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Merge pull request #705 from paulromano/anl-ne-requests

Browse source 
An assortment of fixes
This commit is contained in:
Will Boyd 2016-08-18 19:06:54 -04:00 • committed by GitHub
commit e35b01d9ab
11 changed files with 129 additions and 107 deletions
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14
docs/source/usersguide/install.rst
View file

@ -204,20 +204,22 @@ should be used:
Compiling with MPI
++++++++++++++++++
To compile with MPI, set the :envvar:`FC` environment variable to the path to
the MPI Fortran wrapper. For example, in a bash shell:
To compile with MPI, set the :envvar:`FC` and :envvar:`CC` environment variables
to the path to the MPI Fortran and C wrappers, respectively. For example, in a
bash shell:
.. code-block:: sh
export FC=mpif90
export CC=mpicc
cmake /path/to/openmc
Note that in many shells, an environment variable can be set for a single
command, i.e.
Note that in many shells, environment variables can be set for a single command,
i.e.
.. code-block:: sh
FC=mpif90 cmake /path/to/openmc
FC=mpif90 CC=mpicc cmake /path/to/openmc
Selecting HDF5 Installation
+++++++++++++++++++++++++++
@ -343,7 +345,7 @@ compiler, it is necessary to specify that all objects be compiled with the
.. code-block:: sh
mkdir build && cd build
FC=ifort FFLAGS=-mmic cmake -Dopenmp=on ..
FC=ifort CC=icc FFLAGS=-mmic cmake -Dopenmp=on ..
make
Note that unless an HDF5 build for the Intel Xeon Phi is already on your target

1
openmc/data/thermal.py
View file

@ -33,6 +33,7 @@ _THERMAL_NAMES = {'al': 'c_Al27', 'al27': 'c_Al27',
'orthod': 'c_ortho_D', 'dortho': 'c_ortho_D',
'orthoh': 'c_ortho_H', 'hortho': 'c_ortho_H',
'ouo2': 'c_O_in_UO2', 'o2-u': 'c_O_in_UO2', 'o2/u': 'c_O_in_UO2',
'sio2': 'c_SiO2',
'parad': 'c_para_D', 'dpara': 'c_para_D',
'parah': 'c_para_H', 'hpara': 'c_para_H',
'sch4': 'c_solid_CH4', 'smeth': 'c_solid_CH4',

3
openmc/mgxs/mdgxs.py
View file

@ -793,7 +793,8 @@ class MDGXS(MGXS):
df.rename(columns={'energyout low [MeV]': 'group out'},
inplace=True)
out_groups = np.tile(all_groups, int(df.shape[0] / all_groups.size))
out_groups = np.repeat(all_groups, self.xs_tally.num_scores)
out_groups = np.tile(out_groups, int(df.shape[0] / out_groups.size))
df['group out'] = out_groups
del df['energyout high [MeV]']
columns = ['group in', 'group out']

21
openmc/mgxs/mgxs.py
View file

@ -548,12 +548,6 @@ class MGXS(object):
float
The atomic number density (atom/b-cm) for the nuclide of interest
Raises
-------
ValueError
When the density is requested for a nuclide which is not found in
the spatial domain.
"""
cv.check_type('nuclide', nuclide, basestring)
@ -561,13 +555,7 @@ class MGXS(object):
# Get list of all nuclides in the spatial domain
nuclides = self.domain.get_nuclide_densities()
if nuclide not in nuclides:
msg = 'Unable to get density for nuclide "{0}" which is not in ' \
'{1} "{2}"'.format(nuclide, self.domain_type, self.domain.id)
ValueError(msg)
density = nuclides[nuclide][1]
return density
return nuclides[nuclide][1] if nuclide in nuclides else 0.0
def get_nuclide_densities(self, nuclides='all'):
"""Get an array of atomic number densities in units of atom/b-cm for all
@ -1535,7 +1523,8 @@ class MGXS(object):
df.rename(columns={'energyout low [MeV]': 'group out'},
inplace=True)
out_groups = np.tile(all_groups, int(df.shape[0] / all_groups.size))
out_groups = np.repeat(all_groups, self.xs_tally.num_scores)
out_groups = np.tile(out_groups, int(df.shape[0] / out_groups.size))
df['group out'] = out_groups
del df['energyout high [MeV]']
columns = ['group in', 'group out']
@ -1573,6 +1562,10 @@ class MGXS(object):
df['mean'] /= np.tile(densities, tile_factor)
df['std. dev.'] /= np.tile(densities, tile_factor)
# Replace NaNs by zeros (happens if nuclide density is zero)
df['mean'].replace(np.nan, 0.0, inplace=True)
df['std. dev.'].replace(np.nan, 0.0, inplace=True)
# Sort the dataframe by domain type id (e.g., distribcell id) and
# energy groups such that data is from fast to thermal
if self.domain_type == 'mesh':

