Merge branch 'cmf2' into reaction_object

# Conflicts:
#	cmf/__init__.py
#	cmf/cmf_core_src/cmf_wrap.cpp
#	cmf/cmf_core_src/docstrings.i

cmf/__init__.py

@@ -22,8 +22,7 @@
 from .timetools import StopWatch, datetime_to_cmf, timerange
 
 
-__version__ = '2.0.0b3.reaction_object'
-__compiletime__ = 'Thu Sep 12 17:27:29 2019'
+__version__ = '2.0.0b6'
 
 from .cmf_core import connect_cells_with_flux as __ccwf
 
@@ -41,5 +40,3 @@ def connect_cells_with_flux(cells, connection, start_at_layer=0):
         raise TypeError("flux_connection does not implement the cell_connector protocol")
 
 
-
-

cmf/cmf_core_src/math/real.h

@@ -26,7 +26,6 @@ typedef double real;
 const real REAL_MAX = std::numeric_limits<real>::max();
 #endif
 
-const std::string __compiledate__ = std::string("cmf compiled ") + std::string(__DATE__) + " - " + std::string(__TIME__);
 
 // Some helper functions
 /// Returns the minimum of two values

cmf/cmf_core_src/upslope/surfacewater.cpp

@@ -67,6 +67,30 @@ void DiffusiveSurfaceRunoff::connect_cells( cmf::upslope::Cell& cell1,cmf::upslo
 		new DiffusiveSurfaceRunoff(sw_upper,lower.get_surfacewater(),w);
 	}
 
+}
+/// Returns the square root of the gradient with singularity prevention
+///
+/// \param grad Gradient in m/m
+/// \return sign(grad) * sqrt(grad) but with a flatted singularity at grad = 0
+real sqrt_slope(real grad) {
+
+    const real s_sqrt = sign(grad) * sqrt(std::abs(grad));
+    // linear slope width is a value in which slope range the slope should be altered
+    // to prevent a singularity in dq/ds
+    if (cmf::options.diffusive_slope_singularity_protection > 0.0) {
+        // Only a shortcut for faster writing
+        const real &s0 = cmf::options.diffusive_slope_singularity_protection;
+        // Weight of linear part
+        real w_lin = exp(-square((grad / s0)));
+        // linear part using the slope at s0/4
+        real s_lin = grad / (2. * sqrt(s0 / 4));
+        // Weighted sum of sqrt(s) and a*s
+        return w_lin * s_lin + (1 - w_lin) * s_sqrt;
+    } else {
+        return s_sqrt;
+
+    }
+
 }
 
 real DiffusiveSurfaceRunoff::calc_q( cmf::math::Time t )
@@ -101,21 +125,9 @@ real DiffusiveSurfaceRunoff::calc_q( cmf::math::Time t )
 	// Get slope
 	real grad = dPsi/m_distance;
 
-	// Get signed square root for 
-	real s_sqrt = sign(grad) * sqrt(std::abs(grad));
+	// Get signed square root for gradient
+	real s_sqrt = sqrt_slope(grad);
 
-	// linear slope width is a value in which slope range the slope should be altered
-	// to prevent a singularity in dq/ds
-	if (cmf::options.diffusive_slope_singularity_protection > 0.0) {
-        // Only a shortcut for faster writing
-		const real & s0 = cmf::options.diffusive_slope_singularity_protection;
-        // Weight of linear part
-		real w_lin = exp(-square((grad/s0)));
-        // linear part using the slope at s0/4
-        real s_lin =grad/(2.*sqrt(s0/4));
-        // Weighted sum of sqrt(s) and a*s
-		s_sqrt = w_lin * s_lin + (1-w_lin) * s_sqrt;
-	}
 
 	return prevent_negative_volume(m_flowwidth * pow(d,5/3.) * s_sqrt/left->get_nManning() * 86400.);
 }
@@ -126,3 +138,4 @@ void DiffusiveSurfaceRunoff::NewNodes()
 	wright = SurfaceWater::cast(right_node());
 	owright=OpenWaterStorage::cast(right_node());
 }
+

cmf/cmf_core_src/upslope/surfacewater.h

@@ -133,9 +133,10 @@ namespace cmf {
 			private:
 				static void connect_cells(cmf::upslope::Cell& c1,cmf::upslope::Cell& c2,ptrdiff_t dummy);
 				std::weak_ptr<cmf::upslope::SurfaceWater> wleft;
+                real m_distance, m_flowwidth;
+            protected:
 				virtual real calc_q(cmf::math::Time t);
 				void NewNodes();
-				real m_distance, m_flowwidth;
 			public:
 				/// Creates a KinematicSurfaceRunoff between a SurfaceWater (left) with another (right) node.
 				///
@@ -187,10 +188,11 @@ namespace cmf {
 				std::weak_ptr<cmf::upslope::SurfaceWater> wleft;
 				std::weak_ptr<cmf::river::OpenWaterStorage> owright;
 				std::weak_ptr<cmf::upslope::SurfaceWater> wright;
-				real calc_q(cmf::math::Time t) override;
-				void NewNodes() override;
 				real m_distance, m_flowwidth;
-			public:
+            protected:
+                real calc_q(cmf::math::Time t) override;
+                void NewNodes() override;
+            public:
 				DiffusiveSurfaceRunoff(cmf::upslope::SurfaceWater::ptr left,cmf::water::flux_node::ptr right,real flowwidth,real distance=-1)
 					: flux_connection(left,right,"Diffusive surface runoff"), m_distance(distance), m_flowwidth(flowwidth) {
 

