From ae5c59c072e4e5815f7e9da024ec847a490e4fb2 Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Mon, 16 Dec 2019 18:22:08 +0100
Subject: [PATCH 1/7] Defining rotated nested domain

---
 conf/hermes.conf             | 12 ++++++++++--
 hermesv3_bu/config/config.py | 22 +++++++++++++++++++---
 2 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/conf/hermes.conf b/conf/hermes.conf
index ad9ea14..179e9ef 100755
--- a/conf/hermes.conf
+++ b/conf/hermes.conf
@@ -16,8 +16,8 @@ erase_auxiliary_files = 0
 
 [DOMAIN]
 
-# domain_type=[lcc, rotated, mercator, regular]
-domain_type = lcc
+# domain_type=[lcc, rotated, mercator, regular, rotated_nested]
+domain_type = roated_nested
 # output_type=[MONARCH, CMAQ, WRF_CHEM, DEFAULT]
 output_model = DEFAULT
 output_attributes = <input_dir>/writing/global_attributes_WRF-Chem.csv
@@ -39,6 +39,14 @@ vertical_description = <input_dir>/profiles/vertical/MONARCH_Global_48layers_ver
     # inc_rlat = 0.4
     # inc_rlon = 0.4
 
+# if domain_type == rotated_nested:
+    parent_grid_path = /scratch/Earth/ctena/temporal_coords.nc
+    parent_ratio = 4
+    i_parent_start = 266
+    j_parent_start = 164
+    n_rlat = 212
+    n_rlon = 196
+
 # if domain_type == lcc:
 
     # CALIOPE
diff --git a/hermesv3_bu/config/config.py b/hermesv3_bu/config/config.py
index f99e3e4..4852a63 100755
--- a/hermesv3_bu/config/config.py
+++ b/hermesv3_bu/config/config.py
@@ -74,12 +74,13 @@ class Config(ArgParser):
         p.add_argument('--output_attributes', required=False,
                        help='Path to the file that contains the global attributes.')
 
-        p.add_argument('--domain_type', required=True, help='Type of domain to simulate.',
-                       choices=['lcc', 'rotated', 'mercator', 'regular'])
-
         p.add_argument('--vertical_description', required=True,
                        help='Path to the file that contains the vertical description of the desired output.')
 
+        p.add_argument('--domain_type', required=True, help='Type of domain to simulate.',
+                       choices=['lcc', 'rotated', 'mercator', 'regular', 'rotated_nested'])
+
+
         # Rotated options
         p.add_argument('--centre_lat', required=False, type=float,
                        help='Central geographic latitude of grid (non-rotated degrees). Corresponds to the TPH0D ' +
@@ -100,6 +101,21 @@ class Config(ArgParser):
                        help='Longitudinal grid resolution (rotated degrees). Corresponds to the DLMD parameter  ' +
                             'in NMMB-MONARCH.')
 
+        # Rotated_nested options
+        p.add_argument('--parent_grid_path', required=False, type=str,
+                       help='Path to the netCDF that contains the grid definition.')
+        p.add_argument('--parent_ratio', required=False, type=int,
+                       help='Ratio between the parent and the nested domain.')
+        p.add_argument('--i_parent_start', required=False, type=int,
+                       help='Location of the I to start the nested.')
+        p.add_argument('--j_parent_start', required=False, type=int,
+                       help='Location of the J to start the nested.')
+        p.add_argument('--n_rlat', required=False, type=int,
+                       help='Number of rotated latitude points.')
+        p.add_argument('--n_rlon', required=False, type=int,
+                       help='Number of rotated longitude points.')
+
+
         # Lambert conformal conic options
         p.add_argument('--lat_1', required=False, type=float,
                        help='Standard parallel 1 (in deg). Corresponds to the P_ALP parameter of the GRIDDESC file.')
-- 
GitLab


From b3c92a11d010d451fe472fc89b24952fd273ca15 Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Wed, 15 Jan 2020 18:48:11 +0100
Subject: [PATCH 2/7] Adding Rotated nested grid

