Merge pull request #49 from noaa-ocs-modeling/develop

read and write JSON configuration files, remove virtual nodes flag, add cleanup script, write single `fort.14`

README.md

@@ -36,83 +36,109 @@ The following code (`examples/hera/hera_shinnecock_ike.py`) creates a configurat
 on Hera, over a small Shinnecock Inlet mesh:
 
 ```python
+#! /usr/bin/env python
+
 from datetime import datetime, timedelta
 from pathlib import Path
-import sys
 
 from adcircpy import Tides
 from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
-from nemspy import ModelingSystem
-from nemspy.model import ADCIRCEntry, AtmosphericMeshEntry, WaveMeshEntry
-
-sys.path.append((Path(__file__).parent / '..').absolute())
 
-from coupledmodeldriver.adcirc import write_adcirc_configurations
+from coupledmodeldriver.adcirc.nems_adcirc import (
+    ADCIRCCoupledRunConfiguration,
+    generate_nems_adcirc_configuration,
+)
 from coupledmodeldriver.platforms import Platform
 
 # paths to compiled `NEMS.x` and `adcprep`
 NEMS_EXECUTABLE = '/scratch2/COASTAL/coastal/save/shared/repositories/ADC-WW3-NWM-NEMS/ALLBIN_INSTALL/NEMS-adcirc_atmesh_ww3data.x'
 ADCPREP_EXECUTABLE = '/scratch2/COASTAL/coastal/save/shared/repositories/ADC-WW3-NWM-NEMS/ALLBIN_INSTALL/adcprep'
 
 # directory containing input ADCIRC mesh nodes (`fort.14`) and (optionally) mesh values (`fort.13`)
-MESH_DIRECTORY = Path('/scratch2/COASTAL/coastal/save/shared/models') / 'meshes' / 'shinnecock' / 'grid_v1'
+MESH_DIRECTORY = (
+        Path('/scratch2/COASTAL/coastal/save/shared/models') / 'meshes' / 'shinnecock' / 'grid_v1'
+)
 
 # directory containing input atmospheric mesh forcings (`wind_atm_fin_ch_time_vec.nc`) and WaveWatch III forcings (`ww3.Constant.20151214_sxy_ike_date.nc`)
-FORCINGS_DIRECTORY = Path('/scratch2/COASTAL/coastal/save/shared/models') / 'forcings' / 'shinnecock' / 'ike'
+FORCINGS_DIRECTORY = (
+        Path('/scratch2/COASTAL/coastal/save/shared/models') / 'forcings' / 'shinnecock' / 'ike'
+)
 
 # directory to which to write configuration
-OUTPUT_DIRECTORY = Path(__file__).parent.parent / 'data' / 'configuration' / 'hera_shinnecock_ike'
+OUTPUT_DIRECTORY = (
+        Path(__file__).parent.parent / 'data' / 'configuration' / 'hera_shinnecock_ike'
+)
 
 HAMTIDE_DIRECTORY = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/hamtide'
+TPXO_FILENAME = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc'
+
+platform = Platform.HERA
+adcirc_processors = 11
+modeled_start_time = datetime(2008, 8, 23)
+modeled_duration = timedelta(days=14.5)
+modeled_timestep = timedelta(seconds=2)
+tidal_spinup_duration = timedelta(days=12.5)
+nems_interval = timedelta(hours=1)
+job_duration = timedelta(hours=6)
 
 # dictionary defining runs with ADCIRC value perturbations - in this case, a single run with no perturbation
 runs = {f'test_case_1': (None, None)}
 
-# initialize `nemspy` configuration object with forcing file locations, start and end times,  and processor assignment
-nems = ModelingSystem(
-    start_time=datetime(2008, 8, 23),
-    end_time=datetime(2008, 8, 23) + timedelta(days=14.5),
-    interval=timedelta(hours=1),
-    atm=AtmosphericMeshEntry(filename=FORCINGS_DIRECTORY / 'wind_atm_fin_ch_time_vec.nc', processors=1),
-    wav=WaveMeshEntry(filename=FORCINGS_DIRECTORY / 'ww3.Constant.20151214_sxy_ike_date.nc', processors=1),
-    ocn=ADCIRCEntry(processors=11),
-)
-
 # describe connections between coupled components
-nems.connect('ATM', 'OCN')
-nems.connect('WAV', 'OCN')
-nems.sequence = [
+nems_connections = ['ATM -> OCN', 'WAV -> OCN']
+nems_mediations = None
+nems_sequence = [
     'ATM -> OCN',
     'WAV -> OCN',
     'ATM',
     'WAV',
     'OCN',
 ]
 
+slurm_email_address = '[email protected]'
+
 # initialize `adcircpy` forcing objects
 tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=HAMTIDE_DIRECTORY)
 tidal_forcing.use_all()
-wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
-wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)
-
-# send run information to `adcircpy` and write the resulting configuration to output directory
-write_adcirc_configurations(
-    nems,
-    runs,
-    MESH_DIRECTORY,
-    OUTPUT_DIRECTORY,
-    nems_executable=NEMS_EXECUTABLE,
-    adcprep_executable=ADCPREP_EXECUTABLE,
-    email_address='[email protected]',
-    platform=Platform.HERA,
-    spinup=timedelta(days=12.5),
-    forcings=[tidal_forcing, wind_forcing, wave_forcing],
-    overwrite=True,
-    use_original_mesh=False,
-    verbose=True,
+wind_forcing = AtmosphericMeshForcing(
+    filename=FORCINGS_DIRECTORY / 'wind_atm_fin_ch_time_vec.nc',
+    nws=17,
+    interval_seconds=3600,
+)
+wave_forcing = WaveWatch3DataForcing(
+    filename=FORCINGS_DIRECTORY / 'ww3.Constant.20151214_sxy_ike_date.nc',
+    nrs=5,
+    interval_seconds=3600,
+)
+forcings = [tidal_forcing, wind_forcing, wave_forcing]
+
+configuration = ADCIRCCoupledRunConfiguration(
+    fort13=MESH_DIRECTORY / 'fort.13',
+    fort14=MESH_DIRECTORY / 'fort.14',
+    modeled_start_time=modeled_start_time,
+    modeled_end_time=modeled_start_time + modeled_duration,
+    modeled_timestep=modeled_timestep,
+    nems_interval=nems_interval,
+    nems_connections=nems_connections,
+    nems_mediations=nems_mediations,
+    nems_sequence=nems_sequence,
+    tidal_spinup_duration=tidal_spinup_duration,
+    platform=platform,
+    runs=runs,
+    forcings=forcings,
+    adcirc_processors=adcirc_processors,
+    slurm_partition=None,
+    slurm_job_duration=job_duration,
+    slurm_email_address=slurm_email_address,
+    nems_executable=None,
+    adcprep_executable=None,
+    source_filename=None,
 )
+
+configuration.write_directory(OUTPUT_DIRECTORY, overwrite=True)
+generate_nems_adcirc_configuration(OUTPUT_DIRECTORY, overwrite=True)
 ```
 
