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Merge pull request #326 from matt-frey/develop
Add 3D model
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| ## How to contribute to EPIC | ||
| Hi there. The core developers of EPIC thank you for your contribution. We have some guidelines though which we like you to follow before opening pull request. | ||
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| <!-- 29 November 2021 --> | ||
| <!-- https://stackoverflow.com/questions/11948245/markdown-to-create-pages-and-table-of-contents?page=1&tab=votes#tab-top --> | ||
| #### Table of Contents | ||
| 1. [Unit Testing](#unit-testing) | ||
| 2. [Coding Style](#coding-style) | ||
| 2. [Opening a pull request](#pull-request) | ||
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| ### Unit Testing <a name="unit-testing"></a> | ||
| Please write unit tests for newly added features and routines. All unit tests are located in the directory `unit-tests`. | ||
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| ### Coding Style <a name="coding-style"></a> | ||
| Please follow our coding style when contributing to EPIC. | ||
| * use an indentation of 4 spaces | ||
| * use lower case letters only | ||
| * names of variables and subroutines / functions that consists of multiple words should be separated by underscores, e.g. `this_is_my_subroutine` | ||
| * add a whitespace character before and after mathematical operations, e.g. `i = i + 1` | ||
| * add a whitespace character after `if` and `while`, e.g. `if (i == 0)` | ||
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| ### Opening a pull request <a name="pull-request"></a> | ||
| Developers should fork the main repo and work with the branch `develop`. We only accept pull requests into `develop` of this repository. From time to time we pull all changes in `develop` into `main` and publish a release. |
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| # transpose the fields too! | ||
| import xarray as xr | ||
| import argparse | ||
| import os.path | ||
| import netCDF4 as nc | ||
| import numpy as np | ||
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| parser = argparse.ArgumentParser() | ||
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| parser.add_argument("input_file_name", type=str) | ||
| args = parser.parse_args() | ||
| input_file_name = args.input_file_name | ||
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| file_root, file_ext = os.path.splitext(input_file_name) | ||
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| if not (file_ext == ".hdf5"): | ||
| raise argparse.ArgumentTypeError('Argument filename must end on ".hdf5"') | ||
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| ds_nc=nc.Dataset(input_file_name) | ||
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| # set up time array | ||
| tstep_keys=[] | ||
| for key in ds_nc.groups.keys(): | ||
| if 'step#' in key: | ||
| tstep_keys.append(key) | ||
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| tlen=len(tstep_keys) | ||
| time_array=np.zeros(tlen) | ||
| for i_time in range(tlen): | ||
| time_array[i_time]=ds_nc.groups[tstep_keys[i_time]].t | ||
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| # set up spatial arrays | ||
| extent=ds_nc.groups['box'].extent | ||
| origin=ds_nc.groups['box'].origin | ||
| ncells=ds_nc.groups['box'].ncells | ||
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| x_array=np.linspace(origin[0],origin[0]+extent[0],ncells[0]+1)[:-1] | ||
| y_array=np.linspace(origin[1],origin[1]+extent[1],ncells[1]+1)[:-1] | ||
| z_array=np.linspace(origin[2],origin[2]+extent[2],ncells[2]+1) | ||
| elem_array=range(3) | ||
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| step0=ds_nc.groups[tstep_keys[0]] | ||
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| ds_xr = xr.Dataset() | ||
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| for variable in step0.variables: | ||
| n_dims=len(np.shape(step0[variable][:])) | ||
| if(n_dims==3): | ||
| ds_xr[variable] = xr.DataArray(coords=[time_array, z_array, y_array, x_array], dims=["time", "z","y","x"]) | ||
| elif(n_dims==4): | ||
| ds_xr[variable] = xr.DataArray(coords=[time_array, z_array, y_array, x_array, elem_array], dims=["time", "z","y","x", "index"]) | ||
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| ds_xr['diffB'] = xr.DataArray(coords=[time_array, z_array, y_array, x_array], dims=["time", "z","y","x"]) | ||
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| for i_time in range(tlen): | ||
| this_step=ds_nc.groups[tstep_keys[i_time]] | ||
| for variable in this_step.variables: | ||
| ds_xr[variable][i_time]=np.transpose(this_step[variable][:]) | ||
| if 'dry buoyancy' in this_step.variables: | ||
| ds_xr['diffB'][i_time]=np.transpose(this_step['total buoyancy'][:])-np.transpose(this_step['dry buoyancy'][:]) | ||
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| ds_xr.to_netcdf(file_root + ".nc") |
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| ``` | ||
| &EPIC | ||
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| field_file = 'moist.hdf5' ! input field file | ||
| field_tol = 1.0e-9 ! tolerance for parcel generation | ||
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| ! | ||
| ! h5 output info | ||
| ! | ||
| output%h5_field_freq = 50 ![s] write after these many seconds to the field HDF5 file | ||
| output%h5_parcel_freq = 50 ![s] write after these many seconds to the parcel HDF5 file | ||
| output%h5_parcel_stats_freq = 50 ![s] write after these many seconds to parcel stats HDF5 file | ||
