ncrystal_endf2ncmat issue

[ramic-k]

Hi Thomas,

I think I have found an issue when converting ENDF to .NCMAT

The command used was: ncrystal_endf2ncmat tsl-H_in_MgH2_sg136_Magnesium_Hydride-iel98.endf --secondary tsl-Mg_in_MgH2_sg136_Magnesium_Hydride-iel98.endf:1/3 --outbn MgH2_converted

and the error was:

ncrystal_endf2ncmat tsl-H_in_MgH2_sg136_Magnesium_Hydride-iel98.endf --secondary tsl-Mg_in_MgH2_sg136_Magnesium_Hydride-iel98.endf:1/3 --outbn MgH2_converted Attempting to load ENDF file tsl-H_in_MgH2_sg136_Magnesium_Hydride-iel98.endf... Reading MF=1, MT=451 Descriptive Data Reading MF=7, MT=2 (z,elastic) Reading MF=7, MT=4 (z,n) Performing a few sanity checks... Traceback (most recent call last): File "/home/kemal/Desktop/final_njoy_ncrystal/install/bin/ncrystal_endf2ncmat", line 577, in <module> p1=parse_endf_file(args.ENDFFILE) File "/home/kemal/Desktop/final_njoy_ncrystal/install/bin/ncrystal_endf2ncmat", line 215, in parse_endf_file element_name=guessElementName(data.target['ZA'],data.target['mass']) File "/home/kemal/Desktop/final_njoy_ncrystal/install/bin/ncrystal_endf2ncmat", line 115, in guessElementName guess_by_mass = guessElementFromMass(mass_amu) File "/home/kemal/Desktop/final_njoy_ncrystal/install/bin/ncrystal_endf2ncmat", line 98, in guessElementFromMass elem_data=[ (abs(d.averageMassAMU()-mass_amu),d) for d in [NCrystal.atomDB(z,throwOnErrors=False) for z in range(1,120)] if d ] File "/home/kemal/Desktop/final_njoy_ncrystal/install/bin/ncrystal_endf2ncmat", line 98, in <listcomp> elem_data=[ (abs(d.averageMassAMU()-mass_amu),d) for d in [NCrystal.atomDB(z,throwOnErrors=False) for z in range(1,120)] if d ] File "/home/kemal/Desktop/final_njoy_ncrystal/install/share/NCrystal/python/NCrystal/__init__.py", line 1932, in atomDB rawatomdata=_rawfct['ncrystal_create_atomdata_fromdb'](*key) File "/home/kemal/Desktop/final_njoy_ncrystal/install/share/NCrystal/python/NCrystal/__init__.py", line 256, in fcte _raise_err() File "/home/kemal/Desktop/final_njoy_ncrystal/install/share/NCrystal/python/NCrystal/__init__.py", line 234, in _raise_err raise e NCrystal.NCBadInput: Attempt to initialise shared_obj<T> object with null pointer is illegal

[tkittel]

Thanks @ramic-k . It will be a few weeks before I can take a look, please provide the relevant input files for reproducing the problem (a url or attached here?).

[tkittel]

And I assume it was NCrystal v2.6.1?

[ramic-k]

Yup, the latest and greatest version of NCrystal.

tsl-H_in_MgH2_sg136_Magnesium_Hydride-iel98_endf.txt tsl-Mg_in_MgH2_sg136_Magnesium_Hydride-iel98_endf.txt

[tkittel]

So I found the issue in ncrystal.cc, but there is another issue with your input files, you have messed up the text section near the top, in lines 35+36+43:

