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python 2/3 portability changes for log class from Pizza.py

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This commit is contained in:
Axel Kohlmeyer
2022-08-20 21:42:45 -04:00
parent 057dff375c
commit 1f37087156
2 changed files with 38 additions and 32 deletions
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4
tools/python/pizza/dump.py
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@ -319,8 +319,8 @@ class dump:
# if fail, try next file # if fail, try next file
# if new snapshot time stamp already exists, read next snapshot # if new snapshot time stamp already exists, read next snapshot
while 1: while True:
f = open(self.flist[self.nextfile],'rb') f = open(self.flist[self.nextfile],'r')
f.seek(self.eof) f.seek(self.eof)
snap = self.read_snapshot(f) snap = self.read_snapshot(f)
if not snap: if not snap:

66
tools/python/pizza/log.py
View File

@ -13,25 +13,25 @@ from __future__ import print_function
oneline = "Read LAMMPS log files and extract thermodynamic data" oneline = "Read LAMMPS log files and extract thermodynamic data"
docstr = """ docstr = """
l = log("file1") read in one or more log files l = log("file1") read in one or more log files
l = log("log1 log2.gz") can be gzipped l = log("log1 log2.gz") can be gzipped
l = log("file*") wildcard expands to multiple files l = log("file*") wildcard expands to multiple files
l = log("log.lammps",0) two args = store filename, but don't read l = log("log.lammps",0) two args = store filename, but don't read
incomplete and duplicate thermo entries are deleted incomplete and duplicate thermo entries are deleted
time = l.next() read new thermo info from file time = l.next() read new thermo info from file
used with 2-argument constructor to allow reading thermo incrementally used with 2-argument constructor to allow reading thermo incrementally
return time stamp of last thermo read return time stamp of last thermo read
return -1 if no new thermo since last read return -1 if no new thermo since last read
nvec = l.nvec # of vectors of thermo info nvec = l.nvec # of vectors of thermo info
nlen = l.nlen length of each vectors nlen = l.nlen length of each vectors
names = l.names list of vector names names = l.names list of vector names
t,pe,... = l.get("Time","KE",...) return one or more vectors of values t,pe,... = l.get("Time","KE",...) return one or more vectors of values
l.write("file.txt") write all vectors to a file l.write("file.txt",0) write all vectors to a file, done write header comment
l.write("file.txt","Time","PE",...) write listed vectors to a file l.write("file.txt",1,"Time","PE",...) write listed vectors to a file, include header comment
get and write allow abbreviated (uniquely) vector names get and write allow abbreviated (uniquely) vector names
""" """
@ -79,14 +79,14 @@ class log:
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(arglist) == 1: if len(self.flist) == 0 and len(arglist) == 1:
raise Exception("no log file specified") raise ValueError("No log files specified or specified files do not exist")
if len(arglist) == 1: if len(arglist) == 1:
self.increment = 0 self.increment = 0
self.read_all() self.read_all()
else: else:
if len(self.flist) > 1: if len(self.flist) > 1:
raise Exception("can only incrementally read one log file") raise ValueError("Can only read one log file incrementally")
self.increment = 1 self.increment = 1
self.eof = 0 self.eof = 0
@ -114,7 +114,9 @@ class log:
if not self.increment: raise Exception("cannot read incrementally") if not self.increment: raise Exception("cannot read incrementally")
if self.nvec == 0: if self.nvec == 0:
try: open(self.flist[0],'r') try:
fp = open(self.flist[0],'r')
fp.close()
except: return -1 except: return -1
self.read_header(self.flist[0]) self.read_header(self.flist[0])
if self.nvec == 0: return -1 if self.nvec == 0: return -1
@ -126,7 +128,7 @@ class log:
def get(self,*keys): def get(self,*keys):
if len(keys) == 0: if len(keys) == 0:
raise Exception( "no log vectors specified" ) raise Exception("no log vectors specified" )
colmap = [] colmap = []
for key in keys: for key in keys:
@ -141,7 +143,7 @@ class log:
if count == 1: if count == 1:
