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Improve Python 3 compatibility of pizza tools and simplify read_snapshot code

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This commit is contained in:
Richard Berger
2017-03-16 01:38:05 -04:00
parent 36da9223ec
commit ef940d226c
2 changed files with 41 additions and 34 deletions
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66
python/examples/pizza/dump.py
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@ -146,6 +146,8 @@ d.extra(data) extract bond/tri/line list from data
# History # History
# 8/05, Steve Plimpton (SNL): original version # 8/05, Steve Plimpton (SNL): original version
# 12/09, David Hart (SNL): allow use of NumPy or Numeric # 12/09, David Hart (SNL): allow use of NumPy or Numeric
# 03/17, Richard Berger (Temple U): improve Python 3 compatibility,
# simplify read_snapshot by using reshape
# ToDo list # ToDo list
# try to optimize this line in read_snap: words += f.readline().split() # try to optimize this line in read_snap: words += f.readline().split()
@ -224,7 +226,7 @@ class dump:
self.flist = [] self.flist = []
for word in words: self.flist += glob.glob(word) for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1: if len(self.flist) == 0 and len(list) == 1:
raise StandardError("no dump file specified") raise Exception("no dump file specified")
if len(list) == 1: if len(list) == 1:
self.increment = 0 self.increment = 0
@ -299,7 +301,7 @@ class dump:
def next(self): def next(self):
if not self.increment: raise StandardError("cannot read incrementally") if not self.increment: raise Exception("cannot read incrementally")
# read next snapshot in current file using eof as pointer # read next snapshot in current file using eof as pointer
# if fail, try next file # if fail, try next file
@ -344,13 +346,13 @@ class dump:
try: try:
snap = Snap() snap = Snap()
item = f.readline() item = f.readline()
snap.time = int(f.readline().split()[0]) # just grab 1st field snap.time = int(f.readline().decode().split()[0]) # just grab 1st field
item = f.readline() item = f.readline()
snap.natoms = int(f.readline()) snap.natoms = int(f.readline().decode())
snap.aselect = np.zeros(snap.natoms) snap.aselect = np.zeros(snap.natoms)
item = f.readline() item = f.readline().decode()
words = f.readline().split() words = f.readline().split()
snap.xlo,snap.xhi = float(words[0]),float(words[1]) snap.xlo,snap.xhi = float(words[0]),float(words[1])
words = f.readline().split() words = f.readline().split()
@ -358,7 +360,7 @@ class dump:
words = f.readline().split() words = f.readline().split()
snap.zlo,snap.zhi = float(words[0]),float(words[1]) snap.zlo,snap.zhi = float(words[0]),float(words[1])
item = f.readline() item = f.readline().decode()
if len(self.names) == 0: if len(self.names) == 0:
words = item.split()[2:] words = item.split()[2:]
if len(words): if len(words):
@ -372,24 +374,22 @@ class dump:
else: self.names[words[i]] = i else: self.names[words[i]] = i
if snap.natoms: if snap.natoms:
words = f.readline().split() words = f.readline().decode().split()
ncol = len(words) ncol = len(words)
for i in range(1,snap.natoms): for i in range(1,snap.natoms):
words += f.readline().split() words += f.readline().decode().split()
floats = map(float,words) floats = map(float,words)
if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float) if oldnumeric:
else: atoms = np.zeros((snap.natoms,ncol),np.float) atom_data = np.array(list(floats),np.Float)
start = 0 else:
stop = ncol atom_data = np.array(list(floats),np.float)
for i in range(snap.natoms):
atoms[i] = floats[start:stop] snap.atoms = atom_data.reshape((snap.natoms, ncol))
start = stop else:
stop += ncol snap.atoms = None
else: atoms = None
snap.atoms = atoms
return snap return snap
except: except:
return 0 return None
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# decide if snapshot i is scaled/unscaled from coords of first and last atom # decide if snapshot i is scaled/unscaled from coords of first and last atom
@ -417,7 +417,7 @@ class dump:
def map(self,*pairs): def map(self,*pairs):
if len(pairs) % 2 != 0: if len(pairs) % 2 != 0:
raise StandardError("dump map() requires pairs of mappings") raise Exception("dump map() requires pairs of mappings")
for i in range(0,len(pairs),2): for i in range(0,len(pairs),2):
j = i + 1 j = i + 1
self.names[pairs[j]] = pairs[i]-1 self.names[pairs[j]] = pairs[i]-1
@ -734,7 +734,7 @@ class dump:
for snap in self.snaps: for snap in self.snaps:
if not snap.tselect: continue if not snap.tselect: continue
if snap.nselect != len(vec): if snap.nselect != len(vec):
