fix: adia0D example can run

examples/adiabaticparcel/as2017.py

@@ -8,7 +8,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Friday 12th April 2024
+Last Modified: Thursday 18th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -80,30 +80,28 @@
 
 # parameters to edit in model configuration and plotting
 params1 = {
-    "W_AVG": 1,
-    "T_HALF": 150,
+    "W_avg": 1,
+    "TAU_half": 150,
     "T_END": 300,
     "COUPLTSTEP": 1,
     "OBSTSTEP": 2,
-    "lwdth": 2,
 }
 params2 = {
-    "W_AVG": 0.5,
-    "T_HALF": 300,
+    "W_avg": 0.5,
+    "TAU_half": 300,
     "T_END": 600,
     "COUPLTSTEP": 1,
     "OBSTSTEP": 2,
-    "lwdth": 1,
 }
 params3 = {
-    "W_AVG": 0.002,
-    "T_HALF": 75000,
+    "W_avg": 0.002,
+    "TAU_half": 75000,
     "T_END": 150000,
     "COUPLTSTEP": 3,
     "OBSTSTEP": 750,
-    "lwdth": 0.5,
 }
 paramslist = [params1, params2, params3]
+lwdths = [2, 1, 0.5]
 
 def displacement(time, w_avg, thalf):
     '''displacement z given velocity, w, is sinusoidal
@@ -163,16 +161,16 @@ def displacement(time, w_avg, thalf):
         plt.close()
 
     fig, axs = plt.subplots(nrows=3, ncols=1, figsize=(5, 16))
-    for params in paramslist:
+    for params, lwdth in zip(paramslist, lwdths):
 
         ### edit relevant setup file parameters
         params["zarrbasedir"] = binpath+"as2017_sol"+str(runnum)+".zarr"
-        params["setuptxt"] = binpath+"as2017_setup.txt"
+        params["setup_filename"] = binpath+"as2017_setup.txt"
         editconfigfile.edit_config_params(configfile, params)
 
         ### delete any existing dataset
         os.system("rm -rf "+params["zarrbasedir"])
-        os.system("rm "+params["setuptxt"])
+        os.system("rm "+params["setup_filename"])
 
         ### run model
         os.chdir(path2build)
@@ -197,18 +195,18 @@ def displacement(time, w_avg, thalf):
         supersat = thermo.supersaturation()
         time = pyzarr.get_time(dataset).secs
         sddata = pyzarr.get_supers(dataset, consts)
-        zprof = displacement(time, config["W_AVG"], config["T_HALF"])
+        zprof = displacement(time, config["W_avg"], config["TAU_half"])
 
         attrs = ["radius", "xi", "msol"]
         sd0 = sdtracing.attributes_for1superdroplet(sddata, 0, attrs)
         numconc = np.sum(sddata["xi"][0])/gbxs["domainvol"]/1e6  # [/cm^3]
 
         ### plot results
-        wlab = "<w> = {:.1f}".format(config["W_AVG"]*100)+"cm s$^{-1}$"
+        wlab = "<w> = {:.1f}".format(config["W_avg"]*100)+"cm s$^{-1}$"
         axs = as2017fig.condensation_validation_subplots(axs, time, sd0["radius"],
                                                    supersat[:, 0, 0, 0],
                                                    zprof,
-                                                   lwdth=params["lwdth"],
+                                                   lwdth=lwdth,
                                                    lab=wlab)
 
         runnum += 1

examples/adiabaticparcel/cuspbifurc.py

@@ -6,7 +6,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Friday 12th April 2024
+Last Modified: Thursday 18th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -149,7 +149,7 @@ def displacement(time, w_avg, thalf):
 supersat = thermo.supersaturation()
 time = pyzarr.get_time(dataset).secs
 sddata = pyzarr.get_supers(dataset, consts)
-zprof = displacement(time, config["W_AVG"], config["T_HALF"])
+zprof = displacement(time, config["W_avg"], config["TAU_half"])
 
 ### plot results
 # sample drops to plot from whole range of SD ids
@@ -169,5 +169,5 @@ def displacement(time, w_avg, thalf):
                                 thermo.temp[:, 0, 0, 0],
                                 supersat[:, 0, 0, 0],
                                 sddata.IONIC, sddata.MR_SOL,
-                                config["W_AVG"], numconc,
+                                config["W_avg"], numconc,
                                 savename2)

examples/adiabaticparcel/src/config/as2017_config.yaml

@@ -1,4 +1,3 @@
----
 # ----- CLEO -----
 # File: config.yaml
 # Project: config
@@ -24,52 +23,52 @@
 