---
 conf/hermes.conf                         |   4 +-
 hermesv3_bu/config/config.py             |   5 +-
 hermesv3_bu/grids/grid.py                |   6 +
 hermesv3_bu/grids/grid_rotated.py        |   2 +-
 hermesv3_bu/grids/grid_rotated_nested.py | 194 +++++++++++++++++++++++
 5 files changed, 206 insertions(+), 5 deletions(-)
 create mode 100755 hermesv3_bu/grids/grid_rotated_nested.py

diff --git a/conf/hermes.conf b/conf/hermes.conf
index 179e9ef..d14ae8f 100755
--- a/conf/hermes.conf
+++ b/conf/hermes.conf
@@ -9,7 +9,7 @@ start_date = 2016/11/29 00:00:00
 # ----- end_date = start_date [DEFAULT] -----
 # end_date = 2010/01/01 00:00:00
 output_timestep_num = 24
-auxiliary_files_path = /scratch/Earth/HERMESv3_BU_aux/<domain_type>_<resolution>_test
+auxiliary_files_path = /scratch/Earth/ctena/HERMESv3_BU_aux/<domain_type>_<resolution>_test
 first_time = 0
 erase_auxiliary_files = 0
 
@@ -17,7 +17,7 @@ erase_auxiliary_files = 0
 [DOMAIN]
 
 # domain_type=[lcc, rotated, mercator, regular, rotated_nested]
-domain_type = roated_nested
+domain_type = rotated_nested
 # output_type=[MONARCH, CMAQ, WRF_CHEM, DEFAULT]
 output_model = DEFAULT
 output_attributes = <input_dir>/writing/global_attributes_WRF-Chem.csv
diff --git a/hermesv3_bu/config/config.py b/hermesv3_bu/config/config.py
index 4852a63..4def471 100755
--- a/hermesv3_bu/config/config.py
+++ b/hermesv3_bu/config/config.py
@@ -80,7 +80,6 @@ class Config(ArgParser):
         p.add_argument('--domain_type', required=True, help='Type of domain to simulate.',
                        choices=['lcc', 'rotated', 'mercator', 'regular', 'rotated_nested'])
 
-
         # Rotated options
         p.add_argument('--centre_lat', required=False, type=float,
                        help='Central geographic latitude of grid (non-rotated degrees). Corresponds to the TPH0D ' +
@@ -115,7 +114,6 @@ class Config(ArgParser):
         p.add_argument('--n_rlon', required=False, type=int,
                        help='Number of rotated longitude points.')
 
-
         # Lambert conformal conic options
         p.add_argument('--lat_1', required=False, type=float,
                        help='Standard parallel 1 (in deg). Corresponds to the P_ALP parameter of the GRIDDESC file.')
@@ -702,6 +700,9 @@ class Config(ArgParser):
                 elif arguments.domain_type == 'rotated':
                     arguments.__dict__[item] = arguments.__dict__[item].replace('<resolution>', '{1}_{2}'.format(
                         item, arguments.inc_rlat, arguments.inc_rlon))
+                elif arguments.domain_type == 'rotated_nested':
+                    arguments.__dict__[item] = arguments.__dict__[item].replace('<resolution>', '{1}_{2}'.format(
+                        item, arguments.n_rlat, arguments.n_rlon))
                 elif arguments.domain_type == 'lcc' or arguments.domain_type == 'mercator':
                     arguments.__dict__[item] = arguments.__dict__[item].replace('<resolution>', '{1}_{2}'.format(
                         item, arguments.inc_x, arguments.inc_y))
diff --git a/hermesv3_bu/grids/grid.py b/hermesv3_bu/grids/grid.py
index 6dea082..6803fe4 100755
--- a/hermesv3_bu/grids/grid.py
+++ b/hermesv3_bu/grids/grid.py
@@ -45,6 +45,12 @@ def select_grid(comm, logger, arguments):
                 logger, arguments.auxiliary_files_path, arguments.output_timestep_num,
                 arguments.vertical_description, arguments.centre_lat, arguments.centre_lon, arguments.west_boundary,
                 arguments.south_boundary, arguments.inc_rlat, arguments.inc_rlon)
+        elif arguments.domain_type == 'rotated_nested':
+            from hermesv3_bu.grids.grid_rotated_nested import RotatedNestedGrid
+            grid = RotatedNestedGrid(
+                logger, arguments.auxiliary_files_path, arguments.output_timestep_num,
+                arguments.vertical_description, arguments.parent_grid_path, arguments.parent_ratio,
+                arguments.i_parent_start, arguments.j_parent_start, arguments.n_rlat, arguments.n_rlon)
 