12 ******************************************************************   8 1451   11
 13 *                                                                *   8 1451   12
 14 *  Generated with NJOY+NCrystal                                  *   8 1451   13
 15 *                                                                *   8 1451   14
 16 ******************************************************************   8 1451   15
 17 *                                                                *   8 1451   16
 18 *  Temperatures:                                                 *   8 1451   17
 19 *       296.0 K                                                  *   8 1451   18
 20 *                                                                *   8 1451   19
 21 ******************************************************************   8 1451   20
 22 *                                                                *   8 1451   21
 23  *Crystal structure obtained from:                               *   8 1451   22
 24 * https://www.materialsproject.org/materials/mp-23710/           *   8 1451   23
 25 *                                                                *   8 1451   24
 26 * Phonon spectrum calculations were performed, by Davide Campi   *   8 1451   25
 27 * and Marco Bernasconi from University of Milano-Bicocca, within *   8 1451   26
 28 * Density Functional Perturbation Theory (DFPT) by using the     *   8 1451   27
 29 * Perdew-Burke- Ernzerhof (PBE) approximation to the exchange    *   8 1451   28
 30 * and correlation energy functional. Ultrasoft pseudo-potentials *   8 1451   29
 31 * and a plane wave expansion of Kohn-Sham orbitals up to a       *   8 1451   30
 32 * kinetic cutoff of 60 Ry was employed, as implemented in the    *   8 1451   31
 33 * Quantum-ESPRESSO package.                                      *   8 1451   32
 34 * In the electronic structure calculations, the Brillouin zone   *   8 1451   33
 35 * (BZ) integration was performed over a uniform Γ-centered          8 1451   34
 36 * 10×10×14 k-point mesh [16].                                      8 1451   35
 37 *                                                                *   8 1451   36
 38 * References:                                                    *   8 1451   37
 39 *                                                                *   8 1451   38
 40 *  [1]: "Phonons and related crystal properties from             *   8 1451   39
 41 *       density-functional perturbation theory"                  *   8 1451   40
 42 *       Baroni, S., De Gironcoli, S., Dal Corso, A.,             *   8 1451   41
 43 *       Giannozzi, P. Reviews of Modern Physics 73, 515–562.       8 1451   42
 44 *       doi: 10. 1103/RevModPhys.73.515 , arXiv:0012092v1        *   8 1451   43
 45 *  [2]: "QUANTUM ESPRESSO: a modular and open-source software    *   8 1451   44
 46 *       project for quantum simulations of materials"            *   8 1451   45
 47 *       Giannozzi, P., Baroni, S., et al.,                       *   8 1451   46
 48 *       2009. Q. J. Phys.: Condens. Mat- ter 21, 395502.         *   8 1451   47
 49 *                                                                *   8 1451   48
 50 ******************************************************************   8 1451   49

Fixing it up by hand, everything seems to work. I also changes the Γ to spell out "Gamma", since I am not convinced that Fortran code will appreciate the multi-byte characters. In fact, you should probably check that the file is pure ascii and not utf-8 (you can run the command "file myfilename.endf". If it says UTF-8, you are not done yet.

And a few lines further down the file you have the most serious issue yet: Once again my surname is mis-spelled!!! ;-)

I'll post the fix for ncrystal.cc here shortly, in case you need if before NCrystal v2.7.0 is out.

[ramic-k]

Thanks Thomas! You are saving me a lot of hassle here :D

We shall be regenerating all the files soon, so any typos shall be fixed, including your glorious surname.

[tkittel]

For reference the fixes needed for ncrystal.cc and ncrystal_endf2ncmat are pasted here, in case you can't wait 1-2 days for NCrystal v2.7.0:

@@ -1448,7 +1448,9 @@ void ncrystal_info_getcomponent( ncrystal_info_t ci, unsigned icomponent,
 ncrystal_atomdata_t ncrystal_create_atomdata_fromdb( unsigned z, unsigned a )
 {
   try {
-    return ncc::createNewCHandle<ncc::Wrapped_AtomData>( NC::AtomDB::getIsotopeOrNatElem(z,a) );
+    auto opt_atomdatasp = NC::AtomDB::getIsotopeOrNatElem(z,a);
+    if ( opt_atomdatasp != nullptr )
+      return ncc::createNewCHandle<ncc::Wrapped_AtomData>( std::move(opt_atomdatasp) );
   } NCCATCH;
   return {nullptr};
 }
@@ -1463,8 +1465,11 @@ ncrystal_atomdata_t ncrystal_create_atomdata_fromdbstr( const char* name )
       z = symb.Z();
       a = symb.A();
     }
-    if (z)
-      return ncc::createNewCHandle<ncc::Wrapped_AtomData>( NC::AtomDB::getIsotopeOrNatElem(z,a) );
+    if (z) {
+      auto opt_atomdatasp = NC::AtomDB::getIsotopeOrNatElem(z,a);
+      if ( opt_atomdatasp != nullptr )
+        return ncc::createNewCHandle<ncc::Wrapped_AtomData>( std::move(opt_atomdatasp) );
+    }
   } NCCATCH;
   return {nullptr};
 }

And

@@ -113,7 +113,7 @@ def guessElementName(ZA,mass_amu):
     if ZA in (112,113):
         return 'D'#ortho-D or para-D
     guess_by_mass = guessElementFromMass(mass_amu)
-    guess_by_z = elementZToName(z) if (z>0 and z<120) else None
+    guess_by_z = elementZToName(Z) if (Z>0 and Z<120) else None
     if guess_by_z:
         if guess_by_z!=guess_by_mass:
             raise SystemExit(f"ERROR: Mass and Z guess gives different element name (Z={Z}=>'{guess_by_z}', mass={mass_amu}amu=>'{guess_by_mass}')")

[tkittel]

NCrystal v2.7.0 is out, closing here.