mirror of https://gitlab.com/scemama/eplf
Started to work on grid partitioning
This commit is contained in:
Anthony Scemama
parent
f463cb672e
commit
472865bb69
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@ -63,4 +63,5 @@ compute
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density logical
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density_grad logical
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density_lapl logical
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elf_partition logical
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@ -14,6 +14,39 @@ import tempfile
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editor = os.getenv("EDITOR",default="vi")
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## Data cleaning
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##################
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class Cleaner(object):
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def __init__(self,inp,name):
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self.dir = inp.name
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self.name = name.lower()
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self.inp = inp
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def action(self):
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raise TypeError
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def clean(self):
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print "Removing "+self.name
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self.action()
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class GridDataCleaner(Cleaner):
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def action(self):
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os.system("rm -f %s/grid_data/%s.gz"%(self.dir,self.name) )
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class AllCleaner(Cleaner):
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def action(self):
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os.system("rm -rf %s/grid"%(self.dir) )
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os.system("rm -rf %s/grid_data"%(self.dir) )
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def clear(x,inp):
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d = { "all": AllCleaner,
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}
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if x in d.keys():
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type = d[x]
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else:
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type = GridDataCleaner
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type(inp,x.replace("_"," ")).clean()
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## Data editing
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###############
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@ -70,29 +103,29 @@ class GridEditor(Editor):
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self.opposite = self.inp.opposite
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self.step_size = self.inp.step_size
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self.point_num = self.inp.point_num
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if self.origin is None:
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self.origin = [ 0., 0., 0. ]
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for l in xrange(3):
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self.origin[l] = self.inp.nucl_coord[l][1]
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for i in self.inp.nucl_coord[l]:
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self.origin[l] = min(self.origin[l],i)
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self.origin[l] -= 4.
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if self.opposite is None:
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self.opposite = [ 0., 0., 0. ]
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for l in xrange(3):
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self.opposite[l] = self.inp.nucl_coord[l][1]
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for i in self.inp.nucl_coord[l]:
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self.opposite[l] = max(self.opposite[l],i)
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self.opposite[l] += 4.
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if self.step_size is None:
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self.step_size = [ 0., 0., 0. ]
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for l in xrange(3):
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self.step_size[l] = (self.opposite[l] - self.origin[l])/float(self.point_num[l])
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# if self.origin is None:
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# self.origin = [ 0., 0., 0. ]
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# for l in xrange(3):
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# self.origin[l] = self.inp.nucl_coord[l][1]
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# for i in self.inp.nucl_coord[l]:
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# self.origin[l] = min(self.origin[l],i)
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# self.origin[l] -= 4.
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# if self.opposite is None:
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# self.opposite = [ 0., 0., 0. ]
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# for l in xrange(3):
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# self.opposite[l] = self.inp.nucl_coord[l][1]
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# for i in self.inp.nucl_coord[l]:
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# self.opposite[l] = max(self.opposite[l],i)
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# self.opposite[l] += 4.
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# if self.step_size is None:
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# self.step_size = [ 0., 0., 0. ]
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# for l in xrange(3):
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# self.step_size[l] = (self.opposite[l] - self.origin[l])/float(self.point_num[l])
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self.inp.point_num = self.point_num
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self.inp.origin = self.origin
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self.inp.opposite = self.opposite
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self.inp.step_size = self.step_size
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# self.inp.point_num = self.point_num
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# self.inp.origin = self.origin
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# self.inp.opposite = self.opposite
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# self.inp.step_size = self.step_size
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edit_temp_file(self.inp,self.write_grid_file,self.read_grid_file)
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def write_grid_file(self,file,inp):
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@ -101,33 +134,49 @@ class GridEditor(Editor):
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print >>file, "###########################"
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print >>file, ""
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print >>file, "# Number of points along x, y, z"
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print >>file, "%d %d %d"%tuple(self.point_num)
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if self.point_num is None:
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print >>file, "Default"
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else:
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print >>file, "%d %d %d"%tuple(self.point_num)
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print >>file, ""
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print >>file, "# Coordinates of the origin (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.origin)
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if self.origin is None:
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print >>file, "Default"
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else:
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print >>file, "%f %f %f"%tuple(self.origin)
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print >>file, ""
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print >>file, "# Coordinates of the opposite point (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.opposite)
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if self.opposite is None:
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print >>file, "Default"
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else:
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print >>file, "%f %f %f"%tuple(self.opposite)
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print >>file, ""
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print >>file, "# Step sizes (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.step_size)
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if self.step_size is None:
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print >>file, "Default"
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else:
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print >>file, "%f %f %f"%tuple(self.step_size)
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def read_grid_file(self,file,inp):
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lines = file.readlines()
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lines = filter(lambda x: len(x.strip())>0,lines)
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lines = filter(lambda x: not x.startswith("#"),lines)
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buffer = lines.pop(0).split()
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self.inp.point_num = map(int,buffer)
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buffer = lines.pop(0).lower().split()
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if buffer[0] != "default":
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self.inp.point_num = map(int,buffer)
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buffer = lines.pop(0).split()
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self.inp.origin = map(float,buffer)
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buffer = lines.pop(0).lower().split()
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if buffer[0] != "default":
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self.inp.origin = map(float,buffer)
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buffer = lines.pop(0).split()
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self.inp.opposite = map(float,buffer)
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buffer = lines.pop(0).lower().split()
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if buffer[0] != "default":
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self.inp.opposite = map(float,buffer)
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buffer = lines.pop(0).split()
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self.inp.step_size = self.step_size
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buffer = lines.pop(0).lower().split()
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if buffer[0] != "default":
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self.inp.step_size = self.step_size
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@ -150,9 +199,15 @@ def write_main_file(file,inp):
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print >>file, '# edit(geometry)'
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print >>file, '# edit(grid_parameters)'
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print >>file, ""
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compute = filter(lambda x: x.startswith("compute"),rw_data)
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print >>file, "# Clear"
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print >>file, "# --------------------\n"
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print >>file, '# clear(all)'
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for p in compute:
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print >>file, '# clear(%s)'%(p[8:])
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print >>file, ""
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print >>file, "# Computation"
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print >>file, "# --------------------\n"
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compute = filter(lambda x: x.startswith("compute"),rw_data)
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compute = filter(lambda x: not x.endswith("_grad"),compute)
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compute = filter(lambda x: not x.endswith("_lapl"),compute)
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for p in compute:
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@ -177,7 +232,8 @@ def read_main_file(file,inp):
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line = line.replace("(x) ","=True inp.compute_")
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buffer = line.split()
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line = ' '.join([buffer[1].lower(),buffer[0]])
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elif line.startswith("edit"):
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elif line.startswith("edit") \
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or line.startswith("clear"):
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line = line.replace("(","('").replace(")","',inp)").lower()
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exec line
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@ -19,5 +19,5 @@ SUBST [ X ]
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density;;
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density_grad;;
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density_lapl;;
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elf_partition;;
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END_TEMPLATE
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@ -30,6 +30,7 @@ data = [ \
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("compute_density" , "logical" , "" ),
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("compute_density_grad" , "logical" , "" ),
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("compute_density_lapl" , "logical" , "" ),
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("compute_elf_partition" , "logical" , "" ),
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("grid_data_eplf" , "real" , "(grid_x_num,grid_y_num,grid_z_num)" ),
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("grid_data_eplf_grad" , "real" , "(grid_x_num,grid_y_num,grid_z_num,4)" ),
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("grid_data_eplf_lapl" , "real" , "(grid_x_num,grid_y_num,grid_z_num)" ),
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@ -81,6 +81,13 @@ BEGIN_PROVIDER [ real, grid_$X, (grid_x_num,grid_y_num,grid_z_num) ]
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integer :: ix, iy, iz
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integer :: ibegin, iend
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real, parameter :: UNDEFINED=123456789.123456789
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grid_$X(1,1,1) = UNDEFINED
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call get_grid_data_$X(grid_$X)
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if (grid_$X(1,1,1) /= UNDEFINED) then
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return
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endif
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do iz=1,grid_z_num
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do iy=1,grid_y_num
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@ -114,60 +121,27 @@ BEGIN_PROVIDER [ real, grid_$X, (grid_x_num,grid_y_num,grid_z_num) ]
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enddo
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IRP_IF MPI
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! integer :: dim, ierr
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! do iz=1,grid_z_num
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! real :: buffer(grid_x_num*grid_y_num+1)
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! icount = 0
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! do iy=1,grid_y_num
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! do ix=1,grid_x_num
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! buffer(icount+ix) = grid_$X(ix,iy,iz)
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! enddo
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! icount = icount + grid_x_num
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! enddo
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! dim = grid_x_num * grid_y_num
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! call MPI_REDUCE(buffer,grid_$X(1,1,iz),dim,mpi_real, &
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! mpi_sum,0,MPI_COMM_WORLD,ierr)
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! if (ierr /= MPI_SUCCESS) then
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! call abrt(irp_here,'Unable to fetch buffer')
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! endif
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! call barrier
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! enddo
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! integer :: dim, ierr
