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qiangshuqiangshu
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Enhance tracer module handling
Summarize tracer modules and number of tracers according to the module section at the begining of the yaml file. Add module id and number of tracers checking for each open boundary that has tracer specification
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Lines changed: 71 additions & 31 deletions

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‎schimpy/bctide.py‎

Lines changed: 71 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,6 @@
1111
import numbers
1212
import numpy as np
1313
import click
14-
import datetime
1514

1615

1716
__all__ = ["load_boundary"]
@@ -210,10 +209,32 @@ def __init__(self, hgrid,bc_yaml=None,boundary_segments=None):
210209
"none": 0,
211210
}
212211

213-
## also reading tracer modules defined in the bctides yaml here
212+
## also read in tracer modules defined in the bctides yaml here
214213
self.tracer_modules = bc_yaml.get("modules", [])
215-
216-
214+
## find out number of tracer modules and set up tracer order list
215+
## accroding to the self.tracer_lst defined above, if module not found
216+
## module section in yaml file looks like:
217+
## modules:
218+
## - name: GEN
219+
## num_tracers: 1
220+
## - name: SED
221+
## num_tracers: 5
222+
223+
self.tracer_mod_pos = {}
224+
self.tracer_mod_num = {}
225+
tracer_mods = []
226+
for mod in self.tracer_modules:
227+
mod_id = mod.get("name")
228+
num_tracers = mod.get("num_tracers", 0)
229+
if mod_id in self.tracer_lst.keys():
230+
tracer_mods.append(mod_id)
231+
self.tracer_mod_num[mod_id] = num_tracers
232+
else:
233+
raise ValueError("tracer module %s not recognized" % mod)
234+
tracer_mods.sort(key=lambda d: self.tracer_lst[d])
235+
for kk in range(len(tracer_mods)):
236+
self.tracer_mod_pos[tracer_mods[kk]] = kk
237+
217238

218239
def _norm_earth(self,consts):
219240
out = []
@@ -593,28 +614,28 @@ def write_bctides(self, bctides_file):
593614
% (bname_yaml, bname_hgrid)
594615
)
595616

596-
num_tracer_mod = 0
597-
tracer_mods = []
598-
tracer_mod_pos = {}
599-
for i in range(num_open_boundaries):
600-
if "tracers" in self.open_boundaries[i].keys():
601-
boundary_tracer_mod_num = len(
602-
self.open_boundaries[i]["tracers"]
603-
)
604-
if boundary_tracer_mod_num > num_tracer_mod:
605-
num_tracer_mod = boundary_tracer_mod_num
606-
for j in range(boundary_tracer_mod_num):
607-
tracer_mod = self.open_boundaries[i]["tracers"][j]["tracer"]
608-
if not (tracer_mod in self.tracer_lst.keys()):
609-
raise ValueError(
610-
tracer_mod + " is not a supported tracer module\n"
611-
)
612-
else:
613-
if not (tracer_mod in tracer_mods):
614-
tracer_mods.append(tracer_mod)
615-
tracer_mods.sort(key=lambda d: self.tracer_lst[d])
616-
for kk in range(len(tracer_mods)):
617-
tracer_mod_pos[tracer_mods[kk]] = kk
617+
# num_tracer_mod = 0
618+
# tracer_mods = []
619+
# tracer_mod_pos = {}
620+
# for i in range(num_open_boundaries):
621+
# if "tracers" in self.open_boundaries[i].keys():
622+
# boundary_tracer_mod_num = len(
623+
# self.open_boundaries[i]["tracers"]
624+
# )
625+
# if boundary_tracer_mod_num > num_tracer_mod:
626+
# num_tracer_mod = boundary_tracer_mod_num
627+
# for j in range(boundary_tracer_mod_num):
628+
# tracer_mod = self.open_boundaries[i]["tracers"][j]["tracer"]
629+
# if not (tracer_mod in self.tracer_lst.keys()):
630+
# raise ValueError(
631+
# tracer_mod + " is not a supported tracer module\n"
632+
# )
633+
# else:
634+
# if not (tracer_mod in tracer_mods):
635+
# tracer_mods.append(tracer_mod)
636+
# tracer_mods.sort(key=lambda d: self.tracer_lst[d])
637+
# for kk in range(len(tracer_mods)):
638+
# tracer_mod_pos[tracer_mods[kk]] = kk
618639

