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Add variable to specify ZAID-format #187

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merged 8 commits into from
Jan 30, 2023
Merged

Add variable to specify ZAID-format #187

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2777bcc
handle differente zaid conventions in SerpentDepcode
yardasol Jan 18, 2023
e90fe06
update docpages and release notes
yardasol Jan 18, 2023
2c5d14b
add nndc convention
yardasol Jan 18, 2023
fb05f57
add tests
yardasol Jan 18, 2023
0d4b94b
update example inputfiles
yardasol Jan 18, 2023
710516b
update releasenotes
yardasol Jan 18, 2023
62d423b
Merge remote-tracking branch 'upstream/master' into flexible-zaid-con…
yardasol Jan 19, 2023
95de3cc
fix description of zaid_convention in the docpages
yardasol Jan 19, 2023
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16 changes: 16 additions & 0 deletions doc/fileformatspec/depcode_input.rst
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Expand Up @@ -95,6 +95,22 @@ Serpent-specific properties
:pattern:
``^(.\\/)*(.*)$``

``zaid_convention``
~~~~~~~~~~~~~~~~~~~

:description:
ZAID naming convention for nuclide codes. 'serpent': The third digit in ZA for nuclides in isomeric states is 3 (e.g. 47310 for for Ag-110m). 'mcnp': ZA = Z*1000 + A + (300 + 100*m). where m is the mth isomeric state (e.g. 47510 for Ag-110m). 'nndc': Identical to 'mcnp', except Am242m1 is 95242 and Am242 is 95642


:type:
``string``

:enum:
"serpent", "mcnp", "nndc"

:default:
"mcnp"


.. _openmc_specific_properties:

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4 changes: 4 additions & 0 deletions doc/releasenotes/v0.5.0.rst
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Expand Up @@ -64,6 +64,8 @@ Bug Fixes
..
Describe any bug fixes.

- `Fix bug where Serpent2 material temperatures are hardcoded to 900K in the JEFF 3.1.2 library format. <https://github.com/arfc/saltproc/pull/178>`
- `Fix bug where using MCNP-style ZAID codes results in an error in various SerpentDepcode functions <https://github.com/arfc/saltproc/issues/187>`



Expand Down Expand Up @@ -98,6 +100,7 @@ Python API Changes
- Input file format changes:

- Added default values for certain input parameters
- Adds a ``zaid_convention`` input parameter
- Added depletion settings for OpenMC
- ``num_depsteps`` → ``n_depletion_steps``
- ``depcode['template_inputfile_path']`` → ``depcode['template_input_file_path']``
Expand Down Expand Up @@ -167,6 +170,7 @@ Python API Changes
- (new function) → ``get_neutron_settings()``
- (new function) → ``_get_burnable_materials_file()``
- (new function) → ``_get_burnable_material_card_data()``
- (new parameter) → ``zaid_convention``


- ``OpenMCDepcode`` is a ``Depcode`` subclass that interfaces with ``openmc``. This class implements the following functions
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3 changes: 2 additions & 1 deletion examples/msbr/msbr_main.json
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Expand Up @@ -5,7 +5,8 @@
"depcode": {
"codename": "serpent",
"template_input_file_path": "msbr.serpent",
"geo_file_paths": ["geometry/msbr_full.ini"]
"geo_file_paths": ["geometry/msbr_full.ini"],
"zaid_convention": "serpent"
},
"simulation": {
"sim_name": "msbr_kl_100_simulation"
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3 changes: 2 additions & 1 deletion examples/tap/tap_main.json
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Expand Up @@ -21,7 +21,8 @@
"geometry/1338.ini",
"geometry/1498.ini",
"geometry/1668_all.ini"
]
],
"zaid_convention": "serpent"
},
"simulation": {
"sim_name": "tap_example_simulation",
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8 changes: 7 additions & 1 deletion saltproc/input_schema.json
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Expand Up @@ -54,7 +54,13 @@
"exec_path": {
"default": "sss2"},
"template_input_file_path": {
"pattern": "^(.\\/)*(.*)$"}
"pattern": "^(.\\/)*(.*)$"},
"zaid_convention": {
"description": "ZAID naming convention for nuclide codes. 'serpent': The third digit in ZA for nuclides in isomeric states is 3 (e.g. 47310 for for Ag-110m). 'mcnp': ZA = Z*1000 + A + (300 + 100*m). where m is the mth isomeric state (e.g. 47510 for Ag-110m). 'nndc': Identical to 'mcnp', except Am242m1 is 95242 and Am242 is 95642",
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I'm curious why you included NNDC in this, when it looks like your stuff just uses Serpent and OpenMC.

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@yardasol yardasol Jan 20, 2023 •
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NNDC provides cross section libraries using their own ZAID convention for metastable nuclides. It is slightly different than the convention used by cross section libraries shipped with MCNP. Notice that this variable only appears in the depcode object if codename is serpent. This is because Serpent uses ZAID codes to get cross section data for nuclides. This variable has no effect on how OpenMC will handle it's XS libraries, as that is all internally consistent within OpenMC.