         elif arguments.domain_type == 'mercator':
             from hermesv3_bu.grids.grid_mercator import MercatorGrid
diff --git a/hermesv3_bu/grids/grid_rotated.py b/hermesv3_bu/grids/grid_rotated.py
index 2195707..5d1fbec 100755
--- a/hermesv3_bu/grids/grid_rotated.py
+++ b/hermesv3_bu/grids/grid_rotated.py
@@ -172,7 +172,7 @@ class RotatedGrid(Grid):
                                 boundary_latitudes=self.boundary_latitudes,
                                 boundary_longitudes=self.boundary_longitudes,
                                 rotated=True, rotated_lats=self.rlat, rotated_lons=self.rlon,
-                                north_pole_lat=90 - self.attributes['new_pole_latitude_degrees'],
+                                north_pole_lat=self.attributes['new_pole_latitude_degrees'],
                                 north_pole_lon=self.attributes['new_pole_longitude_degrees'])
         self.logger.write_log("\tGrid created at '{0}'".format(self.netcdf_path), 3)
         self.logger.write_time_log('RotatedGrid', 'write_netcdf', timeit.default_timer() - spent_time, 3)
diff --git a/hermesv3_bu/grids/grid_rotated_nested.py b/hermesv3_bu/grids/grid_rotated_nested.py
new file mode 100755
index 0000000..90dd3df
--- /dev/null
+++ b/hermesv3_bu/grids/grid_rotated_nested.py
@@ -0,0 +1,194 @@
+#!/usr/bin/env python
+
+import os
+import timeit
+from hermesv3_bu.grids.grid import Grid
+import numpy as np
+import math
+
+from hermesv3_bu.logger.log import Log
+
+
+class RotatedNestedGrid(Grid):
+    def __init__(self, logger, auxiliary_path, tstep_num, vertical_description_path, parent_grid_path, parent_ratio,
+                 i_parent_start, j_parent_start, n_rlat, n_rlon):
+        """
+
+        :param logger: Logger.
+        :type logger: Log
+
+        :param auxiliary_path:
+        :param tstep_num:
+        :param vertical_description_path:
+
+        """
+        spent_time = timeit.default_timer()
+
+        self.rlat = None
+        self.rlon = None
+
+        logger.write_log('Rotated Nested grid selected.')
+        self.grid_type = 'Rotated_nested'
+
+        attributes = {'parent_grid_path': parent_grid_path, 'parent_ratio': parent_ratio,
+                      'i_parent_start': i_parent_start, 'j_parent_start': j_parent_start,
+                      'n_rlat': n_rlat, 'n_rlon': n_rlon, 'crs': {'init': 'epsg:4326'}}
+        attributes = self.get_parent_attributes(attributes)
+
+        # Initialises with parent class
+        super(RotatedNestedGrid, self).__init__(logger, attributes, auxiliary_path, vertical_description_path)
+
+        self.shape = (tstep_num, len(self.vertical_desctiption), attributes['n_rlat'], attributes['n_rlon'])
+        self.logger.write_time_log('RotatedNestedGrid', '__init__', timeit.default_timer() - spent_time, 3)
+
+    @staticmethod
+    def get_parent_attributes(attributes):
+        from netCDF4 import Dataset
+
+        netcdf = Dataset(attributes['parent_grid_path'], mode='r')
+
+        rlat = netcdf.variables['rlat'][:]
+        attributes['inc_rlat'] = (rlat[1] - rlat[0]) / attributes['parent_ratio']
+        attributes['1st_rlat'] = rlat[int(attributes['j_parent_start'])]
+
+        rlon = netcdf.variables['rlon'][:]
