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Allow .castep files corresponding to fixed lattice parameter MD runs … #11

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Allow .castep files corresponding to fixed lattice parameter MD runs … #11

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28 changes: 26 additions & 2 deletions castep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,13 @@
\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s*\n""",
re.VERBOSE)

# New regular expression targeting just the 'Unit Cell' section
dotcastep_latt_fixed_RE = re.compile(r"""\s+Unit\sCell\s*\n\s+\-+\s*\n
\s+Real\sLattice\(A\)\s+Reciprocal\sLattice\(1/A\)\s*\n
\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s*\n
\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s*\n
\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s+([\+\-]?\d+.\d+)\s*\n""", re.VERBOSE)

# Start of the 'final configuration'
dotcastep_infinal_RE = re.compile(r"BFGS\s*: Final Configuration:")

Expand All @@ -37,8 +44,18 @@ def parse_dotcastep(seedname):
file. List of atoms may be empty (e.g. MgO)
"""
dotCastep = open(seedname+".castep","r")
# Find the lattice
latticeblock = dotcastep_latt_RE.findall(dotCastep.read())[-1] # Get the last block - handle concat restarts
# Find the lattice. First attempt to locate 'Final Configuration' followed by 'Unit Cell'
latticeblock = dotcastep_latt_RE.findall(dotCastep.read()) # Get the last block - handle concat restarts
if latticeblock:
print("Lattice block identified after 'Final Configuration'")
latticeblock = latticeblock[-1]
else:
print("No 'Unit Cell' after 'Final Configuration' - assuming fixed lattice relaxation.")
# If 'Unit Cell' does not proceed 'Final Configuration', unit cell parameters may have been fixed (using
# FIX_ALL_CELL in .cell file). This may occur e.g. if a grid method was used to optimize geometry followed
# by a fixed lattice paramter relaxation. In this case rewind and look instead just for 'Unit Cell'
dotCastep.seek(0)
latticeblock = dotcastep_latt_fixed_RE.findall(dotCastep.read())[-1]
lattice = []
lattice.append([float(latticeblock[0]), float(latticeblock[1]), float(latticeblock[2])])
lattice.append([float(latticeblock[6]), float(latticeblock[7]), float(latticeblock[8])])
Expand Down Expand Up @@ -121,6 +138,13 @@ def get_stress_dotcastep(filename):
s(3,2), s(3,1), s(2,1).
"""
dotCastep = open(filename,"r")
# ---- by Andy ---- original code for python 2.5. the below seems to fix behaviour for python 3.8.5 (commented a line out below)
#print('filename=',filename)
#findAllMatches = stressRE.findall(dotCastep.read())
#stressData = findAllMatches[0]
#print('stressData=',stressData)
#quit()
# -----------------
stressData = stressRE.findall(dotCastep.read())[0]
dotCastep.close()
units = stressData[0]
Expand Down