Updated to be compliant with PICMI Python standard

4 files changed, 65 insertions, 162 deletions

diff --git a/Python/pywarpx/AMReX.py b/Python/pywarpx/AMReX.py
index dac675129..581133695 100644
--- a/Python/pywarpx/AMReX.py
+++ b/Python/pywarpx/AMReX.py
@@ -6,7 +6,7 @@ from .Geometry import geometry
 from .Algo import algo
 from .Langmuirwave import langmuirwave
 from .Interpolation import interpolation
-from .Particles import particles, electrons
+from .Particles import particles, particles_list
 
 import ctypes
 from ._libwarpx import libwarpx
@@ -23,7 +23,9 @@ class AMReX(object):
         argv += langmuirwave.attrlist()
         argv += interpolation.attrlist()
         argv += particles.attrlist()
-        argv += electrons.attrlist()
+
+        for particle in particles_list:
+            argv += particle.attrlist()
 
         amrex_init(argv)
 
diff --git a/Python/pywarpx/PICMI.py b/Python/pywarpx/PICMI.py
index 3e7e7185f..95bb758dc 100644
--- a/Python/pywarpx/PICMI.py
+++ b/Python/pywarpx/PICMI.py
@@ -1,74 +1,14 @@
 """Classes following the PICMI standard
 """
+from PICMI_Base import *
 import numpy as np
 from pywarpx import *
 
-pi = 3.14159265358979323  # ratio of a circle's circumference to its diameter
-euler = 0.57721566490153386  # Euler-Masceroni constant. Base of the natural logarithm.
-amu = 1.660538921e-27  # Atomic Mass Unit [kg]
-clight = 2.99792458e+8  # Speed of light in vacuum (exact) [m/s]
-echarge = 1.602176565e-19  # Elementary charge [C]
-emass = 9.10938291e-31  # Electron mass [kg]
-mu0 = 4.e-7*pi  # Permeability of free space [kg.m/(s.s.A.A)=H/m=T.m/A]
-eps0 = 1./(mu0*clight*clight)  # Permittivity of free space [F/m]
-boltzmann = 1.3806488e-23  # Boltzmann's constant [J/K]
-avogadro = 6.02214129e23  # Avogadro's Number [atoms/mole]
-planck = 6.62606957e-34  # Planck's constant [J.s]
-
-class Grid(object):
-    """
-    - `Grid`
-      - **type**: *object*
-      - `Nx=nx` - **type**: *integer* - "Number of cells along X (Nb nodes=nx+1)."
-      - `Ny=ny` - **type**: *integer* - "Number of cells along Y (Nb nodes=ny+1)."
-      - `Nr=nr` - **type**: *integer* - "Number of cells along R (Nb nodes=nr+1)."
-      - `Nz=nz` - **type**: *integer* - "Number of cells along Z (Nb nodes=nz+1)."
-      - `Nm=nm` - **type**: *integer* - "Number of azimuthal modes."
-      - `Xmin=xmin` - **type**: *double* - "Position of first node along X."
-      - `Xmax=xmax` - **type**: *double* - "Position of last node along X."
-      - `Ymin=ymin` - **type**: *double* - "Position of first node along Y."
-      - `Ymax=ymax` - **type**: *double* - "Position of last node along Y."
-      - `Rmax=rmax` - **type**: *double* - "Position of last node along R."
-      - `Zmin=zmin` - **type**: *double* - "Position of first node along Z."
-      - `Zmax=zmax` - **type**: *double* - "Position of last node along Z."
-      - `bcxmin` - **type**: *string* - "Boundary condition at min X: periodic/open/dirichlet/neumann."
-      - `bcxmax` - **type**: *string* - "Boundary condition at max X: periodic/open/dirichlet/neumann."
-      - `bcymin` - **type**: *string* - "Boundary condition at min Y: periodic/open/dirichlet/neumann."
-      - `bcymax` - **type**: *string* - "Boundary condition at max Y: periodic/open/dirichlet/neumann."
-      - `bcrmax` - **type**: *string* - "Boundary condition at max R: open/dirichlet/neumann."
-      - `bczmin` - **type**: *string* - "Boundary condition at min Z: periodic/open/dirichlet/neumann."
-      - `bczmax` - **type**: *string* - "Boundary condition at max Z: periodic/open/dirichlet/neumann."
-
-      - max_grid_size
-      - max_level
-      - coord_sys
-    """
-
-    def __init__(self, nx=None, ny=None, nr=None, nz=None, nm=None,
-                 xmin=None, xmax=None, ymin=None, ymax=None, rmax=None, zmin=None, zmax=None,
-                 bcxmin=None, bcxmax=None, bcymin=None, bcymax=None, bcrmax=None, bczmin=None, bczmax=None,
-                 **kw):
-        self.nx = nx
-        self.ny = ny
-        self.nr = nr
-        self.nz = nz
-        self.nm = nm
-        self.xmin = xmin
-        self.xmax = xmax
-        self.ymin = ymin
-        self.ymax = ymax
-        self.rmax = rmax
-        self.zmin = zmin
-        self.zmax = zmax
-        self.bcxmin = bcxmin
-        self.bcxmax = bcxmax
-        self.bcymin = bcymin
-        self.bcymax = bcymax
-        self.bcrmax = bcrmax
-        self.bczmin = bczmin
-        self.bczmax = bczmax
-
-        amr.n_cell = '%d  %d  %d'%(nx, ny, nz)
+
+class Grid(PICMI_Grid):
+    def init(self, **kw):
+
+        amr.n_cell = '%d  %d  %d'%(self.nx, self.ny, self.nz)
 