 ### Initialisation Parameters ###
 inputfiles:
-  constants_filename : ../libs/cleoconstants.hpp           # name of file for values of physical constants
-  grid_filename : ./share/as2017_dimlessGBxboundaries.dat  # binary filename for initialisation of GBxs / GbxMaps
+  constants_filename: ../libs/cleoconstants.hpp            # name of file for values of physical constants
+  grid_filename: ./share/as2017_dimlessGBxboundaries.dat   # binary filename for initialisation of GBxs / GbxMaps
 
 initsupers:
-  type : frombinary                                        # type of initialisation of super-droplets
-  initsupers_filename : ./share/as2017_dimlessSDsinit.dat  # binary filename for initialisation of SDs
-  totnsupers : 64                                          # initial total no. of SDs
+  type: frombinary                                         # type of initialisation of super-droplets
+  initsupers_filename: ./share/as2017_dimlessSDsinit.dat   # binary filename for initialisation of SDs
+  totnsupers: 64                                           # initial total no. of SDs
 
 ### Output Parameters ###
 outputdata:
-  setup_filename : /home/m/m300950/CLEO/build_adia0D//bin/as2017_setup.txt  # .txt filename to copy configuration to
-  stats_filename : /home/m/m300950/CLEO/build_adia0D//bin/as2017_stats.txt  # .txt file to output runtime statistics to
-  zarrbasedir : /home/m/m300950/CLEO/build_adia0D//bin/as2017_sol8.zarr     # zarr store base directory
-  maxchunk : 2500000                                                        # maximum no. of elements in chunks of zarr store array
+  setup_filename: /home/m/m300950/CLEO/build_adia0D//bin/as2017_setup.txt   # .txt filename to copy configuration to
+  stats_filename: /home/m/m300950/CLEO/build_adia0D//bin/as2017_stats.txt   # .txt file to output runtime statistics to
+  zarrbasedir: /home/m/m300950/CLEO/build_adia0D//bin/as2017_sol2.zarr      # zarr store base directory
+  maxchunk: 2500000                                                         # maximum no. of elements in chunks of zarr store array
 
 ### SDM Runtime Parameters ###
 domain:
-  nspacedims : 0                                       # no. of spatial dimensions to model
-  ngbxs : 1                                            # total number of Gbxs
+  nspacedims: 0                                        # no. of spatial dimensions to model
+  ngbxs: 1                                             # total number of Gbxs
 
 timesteps:
-  CONDTSTEP : 1                                        # time between SD condensation [s]
-  COLLTSTEP : 1                                        # time between SD collision [s]
-  MOTIONTSTEP : 1                                      # time between SDM motion [s]
-  COUPLTSTEP : 3                                       # time between dynamic couplings [s]
-  OBSTSTEP : 750                                       # time between SDM observations [s]
-  T_END : 150000                                       # time span of integration from 0s to T_END [s]
+  CONDTSTEP: 1                                         # time between SD condensation [s]
+  COLLTSTEP: 1                                         # time between SD collision [s]
+  MOTIONTSTEP: 1                                       # time between SDM motion [s]
+  COUPLTSTEP: 3                                        # time between dynamic couplings [s]
+  OBSTSTEP: 750                                        # time between SDM observations [s]
+  T_END: 150000                                        # time span of integration from 0s to T_END [s]
 
 ### Microphysics Parameters ###
 microphysics:
   condensation:
-    do_alter_thermo : true                             # true = cond/evap alters the thermodynamic state
-    niters : 2                                         # no. iterations of Newton Raphson Method before testing for convergence
-    SUBTSTEP : 0.1                                     # smallest subtimestep in cases of substepping [s]
-    rtol : 0.0                                         # relative tolerance for implicit Euler integration
-    atol : 0.01                                        # abolute tolerance for implicit Euler integration
+    do_alter_thermo: true                              # true = cond/evap alters the thermodynamic state
+    niters: 2                                          # no. iterations of Newton Raphson Method before testing for convergence
+    SUBTSTEP: 0.1                                      # smallest subtimestep in cases of substepping [s]
+    rtol: 0.0                                          # relative tolerance for implicit Euler integration
+    atol: 0.01                                         # abolute tolerance for implicit Euler integration
 
 ### Coupled Dynamics Parameters ###
 coupled_dynamics:
-  type : cvode                                          # type of coupled dynamics to configure
+  type: cvode                                           # type of coupled dynamics to configure
   # initial (uniform) thermodynamic conditions #
-  P_init : 100000.0                                     # initial pressure [Pa]
-  TEMP_init : 273.15                                    # initial temperature [T]
-  relh_init : 98.0                                      # initial relative humidity (%)
+  P_init: 100000.0                                      # initial pressure [Pa]
+  TEMP_init: 273.15                                     # initial temperature [T]
+  relh_init: 98.0                                       # initial relative humidity (%)
   # ODE solver parameters #
-  W_avg : 0.002                                         # average amplitude of sinusoidal w [m/s] (dP/dt ~ w*dP/dz)
-  TAU_half : 75000                                      # timescale for w sinusoid, tau_half = TAU_HALF/pi [s]
-  rtol : 1e-6                                           # relative tolerance for integration of [P, T, qv, qc] ODEs
-  atol : 1e-6                                           # relative tolerance for integration of [P, T, qv, qc] ODEs
+  W_avg: 0.002                                          # average amplitude of sinusoidal w [m/s] (dP/dt ~ w*dP/dz)
+  TAU_half: 75000                                       # timescale for w sinusoid, tau_half = TAU_half/pi [s]
+  rtol: 1e-6                                            # relative tolerance for integration of [P, T, qv, qc] ODEs
+  atol: 1e-6                                            # relative tolerance for integration of [P, T, qv, qc] ODEs

examples/adiabaticparcel/src/config/cuspbifurc_config.yaml

@@ -70,6 +70,6 @@ coupled_dynamics:
   relh_init : 98.0                                      # initial relative humidity (%)
   # ODE solver parameters #
   W_avg : 0.002                                         # average amplitude of sinusoidal w [m/s] (dP/dt ~ w*dP/dz)
-  TAU_half : 75000                                      # timescale for w sinusoid, tau_half = TAU_HALF/pi [s]
+  TAU_half : 75000                                      # timescale for w sinusoid, tau_half = TAU_half/pi [s]
   rtol : 1e-6                                           # relative tolerance for integration of [P, T, qv, qc] ODEs
   atol : 1e-6                                           # relative tolerance for integration of [P, T, qv, qc] ODEs

examples/exampleplotting/plotssrc/as2017fig.py

@@ -6,7 +6,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Friday 17th November 2023
+Last Modified: Wednesday 17th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -100,7 +100,7 @@ def condensation_validation_subplots(axs, time, radius, supersat, zprof,
     return axs
 
 def arabas_shima_2017_fig(time, zprof, radius, msol, temp, supersat,
-                          IONIC, MR_SOL, W_AVG, numconc, savename=""):
+                          IONIC, MR_SOL, W_avg, numconc, savename=""):
     ''' plots the same plots as in Figure 5 of
     "On the CCN (de)activation nonlinearities"
     S. Arabas and S. Shima 2017 to check radius
@@ -118,7 +118,7 @@ def arabas_shima_2017_fig(time, zprof, radius, msol, temp, supersat,
 
     textlab = "N = "+str(numconc)+"cm$^{-3}$\n" +\
               "r$_{dry}$ = "+"{:.2g}\u03BCm\n".format(radius[0]) +\
-              "<w> = {:.1f}".format(W_AVG*100)+"cm s$^{-1}$"
+              "<w> = {:.1f}".format(W_avg*100)+"cm s$^{-1}$"
     axs[0].text(0.03, 0.82, textlab, transform=axs[0].transAxes)
 
     axs[0].set_xlim([-1, 1])