+        attributes['inc_rlon'] = (rlon[1] - rlon[0]) / attributes['parent_ratio']
+        attributes['1st_rlon'] = rlon[attributes['i_parent_start']]
+
+        rotated_pole = netcdf.variables['rotated_pole']
+        attributes['parent'] = {'new_pole_longitude_degrees': rotated_pole.grid_north_pole_longitude,
+                                'new_pole_latitude_degrees': 90 - rotated_pole.grid_north_pole_latitude}
+
+        return attributes
+
+    def create_regular_rotated(self):
+        """
+        Create a regular grid on the rotated domain.
+
+        :return: center_latitudes, center_longitudes, corner_latitudes, corner_longitudes
+        :rtype: tuple
+        """
+        spent_time = timeit.default_timer()
+
+        center_latitudes = np.linspace(self.attributes['1st_rlat'], self.attributes['1st_rlat'] +
+                                       (self.attributes['inc_rlat'] * (self.attributes['n_rlat'] - 1)),
+                                       self.attributes['n_rlat'], dtype=np.float)
+        center_longitudes = np.linspace(self.attributes['1st_rlon'], self.attributes['1st_rlon'] +
+                                        (self.attributes['inc_rlon'] * (self.attributes['n_rlon'] - 1)),
+                                        self.attributes['n_rlon'], dtype=np.float)
+
+        corner_latitudes = self.create_bounds(center_latitudes, self.attributes['inc_rlat'], number_vertices=4,
+                                              inverse=True)
+        corner_longitudes = self.create_bounds(center_longitudes, self.attributes['inc_rlon'], number_vertices=4)
+
+        self.logger.write_time_log('RotatedNestedGrid', 'create_regular_rotated', timeit.default_timer() - spent_time, 3)
+        return center_latitudes, center_longitudes, corner_latitudes, corner_longitudes
+
+    def create_coords(self):
+        """
+        Create the coordinates for a rotated domain.
+        """
+        spent_time = timeit.default_timer()
+        # Create rotated coordinates
+        (self.rlat, self.rlon, br_lats_single, br_lons_single) = self.create_regular_rotated()
+
+        # 1D to 2D
+        c_lats = np.array([self.rlat] * len(self.rlon)).T
+        c_lons = np.array([self.rlon] * len(self.rlat))
+
+        # Create rotated boundary coordinates
+        b_lats = super(RotatedNestedGrid, self).create_bounds(c_lats, self.attributes['inc_rlat'], number_vertices=4,
+                                                        inverse=True)
+        b_lons = super(RotatedNestedGrid, self).create_bounds(c_lons, self.attributes['inc_rlon'], number_vertices=4)
+
+        # Rotated to Lat-Lon
+        self.boundary_longitudes, self.boundary_latitudes = self.rotated2latlon(b_lons, b_lats)
+        self.center_longitudes, self.center_latitudes = self.rotated2latlon(c_lons, c_lats)
+
+        self.logger.write_time_log('RotatedNestedGrid', 'create_coords', timeit.default_timer() - spent_time, 3)
+        return True
+
+    def rotated2latlon(self, lon_deg, lat_deg, lon_min=-180):
+        """
+        Calculate the unrotated coordinates using the rotated ones.
+
+        :param lon_deg: Rotated longitude coordinate.
+        :type lon_deg: numpy.array
+
