add coordinate generation template code

pynemo/tests/coord_gen.py

+#!/usr/bin/env python2
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Mar 11 11:16:57 2020
+
+example grid set up
+
+@author: jdha
+"""
+
+
+
+def set_hgrid(dx, dy, jpi, jpj, zoffx, zoffy):
+    # Set grid positions [km]
+    latt = np.zeros((jpi, jpj))
+    lont = np.zeros((jpi, jpj))
+    lonu = np.zeros((jpi, jpj))
+    latu = np.zeros((jpi, jpj))
+    lonv = np.zeros((jpi, jpj))
+    latv = np.zeros((jpi, jpj))
+    lonf = np.zeros((jpi, jpj))
+    latf = np.zeros((jpi, jpj))
+
+    for i in range(0, jpi):
+        lont[i, :] = zoffx * dx * 1.e-3 + dx * 1.e-3 * np.float(i)
+        lonu[i, :] = zoffx * dx * 1.e-3 + dx * 1.e-3 * (np.float(i) + 0.5)
+
+    for j in range(0, jpj):
+        latt[:, j] = zoffy * dy * 1.e-3 + dy * 1.e-3 * float(j)
+        latv[:, j] = zoffy * dy * 1.e-3 + dy * 1.e-3 * (float(j) + 0.5)
+
+    lonv = lont
+    lonf = lonu
+    latu = latt
+    latf = latv
+
+    e1t = np.ones((jpi, jpj)) * dx
+    e2t = np.ones((jpi, jpj)) * dy
+    e1u = np.ones((jpi, jpj)) * dx
+    e2u = np.ones((jpi, jpj)) * dy
+    e1v = np.ones((jpi, jpj)) * dx
+    e2v = np.ones((jpi, jpj)) * dy
+    e1f = np.ones((jpi, jpj)) * dx
+    e2f = np.ones((jpi, jpj)) * dy
+
+    # Set bathymetry [m]:
+    batt = 500. + 0.5 * 1500. * (1.0 + np.tanh((lont - 40.) / 7.))
+
+    # Set surface mask:
+    ktop = np.zeros((jpi, jpj))
+    ktop[1:jpi - 1, nghost + 1:jpj - nghost - 1] = 1
+    batt = np.where((ktop == 0.), 0., batt)
+
+    # Set coriolis parameter:
+    ff_t = np.zeros((jpi, jpj))
+    ff_f = np.zeros((jpi, jpj))
+
+    return lont, latt, lonu, latu, lonv, latv, lonf, latf, \
+           e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f, batt, ktop, ff_f, ff_t
+           
+           
+def write_coord(fileout, lont, latt, lonu, latu, lonv, latv, lonf, latf,
+                e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f):
+    ''' 
+    Writes out a NEMO formatted coordinates file.
+    
+    Args:
+        fileout         (string): filename
+        lon[t/u/v/f](np.ndarray): longitude array at [t/u/v/f]-points (2D)
+        lat[t/u/v/f](np.ndarray): latitude array at [t/u/v/f]-points (2D)
+        e1[t/u/v/f] (np.ndarray): zonal scale factors at [t/u/v/f]-points
+        e2[t/u/v/f] (np.ndarray): meridional scale factors at [t/u/v/f]-points
+            
+    Returns:
+    '''
+    
+    # Open pointer to netcdf file
+    dataset = Dataset(fileout, 'w', format='NETCDF4_CLASSIC')
+    
+    # Get input size and create appropriate dimensions
+    # TODO: add some sort of error handling
+    nx, ny = np.shape(lont)
+    dataset.createDimension('x', nx)
+    dataset.createDimension('y', ny)
+    
+    # Create Variables   
+    nav_lon = dataset.createVariable('nav_lon', np.float32, ('y', 'x'))
+    nav_lat = dataset.createVariable('nav_lat', np.float32, ('y', 'x'))
+    
+    glamt = dataset.createVariable('glamt', np.float64, ('y', 'x'))
+    glamu = dataset.createVariable('glamu', np.float64, ('y', 'x'))
+    glamv = dataset.createVariable('glamv', np.float64, ('y', 'x'))
+    glamf = dataset.createVariable('glamf', np.float64, ('y', 'x'))
+    gphit = dataset.createVariable('gphit', np.float64, ('y', 'x'))
+    gphiu = dataset.createVariable('gphiu', np.float64, ('y', 'x'))
+    gphiv = dataset.createVariable('gphiv', np.float64, ('y', 'x'))
+    gphif = dataset.createVariable('gphif', np.float64, ('y', 'x'))
+    
+    ge1t = dataset.createVariable('e1t', np.float64, ('y', 'x'))
+    ge1u = dataset.createVariable('e1u', np.float64, ('y', 'x'))
+    ge1v = dataset.createVariable('e1v', np.float64, ('y', 'x'))
+    ge1f = dataset.createVariable('e1f', np.float64, ('y', 'x'))
+    ge2t = dataset.createVariable('e2t', np.float64, ('y', 'x'))
+    ge2u = dataset.createVariable('e2u', np.float64, ('y', 'x'))
+    ge2v = dataset.createVariable('e2v', np.float64, ('y', 'x'))
+    ge2f = dataset.createVariable('e2f', np.float64, ('y', 'x'))
+    
+    nav_lon.units, nav_lon.long_name = 'km', 'X'
+    nav_lat.units, nav_lat.long_name = 'km', 'Y'
+    
+    # Populate file with input data 
+    # TODO: do we need to transpose?