raise StandardError("vec length does not match # of selected atoms") raise Exception("vec length does not match # of selected atoms")
atoms = snap.atoms atoms = snap.atoms
m = 0 m = 0
for i in range(snap.natoms): for i in range(snap.natoms):
@ -800,7 +800,7 @@ class dump:
def atom(self,n,*list): def atom(self,n,*list):
if len(list) == 0: if len(list) == 0:
raise StandardError("no columns specified") raise Exception("no columns specified")
columns = [] columns = []
values = [] values = []
for name in list: for name in list:
@ -816,7 +816,7 @@ class dump:
for i in range(snap.natoms): for i in range(snap.natoms):
if atoms[i][id] == n: break if atoms[i][id] == n: break
if atoms[i][id] != n: if atoms[i][id] != n:
raise StandardError("could not find atom ID in snapshot") raise Exception("could not find atom ID in snapshot")
for j in range(ncol): for j in range(ncol):
values[j][m] = atoms[i][columns[j]] values[j][m] = atoms[i][columns[j]]
m += 1 m += 1
@ -831,7 +831,7 @@ class dump:
snap = self.snaps[self.findtime(n)] snap = self.snaps[self.findtime(n)]
if len(list) == 0: if len(list) == 0:
raise StandardError("no columns specified") raise Exception("no columns specified")
columns = [] columns = []
values = [] values = []
for name in list: for name in list:
@ -957,9 +957,9 @@ class dump:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def findtime(self,n): def findtime(self,n):
for i in range(self.nsnaps): for i, snap in enumerate(self.snaps):
if self.snaps[i].time == n: return i if snap.time == n: return i
raise StandardError("no step %d exists" % n) raise Exception("no step %d exists" % n)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# return maximum box size across all selected snapshots # return maximum box size across all selected snapshots
@ -1008,7 +1008,7 @@ class dump:
nbonds = int(f.readline()) nbonds = int(f.readline())
item = f.readline() item = f.readline()
if not re.search("BONDS",item): if not re.search("BONDS",item):
raise StandardError("could not read bonds from dump file") raise Exception("could not read bonds from dump file")
words = f.readline().split() words = f.readline().split()
ncol = len(words) ncol = len(words)
@ -1031,7 +1031,7 @@ class dump:
self.bondflag = 1 self.bondflag = 1
self.bondlist = bondlist self.bondlist = bondlist
except: except:
raise StandardError("could not read from bond dump file") raise Exception("could not read from bond dump file")
# request bonds from data object # request bonds from data object
@ -1047,7 +1047,7 @@ class dump:
self.bondflag = 1 self.bondflag = 1
self.bondlist = bondlist self.bondlist = bondlist
except: except:
raise StandardError("could not extract bonds from data object") raise Exception("could not extract bonds from data object")
# request tris/lines from cdata object # request tris/lines from cdata object
@ -1061,7 +1061,7 @@ class dump:
self.lineflag = 1 self.lineflag = 1
self.linelist = lines self.linelist = lines
except: except:
raise StandardError("could not extract tris/lines from cdata object") raise Exception("could not extract tris/lines from cdata object")
# request tris from mdump object # request tris from mdump object
@ -1070,10 +1070,10 @@ class dump:
self.triflag = 2 self.triflag = 2
self.triobj = arg self.triobj = arg
except: except:
raise StandardError("could not extract tris from mdump object") raise Exception("could not extract tris from mdump object")
else: else:
raise StandardError("unrecognized argument to dump.extra()") raise Exception("unrecognized argument to dump.extra()")
# -------------------------------------------------------------------- # --------------------------------------------------------------------

9
python/examples/pizza/pdbfile.py
View File

@ -54,6 +54,7 @@ index,time,flag = p.iterator(1)
# History # History
# 8/05, Steve Plimpton (SNL): original version # 8/05, Steve Plimpton (SNL): original version
# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
# ToDo list # ToDo list
# for generic PDB file (no template) from a LJ unit system, # for generic PDB file (no template) from a LJ unit system,
@ -68,6 +69,12 @@ index,time,flag = p.iterator(1)
# Imports and external programs # Imports and external programs
import sys, types, glob, urllib import sys, types, glob, urllib
PY3 = sys.version_info[0] == 3
if PY3:
string_types = str,
else:
string_types = basestring
# Class definition # Class definition
@ -77,7 +84,7 @@ class pdbfile:
def __init__(self,*args): def __init__(self,*args):
if len(args) == 1: if len(args) == 1:
if type(args[0]) is types.StringType: if type(args[0]) is string_types:
filestr = args[0] filestr = args[0]
self.data = None self.data = None
else: else: