Merge branch 'master' of github.com:exoclime/THOR-dev

.clang-format

@@ -22,13 +22,13 @@ AlignOperands: true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: false
 
-AllowShortBlocksOnASingleLine: true
-AllowShortCaseLabelsOnASingleLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
 
-AllowShortFunctionsOnASingleLine: InlineOnly
+AllowShortFunctionsOnASingleLine: None
 
-AllowShortIfStatementsOnASingleLine: true
-AllowShortLoopsOnASingleLine: true
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
 
 AlwaysBreakAfterReturnType: None
 
@@ -68,7 +68,7 @@ BreakStringLiterals: true
 # limit of lign break
 # 0: no limit
 # the original code, didn't always use it (used for function calls and declarations, not for formulas), should we use one?
-ColumnLimit: 0
+ColumnLimit: 100
 
 # CommentPragmas: str
 CompactNamespaces: true

Makefile

@@ -77,7 +77,7 @@ ifeq ($(COMP), nvcc)
 	CC_comp_flag = -dc
 	ccbin :=
 	# ccbin := -ccbin g++-5
-	CDB := none 
+	CDB := none
 	arch := -arch sm_$(SM)
 	dependencies_flags = --generate-dependencies
 
@@ -356,9 +356,9 @@ clean:
 	-$(RM) $(BINDIR)/release/esp
 	-$(RM) $(BINDIR)/prof/esp
 	@echo $(CYAN)clean up objects files and dependencies $(END)
-	-$(RM) $(OBJDIR)/debug/*.o $(OBJDIR)/debug/*.d $(OBJDIR)/debug/*.o.json
-	-$(RM) $(OBJDIR)/release/*.o $(OBJDIR)/release/*.d $(OBJDIR)/release/*.o.json
-	-$(RM) $(OBJDIR)/prof/*.o $(OBJDIR)/prof/*.d $(OBJDIR)/prof/*.o.json
+	-$(RM) $(OBJDIR)/debug/*.o $(OBJDIR)/debug/*.d $(OBJDIR)/debug/*.d.* $(OBJDIR)/debug/*.o.json
+	-$(RM) $(OBJDIR)/release/*.o $(OBJDIR)/release/*.d $(OBJDIR)/release/*.d.* $(OBJDIR)/release/*.o.json
+	-$(RM) $(OBJDIR)/prof/*.o $(OBJDIR)/prof/*.d $(OBJDIR)/prof/*.d.* $(OBJDIR)/prof/*.o.json
 	@echo $(CYAN)clean up tests binaries $(END)
 	-$(RM) $(BINDIR)/tests/cmdargs_test
 	-$(RM) $(BINDIR)/tests/storage_test

README.md

@@ -18,10 +18,14 @@ Current code owners: Joao Mendonca: [email protected], Russell Deitrick
    $ cd THOR
    $ cp Makefile.conf.template Makefile.conf
 ```
-Find the `SM` value of your Nvidia GPU. Then open `Makefile.conf` in a text editor and edit like so:
+Find the `SM` value of your Nvidia GPU. Decide if you want to run without any physics module `empty` physics module, or the one with radiative transfer, the `multi` module. Then open `Makefile.conf` in a text editor and edit like so:
 ```
-MODULES_SRC := src/physics/managers/multi/
+MODULES_SRC := src/physics/managers/<module_type>/
 SM:=<SM value of your card> 
+
+``` 
+Set `module_type`to `empty` (default) or `multi`.
+
 ```
 Then head back to the command line and
 ```sh

changelog.md

@@ -0,0 +1,24 @@
+# changes since v2.0.0
+
+ * argument parser fails and complains when wrong number of argument for keys
+ * added test script to run multiple sims
+ * fix conservation output (was not copied back before output)
+ * clean up RT module startup output
+ * added new routines to mjolnir/hamarr (KE, SR)
+ * fixed issues in regrid
+ * changed many of the plot functions to use regrid data (some still need work)
+ * added entropy to global & grid conservation outputs
+ * fixed pot temp update error in Density_Pressure_Eqs_Poles *major*
+ * started generalizing plot functions in hamarr to make adding new quantities easier
+ * added acoustic wave experiment from Tomita & Satoh 2004
+ * added gravity wave experiment from Tomita & Satoh 2004
+ * added python scripts to allow editing of initial h5 files (preliminary)
+ * removed TPprof option, which didn't work as desired anyway: users should use the python tools to edit initial h5 files if non-isothermal initial state is needed
+ * removal of spurious vertical component of horizontal momentum diffusion has been moved
+ to a separate function "Correct_Horizontal" to avoid potential issues related to the order
+ in which threads are called
+ * incorrect diffusion quantity (diffmh_d) was being passed to Momentum_Eq in the dynamical core, changed now to correct value (DivM_d)
+ * added crash_report tool that dumps location of nans when the model crashes
+ * further updates to python plotting tools to make them more flexible
+ * added "custom_example.py" to mjolnir to demonstrate how to make multipanel plots with the python tools
+ * grid output now contains differential operators grad, div, and vertical component of curl (the latter is not used by the model, but may be useful in post-processing)

ifile/deephj.thr

@@ -50,10 +50,6 @@ Tmean = 1759
 # Reference surface pressure [Pa]
 P_ref = 22000000.0
 
-# Initialize atmosphere with Guillot TP profile (0 = isothermal)?
-TPprof = 0
-
-
 #-- Grid options -------------------------------------------------------------#
 # Altitude of the top of the model domain [m]
 Top_altitude = 8e6
@@ -79,6 +75,9 @@ DivDampP =    true
 
