Updated this branch with the restructured Python module taken from th…

…e OOPrestructure branch

examples/symba_chambers2013/aescattermovie.py

@@ -0,0 +1,116 @@
+import swiftest.io as swio
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import animation
+import matplotlib.colors as mcolors
+
+radscale = 20
+xmin = 1.0
+xmax = 10.0
+ymin = 1e-6
+ymax = 1.0
+
+class AnimatedScatter(object):
+    """An animated scatter plot using matplotlib.animations.FuncAnimation."""
+    def __init__(self, ds, param):
+        #outf = 'aescatter.mp4'
+
+        frame = 0
+        nframes = ds['time'].size
+        self.ds = ds
+        self.param = param
+        self.ds['Mass'] = self.ds['Mass'] / param['GU']
+        self.ds['radmarker'] = self.ds['Radius'].fillna(0)
+        self.ds['radmarker'] = self.ds['radmarker'] / self.ds['radmarker'].max() * radscale
+
+        self.clist = {'Initial conditions' : 'xkcd:faded blue',
+                      'Disruption' : 'xkcd:marigold',
+                      'Supercatastrophic' : 'xkcd:shocking pink',
+                      'Hit and run fragment' : 'xkcd:baby poop green'}
+
+        self.stream = self.data_stream(frame)
+        # Setup the figure and axes...
+        self.fig, self.ax = plt.subplots(figsize=(8,4.5))
+        # Then setup FuncAnimation.
+        self.ani = animation.FuncAnimation(self.fig, self.update, interval=1, frames=nframes,
+                                          init_func=self.setup_plot, blit=True)
+        self.ani.save('aescatter.mp4', fps=60, dpi=300,
+                      extra_args=['-vcodec', 'libx264'])
+        print('Finished writing aescattter.mp4')
+
+    def scatters(self, pl, radmarker, origin):
+        scat = []
+        for key, value in self.clist.items():
+            idx = origin == value
+            s = self.ax.scatter(pl[idx, 0], pl[idx, 1], marker='o', s=radmarker[idx], c=value, alpha=0.25, label=key)
+            scat.append(s)
+        return scat
+
+    def setup_plot(self):
+        # First frame
+        """Initial drawing of the scatter plot."""
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(0))
+
+        # set up the figure
+        self.ax = plt.axes(xlim=(xmin, xmax), ylim=(ymin, ymax))
+        self.ax.margins(x=10, y=1)
+        self.ax.set_xlabel('Semi Major Axis (AU)', fontsize='16', labelpad=1)
+        self.ax.set_ylabel('Eccentricity', fontsize='16', labelpad=1)
+        self.ax.set_yscale('log')
+
+        self.title = self.ax.text(0.50, 1.05, "", bbox={'facecolor': 'w', 'alpha': 0.5, 'pad': 5}, transform=self.ax.transAxes,
+                        ha="center")
+
+        self.title.set_text(f'Time = ${t / 24 / 3600:4.1f}$ days with ${npl:f}$ particles')
+        slist = self.scatters(pl, radmarker, origin)
+        self.s0 = slist[0]
+        self.s1 = slist[1]
+        self.s2 = slist[2]
+        self.s3 = slist[3]
+        self.ax.legend(loc='upper right')
+        return self.s0, self.s1, self.s2, self.s3, self.title
+
+    def data_stream(self, frame=0):
+        while True:
+            d = self.ds.isel(time=frame)
+            Radius = d['radmarker'].values
+            Mass = d['Mass'].values
+            a = d['a'].values 
+            e = d['e'].values
+            name = d['id'].values
+            npl = d['npl'].values
+            radmarker = d['radmarker']
+            origin = d['origin_type']
+
+            t = self.ds.coords['time'].values[frame]
+
+            frame += 1
+            yield t, name, Mass, Radius, npl, np.c_[a, e], radmarker, origin
+
+    def update(self,frame):
+        """Update the scatter plot."""
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(frame))
+
+        self.title.set_text(f'Time = ${t / 24 / 3600:4.1f}$ days with ${npl:4.0f}$ particles')
+
+        # We need to return the updated artist for FuncAnimation to draw..
+        # Note that it expects a sequence of artists, thus the trailing comma.
+        s = [self.s0, self.s1, self.s2, self.s3]
+        for i, (key, value) in enumerate(self.clist.items()):
+            idx = origin == key
+            s[i].set_sizes(radmarker[idx])
+            s[i].set_offsets(pl[idx,:])
+            s[i].set_facecolor(value)
+
+        self.s0 = s[0]
+        self.s1 = s[1]
+        self.s2 = s[2]
+        self.s3 = s[3]
+        return self.s0, self.s1, self.s2, self.s3, self.title,
+
+
+param = swio.read_swiftest_param("param.in")
+marsdisk = swio.swiftest2xr(param)
+print('Making animation')
+anim = AnimatedScatter(marsdisk,param)
+print('Animation finished')

