用于处理 ADCIRC 输入和输出文件的 Python 包

项目描述

ADCIRCPy

用于自动化 ADCIRC 模型运行的 Python 库。

文档可以在https://adcircpy.readthedocs.io找到

组织/责任

ADCIRCpy 目前由美国联邦政府机构国家海洋和大气管理局 (NOAA)下属的海岸调查办公室 (OCS)的沿海海洋建模处 (CMMB)维护。它主要由@jreniel开发。

扎卡里·伯内特（领导） - zachary.burnett@noaa.gov
Jaime Calzada - jrcalzada@vims.edu

安装

请使用 Python>=3.6 的虚拟环境。您可以使用 conda 或操作系统的 Python 为应用程序提供虚拟环境。

您可以通过 pip 安装应用程序。这将安装最新的标记版本。

pip install adcircpy

或者，您可以通过克隆然后运行来手动安装 repo

pip install .

用法

命令行界面 (CLI)

该程序公开了一些可从命令行界面获得的命令。您可以将-h标志传递给任何此命令以探索它们的功能。

tide_gen
plot_mesh
tidal_run
best_track_run
best_track_file
plot_maxele
plot_fort61
fort63

例子

生成潮汐成分模板

tide_gen您可以通过执行命令并通过传递网格、开始日期和运行天数作为参数来快速为您的网格创建潮汐分量表。默认情况下，此函数从HAMTIDE数据库中获取数据。

tide_gen \
    /path/to/your/fort.14 \
    2021-02-26T00:00:00 \
    15 \
    --mesh-crs='epsg:4326'

为飓风桑迪 (AL182012) 运行最佳赛道

创建 ADCIRC 输入文件包括飓风桑迪的潮汐和风暴数据：

best_track_run \
    /path/to/your/fort.14 \
    Sandy2012 \
    --fort13=/path/to/your/fort.13 \
    --crs=EPSG:4326 \
    --output-directory=/path/where/you/want/the/files \
    --constituents=all \
    --spinup-days=15.0 \
    --elev=30. \
    --mete=30. \
    --velo=30. \
    --skip-run

请注意，由于 fort.14 不包含正确操作所需的坐标参考系统信息，因此需要 --crs 标志。EPSG:4326表示网格在 WGS84（纬度/经度）中。请注意，反冲代表 shell 的“在下一行继续”。您可以在排除反斜杠后将上面的命令写在一行上。

绘制结果

这是使用包进行快速绘图的两个示例。这些在此处仅作为说明性示例给出。支持比此示例更多的文件类型，但该程序尚不支持每种输出输入/输出文件类型。作为用户，我们鼓励您探索可用的内容并提出改进建议并做出贡献。

plot_fort61 /path/to/fort.61.nc MSL --show --coops-only

plot_mesh /path/to/fort.14 --show-elements

Python API

有关使用示例，请参见示例目录。

`example_1.py`

以下代码通过执行以下操作构建简单的 ADCIRC 运行配置：

读取fort.14网格文件（特别是 Shinnecock Inlet 的测试网格）
向网格添加潮汐强迫
使用网格创建AdcircRun驱动程序对象，包括开始和结束日期
覆盖结果中的默认模型选项fort.15
如果存在则运行 ADCIRC，否则将配置写入磁盘

from datetime import datetime, timedelta
from pathlib import Path
import shutil

from adcircpy import AdcircMesh, AdcircRun, Tides
from adcircpy.utilities import download_mesh, get_logger

LOGGER = get_logger(__name__)

DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'shinnecock'
OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_1'

MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'

download_mesh(
    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
    directory=MESH_DIRECTORY,
    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
)

# open mesh file
mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)

# initialize tidal forcing and constituents
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)

# set simulation dates
duration = timedelta(days=5)
start_date = datetime(2015, 12, 14)
end_date = start_date + duration

# instantiate driver object
driver = AdcircRun(mesh, start_date, end_date)

# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))

