:
-    ElIncScatter( const Info& );
+    //Construct from Info. For special use-cases it is possible to apply an
+    //overall cross section scale-factor (>0.0), and to optionally use the total
+    //scattering cross section, rather than just sigma_incoherent:
+    //
+    //Two constructors based on Info objects are available, one taking the MSD
+    //information from AtomInfo, and getting them from integration of VDOS
+    //curves (.
+    struct msd_from_atominfo_t {};
+    struct msd_from_dyninfo_t {};
+    ElIncScatter( msd_from_atominfo_t, const Info&, double scale_factor = 1.0, bool use_total_xsect = false );
+    ElIncScatter( msd_from_dyninfo_t, const Info&, double scale_factor = 1.0, bool use_total_xsect = false );
 
     //Constructor similar to the ElIncXS constructor:
     ElIncScatter( const VectD& elements_meanSqDisp,

ncrystal_core/include/NCrystal/ncrystal.h

@@ -473,10 +473,10 @@ extern "C" {
 #  undef NCRYSTAL_VERSION_STR
 #endif
 #define NCRYSTAL_VERSION_MAJOR 2
-#define NCRYSTAL_VERSION_MINOR 5
-#define NCRYSTAL_VERSION_PATCH 81
-#define NCRYSTAL_VERSION   2005081 /* (1000000*MAJOR+1000*MINOR+PATCH)             */
-#define NCRYSTAL_VERSION_STR "2.5.81"
+#define NCRYSTAL_VERSION_MINOR 6
+#define NCRYSTAL_VERSION_PATCH 0
+#define NCRYSTAL_VERSION   2006000 /* (1000000*MAJOR+1000*MINOR+PATCH)             */
+#define NCRYSTAL_VERSION_STR "2.6.0"
   NCRYSTAL_API int ncrystal_version(); /* returns NCRYSTAL_VERSION                  */
   NCRYSTAL_API const char * ncrystal_version_str(); /* returns NCRYSTAL_VERSION_STR */
 

ncrystal_core/src/NCElIncScatter.cc

@@ -20,17 +20,23 @@
 ////////////////////////////////////////////////////////////////////////////////
 
 #include "NCrystal/internal/NCElIncScatter.hh"
+#include "NCrystal/internal/NCVDOSEval.hh"
 #include "NCrystal/NCInfo.hh"
 #include "NCrystal/internal/NCElIncXS.hh"
 #include "NCrystal/internal/NCRandUtils.hh"
 #include "NCrystal/internal/NCDebyeMSD.hh"
 #include "NCrystal/internal/NCSpan.hh"
+#include "NCrystal/internal/NCDebyeMSD.hh"
+#include <iostream>
+
 namespace NC = NCrystal;
 
 NC::ElIncScatter::~ElIncScatter() = default;
 
-NC::ElIncScatter::ElIncScatter( const Info& ci )
+NC::ElIncScatter::ElIncScatter( msd_from_atominfo_t, const Info& ci, double scale_factor, bool use_total_xsect )
 {
+  nc_assert_always( !(scale_factor<=0.0) );
+
   if ( !ci.hasAtomInfo() )
     NCRYSTAL_THROW(MissingInfo,"Passed Info object lacks AtomInfo information"
                    " (elastic-incoherent model only works with crystalline materials).");
@@ -56,8 +62,11 @@ NC::ElIncScatter::ElIncScatter( const Info& ci )
     ntot += ai.numberPerUnitCell();
 
   for ( const auto& ai : atominfos ) {
-    scale.push_back(double(ai.numberPerUnitCell())/ntot);
-    bixs.push_back(ai.atomData().incoherentXS().get());
+    scale.push_back(double(ai.numberPerUnitCell())*scale_factor/ntot);
+    if (use_total_xsect)
+      bixs.push_back(ai.atomData().scatteringXS().get());
+    else
+      bixs.push_back(ai.atomData().incoherentXS().get());
     if ( ai.msd().has_value() ) {
       msd.push_back( ai.msd().value() );
     } else {
@@ -76,6 +85,45 @@ NC::ElIncScatter::ElIncScatter( const Info& ci )
   m_elincxs = std::make_unique<ElIncXS>( msd, bixs, scale );
 }
 
