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update log pizza.py files to python 3

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This commit is contained in:
ali
2022-02-21 17:25:13 -06:00
parent 7ea26161f7
commit 5c297fa4d1
3 changed files with 49 additions and 50 deletions
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2
tools/python/log2txt.py
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@ -16,7 +16,7 @@ sys.path.append(path)
from log import log from log import log
if len(sys.argv) < 3: if len(sys.argv) < 3:
raise StandardError, "Syntax: log2txt.py log.lammps data.txt X Y ..." raise Exception("Syntax: log2txt.py log.lammps data.txt X Y ...")
logfile = sys.argv[1] logfile = sys.argv[1]
datafile = sys.argv[2] datafile = sys.argv[2]

2
tools/python/logplot.py
View File

@ -15,7 +15,7 @@ from log import log
from gnu import gnu from gnu import gnu
if len(sys.argv) != 4: if len(sys.argv) != 4:
raise StandardError, "Syntax: logplot.py log.lammps X Y" raise Exception("Syntax: logplot.py log.lammps X Y")
logfile = sys.argv[1] logfile = sys.argv[1]
xlabel = sys.argv[2] xlabel = sys.argv[2]

95
tools/python/pizza/log.py
View File

@ -64,7 +64,7 @@ class log:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def __init__(self,*list): def __init__(self,*arglist):
self.nvec = 0 self.nvec = 0
self.names = [] self.names = []
self.ptr = {} self.ptr = {}
@ -72,18 +72,18 @@ class log:
# flist = list of all log file names # flist = list of all log file names
words = list[0].split() words = arglist[0].split()
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(arglist) == 1:
raise StandardError,"no log file specified" raise Exception("no log file specified")
if len(list) == 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 StandardError,"can only incrementally read one log file" raise Exception("can only incrementally read one log file")
self.increment = 1 self.increment = 1
self.eof = 0 self.eof = 0
@ -92,24 +92,23 @@ class log:
def read_all(self): def read_all(self):
self.read_header(self.flist[0]) self.read_header(self.flist[0])
if self.nvec == 0: raise StandardError,"log file has no values" if self.nvec == 0: raise Exception("log file has no values")
# read all files # read all files
for file in self.flist: self.read_one(file) for file in self.flist: self.read_one(file)
print
# sort entries by timestep, cull duplicates # sort entries by timestep, cull duplicates
self.data.sort(self.compare) self.data.sort(key=(lambda elem: elem[0]))
self.cull() self.cull()
self.nlen = len(self.data) self.nlen = len(self.data)
print "read %d log entries" % self.nlen print("read %d log entries" % self.nlen)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def next(self): def next(self):
if not self.increment: raise StandardError,"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: open(self.flist[0],'r')
@ -124,12 +123,12 @@ class log:
def get(self,*keys): def get(self,*keys):
if len(keys) == 0: if len(keys) == 0:
raise StandardError, "no log vectors specified" raise Exception( "no log vectors specified" )
map = [] colmap = []
for key in keys: for key in keys:
if self.ptr.has_key(key): if key in self.ptr:
map.append(self.ptr[key]) colmap.append(self.ptr[key])
else: else:
count = 0 count = 0
for i in range(self.nvec): for i in range(self.nvec):
@ -137,15 +136,15 @@ class log:
count += 1 count += 1
index = i index = i
if count == 1: if count == 1:
map.append(index) colmap.append(index)
else: else:
raise StandardError, "unique log vector %s not found" % key raise Exception( "unique log vector %s not found" % key)
vecs = [] vecs = []
for i in range(len(keys)): for i in range(len(keys)):
vecs.append(self.nlen * [0]) vecs.append(self.nlen * [0])
for j in xrange(self.nlen): for j in range(self.nlen):
vecs[i][j] = self.data[j][map[i]] vecs[i][j] = self.data[j][colmap[i]]
if len(keys) == 1: return vecs[0] if len(keys) == 1: return vecs[0]
