work in progress

.gitignore

@@ -23,4 +23,11 @@ docs/site/
 # environment.
 Manifest.toml
 
-.vscode
+.vscode
+
+#Julia system image
+JuliaSysimage.dll
+
+#python stuff
+__pycache__
+*.pyc

Project.toml

@@ -5,6 +5,7 @@ version = "0.1.2"
 
 [deps]
 ApproxFun = "28f2ccd6-bb30-5033-b560-165f7b14dc2f"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -15,3 +16,4 @@ Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
+TruncatedStacktraces = "781d530d-4396-4725-bb49-402e4bee1e77"

Python Burgers example/benchmarkedBurgers.py

@@ -0,0 +1,352 @@
+# 2nd-order accurate finite-volume implementation of the inviscid Burger's
+# equation with piecewise linear slope reconstruction
+#
+# We are solving u_t + u u_x = 0 with outflow boundary conditions
+#
+# M. Zingale (2013-03-26)
+
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+import sys
+import time
+import cProfile
+from memory_profiler import profile
+from pympler import asizeof
+from pympler import muppy
+from pympler import summary
+from pympler import classtracker
+import tracemalloc
+import linecache
+import os
+
+mpl.rcParams['mathtext.fontset'] = 'cm'
+mpl.rcParams['mathtext.rm'] = 'serif'
+
+mpl.rcParams['font.size'] = 12
+mpl.rcParams['legend.fontsize'] = 'large'
+mpl.rcParams['figure.titlesize'] = 'medium'
+
+class Grid1d(object):
+    def __init__(self, nx, ng, xmin=0.0, xmax=1.0, bc="outflow"):
+
+        self.nx = nx
+        self.ng = ng
+
+        self.xmin = xmin
+        self.xmax = xmax
+
+        self.bc=bc
+
+        # python is zero-based.  Make easy intergers to know where the
+        # real data lives
+        self.ilo = ng
+        self.ihi = ng+nx-1
+
+        # physical coords -- cell-centered, left and right edges
+        self.dx = (xmax - xmin)/(nx)
+        self.x = xmin + (np.arange(nx+2*ng)-ng+0.5)*self.dx
+
+        # storage for the solution
+        self.u = np.zeros((nx+2*ng), dtype=np.float64)
+
+    def scratch_array(self):
+        """ return a scratch array dimensioned for our grid """
+        return np.zeros((self.nx+2*self.ng), dtype=np.float64)
+
+    def fill_BCs(self):
+        """ fill all ghostcells as periodic """
+
+        if self.bc == "periodic":
+
+            # left boundary
+            self.u[0:self.ilo] = self.u[self.ihi-self.ng+1:self.ihi+1]
+
+            # right boundary
+            self.u[self.ihi+1:] = self.u[self.ilo:self.ilo+self.ng]
+
+        elif self.bc == "outflow":
+
+            # left boundary
+            self.u[0:self.ilo] = self.u[self.ilo]
+
+            # right boundary
+            self.u[self.ihi+1:] = self.u[self.ihi]
+
+        else:
+            sys.exit("invalid BC")
+
+
+    def norm(self, e):
+        """ return the norm of quantity e which lives on the grid """
+        if len(e) != 2*self.ng + self.nx:
+            return None
+
+        return np.sqrt(self.dx*np.sum(e[self.ilo:self.ihi+1]**2))
+
+
+class Simulation(object):
+
+    def __init__(self, grid):
+        self.grid = grid
+        self.t = 0.0
+
+
+    def init_cond(self, type="tophat"):
+
+        if type == "tophat":
+            self.grid.u[np.logical_and(self.grid.x >= 0.333,
+                                          self.grid.x <= 0.666)] = 1.0
+
+        elif type == "sine":
+            self.grid.u[:] = 1.0
+
+            index = np.logical_and(self.grid.x >= 0.333,
+                                      self.grid.x <= 0.666)
+            self.grid.u[index] += \
+                0.5*np.sin(2.0*np.pi*(self.grid.x[index]-0.333)/0.333)
+
+        elif type == "rarefaction":
+            self.grid.u[:] = 1.0
