Update Galaxia names and fix examples

Author: LourensVeen

examples/examples_galaxia/evolution_cluster.py

@@ -18,7 +18,7 @@
 from amuse.community.seba.interface import SeBa
 from amuse.ext.composition_methods import LEAPFROG
 from amuse.ext.rotating_bridge import Rotating_Bridge
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 from matplotlib import pyplot
 
 
@@ -130,7 +130,7 @@ def galactic_model(self):
          The axisymmetric component has its defaul values from Allen &
          Santillan (1990).
          '''
-        galaxy = BarAndSpirals3D()
+        galaxy = Galaxia()
         galaxy.kinetic_energy = quantities.zero
         galaxy.potential_energy = quantities.zero
         galaxy.parameters.spiral_contribution = True

examples/examples_galaxia/orbit_one_star.py

@@ -11,7 +11,7 @@
 from amuse import datamodel
 from amuse.units import quantities, units
 from amuse.ext.rotating_bridge import Rotating_Bridge
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 from amuse.ext.composition_methods import (
         SPLIT_6TH_SS_M13, SPLIT_4TH_S_M6
         )
@@ -110,7 +110,7 @@ def galaxy(self):
         # The bar does not grow adiabatically
         # The axisymmetric component has its defaul values from Allen &
         # Santillan (1990).
-        galaxy = BarAndSpirals3D()
+        galaxy = Galaxia()
         galaxy.kinetic_energy = quantities.zero
         galaxy.potential_energy = quantities.zero
         galaxy.parameters.bar_contribution = True

examples/examples_galaxia/resonances.py

@@ -7,7 +7,7 @@
 
 import numpy
 from amuse.units import units
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 from matplotlib import rc
 import matplotlib.pyplot as plt
 
@@ -34,7 +34,7 @@ def plot_resonances(r, omega_c, ilr2, olr2, ilr4, olr4):
     xticks = numpy.arange(0, 15, 1)
     ax.set_xlim(0, 15)
     ax.set_ylim(0, 100)
-    ax.set_ylabel("$\Omega$ $[kms^{-1}kpc^{-1}]$")
+    ax.set_ylabel("$\\Omega$ $[kms^{-1}kpc^{-1}]$")
     ax.set_xlabel("R [Kpc]")
     plt.yticks(yticks)
     plt.xticks(xticks)
@@ -45,7 +45,7 @@ def plot_resonances(r, omega_c, ilr2, olr2, ilr4, olr4):
 if __name__ in('__main__', '__plot__'):
 
     # Axisymmetric model of the Galaxy with default values
-    MW = BarAndSpirals3D()
+    MW = Galaxia()
     MW.commit_parameters()
 
     r = numpy.arange(0.001, 15, 0.005) | units.kpc

examples/examples_galaxia/rotation_curve_Milky_Way.py

@@ -5,7 +5,7 @@
 # ---------------------------------------------------------------------------
 
 from amuse.units import units
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 import numpy
 from matplotlib import pyplot
 
@@ -24,7 +24,7 @@ def galaxy_model_with_bar_and_spirals(
         fiducial_radius=8 | units.kpc):
     # Galaxy model that uses a three dimensional bar (no adiabatic growing)
     # and the C&G model for the spiral arms
-    galaxy = BarAndSpirals3D()
+    galaxy = Galaxia()
     galaxy.parameters.bar_contribution = True
     galaxy.parameters.bar_phase = initial_phase_bar_and_SA
     galaxy.parameters.mass_bar = mass_bar
@@ -46,7 +46,7 @@ def galaxy_model_with_bar_and_spirals(
 
 def galaxy_model_purely_axisymmetric():
     # Axisymmetric Galaxy model with default values
-    galaxy = BarAndSpirals3D()
+    galaxy = Galaxia()
     galaxy.commit_parameters()
     return galaxy
 

examples/examples_galaxia/utility_functions.py

@@ -8,7 +8,7 @@
 # ---------------------------------------------------------------------------
 
 from amuse.units import units
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 import numpy
 from amuse.units.quantities import VectorQuantity
 
@@ -31,7 +31,7 @@ def galaxy_model(
     # The bar does not grow adiabatically
     # The axisymmetric component has its default values from Allen & Santillan
     # (1990).
-    galaxy = BarAndSpirals3D()
+    galaxy = Galaxia()
     galaxy.parameters.bar_contribution = True
     galaxy.parameters.bar_phase = initial_phase_bar
     galaxy.parameters.omega_bar = pattern_speed_bar

examples/textbook/Sun_and_M67_in_the_Galaxy.py

@@ -4,7 +4,7 @@
 from amuse import datamodel
 from amuse.units import quantities
 from amuse.ext.rotating_bridge import Rotating_Bridge
-from amuse.community.galaxia.interface import BarAndSpirals3D
+from amuse.community.galaxia.interface import Galaxia
 from amuse.ext.composition_methods import *
 