colmap.append(index) colmap.append(index)
else: else:
raise Exception( "unique log vector %s not found" % key) raise ValueError("unique log vector %s not found" % key)
vecs = [] vecs = []
for i in range(len(keys)): for i in range(len(keys)):
@ -210,14 +212,16 @@ class log:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def read_header(self,file): def read_header(self, file):
str_multi = "----- Step" str_multi = "----- Step"
str_one = "Step " str_one = "Step "
if file[-3:] == ".gz": if file[-3:] == ".gz":
txt = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r').read() fp = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
txt = fp.read()
else: else:
txt = open(file).read() fp = open(file)
txt = fp.read()
if txt.find(str_multi) >= 0: if txt.find(str_multi) >= 0:
self.firststr = str_multi self.firststr = str_multi
@ -226,6 +230,7 @@ class log:
self.firststr = str_one self.firststr = str_one
self.style = 2 self.style = 2
else: else:
fp.close()
return return
if self.style == 1: if self.style == 1:
@ -252,6 +257,7 @@ class log:
self.ptr[words[i]] = i self.ptr[words[i]] = i
self.nvec = len(self.names) self.nvec = len(self.names)
fp.close()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -262,9 +268,9 @@ class log:
file = arglist[0] file = arglist[0]
if file[-3:] == ".gz": if file[-3:] == ".gz":
f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb') f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
else: else:
f = open(file,'rb') f = open(file,'r')
if len(arglist) == 2: f.seek(arglist[1]) if len(arglist) == 2: f.seek(arglist[1])
txt = f.read() txt = f.read()
@ -282,12 +288,12 @@ class log:
# set start = position in file to start looking for next chunk # set start = position in file to start looking for next chunk
# rewind eof if final entry is incomplete # rewind eof if final entry is incomplete
s1 = txt.find(self.firststr.encode('utf-8'),start) s1 = txt.find(self.firststr,start)
s2 = txt.find("Loop time of".encode('utf-8'),start+1) s2 = txt.find("Loop time of",start+1)
if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2 if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
if self.style == 2: if self.style == 2:
s1 = txt.find("\n".encode('utf-8'),s1) + 1 s1 = txt.find("\n",s1) + 1
elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1 elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
s1 = 0 s1 = 0
elif s1 == -1 and s2 >= 0: # found s2, but no s1 elif s1 == -1 and s2 >= 0: # found s2, but no s1
@ -296,16 +302,16 @@ class log:
elif s1 >= 0 and s2 == -1: # found s1, but no s2 elif s1 >= 0 and s2 == -1: # found s1, but no s2
last = 1 last = 1
if self.style == 1: if self.style == 1:
s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1 s2 = txt.rfind("\n--",s1) + 1
else: else:
s1 = txt.find("\n".encode('utf-8'),s1) + 1 s1 = txt.find("\n",s1) + 1
s2 = txt.rfind("\n".encode('utf-8'),s1) + 1 s2 = txt.rfind("\n",s1) + 1
eof -= len(txt) - s2 eof -= len(txt) - s2
elif s1 == -1 and s2 == -1: # found neither elif s1 == -1 and s2 == -1: # found neither
# could be end-of-file section # could be end-of-file section
# or entire read was one chunk # or entire read was one chunk
if txt.find("Loop time of".encode('utf-8'),start) == start: # end of file, so exit if txt.find("Loop time of",start) == start: # end of file, so exit
eof -= len(txt) - start # reset eof to "Loop" eof -= len(txt) - start # reset eof to "Loop"
break break
@ -325,7 +331,7 @@ class log:
# parse each entry for numeric fields, append to data # parse each entry for numeric fields, append to data
if self.style == 1: if self.style == 1:
sections = chunk.split("\n--".encode('utf-8')) sections = chunk.split("\n--")
pat1 = re.compile("Step\s*(\S*)\s") pat1 = re.compile("Step\s*(\S*)\s")
pat2 = re.compile("=\s*(\S*)") pat2 = re.compile("=\s*(\S*)")
for section in sections: for section in sections:
@ -335,7 +341,7 @@ class log:
self.data.append(list(map(float,words))) self.data.append(list(map(float,words)))
else: else:
lines = chunk.split("\n".encode('utf-8')) lines = chunk.split("\n")
for line in lines: for line in lines:
words = line.split() words = line.split()
self.data.append(list(map(float,words))) self.data.append(list(map(float,words)))