619640
for i in range(num_open_boundaries):
620641
print("processing open boundary %s " % self.open_boundaries[i]["name"])
@@ -693,7 +714,7 @@ def write_bctides(self, bctides_file):
693714
)
694715

695716
## output tracer boundary
696-
tracer_boundary_sources = [0] * num_tracer_mod
717+
tracer_boundary_sources = [0] * len(self.tracer_mod_pos)
697718
## this list save sorted tracer boundary index according to SCHISM code order
698719
tracer_boundary_lst_sorted = []
699720
if "tracers" in self.open_boundaries[i].keys():
@@ -702,11 +723,30 @@ def write_bctides(self, bctides_file):
702723
)
703724
for j in range(boundary_tracer_mod_num):
704725
tracer_boundary = self.open_boundaries[i]["tracers"][j]["source"]
705-
tracer_mod = self.open_boundaries[i]["tracers"][j]["tracer"]
726+
tracer_mod = self.open_boundaries[i]["tracers"][j]["module"]
727+
## if tracer mod not in self.tracer_mod_pos, raise error
728+
if not (tracer_mod in self.tracer_mod_pos.keys()):
729+
raise ValueError(
730+
tracer_mod + " is not in specified tracer module list at the begining \
731+
of bctide yamal\n")
732+
706733
tracer_boundary_key = tracer_boundary
734+
## set boundary key to "constant" if source is a number or list of numbers
707735
if isinstance(tracer_boundary, numbers.Number):
708736
tracer_boundary_key = "constant"
709737
elif isinstance(tracer_boundary, list):
738+
boundary_tracer_mod_num = len(tracer_boundary)
739+
## if curent tracer mod has multiple tracers, check if the
740+
## length of tracer_boundary match the number of tracers defined
741+
## in self.tracer_mod_num
742+
if boundary_tracer_mod_num != self.tracer_mod_num[tracer_mod]:
743+
raise ValueError( self.open_boundaries[i]["name"] + ": "
744+
tracer_mod + " boundary source length "
745+
+ str(boundary_tracer_mod_num)
746+
+ " does not match number of tracers defined in module section: "
747+
+ str(self.tracer_mod_num[tracer_mod])
748+
)
749+
710750
if all(
711751
isinstance(x, numbers.Number)
712752
for x in tracer_boundary
@@ -720,12 +760,12 @@ def write_bctides(self, bctides_file):
720760
+ " boundary is not supported"
721761
)
722762
tracer_boundary_source = self.tracer_source[tracer_boundary_key]
723-
pos = tracer_mod_pos[tracer_mod]
763+
pos = self.tracer_mod_pos[tracer_mod]
724764
tracer_boundary_sources[pos] = tracer_boundary_source
725765
tracer_boundary_lst_sorted.append(j)
726766

727767
tracer_boundary_lst_sorted.sort(
728-
key=lambda jj: tracer_mod_pos[
768+
key=lambda jj: self.tracer_mod_pos[
729769
self.open_boundaries[i]["tracers"][jj]["tracer"]
730770
]
731771
)
@@ -734,7 +774,7 @@ def write_bctides(self, bctides_file):
734774
outf.write(str(vel_id) + " ")
735775
outf.write(str(temp_id) + " ")
736776
outf.write(str(salt_id) + " ")
737-
for ii in range(num_tracer_mod):
777+
for ii in range(len(self.tracer_mod_pos)):
738778
outf.write(str(tracer_boundary_sources[ii]) + " ")
739779
outf.write("\n")
740780

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