 This code will generate a directory `hera_shinnecock_ike/` with the following structure:
@@ -121,19 +147,27 @@ This code will generate a directory `hera_shinnecock_ike/` with the following st
 📦 hera_shinnecock_ike/
 ┣ 📂 coldstart/
 ┃  ┣ 📜 fort.13
-┃  ┣ 📜 fort.14
+┃  ┣ 🔗 fort.14 -> ../fort.14
 ┃  ┗ 📜 fort.15
 ┣ 📂 runs/
 ┃  ┗ 📂 test_case_1/
 ┃    ┣ 📜 fort.13
-┃    ┣ 📜 fort.14
+┃    ┣ 🔗 fort.14 -> ../../fort.14
 ┃    ┗ 📜 fort.15
+┣ 📜 configure_modeldriver.json
+┣ 📜 configure_nems.json
+┣ 📜 configure_slurm.json
+┣ 📜 configure_adcirc.json
+┣ 📜 configure_tidal_forcing.json
+┣ 📜 configure_atmesh.json
+┣ 📜 configure_ww3data.json
 ┣ 📜 nems.configure.coldstart
 ┣ 📜 nems.configure.hotstart
 ┣ 📜 config.rc.coldstart
 ┣ 📜 config.rc.hotstart
 ┣ 📜 model_configure.coldstart
 ┣ 📜 model_configure.hotstart
+┣ 📜 fort.14
 ┣ 📜 job_adcprep_hera.job
 ┣ 📜 job_nems_adcirc_hera.job.coldstart
 ┣ 📜 job_nems_adcirc_hera.job.hotstart
@@ -180,7 +214,13 @@ This will first create symbolic links to populate configuration directories (by
 ┃    ┣ 🔗 setup.sh -> ../../setup.sh.hotstart
 ┃    ┣ 🔗 hera_adcprep.job -> ../../job_adcprep_hera.job
 ┃    ┗ 🔗 hera_nems_adcirc.job -> ../../job_nems_adcirc_hera.job.hotstart
-┣ 📜 nems.configure.coldstart
+┣ 📜 configure_modeldriver.json
+┣ 📜 configure_nems.json
+┣ 📜 configure_slurm.json
+┣ 📜 configure_adcirc.json
+┣ 📜 configure_tidal_forcing.json
+┣ 📜 configure_atmesh.json
+┣ 📜 configure_ww3data.json
 ┣ 📜 nems.configure.hotstart
 ┣ 📜 config.rc.coldstart
 ┣ 📜 config.rc.hotstart