+NC::ElIncScatter::ElIncScatter( msd_from_dyninfo_t, const Info& info, double scale_factor, bool use_total_xsect )
+{
+  VectD msd, bixs, scale;
+  msd.reserve(info.getDynamicInfoList().size());
+  bixs.reserve(info.getDynamicInfoList().size());
+  scale.reserve(info.getDynamicInfoList().size());
+
+  nc_assert_always( !(scale_factor<=0.0) );
+  unsigned nmissing = 0;
+  for ( auto& di : info.getDynamicInfoList() ) {
+    double msd_value(0.0);
+    if ( dynamic_cast<const DI_VDOS*>(di.get()) ) {
+      msd_value = VDOSEval( static_cast<const DI_VDOS*>(di.get())->vdosData() ).getMSD();
+    } else if ( dynamic_cast<const DI_VDOSDebye*>(di.get()) ) {
+      if ( !info.hasTemperature() )
+        NCRYSTAL_THROW(MissingInfo,"Requested to evaluate atomic mean-squared-displacements for a material without a temperature value.");
+      msd_value = debyeIsotropicMSD( static_cast<const DI_VDOSDebye*>(di.get())->debyeTemperature(),
+                                     info.getTemperature(),
+                                     di->atomData().averageMassAMU() );
+    } else {
+      ++nmissing;
+    }
+    if ( msd_value ) {
+      msd.push_back( msd_value );
+      scale.push_back( di->fraction() * scale_factor );
+      if (use_total_xsect)
+        bixs.push_back(di->atomData().scatteringXS().get());
+      else
+        bixs.push_back(di->atomData().incoherentXS().get());
+    }
+  }
+
+  m_elincxs = std::make_unique<ElIncXS>( msd, bixs, scale );
+
+  if ( nmissing > 0 )
+    std::cout<<"NCrystal WARNING: Requested to create incoherent-elastic component from dynamic information in material where "<<nmissing
+             <<" atom"<<(nmissing==1?"":"s")<<" do not have the necessary information."<<std::endl;
+}
+
 NC::ElIncScatter::ElIncScatter( const VectD& elements_meanSqDisp,
                                 const VectD& elements_boundincohxs,
                                 const VectD& elements_scale )

ncrystal_core/src/NCStdScatFact.cc

@@ -32,6 +32,7 @@
 #include "NCrystal/internal/NCElIncScatter.hh"
 #include "NCrystal/internal/NCSABScatter.hh"
 #include "NCrystal/internal/NCSABFactory.hh"
+#include "NCrystal/internal/NCString.hh"//for safe_str2dbl
 
 namespace NC = NCrystal;
 
@@ -116,9 +117,62 @@ namespace NCrystal {
       if ( cfg.get_incoh_elas() && info.isCrystalline() ) {
         const bool has_msd = info.hasAtomMSD() || ( info.hasTemperature() && info.hasDebyeTemperature() );
         if ( has_msd )
-          components.push_back({1.0,makeSO<ElIncScatter>(info)});
+          components.push_back({1.0,makeSO<ElIncScatter>(ElIncScatter::msd_from_atominfo_t(),info)});
       }
 
