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suspendtools
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further improved serial

This commit is contained in:
Michael Krayer 2022-03-25 16:39:14 +01:00
parent c072e41677
commit b91f5e95bb
2 changed files with 112 additions and 28 deletions
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19
field.py
View File

@ -202,7 +202,7 @@ class Field3d:
r._dim = dim
return r
def save(self,file,name='Field3d',truncate=False):
def save(self,file,name='Field3d',truncate=False,single_precision=False):
import h5py
is_open = isinstance(file,(h5py.File,h5py.Group))
flag = 'w' if truncate else 'a'
@ -210,7 +210,10 @@ class Field3d:
g = f.create_group(name)
g.create_dataset('origin',data=self.origin)
g.create_dataset('spacing',data=self.spacing)
g.create_dataset('data',data=self.data)
if single_precision:
g.create_dataset('data',data=self.data,dtype='f4')
else:
g.create_dataset('data',data=self.data)
if not is_open: f.close()
return
@ -590,6 +593,18 @@ class Field3d:
val += c[ii,jj,kk]*self.data[i0+ii,j0+jj,k0+kk]
return val
def scipy_interpolate(self,pts,oob_fill=None):
from scipy.interpolate import RegularGridInterpolator
if oob_fill is None:
bounds_error = True
fill_value = None
else:
bounds_error = False
fill_value = oob_fill
rgi = RegularGridInterpolator(self.grid(),self.data,method='linear',
bounds_error=bounds_error,fill_value=fill_value)
return rgi(pts)
@staticmethod
def padding(origin,spacing,dim,padding,numpad):
if isinstance(numpad,int):

