Droplet no quant

README.md

@@ -8,10 +8,10 @@ A Python library for network dynamics modeling and HPC simulation.
 [![Build Status](https://travis-ci.org/dpploy/cortix.svg?branch=master)](https://travis-ci.org/dpploy/cortix)
 [![PyPI version](https://badge.fury.io/py/cortix.svg)](https://badge.fury.io/py/cortix)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/Django.svg)](https://badge.fury.io/py/cortix)
-
 [![codecov](https://codecov.io/gh/dpploy/cortix/branch/master/graph/badge.svg)](https://codecov.io/gh/dpploy/cortix)
 
-![](cortix/docs/cortix-cover.png)
+
+![](https://cortix.org/cortix-cover.png)
 
 ## What is Cortix?
 

cortix/examples/droplet_swirl/droplet.py

@@ -9,9 +9,6 @@
 import scipy.constants as const
 from scipy.integrate import odeint
 from cortix.src.module import Module
-from cortix.support.phase import Phase
-from cortix.support.specie import Specie
-from cortix.support.quantity import Quantity
 
 class Droplet(Module):
     '''
@@ -24,7 +21,7 @@ class Droplet(Module):
     `visualization` sends data to a visualization module.
     '''
 
-    def __init__(self):
+    def __init__(self, save=True):
         '''
         Attributes
         ----------
@@ -34,6 +31,8 @@ def __init__(self):
         show_time: tuple
             Two-element tuple, `(bool,float)`, `True` will print to standard
             output.
+        save: bool
+            Save droplet history across time
         '''
 
         super().__init__()
@@ -47,9 +46,11 @@ def __init__(self):
 
         self.bounce = True
         self.slip   = True
+        self.save   = save
 
-        species = list()
-        quantities = list()
+        if self.save:
+            self.positions = []
+            self.velocities = []
 
         self.ode_params = dict()
 
@@ -59,42 +60,12 @@ def __init__(self):
         self.ode_params['droplet-xsec-area'] = np.pi * (self.droplet_diameter/2.0)**2
         self.ode_params['gravity'] = const.g
 
-        # Species in the liquid phase
-        water = Specie(name='water', formula_name='H2O(l)', phase='liquid', \
-                atoms=['2*H','O'])
-        water.massCC =  0.99965 # [g/cc]
-        water.massCCUnit = 'g/cc'
-        water.molarCCUnit = 'mole/cc'
-        species.append(water)
 
-        droplet_mass = 4/3 * np.pi * (self.droplet_diameter/2)**3 * water.massCC * \
+        water_massCC =  0.99965 # [g/cc]
+        droplet_mass = 4/3 * np.pi * (self.droplet_diameter/2)**3 * water_massCC * \
                 const.gram / const.centi**3  # [kg]
         self.ode_params['droplet-mass'] = droplet_mass
 
-        # Spatial position
-        x_0 = np.zeros(3)
-        position = Quantity(name='position', formalName='Pos.', unit='m', value=x_0)
-        quantities.append(position)
-
-        # Velocity
-        v_0 = np.zeros(3)
-        velocity = Quantity(name='velocity', formalName='Veloc.', unit='m/s', value=v_0)
-        quantities.append(velocity)
-
-        # Speed
-        speed = Quantity(name='speed', formalName='Speed', unit='m/s', value=0.0)
-        quantities.append(speed)
-
-        # Radial position
-        radial_pos = Quantity(name='radial-position', formalName='Radius', unit='m', \
-                value=np.linalg.norm(x_0[0:2]))
-        quantities.append(radial_pos)
-
-        # Liquid phase 
-        self.liquid_phase = Phase(self.initial_time, time_unit='s', species=species, \
-                quantities=quantities)
-        self.liquid_phase.SetValue('water', water.massCC, self.initial_time)
-
         # Domain box dimensions: LxLxH m^3 box with given H.
         # Origin of cartesian coordinate system at the bottom of the box. 
         # z coordinate pointing upwards. -L <= x <= L, -L <= y <= L, 
@@ -104,11 +75,9 @@ def __init__(self):
         # Random positioning of the droplet constrained to a box sub-region.
         x_0 = (2 * np.random.random(3) - np.ones(3)) * self.box_half_length / 4.0
         x_0[2] = self.box_height
-        self.liquid_phase.SetValue('position', x_0, self.initial_time)
 