demo/cmf2d.py

@@ -9,7 +9,7 @@
 import numpy as np
 from argparse import ArgumentParser
 from datetime import datetime, timedelta
-
+from matplotlib import cm
 try:
     import pylab
     import cmf.draw
@@ -176,7 +176,7 @@ def run(p, outlet, until, dt=cmf.day):
     outflow = cmf.timeseries(solver.t, dt)
     for t in solver.run(solver.t, solver.t + until, dt):
         outflow.add(outlet(t))
-        print("%20s - %6.1f l/day" % (t, outlet(t) * 1e3))
+        print("%20s - %6.1f l/day - %6.2f Wetness" % (t, outlet(t) * 1e3, p.cells[0].layers[0].Wetness))
     return outflow, solver.info
 
 
@@ -186,12 +186,12 @@ def animate(p, outlet, until, dt=cmf.day):
 
     solver = cmf.CVodeKrylov(p, 1e-9)
     solver.t = cmf.Time(1, 1, 1980)
-    hp = HillPlot(p, solver.t)
+    hp = HillPlot(p, solver.t, cmap=cm.viridis_r)
     hp.scale = 1000
 
     def integration():
         for t in solver.run(solver.t, solver.t + until, dt):
-            print(t)
+            print("%20s - %6.1f l/day - %6.2f Wetness" % (t, outlet(t) * 1e3, p.cells[0].layers[0].wetness))
             yield t
 
     anim = hp.get_animator(integration)

demo/parkinglot.py

@@ -39,7 +39,7 @@
     c.add_layer(0.1, cmf.VanGenuchtenMualem(Ksat=0.005))
     c.install_connection(cmf.GreenAmptInfiltration)
 
-cmf.DiffusiveSurfaceRunoff.set_linear_slope(1e-4)
+# cmf.DiffusiveSurfaceRunoff.set_linear_slope(1e-4)
 cmf.connect_cells_with_flux(p, cmf.DiffusiveSurfaceRunoff)
 outlet = p.NewOutlet('outlet', -length, 0, -slope * length)
 
@@ -67,7 +67,7 @@ def getpot():
 # %%
 fig, ax = plt.subplots()
 img = ax.imshow(getdepth(), cmap=plt.cm.Blues, aspect='equal',
-                vmin=0.0, vmax=0.01, origin='bottom', interpolation='nearest',
+                vmin=0.0, vmax=0.01, origin='lower', interpolation='nearest',
                 extent=(-length / 2, (size[0] - .5) * length, -length / 2, length * (size[1] - .5)))
 fluxdir = cmf.cell_flux_directions(p, solver.t)
 pos = cmf.cell_positions(p.cells)

documentation/installation/CmfInstallUbuntu.md

@@ -4,87 +4,10 @@
 
 # Install cmf on a Linux with sudo privileges
 
-First you need to make sure that the dependencies of cmf are fullfilled.
-It is good practise to get ppackages from your Linux distribution, if
-they are available and to get only those packages, that you can't get
-from your distribution to install directly in Python. Any package
-installed by your OS package manager will be updated by the OS, while
-other packages need to get updated by yourself.
 
-I am working mostly with Ubuntu variants, hence i can't say anything
-about other Linux package managers. However an internet search like
-"apt-get fedora" will help.
 
-## Python 2.7 
 
-You need sudo privileges to install the dependencies for the system. You
-will need `python-dev` and `numpy`. Recommended are `matplotlib`,
-`scipy`and `pandas`.
-
-### Dependencies of cmf from the Ubuntu package manager
-
-    #!sh
-    sudo apt-get install python-dev python-numpy python-scipy python-pandas python-matplotlib
-
-### Get dependencies from the Python Package Index (PyPI)
-
-Follow this steps if you can't get the packages from your OS or if you
-do not have sudo privileges. This text assumes you want everything only
-installed for yourself and not for other users.
-
-First check your python version:
-
-    #!sh
-    python --version
-
-If the version is \<=2.7.8 then get the program `pip` to install more
-packages.For higher versions, `pip` is already part of Python
-
-    #!sh
-    wget https://bootstrap.pypa.io/get-pip.py
-    python get-pip.py --user
-
-The next steps are only needed if you did not used the `apt-get`
-commands from above:
-
-    #!sh
-    pip install numpy --user
-    pip install matplotlib --user
-    pip install scipy --user
-    pip install pandas --user
-
-### Compile cmf
-
-Get the source code from CmfDownload and unzip it to /cmf-source
-
-    #!sh
-    cd cmf-source
-    python setup.py install --user
-    cd .. # Important! You cannot test your installation from the source folder
-
-or, without multi core processor support (without OpenMP)
-
-    #!sh
-    cd cmf-source
-    python setup.py install noopenmp --user
-    cd .. # Important! You cannot test your installation from the source folder
-
-## Adding geometric support to CMF 
-
-To added geometric features to cmf, you need to install the geos library
-and shapely. For the geos library, you need sudo privileges
-
-    #!sh
-    wget http://download.osgeo.org/geos/geos-3.2.2.tar.bz2
-    tar -xjf geos-3.2.2.tar.bz2
-    cd geos-3.2.2
-    ./configure
-    make
-    sudo make install
-    cd ..
-    pip install shapely --user
-
-## Python 3.5 
+## Python 3.7 and higher 
 
 Work in progress..