| output%h5_field_stats_freq = 50 ![s] write after these many seconds to the field stats HDF5 file | ||
| output%h5_write_fields = .true. ! enable / disable field dump | ||
| output%h5_write_parcels = .true. ! enable / disable parcel dump | ||
| output%h5_write_parcel_stats = .true. ! enable / disable parcel statistics | ||
| output%h5_write_field_stats = .true. ! enable / disable field statistics | ||
| output%h5_overwrite = .true. ! replace existing HDF5 files | ||
| output%h5_basename = 'moist' ! HDF5 output base name | ||
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| ! | ||
| ! parcel info | ||
| ! | ||
| parcel%n_per_cell = 8 ! initial number of parcels per cell | ||
| parcel%lambda_max = 5.0 ! maximum parcel aspect ratio | ||
| parcel%min_vratio = 36.0 ! minimum ratio of grid cell volume / parcel volume | ||
| parcel%max_vratio = 2.89 ! maximum ratio of grid cell volume / parcel volume | ||
| parcel%correction_iters = 2 ! how many parcel correction iterations | ||
| parcel%gradient_pref = 1.8 ! gradient correction prefactor | ||
| parcel%max_compression = 0.5 ! gradient correction maximum compression | ||
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| ! | ||
| ! stepper info | ||
| ! | ||
| time%limit = 2000.0 ! time limit (s) | ||
| time%alpha = 0.2 ! scaling factor for the strain and buoyancy gradient time step | ||
| time%precise_stop = .false. ! time limit exact | ||
| / |
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| &MODELS | ||
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| model = 'MoistPlume' | ||
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| h5fname = 'moist.hdf5' | ||
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| box%ncells = 32, 32, 32 | ||
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| box%extent = 6280, 6280, 6280 | ||
| box%origin = 0, 0, 0 | ||
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| moist%H = 0.8 | ||
| moist%z_c = 2500 | ||
| moist%mu = 0.9 | ||
| moist%z_d = 4000 | ||
| moist%z_m = 5000 | ||
| moist%r_plume = 800 | ||
| moist%e_values = 0.3, -0.4, 0.5 | ||
| moist%l_condense = 1000.0 | ||
| moist%q0 = 0.015 | ||
| moist%theta_l0 = 288.0 | ||
| / |
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| ``` | ||
| &EPIC | ||
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| field_file = 'robert3d.hdf5' ! input field file | ||
| field_tol = 1.0e-9 ! tolerance for parcel generation | ||
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| ! | ||
| ! h5 output info | ||
| ! | ||
| output%h5_field_freq = 30 ![s] write after these many seconds to the field HDF5 file | ||
| output%h5_parcel_freq = 30 ![s] write after these many seconds to the parcel HDF5 file | ||
| output%h5_parcel_stats_freq = 30 ![s] write after these many seconds to parcel stats HDF5 file | ||
| output%h5_field_stats_freq = 30 ![s] write after these many seconds to the field stats HDF5 file | ||
| output%h5_write_fields = .true. ! enable / disable field dump | ||
| output%h5_write_parcels = .true. ! enable / disable parcel dump | ||
| output%h5_write_parcel_stats = .true. ! enable / disable parcel statistics | ||
| output%h5_write_field_stats = .true. ! enable / disable field statistics | ||
| output%h5_overwrite = .true. ! replace existing HDF5 files | ||
| output%h5_basename = 'robert3d' ! HDF5 output base name | ||
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| ! | ||
| ! parcel info | ||
| ! | ||
| parcel%n_per_cell = 8 ! initial number of parcels per cell | ||
| parcel%lambda_max = 5.0 ! maximum parcel aspect ratio | ||
| parcel%min_vratio = 36.0 ! minimum ratio of grid cell volume / parcel volume | ||
| parcel%max_vratio = 2.89 ! maximum ratio of grid cell volume / parcel volume | ||
| parcel%correction_iters = 2 ! how many parcel correction iterations | ||
| parcel%gradient_pref = 1.8 ! gradient correction prefactor | ||
| parcel%max_compression = 0.5 ! gradient correction maximum compression | ||
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| ! | ||
| ! stepper info | ||
| ! | ||
| time%limit = 1600.0 ! time limit (s) | ||
| time%alpha = 0.2 ! scaling factor for the strain and buoyancy gradient time step | ||
| time%precise_stop = .false. ! time limit exact | ||
| / |
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| &MODELS | ||
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| model = 'Robert' | ||
| h5fname = 'robert3d.hdf5' | ||
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| box%ncells = 32, 32, 32 | ||
| box%extent = 1000, 1000, 1000 | ||
| box%origin = -500.0, -500.0, 0.0 | ||
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| robert_flow%n_bubbles = 3 | ||
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| robert_flow%bubbles(1)%dtheta_max = 0.5 | ||
| robert_flow%bubbles(1)%center = 0.0, 0.0, 300.0 | ||
| robert_flow%bubbles(1)%radius = 150.0 | ||
| robert_flow%bubbles(1)%width = 50.0 | ||
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| robert_flow%bubbles(2)%dtheta_max = -0.15 | ||
| robert_flow%bubbles(2)%center = 60.0, 60.0, 640.0 | ||
| robert_flow%bubbles(2)%radius = 0.0 | ||
| robert_flow%bubbles(2)%width = 50.0 | ||
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| robert_flow%bubbles(3)%dtheta_max = -0.35 | ||
| robert_flow%bubbles(3)%center = -95.0, -80.0, 780.0 | ||
| robert_flow%bubbles(3)%radius = 0.0 | ||
| robert_flow%bubbles(3)%width = 70.0 | ||
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| / |
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