Merge pull request #282 from RudolfWeeber/py_cleanup

Py cleanup

src/python/espressomd/Makefile.am

@@ -43,13 +43,11 @@ PYXFILES =  \
 	particle_data.pyx \
 	analyze.pyx \
 	cellsystem.pyx \
-	changeVolume.pyx \
 	code_info.pyx \
 	cuda_init.pyx \
 	debye_hueckel.pyx \
 	integrate.pyx \
 	interactions.pyx \
-	invalidateSystem.pyx \
 	thermostat.pyx \
 	utils.pyx
 

src/python/espressomd/__init__.py

@@ -35,3 +35,4 @@
 espressomd._init.setup()
 
 from espressomd.system import System
+from espressomd.code_info import features

src/python/espressomd/_system.pxd

@@ -18,3 +18,5 @@
 #  
 import particle_data
 
+cdef extern from "grid.hpp":
+    cdef void rescale_boxl(int dir, double d_new)

src/python/espressomd/_system.pyx

@@ -340,7 +340,31 @@ cdef class System:
             global max_cut_bonded
             return max_cut_bonded
 
+
+    def changeVolumeAndRescaleParticles(dNew, dir="xyz"):
+      """Change box size and rescale particle coordinates
+         changeVolumeAndRescaleParticles(dNew, dir="xyz")
+	 dNew: new length, dir=coordinate tow work on, "xyz" for isotropic
+      """
+      if dNew<0:
+        raise ValueError("No negative lengths")
+      if dir=="xyz":
+        dNew=dNew**(1./3.)
+        rescale_boxl(3, dNew)
+      elif dir=="x":
+        rescale_boxl(0, dNew)
+      elif dir=="y":
+        rescale_boxl(1, dNew)
+      elif dir=="z":
+        rescale_boxl(2, dNew)
+      else:
+        raise ValueError('Usage: changeVolume { <V_new> | <L_new> { "x" | "y" | "z" | "xyz" } }')
+
+
+
+
 #lbfluid=lb.DeviceList()
 IF CUDA == 1:
     cu=cuda_init.CudaInitHandle()
 
+

src/python/espressomd/analyze.pyx

@@ -30,29 +30,30 @@ from libcpp.vector cimport vector #import std::vector as vector
 #
 # Minimal distance between particles
 #
+
 def mindist(system, p1 = 'default', p2 = 'default'):
+  """Minimal distance between particles
+    mindist(p1="default",p2="default")
+    
+    p1, p2: lists of particle types
+  """
 
   cdef IntList* set1
   cdef IntList* set2
 
   if p1 == 'default' and p2 == 'default':
     result = c_analyze.mindist(NULL,NULL)
-  elif p1 == 'default' and not p2 == 'default':
-    print 'usage: mindist([typelist],[typelist])'
-    return 0
-  elif not p1 == 'default' and p2 == 'default':
-    print 'usage: mindist([typelist],[typelist])'
-    return 0
+  elif (p1 == 'default' and not p2 == 'default') or \
+       (not p1 == 'default' and p2 == 'default'):
+    raise Exception("Both, p1 and p2 have to be specified\n"+__doc__)
   else:
     for i in range(len(p1)):
       if not isinstance(p1[i],int):
-        print 'usage: mindist([typelist],[typelist])'
-        return 0
+        raise ValueError("Particle types in p1 and p2 have to be of type int: "+str(p1[i]))
 
     for i in range(len(p2)):
       if not isinstance(p2[i],int):
-        print 'usage: mindist([typelist],[typelist])'
-        return 0
+        raise ValueError("Particle types in p1 and p2 have to be of type int"+str(p2[i]))
 
     set1 = create_IntList_from_python_object(p1)
     set2 = create_IntList_from_python_object(p2)
@@ -71,28 +72,50 @@ def mindist(system, p1 = 'default', p2 = 'default'):
 #
 # Distance to particle or point
 #
-def distto(system, id_or_pos):
+def distto(system, id=None,pos=None):
+  """"Distance to particle or point
+      distto(id=None,pos=None)
+      id: id of the particle
+      pos: position as array
+  """
+
+  if id==None and pos==None:
+    raise Exception("Either id or pos have to be specified\n"+__doc__)
+
+  if id !=None and pos != None:
+    raise Exception("Only one of id or pos may be specified\n"+__doc__)
+
+
   cdef double cpos[3]
   if system.n_part == 0:
-    print  'no particles'
-    return 'no particles'
+    raise Exception("no particles")
 
-  # check if id_or_pos is position or particle id
-  if isinstance(id_or_pos,int):
-    _id = id_or_pos
-    _pos = particle_data.ParticleHandle(id_or_pos).pos
+
+  # Get position 
+  # If particle id specified
+  if id !=None:
+    if not isinstance(id,int):
+      raise ValueError("Id has to be an integer")
+    _pos = system.part[id].pos
     for i in range(3):
       cpos[i] = _pos[i]
   else:
     for i in range(3):
-      cpos[i] = id_or_pos[i]
+      cpos[i] = pos[i]
       _id = -1
   return c_analyze.distto(cpos,_id)
 