-        # Droplet Initial velocity = 0 -> placed still in the flow
-        self.liquid_phase.SetValue('velocity', np.array([0.0,0.0,0.0]), \
-                self.initial_time)
+        self.initial_pos = self.position = x_0
+        self.velocity = np.zeros(3)
 
         # Default value for the medium surrounding the droplet if data is not passed
         # through a conneted port.
@@ -132,16 +101,11 @@ def run(self, *args):
 
             # Interactions in the external-flow port
             #---------------------------------------
-
-            position = self.liquid_phase.GetValue('position')
-            self.send( (time,position), 'external-flow' )
-
-            (check_time, velocity,fluid_props) = self.recv( 'external-flow' )
+            self.send((time, self.position), 'external-flow')
+            (check_time, velocity,fluid_props) = self.recv('external-flow')
 
             assert abs(check_time-time) <= 1e-6
             self.ode_params['flow-velocity'] = velocity
-            #medium_mass_density  = fluid_props.mass_density  # see Vortex
-            #medium_dyn_viscosity = fluid_props.dyn_viscosity # see Vortex
             medium_mass_density  = fluid_props[0]
             medium_dyn_viscosity = fluid_props[1]
 
@@ -156,12 +120,12 @@ def run(self, *args):
             # Interactions in the visualization port
             #---------------------------------------
 
-            self.send( position, 'visualization' )
+            self.send(self.position, 'visualization' )
 
             # Evolve droplet state to next time stamp
             #----------------------------------------
 
-            time = self.__step( time )
+            time = self.__step(time)
 
         self.send('DONE', 'visualization') # this should not be needed: TODO
         return
@@ -229,10 +193,7 @@ def __step(self, time=0.0):
         '''
 
         if not self.bottom_impact:
-
-           x_0 = self.liquid_phase.GetValue('position', time)
-           v_0 = self.liquid_phase.GetValue('velocity', time)
-           u_vec_0 = np.concatenate((x_0,v_0))
+           u_vec_0 = np.concatenate((self.position,self.velocity))
 
            t_interval_sec = np.linspace(0.0, self.time_step, num=2)
 
@@ -248,12 +209,8 @@ def __step(self, time=0.0):
 
            u_vec = u_vec_hist[1,:]  # solution vector at final time step
 
-        values = self.liquid_phase.GetRow(time) # values at previous time
-
         time += self.time_step
 
-        self.liquid_phase.AddRow(time, values)
-
         if not self.bottom_impact:
 
             # Ground impact with bouncing drop
@@ -271,11 +228,14 @@ def __step(self, time=0.0):
                 u_vec[3:] = 0.0  # zero velocity
                 self.bottom_impact = True
 
+
+            # Save values (if necessary)
+            if self.save:
+                self.positions.append(self.position)
+                self.velocities.append(self.velocity)
+
             # Update current values
-            self.liquid_phase.SetValue('position', u_vec[0:3], time)
-            self.liquid_phase.SetValue('velocity', u_vec[3:], time)
-            self.liquid_phase.SetValue('speed', np.linalg.norm(u_vec[3:]), time)
-            self.liquid_phase.SetValue('radial-position', np.linalg.norm(u_vec[0:2]),
-                    time)
+            self.position = u_vec[0:3]
+            self.velocity = u_vec[3:]
 
         return time

cortix/examples/droplet_swirl/run_droplet_swirl.py

@@ -10,7 +10,7 @@
 To run this case using MPI you should compute the number of
 processes as follows:
 
-    `nprocs = n_droplets + 1 vortex + 1 cortix`
+    `nprocs = 2 * n_droplets + 1 cortix`
 
 then issue the MPI run command as follows (replace `nprocs` with a number):
 
@@ -25,14 +25,13 @@
 
 import scipy.constants as const
 
-
 from cortix import Cortix
 from cortix import Network
 from cortix.examples.droplet_swirl.droplet import Droplet
 from cortix.examples.droplet_swirl.vortex import Vortex
 
 
-def main():
+def main(n_droplets=5, end_time = 3 * const.minute, time_step = 0.2, create_plots=True):
     '''Cortix run file for a `Droplet`-`Vortex` network.
 