 from prepare_figure import *
@@ -33,7 +33,7 @@ def kinetic_energy(self):
 class IntegrateOrbit(object):
     """
     This class makes the integration of the Sun in the Milky Way
-    by using BarAndSpirals3D. 
+    by using Galaxia.
     galaxy(): Function that sets the desired Galactic model. Any question on the parameters, contact me
     creation_particles_noinertial(): creates a parti le set in a rotating frame
     noinertial_to_inertial(): converts data from rotating to inertial frame
@@ -64,7 +64,7 @@ def __init__(self, t_end= 10 |units.Myr, dt_bridge=0.5 |units.Myr, method= SPLIT
 
     def galaxy(self):
         global I
-        galaxy= BarAndSpirals3D(redirection='file', redirect_stdout_file="GAL{0}.log".format(I))
+        galaxy= Galaxia(redirection='file', redirect_stdout_file="GAL{0}.log".format(I))
         I = I + 1
         galaxy.kinetic_energy=quantities.zero
         galaxy.potential_energy=quantities.zero
@@ -182,7 +182,8 @@ def get_pos_vel_and_orbit(self, particle_set):
 
             x = particle_set.x
             y = particle_set.y
-            write_set_to_file(particle_set.savepoint(self.time), filename, "hdf5")
+            write_set_to_file(particle_set.savepoint(self.time), filename, "hdf5",
+                              append_to_file=True)
 
 
         print("minimum", tmin.in_(units.Myr), dmin.in_(units.parsec))

examples/textbook/solar_cluster_in_galaxy_potential.py

@@ -5,7 +5,6 @@
 from amuse.units.optparse import OptionParser
 from amuse.units import quantities
 
-from amuse.community.galaxia.interface import BarAndSpirals3D
 from amuse.ext.composition_methods import *
 from matplotlib import pyplot
 

examples/textbook/solar_cluster_in_semilive_galaxy.py

@@ -5,7 +5,6 @@
 from amuse.units.optparse import OptionParser
 from amuse.units import quantities
 
-from amuse.community.galaxia.interface import BarAndSpirals3D
 from amuse.ext.composition_methods import *
 from matplotlib import pyplot
 from prepare_figure import figure_frame, get_distinct
@@ -178,7 +177,7 @@ def evolve_cluster_in_potential(gravity, t_end, dt,
     if filename:
         write_set_to_file(sun, filename, "hdf5", timestamp = time,
                           append_to_file=False)
-        write_set_to_file(GMCs, filename, "hdf5", timestamp = time)
+        write_set_to_file(GMCs, filename, "hdf5", timestamp = time, append_to_file=True)
 
     x = []
     y = []
@@ -189,8 +188,10 @@ def evolve_cluster_in_potential(gravity, t_end, dt,
         for ch in channels_to_framework:
             ch.copy()
         if filename:
-            write_set_to_file(sun, filename, "hdf5", timestamp = time)
-            write_set_to_file(GMCs, filename, "hdf5", timestamp = time)
+            write_set_to_file(sun, filename, "hdf5", timestamp = time,
+                              append_to_file=True)
+            write_set_to_file(GMCs, filename, "hdf5", timestamp = time,
+                              append_to_file=True)
 
         x.append(gravity.particles[0].x.value_in(units.kpc))
         y.append(gravity.particles[0].y.value_in(units.kpc))
@@ -278,8 +279,8 @@ def make_giant_molecular_clouds(Ngmc):
     print("Masses:", MGMCs.in_(units.MSun), MGalaxy.in_(units.MSun), \
           MGMCs/MGalaxy)
     GMCs = ProtoPlanetaryDisk(len(masses), convert_nbody=converter,
-                              Rmin=Rin.value_in(units.kpc), 
-                              Rmax=Rout.value_in(units.kpc),
+                              radius_min=Rin.value_in(units.kpc),
+                              radius_max=Rout.value_in(units.kpc),
                               q_out=30.0, discfraction=MGMCs/MGalaxy).result
 
     #second population of GMCs
@@ -289,8 +290,8 @@ def make_giant_molecular_clouds(Ngmc):
     GMCs.mass = masses
     MGMCs = masses.sum()
     thin_disk_GMCs = ProtoPlanetaryDisk(N_thin_disk, convert_nbody=converter,
-                              Rmin=Rin.value_in(units.kpc), 
-                              Rmax=2*Rout.value_in(units.kpc),
+                              radius_min=Rin.value_in(units.kpc),
+                              radius_max=2*Rout.value_in(units.kpc),
                               q_out=10.0, discfraction=MGMCs/MGalaxy).result
     thin_disk_GMCs.masses = masses
     GMCs.add_particles(thin_disk_GMCs)

src/amuse/community/galaxia/__init__.py

@@ -1 +1 @@
-from .interface import Galaxia
+from .interface import BarAndSpirals3D, Barandspirals3d, Galaxia

src/amuse/community/galaxia/interface.py

@@ -1,7 +1,7 @@
 from amuse.support.import_helper import load_code
 
+GalaxiaInterface = load_code("galaxia", "GalaxiaInterface")
+Galaxia = load_code("galaxia", "Galaxia")
 
-BarAndSpiralsInterface = load_code("galaxia", "BarAndSpiralsInterface")
-BarAndSpirals3D = load_code("galaxia", "BarAndSpirals3D")
-
-Barandspirals3d = BarAndSpirals3D
+Barandspirals3d = Galaxia
+BarAndSpirals3D = Galaxia