 # get all particles in neighborhood r_catch of pos and return their ids
 # in il. plane can be used to specify the distance in the xy, xz or yz
 # plane
 def nbhood(self, pos=None, r_catch=None, plane = '3d'):
+  """nbhood(pos=None, r_catch=None, plane = '3d'):
+     get all particles in neighborhood r_catch of pos and return their ids
+     in il. plane can be used to specify the distance in the xy, xz or yz
+     plane
+     nbhood(pos=None, r_catch=None, plane = '3d'):
+  """
+
   cdef int planedims[3]
   cdef IntList* il=NULL
   cdef double c_pos[3]
@@ -124,18 +147,23 @@ def nbhood(self, pos=None, r_catch=None, plane = '3d'):
   free(il)
   return result
 
+
+
 #
 # Pressure analysis
 #
 def pressure(self, pressure_type = 'all', id1 = 'default', id2 = 'default', v_comp=False):
+  """Pewaauew
+     pressure(pressure_type = 'all', id1 = 'default', id2 = 'default', v_comp=False)
+  """
   cdef vector[string] pressure_labels
   cdef vector[double] pressures
 
   checkTypeOrExcept(v_comp, 1, bool, "v_comp must be a boolean")
 
   if pressure_type=='all':
     c_analyze.analyze_pressure_all(pressure_labels, pressures, v_comp)
-    return pressure_labels, pressures
+    return dict(zip(pressure_labels, pressures))
   elif id1 == 'default' and id2 == 'default':
     pressure = c_analyze.analyze_pressure(pressure_type, v_comp)
     return pressure
@@ -150,14 +178,15 @@ def pressure(self, pressure_type = 'all', id1 = 'default', id2 = 'default', v_co
     return pressure
 
 def stress_tensor(self, stress_type = 'all', id1 = 'default', id2 = 'default', v_comp=False):
+  """stress_tensor(self, stress_type = 'all', id1 = 'default', id2 = 'default', v_comp=False)"""
   cdef vector[string] stress_labels
   cdef vector[double] stresses
 
   checkTypeOrExcept(v_comp, 1, bool, "v_comp must be a boolean")
 
   if stress_type=='all':
     c_analyze.analyze_stress_tensor_all(stress_labels, stresses, v_comp)
-    return stress_labels, stresses
+    return dict(zip(stress_labels, stresses))
   elif id1 == 'default' and id2 == 'default':
     if (c_analyze.analyze_stress_tensor(stress_type, v_comp, stresses)):
       raise Exception("Error while calculating stress tensor")
@@ -175,6 +204,9 @@ def stress_tensor(self, stress_type = 'all', id1 = 'default', id2 = 'default', v
     return stresses
 
 def local_stress_tensor(self, periodicity=(1, 1, 1), range_start=(0.0, 0.0, 0.0), stress_range=(1.0, 1.0, 1.0), bins=(1, 1, 1)):
+  """local_stress_tensor(periodicity=(1, 1, 1), range_start=(0.0, 0.0, 0.0), stress_range=(1.0, 1.0, 1.0), bins=(1, 1, 1))
+  """
+
   cdef DoubleList* local_stress_tensor=NULL
   cdef int[3] c_periodicity, c_bins
   cdef double[3] c_range_start, c_stress_range
@@ -195,9 +227,9 @@ def local_stress_tensor(self, periodicity=(1, 1, 1), range_start=(0.0, 0.0, 0.0)
 # Energy analysis
 #
 def energy(system, etype = 'all', id1 = 'default', id2 = 'default'):
+  """energy(system, etype = 'all', id1 = 'default', id2 = 'default')"""
   if system.n_part == 0:
-    print  'no particles'
-    return 'no particles'
+    raise Exception('no particles')
 
   if c_analyze.total_energy.init_status == 0:
     c_analyze.init_energies(&c_analyze.total_energy)

src/python/espressomd/cellsystem.pyx

@@ -19,10 +19,13 @@
 cimport cellsystem
 
 cdef class Cellsystem:
-    def __init__(self):
-        pass
+
 
     def setDomainDecomposition(self, useVerletList=True):
+        """Activates domain decomposition cell system
+        setDomainDecomposition(useVerletList=True)
+        """
+
         useVerletList=bool(useVerletList)
 
         ### should work with global_variables.dd
@@ -41,12 +44,16 @@ cdef class Cellsystem:
         return True
 
     def setNsquare(self):
+        """Activates the nsquare force calculation
+        """
         mpi_bcast_cell_structure(CELL_STRUCTURE_NSQUARE)
         # @TODO: gathering should be interface independent
         # return mpi_gather_runtime_errors(interp, TCL_OK)
         return True
 
     def setLayered(self, nLayers=""):
+        """setLayered(nLayers="")
+        Set the layerd cell system with nLayers layers"""
         if nLayers!="":
             if not isinstance(nLayers, int):
                 raise ValueError("layer height should be positive")