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Methods defined here:
- __init__(self)
- getCenter(self)
- getCharge(self)
- getCoarseGridDims(self)
- getConstant(self, name)
- Get a constant value; raises KeyError if constant not found
- getFineGridDims(self)
- getFineGridPoints(self)
- getFocus(self)
- getLength(self)
- getMax(self)
- getMin(self)
- getProcGrid(self)
- getSmallest(self)
- parseInput(self, filename)
- Parse input structure file in PDB or PQR format
- printResults(self)
- Return a string with the formatted results
- runPsize(self, filename)
- Parse input PQR file and set parameters
- setAll(self)
- Set up all of the things calculated individually above
- setCenter(self, maxlen, minlen)
- Compute molecule center
- setCoarseGridDims(self, olen)
- Compute coarse mesh dimensions
- setConstant(self, name, value)
- Set a constant to a value; returns 0 if constant not found
- setFineGridDims(self, olen, clen)
- Compute fine mesh dimensions
- setFineGridPoints(self, flen)
- Compute mesh grid points, assuming 4 levels in MG hierarchy
- setFocus(self, flen, np, clen)
- Calculate the number of levels of focusing required for each
processor subdomain
- setLength(self, maxlen, minlen)
- Compute molecule dimensions
- setProcGrid(self, n, nsmall)
- Calculate the number of processors required to span each
dimension
- setSmallest(self, n)
- Compute parallel division in case memory requirement above ceiling
Find the smallest dimension and see if the number of grid points in
that dimension will fit below the memory ceiling
Reduce nsmall until an nsmall^3 domain will fit into memory
Data and non-method functions defined here:
- __doc__ = None
- __module__ = 'psize'
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