+        :param lat_deg: Rotated latitude coordinate.
+        :type lat_deg: numpy.array
+
+        :param lon_min: Minimum value for the longitudes: -180 (-180 to 180) or 0 (0 to 360)
+        :type lon_min: float
+
+        :return: Unrotated coordinates. Longitudes, Latitudes
+        :rtype: tuple(numpy.array, numpy.array)
+        """
+        spent_time = timeit.default_timer()
+        degrees_to_radians = math.pi / 180.
+        # radians_to_degrees = 180. / math.pi
+
+        # Positive east to negative east
+        # self.new_pole_longitude_degrees -= 180
+
+        tph0 = self.attributes['parent']['new_pole_latitude_degrees'] * degrees_to_radians
+        tlm = lon_deg * degrees_to_radians
+        tph = lat_deg * degrees_to_radians
+        tlm0d = self.attributes['parent']['new_pole_longitude_degrees']
+        ctph0 = np.cos(tph0)
+        stph0 = np.sin(tph0)
+
+        stlm = np.sin(tlm)
+        ctlm = np.cos(tlm)
+        stph = np.sin(tph)
+        ctph = np.cos(tph)
+
+        # Latitude
+        sph = (ctph0 * stph) + (stph0 * ctph * ctlm)
+        # if sph > 1.:
+        #     sph = 1.
+        # if sph < -1.:
+        #     sph = -1.
+        sph[sph > 1.] = 1.
+        sph[sph < -1.] = -1.
+
+        aph = np.arcsin(sph)
+        aphd = aph / degrees_to_radians
+
+        # Longitude
+        anum = ctph * stlm
+        denom = (ctlm * ctph - stph0 * sph) / ctph0
+        relm = np.arctan2(anum, denom) - math.pi
+        almd = relm / degrees_to_radians + tlm0d
+
+        # if almd < min_lon:
+        #     almd += 360
+        # elif almd > max_lon:
+        #     almd -= 360
+        almd[almd > (lon_min + 360)] -= 360
+        almd[almd < lon_min] += 360
+
+        self.logger.write_time_log('RotatedNestedGrid', 'rotated2latlon', timeit.default_timer() - spent_time, 3)
+
+        return almd, aphd
+
+    def write_netcdf(self):
+        """
+        Write a rotated grid NetCDF with empty data
+        """
+        from hermesv3_bu.io_server.io_netcdf import write_coords_netcdf
+        spent_time = timeit.default_timer()
+        if not os.path.exists(self.netcdf_path):
+            if not os.path.exists(os.path.dirname(self.netcdf_path)):
+                os.makedirs(os.path.dirname(self.netcdf_path))
+            # Writes an auxiliary empty NetCDF only with the coordinates and an empty variable.
+            write_coords_netcdf(self.netcdf_path, self.center_latitudes, self.center_longitudes,
+                                [{'name': 'var_aux', 'units': '', 'data': 0}],
+                                boundary_latitudes=self.boundary_latitudes,
+                                boundary_longitudes=self.boundary_longitudes,
+                                rotated=True, rotated_lats=self.rlat, rotated_lons=self.rlon,
+                                north_pole_lat=90 - self.attributes['parent']['new_pole_latitude_degrees'],
+                                north_pole_lon=self.attributes['parent']['new_pole_longitude_degrees'])
+        self.logger.write_log("\tGrid created at '{0}'".format(self.netcdf_path), 3)
+        self.logger.write_time_log('RotatedNestedGrid', 'write_netcdf', timeit.default_timer() - spent_time, 3)
+        return True
-- 
GitLab