examples/symba_clement2018/aescattermovie.py

@@ -0,0 +1,116 @@
+import swiftest.io as swio
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import animation
+import matplotlib.colors as mcolors
+
+radscale = 20
+xmin = 1.0
+xmax = 10.0
+ymin = 1e-6
+ymax = 1.0
+
+class AnimatedScatter(object):
+    """An animated scatter plot using matplotlib.animations.FuncAnimation."""
+    def __init__(self, ds, param):
+        #outf = 'aescatter.mp4'
+
+        frame = 0
+        nframes = ds['time'].size
+        self.ds = ds
+        self.param = param
+        self.ds['Mass'] = self.ds['Mass'] / param['GU']
+        self.ds['radmarker'] = self.ds['Radius'].fillna(0)
+        self.ds['radmarker'] = self.ds['radmarker'] / self.ds['radmarker'].max() * radscale
+
+        self.clist = {'Initial conditions' : 'xkcd:faded blue',
+                      'Disruption' : 'xkcd:marigold',
+                      'Supercatastrophic' : 'xkcd:shocking pink',
+                      'Hit and run fragment' : 'xkcd:baby poop green'}
+
+        self.stream = self.data_stream(frame)
+        # Setup the figure and axes...
+        self.fig, self.ax = plt.subplots(figsize=(8,4.5))
+        # Then setup FuncAnimation.
+        self.ani = animation.FuncAnimation(self.fig, self.update, interval=1, frames=nframes,
+                                          init_func=self.setup_plot, blit=True)
+        self.ani.save('aescatter.mp4', fps=60, dpi=300,
+                      extra_args=['-vcodec', 'libx264'])
+        print('Finished writing aescattter.mp4')
+
+    def scatters(self, pl, radmarker, origin):
+        scat = []
+        for key, value in self.clist.items():
+            idx = origin == value
+            s = self.ax.scatter(pl[idx, 0], pl[idx, 1], marker='o', s=radmarker[idx], c=value, alpha=0.25, label=key)
+            scat.append(s)
+        return scat
+
+    def setup_plot(self):
+        # First frame
+        """Initial drawing of the scatter plot."""
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(0))
+
+        # set up the figure
+        self.ax = plt.axes(xlim=(xmin, xmax), ylim=(ymin, ymax))
+        self.ax.margins(x=10, y=1)
+        self.ax.set_xlabel('Semi Major Axis (AU)', fontsize='16', labelpad=1)
+        self.ax.set_ylabel('Eccentricity', fontsize='16', labelpad=1)
+        self.ax.set_yscale('log')
+
+        self.title = self.ax.text(0.50, 1.05, "", bbox={'facecolor': 'w', 'alpha': 0.5, 'pad': 5}, transform=self.ax.transAxes,
+                        ha="center")
+
+        self.title.set_text(f'Time = ${t / 24 / 3600:4.1f}$ days with ${npl:f}$ particles')
+        slist = self.scatters(pl, radmarker, origin)
+        self.s0 = slist[0]
+        self.s1 = slist[1]
+        self.s2 = slist[2]
+        self.s3 = slist[3]
+        self.ax.legend(loc='upper right')
+        return self.s0, self.s1, self.s2, self.s3, self.title
+
+    def data_stream(self, frame=0):
+        while True:
+            d = self.ds.isel(time=frame)
+            Radius = d['radmarker'].values
+            Mass = d['Mass'].values
+            a = d['a'].values 
+            e = d['e'].values
+            name = d['id'].values
+            npl = d['npl'].values
+            radmarker = d['radmarker']
+            origin = d['origin_type']
+
+            t = self.ds.coords['time'].values[frame]
+
+            frame += 1
+            yield t, name, Mass, Radius, npl, np.c_[a, e], radmarker, origin
+
+    def update(self,frame):
+        """Update the scatter plot."""
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(frame))
+
+        self.title.set_text(f'Time = ${t / 24 / 3600:4.1f}$ days with ${npl:4.0f}$ particles')
+
+        # We need to return the updated artist for FuncAnimation to draw..
+        # Note that it expects a sequence of artists, thus the trailing comma.
+        s = [self.s0, self.s1, self.s2, self.s3]
+        for i, (key, value) in enumerate(self.clist.items()):
+            idx = origin == key
+            s[i].set_sizes(radmarker[idx])
+            s[i].set_offsets(pl[idx,:])
+            s[i].set_facecolor(value)
+
+        self.s0 = s[0]
+        self.s1 = s[1]
+        self.s2 = s[2]
+        self.s3 = s[3]
+        return self.s0, self.s1, self.s2, self.s3, self.title,
+
+
+param = swio.read_swiftest_param("param.in")
+marsdisk = swio.swiftest2xr(param)
+print('Making animation')
+anim = AnimatedScatter(marsdisk,param)
+print('Animation finished')