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! real :: buffer(grid_x_num*grid_y_num*grid_z_num)
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! icount = 0
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! do iz=1,grid_z_num
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! do iy=1,grid_y_num
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! do ix=1,grid_x_num
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! buffer(icount+ix) = grid_$X(ix,iy,iz)
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! enddo
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! icount = icount + grid_x_num
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! enddo
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! enddo
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! dim = grid_x_num * grid_y_num * grid_y_num
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! call MPI_REDUCE(buffer,grid_$X,dim,mpi_real, &
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! mpi_sum,0,MPI_COMM_WORLD,ierr)
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! if (ierr /= MPI_SUCCESS) then
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! call abrt(irp_here,'Unable to fetch buffer')
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! endif
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integer :: dim, ierr
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dim = grid_x_num
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do iz=1,grid_z_num
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real :: buffer(grid_x_num)
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real :: buffer(grid_x_num*grid_y_num+1)
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icount = 0
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do iy=1,grid_y_num
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do ix=1,grid_x_num
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buffer(ix) = grid_$X(ix,iy,iz)
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buffer(icount+ix) = grid_$X(ix,iy,iz)
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enddo
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call MPI_REDUCE(buffer,grid_$X(1,iy,iz),dim,mpi_real, &
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mpi_sum,0,MPI_COMM_WORLD,ierr)
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if (ierr /= MPI_SUCCESS) then
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call abrt(irp_here,'Unable to fetch buffer')
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endif
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call barrier
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icount = icount + grid_x_num
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enddo
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dim = grid_x_num * grid_y_num
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call MPI_REDUCE(buffer,grid_$X(1,1,iz),dim,mpi_real, &
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mpi_sum,0,MPI_COMM_WORLD,ierr)
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if (ierr /= MPI_SUCCESS) then
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call abrt(irp_here,'Unable to fetch buffer')
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endif
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call barrier
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enddo
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IRP_ENDIF
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call set_grid_data_$X(grid_$X)
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END_PROVIDER
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@ -188,6 +162,13 @@ END_PROVIDER
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integer :: ix, iy, iz, it
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integer :: ibegin, iend
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real, parameter :: UNDEFINED=123456789.123456789
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grid_$X_lapl(1,1,1) = UNDEFINED
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call get_grid_data_$X_lapl(grid_$X)
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if (grid_$X_lapl(1,1,1) /= UNDEFINED) then
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return
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endif
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do iz=1,grid_z_num
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do iy=1,grid_y_num
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@ -256,6 +237,8 @@ END_PROVIDER
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enddo
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enddo
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IRP_ENDIF
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call set_grid_data_$X_grad(grid_$X_grad)
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call set_grid_data_$X_lapl(grid_$X_lapl)
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END_PROVIDER
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@ -265,3 +248,14 @@ SUBST [ X ]
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density;;
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END_TEMPLATE
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IRP_IF caca
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BEGIN_PROVIDER [ integer, grid_partition_$X, (grid_x_num,grid_y_num,grid_z_num) ]
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implicit none
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BEGIN_DOC
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! Create the topological partition of $X
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END_DOC
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END_PROVIDER
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IRP_ENDIF
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@ -3,34 +3,34 @@ program eplf
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provide mpi_rank
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if (comp_eplf) then
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call set_grid_data_eplf(grid_eplf)
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PROVIDE grid_eplf
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FREE grid_eplf
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endif
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if (comp_eplf_grad.or.comp_eplf_lapl) then
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call set_grid_data_eplf_grad(grid_eplf_grad)
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call set_grid_data_eplf_lapl(grid_eplf_lapl)
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PROVIDE grid_eplf_grad
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PROVIDE grid_eplf_lapl
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FREE grid_eplf_grad
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FREE grid_eplf_lapl
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endif
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if (comp_elf) then
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call set_grid_data_elf(grid_elf)
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PROVIDE grid_elf
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FREE grid_elf
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endif
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if (comp_elf_grad.or.comp_elf_lapl) then
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call set_grid_data_elf_grad(grid_elf_grad)
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call set_grid_data_elf_lapl(grid_elf_lapl)
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PROVIDE grid_elf_grad
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PROVIDE grid_elf_lapl
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FREE grid_elf_grad
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FREE grid_elf_lapl
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endif
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if (comp_density) then
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call set_grid_data_density(grid_density)
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PROVIDE grid_density
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FREE grid_density
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endif
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if (comp_density_grad.or.comp_density_lapl) then
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call set_grid_data_density_grad(grid_density_grad)
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call set_grid_data_density_lapl(grid_density_lapl)
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PROVIDE grid_density_grad
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PROVIDE grid_density_lapl
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FREE grid_density_grad
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FREE grid_density_lapl
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endif
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