python 2/3 portability changes for log class from Pizza.py
This commit is contained in:
Axel Kohlmeyer
@ -319,8 +319,8 @@ class dump:
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# if fail, try next file
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# if new snapshot time stamp already exists, read next snapshot
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while 1:
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f = open(self.flist[self.nextfile],'rb')
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while True:
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f = open(self.flist[self.nextfile],'r')
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f.seek(self.eof)
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snap = self.read_snapshot(f)
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if not snap:
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@ -13,25 +13,25 @@ from __future__ import print_function
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oneline = "Read LAMMPS log files and extract thermodynamic data"
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docstr = """
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l = log("file1") read in one or more log files
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l = log("log1 log2.gz") can be gzipped
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l = log("file*") wildcard expands to multiple files
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l = log("log.lammps",0) two args = store filename, but don't read
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l = log("file1") read in one or more log files
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l = log("log1 log2.gz") can be gzipped
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l = log("file*") wildcard expands to multiple files
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l = log("log.lammps",0) two args = store filename, but don't read
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incomplete and duplicate thermo entries are deleted
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time = l.next() read new thermo info from file
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time = l.next() read new thermo info from file
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used with 2-argument constructor to allow reading thermo incrementally
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return time stamp of last thermo read
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return -1 if no new thermo since last read
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nvec = l.nvec # of vectors of thermo info
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nlen = l.nlen length of each vectors
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names = l.names list of vector names
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t,pe,... = l.get("Time","KE",...) return one or more vectors of values
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l.write("file.txt") write all vectors to a file
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l.write("file.txt","Time","PE",...) write listed vectors to a file
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nvec = l.nvec # of vectors of thermo info
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nlen = l.nlen length of each vectors
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names = l.names list of vector names
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t,pe,... = l.get("Time","KE",...) return one or more vectors of values
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l.write("file.txt",0) write all vectors to a file, done write header comment
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l.write("file.txt",1,"Time","PE",...) write listed vectors to a file, include header comment
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get and write allow abbreviated (uniquely) vector names
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"""
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@ -79,14 +79,14 @@ class log:
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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(arglist) == 1:
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raise Exception("no log file specified")
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raise ValueError("No log files specified or specified files do not exist")
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if len(arglist) == 1:
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self.increment = 0
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self.read_all()
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else:
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if len(self.flist) > 1:
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raise Exception("can only incrementally read one log file")
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raise ValueError("Can only read one log file incrementally")
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self.increment = 1
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self.eof = 0
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@ -114,7 +114,9 @@ class log:
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if not self.increment: raise Exception("cannot read incrementally")
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if self.nvec == 0:
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try: open(self.flist[0],'r')
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try:
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fp = open(self.flist[0],'r')
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fp.close()
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except: return -1
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self.read_header(self.flist[0])
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if self.nvec == 0: return -1
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@ -126,7 +128,7 @@ class log:
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def get(self,*keys):
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if len(keys) == 0:
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raise Exception( "no log vectors specified" )
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raise Exception("no log vectors specified" )
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colmap = []
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for key in keys:
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@ -141,7 +143,7 @@ class log:
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if count == 1:
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colmap.append(index)
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else:
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raise Exception( "unique log vector %s not found" % key)
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raise ValueError("unique log vector %s not found" % key)
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vecs = []
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for i in range(len(keys)):
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@ -210,14 +212,16 @@ class log:
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# --------------------------------------------------------------------
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def read_header(self,file):
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def read_header(self, file):
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str_multi = "----- Step"
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str_one = "Step "
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if file[-3:] == ".gz":
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txt = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r').read()
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fp = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
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txt = fp.read()
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else:
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txt = open(file).read()
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fp = open(file)
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txt = fp.read()
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if txt.find(str_multi) >= 0:
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self.firststr = str_multi
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@ -226,6 +230,7 @@ class log:
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self.firststr = str_one
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self.style = 2
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else:
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fp.close()
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return
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if self.style == 1:
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@ -252,6 +257,7 @@ class log:
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self.ptr[words[i]] = i
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self.nvec = len(self.names)
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fp.close()
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# --------------------------------------------------------------------
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@ -262,9 +268,9 @@ class log:
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file = arglist[0]
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if file[-3:] == ".gz":
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f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb')
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f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
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else:
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f = open(file,'rb')
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f = open(file,'r')
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if len(arglist) == 2: f.seek(arglist[1])
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txt = f.read()
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@ -282,12 +288,12 @@ class log:
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# set start = position in file to start looking for next chunk
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# rewind eof if final entry is incomplete
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s1 = txt.find(self.firststr.encode('utf-8'),start)
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s2 = txt.find("Loop time of".encode('utf-8'),start+1)
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s1 = txt.find(self.firststr,start)
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s2 = txt.find("Loop time of",start+1)
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if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
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if self.style == 2:
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s1 = txt.find("\n".encode('utf-8'),s1) + 1
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s1 = txt.find("\n",s1) + 1
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elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
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s1 = 0
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elif s1 == -1 and s2 >= 0: # found s2, but no s1
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@ -296,16 +302,16 @@ class log:
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elif s1 >= 0 and s2 == -1: # found s1, but no s2
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last = 1
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if self.style == 1:
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s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1
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s2 = txt.rfind("\n--",s1) + 1
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else:
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s1 = txt.find("\n".encode('utf-8'),s1) + 1
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s2 = txt.rfind("\n".encode('utf-8'),s1) + 1
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s1 = txt.find("\n",s1) + 1
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s2 = txt.rfind("\n",s1) + 1
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eof -= len(txt) - s2
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elif s1 == -1 and s2 == -1: # found neither
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# could be end-of-file section
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# or entire read was one chunk
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if txt.find("Loop time of".encode('utf-8'),start) == start: # end of file, so exit
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if txt.find("Loop time of",start) == start: # end of file, so exit
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eof -= len(txt) - start # reset eof to "Loop"
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break
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@ -325,7 +331,7 @@ class log:
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# parse each entry for numeric fields, append to data
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if self.style == 1:
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sections = chunk.split("\n--".encode('utf-8'))
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sections = chunk.split("\n--")
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pat1 = re.compile("Step\s*(\S*)\s")
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pat2 = re.compile("=\s*(\S*)")
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for section in sections:
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@ -335,7 +341,7 @@ class log:
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self.data.append(list(map(float,words)))
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else:
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lines = chunk.split("\n".encode('utf-8'))
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lines = chunk.split("\n")
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for line in lines:
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words = line.split()
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self.data.append(list(map(float,words)))
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