SPP in c++

.vscode/settings.json

@@ -0,0 +1,71 @@
+{
+    "files.associations": {
+        "algorithm": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "bit": "cpp",
+        "cctype": "cpp",
+        "charconv": "cpp",
+        "chrono": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "compare": "cpp",
+        "concepts": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "exception": "cpp",
+        "format": "cpp",
+        "forward_list": "cpp",
+        "functional": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "ios": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "iterator": "cpp",
+        "limits": "cpp",
+        "list": "cpp",
+        "locale": "cpp",
+        "map": "cpp",
+        "memory": "cpp",
+        "new": "cpp",
+        "optional": "cpp",
+        "ostream": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "string": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "typeinfo": "cpp",
+        "unordered_map": "cpp",
+        "utility": "cpp",
+        "vector": "cpp",
+        "xfacet": "cpp",
+        "xhash": "cpp",
+        "xiosbase": "cpp",
+        "xlocale": "cpp",
+        "xlocbuf": "cpp",
+        "xlocinfo": "cpp",
+        "xlocmes": "cpp",
+        "xlocmon": "cpp",
+        "xlocnum": "cpp",
+        "xloctime": "cpp",
+        "xmemory": "cpp",
+        "xstddef": "cpp",
+        "xstring": "cpp",
+        "xtr1common": "cpp",
+        "xtree": "cpp",
+        "xutility": "cpp"
+    },
+    "C_Cpp.errorSquiggles": "Disabled"
+}

CellModeller/Biophysics/.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "files.associations": {
+        "vector": "cpp"
+    }
+}

CellModeller/Biophysics/BacterialModels/CLBacterium.cl

@@ -101,6 +101,7 @@ float4 quat_rot(float4 q, float4 v) {
 //  axis -- axis about which to rotate
 //  angle -- amount to rotate (radians)
 //  v -- the vector to rotate
+
 float4 rot(float4 axis, float angle, float4 v) {
   float4 q = axis*sin(angle/2.f);
   q.w = cos(angle/2.f);

CellModeller/Biophysics/BacterialModels/CLBacterium.py

@@ -200,6 +200,10 @@ def init_kernels(self):
                 reduce_expr="a+b", map_expr="dot(x[i].s0123,y[i].s0123)+dot(x[i].s4567,y[i].s4567)",
                 arguments="__global float8 *x, __global float8 *y")
 
+        # Add a force along the length dimension only
+        self.add_force = ElementwiseKernel(self.context,
+                                            "float8 *pos, const float mag, const float *force",
+                                            "pos[i].s6 = pos[i].s6 + mag*force[i]", "add_force")
 
     def init_data(self):
         """Set up the data OpenCL will store on the device."""
@@ -231,6 +235,7 @@ def init_data(self):
         self.cell_dlens_dev = cl_array.zeros(self.queue, cell_geom, numpy.float32)
         self.cell_target_dlens_dev = cl_array.zeros(self.queue, cell_geom, numpy.float32)
         self.cell_growth_rates = numpy.zeros(cell_geom, numpy.float32)
+        self.cell_growth_rates_dev = cl_array.zeros(self.queue, cell_geom, numpy.float32)
 
         # cell geometry calculated from l and r
         self.cell_areas_dev = cl_array.zeros(self.queue, cell_geom, numpy.float32)
@@ -449,6 +454,7 @@ def set_cells(self):
         self.cell_dlens_dev[0:self.n_cells].set(self.cell_dlens[0:self.n_cells])
         self.cell_dcenters_dev[0:self.n_cells].set(self.cell_dcenters[0:self.n_cells])
         self.cell_dangs_dev[0:self.n_cells].set(self.cell_dangs[0:self.n_cells])
+        self.cell_growth_rates_dev[0:self.n_cells].set(self.cell_growth_rates[0:self.n_cells])
 
     def set_planes(self):
         """Copy plane pts, norms, and coeffs to the device from local."""
@@ -574,8 +580,6 @@ def step(self, dt):
 
     def sub_tick_init(self, dt):
         # set target dlens (taken from growth rates set by updateCellStates)
-        #self.cell_target_dlens_dev.set(dt*self.cell_growth_rates)
-        #self.cell_dlens_dev.set(dt*self.cell_dlens)
         self.cell_dlens_dev[0:self.n_cells].set(dt*self.cell_growth_rates[0:self.n_cells])
 
         # redefine gridding based on the range of cell positions
@@ -616,7 +620,7 @@ def sub_tick(self, dt):
         self.sub_tick_i += 1
         alpha = 10**(self.sub_tick_i)
         new_cts = self.n_cts - old_n_cts
-        if (new_cts>0 or self.sub_tick_i==0) and self.sub_tick_i<self.max_substeps:
+        if (new_cts>0 or self.sub_tick_i==1) and self.sub_tick_i<self.max_substeps:
             self.build_matrix() # Calculate entries of the matrix
             #print "max cell contacts = %i"%cl_array.max(self.cell_n_cts_dev).get()
             self.CGSSolve(dt, alpha) # invert MTMx to find deltap
@@ -976,7 +980,6 @@ def CGSSolve(self, dt, alpha, substep=False):
                                     self.ct_reldists_dev.data,
                                     self.rhs_dev.data).wait()
 
-
         # res = b-Ax
         self.calculate_Ax(self.BTBx_dev, self.deltap_dev, dt, alpha)
         self.vsub(self.res_dev[0:self.n_cells], self.rhs_dev[0:self.n_cells], self.BTBx_dev[0:self.n_cells])