forked from lijiext/lammps
Improve Python 3 compatibility of pizza tools and simplify read_snapshot code
This commit is contained in:
Richard Berger
parent
36da9223ec
commit
ef940d226c
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@ -146,6 +146,8 @@ d.extra(data) extract bond/tri/line list from data
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# History
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# 8/05, Steve Plimpton (SNL): original version
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# 12/09, David Hart (SNL): allow use of NumPy or Numeric
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# 03/17, Richard Berger (Temple U): improve Python 3 compatibility,
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# simplify read_snapshot by using reshape
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# ToDo list
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# try to optimize this line in read_snap: words += f.readline().split()
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@ -224,7 +226,7 @@ class dump:
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self.flist = []
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for word in words: self.flist += glob.glob(word)
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if len(self.flist) == 0 and len(list) == 1:
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raise StandardError("no dump file specified")
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raise Exception("no dump file specified")
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if len(list) == 1:
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self.increment = 0
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@ -299,7 +301,7 @@ class dump:
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def next(self):
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if not self.increment: raise StandardError("cannot read incrementally")
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if not self.increment: raise Exception("cannot read incrementally")
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# read next snapshot in current file using eof as pointer
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# if fail, try next file
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@ -344,13 +346,13 @@ class dump:
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try:
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snap = Snap()
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item = f.readline()
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snap.time = int(f.readline().split()[0]) # just grab 1st field
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snap.time = int(f.readline().decode().split()[0]) # just grab 1st field
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item = f.readline()
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snap.natoms = int(f.readline())
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snap.natoms = int(f.readline().decode())
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snap.aselect = np.zeros(snap.natoms)
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item = f.readline()
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item = f.readline().decode()
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words = f.readline().split()
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snap.xlo,snap.xhi = float(words[0]),float(words[1])
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words = f.readline().split()
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@ -358,7 +360,7 @@ class dump:
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words = f.readline().split()
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snap.zlo,snap.zhi = float(words[0]),float(words[1])
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item = f.readline()
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item = f.readline().decode()
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if len(self.names) == 0:
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words = item.split()[2:]
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if len(words):
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@ -372,24 +374,22 @@ class dump:
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else: self.names[words[i]] = i
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if snap.natoms:
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words = f.readline().split()
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words = f.readline().decode().split()
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ncol = len(words)
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for i in range(1,snap.natoms):
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words += f.readline().split()
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words += f.readline().decode().split()
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floats = map(float,words)
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if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
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else: atoms = np.zeros((snap.natoms,ncol),np.float)
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start = 0
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stop = ncol
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for i in range(snap.natoms):
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atoms[i] = floats[start:stop]
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start = stop
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stop += ncol
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else: atoms = None
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snap.atoms = atoms
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if oldnumeric:
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atom_data = np.array(list(floats),np.Float)
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else:
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atom_data = np.array(list(floats),np.float)
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snap.atoms = atom_data.reshape((snap.natoms, ncol))
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else:
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snap.atoms = None
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return snap
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except:
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return 0
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return None
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# --------------------------------------------------------------------
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# decide if snapshot i is scaled/unscaled from coords of first and last atom
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@ -417,7 +417,7 @@ class dump:
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def map(self,*pairs):
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if len(pairs) % 2 != 0:
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raise StandardError("dump map() requires pairs of mappings")
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raise Exception("dump map() requires pairs of mappings")
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for i in range(0,len(pairs),2):
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j = i + 1
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self.names[pairs[j]] = pairs[i]-1
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@ -734,7 +734,7 @@ class dump:
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for snap in self.snaps:
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if not snap.tselect: continue
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if snap.nselect != len(vec):
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raise StandardError("vec length does not match # of selected atoms")
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raise Exception("vec length does not match # of selected atoms")
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atoms = snap.atoms
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m = 0
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for i in range(snap.natoms):
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@ -800,7 +800,7 @@ class dump:
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def atom(self,n,*list):
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if len(list) == 0:
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raise StandardError("no columns specified")
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raise Exception("no columns specified")
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columns = []
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values = []
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for name in list:
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@ -816,7 +816,7 @@ class dump:
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for i in range(snap.natoms):
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if atoms[i][id] == n: break
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if atoms[i][id] != n:
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raise StandardError("could not find atom ID in snapshot")
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raise Exception("could not find atom ID in snapshot")
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for j in range(ncol):
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values[j][m] = atoms[i][columns[j]]
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m += 1
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@ -831,7 +831,7 @@ class dump:
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snap = self.snaps[self.findtime(n)]
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if len(list) == 0:
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raise StandardError("no columns specified")
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raise Exception("no columns specified")
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columns = []
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values = []
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for name in list:
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@ -957,9 +957,9 @@ class dump:
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# --------------------------------------------------------------------
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def findtime(self,n):
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for i in range(self.nsnaps):
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if self.snaps[i].time == n: return i
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raise StandardError("no step %d exists" % n)
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for i, snap in enumerate(self.snaps):
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if snap.time == n: return i
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raise Exception("no step %d exists" % n)
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# --------------------------------------------------------------------
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# return maximum box size across all selected snapshots
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@ -1008,7 +1008,7 @@ class dump:
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nbonds = int(f.readline())
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item = f.readline()
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if not re.search("BONDS",item):
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raise StandardError("could not read bonds from dump file")
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raise Exception("could not read bonds from dump file")
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words = f.readline().split()
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ncol = len(words)
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@ -1031,7 +1031,7 @@ class dump:
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self.bondflag = 1
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self.bondlist = bondlist
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except:
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raise StandardError("could not read from bond dump file")
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raise Exception("could not read from bond dump file")
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# request bonds from data object
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@ -1047,7 +1047,7 @@ class dump:
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self.bondflag = 1
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self.bondlist = bondlist
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except:
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raise StandardError("could not extract bonds from data object")
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raise Exception("could not extract bonds from data object")
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# request tris/lines from cdata object
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@ -1061,7 +1061,7 @@ class dump:
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self.lineflag = 1
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self.linelist = lines
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except:
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raise StandardError("could not extract tris/lines from cdata object")
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raise Exception("could not extract tris/lines from cdata object")
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# request tris from mdump object
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@ -1070,10 +1070,10 @@ class dump:
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self.triflag = 2
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self.triobj = arg
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except:
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raise StandardError("could not extract tris from mdump object")
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raise Exception("could not extract tris from mdump object")
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else:
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raise StandardError("unrecognized argument to dump.extra()")
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raise Exception("unrecognized argument to dump.extra()")
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# --------------------------------------------------------------------
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@ -54,6 +54,7 @@ index,time,flag = p.iterator(1)
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# History
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# 8/05, Steve Plimpton (SNL): original version
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# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
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# ToDo list
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# for generic PDB file (no template) from a LJ unit system,
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@ -68,6 +69,12 @@ index,time,flag = p.iterator(1)
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# Imports and external programs
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import sys, types, glob, urllib
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PY3 = sys.version_info[0] == 3
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if PY3:
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string_types = str,
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else:
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string_types = basestring
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# Class definition
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@ -77,7 +84,7 @@ class pdbfile:
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def __init__(self,*args):
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if len(args) == 1:
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if type(args[0]) is types.StringType:
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if type(args[0]) is string_types:
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filestr = args[0]
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self.data = None
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else:
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