+      if ( info.countCustomSections( "SPECIALINCOHELAS" ) > 0 ) {
+        //Special "secret" test code for testing purposes (before we perhaps
+        //decide to make it an official feature). Add @CUSTOM_SPECIALINCOHELAS
+        //section to enable incoherent-elastic treatment in non-crystals.
+        if ( info.countCustomSections( "SPECIALINCOHELAS" ) != 1 )
+          NCRYSTAL_THROW(BadInput,"Only one CUSTOM_SPECIALINCOHELAS section is allowed in input.");
+        bool has_atominfo_msd = info.hasAtomMSD() || ( info.hasTemperature() && info.hasDebyeTemperature() );
+        bool has_dyninfovdos_msd = false;
+        if ( !has_atominfo_msd ) {
+          for ( auto& di : info.getDynamicInfoList() ) {
+            if ( dynamic_cast<const DI_VDOS*>(di.get()) ) {
+              //Allow if even a single VDOS is present (it might for instance be
+              //e.g. H-in-polyethylene where the almost irrelevant C atom is
+              //simply modelled as free gas).
+              has_dyninfovdos_msd = true;
+              break;
+            }
+          }
+        }
+        if (!has_atominfo_msd && !has_dyninfovdos_msd)
+          NCRYSTAL_THROW(BadInput,"Presence of CUSTOM_SPECIALINCOHELAS section requires ability to"
+                         " determine atomic mean squared displacements for all atoms.");
+        if ( info.isCrystalline() )
+          NCRYSTAL_THROW(BadInput,"A @CUSTOM_SPECIALINCOHELAS section can currently only be used when there is otherwise no unit cell information in the input.");
+        if ( cfg.get_incoh_elas() ) {
+          //Decode:
+          //
+          //Syntax is single line with factor (>0.0,<=10.0), followed optionally by the keyword "include_sigma_coh"
+          const auto& cd = info.getCustomSection("SPECIALINCOHELAS");//vector<VectS>
+          if ( cd.size() != 1 )
+            NCRYSTAL_THROW(BadInput,"CUSTOM_SPECIALINCOHELAS section should only have 1 line.");
+          const auto& line = cd.at(0);
+          nc_assert_always(!line.empty());
+          if ( line.empty() || line.size() > 2  )
+            NCRYSTAL_THROW(BadInput,"Bad syntax in CUSTOM_SPECIALINCOHELAS section (too many entries).");
+          double scale_factor;
+          if (!safe_str2dbl( line.at(0), scale_factor ) || !(scale_factor>0.0) || !(scale_factor<=10.0) )
+            NCRYSTAL_THROW(BadInput,"Invalid scale factor in CUSTOM_SPECIALINCOHELAS section. Value should be in interval (0.0,10.0].");
+          bool include_sigma_coh(false);
+          if ( line.size()==2 )  {
+            if ( line.at(1)!="include_sigma_coh" )
+              NCRYSTAL_THROW2(BadInput,"Invalid keyword in CUSTOM_SPECIALINCOHELAS section. Syntax requires either"
+                              " just the scale factor, or a scale factor followed by the keyword \"include_sigma_coh\".");
+            include_sigma_coh = true;
+          }
+          if (has_atominfo_msd)
+            components.push_back({1.0,makeSO<ElIncScatter>(ElIncScatter::msd_from_atominfo_t(),info,scale_factor, include_sigma_coh)});
+          else
+            components.push_back({1.0,makeSO<ElIncScatter>(ElIncScatter::msd_from_dyninfo_t(),info,scale_factor, include_sigma_coh)});
+        }
+      }
+
+
       ///////////////////////////////////////////////////////////////////////////////////////////////////////////
       //Coherent-elastic (Bragg) component:
       if ( cfg.get_coh_elas() && info.isCrystalline() && info.hasHKLInfo() ) {

ncrystal_mcstas/NCrystal_sample.comp

@@ -25,7 +25,7 @@
 * %I
 *
 * Written by: NCrystal developers
-* Version: 2.5.81
+* Version: 2.6.0
 * Origin: NCrystal Developers (European Spallation Source ERIC and DTU Nutech)
 *
 * McStas sample component for the NCrystal scattering library. Find more

ncrystal_python/__init__.py

@@ -52,7 +52,7 @@
 ################################################################################
 
 __license__ = "Apache 2.0, http://www.apache.org/licenses/LICENSE-2.0"
-__version__ = '2.5.81'
+__version__ = '2.6.0'
 __status__ = "Production"
 __author__ = "NCrystal developers (Thomas Kittelmann, Xiao Xiao Cai)"
 __copyright__ = "Copyright 2015-2021 %s"%__author__