19
openmc/volume.py
View file

@ -1,6 +1,7 @@
from collections import Iterable, Mapping
from numbers import Real, Integral
from xml.etree import ElementTree as ET
from warnings import warn
import numpy as np
import pandas as pd
@ -68,10 +69,26 @@ class VolumeCalculation(object):
self.samples = samples
if lower_left is not None:
self.lower_left = lower_left
if upper_right is None:
raise ValueError('Both lower-left and upper-right coordinates '
'should be specified')
# For cell domains, try to compute bounding box and make sure
# user-specified one is valid
if self.domain_type == 'cell':
for c in domains:
if c.region is None:
continue
ll, ur = c.region.bounding_box
if np.any(np.isinf(ll)) or np.any(np.isinf(ur)):
continue
if (np.any(np.asarray(lower_left) > ll) or
np.any(np.asarray(upper_right) < ur)):
warn("Specified bounding box is smaller than computed "
"bounding box for cell {}. Volume calculation may "
"be incorrect!".format(c.id))
self.lower_left = lower_left
self.upper_right = upper_right
else:
if self.domain_type == 'cell':

3
src/constants.F90
View file

@ -54,7 +54,8 @@ module constants
! Maximum number of external source spatial resamples to encounter before an
! error is thrown.
integer, parameter :: MAX_EXTSRC_RESAMPLES = 10000
integer, parameter :: EXTSRC_REJECT_THRESHOLD = 10000
real(8), parameter :: EXTSRC_REJECT_FRACTION = 0.05
! ============================================================================
! PHYSICAL CONSTANTS

2
src/relaxng/settings.rnc
View file

@ -153,7 +153,7 @@ element settings {
attribute lower_left { list { xsd:double+ } }) &
(element upper_right { list { xsd:double+ } } |
attribute upper_right { list { xsd:double+ } })
}+ &
}* &
element uniform_fs{
(element dimension { list { xsd:positiveInteger+ } } |

4
src/relaxng/settings.rng
View file

@ -625,7 +625,7 @@
<data type="positiveInteger"/>
</element>
</optional>
<oneOrMore>
<zeroOrMore>
<element name="volume_calc">
<interleave>
<choice>
@ -694,7 +694,7 @@
</choice>
</interleave>
</element>
</oneOrMore>
</zeroOrMore>
<optional>
<element name="uniform_fs">
<interleave>

23
src/source.F90
View file

@ -107,7 +107,8 @@ contains
real(8) :: r(3) ! sampled coordinates
logical :: found ! Does the source particle exist within geometry?
type(Particle) :: p ! Temporary particle for using find_cell
integer, save :: num_resamples = 0 ! Number of resamples encountered
integer, save :: n_accept = 0 ! Number of samples accepted
integer, save :: n_reject = 0 ! Number of samples rejected
! Set weight to one by default
site % wgt = ONE
@ -143,13 +144,6 @@ contains
! Now search to see if location exists in geometry
call find_cell(p, found)
if (.not. found) then
num_resamples = num_resamples + 1
if (num_resamples == MAX_EXTSRC_RESAMPLES) then
call fatal_error("Maximum number of external source spatial &
&resamples reached!")
end if
end if
! Check if spatial site is in fissionable material
select type (space => external_source(i) % space)
@ -162,8 +156,21 @@ contains
end if
end if
end select
! Check for rejection
if (.not. found) then
n_reject = n_reject + 1
if (n_reject >= EXTSRC_REJECT_THRESHOLD .and. &
real(n_accept, 8)/n_reject <= EXTSRC_REJECT_FRACTION) then
call fatal_error("More than 95% of external source sites sampled &
&were rejected. Please check your external source definition.")
end if
end if
end do
! Increment number of accepted samples
n_accept = n_accept + 1
call p % clear()
! Sample angle