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"type": "string",
"enum": ["serpent", "mcnp", "nndc"],
"default": "mcnp"
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}
}
}
},
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79 changes: 59 additions & 20 deletions saltproc/serpent_depcode.py
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Expand Up @@ -41,7 +41,8 @@ def __init__(self,
output_path,
exec_path,
template_input_file_path,
geo_file_paths):
geo_file_paths,
zaid_convention):
"""Initialize a SerpentDepcode object.

Parameters
Expand All @@ -52,10 +53,21 @@ def __init__(self,
Path to Serpent2 executable.
template_input_file_path : str
Path to user input file for Serpent2
geo_file_paths : str or list, optional
geo_file_paths : str or list
Path to file that contains the reactor geometry.
List of `str` if reactivity control by
switching geometry is `On` or just `str` otherwise.
zaid_convention : str
ZAID naming convention for nuclide codes.

'serpent' - The third digit in ZA for nuclides in isomeric states
is 3 (e.g. 47310 for for Ag-110m).

'mcnp' - ZA = Z*1000 + A + (300 + 100*m). where m is the mth
isomeric state (e.g. 47510 for Ag-110m)

'nndc' - Identical to 'mcnp', except Am242m1 is 95242 and Am242
is 95642

"""
super().__init__("serpent",
Expand All @@ -66,6 +78,7 @@ def __init__(self,
self.runtime_inputfile = \
str((output_path / 'runtime_input.serpent').resolve())
self.runtime_matfile = str((output_path / 'runtime_mat.ini').resolve())
self.zaid_convention = zaid_convention

def get_neutron_settings(self, file_lines):
"""Get neutron settings (no. of neutrons per cycle, no. of active and
Expand Down Expand Up @@ -175,20 +188,33 @@ def convert_nuclide_code_to_name(self, nuc_code):
"""

if '.' in str(nuc_code):
nuc_code = pyname.zzzaaa_to_id(int(nuc_code.split('.')[0]))
nuc_code = int(nuc_code.split('.')[0])
if self.zaid_convention == 'serpent':
nuc_code = pyname.zzzaaa_to_id(nuc_code)
if self.zaid_convention in ('mcnp', 'nndc'):
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Consider changing to elif here, then you could add an else statement to make sure self.zaid_convention is an expected value.

if self.zaid_convention == 'mcnp' and nuc_code in (95242, 95642):
if nuc_code == 95242:
nuc_code = 95642
else:
nuc_code = 95242
Comment on lines +195 to +199
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Based on your documentation I thought 95642 was for the NNDC ZAIDs, not the OpenMC ones. This function makes it seem the opposite.

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This has nothing to do with OpenMC. It is all about where the nuclide cross section data is sourced from, since their ZAIDs will have slightly different conventions for metastable isotopes. This is a bit confusing so I'm going to go through this step-by-step.

  1. Recall that the standard nndc convention is identical to the mcnp convention, except in the case of Am-242 and Am-242m. The mcnp convention for ZAIDs of metastable isotopes is ZA = Z * 1000 + (A + 300 + 100*m). This means that Ag-110m has ZA = 47510, and Am-242m has ZA = 95642. In the nndc convention, for whatever reason, the ZA for Am-242m and Am242 are swapped, so ZA(Am242) = 95642, and ZA(Am242m) = 95242.
  2. PyNE's nucname module contains functions for handling ZAID codes. One such function is nucname.mcnp_to_id, which converts the ZAID code in mcnp convention to PyNEs internal id format. However, during testing, I noticed that this function actually converts ZAID codes in nndc convention! That is, will convert 95242 to 952420001, and 95642 to 952420000, but convert everything else normally. So if we are using the mcnp convention, we'll need to input the wrong ZAID code to get the right PyNE id. Does that make sense?

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That all mostly makes sense (I meant to say MCNP, but had OpenMC on my mind when I made the comment, apologies). Just to make sure I understand this correctly:

In MCNP:

  • Am242 = 95242
  • Am242m = 95642
    In NNDC:
  • Am242 = 95642
  • Am242m = 95242.

Your function here says that if you are using MCNP and you give it 95242 (Am242 in MCNP), then it converts it to 95642 (Am242m in MCNP). If you give it 95642 (Am242m in MCNP), then it converts it to 95242 (Am242). So that gets switched. This assumes that you are providing NNDC nomenclature and trying to use MCNP. What if you are using MCNP nomenclature already and don't need to switch it?

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You have the first right.

This assumes that you are providing NNDC nomenclature and trying to use MCNP. What if you are using MCNP nomenclature already and don't need to switch it?

