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This dummy project required the execution of the following python scripts before the simulations are submitted:.
Create_grid.py
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import os import shutil path_bot = snakemake.input.path_bot path_fxw = snakemake.input.path_fxw output_bot = snakemake.output.output_bot output_fxw = snakemake.output.output_fxw ## In this demo only files are copied, but in reality bed and fxw are created based on external data. shutil.copyfile(path_bot, output_bot) shutil.copyfile(path_fxw, output_fxw) |
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create_output_locations.py
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import os
import shutil
path_p1 = snakemake.input.path_p1
path_p2 = snakemake.input.path_p2
output_p1 = snakemake.output.output_p1
output_p2 = snakemake.output.output_p2
## In this demo only files are copied, but in reality bed and fxw are created based on external data.
shutil.copyfile(path_p1, output_p1)
shutil.copyfile(path_p2, output_p2) |
create_sims.py
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import os
import numpy as np
from shutil import copyfile
from mako.template import Template
def render_template(data,template):
'''
Render template
input:
data: dictionary with variables to render
template: template file
'''
with open(template) as f:
template = f.read()
##
tmpl = Template(text=template)
with open(os.path.join(data['output_path'], '{}.{}'.format(data['fname'],data['extension']) ),mode='w') as f:
f.write(tmpl.render(**data))
path_sims = snakemake.output.path_sims
path_template = snakemake.input.path_template
## if file exists overwrite
overwrite = False
swan_template = 'swan_template_final.swn'
# =============================================================================
# wave conditions
# =============================================================================
wind_speed_list = [30, 20]
# =============================================================================
# create sims
# =============================================================================
## template file
template = os.path.join(path_template,swan_template)
run_condition = {'water_level':[],
'wind_speed':[],
'wind_dir':[]}
## make combinations
for ii, item in enumerate(wind_speed_list):
## get conditions
wind_speed = item
fname = 'U{}'.format(wind_speed)
## data for template
data = {'output_path':os.path.dirname(path_sims[ii]),
'extension':'swn',
'variant':'A',
'fname':fname,
'wind_speed': wind_speed,
'wind_dir': 180,
'water_level': 0}
## skip if file already exists
if os.path.exists(os.path.join(path_sims[ii], '{}.swn'.format(fname))) and overwrite:
print('skipped {}'.format(fname))
continue
## render template
render_template(data,template)
## copy swan_run
copyfile(os.path.join(path_template,'swan4131A1c7.sh'), os.path.join(os.path.dirname(path_sims[ii]),'swan4131A1c7.sh'))
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