+    nav_lon[:, :] = lont.T
+    nav_lat[:, :] = latt.T
+
+    glamt[:, :] = lont.T
+    glamu[:, :] = lonu.T
+    glamv[:, :] = lonv.T
+    glamf[:, :] = lonf.T
+    gphit[:, :] = latt.T
+    gphiu[:, :] = latu.T
+    gphiv[:, :] = latv.T
+    gphif[:, :] = latf.T
+
+    ge1t[:, :] = e1t.T
+    ge1u[:, :] = e1u.T
+    ge1v[:, :] = e1v.T
+    ge1f[:, :] = e1f.T
+    ge2t[:, :] = e2t.T
+    ge2u[:, :] = e2u.T
+    ge2v[:, :] = e2v.T
+    ge2f[:, :] = e2f.T
+
+    # Close off pointer
+    dataset.close()
+
+def write_domcfg(fileout, ln_zco, ln_zps, ln_sco, ln_isfcav, jperio, bat, 
+                 lont, latt, lonu, latu, lonv, latv, lonf, latf,
+                 e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f, ff_f, ff_t,
+                 dept_1d, e3t_1d, e3w_1d, e3t, e3u, e3v, e3f, e3w, e3uw, e3vw,
+                 ktop, kbot):
+    ''' 
+    Writes out a NEMO formatted domcfg file.
+    
+    Args:
+        fileout         (string): filename
+        ln_zco         (logical): vertical coordinate flag [z-level]
+        ln_zps         (logical): vertical coordinate flag [z-partial-step]
+        ln_sco         (logical): vertical coordinate flag [sigma]
+        ln_isfcav      (logical): ice cavity flag
+        jperio             (int): domain type
+        bat         (np.ndarray): bathymetry array at t-points (2D)
+        lon[t/u/v/f](np.ndarray): longitude array at [t/u/v/f]-points (2D)
+        lat[t/u/v/f](np.ndarray): latitude array at [t/u/v/f]-points (2D)
+        e1[t/u/v/f] (np.ndarray): zonal scale factors at [t/u/v/f]-points
+        e2[t/u/v/f] (np.ndarray): meridional scale factors at [t/u/v/f]-points
+        ff_[f/t]    (np.ndarray): coriolis parameter at [t/f]-points
+        dept_1d     (np.ndarray): 1D depth levels at t-points
+        e3[t/w]_1d  (np.ndarray): 1D vertical scale factors at [t/w]-points
+        e3[t/u/v/f] (np.ndarray): vertcal scale factors at [t/u/v/f]-points
+        e3[w/uw/vw] (np.ndarray): vertcal scale factors at [w/uw/vw]-points
+        ktop        (np.ndarray): upper most wet point
+        kbot        (np.ndarray): lower most wet point
+            
+    Returns:
+    '''
+    
+    # Open pointer to netcdf file
+    dataset = Dataset(fileout, 'w', format='NETCDF4_CLASSIC')
+    
+    # Get input size and create appropriate dimensions
+    # TODO: add some sort of error handling
+    nx, ny, nz = np.shape(e3t)
+    dataset.createDimension('x', nx)
+    dataset.createDimension('y', ny)
+    dataset.createDimension('z', nz)
+    
+    # create Variables 
+    nav_lon = dataset.createVariable('nav_lon', np.float32, ('y', 'x'))
+    nav_lat = dataset.createVariable('nav_lat', np.float32, ('y', 'x'))
+    nav_lev = dataset.createVariable('nav_lev', np.float32, 'z')
+    
+    giglo = dataset.createVariable('jpiglo', "i4")
+    gjglo = dataset.createVariable('jpjglo', "i4")
+    gkglo = dataset.createVariable('jpkglo', "i4")
+    
+    gperio = dataset.createVariable('jperio', "i4")
+    
+    gzco = dataset.createVariable('ln_zco', "i4")
+    gzps = dataset.createVariable('ln_zps', "i4")
+    gsco = dataset.createVariable('ln_sco', "i4")
+    gcav = dataset.createVariable('ln_isfcav', "i4")
+
+    ge3t1d = dataset.createVariable('e3t_1d', np.float64, 'z')
+    ge3w1d = dataset.createVariable('e3w_1d', np.float64, 'z')