libs/initialise/optional_config_params.hpp

@@ -9,7 +9,7 @@
  * Author: Clara Bayley (CB)
  * Additional Contributors:
  * -----
- * Last Modified: Wednesday 17th April 2024
+ * Last Modified: Thursday 18th April 2024
  * Modified By: CB
  * -----
  * License: BSD 3-Clause "New" or "Revised" License
@@ -100,7 +100,7 @@ struct OptionalConfigParams {
     double relh_init = NaNVals::dbl(); /**< initial relative humidity (%) */
     /* ODE solver parameters */
     double W_avg = NaNVals::dbl(); /**< average amplitude of sinusoidal w [m/s] (dP/dt ~ w*dP/dz) */
-    double TAU_half = NaNVals::dbl(); /**< timescale for w sinusoid, tau_half = TAU_HALF/pi [s] */
+    double TAU_half = NaNVals::dbl(); /**< timescale for w sinusoid, tau_half = TAU_half/pi [s] */
     double rtol = NaNVals::dbl(); /**< relative tolerance for integration of [P, T, qv, qc] ODEs */
     double atol = NaNVals::dbl(); /**< absolute tolerances for integration of [P, T, qv, qc] ODEs */
   } cvodedynamics;

pySD/editconfigfile.py

@@ -9,7 +9,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Wednesday 17th April 2024
+Last Modified: Thursday 18th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -24,19 +24,21 @@ def update_param(node, param, new_value):
     '''Function to recursively searches for 'param' key in YAML node
     and updates it's value to with 'new_value' when found '''
 
-    is_success = False
     if isinstance(node, dict):
         if param in node:
             node[param] = new_value # update value
-            is_success = True
+            return True
         else:
             for key, val in node.items():
-                update_param(val, param, new_value)
+                is_success = update_param(val, param, new_value)
+                if is_success:
+                    return True
     elif isinstance(node, list):
         for item in node:
-            update_param(item, param, new_value)
-
-    return is_success
+            is_success = update_param(item, param, new_value)
+            if is_success:
+                    return True
+    return False
 
 def edit_config_params(filename, params2change):
     ''' rewrites config YAML file with key,value pairs listed in params2change updated to new values
@@ -51,9 +53,8 @@ def edit_config_params(filename, params2change):
     # Update the parameters from the YAML file
     for param, new_value in params2change.items():
         is_success = update_param(data, param, new_value)
-
         if not is_success:
-          errmsg = param+"could not be updated to new value: "+str(new_value)
+          errmsg = param+" could not be updated to new value: "+str(new_value)
           raise ValueError(errmsg)
 
     # Overwrite the YAML file

pySD/gbxboundariesbinary_src/create_gbxboundaries.py

@@ -6,7 +6,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Tuesday 24th October 2023
+Last Modified: Wednesday 17th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -23,8 +23,7 @@
 from .. import cxx2py, writebinary
 
 def get_COORD0_from_constsfile(constsfile, returnconsts=False):
-  ''' create values from constants file & config file
-  required as inputs to create initial
+  ''' create values from constants file required as inputs to create initial
   superdroplet conditions '''
 
   consts = cxx2py.read_cxxconsts_into_floats(constsfile)

pySD/gbxboundariesbinary_src/read_gbxboundaries.py

@@ -1,3 +1,23 @@
+'''
+Copyright (c) 2024 MPI-M, Clara Bayley
+
+
+----- CLEO -----
+File: read_gbxboundaries.py
+Project: gbxboundariesbinary_src
+Created Date: Wednesday 17th January 2024
+Author: Clara Bayley (CB)
+Additional Contributors:
+-----
+Last Modified: Wednesday 17th April 2024
+Modified By: CB
+-----
+License: BSD 3-Clause "New" or "Revised" License
+https://opensource.org/licenses/BSD-3-Clause
+-----
+File Description:
+'''
+
 import numpy as np
 import matplotlib.pyplot as plt
 
@@ -248,9 +268,7 @@ def grid_dimensions(gbxbounds):
     return extents, spacings, griddims
 
 def print_domain_info(constsfile, gridfile):
-    ''' create values from constants file & config file
-    required as inputs to create initial
-    superdroplet conditions '''
+    ''' prints information about domain reda from gridfile and constants file '''
 
     isprint=True
     COORD0 = get_COORD0_from_constsfile(constsfile)

pySD/sdmout_src/ensembzarr.py

@@ -6,7 +6,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Friday 19th January 2024
+Last Modified: Thursday 18th April 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -54,7 +54,7 @@ def write_ensemb_setupfile(ensembsetupfile, setupfile, datasets):
   os.system('cp '+setupfile+" "+ensembsetupfile)
   params = {
     "initsupers_filename" : "[ensemble, see below]",
-    "setuptxt" : "[ensemble, see below]",
+    "setup_filename" : "[ensemble, see below]",
     "zarrbasedir" : "[ensemble, see below]",
     "stats_filename" : "[ensemble, see below]"
     }