examples/symba_mars_disk/aescattermovie.py

@@ -1,4 +1,4 @@
-import swiftestio as swio
+import swiftest.io as swio
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib import animation
@@ -13,15 +13,15 @@
 
 class AnimatedScatter(object):
     """An animated scatter plot using matplotlib.animations.FuncAnimation."""
-    def __init__(self, ds, config):
+    def __init__(self, ds, param):
         #outf = 'aescatter.mp4'
 
         frame = 0
         nframes = ds['time'].size
         self.ds = ds
-        self.config = config
-        self.ds['mass'] = self.ds['mass'] / config['GU']
-        self.ds['radmarker'] = self.ds['radius'].fillna(0)
+        self.param = param
+        self.ds['Mass'] = self.ds['Mass'] / param['GU']
+        self.ds['radmarker'] = self.ds['Radius'].fillna(0)
         self.ds['radmarker'] = self.ds['radmarker'] / self.ds['radmarker'].max() * radscale
 
         self.clist = {'Initial conditions' : 'xkcd:faded blue',
@@ -50,7 +50,7 @@ def scatters(self, pl, radmarker, origin):
     def setup_plot(self):
         # First frame
         """Initial drawing of the scatter plot."""
-        t, name, mass, radius, npl, pl, radmarker, origin = next(self.data_stream(0))
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(0))
 
         # set up the figure
         self.ax = plt.axes(xlim=(xmin, xmax), ylim=(ymin, ymax))
@@ -74,8 +74,8 @@ def setup_plot(self):
     def data_stream(self, frame=0):
         while True:
             d = self.ds.isel(time=frame)
-            radius = d['radmarker'].values
-            mass = d['mass'].values
+            Radius = d['radmarker'].values
+            Mass = d['Mass'].values
             a = d['a'].values / RMars
             e = d['e'].values
             name = d['id'].values
@@ -86,11 +86,11 @@ def data_stream(self, frame=0):
             t = self.ds.coords['time'].values[frame]
 
             frame += 1
-            yield t, name, mass, radius, npl, np.c_[a, e], radmarker, origin
+            yield t, name, Mass, Radius, npl, np.c_[a, e], radmarker, origin
 
     def update(self,frame):
         """Update the scatter plot."""
-        t, name, mass, radius, npl, pl, radmarker, origin = next(self.data_stream(frame))
+        t, name, Mass, Radius, npl, pl, radmarker, origin = next(self.data_stream(frame))
 
         self.title.set_text(f'Time = ${t / 24 / 3600:4.1f}$ days with ${npl:4.0f}$ particles')
 
@@ -110,8 +110,8 @@ def update(self,frame):
         return self.s0, self.s1, self.s2, self.s3, self.title,
 