144
tests/test_mgxs_library_no_nuclides/results_true.dat
View file

@ -29,39 +29,39 @@
1 10000 1 total 0.385188 0.026946
0 10000 2 total 0.412389 0.015425
material group in group out nuclide moment mean std. dev.
9 10000 1 1 total P0 -0.000207 0.000149
11 10000 1 1 total P1 0.000234 0.000128
13 10000 1 1 total P2 0.051870 0.006983
12 10000 1 1 total P0 0.384199 0.027001
13 10000 1 1 total P1 0.051870 0.006983
14 10000 1 1 total P2 0.020069 0.002846
15 10000 1 1 total P3 0.009478 0.002234
8 10000 1 2 total P0 0.000989 0.000482
10 10000 1 2 total P1 -0.000103 0.000184
12 10000 1 2 total P2 0.384199 0.027001
14 10000 1 2 total P3 0.020069 0.002846
1 10000 2 1 total P0 0.016482 0.004502
3 10000 2 1 total P1 -0.010499 0.010438
5 10000 2 1 total P2 -0.000768 0.000768
9 10000 1 2 total P1 -0.000207 0.000149
10 10000 1 2 total P2 -0.000103 0.000184
11 10000 1 2 total P3 0.000234 0.000128
4 10000 2 1 total P0 0.000925 0.000925
5 10000 2 1 total P1 -0.000768 0.000768
6 10000 2 1 total P2 0.000494 0.000494
7 10000 2 1 total P3 -0.000171 0.000172
0 10000 2 2 total P0 0.411465 0.015245
2 10000 2 2 total P1 0.006371 0.010551
4 10000 2 2 total P2 0.000925 0.000925
6 10000 2 2 total P3 0.000494 0.000494
1 10000 2 2 total P1 0.016482 0.004502
2 10000 2 2 total P2 0.006371 0.010551
3 10000 2 2 total P3 -0.010499 0.010438
material group in group out nuclide moment mean std. dev.
9 10000 1 1 total P0 -0.000207 0.000149
11 10000 1 1 total P1 0.000234 0.000128
13 10000 1 1 total P2 0.051870 0.006983
12 10000 1 1 total P0 0.384199 0.027001
13 10000 1 1 total P1 0.051870 0.006983
14 10000 1 1 total P2 0.020069 0.002846
15 10000 1 1 total P3 0.009478 0.002234
8 10000 1 2 total P0 0.000989 0.000482
10 10000 1 2 total P1 -0.000103 0.000184
12 10000 1 2 total P2 0.384199 0.027001
14 10000 1 2 total P3 0.020069 0.002846
1 10000 2 1 total P0 0.016482 0.004502
3 10000 2 1 total P1 -0.010499 0.010438
5 10000 2 1 total P2 -0.000768 0.000768
9 10000 1 2 total P1 -0.000207 0.000149
10 10000 1 2 total P2 -0.000103 0.000184
11 10000 1 2 total P3 0.000234 0.000128
4 10000 2 1 total P0 0.000925 0.000925
5 10000 2 1 total P1 -0.000768 0.000768
6 10000 2 1 total P2 0.000494 0.000494
7 10000 2 1 total P3 -0.000171 0.000172
0 10000 2 2 total P0 0.411465 0.015245
2 10000 2 2 total P1 0.006371 0.010551
4 10000 2 2 total P2 0.000925 0.000925
6 10000 2 2 total P3 0.000494 0.000494
1 10000 2 2 total P1 0.016482 0.004502
2 10000 2 2 total P2 0.006371 0.010551
3 10000 2 2 total P3 -0.010499 0.010438
material group in group out nuclide mean std. dev.
3 10000 1 1 total 1.0 0.078516
2 10000 1 2 total 1.0 0.687184
@ -154,39 +154,39 @@
1 10001 1 total 0.310121 0.033788
