bugfix: fixed size of the readable portion of chunk['data'] (now it works also when no ghost cells are present)
This commit is contained in:
Tiago Pestana
parent
c75092dfc7
commit
a0643f951b
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@ -146,8 +146,8 @@ class ibmppp:
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self.__localChunkSize[key][1] = self.__localChunkBounds[key][3] - self.__localChunkBounds[key][2] + 1
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self.__localChunkSize[key][2] = self.__localChunkBounds[key][5] - self.__localChunkBounds[key][4] + 1
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# Verify that local grid size is not smaller than ghost cell size
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if (self.__localChunkSize[key][0]<self.__nghx or
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self.__localChunkSize[key][1]<self.__nghy or
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if (self.__localChunkSize[key][0]<self.__nghx or
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self.__localChunkSize[key][1]<self.__nghy or
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self.__localChunkSize[key][2]<self.__nghz):
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raise ValueError('Local grid size must be greater than number of ghost cells in each direction!')
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# Initialize neighbor array
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@ -191,17 +191,17 @@ class ibmppp:
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(np.arange(-self.__nghx,0)*self.__dx[key]+self.grid[key][0][self.__localChunkBounds[key][0]-1], # lower ghost cells
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self.grid[key][0][self.__localChunkBounds[key][0]-1:self.__localChunkBounds[key][1]], # chunk grid
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np.arange(1,self.__nghx+1)*self.__dx[key]+self.grid[key][0][self.__localChunkBounds[key][1]-1]) # upper ghost cells
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)
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)
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self.localGrid[key][1] = np.concatenate(
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(np.arange(-self.__nghy,0)*self.__dx[key]+self.grid[key][1][self.__localChunkBounds[key][2]-1], # lower ghost cells
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self.grid[key][1][self.__localChunkBounds[key][2]-1:self.__localChunkBounds[key][3]], # chunk grid
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np.arange(1,self.__nghy+1)*self.__dx[key]+self.grid[key][1][self.__localChunkBounds[key][3]-1]) # upper ghost cells
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)
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)
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self.localGrid[key][2] = np.concatenate(
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(np.arange(-self.__nghz,0)*self.__dx[key]+self.grid[key][2][self.__localChunkBounds[key][4]-1], # lower ghost cells
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self.grid[key][2][self.__localChunkBounds[key][4]-1:self.__localChunkBounds[key][5]], # chunk grid
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np.arange(1,self.__nghz+1)*self.__dx[key]+self.grid[key][2][self.__localChunkBounds[key][5]-1]) # upper ghost cells
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)
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)
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def loadParticles(self):
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'''Reads particles from file and distributes them to the correct processor.'''
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@ -260,9 +260,9 @@ class ibmppp:
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# Find particles which affect that chunk
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li_part = ((pp[col['x'],:]>=bdmin[0]-pp[col['r'],:]) &
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(pp[col['x'],:]<=bdmax[0]+pp[col['r'],:]) &
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(pp[col['y'],:]>=bdmin[1]-pp[col['r'],:]) &
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(pp[col['y'],:]>=bdmin[1]-pp[col['r'],:]) &
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(pp[col['y'],:]<=bdmax[1]+pp[col['r'],:]) &
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(pp[col['z'],:]>=bdmin[2]-pp[col['r'],:]) &
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(pp[col['z'],:]>=bdmin[2]-pp[col['r'],:]) &
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(pp[col['z'],:]<=bdmax[2]+pp[col['r'],:]))
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# Send them to that processor
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sendbuf = (np.ascontiguousarray(pp[:,li_part]),col)
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@ -291,19 +291,19 @@ class ibmppp:
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# Also determine file which contains the desired field as well as the
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# dataset ID
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if key[0]=='u':
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filebase = self.__dir_base+'uvwp.'
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filebase = self.__dir_base+'/uvwp.'
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dset = 1
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elif key[0]=='v':
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filebase = self.__dir_base+'uvwp.'
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filebase = self.__dir_base+'/uvwp.'
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dset = 2
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elif key[0]=='w':
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filebase = self.__dir_base+'uvwp.'
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filebase = self.__dir_base+'/uvwp.'
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dset = 3
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elif key[0]=='p':
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filebase = self.__dir_base+'uvwp.'
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filebase = self.__dir_base+'/uvwp.'
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dset = 4
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elif key[0]=='s':
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filebase = self.__dir_base+'scal.'
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filebase = self.__dir_base+'/scal.'