else: return vecs else: return vecs
@ -154,10 +153,10 @@ class log:
def write(self,filename,*keys): def write(self,filename,*keys):
if len(keys): if len(keys):
map = [] colmap = []
for key in keys: for key in keys:
if self.ptr.has_key(key): if key in self.ptr:
map.append(self.ptr[key]) colmap.append(self.ptr[key])
else: else:
count = 0 count = 0
for i in range(self.nvec): for i in range(self.nvec):
@ -165,17 +164,18 @@ class log:
count += 1 count += 1
index = i index = i
if count == 1: if count == 1:
map.append(index) colmap.append(index)
else: else:
raise StandardError, "unique log vector %s not found" % key raise Exception( "unique log vector %s not found" % key)
else: else:
map = range(self.nvec) colmap = range(self.nvec)
f = open(filename,"w") f = open(filename,"w")
for i in xrange(self.nlen): # write data
for j in xrange(len(map)): for i in range(self.nlen):
print >>f,self.data[i][map[j]], for j in range(len(colmap)):
print >>f print(self.data[i][colmap[j]],file=f,end=" "),
print("\n",file=f,end="")
f.close() f.close()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -243,18 +243,18 @@ class log:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def read_one(self,*list): def read_one(self,*arglist):
# if 2nd arg exists set file ptr to that value # if 2nd arg exists set file ptr io that value
# read entire (rest of) file into txt # read entire (rest of) file into txt
file = list[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),'rb')
else: else:
f = open(file,'rb') f = open(file,'rb')
if len(list) == 2: f.seek(list[1]) if len(arglist) == 2: f.seek(arglist[1])
txt = f.read() txt = f.read()
if file[-3:] == ".gz": eof = 0 if file[-3:] == ".gz": eof = 0
else: eof = f.tell() else: eof = f.tell()
@ -270,12 +270,12 @@ 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,start) s1 = txt.find(self.firststr.encode('utf-8'),start)
s2 = txt.find("Loop time of",start+1) s2 = txt.find("Loop time of".encode('utf-8'),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",s1) + 1 s1 = txt.find("\n".encode('utf-8'),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
@ -284,25 +284,25 @@ 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--",s1) + 1 s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1
else: else:
s1 = txt.find("\n",s1) + 1 s1 = txt.find("\n".encode('utf-8'),s1) + 1
s2 = txt.rfind("\n",s1) + 1 s2 = txt.rfind("\n".encode('utf-8'),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",start) == start: # end of file, so exit if txt.find("Loop time of".encode('utf-8'),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
last = 1 # entire read is a chunk last = 1 # entire read is a chunk
s1 = 0 s1 = 0
if self.style == 1: if self.style == 1:
s2 = txt.rfind("\n--",s1) + 1 s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1
else: else:
s2 = txt.rfind("\n",s1) + 1 s2 = txt.rfind("\n".encode('utf-8'),s1) + 1
eof -= len(txt) - s2 eof -= len(txt) - s2
if s1 == s2: break if s1 == s2: break
@ -313,24 +313,23 @@ 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--") sections = chunk.split("\n--".encode('utf-8'))
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:
word1 = [re.search(pat1,section).group(1)] word1 = [re.search(pat1,section).group(1)]
word2 = re.findall(pat2,section) word2 = re.findall(pat2,section)
words = word1 + word2 words = word1 + word2
self.data.append(map(float,words)) self.data.append(list(map(float,words)))
else: else:
lines = chunk.split("\n") lines = chunk.split("\n".encode('utf-8'))
for line in lines: for line in lines:
words = line.split() words = line.split()
self.data.append(map(float,words)) self.data.append(list(map(float,words)))
# print last timestep of chunk # print last timestep of chunk
print(int(self.data[len(self.data)-1][0]),)
print int(self.data[len(self.data)-1][0]),
sys.stdout.flush() sys.stdout.flush()
return eof return eof