The reason we do the swap is because PyNE assumes an nndc format for nucname.mcnp_to_id and other mcnp-related functions. That is, there is a discrepancy between our understanding of the mncp convention and what PyNE's understanding of the mcnp convention. PyNE's mcnp convention is equivalent to our nndc convention. So if we want to use our mcnp convention, we have to swap the ZAIDs for Am242 and Am242m that we input into the mcnp-related functions in PyNE to get the correct outputs (ZAIDs and nuclide names).

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That makes sense. I'm making sure that there is no situation in which these ZAIDs would be switched when they don't have to be.

nuc_code = pyname.mcnp_to_id(nuc_code)

zz = pyname.znum(nuc_code)
aa = pyname.anum(nuc_code)
aa_str = str(aa)
if aa > 300:
if zz > 76:
aa_str = str(aa - 100) + 'm1'
aa = aa - 100
else:
aa_str = str(aa - 200) + 'm1'
aa = aa - 200
nuc_zzaaam = str(zz) + str(aa) + '1'
elif aa == 0:
aa_str = 'nat'
if self.zaid_convention == 'serpent':
if aa > 300:
if zz > 76:
aa_str = str(aa - 100) + 'm1'
else:
aa_str = str(aa - 200) + 'm1'
elif aa == 0:
aa_str = 'nat'
if self.zaid_convention in ('mcnp', 'nndc'):
mm = pyname.snum(nuc_code)
if mm != 0:
aa_str = str(aa) + f'm{mm}'

nuc_name = pyname.zz_name[zz] + aa_str
else:
meta_flag = pyname.snum(nuc_code)
Expand Down Expand Up @@ -233,10 +259,23 @@ def map_nuclide_code_zam_to_serpent(self):
line = line.split()
nuc_code = line[2]
if '.' in str(nuc_code):
nuc_code = pyname.zzzaaa_to_id(int(nuc_code.split('.')[0]))

zzaaam = \
self.convert_nuclide_code_to_zam(pyname.zzaaam(nuc_code))
nuc_code = int(nuc_code.split('.')[0])
# In MCNP format the ground state of Am-242 is 95242,
# but PyNE seems to disagree
if self.zaid_convention == 'serpent':
nuc_code = pyname.zzzaaa_to_id(nuc_code)
zzaaam = \
self.convert_nuclide_code_to_zam(pyname.zzaaam(nuc_code))
if self.zaid_convention == 'nndc' or self.zaid_convention == 'mcnp':
if self.zaid_convention == 'mcnp' and nuc_code in (95242, 95642):
if nuc_code == 95242:
nuc_code = 95642
else:
nuc_code = 95242
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nuc_code = pyname.mcnp_to_id(nuc_code)
zzaaam = pyname.zzaaam(nuc_code)
else:
zzaaam = int(nuc_code)

nuc_code_map.update({zzaaam: line[2]})
return nuc_code_map
Expand Down Expand Up @@ -436,15 +475,15 @@ def run_depletion_step(self, cores, nodes):
args = (self.exec_path, '-omp', str(cores), self.runtime_inputfile)
print('Running %s' % (self.codename))
try:
subprocess.check_output(
subprocess.run(
args,
cwd=os.path.split(self.template_input_file_path)[0],
stderr=subprocess.STDOUT)
capture_output=True)
print('Finished Serpent2 Run')
except subprocess.CalledProcessError as error:
print(error.output.decode("utf-8"))
raise RuntimeError('\n %s RUN FAILED\n see error message above'
% (self.codename))
print('Finished Serpent2 Run')

def convert_nuclide_code_to_zam(self, nuc_code):
"""Converts nuclide code from Serpent2 format to zam format.
Expand Down
3 changes: 2 additions & 1 deletion tests/integration_tests/run_constant_reprocessing/tap_input.json
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Expand Up @@ -5,7 +5,8 @@
"depcode": {
"codename": "serpent",
"template_input_file_path": "tap_template.ini",
"geo_file_paths": ["tap_geometry_base.ini"]
"geo_file_paths": ["tap_geometry_base.ini"],
"zaid_convention": "serpent"
},
"simulation": {
"sim_name": "tap_constant_reprocessing"
Expand Down
3 changes: 2 additions & 1 deletion tests/integration_tests/run_no_reprocessing/test_input.json
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Expand Up @@ -5,7 +5,8 @@
"depcode": {
"codename": "serpent",
"template_input_file_path": "test_input.ini",
"geo_file_paths": ["../../serpent_data/tap_geometry_base.ini"]
"geo_file_paths": ["../../serpent_data/tap_geometry_base.ini"],
"zaid_convention": "serpent"
},
"simulation": {
"sim_name": "test_no_reprocessing",
Expand Down
3 changes: 2 additions & 1 deletion tests/serpent_data/tap_input.json
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Expand Up @@ -5,7 +5,8 @@
"depcode": {
"codename": "serpent",
"template_input_file_path": "tap_template.ini",
"geo_file_paths": ["tap_geometry_base.ini"]
"geo_file_paths": ["tap_geometry_base.ini"],
"zaid_convention": "serpent"
},
"simulation": {
"sim_name": "tap_test_simulation_serpent"
Expand Down
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