modernize tinker2lmp scripts so they run with both python2.7 and python3.x
This commit is contained in:
Axel Kohlmeyer
@ -3,16 +3,17 @@
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#
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# Copyright (2005) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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# data tool
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from __future__ import print_function
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oneline = "Read, write, manipulate LAMMPS data files"
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docstr = """
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d = data("data.poly") read a LAMMPS data file, can be gzipped
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d = data() create an empty data file
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d = data() create an empty data file
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d.map(1,"id",3,"x") assign names to atom columns (1-N)
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@ -26,17 +27,17 @@ d.reorder("Atoms",1,3,2,4,5) reorder columns (1-N) in a data file section
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1,3,2,4,5 = new order of previous columns, can delete columns this way
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d.title = "My LAMMPS data file" set title of the data file
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d.title = "My LAMMPS data file" set title of the data file
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d.headers["atoms"] = 1500 set a header value
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d.sections["Bonds"] = lines set a section to list of lines (with newlines)
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d.delete("bonds") delete a keyword or section of data file
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d.delete("bonds") delete a keyword or section of data file
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d.delete("Bonds")
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d.replace("Atoms",5,vec) replace Nth column of section with vector
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d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N
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d.replace("Atoms",5,vec) replace Nth column of section with vector
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d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N
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newxyz assumes id,x,y,z are defined in both data and dump files
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also replaces ix,iy,iz if they are defined
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index,time,flag = d.iterator(0/1) loop over single data file snapshot
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time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects
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@ -53,7 +54,7 @@ time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects
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NULL if bonds do not exist
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tris = NULL
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lines = NULL
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d.write("data.new") write a LAMMPS data file
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"""
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@ -65,7 +66,7 @@ d.write("data.new") write a LAMMPS data file
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# Variables
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# title = 1st line of data file
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# names = dictionary with atom attributes as keys, col #s as values
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# names = dictionary with atom attributes as keys, col #s as values
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# headers = dictionary with header name as key, value or tuple as values
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# sections = dictionary with section name as key, array of lines as values
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# nselect = 1 = # of snapshots
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@ -79,13 +80,13 @@ except: PIZZA_GUNZIP = "gunzip"
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# Class definition
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class data:
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class data(object):
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# --------------------------------------------------------------------
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def __init__(self,*list):
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self.nselect = 1
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if len(list) == 0:
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self.title = "LAMMPS data file"
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self.names = {}
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@ -99,7 +100,7 @@ class data:
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self.title = f.readline()
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self.names = {}
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headers = {}
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while 1:
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line = f.readline()
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@ -109,16 +110,16 @@ class data:
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found = 0
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for keyword in hkeywords:
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if line.find(keyword) >= 0:
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found = 1
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words = line.split()
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if keyword == "xlo xhi" or keyword == "ylo yhi" or \
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keyword == "zlo zhi":
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headers[keyword] = (float(words[0]),float(words[1]))
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elif keyword == "xy xz yz":
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headers[keyword] = \
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found = 1
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words = line.split()
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if keyword == "xlo xhi" or keyword == "ylo yhi" or \
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keyword == "zlo zhi":
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headers[keyword] = (float(words[0]),float(words[1]))
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elif keyword == "xy xz yz":
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headers[keyword] = \
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(float(words[0]),float(words[1]),float(words[2]))
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else:
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headers[keyword] = int(words[0])
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headers[keyword] = int(words[0])
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if not found:
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break
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@ -128,22 +129,21 @@ class data:
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for pair in skeywords:
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keyword,length = pair[0],pair[1]
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if keyword == line:
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found = 1
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if not headers.has_key(length):
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raise StandardError, \
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"data section %s has no matching header value" % line
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f.readline()
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found = 1
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if length not in headers:
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raise (Exception, "data section %s has no matching header value" % line)
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f.readline()
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list = []
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for i in xrange(headers[length]): list.append(f.readline())
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for i in range(headers[length]): list.append(f.readline())
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sections[keyword] = list
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if not found:
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raise StandardError,"invalid section %s in data file" % line
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raise (Exception,"invalid section %s in data file" % line)
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f.readline()
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line = f.readline()
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if not line:
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break
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line = line.strip()
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f.close()
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self.headers = headers
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self.sections = sections
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@ -153,7 +153,7 @@ class data:
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def map(self,*pairs):
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if len(pairs) % 2 != 0:
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raise StandardError, "data map() requires pairs of mappings"
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raise Exception("data 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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@ -168,7 +168,7 @@ class data:
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lines = self.sections[field]
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for line in lines:
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words = line.split()
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values = map(float,words)
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values = list(map(float,words))
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array.append(values)
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return array
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elif len(list) == 2:
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@ -181,7 +181,7 @@ class data:
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vec.append(float(words[n]))
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return vec
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else:
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raise StandardError, "invalid arguments for data.get()"
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raise Exception("invalid arguments for data.get()")
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# --------------------------------------------------------------------
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# reorder columns in a data file field
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@ -192,10 +192,10 @@ class data:
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oldlines = self.sections[name]
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newlines = natoms*[""]
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for index in order:
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for i in xrange(len(newlines)):
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for i in range(len(newlines)):
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words = oldlines[i].split()
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newlines[i] += words[index-1] + " "
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for i in xrange(len(newlines)):
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for i in range(len(newlines)):
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newlines[i] += "\n"
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self.sections[name] = newlines
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@ -206,7 +206,7 @@ class data:
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lines = self.sections[name]
