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Merged
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Mar 26, 2017
Merged

Add support for short-term archiving #153

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16 changes: 15 additions & 1 deletion config.default
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,21 @@ preprocessedReferenceRunName = None

# directory containing model results
baseDirectory = /dir/to/model/output
# names of namelist and streams files. If not in baseDirectory, give full path

# Note: an absolute path can be supplied for any of these subdirectories.
# A relative path is assumed to be relative to baseDirectory.
# By default, results are assumed to be directly in baseDirectory,
# i.e. <baseDirecory>/./

# subdirectory containing restart files
runSubdirectory = .
# subdirectory for ocean history files
oceanHistorySubdirectory = .
# subdirectory for sea ice history files
seaIceHistorySubdirectory = .

# names of namelist and streams files, either a path relative to baseDirectory
# or an absolute path.
oceanNamelistFileName = mpas-o_in
oceanStreamsFileName = streams.ocean
seaIceNamelistFileName = mpas-cice_in
Expand Down
77 changes: 36 additions & 41 deletions mpas_analysis/ocean/meridional_overturning_circulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@

Authors
-------
Milena Veneziani, Mark Petersen, Phillip Wolfram
Milena Veneziani, Mark Petersen, Phillip Wolfram, Xylar Asay-Davis

Last Modified
-------------
03/14/2017
03/23/2017
"""

import xarray as xr
Expand All @@ -24,17 +24,18 @@
from ..shared.plot.plotting import plot_vertical_section,\
timeseries_analysis_plot, setup_colormap

from ..shared.io import NameList, StreamsFile
from ..shared.io.utility import buildConfigFullPath
from ..shared.io.utility import build_config_full_path

from ..shared.generalized_reader.generalized_reader \
import open_multifile_dataset

from ..shared.timekeeping.utility import get_simulation_start_time, \
days_to_datetime

from ..shared.analysis_task import setup_task

def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{

def moc_streamfunction(config): # {{{
"""
Process MOC analysis member data if available, or compute MOC at
post-processing if not. Plots streamfunction climatolgoical sections
Expand All @@ -56,22 +57,18 @@ def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{

Authors
-------
Milena Veneziani, Mark Petersen, Phillip J. Wolfram
Milena Veneziani, Mark Petersen, Phillip J. Wolfram, Xylar Asay-Davis

Last Modified
-------------
03/14/2017
03/23/2017
"""

# **** Initial settings ****
# read parameters from config file
inDirectory = config.get('input', 'baseDirectory')

namelistFileName = config.get('input', 'oceanNamelistFileName')
namelist = NameList(namelistFileName, path=inDirectory)

streamsFileName = config.get('input', 'oceanStreamsFileName')
streams = StreamsFile(streamsFileName, streamsdir=inDirectory)
# perform common setup for the task
namelist, runStreams, historyStreams, calendar, streamMap, \
variableMap, plotsDirectory = setup_task(config, componentName='ocean')

timeSeriesStatsMonthlyAnalysisMemberFlag = namelist.get(
'config_am_timeseriesstatsmonthly_enable')
Expand All @@ -83,14 +80,13 @@ def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{
# Get a list of timeSeriesStats output files from the streams file,
# reading only those that are between the start and end dates
# First a list necessary for the streamfunctionMOC climatology
streamName = streams.find_stream(streamMap['timeSeriesStats'])
streamName = historyStreams.find_stream(streamMap['timeSeriesStats'])
startDateClimo = config.get('climatology', 'startDate')
endDateClimo = config.get('climatology', 'endDate')
calendar = namelist.get('config_calendar_type')
inputFilesClimo = streams.readpath(streamName,
startDate=startDateClimo,
endDate=endDateClimo,
calendar=calendar)
inputFilesClimo = historyStreams.readpath(streamName,
startDate=startDateClimo,
endDate=endDateClimo,
calendar=calendar)
print '\n List of files for climatologies:\n{} through {}'.format(
inputFilesClimo[0], inputFilesClimo[-1])
startYearClimo = config.getint('climatology', 'startYear')
Expand All @@ -105,10 +101,10 @@ def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{
# Then a list necessary for the streamfunctionMOC Atlantic timeseries
startDateTseries = config.get('timeSeries', 'startDate')
endDateTseries = config.get('timeSeries', 'endDate')
inputFilesTseries = streams.readpath(streamName,
startDate=startDateTseries,
endDate=endDateTseries,
calendar=calendar)
inputFilesTseries = historyStreams.readpath(streamName,
startDate=startDateTseries,
endDate=endDateTseries,
calendar=calendar)
print '\n List of files for timeSeries:\n{} through {}'.format(
inputFilesTseries[0], inputFilesTseries[-1])
startYearTseries = config.getint('timeSeries', 'startYear')
Expand All @@ -133,15 +129,14 @@ def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{
# streams, calendar, sectionName, dictClimo, dictTseries)
else:
mocDictClimo, dictRegion = _compute_moc_climo_postprocess(
config, streams, variableMap, calendar, sectionName, regionNames,
dictClimo)
config, runStreams, variableMap, calendar, sectionName,
regionNames, dictClimo)
dsMOCTimeSeries = _compute_moc_time_series_postprocess(
config, streams, variableMap, calendar, sectionName, regionNames,
dictTseries, mocDictClimo, dictRegion)
config, runStreams, variableMap, calendar, sectionName,
regionNames, dictTseries, mocDictClimo, dictRegion)