From 7d020381bf2b83eea9658303b3fa3f2e00c34fcd Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Mon, 20 Jan 2020 17:56:21 +0100
Subject: [PATCH 3/7] Adding Rotated nested grid

---
 conf/hermes.conf                         | 10 ++++++----
 hermesv3_bu/grids/grid_rotated_nested.py | 15 +++++++++------
 hermesv3_bu/writer/default_writer.py     |  8 ++++----
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/conf/hermes.conf b/conf/hermes.conf
index d14ae8f..364be0d 100755
--- a/conf/hermes.conf
+++ b/conf/hermes.conf
@@ -42,10 +42,12 @@ vertical_description = <input_dir>/profiles/vertical/MONARCH_Global_48layers_ver
 # if domain_type == rotated_nested:
     parent_grid_path = /scratch/Earth/ctena/temporal_coords.nc
     parent_ratio = 4
-    i_parent_start = 266
-    j_parent_start = 164
-    n_rlat = 212
-    n_rlon = 196
+    # i -> lon
+    i_parent_start = 200
+    # j -> lat
+    j_parent_start = 100
+    n_rlat = 400
+    n_rlon = 400
 
 # if domain_type == lcc:
 
diff --git a/hermesv3_bu/grids/grid_rotated_nested.py b/hermesv3_bu/grids/grid_rotated_nested.py
index 90dd3df..13cf552 100755
--- a/hermesv3_bu/grids/grid_rotated_nested.py
+++ b/hermesv3_bu/grids/grid_rotated_nested.py
@@ -47,6 +47,7 @@ class RotatedNestedGrid(Grid):
 
         netcdf = Dataset(attributes['parent_grid_path'], mode='r')
 
+        # TODO check if the i_parent start, j_parent_start begin in 0 or in 1
         rlat = netcdf.variables['rlat'][:]
         attributes['inc_rlat'] = (rlat[1] - rlat[0]) / attributes['parent_ratio']
         attributes['1st_rlat'] = rlat[int(attributes['j_parent_start'])]
@@ -56,8 +57,10 @@ class RotatedNestedGrid(Grid):
         attributes['1st_rlon'] = rlon[attributes['i_parent_start']]
 
         rotated_pole = netcdf.variables['rotated_pole']
-        attributes['parent'] = {'new_pole_longitude_degrees': rotated_pole.grid_north_pole_longitude,
-                                'new_pole_latitude_degrees': 90 - rotated_pole.grid_north_pole_latitude}
+        attributes['new_pole_longitude_degrees'] = rotated_pole.grid_north_pole_longitude
+        attributes['new_pole_latitude_degrees'] = 90 - rotated_pole.grid_north_pole_latitude
+
+        netcdf.close()
 
         return attributes
 
@@ -131,10 +134,10 @@ class RotatedNestedGrid(Grid):
         # Positive east to negative east
         # self.new_pole_longitude_degrees -= 180
 
-        tph0 = self.attributes['parent']['new_pole_latitude_degrees'] * degrees_to_radians
+        tph0 = self.attributes['new_pole_latitude_degrees'] * degrees_to_radians
         tlm = lon_deg * degrees_to_radians
         tph = lat_deg * degrees_to_radians
-        tlm0d = self.attributes['parent']['new_pole_longitude_degrees']
+        tlm0d = self.attributes['new_pole_longitude_degrees']
         ctph0 = np.cos(tph0)
         stph0 = np.sin(tph0)
 
@@ -187,8 +190,8 @@ class RotatedNestedGrid(Grid):
                                 boundary_latitudes=self.boundary_latitudes,
                                 boundary_longitudes=self.boundary_longitudes,
                                 rotated=True, rotated_lats=self.rlat, rotated_lons=self.rlon,
-                                north_pole_lat=90 - self.attributes['parent']['new_pole_latitude_degrees'],
-                                north_pole_lon=self.attributes['parent']['new_pole_longitude_degrees'])
+                                north_pole_lat=90 - self.attributes['new_pole_latitude_degrees'],
+                                north_pole_lon=self.attributes['new_pole_longitude_degrees'])
         self.logger.write_log("\tGrid created at '{0}'".format(self.netcdf_path), 3)
         self.logger.write_time_log('RotatedNestedGrid', 'write_netcdf', timeit.default_timer() - spent_time, 3)
         return True
diff --git a/hermesv3_bu/writer/default_writer.py b/hermesv3_bu/writer/default_writer.py
index 5bde50b..1f2546f 100755
--- a/hermesv3_bu/writer/default_writer.py
+++ b/hermesv3_bu/writer/default_writer.py
@@ -110,7 +110,7 @@ class DefaultWriter(Writer):
             var_dim = ('y', 'x',)
             lat_dim = lon_dim = var_dim
 
-        elif self.grid.grid_type == 'Rotated':
+        elif self.grid.grid_type in ['Rotated', 'Rotated_nested']:
             netcdf.createDimension('rlat', len(self.grid.rlat))
             netcdf.createDimension('rlon', len(self.grid.rlon))
             var_dim = ('rlat', 'rlon')
@@ -177,7 +177,7 @@ class DefaultWriter(Writer):
             y_var.standard_name = "projection_y_coordinate"
             y_var[:] = self.grid.y
 