# override default options so the resulting `fort.15` matches the original Shinnecock test case options
driver.timestep = 6.0
driver.DRAMP = 2.0
driver.TOUTGE = 3.8
driver.TOUTGV = 3.8
driver.smagorinsky = False
driver.horizontal_mixing_coefficient = 5.0
driver.gwce_solution_scheme = 'semi-implicit-legacy'

if shutil.which('padcirc') is not None:
    driver.run(OUTPUT_DIRECTORY, overwrite=True)
elif shutil.which('adcirc') is not None:
    driver.run(OUTPUT_DIRECTORY, overwrite=True, nproc=1)
else:
    LOGGER.warning(
        'ADCIRC binaries were not found in PATH. '
        'ADCIRC will not run. Writing files to disk...'
    )
    driver.write(OUTPUT_DIRECTORY, overwrite=True)

`example_2.py`

下面的代码与example_1.py上面的代码类似，不同之处在于它向网格添加了静态 Manning 的 N 系数。

from datetime import datetime, timedelta
from pathlib import Path
import shutil

import numpy

from adcircpy import AdcircMesh, AdcircRun, Tides
from adcircpy.utilities import download_mesh, get_logger

LOGGER = get_logger(__name__)

DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_2'

MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'

download_mesh(
    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
    directory=MESH_DIRECTORY,
    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
)

# open mesh file
mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)

# generate tau0 factor
mesh.generate_tau0()

# also add Manning's N to the domain (constant for this example)
mesh.mannings_n_at_sea_floor = numpy.full(mesh.values.shape, 0.025)

# initialize tidal forcing and constituents
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)

# set simulation dates
spinup_time = timedelta(days=2)
duration = timedelta(days=3)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + duration

# instantiate driver object
driver = AdcircRun(mesh, start_date, end_date, spinup_time)

# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))

# override default options
driver.timestep = 4.0

if shutil.which('padcirc') is not None:
    driver.run(OUTPUT_DIRECTORY, overwrite=True)
elif shutil.which('adcirc') is not None:
    driver.run(OUTPUT_DIRECTORY, overwrite=True, nproc=1)
else:
    LOGGER.warning(
        'ADCIRC binaries were not found in PATH. '
        'ADCIRC will not run. Writing files to disk...'
    )
    driver.write(OUTPUT_DIRECTORY, overwrite=True)

`example_3.py`

下面的代码与example_1.py上面的类似，除了它添加了 HURDAT BestTrack 风力，还构建了一个 Slurm 作业脚本以提交给作业管理器。

from datetime import datetime, timedelta
from pathlib import Path

from adcircpy import AdcircMesh, AdcircRun, Tides
from adcircpy.forcing.winds import BestTrackForcing
from adcircpy.server import SlurmConfig
from adcircpy.utilities import download_mesh

DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_3'

MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'

download_mesh(
    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
    directory=MESH_DIRECTORY,
    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
)

# open mesh file
mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)

# initialize tidal forcing and constituents
tidal_forcing = Tides()
tidal_forcing.use_all()
mesh.add_forcing(tidal_forcing)

# initialize wind forcing
wind_forcing = BestTrackForcing('Sandy2012')
mesh.add_forcing(wind_forcing)

# initialize Slurm configuration
slurm = SlurmConfig(
    account='account',
    ntasks=1000,
    run_name='adcircpy/examples/example_3.py',
    partition='partition',
    walltime=timedelta(hours=8),
    mail_type='all',
    mail_user='example@email.gov',
    log_filename='example_3.log',
    modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
    path_prefix='$HOME/adcirc/build',
)

# set simulation dates
spinup_time = timedelta(days=15)
duration = timedelta(days=3)
start_date = datetime(2012, 10, 21, 18)
end_date = start_date + duration

# instantiate driver object
driver = AdcircRun(mesh, start_date, end_date, spinup_time, server_config=slurm)

# write driver state to disk
driver.write(OUTPUT_DIRECTORY, overwrite=True)

`example_4.py`

下面的代码类似于example_3.py上面的，除了它使用 ATMESH 风力和 WW3DATA 波浪强迫。

from datetime import datetime, timedelta
from pathlib import Path

from adcircpy import AdcircMesh, AdcircRun, Tides
from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
from adcircpy.server import SlurmConfig
from adcircpy.utilities import download_mesh

DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_4'

MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'

download_mesh(
    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
    directory=MESH_DIRECTORY,
    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
)

# open mesh file
mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)

# initialize tidal forcing and constituents
tidal_forcing = Tides()
tidal_forcing.use_all()
mesh.add_forcing(tidal_forcing)