 # Strength of diffusion
 Diffc = 0.02
+
+# Strength of divergence damping
+DivDampc = 0.02
 #########################################################
 
 

ifile/earth_acoustic_test.thr

@@ -0,0 +1,189 @@
+# config file for THOR
+# config format version
+config_version = 1
+
+# earth acoustic wave test (Tomita & Satoh 2004)
+
+
+#-- Time stepping and output options -----------------------------------------#
+# number of steps
+num_steps = 96
+
+# length of timesteps in seconds
+timestep = 1800
+
+# output
+# output every n steps
+n_out = 2
+
+# output directory (relative to current working directory)
+# defaults to 'results'
+results_path = acoustic_test_divdonly
+
+# calculate and output quantities we hope to conserve
+# angular momentum, energy, mass, (entropy soon)
+conservation = true
+
+
+#-- Planetary parameters -----------------------------------------------------#
+# name of simulation for output files
+simulation_ID = Earth
+
+# Radius [m]
+radius = 6371000.0
+
+# Rotation rate [rad s^-1]
+rotation_rate = 0
+
+# Gravitational acceleration [m/s^2]
+gravitation = 9.8
+
+# Gas constant [J/(Kg K)] (R_univ/mean_molecular_mass)
+Rd = 287.0
+
+# Specific heat capacities [J/(Kg K)]
+Cp = 1005.0
+
+# Mean atmospheric temperature [K]
+Tmean = 300.0
+
+# Reference surface pressure [Pa] (pressure at bottom of model)
+P_ref = 100000.0
+
+#-- Grid options -------------------------------------------------------------#
+# Altitude of the top of the model domain [m]
+Top_altitude = 10000.0
+
+# Horizontal resolution level.
+glevel = 5
+
+# Number of vertical layers
+vlevel = 20
+
+# Spring dynamics
+spring_dynamics = true
+
+# Parameter beta for spring dynamics
+spring_beta = 1.15
+
+## diffusion ############################################
+# Hyper-diffusion
+HyDiff  =    false
+
+# Divergence-damping
+DivDampP =    true
+
+# Strength of diffusion
+Diffc = 0.02
+
+# Strength of divergence damping
+DivDampc = 0.02
+#########################################################
+
+
+#-- Model options ------------------------------------------------------------#
+# Non-hydrostatic parameter
+NonHydro = true
+
+# Deep atmosphere (scale quantities for altitude + radius)
+DeepModel = true
+
+# Initial conditions
+rest = true
+
+# initial conditions file, used if rest is set to false
+# (path relative to current working directory)
+# defaults to 'ifile/esp_initial.h5'
+initial =ifile/esp_initial.h5
+
+# Core benchmark tests
+# Held-Suarez test for Earth == HeldSuarez
+# Benchmark test for shallow hot Jupiter == ShallowHotJupiter
+# Benchmark test for deep hot Jupiter == DeepHotJupiter
+# Benchmark test for tidally locked Earth == TidallyLockedEarth
+# No benchmark test == NoBenchmark (model is then forced with grey RT by default)
+core_benchmark = AcousticTest
+
+# Switch off dynamical core (gcm)
+# This is useful for testing/debugging physics modules
+gcm_off = false
+
+# enable convective adjustment scheme
+conv_adj = 0
+
+
+#-- Sponge layer (Rayleigh drag) ---------------------------------------------#
+# use sponge layer (Rayleigh drag) at top of atmosphere?
+SpongeLayer = false
+
+# latitude rings (zonal mean is calculated over these)
+nlat = 20
+
+# bottom of sponge layer (fractional height)
+ns_sponge = 0.75
+
+# strength of sponge layer (1/damping time)
+Rv_sponge = 1e-5
+
+# shrink sponge by half after some time (experimental)
+#shrink_sponge = true
+
+# when to shrink sponge (days)
+#t_shrink = 1
+
+
+#-- Radiative transfer options (core_benchmark = NoBenchmark) --------------------------#
+radiative_transfer = false
+## RT parameters #######################################
+# stellar temperature (k)
+Tstar = 5800
+
+# orbital distance or semi-major axis (au)
+planet_star_dist = 1
+
+# radius of host star (R_sun)
+radius_star = 1
+
+# bond albedo of planet
+albedo = 0.3
+
+# grey opt. depth of thermal wavelengths (at ref pressure)
+taulw = 10
+
+# grey opt. depth of incoming stellar flux (at ref pressure)
+tausw = 1.67
+
+# temperature of internal heat flux (bottom boundary) (K)
+Tlow = 50
+
+# diffusivity factor
+diff_fac = 0.5
+#########################################################
+
+## insolation (orbit + spin-state) parameters ###########
+# synchronous rotation (tidally-locking at 1:1)
+sync_rot = true
+
+# mean motion of orbit (if sync_rot=false and ecc>0) (rad/s)
+#mean_motion = 1.98e-7
+
+# initial substellar longitude (deg)
+#alpha_i = 0
+
+# initial orbital position (deg)
+#true_long_i = 0
+
+# eccentricity of orbit
+#ecc = 0
+
+# obliquity (axial-tilt) (deg)
+#obliquity = 0
+
+# longitude of periastron (relative to equinox) (deg)
+# (stupid Earth convention applies)
+#longp = 0
+#########################################################
+
+#-- Device options -----------------------------------------------------------#
+# GPU ID number
+GPU_ID_N = 0