+    gitop = dataset.createVariable('top_level', "i4", ('y', 'x'))
+    gibot = dataset.createVariable('bottom_level', "i4", ('y', 'x'))
+    gbat = dataset.createVariable('Bathymetry', np.float64, ('y', 'x'))
+    glamt = dataset.createVariable('glamt', np.float64, ('y', 'x'))
+    glamu = dataset.createVariable('glamu', np.float64, ('y', 'x'))
+    glamv = dataset.createVariable('glamv', np.float64, ('y', 'x'))
+    glamf = dataset.createVariable('glamf', np.float64, ('y', 'x'))
+    gphit = dataset.createVariable('gphit', np.float64, ('y', 'x'))
+    gphiu = dataset.createVariable('gphiu', np.float64, ('y', 'x'))
+    gphiv = dataset.createVariable('gphiv', np.float64, ('y', 'x'))
+    gphif = dataset.createVariable('gphif', np.float64, ('y', 'x'))
+    ge1t = dataset.createVariable('e1t', np.float64, ('y', 'x'))
+    ge1u = dataset.createVariable('e1u', np.float64, ('y', 'x'))
+    ge1v = dataset.createVariable('e1v', np.float64, ('y', 'x'))
+    ge1f = dataset.createVariable('e1f', np.float64, ('y', 'x'))
+    ge2t = dataset.createVariable('e2t', np.float64, ('y', 'x'))
+    ge2u = dataset.createVariable('e2u', np.float64, ('y', 'x'))
+    ge2v = dataset.createVariable('e2v', np.float64, ('y', 'x'))
+    ge2f = dataset.createVariable('e2f', np.float64, ('y', 'x'))
+    gfff = dataset.createVariable('ff_f', np.float64, ('y', 'x'))
+    gfft = dataset.createVariable('ff_t', np.float64, ('y', 'x'))
+    ge3t = dataset.createVariable('e3t_0', np.float64, ('z', 'y', 'x'))
+    ge3w = dataset.createVariable('e3w_0', np.float64, ('z', 'y', 'x'))
+    ge3u = dataset.createVariable('e3u_0', np.float64, ('z', 'y', 'x'))
+    ge3v = dataset.createVariable('e3v_0', np.float64, ('z', 'y', 'x'))
+    ge3f = dataset.createVariable('e3f_0', np.float64, ('z', 'y', 'x'))
+    ge3uw = dataset.createVariable('e3uw_0', np.float64, ('z', 'y', 'x'))
+    ge3vw = dataset.createVariable('e3vw_0', np.float64, ('z', 'y', 'x'))
+
+    nav_lon.units, nav_lon.long_name = 'km', 'X'
+    nav_lat.units, nav_lat.long_name = 'km', 'Y'
+
+    # Populate file with input data 
+    giglo[:] = nx
+    gjglo[:] = ny
+    gkglo[:] = nz
+    
+    gzco[:] = ln_zco
+    gzps[:] = ln_zps
+    gsco[:] = ln_sco
+    gcav[:] = ln_isfcav
+    
+    gperio[:] = jperio
+
+    # TODO: do we need to transpose?
+    nav_lon[:, :] = lont.T
+    nav_lat[:, :] = latt.T
+    nav_lev[:]    = dept_1d
+    
+    ge3t1d[:] = e3t_1d
+    ge3w1d[:] = e3w_1d
+    
+    gitop[:, :] = ktop.T
+    gibot[:, :] = kbot.T
+    
+    gbat[:, :] = bat.T
+    
+    glamt[:, :] = lont.T
+    glamu[:, :] = lonu.T
+    glamv[:, :] = lonv.T
+    glamf[:, :] = lonf.T
+    gphit[:, :] = latt.T
+    gphiu[:, :] = latu.T
+    gphiv[:, :] = latv.T
+    gphif[:, :] = latf.T
+    
+    ge1t[:, :] = e1t.T
+    ge1u[:, :] = e1u.T
+    ge1v[:, :] = e1v.T
+    ge1f[:, :] = e1f.T
+    ge2t[:, :] = e2t.T
+    ge2u[:, :] = e2u.T
+    ge2v[:, :] = e2v.T
+    ge2f[:, :] = e2f.T
+    gfff[:, :] = ff_f.T
+    gfft[:, :] = ff_t.T
+    
+    ge3t[:, :, :]  = e3t.T
+    ge3w[:, :, :]  = e3w.T
+    ge3u[:, :, :]  = e3u.T
+    ge3v[:, :, :]  = e3v.T
+    ge3f[:, :, :]  = e3f.T
+    ge3uw[:, :, :] = e3uw.T
+    ge3vw[:, :, :] = e3vw.T
+    
+    # Close off pointer
+    dataset.close()
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