         # Maximum allowable size of each subdomain in the problem domain; 
         #    this is used to decompose the domain for parallel calculations.
@@ -79,97 +19,45 @@ class Grid(object):
 
         # Geometry
         geometry.coord_sys = kw.get('coord_sys', 0)  # 0: Cartesian
-        geometry.is_periodic = '%d %d %d'%(bcxmin=='periodic', bcymin=='periodic', bczmin=='periodic')  # Is periodic?  
-        geometry.prob_lo = '%7.0e %7.0e %7.0e'%(xmin, ymin, zmin)  # physical domain
-        geometry.prob_hi = '%7.0e %7.0e %7.0e'%(xmax, ymax, zmax)
-
-
-class EM_solver(object):
-    Methods_list = ['Yee', 'CK', 'CKC', 'Lehe', 'PSTD', 'PSATD', 'GPSTD']
-    def __init__(self, Method=None,
-                 norderx=None, nordery=None, norderr=None, norderz=None,
-                 l_nodal=None,
-                 current_deposition_algo=None, charge_deposition_algo=None,
-                 field_gathering_algo=None, particle_pusher_algo=None, **kw):
-
-        assert Method is None or Method in EM_solver.Methods_list, Exception('Method has incorrect value')
-
-        if current_deposition_algo is not None:
-            algo.current_deposition = current_deposition_algo
-        if charge_deposition_algo is not None:
-            algo.charge_deposition = charge_deposition_algo
-        if field_gathering_algo is not None:
-            algo.field_gathering = field_gathering_algo
-        if particle_pusher_algo is not None:
-            algo.particle_pusher = particle_pusher_algo
-
-
-class Particle(object):
-    def __init__(self, Charge=None, charge=None, Q=None, q=None,
-                 Mass=None, mass=None, M=None, m=None,
-                 Symbol=None, symbol=None, S=None, s=None,
-                 Name=None, name=None, N=None, n=None, **kw):
-        # --- Accept multpiple names, but use 'charge', 'mass', 'symbol', 'name' internally.
-        if Charge is not None: charge = Charge
-        if Q is not None: charge = Q
-        if q is not None: charge = q
-        if Mass is not None: mass = Mass
-        if M is not None: mass = M
-        if m is not None: mass = m
-        if Symbol is not None: symbol = Symbol
-        if S is not None: symbol = S
-        if s is not None: symbol = s
-        if Name is not None: name = Name
-        if N is not None: name = N
-        if n is not None: name = n
-        self.charge = charge
-        self.mass = mass
-        self.symbol = symbol
-
-Electron = Particle(q=-echarge, m=emass, symbol='e-', name='Electron')
-Positron = Particle(q=echarge, m=emass, symbol='e+', name='Positron')
-Proton = Particle(q=echarge, m=1.6726231e-27, symbol='p', name='Proton')
-AntiProton = Particle(q=-echarge, m=1.6726231e-27, symbol='p-', name='Antiproton')
-Neutron = Particle(q=0. , m=1.6749286e-27, symbol='n', name='Neutron')
-Muon = Particle(q=-echarge, m=1.883531475e-28, symbol='mu-', name='Muon')
-Antimuon = Particle(q=echarge, m=1.883531475e-28, symbol='mu+', name='Antimuon')
-Photon = Particle(q=0., m=0., symbol='gnu', name='Photon')
-    
-
-class Species(object):
-    def __init__(self,
-                  Type=None, type=None,
-                  Name=None, name=None,
-                  Sid=None, sid=None,
-                  Charge_state=None, charge_state=None,
-                  Charge=None, charge=None, Q=None, q=None,
-                  Mass=None, mass=None, M=None, m=None,
-                  Weight=None, weight=None, W=None, w=None, **kw):
-        # --- Accept multpiple names, but use 'type', 'name', 'sid', 'charge_state', 'charge', 'mass', 'weight'
-        if Type is not None: type = Type
-        if Name is not None: name = Name
-        if Sid is not None: sid = Sid
-        if Charge_state is not None: charge_state = Charge_state
-        if Charge is not None: charge = Charge
-        if Q is not None: charge = Q
-        if q is not None: charge = q
-        if Mass is not None: mass = Mass
-        if M is not None: mass = M
-        if m is not None: mass = m
-        if Weight is not None: weight = Weight
-        if W is not None: weight = W
-        if w is not None: weight = w
-        self.type = type
-        self.name = name
-        self.sid = sid
-        self.charg_state = charg_state
-        self.charge = charge
-        self.mass = mass
-        self.weight = weight
+        geometry.is_periodic = '%d %d %d'%(self.bcxmin=='periodic', self.bcymin=='periodic', self.bczmin=='periodic')  # Is periodic?  
+        geometry.prob_lo = '%7.0e %7.0e %7.0e'%(self.xmin, self.ymin, self.zmin)  # physical domain
+        geometry.prob_hi = '%7.0e %7.0e %7.0e'%(self.xmax, self.ymax, self.zmax)
+
+    def getxmin(self):
+        return warpx.getProbLo(0)
+    def getxmax(self):
+        return warpx.getProbHi(0)
+    def getymin(self):
+        return warpx.getProbLo(1)
+    def getymax(self):
+        return warpx.getProbHi(1)
+    def getzmin(self):
+        return warpx.getProbLo(2)
+    def getzmax(self):
+        return warpx.getProbHi(2)
+
+class EM_solver(PICMI_EM_solver):
+    def init(self, **kw):
+
+        if self.current_deposition_algo is not None:
+            algo.current_deposition = self.current_deposition_algo
+        if self.charge_deposition_algo is not None:
+            algo.charge_deposition = self.charge_deposition_algo
+        if self.field_gathering_algo is not None:
+            algo.field_gathering = self.field_gathering_algo
+        if self.particle_pusher_algo is not None:
+            algo.particle_pusher = self.particle_pusher_algo
+
+
+class Species(PICMI_Species):
+    def init(self, **kw):
 
