Merge branch 'master' of ssh://git.penic.eu:29418/trisurf-manager

Samo Penic

2018-07-05 f9d768c731d86b2af9edfad4ef16f1dd8b359ffb

 trisurf/wrapper.py

@@ -82,10 +82,11 @@
      ('znorm', c_double),
      ('area', c_double),
      ('volume', c_double),
      ('energy', c_double),
   ]

class ts_triangle_list(Structure):
   _fields_=[('n',c_uint),('tria', POINTER(POINTER(ts_triangle)))]
   _fields_=[('n',c_uint),('a0',c_double),('tria', POINTER(POINTER(ts_triangle))),]


ts_cell._fields_=[
@@ -145,6 +146,8 @@
      ('pswitch',c_long),
      ('constvolswitch',c_long),
      ('constareaswitch',c_long),
      ('stretchswitch',c_long),
      ('xkA0',c_double),
      ('constvolprecision',c_double),
      ('multiprocessing',c_char_p),
      ('brezveze0',c_long),
@@ -199,9 +202,113 @@
ts_cluster._fields_=[('nvtx',c_uint),('idx',c_uint),('vtx', POINTER(POINTER(ts_vertex)))]

class ts_cluster_list(Structure):
   _fields_=[('n',c_uint),('poly',POINTER(POINTER(ts_cluster)))]
   _fields_=[('n',c_uint),('cluster',POINTER(POINTER(ts_cluster)))]




ts=CDLL('libtrisurf.so')



#function call wrappers
def create_vesicle_from_tape(tape):
   """Using pointer for tape, it creates a vesicle, returning pointer to it."""
   ts.create_vesicle_from_tape.argtype=POINTER(ts_tape)
   ts.create_vesicle_from_tape.restype=POINTER(ts_vesicle)
   return ts.create_vesicle_from_tape(tape)

def parsetape(filename='tape'):
   """Loads tape with  filename (if not given it defaults to 'tape'). It returns a pointer to structure for tape"""
   ts.parsetape.restype=POINTER(ts_tape)
   ts.parsetape.argtype=[c_char_p]
   return ts.parsetape(filename.encode('ascii'))

def parseDump(filename):
   """Loads a vtu file with 'filename' and creates a vesicle returning pointer to it"""
   ts.parseDump.argtype=[c_char_p]
   ts.parseDump.restype=POINTER(ts_vesicle)
   vesicle=ts.parseDump(filename.encode('ascii'))
   return vesicle

def single_timestep(vesicle):
   """Makes a single timestep in simulations. Returns a tuple of vmsrt and bfrt (vertex move success rate and bond flip success rate)"""
   ts.single_timestep.argtype=[POINTER(ts_vesicle),POINTER(c_double),POINTER(c_double)]
   vmsrt=c_double(0.0)
   bfsrt=c_double(0.0)
   ts.single_timestep(vesicle,byref(vmsrt),byref(bfsrt))
   return (vmsrt.value, bfsrt.value)

def write_vertex_xml_file(vesicle,timestep_no=0):
   """Writes a vesicle into file with filename 'timestep_XXXXXX.vtu', where XXXXXX is a leading zeroed number given with timestep_no parameter (defaults to 0 if not given"""
   ts.write_vertex_xml_file.argtypes=[POINTER(ts_vesicle),c_int]
   ts.write_vertex_xml_file(vesicle,c_int(timestep_no))


def vesicle_free(vesicle):
   """Free memory of the whole vesicle"""
   ts.vesicle_free.argtype=[POINTER(ts_vesicle)]
   ts.vesicle_free(vesicle)

def vesicle_volume(vesicle):
   ts.vesicle_volume.argtype=[POINTER(ts_vesicle)]
   ts.vesicle_volume(vesicle)

def vesicle_area(vesicle):
   ts.vesicle_area.argtype=[POINTER(ts_vesicle)]
   ts.vesicle_area(vesicle)

def gyration_eigen(vesicle):
   ts.gyration_eigen.argtype=[POINTER(ts_vesicle), POINTER(c_double), POINTER(c_double), POINTER(c_double)]
   l1=c_double(0.0)
   l2=c_double(0.0)
   l3=c_double(0.0)
   ts.gyration_eigen(vesicle , byref(l1), byref(l2), byref(l3))
   return (l1.value, l2.value, l3.value)

def vesicle_meancurvature(vesicle):
   ts.vesicle_meancurvature.argtype=[POINTER(ts_vesicle)]
   ts.vesicle_meancurvature.restype=c_double
   return ts.vesicle_meancurvature(vesicle)

def init_cluster_list():
   ts.init_cluster_list.restype=POINTER(ts_cluster_list)
   ret=ts.init_cluster_list()
   return ret

def clusterize_vesicle(vesicle, cluster_list):
   ts.clusterize_vesicle.argtype=[POINTER(ts_vesicle), POINTER(ts_cluster_list)]
   ts.clusterize_vesicle(vesicle, cluster_list)

def cluster_list_free(cluster_list):
   """Free memory of cluster list"""
   ts.cluster_list_free.argtype=[POINTER(ts_cluster_list)]
   ts.cluster_list_free(cluster_list)

def stretchenergy(vesicle, triangle):
   ts.stretchenergy.argtype=[POINTER(ts_vesicle), POINTER(ts_triangle)]
   ts.stretchenergy(vesicle,triangle)

def get_absolute_ulm2(vesicle,l,m):
   ts.get_absolute_ulm2.argtype=[POINTER(ts_vesicle), c_double, c_double]
   ts.get_absolute_ulm2.restype=c_double
   ret=ts.get_absolute_ulm2(vesicle,l,m)
   return ret

def getR0(vesicle):
   ts.getR0.argtype=[POINTER(ts_vesicle)]
   ts.getR0.restype=c_double
   r0=ts.getR0(vesicle)
   return r0

def preparationSh(vesicle,r0):
   ts.preparationSh.argtype=[POINTER(ts_vesicle), c_double]
   ts.preparationSh(vesicle,float(r0))

def calculateUlmComplex(vesicle):
   ts.calculateUlmComplex.argtype=[POINTER(ts_vesicle)]
   ts.calculateUlmComplex(vesicle)

def solve_for_ulm2(vesicle):
   ts.solve_for_ulm2.argtype=[POINTER(ts_vesicle)]
   ts.solve_for_ulm2(vesicle)