# initialize atmospheric mesh forcings (for NUOPC coupling)
wind_forcing = AtmosphericMeshForcing(
    filename='Wind_HWRF_SANDY_Nov2018_ExtendedSmoothT.nc', nws=17, interval_seconds=3600,
)
mesh.add_forcing(wind_forcing)

# initialize wave mesh forcings (for NUOPC coupling)
wave_forcing = WaveWatch3DataForcing(
    filename='ww3.HWRF.NOV2018.2012_sxy.nc', nrs=5, interval_seconds=3600,
)
mesh.add_forcing(wave_forcing)

# initialize Slurm configuration
slurm = SlurmConfig(
    account='account',
    ntasks=1000,
    run_name='adcircpy/examples/example_4.py',
    partition='partition',
    walltime=timedelta(hours=8),
    mail_type='all',
    mail_user='example@email.gov',
    log_filename='example_4.log',
    modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
    path_prefix='$HOME/adcirc/build',
)

# instantiate driver object
driver = AdcircRun(
    mesh=mesh,
    start_date=datetime.now(),
    end_date=timedelta(days=7),
    spinup_time=timedelta(days=5),
    server_config=slurm,
)

# write driver state to disk
driver.write(OUTPUT_DIRECTORY, overwrite=True)

引文

Calzada, J., Burnett, Z., Moghimi, S., Myers, E., & Pe’eri, S. (2021). ADCIRCpy: A Python API to generate ADCIRC model input files (Technical Memorandum No. 41; NOAA NOS OCS). National Oceanic and Atmospheric Administation.

@techreport{calzadaADCIRCpyPythonAPI2021,
    type = {Technical {{Memorandum}}},
    title = {{{ADCIRCpy}}: A {{Python API}} to Generate {{ADCIRC}} Model Input Files},
    author = {Calzada, Jaime and Burnett, Zachary and Moghimi, Saeed and Myers, Edward and Pe'eri, Shachak},
    year = {2021},
    month = dec,
    number = {41},
    institution = {{National Oceanic and Atmospheric Administation}},
    abstract = {The Advanced Circulation Model (ADCIRC) is a Fortran program used for modeling ocean circulation due to tides, surface waves and atmospheric forcings. However, the input formats and configuration are inflexible and not straight forward for operational implementation, making rapid iteration of model testing, ensemble configuration, and model coupling complicated. Here, we introduce a flexible abstraction of model inputs and outputs written in Python, called ADCIRCpy, that provides a simpler user interface for automatically generating ADCIRC configuration to a variety of inputs and model scenarios. This documentation outlines 1. the needs for such an abstraction, 2. the peculiarities and challenges with the ADCIRC model that necessitate custom logic, and 3. methodologies for generalizing user input in such a way as to make generating model configurations consistent, fast, and efficient.}
}

致谢

ADCIRCpy 的大部分内容是由 Jaime Calzada @jreniel编写的。

项目详情

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1.10b0 预发布

2020 年 8 月 12 日

这个版本

1.2.1

2022 年 4 月 22 日

1.2.0

2022 年 4 月 20 日

1.1.4

2022 年 3 月 10 日

1.1.3

2022 年 3 月 8 日

1.1.2

2022 年 2 月 22 日

1.1.1

adcircpy 1.2.1

导航

项目链接

统计数据

Meta

Maintainers

分类

项目描述

ADCIRCPy

用于自动化 ADCIRC 模型运行的 Python 库。

组织/责任

安装

用法

命令行界面 (CLI)

例子

生成潮汐成分模板

为飓风桑迪 (AL182012) 运行最佳赛道

绘制结果

Python API

`example_1.py`

`example_2.py`

`example_3.py`

`example_4.py`

引文

致谢

项目详情

项目链接

统计数据

元

维护者

分类器

发布历史发布通知| RSS订阅

adcircpy 1.2.1

导航

项目链接

统计数据

Meta

Maintainers

分类

项目描述

ADCIRCPy

用于自动化 ADCIRC 模型运行的 Python 库。

组织/责任

安装

用法

命令行界面 (CLI)

例子

生成潮汐成分模板

为飓风桑迪 (AL182012) 运行最佳赛道

绘制结果

Python API

example_1.py

example_2.py

example_3.py

example_4.py

引文

致谢

项目详情

项目链接

统计数据

元

维护者

分类器

发布历史 发布通知| RSS订阅

`example_1.py`

`example_2.py`

`example_3.py`

`example_4.py`

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