+            self.grid.u[self.grid.x > 0.5] = 2.0
+
+
+    def timestep(self, C):
+        return C*self.grid.dx/max(abs(self.grid.u[self.grid.ilo:
+                                                  self.grid.ihi+1]))
+
+    def states(self, dt):
+        """ compute the left and right interface states """
+
+        g = self.grid
+        # compute the piecewise linear slopes -- 2nd order MC limiter
+        # we pick a range of cells that includes 1 ghost cell on either
+        # side
+        ib = g.ilo-1
+        ie = g.ihi+1
+
+        u = g.u
+
+        # this is the MC limiter from van Leer (1977), as given in
+        # LeVeque (2002).  Note that this is slightly different than
+        # the expression from Colella (1990)
+
+        dc = g.scratch_array()
+        dl = g.scratch_array()
+        dr = g.scratch_array()
+
+        dc[ib:ie+1] = 0.5*(u[ib+1:ie+2] - u[ib-1:ie  ])
+        dl[ib:ie+1] = u[ib+1:ie+2] - u[ib  :ie+1]
+        dr[ib:ie+1] = u[ib  :ie+1] - u[ib-1:ie  ]
+
+        # these where's do a minmod()
+        d1 = 2.0*np.where(np.fabs(dl) < np.fabs(dr), dl, dr)
+        d2 = np.where(np.fabs(dc) < np.fabs(d1), dc, d1)
+        ldeltau = np.where(dl*dr > 0.0, d2, 0.0)
+
+        # now the interface states.  Note that there are 1 more interfaces
+        # than zones
+        ul = g.scratch_array()
+        ur = g.scratch_array()
+
+        # are these indices right?
+        #
+        #  --+-----------------+------------------+
+        #     ^       i       ^ ^        i+1
+        #     ur(i)     ul(i+1) ur(i+1)
+        #
+        ur[ib:ie+2] = u[ib:ie+2] - \
+                      0.5*(1.0 + u[ib:ie+2]*dt/self.grid.dx)*ldeltau[ib:ie+2]
+
+        ul[ib+1:ie+2] = u[ib:ie+1] + \
+                        0.5*(1.0 - u[ib:ie+1]*dt/self.grid.dx)*ldeltau[ib:ie+1]
+
+        return ul, ur
+
+
+    def riemann(self, ul, ur):
+        """
+        Riemann problem for Burgers' equation.
+        """
+
+        S = 0.5*(ul + ur)
+        ushock = np.where(S > 0.0, ul, ur)
+        ushock = np.where(S == 0.0, 0.0, ushock)
+
+        # rarefaction solution
+        urare = np.where(ur <= 0.0, ur, 0.0)
+        urare = np.where(ul >= 0.0, ul, urare)
+
+        us = np.where(ul > ur, ushock, urare)
+
+        return 0.5*us*us
+
+    def update(self, dt, flux):
+        """ conservative update """
+
+        g = self.grid
+
+        unew = g.scratch_array()
+
+        unew[g.ilo:g.ihi+1] = g.u[g.ilo:g.ihi+1] + \
+            dt/g.dx * (flux[g.ilo:g.ihi+1] - flux[g.ilo+1:g.ihi+2])
+
+        return unew
+
+    def evolve(self, C, tmax):
+
+        self.t = 0.0
+
+        g = self.grid
+
+        # main evolution loop
+        while (self.t < tmax):
+
+            # fill the boundary conditions
+            g.fill_BCs()
+
+            # get the timestep
+            dt = self.timestep(C)
+
+            if (self.t + dt > tmax):
+                dt = tmax - self.t
+
+            # get the interface states
+            ul, ur = self.states(dt)
+
+            # solve the Riemann problem at all interfaces
+            flux = self.riemann(ul, ur)
+
+            # do the conservative update
+            unew = self.update(dt, flux)
+
+            self.grid.u[:] = unew[:]
+
+            self.t += dt
+
+def display_top(snapshot, key_type='lineno', limit=10):
+    snapshot = snapshot.filter_traces((
+        tracemalloc.Filter(False, "<frozen importlib._bootstrap>"),
+        tracemalloc.Filter(False, "<unknown>"),
+    ))
+    top_stats = snapshot.statistics(key_type)
+
+    other = top_stats[limit:]
+    if other:
+        size = sum(stat.size for stat in other)
+        print("%s other: %.1f KiB" % (len(other), size / 1024))
+    total = sum(stat.size for stat in top_stats)
+    print("Total allocated size: %.1f KiB" % (total / 1024))
+
+def main():
+    #-----------------------------------------------------------------------------
+    # sine
+
+    tracemalloc.start()
+
+    xmin = 0.0
+    xmax = 1.0
+    nx = 256
+    ng = 2
+    g = Grid1d(nx, ng, bc="periodic")
+
+    # maximum evolution time based on period for unit velocity
+    tmax = (xmax - xmin)/1.0
+
+    C = 0.8
+
+    plt.clf()
+
+    s = Simulation(g)
+
+    start = time.perf_counter()
+
+    for i in range(0, 10):
+        tend = (i+1)*0.02*tmax
+        s.init_cond("sine")
+
+        uinit = s.grid.u.copy()
+
+        s.evolve(C, tend)
+
+        c = 1.0 - (0.1 + i*0.1)
+        g = s.grid
+        #plt.plot(g.x[g.ilo:g.ihi+1], g.u[g.ilo:g.ihi+1], color=str(c))
+
+    timeTaken = time.perf_counter() - start
+
+    g = s.grid
+
+    plt.plot(g.x[g.ilo:g.ihi+1], uinit[g.ilo:g.ihi+1], ls=":", color="0.9", zorder=-1)
+
+    xs = g.x[g.ilo:g.ihi+1]
+    #us = uinit[g.ilo:g.ihi+1]
+    us = g.u[g.ilo:g.ihi+1]
+
+    plt.xlabel("$x$")
+    plt.ylabel("$u$")
+    plt.savefig("fv-burger-sine.pdf")
+
+    f = open('python-xs.txt','w')
+    for i in range(len(xs)):
+        f.write(str(xs[i]) + '\n')
+    f.close()
+
+    f = open('python-us.txt','w')
+    for i in range(len(us)):
+        f.write(str(us[i]) + '\n')
+    f.close()
+
+    snapshot = tracemalloc.take_snapshot()
+
+    display_top(snapshot)
+
+    print(asizeof.asizeof(g))
+    print(asizeof.asizeof(s))
+
+    tracemalloc.stop()
+
+    return timeTaken
+
+
+    #-----------------------------------------------------------------------------
+    # rarefaction
+    """
+    xmin = 0.0
+    xmax = 1.0
+    nx = 256
+    ng = 2
+    g = Grid1d(nx, ng, bc="outflow")
+
+    # maximum evolution time based on period for unit velocity
+    tmax = (xmax - xmin)/1.0
+
+    C = 0.8
+
+    plt.clf()
+
+    s = Simulation(g)
+
+    for i in range(0, 10):
+        tend = (i+1)*0.02*tmax
+
+        s.init_cond("rarefaction")
+
+        uinit = s.grid.u.copy()
+
+        s.evolve(C, tend)
+
+        c = 1.0 - (0.1 + i*0.1)
+        plt.plot(g.x[g.ilo:g.ihi+1], g.u[g.ilo:g.ihi+1], color=str(c))
+
+
+    plt.plot(g.x[g.ilo:g.ihi+1], uinit[g.ilo:g.ihi+1], ls=":", color="0.9", zorder=-1)
+
+    plt.xlabel("$x$")
+    plt.ylabel("$u$")
+
+    plt.savefig("fv-burger-rarefaction.pdf")"""
+
+if __name__ == "__main__":
+    main()
+

Python Burgers example/mprof0

@@ -0,0 +1,10 @@
+Filename: C:\Users\alice\AppData\Local\Programs\Python\Python310\lib\site-packages\memory_profiler.py
+
+Line #    Mem usage    Increment  Occurrences   Line Contents
+=============================================================
+  1185    132.2 MiB    132.2 MiB           1               @wraps(wrapped=func)
+  1186                                                     def wrapper(*args, **kwargs):
+  1187    132.2 MiB      0.0 MiB           1                   prof = get_prof()
+  1188    132.2 MiB     -0.0 MiB           1                   val = prof(func)(*args, **kwargs)
+  1189    132.2 MiB      0.0 MiB           1                   show_results_bound(prof)
+  1190    132.2 MiB      0.0 MiB           1                   return val

Python Burgers example/mprofile_20230427223539.dat

@@ -0,0 +1,4 @@
+CMDLINE C:\Users\alice\AppData\Local\Programs\Python\Python310\python.exe run-burgers.py
+MEM 1.593750 1682631339.4155
+MEM 12.250000 1682631339.5263
+MEM 18.988281 1682631339.6373