     Attributes
@@ -54,12 +53,6 @@ def main():
     '''
 
     # Configuration Parameters
-    n_droplets = 5
-    end_time   = 3*const.minute
-    time_step  = 0.2
-
-    create_plots = True
-
     if n_droplets >= 2000:
         create_plots = False
 
@@ -81,15 +74,13 @@ def main():
         vortex.plot_velocity()
 
     for i in range(n_droplets):
-
         # Droplet modules (multiple).
-        droplet = Droplet()
+        droplet = Droplet(save=create_plots)
         swirl.network.module(droplet)
         droplet.end_time = end_time
         droplet.time_step = time_step
         droplet.bounce = False
         droplet.slip = False
-        droplet.save = True
 
         # Network port connectivity (connect modules through their ports)
         swirl.network.connect( [droplet,'external-flow'],
@@ -111,10 +102,11 @@ def main():
 
             from mpl_toolkits.mplot3d import Axes3D
             import matplotlib.pyplot as plt
+            import numpy as np
 
             positions = list()
             for m in swirl.network.modules[1:]:
-                positions.append(m.liquid_phase.get_quantity_history('position')[0].value)
+                positions.append(m.positions)
 
             fig = plt.figure(1)
             ax = fig.add_subplot(111,projection='3d')
@@ -131,26 +123,26 @@ def main():
 
             # All droplets' speed
             fig = plt.figure(2)
-            plt.xlabel('Time [min]')
+            plt.xlabel('Time')
             plt.ylabel('Speed [m/s]')
             plt.title('All Droplets')
 
             for m in modules[1:]:
-                speed = m.liquid_phase.get_quantity_history('speed')[0].value
-                plt.plot(list(speed.index/60), speed.tolist())
+                speeds = [np.linalg.norm(vel) for vel in m.velocities]
+                plt.plot(speeds)
 
             plt.grid()
             fig.savefig('speeds.png', dpi=300)
 
             # All droplets' radial position
             fig = plt.figure(3)
-            plt.xlabel('Time [min]')
+            plt.xlabel('Time')
             plt.ylabel('Radial Position [m]')
             plt.title('All Droplets')
 
             for m in modules[1:]:
-                radial_pos = m.liquid_phase.get_quantity_history('radial-position')[0].value
-                plt.plot(list(radial_pos.index/60)[1:], radial_pos.tolist()[1:])
+                radial_pos = [np.linalg.norm(pos[0:2]) for pos in m.positions]
+                plt.plot(radial_pos[1:])
 
             plt.grid()
             fig.savefig('radialpos.png', dpi=300)
@@ -159,4 +151,6 @@ def main():
     swirl.close()
 
 if __name__ == '__main__':
-    main()
+    import sys
+    num_drops = int(sys.argv[1]) if len(sys.argv) > 1 else 5
+    main(n_droplets=num_drops, create_plots=True)

cortix/src/cortix_main.py

@@ -59,15 +59,13 @@ def __init__(self, use_mpi=False, splash=False, log_filename='cortix'):
 
         self.__network = None
         self.log_filename = log_filename
+
         # Fall back to multiprocessing if mpi4py is not available
         if self.use_mpi:
-            try:
                 from mpi4py import MPI
                 self.comm = MPI.COMM_WORLD
                 self.rank = self.comm.Get_rank()
                 self.size = self.comm.size
-            except ImportError:
-                self.use_mpi = False
 
         # Setup the global logger 
         self.__create_logger()

cortix/src/module.py

@@ -23,7 +23,7 @@ class Module:
 
     '''
 
-    def __init__(self):
+    def __init__(self, save=True):
         '''Module super class constructor.
 
         Note
@@ -66,7 +66,7 @@ def __init__(self):
         self.use_multiprocessing = True
         self.ports = list()
         self.log = logging.getLogger('cortix')
-        self.save = False
+        self.save = save
 
         self.id = None