Various fixes to conform to Python PICMI standard

5 files changed, 72 insertions, 36 deletions

diff --git a/Python/pywarpx/AMReX.py b/Python/pywarpx/AMReX.py
index 581133695..bdadc49bd 100644
--- a/Python/pywarpx/AMReX.py
+++ b/Python/pywarpx/AMReX.py
@@ -6,6 +6,7 @@ from .Geometry import geometry
 from .Algo import algo
 from .Langmuirwave import langmuirwave
 from .Interpolation import interpolation
+from . import Particles
 from .Particles import particles, particles_list
 
 import ctypes
@@ -24,6 +25,12 @@ class AMReX(object):
         argv += interpolation.attrlist()
         argv += particles.attrlist()
 
+        if not particles_list:
+            # --- This is needed in case only species_names has been set,
+            # --- assuming that only the built in particle types are being used.
+            for pstring in particles.species_names.split(' '):
+                particles_list.append(getattr(Particles, pstring))
+
         for particle in particles_list:
             argv += particle.attrlist()
 
diff --git a/Python/pywarpx/Bucket.py b/Python/pywarpx/Bucket.py
index 2f4a1704c..916b030d1 100644
--- a/Python/pywarpx/Bucket.py
+++ b/Python/pywarpx/Bucket.py
@@ -25,7 +25,9 @@ class Bucket(object):
         "Concatenate the attributes into a string"
         result = []
         for attr, value in self.argvattrs.iteritems():
-            attrstring = '{0}.{1}={2} '.format(self.instancename, attr, value)
+            # --- repr is applied to value so that for floats, all of the digits are included.
+            # --- The strip is then needed when value is a string.
+            attrstring = '{0}.{1}={2} '.format(self.instancename, attr, repr(value).strip("'\""))
             result += [attrstring]
         return result
 
diff --git a/Python/pywarpx/PGroup.py b/Python/pywarpx/PGroup.py
index cbc30943b..fa8572c0a 100644
--- a/Python/pywarpx/PGroup.py
+++ b/Python/pywarpx/PGroup.py
@@ -6,8 +6,9 @@ class PGroup(object):
     """Implements a class that has the same API as a warp ParticleGroup instance.
     """
 
-    def __init__(self, igroup):
+    def __init__(self, igroup, ispecie):
         self.igroup = igroup
+        self.ispecie = ispecie
         self.ns = 1 # Number of species
 
         self.gallot()
@@ -75,81 +76,85 @@ class PGroup(object):
         return self.nps.sum()
     npmax = property(getnpmax)
 
-    def getxp(self, js=0):
-        return _libwarpx.get_particle_x(js)[self.igroup]
+    def getxp(self):
+        return _libwarpx.get_particle_x(self.ispecie)[self.igroup]
     xp = property(getxp)
 
-    def getyp(self, js=0):
-        return _libwarpx.get_particle_y(js)[self.igroup]
+    def getyp(self):
+        return _libwarpx.get_particle_y(self.ispecie)[self.igroup]
     yp = property(getyp)
 
-    def getzp(self, js=0):
-        return _libwarpx.get_particle_z(js)[self.igroup]
+    def getzp(self):
+        return _libwarpx.get_particle_z(self.ispecie)[self.igroup]
     zp = property(getzp)
 
-    def getuxp(self, js=0):
-        return _libwarpx.get_particle_ux(js)[self.igroup]
+    def getuxp(self):
+        return _libwarpx.get_particle_ux(self.ispecie)[self.igroup]
     uxp = property(getuxp)
 
-    def getuyp(self, js=0):
-        return _libwarpx.get_particle_uy(js)[self.igroup]
+    def getuyp(self):
+        return _libwarpx.get_particle_uy(self.ispecie)[self.igroup]
     uyp = property(getuyp)
 
-    def getuzp(self, js=0):
-        return _libwarpx.get_particle_uz(js)[self.igroup]
+    def getuzp(self):
+        return _libwarpx.get_particle_uz(self.ispecie)[self.igroup]
     uzp = property(getuzp)
 
-    def getpid(self, js=0):
-        id = _libwarpx.get_particle_id(js)[self.igroup]
+    def getpid(self):
+        id = _libwarpx.get_particle_id(self.ispecie)[self.igroup]
         pid = np.array([id]).T
         return pid
     pid = property(getpid)
 
-    def getgaminv(self, js=0):
-        uxp = self.getuxp(js)
-        uyp = self.getuyp(js)
-        uzp = self.getuzp(js)
+    def getgaminv(self):
+        uxp = self.getuxp()
+        uyp = self.getuyp()
+        uzp = self.getuzp()
         return np.sqrt(1. - (uxp**2 + uyp**2 + uzp**2)/_libwarpx.clight**2)
     gaminv = property(getgaminv)
 
-    def getex(self, js=0):
-        return _libwarpx.get_particle_Ex(js)[self.igroup]
+    def getex(self):
+        return _libwarpx.get_particle_Ex(self.ispecie)[self.igroup]
     ex = property(getex)
 