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newlines = []
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j = icol - 1
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for i in xrange(len(lines)):
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for i in range(len(lines)):
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line = lines[i]
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words = line.split()
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words[j] = str(vector[i])
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@ -228,48 +228,48 @@ class data:
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self.replace("Atoms",self.names['x']+1,x)
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self.replace("Atoms",self.names['y']+1,y)
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self.replace("Atoms",self.names['z']+1,z)
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if dm.names.has_key("ix") and self.names.has_key("ix"):
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if "ix" in dm.names and "ix" in self.names:
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ix,iy,iz = dm.vecs(ntime,"ix","iy","iz")
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self.replace("Atoms",self.names['ix']+1,ix)
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self.replace("Atoms",self.names['iy']+1,iy)
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self.replace("Atoms",self.names['iz']+1,iz)
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# --------------------------------------------------------------------
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# delete header value or section from data file
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def delete(self,keyword):
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if self.headers.has_key(keyword): del self.headers[keyword]
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elif self.sections.has_key(keyword): del self.sections[keyword]
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else: raise StandardError, "keyword not found in data object"
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if keyword in self.headers: del self.headers[keyword]
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elif keyword in self.sections: del self.sections[keyword]
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else: raise Exception("keyword not found in data object")
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# --------------------------------------------------------------------
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# write out a LAMMPS data file
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def write(self,file):
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f = open(file,"w")
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print >>f,self.title
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print(self.title, file=f)
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# write any keywords in standard list hkeywords
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# in the order they are in hkeywords
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# then write any extra keywords at end of header section
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for keyword in hkeywords:
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if self.headers.has_key(keyword):
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if keyword in self.headers:
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if keyword == "xlo xhi" or keyword == "ylo yhi" or \
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keyword == "zlo zhi":
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pair = self.headers[keyword]
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print >>f,pair[0],pair[1],keyword
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pair = self.headers[keyword]
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print(pair[0],pair[1],keyword, file=f)
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elif keyword == "xy xz yz":
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triple = self.headers[keyword]
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print >>f,triple[0],triple[1],triple[2],keyword
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triple = self.headers[keyword]
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print(triple[0],triple[1],triple[2],keyword, file=f)
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else:
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print >>f,self.headers[keyword],keyword
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print(self.headers[keyword],keyword, file=f)
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for keyword in self.headers.keys():
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for keyword in list(self.headers.keys()):
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if keyword not in hkeywords:
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print >>f,self.headers[keyword],keyword
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print(self.headers[keyword],keyword, file=f)
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# write any sections in standard list skeywords
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# in the order they are in skeywords
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@ -277,18 +277,18 @@ class data:
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for pair in skeywords:
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keyword = pair[0]
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if self.sections.has_key(keyword):
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print >>f,"\n%s\n" % keyword
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if keyword in self.sections:
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print("\n%s\n" % keyword, file=f)
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for line in self.sections[keyword]:
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print >>f,line,
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print(line, end='', file=f)
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skeyfirst = [pair[0] for pair in skeywords]
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for keyword in self.sections.keys():
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for keyword in list(self.sections.keys()):
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if keyword not in skeyfirst:
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print >>f,"\n%s\n" % keyword
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print("\n%s\n" % keyword, file=f)
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for line in self.sections[keyword]:
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print >>f,line,
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print(line, end='', file=f)
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f.close()
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@ -304,20 +304,20 @@ class data:
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def findtime(self,n):
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if n == 0: return 0
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raise StandardError, "no step %d exists" % (n)
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raise(Exception, "no step %d exists" % (n))
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# --------------------------------------------------------------------
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# return list of atoms and bonds to viz for data object
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def viz(self,isnap):
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if isnap: raise StandardError, "cannot call data.viz() with isnap != 0"
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if isnap: raise Exception("cannot call data.viz() with isnap != 0")
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id = self.names["id"]
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type = self.names["type"]
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x = self.names["x"]
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y = self.names["y"]
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z = self.names["z"]
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xlohi = self.headers["xlo xhi"]
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ylohi = self.headers["ylo yhi"]
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zlohi = self.headers["zlo zhi"]
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@ -336,7 +336,7 @@ class data:
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# assumes atoms are sorted so can lookup up the 2 atoms in each bond
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bonds = []
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if self.sections.has_key("Bonds"):
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if "Bonds" in self.sections:
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bondlines = self.sections["Bonds"]
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for line in bondlines:
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words = line.split()
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@ -349,8 +349,8 @@ class data:
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float(atom1words[z]),
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float(atom2words[x]),float(atom2words[y]),
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float(atom2words[z]),
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float(atom1words[type]),float(atom2words[type])])
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float(atom1words[type]),float(atom2words[type])])
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tris = []
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lines = []
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return 0,box,atoms,bonds,tris,lines
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@ -375,8 +375,8 @@ class data:
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hkeywords = ["atoms","ellipsoids","lines","triangles","bodies",
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"bonds","angles","dihedrals","impropers",
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"atom types","bond types","angle types","dihedral types",
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"improper types",
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"atom types","bond types","angle types","dihedral types",
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"improper types",
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"xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
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skeywords = [["Masses","atom types"],
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@ -384,14 +384,14 @@ skeywords = [["Masses","atom types"],
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["Lines","lines"],["Triangles","triangles"],["Bodies","bodies"],
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["Velocities","atoms"],
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["Bonds","bonds"],
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["Angles","angles"],
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["Angles","angles"],
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["Dihedrals","dihedrals"],
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["Impropers","impropers"],
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["Impropers","impropers"],
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["Pair Coeffs","atom types"],
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["Bond Coeffs","bond types"],
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["Bond Coeffs","bond types"],
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["Angle Coeffs","angle types"],
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["Dihedral Coeffs","dihedral types"],
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["Improper Coeffs","improper types"],
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["Dihedral Coeffs","dihedral types"],
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["Improper Coeffs","improper types"],
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["BondBond Coeffs","angle types"],
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["BondAngle Coeffs","angle types"],
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["MiddleBondTorsion Coeffs","dihedral types"],
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