-        elif self.grid.grid_type == 'Rotated':
+        elif self.grid.grid_type in ['Rotated', 'Rotated_nested']:
             self.logger.write_log('\t\tCreating rlat variable', message_level=3)
             rlat = netcdf.createVariable('rlat', np.float64, ('rlat',))
             rlat.long_name = "latitude in rotated pole grid"
@@ -224,7 +224,7 @@ class DefaultWriter(Writer):
                 var.grid_mapping = 'Latitude_Longitude'
             elif self.grid.grid_type == 'Lambert Conformal Conic':
                 var.grid_mapping = 'Lambert_Conformal'
-            elif self.grid.grid_type == 'Rotated':
+            elif self.grid.grid_type in ['Rotated', 'Rotated_nested']:
                 var.grid_mapping = 'rotated_pole'
             elif self.grid.grid_type == 'Mercator':
                 var.grid_mapping = 'mercator'
@@ -247,7 +247,7 @@ class DefaultWriter(Writer):
             mapping.longitude_of_central_meridian = self.grid.attributes['lon_0']
             mapping.latitude_of_projection_origin = self.grid.attributes['lat_0']
 
-        elif self.grid.grid_type == 'Rotated':
+        elif self.grid.grid_type in ['Rotated', 'Rotated_nested']:
             mapping = netcdf.createVariable('rotated_pole', 'c')
             mapping.grid_mapping_name = 'rotated_latitude_longitude'
             mapping.grid_north_pole_latitude = 90 - self.grid.attributes['new_pole_latitude_degrees']
-- 
GitLab


From ecda0f044a8f74169e8234d3541b052397da9a2b Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Wed, 12 Feb 2020 12:05:46 +0100
Subject: [PATCH 4/7] Added rotated-nested on monarch writer

---
 hermesv3_bu/writer/monarch_writer.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hermesv3_bu/writer/monarch_writer.py b/hermesv3_bu/writer/monarch_writer.py
index 3e43f0d..3975620 100755
--- a/hermesv3_bu/writer/monarch_writer.py
+++ b/hermesv3_bu/writer/monarch_writer.py
@@ -62,8 +62,8 @@ class MonarchWriter(Writer):
         super(MonarchWriter, self).__init__(comm_world, comm_write, logger, netcdf_path, grid, date_array,
                                             pollutant_info, rank_distribution, emission_summary)
 
-        if self.grid.grid_type not in ['Rotated']:
-            error_exit("ERROR: Only Rotated grid is implemented for MONARCH. " +
+        if self.grid.grid_type not in ['Rotated', 'Rotated_nested']:
+            error_exit("ERROR: Only Rotated or Rotated-nested grid is implemented for MONARCH. " +
                        "The current grid type is '{0}'".format(self.grid.grid_type))
 
         for i, (pollutant, variable) in enumerate(self.pollutant_info.iterrows()):
-- 
GitLab


From 1a61f0d344d9697d1444099e0b9ffa83fd464f3c Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Wed, 12 Feb 2020 13:49:06 +0100
Subject: [PATCH 5/7] PEP8 corrections

---
 hermesv3_bu/grids/grid_rotated_nested.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/hermesv3_bu/grids/grid_rotated_nested.py b/hermesv3_bu/grids/grid_rotated_nested.py
index 13cf552..2630173 100755
--- a/hermesv3_bu/grids/grid_rotated_nested.py
+++ b/hermesv3_bu/grids/grid_rotated_nested.py
@@ -84,7 +84,8 @@ class RotatedNestedGrid(Grid):
                                               inverse=True)
         corner_longitudes = self.create_bounds(center_longitudes, self.attributes['inc_rlon'], number_vertices=4)
 
