Simulation of flexible fibers.

README.rst

@@ -94,6 +94,8 @@ basic examples.  Some of the formulations available are:
    pp. 124--149)
 -  `Akinci <http://doi.acm.org/10.1145/2185520.2185558>`_ (Akinci et al. ACM
    Trans. Graph., 2012, pp. 62:1--62:8)
+-  `Direct Fiber Simulation <https://doi.org/10.3390/jcs4020077>`_ for
+   fiber suspensions (Meyer et al. 2020, JCS, 4(2), pp. 77)
 
 Boundary conditions from the following papers are implemented:
 

pysph/base/gpu_domain_manager.py

@@ -14,8 +14,10 @@
 class GPUDomainManager(DomainManagerBase):
     def __init__(self, xmin=-1000., xmax=1000., ymin=0.,
                  ymax=0., zmin=0., zmax=0.,
-                 periodic_in_x=False, periodic_in_y=False,
-                 periodic_in_z=False, n_layers=2.0, backend=None, props=None,
+                 periodic_in_x=False, periodic_in_y=False, periodic_in_z=False,
+                 gamma_yx=0.0, gamma_zx=0.0, gamma_zy=0.0,
+                 n_layers=2.0, backend=None, props=None,
+                 dt=0.0, calls_per_step=2,
                  mirror_in_x=False, mirror_in_y=False, mirror_in_z=False):
         """Constructor"""
         DomainManagerBase.__init__(self, xmin=xmin, xmax=xmax,

pysph/base/nnps_base.pxd

@@ -138,7 +138,7 @@ cpdef UIntArray arange_uint(int start, int stop=*)
 
 # Basic particle array wrapper used for NNPS
 cdef class NNPSParticleArrayWrapper:
-    cdef public DoubleArray x,y,z,h
+    cdef public DoubleArray x,y,z,u,v,w,h
     cdef public UIntArray gid
     cdef public IntArray tag
     cdef public ParticleArray pa
@@ -164,6 +164,10 @@ cdef class DomainManagerBase:
     cdef public double ytranslate
     cdef public double ztranslate
 
+    cdef public double gamma_yx
+    cdef public double gamma_zx
+    cdef public double gamma_zy
+
     cdef public int dim
     cdef public bint periodic_in_x, periodic_in_y, periodic_in_z
     cdef public bint is_periodic
@@ -180,8 +184,14 @@ cdef class DomainManagerBase:
     cdef public double radius_scale  # Radius scale for kernel
     cdef public double n_layers      # Number of layers of ghost particles
 
+    cdef public double t             # Time for Lees-Edwards BC
+    cdef public double dt            # Time step for Lees-Edwards BC
+    cdef public int calls_per_step   # Number of calls per step
+    cdef public int loops            # loop counter
+
     #cdef double dbl_max              # Maximum value of double
 
+
     # remove ghost particles from a previous iteration
     cpdef _remove_ghosts(self)
 
@@ -199,6 +209,10 @@ cdef class CPUDomainManager(DomainManagerBase):
     # Convenience function to add a value to a carray
     cdef _add_to_array(self, DoubleArray arr, double disp, int start=*)
 
+    # Functions to shift ghost particle periodically in a direction
+    cdef _shift_periodic(self, DoubleArray arr, double disp, double min_pos,
+                         double max_pos, int start=*)
+
     # Convenience function to multiply a value to a carray
     cdef _mul_to_array(self, DoubleArray arr, double val)