 
-config = swio.read_swiftest_config("param.in")
-marsdisk = swio.swiftest2xr(config)
+param = swio.read_swiftest_param("param.in")
+marsdisk = swio.swiftest2xr(param)
 print('Making animation')
-anim = AnimatedScatter(marsdisk,config)
+anim = AnimatedScatter(marsdisk,param)
 print('Animation finished')

python/swiftest/README.md

@@ -0,0 +1,2 @@
+swiftest
+Documentation TBD

python/swiftest/requirements.txt

@@ -0,0 +1,86 @@
+argon2-cffi @ file:///tmp/build/80754af9/argon2-cffi_1613036642480/work
+astropy==4.2.1
+astroquery==0.4.2
+async-generator==1.10
+attrs @ file:///tmp/build/80754af9/attrs_1620827162558/work
+backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
+beautifulsoup4==4.9.3
+bleach @ file:///tmp/build/80754af9/bleach_1612211392645/work
+certifi==2021.5.30
+cffi @ file:///tmp/build/80754af9/cffi_1613246939562/work
+chardet==4.0.0
+cryptography==3.4.7
+cycler==0.10.0
+decorator @ file:///tmp/build/80754af9/decorator_1621259047763/work
+defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
+entrypoints==0.3
+html5lib==1.1
+idna==2.10
+importlib-metadata==4.5.0
+ipykernel==5.5.5
+ipython @ file:///tmp/build/80754af9/ipython_1617118429768/work
+ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
+ipywidgets @ file:///tmp/build/80754af9/ipywidgets_1610481889018/work
+jedi==0.17.0
+jeepney==0.6.0
+Jinja2 @ file:///tmp/build/80754af9/jinja2_1621238361758/work
+jsonschema @ file:///tmp/build/80754af9/jsonschema_1602607155483/work
+jupyter==1.0.0
+jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1616770841739/work
+jupyter-console @ file:///tmp/build/80754af9/jupyter_console_1616615302928/work
+jupyter-core @ file:///tmp/build/80754af9/jupyter_core_1612213308260/work
+jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
+jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
+keyring==23.0.1
+kiwisolver @ file:///tmp/build/80754af9/kiwisolver_1612282414123/work
+MarkupSafe @ file:///tmp/build/80754af9/markupsafe_1621528142364/work
+matplotlib==3.4.2
+mistune @ file:///tmp/build/80754af9/mistune_1594373098390/work
+mkl-random @ file:///tmp/build/80754af9/mkl_random_1618853974840/work
+mkl-service==2.3.0
+nbclient @ file:///tmp/build/80754af9/nbclient_1614364831625/work
+nbconvert @ file:///tmp/build/80754af9/nbconvert_1601914821128/work
+nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
+nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
+notebook @ file:///tmp/build/80754af9/notebook_1621523661196/work
+numpy==1.20.3
+olefile==0.46
+packaging @ file:///tmp/build/80754af9/packaging_1611952188834/work
+pandas==1.2.4
+pandocfilters @ file:///tmp/build/80754af9/pandocfilters_1605120451932/work
+parso @ file:///tmp/build/80754af9/parso_1617223946239/work
+pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
+pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
+Pillow @ file:///tmp/build/80754af9/pillow_1617386154241/work
+prometheus-client @ file:///tmp/build/80754af9/prometheus_client_1623189609245/work
+prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1616415428029/work
+ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
+pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
+pyerfa==2.0.0
+Pygments @ file:///tmp/build/80754af9/pygments_1621606182707/work
+pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
+pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1600141707582/work
+pySLALIB==1.0.4
+python-dateutil @ file:///home/ktietz/src/ci/python-dateutil_1611928101742/work
+pytz @ file:///tmp/build/80754af9/pytz_1612215392582/work
+pyvo==1.1
+pyzmq==20.0.0
+qtconsole @ file:///tmp/build/80754af9/qtconsole_1623278325812/work
+QtPy==1.9.0
+requests==2.25.1
+scipy==1.6.3
+Send2Trash @ file:///tmp/build/80754af9/send2trash_1607525499227/work
+six @ file:///tmp/build/80754af9/six_1623709665295/work
+soupsieve==2.2.1
+-e git+https://github.itap.purdue.edu/MintonGroup/swiftest.git@19f9e7d0b735f38b5b2e0f5d21fe9b4fb2b79838#egg=swiftest&subdirectory=python/swiftest
+terminado==0.9.4
+testpath @ file:///home/ktietz/src/ci/testpath_1611930608132/work
+tornado @ file:///tmp/build/80754af9/tornado_1606942283357/work
+traitlets @ file:///home/ktietz/src/ci/traitlets_1611929699868/work
+typing-extensions==3.10.0.0
+urllib3==1.26.5
+wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work
+webencodings==0.5.1
+widgetsnbextension==3.5.1
+xarray==0.18.2
+zipp @ file:///tmp/build/80754af9/zipp_1615904174917/work