-        self.logger.write_time_log('RotatedNestedGrid', 'create_regular_rotated', timeit.default_timer() - spent_time, 3)
+        self.logger.write_time_log('RotatedNestedGrid', 'create_regular_rotated',
+                                   timeit.default_timer() - spent_time, 3)
         return center_latitudes, center_longitudes, corner_latitudes, corner_longitudes
 
     def create_coords(self):
@@ -101,7 +102,7 @@ class RotatedNestedGrid(Grid):
 
         # Create rotated boundary coordinates
         b_lats = super(RotatedNestedGrid, self).create_bounds(c_lats, self.attributes['inc_rlat'], number_vertices=4,
-                                                        inverse=True)
+                                                              inverse=True)
         b_lons = super(RotatedNestedGrid, self).create_bounds(c_lons, self.attributes['inc_rlon'], number_vertices=4)
 
         # Rotated to Lat-Lon
-- 
GitLab


From 5d088b77618daa8513c8bdf35b00312d3dbe32e5 Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Thu, 13 Feb 2020 10:45:49 +0100
Subject: [PATCH 6/7] Substracting 1 to the i_parent and j_parent start

---
 hermesv3_bu/grids/grid_rotated_nested.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/hermesv3_bu/grids/grid_rotated_nested.py b/hermesv3_bu/grids/grid_rotated_nested.py
index 2630173..9b5ed39 100755
--- a/hermesv3_bu/grids/grid_rotated_nested.py
+++ b/hermesv3_bu/grids/grid_rotated_nested.py
@@ -47,14 +47,15 @@ class RotatedNestedGrid(Grid):
 
         netcdf = Dataset(attributes['parent_grid_path'], mode='r')
 
-        # TODO check if the i_parent start, j_parent_start begin in 0 or in 1
         rlat = netcdf.variables['rlat'][:]
         attributes['inc_rlat'] = (rlat[1] - rlat[0]) / attributes['parent_ratio']
-        attributes['1st_rlat'] = rlat[int(attributes['j_parent_start'])]
+        # j_parent_start start the index at 1 so we must - 1
+        attributes['1st_rlat'] = rlat[int(attributes['j_parent_start']) - 1]
 
         rlon = netcdf.variables['rlon'][:]
         attributes['inc_rlon'] = (rlon[1] - rlon[0]) / attributes['parent_ratio']
-        attributes['1st_rlon'] = rlon[attributes['i_parent_start']]
+        # i_parent_start start the index at 1 so we must - 1
+        attributes['1st_rlon'] = rlon[attributes['i_parent_start'] - 1]
 
         rotated_pole = netcdf.variables['rotated_pole']
         attributes['new_pole_longitude_degrees'] = rotated_pole.grid_north_pole_longitude
-- 
GitLab


From 55f4ee99cffc87496b7b072a5fdbe87acb142cb9 Mon Sep 17 00:00:00 2001
From: Carles Tena <carles.tena@bsc.es>
Date: Thu, 13 Feb 2020 14:37:02 +0100
Subject: [PATCH 7/7] Increased the buffer size

---
 hermesv3_bu/writer/writer.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/hermesv3_bu/writer/writer.py b/hermesv3_bu/writer/writer.py
index 0a92322..f7ca833 100755
--- a/hermesv3_bu/writer/writer.py
+++ b/hermesv3_bu/writer/writer.py
@@ -14,6 +14,8 @@ CHUNKING = True
 BALANCED = False
 MPI_TAG_CONSTANT = 10**6
 
+BUFFER_SIZE = 2**28
+
 
 def select_writer(logger, comm_world, arguments, grid, date_array):
     """
@@ -328,7 +330,7 @@ class Writer(object):
             for i_rank in range(self.comm_world.Get_size()):
                 self.logger.write_log(
                     '\tFrom {0} to {1}'.format(i_rank, self.comm_world.Get_rank()), message_level=3)
-                req = self.comm_world.irecv(2**27, source=i_rank, tag=i_rank)
+                req = self.comm_world.irecv(BUFFER_SIZE, source=i_rank, tag=i_rank)
                 dataframe = req.wait()
                 data_list.append(dataframe.reset_index())
 
-- 
GitLab