0 10001 2 total 0.296264 0.043792
material group in group out nuclide moment mean std. dev.
9 10001 1 1 total P0 0.000000 0.000000
11 10001 1 1 total P1 0.000000 0.000000
13 10001 1 1 total P2 0.038230 0.008484
12 10001 1 1 total P0 0.310121 0.033788
13 10001 1 1 total P1 0.038230 0.008484
14 10001 1 1 total P2 0.020745 0.004696
15 10001 1 1 total P3 0.007964 0.003732
8 10001 1 2 total P0 0.000000 0.000000
10 10001 1 2 total P1 0.000000 0.000000
12 10001 1 2 total P2 0.310121 0.033788
14 10001 1 2 total P3 0.020745 0.004696
1 10001 2 1 total P0 -0.011214 0.016180
3 10001 2 1 total P1 -0.003270 0.007329
5 10001 2 1 total P2 0.000000 0.000000
9 10001 1 2 total P1 0.000000 0.000000
10 10001 1 2 total P2 0.000000 0.000000
11 10001 1 2 total P3 0.000000 0.000000
4 10001 2 1 total P0 0.000000 0.000000
5 10001 2 1 total P1 0.000000 0.000000
6 10001 2 1 total P2 0.000000 0.000000
7 10001 2 1 total P3 0.000000 0.000000
0 10001 2 2 total P0 0.296264 0.043792
2 10001 2 2 total P1 0.008837 0.011504
4 10001 2 2 total P2 0.000000 0.000000
6 10001 2 2 total P3 0.000000 0.000000
1 10001 2 2 total P1 -0.011214 0.016180
2 10001 2 2 total P2 0.008837 0.011504
3 10001 2 2 total P3 -0.003270 0.007329
material group in group out nuclide moment mean std. dev.
9 10001 1 1 total P0 0.000000 0.000000
11 10001 1 1 total P1 0.000000 0.000000
13 10001 1 1 total P2 0.038230 0.008484
12 10001 1 1 total P0 0.310121 0.033788
13 10001 1 1 total P1 0.038230 0.008484
14 10001 1 1 total P2 0.020745 0.004696
15 10001 1 1 total P3 0.007964 0.003732
8 10001 1 2 total P0 0.000000 0.000000
10 10001 1 2 total P1 0.000000 0.000000
12 10001 1 2 total P2 0.310121 0.033788
14 10001 1 2 total P3 0.020745 0.004696
1 10001 2 1 total P0 -0.011214 0.016180
3 10001 2 1 total P1 -0.003270 0.007329
5 10001 2 1 total P2 0.000000 0.000000
9 10001 1 2 total P1 0.000000 0.000000
10 10001 1 2 total P2 0.000000 0.000000
11 10001 1 2 total P3 0.000000 0.000000
4 10001 2 1 total P0 0.000000 0.000000
5 10001 2 1 total P1 0.000000 0.000000
6 10001 2 1 total P2 0.000000 0.000000
7 10001 2 1 total P3 0.000000 0.000000
0 10001 2 2 total P0 0.296264 0.043792
2 10001 2 2 total P1 0.008837 0.011504
4 10001 2 2 total P2 0.000000 0.000000
6 10001 2 2 total P3 0.000000 0.000000
1 10001 2 2 total P1 -0.011214 0.016180
2 10001 2 2 total P2 0.008837 0.011504
3 10001 2 2 total P3 -0.003270 0.007329
material group in group out nuclide mean std. dev.
3 10001 1 1 total 1.0 0.108779
2 10001 1 2 total 0.0 0.000000
@ -279,39 +279,39 @@
1 10002 1 total 0.671269 0.026186
0 10002 2 total 2.035388 0.258060
material group in group out nuclide moment mean std. dev.
9 10002 1 1 total P0 0.008758 0.000926