# **** Plot MOC ****
# Define plotting variables
plotsDirectory = buildConfigFullPath(config, 'output', 'plotsSubdirectory')
mainRunName = config.get('runs', 'mainRunName')
movingAveragePoints = config.getint(sectionName, 'movingAveragePoints')
colorbarLabel = '[Sv]'
Expand Down Expand Up @@ -184,10 +179,10 @@ def moc_streamfunction(config, streamMap=None, variableMap=None): # {{{
# }}}


def _load_mesh(streams): # {{{
def _load_mesh(runStreams): # {{{
# Load mesh related variables
try:
restartFile = streams.readpath('restart')[0]
restartFile = runStreams.readpath('restart')[0]
except ValueError:
raise IOError('No MPAS-O restart file found: need at least one '
'restart file for MOC calculation')
Expand All @@ -210,13 +205,13 @@ def _load_mesh(streams): # {{{
refTopDepth, refLayerThickness # }}}


def _compute_moc_climo_postprocess(config, streams, variableMap, calendar,
def _compute_moc_climo_postprocess(config, runStreams, variableMap, calendar,
sectionName, regionNames, dictClimo): # {{{

'''compute mean MOC streamfunction as a post-process'''

dvEdge, areaCell, refBottomDepth, latCell, nVertLevels, \
refTopDepth, refLayerThickness = _load_mesh(streams)
refTopDepth, refLayerThickness = _load_mesh(runStreams)

variableList = ['avgNormalVelocity',
'avgVertVelocityTop']
Expand Down Expand Up @@ -257,9 +252,9 @@ def _compute_moc_climo_postprocess(config, streams, variableMap, calendar,
# Compute and plot annual climatology of MOC streamfunction
print '\n Compute and/or plot post-processed MOC climatological '\
'streamfunction...'
simulationStartTime = get_simulation_start_time(streams)
outputDirectory = buildConfigFullPath(config, 'output',
'mpasClimatologySubdirectory')
simulationStartTime = get_simulation_start_time(runStreams)
outputDirectory = build_config_full_path(config, 'output',
'mpasClimatologySubdirectory')
try:
os.makedirs(outputDirectory)
except OSError:
Expand Down Expand Up @@ -375,7 +370,7 @@ def _compute_moc_climo_postprocess(config, streams, variableMap, calendar,
return mocDictClimo, dictRegion # }}}


def _compute_moc_time_series_postprocess(config, streams, variableMap,
def _compute_moc_time_series_postprocess(config, runStreams, variableMap,
calendar, sectionName, regionNames,
dictTseries, mocDictClimo,
dictRegion): # {{{
Expand All @@ -397,12 +392,12 @@ def write_file(dsMOCTimeSeries):
'time series...'
print ' Load data...'

simulationStartTime = get_simulation_start_time(streams)
simulationStartTime = get_simulation_start_time(runStreams)
variableList = ['avgNormalVelocity',
'avgVertVelocityTop']

dvEdge, areaCell, refBottomDepth, latCell, nVertLevels, \
refTopDepth, refLayerThickness = _load_mesh(streams)
refTopDepth, refLayerThickness = _load_mesh(runStreams)

ds = open_multifile_dataset(fileNames=dictTseries['inputFilesTseries'],
calendar=calendar,
Expand All @@ -422,8 +417,8 @@ def write_file(dsMOCTimeSeries):
transectEdgeMaskSigns = dictRegion['transectEdgeMaskSignsAtlantic']
regionCellMask = dictRegion['AtlanticCellMask']

outputDirectory = buildConfigFullPath(config, 'output',
'timeseriesSubdirectory')
outputDirectory = build_config_full_path(config, 'output',
'timeseriesSubdirectory')
try:
os.makedirs(outputDirectory)
except OSError:
Expand Down
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