-    def getey(self, js=0):
-        return _libwarpx.get_particle_Ey(js)[self.igroup]
+    def getey(self):
+        return _libwarpx.get_particle_Ey(self.ispecie)[self.igroup]
     ey = property(getey)
 
-    def getez(self, js=0):
-        return _libwarpx.get_particle_Ez(js)[self.igroup]
+    def getez(self):
+        return _libwarpx.get_particle_Ez(self.ispecie)[self.igroup]
     ez = property(getez)
 
-    def getbx(self, js=0):
-        return _libwarpx.get_particle_Bx(js)[self.igroup]
+    def getbx(self):
+        return _libwarpx.get_particle_Bx(self.ispecie)[self.igroup]
     bx = property(getbx)
 
-    def getby(self, js=0):
-        return _libwarpx.get_particle_By(js)[self.igroup]
+    def getby(self):
+        return _libwarpx.get_particle_By(self.ispecie)[self.igroup]
     by = property(getby)
 
-    def getbz(self, js=0):
-        return _libwarpx.get_particle_Bz(js)[self.igroup]
+    def getbz(self):
+        return _libwarpx.get_particle_Bz(self.ispecie)[self.igroup]
     bz = property(getbz)
 
 class PGroups(object):
     def __init__(self, ispecie=0):
         self.ispecie = ispecie
-        xall = _libwarpx.get_particle_x(ispecie)
+
+    def setuppgroups(self):
+        xall = _libwarpx.get_particle_x(self.ispecie)
         self.ngroups = len(xall)
 
         self._pgroups = []
         for igroup in range(self.ngroups):
-            self._pgroups.append(PGroup(igroup))
+            self._pgroups.append(PGroup(igroup, self.ispecie))
         
     def __iter__(self):
+        self.setuppgroups()
         for igroup in range(self.ngroups):
             yield self._pgroups[igroup]
 
     def __getitem__(self, key):
+        self.setuppgroups()
         return self._pgroups[key]
 
diff --git a/Python/pywarpx/PICMI.py b/Python/pywarpx/PICMI.py
index 95bb758dc..30957970e 100644
--- a/Python/pywarpx/PICMI.py
+++ b/Python/pywarpx/PICMI.py
@@ -4,6 +4,8 @@ from PICMI_Base import *
 import numpy as np
 from pywarpx import *
 
+codename = 'WarpX'
+
 
 class Grid(PICMI_Grid):
     def init(self, **kw):
@@ -20,8 +22,26 @@ class Grid(PICMI_Grid):
         # Geometry
         geometry.coord_sys = kw.get('coord_sys', 0)  # 0: Cartesian
         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)
+        geometry.prob_lo = '%s %s %s'%(repr(self.xmin), repr(self.ymin), repr(self.zmin))  # physical domain
+        geometry.prob_hi = '%s %s %s'%(repr(self.xmax), repr(self.ymax), repr(self.zmax))
+
+        if self.moving_window_velocity is not None and np.any(self.moving_window_velocity != 0):
+            warpx.do_moving_window = 1
+            if self.moving_window_velocity[0] != 0.:
+                warpx.moving_window_dir = 'x'
+                warpx.moving_window_v = self.moving_window_velocity[0]/clight  # in units of the speed of light
+            if self.moving_window_velocity[1] != 0.:
+                warpx.moving_window_dir = 'y'
+                warpx.moving_window_v = self.moving_window_velocity[1]/clight  # in units of the speed of light
+            if self.moving_window_velocity[2] != 0.:
+                warpx.moving_window_dir = 'z'
+                warpx.moving_window_v = self.moving_window_velocity[2]/clight  # in units of the speed of light
+
+    def getmins(self, **kw):
+        return np.array([warpx.getProbLo(0), warpx.getProbLo(1), warpx.getProbLo(2)])
+
+    def getmaxs(self, **kw):
+        return np.array([warpx.getProbHi(0), warpx.getProbHi(1), warpx.getProbHi(2)])
 
     def getxmin(self):
         return warpx.getProbLo(0)
diff --git a/Python/pywarpx/_libwarpx.py b/Python/pywarpx/_libwarpx.py
index e552a2f58..9dcc879c5 100755
--- a/Python/pywarpx/_libwarpx.py
+++ b/Python/pywarpx/_libwarpx.py
@@ -107,6 +107,8 @@ f.argtypes = (ctypes.c_int, ctypes.c_int,
               ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"),
               ctypes.c_int)
 
+libwarpx.warpx_getProbLo.restype = ctypes.c_double
+libwarpx.warpx_getProbHi.restype = ctypes.c_double
 libwarpx.warpx_getistep.restype = ctypes.c_int
 libwarpx.warpx_gett_new.restype = ctypes.c_double
 libwarpx.warpx_getdt.restype = ctypes.c_double