11 10002 1 1 total P1 -0.003785 0.000817
13 10002 1 1 total P2 0.381167 0.016243
12 10002 1 1 total P0 0.639901 0.024709
13 10002 1 1 total P1 0.381167 0.016243
14 10002 1 1 total P2 0.152392 0.008156
15 10002 1 1 total P3 0.009148 0.003889
8 10002 1 2 total P0 0.031368 0.001728
10 10002 1 2 total P1 -0.002568 0.001014
12 10002 1 2 total P2 0.639901 0.024709
14 10002 1 2 total P3 0.152392 0.008156
1 10002 2 1 total P0 0.509941 0.051236
3 10002 2 1 total P1 0.024988 0.008312
5 10002 2 1 total P2 0.000400 0.000401
9 10002 1 2 total P1 0.008758 0.000926
10 10002 1 2 total P2 -0.002568 0.001014
11 10002 1 2 total P3 -0.003785 0.000817
4 10002 2 1 total P0 0.000443 0.000445
5 10002 2 1 total P1 0.000400 0.000401
6 10002 2 1 total P2 0.000320 0.000321
7 10002 2 1 total P3 0.000214 0.000215
0 10002 2 2 total P0 2.034945 0.257800
2 10002 2 2 total P1 0.111175 0.013020
4 10002 2 2 total P2 0.000443 0.000445
6 10002 2 2 total P3 0.000320 0.000321
1 10002 2 2 total P1 0.509941 0.051236
2 10002 2 2 total P2 0.111175 0.013020
3 10002 2 2 total P3 0.024988 0.008312
material group in group out nuclide moment mean std. dev.
9 10002 1 1 total P0 0.008758 0.000926
11 10002 1 1 total P1 -0.003785 0.000817
13 10002 1 1 total P2 0.381167 0.016243
12 10002 1 1 total P0 0.639901 0.024709
13 10002 1 1 total P1 0.381167 0.016243
14 10002 1 1 total P2 0.152392 0.008156
15 10002 1 1 total P3 0.009148 0.003889
8 10002 1 2 total P0 0.031368 0.001728
10 10002 1 2 total P1 -0.002568 0.001014
12 10002 1 2 total P2 0.639901 0.024709
14 10002 1 2 total P3 0.152392 0.008156
1 10002 2 1 total P0 0.509941 0.051236
3 10002 2 1 total P1 0.024988 0.008312
5 10002 2 1 total P2 0.000400 0.000401
9 10002 1 2 total P1 0.008758 0.000926
10 10002 1 2 total P2 -0.002568 0.001014
11 10002 1 2 total P3 -0.003785 0.000817
4 10002 2 1 total P0 0.000443 0.000445
5 10002 2 1 total P1 0.000400 0.000401
6 10002 2 1 total P2 0.000320 0.000321
7 10002 2 1 total P3 0.000214 0.000215
0 10002 2 2 total P0 2.034945 0.257800
2 10002 2 2 total P1 0.111175 0.013020
4 10002 2 2 total P2 0.000443 0.000445
6 10002 2 2 total P3 0.000320 0.000321
1 10002 2 2 total P1 0.509941 0.051236
2 10002 2 2 total P2 0.111175 0.013020
3 10002 2 2 total P3 0.024988 0.008312
material group in group out nuclide mean std. dev.
3 10002 1 1 total 1.0 0.038609
2 10002 1 2 total 1.0 0.067667

2
tests/test_mgxs_library_nuclides/results_true.dat
View file

@ -1 +1 @@
8142ae4e107002a835999e4ace85c17376f262a7059fc224f3756a2de19aba6ca4c4fa14ca2085c87d7729aa8d6d6f78fdae21ac6dfe33ca303449c769076074
e494320a213b5704a2ac915a2ba504857be91961ceb6735b6ad05d81eb31c44c9584d5bd9d40baececf1dcb5b030e6ecec63cfbd20639baf69bcb596c5c46591