119
serial.py
View File

@ -2,6 +2,7 @@ import numpy as np
import math
from .helper import position_from_rank, rank_from_position, eval_procslice, key_grid
from .field import Field3d
import warnings
class SPP:
"""Serial Python Postprocessor for suspend"""
@ -17,6 +18,7 @@ class SPP:
self.spacing = tuple(spacing)
self.dim = tuple(dim)
self.xperiodic,self.yperiodic,self.zperiodic = periodicity
self.__KEYTMP = '__TMP'
return
@classmethod
@ -90,19 +92,39 @@ class SPP:
f.close()
return
def save_fields(self,file,keys,verbose=False,on_pressure_grid=False,single_precision=False):
'''Save current state to file.'''
import h5py
if not isinstance(keys,(list,tuple,np.ndarray)):
keys = tuple(keys)
if verbose: print('[SPP.save_field] {:s}'.format(file))
f = h5py.File(file,'w')
for key_ in keys:
if verbose: print('[SPP.save_field] saving {:s}'.format(key_))
assert key_ in self.field, \
"Field {} cannot be saved, because it does not exist.".format(key_)
if on_pressure_grid:
tmp = self.shift_to_pressure_grid(key_,key_out=None)
else:
tmp = self.field[key]
tmp.save(f,name=key_,single_precision=single_precision)
f.close()
return
def delete(self,key):
'''Removes a field from memory.'''
import gc
assert not key in ('u','v','w'), "Deleting u,v,w is not permitted."
assert key in self.field, \
"Field {} cannot be deleted, because it does not exist.".format(key)
del self.field[key]
gc.collect()
return
def differentiate(self,key,axis,key_out=None):
def differentiate(self,key,axis,key_out=''):
assert axis<3, "'axis' must be one of 0,1,2."
if key_out is None:
key_out = 'd'+key+('dx','dy','dz')[axis]
if key_out is None: key_out = self.__KEYTMP
if key_out=='': key_out = 'd'+key+('dx','dy','dz')[axis]
shifting_state = self.shifting_state(key,axis=axis)
if shifting_state==-1:
shift_origin = 'after'
@ -114,9 +136,15 @@ class SPP:
raise ValueError("Invalid shifting state.")
self.field[key_out] = self.field[key].derivative(axis,shift_origin=shift_origin)
self.exchange_ghost_cells(key_out)
if key_out==self.__KEYTMP:
tmp = self.field[key_out]
self.delete(key_out)
return tmp
return self.field[key_out]
def qcriterion(self,key_out='Q',from_pressure=False,dtype=np.double):
def qcriterion(self,key_out='Q',from_pressure=False,keep_derivatives=False):
'''Computes Q-criterion'''
if key_out is None: key_out = self.__KEYTMP
if from_pressure:
assert 'p' in self.field, "Pressure field is not loaded."
self.field[key_out] = 0.5*self.field['p'].laplacian(only_keep_interior=False)
@ -124,40 +152,82 @@ class SPP:
assert 'u' in self.field, "Velocity field is not loaded: u"
assert 'v' in self.field, "Velocity field is not loaded: v"
assert 'w' in self.field, "Velocity field is not loaded: w"
self.field[key_out] = Field3d.allocate(self.dim,self.origin,self.spacing,
fill=0.0,dtype=dtype)
self.field[key_out] = Field3d.allocate(self.dim,self.origin,self.spacing,fill=0.0)
keyx = ('x','y','z')
keyu = ('u','v','w')
for ii in range(3):
key_der = 'd'+keyu[ii]+'d'+keyx[ii]
self.differentiate(keyu[ii],ii,key_der)
self.shift_to_pressure_grid(key_der)
self.field[key_out] += self.field[key_der]**2
self.delete(key_der)
if not key_der in self.field:
self.differentiate(keyu[ii],ii,key_out=key_der)
self.shift_to_pressure_grid(key_der,key_out='der')
self.field[key_out] += self.field['der']**2
self.delete('der')
if not keep_derivatives: self.delete(key_der)
#
iip1 = (ii+1)%3
key_der1 = 'd'+keyu[ii]+'d'+keyx[iip1]
key_der2 = 'd'+keyu[iip1]+'d'+keyx[ii]
self.differentiate(keyu[ii],iip1,key_der1)
self.differentiate(keyu[iip1],ii,key_der2)
self.shift_to_pressure_grid(key_der1)
self.shift_to_pressure_grid(key_der2)
self.field[key_out] += 2.0*self.field[key_der1]*self.field[key_der2]
self.delete(key_der1)
self.delete(key_der2)
if not key_der1 in self.field:
self.differentiate(keyu[ii],iip1,key_out=key_der1)
self.shift_to_pressure_grid(key_der1,key_out='der1')
if not keep_derivatives: self.delete(key_der1)
if not key_der2 in self.field:
self.differentiate(keyu[iip1],ii,key_out=key_der2)
self.shift_to_pressure_grid(key_der2,key_out='der2')
if not keep_derivatives: self.delete(key_der2)
self.field[key_out] += 2.0*self.field['der1']*self.field['der2']
self.delete('der1')
self.delete('der2')
self.field[key_out] *= -0.5
return
if key_out==self.__KEYTMP:
tmp = self.field[key_out]
self.delete(key_out)
return tmp
return self.field[key_out]
def vorticity(self,axis,key_out='',keep_derivatives=False):
keyx = ('x','y','z')
keyu = ('u','v','w')
iip1 = (axis+1)%3
iip2 = (axis+2)%3
key_der1 = 'd'+keyu[iip1]+'d'+keyx[iip2]
key_der2 = 'd'+keyu[iip2]+'d'+keyx[iip1]
if key_out is None: key_out = self.__KEYTMP
if key_out=='': key_out = 'om'+keyx[axis]
if not key_der1 in self.field:
self.differentiate(keyu[iip1],iip2,key_out=key_der1)
self.shift_to_pressure_grid(key_der1,key_out='der1')
if not keep_derivatives: self.delete(key_der1)
if not key_der2 in self.field:
self.differentiate(keyu[iip2],iip1,key_out=key_der2)
self.shift_to_pressure_grid(key_der1,key_out='der2')
if not keep_derivatives: self.delete(key_der2)
self.field[key_out] = self.field['der2']-self.field['der1']
self.delete('der1')
self.delete('der2')
if key_out==self.__KEYTMP:
tmp = self.field[key_out]
self.delete(key_out)
return tmp
return self.field[key_out]
def shift_to_pressure_grid(self,key,key_out=None):
from .field import Field3d
if key_out is None:
if key in ('u','v','w'):
raise ValueError("In-place shift of {'u','v','w'} is not permitted.")
key_out = key
if key_out is None: key_out = self.__KEYTMP
if key_out==key:
raise ValueError("In-place shift is not permitted.")
fld_ref = Field3d.pseudo_field(self.dim,self.origin,self.spacing)
rel_shift = self.field[key].relative_shift(fld_ref)
self.field[key_out] = self.field[key].shift_origin(rel_shift)
if self.field[key].has_same_grid(fld_ref):
self.field[key_out] = self.field[key].copy()
else:
rel_shift = self.field[key].relative_shift(fld_ref)
self.field[key_out] = self.field[key].shift_origin(rel_shift)
self.exchange_ghost_cells(key_out)
if key_out==self.__KEYTMP:
tmp = self.field[key_out]
self.delete(key_out)
return tmp
return self.field[key_out]
def shifting_state(self,key,axis=None):
'''Returns the relative shift with respect to domain
@ -200,4 +270,3 @@ class SPP:
self.field[key].data[tuple(sl_out)] = self.field[key].data[tuple(sl_in)]
idx_ += 1
return