         self.species_number = particles.nspecies
         particles.nspecies = particles.nspecies + 1
-        particles.species_names = particles.species_names + ' ' + name
+        particles.species_names = particles.species_names + ' ' + self.name
+
+        self.bucket = Bucket.Bucket(self.name, mass=self.mass, charge=self.charge, injection_style = 'python')
+        Particles.particles_list.append(self.bucket)
 
     def add_particles(self, n=None,
                       x=None, y=None, z=None,
@@ -179,11 +67,18 @@ class Species(object):
         add_particles(self.species_number, x, y, z, ux, uy, uz, pid, unique_particles)
 
 
-class Simulation(object):
-    def __init__(self, plot_int=None, verbose=None, cfl=None):
-        amr.plot_int = plot_int
-        warpx.verbose = verbose
-        warpx.cfl = cfl
+class Simulation(PICMI_Simulation):
+    def set_warpx_attr(self, warpx_obj, attr, kw):
+        value = kw.get(attr, None)
+        if value is not None:
+            setattr(warpx_obj, attr, value)
+            setattr(self, attr, value)
+
+    def init(self, **kw):
+
+        warpx.verbose = self.verbose
+        warpx.cfl = self.cfl
+        amr.plot_int = self.plot_int
 
         self.amrex = AMReX()
         self.amrex.init()
diff --git a/Python/pywarpx/Particles.py b/Python/pywarpx/Particles.py
index bc3feef9c..e7bac7e10 100644
--- a/Python/pywarpx/Particles.py
+++ b/Python/pywarpx/Particles.py
@@ -1,6 +1,7 @@
 from .Bucket import Bucket
 
 particles = Bucket('particles', nspecies=0, species_names='')
+particles_list = []
 
 electrons = Bucket('electrons')
 electrons.charge = "-q_e"
@@ -16,3 +17,8 @@ protons = Bucket('protons')
 protons.charge = "q_e"
 protons.mass = "m_p"
 protons.injection_style = "python"
+
+particle_dict = {'electrons':electrons,
+                 'positrons':positrons,
+                 'protons':protons
+                 }
diff --git a/Python/pywarpx/__init__.py b/Python/pywarpx/__init__.py
index cf79c65a6..f6b5a5bd3 100644
--- a/Python/pywarpx/__init__.py
+++ b/Python/pywarpx/__init__.py
@@ -8,7 +8,7 @@ from .Interpolation import interpolation
 from .Particles import particles
 from .AMReX import AMReX
 
-from .timestepper import TimeStepper
+#from .timestepper import TimeStepper
 from .PGroup import PGroup
 from .PGroup import PGroups