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dset = int(key[1])
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if dset!=1:
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self.fields[key] = None
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@ -348,10 +348,14 @@ class ibmppp:
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if kb1!=chunk['kbeg'] or ke1!=chunk['kbeg']+chunk['nzl']-1:
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raise ValueError('Loaded chunk does not correspond to processor grid (kbeg={}, nzl={} vs kbeg={},nzl={}'.format(kb1,ke1-kb1+1,chunk['kbeg'],chunk['nzl']))
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ngh1 = chunk['ighost']
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ibeg = [i + ngh1 for i in [0,0,0]]
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iend = [i-ngh1 for i in chunk['data'].shape]
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# No need to care about ghost cells here, we communicate them later
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self.field[key][ib1-ib+self.__nghx:ie1-ib+self.__nghx+1,
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jb1-jb+self.__nghy:je1-jb+self.__nghy+1,
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kb1-kb+self.__nghz:ke1-kb+self.__nghz+1] = chunk['data'][ngh1:-ngh1,ngh1:-ngh1,ngh1:-ngh1]
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kb1-kb+self.__nghz:ke1-kb+self.__nghz+1] = chunk['data'][ibeg[0]:iend[0],\
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ibeg[1]:iend[1],\
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ibeg[2]:iend[2]]
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# Exchange ghost cells and set boundary conditions
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self.exchangeGhostCells(key)
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self.imposeBoundaryConditions(key)
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@ -449,7 +453,7 @@ class ibmppp:
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# Construct XDMF filename
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file_xdmf = filename+'_'+key+'.xdmf'
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# Open file and write header
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fid = open(file_xdmf,'w')
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fid = open(file_xdmf,'w')
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fid.write('<?xml version="1.0"?>\n')
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fid.write('<Xdmf Version="2.0">\n')
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fid.write(' <Domain>\n')
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@ -575,7 +579,7 @@ class ibmppp:
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# Construct XDMF filename
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file_xdmf = filename+'_'+key+'.xdmf'
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# Open file and write header
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fid = open(file_xdmf,'w')
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fid = open(file_xdmf,'w')
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fid.write('<?xml version="1.0"?>\n')
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fid.write('<Xdmf Version="2.0">\n')
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fid.write(' <Domain>\n')
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@ -688,7 +692,7 @@ class ibmppp:
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# Construct XDMF filename
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file_xdmf = filename+'.xdmf'
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# Open file
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fid = open(file_xdmf,'w')
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fid = open(file_xdmf,'w')
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# Write header
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fid.write('<?xml version="1.0"?>\n')
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fid.write('<Xdmf Version="2.0">\n')
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@ -832,7 +836,7 @@ class ibmppp:
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self.differentiateField('u','x')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['ux'],'mult',symm2=self.__boundarySymmetries['ux'])
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self.__allocateField('tmp','ux',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 0.5*np.square(self.field['ux'])
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self.field['tmp'] += 0.5*np.square(self.field['ux'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','Q'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','Q')
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self.field['Q'][iout,jout,kout] -= self.field['tmp'][iin,jin,kin]
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@ -844,7 +848,7 @@ class ibmppp:
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self.differentiateField('v','y')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['vy'],'mult',symm2=self.__boundarySymmetries['vy'])
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self.__allocateField('tmp','vy',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 0.5*np.square(self.field['vy'])
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self.field['tmp'] += 0.5*np.square(self.field['vy'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','Q'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','Q')
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self.field['Q'][iout,jout,kout] -= self.field['tmp'][iin,jin,kin]
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@ -856,7 +860,7 @@ class ibmppp:
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self.differentiateField('w','z')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['wz'],'mult',symm2=self.__boundarySymmetries['wz'])
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self.__allocateField('tmp','wz',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 0.5*np.square(self.field['wz'])
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self.field['tmp'] += 0.5*np.square(self.field['wz'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','Q'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','Q')
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self.field['Q'][iout,jout,kout] -= self.field['tmp'][iin,jin,kin]
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@ -981,7 +985,7 @@ class ibmppp:
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self.differentiateField('u','x')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['ux'],'mult',symm2=self.__boundarySymmetries['ux'])
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self.__allocateField('tmp','ux',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 2.0*np.square(self.field['ux'])
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self.field['tmp'] += 2.0*np.square(self.field['ux'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','D'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','D')
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self.field['D'][iout,jout,kout] += self.field['tmp'][iin,jin,kin]
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@ -993,7 +997,7 @@ class ibmppp:
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self.differentiateField('v','y')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['vy'],'mult',symm2=self.__boundarySymmetries['vy'])
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self.__allocateField('tmp','vy',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 2.0*np.square(self.field['vy'])
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self.field['tmp'] += 2.0*np.square(self.field['vy'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','D'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','D')
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self.field['D'][iout,jout,kout] += self.field['tmp'][iin,jin,kin]
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@ -1005,7 +1009,7 @@ class ibmppp:
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self.differentiateField('w','z')
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symm = self.__deriveSymmetry(self.__boundarySymmetries['wz'],'mult',symm2=self.__boundarySymmetries['wz'])
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self.__allocateField('tmp','wz',shift=(0,0,0),symmetry=symm)
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self.field['tmp'] += 2.0*np.square(self.field['wz'])
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self.field['tmp'] += 2.0*np.square(self.field['wz'])
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self.shiftField('tmp',self.__getShiftDirection('tmp','D'))
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iin,jin,kin,iout,jout,kout = self.__sliceCollocated('tmp','D')
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self.field['D'][iout,jout,kout] += self.field['tmp'][iin,jin,kin]
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@ -1306,7 +1310,7 @@ class ibmppp:
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self.grid[key][idir] += shift[idir]*0.5*self.__dx[key]
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self.localGrid[key][idir] += shift[idir]*0.5*self.__dx[key]
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# Perform the interpolation
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if subsequent:
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if subsequent:
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# Three (at maximum) subsequent 1D interpolations.
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# NOTE: This algorithm requires ghost cell communication for each substep, which can be avoided if we shifted in all directions simultaneously!
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# Construct index range of target
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@ -1452,14 +1456,14 @@ class ibmppp:
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self.__symmetrizeWall(key,(0,+1,0))
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self.__symmetrizeWall(key,(0,0,-1))
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self.__symmetrizeWall(key,(0,0,+1))
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def printMemoryUsage(self):
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'''Print estimation of memory usage (max over all processors)'''
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mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024.
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mem = self.__comm.reduce(sendobj=mem,op=MPI.MAX,root=0)
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if self.__rank==0:
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print('Current memory usage: {:8.2f} MiB'.format(mem))
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def printMemoryUsageField(self,key):
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'''Print estimation of memory usage per allocated field.'''
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bytesNumpy = np.dtype(self.__precision).itemsize
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@ -1478,8 +1482,8 @@ class ibmppp:
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# v -> -v v -> -v
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# w -> -w w -> w
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# p -> p p -> p
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self.__boundarySymmetries = {'u': np.zeros((3,3,3),dtype='i'),
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'v': np.zeros((3,3,3),dtype='i'),
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self.__boundarySymmetries = {'u': np.zeros((3,3,3),dtype='i'),
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'v': np.zeros((3,3,3),dtype='i'),
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'w': np.zeros((3,3,3),dtype='i'),
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'p': np.zeros((3,3,3),dtype='i'),
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's1': np.zeros((3,3,3),dtype='i'),
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@ -1679,7 +1683,7 @@ class ibmppp:
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rank_dst = self.__nghbr[ip_dst,jp_dst,kp_dst]
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rank_src = self.__nghbr[ip_src,jp_src,kp_src]
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# [send/recv] create a tag
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tag = ip_dst*100+jp_dst*10+kp_dst
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tag = ip_dst*100+jp_dst*10+kp_dst
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# [send/recv] get the indices of data to be sent/received
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(nxl,nyl,nzl) = self.__localChunkSize[key]
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if positionDst[0]==-1:
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@ -1819,7 +1823,7 @@ class ibmppp:
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@staticmethod
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def __rankFromPosition(ip,jp,kp,nxp,nyp,nzp):
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return ip*nyp*nzp+jp*nzp+kp
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@staticmethod
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def __positionFromRank(rank,nxp,nyp,nzp):
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ip = rank//(nyp*nzp)
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@ -1851,7 +1855,7 @@ class ibmppp:
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def gaussianFilterStencilWidth(sigma=(1,1,1),truncate=4.0):
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if len(sigma)!=3:
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raise ValueError('Expected one value of sigma for each direction, but only got {}.'.format(len(sigma)))
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# Compute stencil width
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# Compute stencil width
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stencil = [0,0,0]
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for ii in range(0,3):
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stencil[ii] = 2*int(truncate*sigma[ii]+0.5)+1
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