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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@ -15,6 +15,7 @@
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# Author: Steve Plimpton
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from __future__ import print_function
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import sys,os,math
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from data import data
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@ -29,20 +30,20 @@ DELTA = 0.001 # delta on LAMMPS shrink-wrap box size, in Angstroms
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def error(txt=""):
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if not txt:
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print "Syntax: tinker2lmp.py -switch args ..."
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print " -xyz file"
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print " -amoeba file"
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print " -hippo file"
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print " -data file"
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print " -bitorsion file"
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print " -nopbc"
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print " -pbc xhi yhi zhi"
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else: print "ERROR:",txt
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print("Syntax: tinker2lmp.py -switch args ...")
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print(" -xyz file")
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print(" -amoeba file")
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print(" -hippo file")
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print(" -data file")
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print(" -bitorsion file")
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print(" -nopbc")
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print(" -pbc xhi yhi zhi")
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else: print("ERROR:",txt)
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#sys.exit()
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# read and store values from a Tinker xyz file
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class XYZfile:
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class XYZfile(object):
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def __init__(self,file):
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lines = open(file,'r').readlines()
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header = lines[0]
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@ -212,7 +213,7 @@ class XYZfile:
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def output(self,outfile):
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fp = open(outfile,'w')
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words = self.header.split()
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print >>fp,self.natoms,"replicated",' '.join(words[1:])
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print(self.natoms,"replicated",' '.join(words[1:]), file=fp)
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id = self.id
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label = self.label
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@ -225,9 +226,9 @@ class XYZfile:
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# NOTE: worry about formatting of line
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for i in range(self.natoms):
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print >>fp,i+1,label[i],x[i],y[i],z[i],type[i],
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for j in bonds[i]: print >>fp,j,
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print >>fp
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print(i+1,label[i],x[i],y[i],z[i],type[i], end=' ', file=fp)
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for j in bonds[i]: print(j, end=' ', file=fp)
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print(file=fp)
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fp.close()
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@ -255,7 +256,7 @@ class XYZfile:
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# scalar force field params in Force Field Definition section
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# bond, angle, dihedral coeffs indexed by Tinker classes
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class PRMfile:
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class PRMfile(object):
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def __init__(self,file):
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lines = open(file,'r').readlines()
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self.nlines = len(lines)
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@ -519,7 +520,7 @@ class PRMfile:
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error("torsion does not have triplets of params: %d %d %d %d" % \
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(class1,class2,class3,class4))
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mfourier = (len(words)-5) / 3
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mfourier = int((len(words)-5)/3)
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oneparams = [class1,class2,class3,class4,mfourier]
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for iset in range(mfourier):
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@ -743,7 +744,7 @@ if pbcflag:
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else:
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xlo = ylo = zlo = BIG
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xhi = yhi = zhi = -BIG
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for i in xrange(natoms):
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for i in range(natoms):
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xlo = min(xlo,float(x[i]))
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ylo = min(ylo,float(y[i]))
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zlo = min(zlo,float(z[i]))
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@ -1097,11 +1098,11 @@ for i,one in enumerate(alist):
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nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
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if nbonds != 3:
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print "Center angle atom has wrong bond count"
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print " angle atom IDs:",atom1,atom2,atom3
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print " angle atom classes:",c1,c2,c3
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print " Tinker FF file param options:",len(params[3])
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print " Nbonds and hydrogen count:",nbonds,hcount
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print("Center angle atom has wrong bond count")
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print(" angle atom IDs:",atom1,atom2,atom3)
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print(" angle atom classes:",c1,c2,c3)
|
||||
print(" Tinker FF file param options:",len(params[3]))
|
||||
print(" Nbonds and hydrogen count:",nbonds,hcount)
|
||||
#sys.exit() NOTE: allow this for now
|
||||
|
||||
if hcount == 0: which = 1
|
||||
@ -1109,22 +1110,22 @@ for i,one in enumerate(alist):
|
||||
which = 2
|
||||
m += 1
|
||||
|
||||
print "3-bond angle"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
print " which:",which,m
|
||||
print("3-bond angle")
|
||||
print(" angle atom IDs:",atom1,atom2,atom3)
|
||||
print(" angle atom classes:",c1,c2,c3)
|
||||
print(" Tinker FF file param options:",len(params[3]))
|
||||
print(" Nbonds and hydrogen count:",nbonds,hcount)
|
||||
print(" which:",which,m)
|
||||
|
||||
elif len(params[3]) == 3:
|
||||
nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
|
||||
|
||||
if nbonds != 4:
|
||||
print "Center angle atom has wrong bond count"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
print("Center angle atom has wrong bond count")
|
||||
print(" angle atom IDs:",atom1,atom2,atom3)
|
||||
print(" angle atom classes:",c1,c2,c3)
|
||||
print(" Tinker FF file param options:",len(params[3]))
|
||||
print(" Nbonds and hydrogen count:",nbonds,hcount)
|
||||
#sys.exit() NOTE: allow this for now
|
||||
|
||||
if hcount == 0: which = 1
|
||||
@ -1170,7 +1171,7 @@ for itype in range(len(aparams)):
|
||||
elif (c3,c2,c1) in badict:
|
||||
n1,n2,r1,r2 = badict[(c3,c2,c1)]
|
||||
else:
|
||||
print "Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3)
|
||||
print("Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3))
|
||||
n1,n2,r1,r2 = 4*[0.0]
|
||||
|
||||
baparams.append((n1,n2,r1,r2))
|
||||
@ -1600,17 +1601,17 @@ if nbitorsions:
|
||||
nbitorsions)
|
||||
|
||||
fp = open(bitorsionfile,'w')
|
||||
print >>fp,"Tinker BiTorsion parameter file for fix bitorsion\n"
|
||||
print >>fp,"%d bitorsion types" % len(bitorsionparams)
|
||||
print("Tinker BiTorsion parameter file for fix bitorsion\n", file=fp)
|
||||
print("%d bitorsion types" % len(bitorsionparams), file=fp)
|
||||
itype = 0
|
||||
for nx,ny,array in bitorsionparams:
|
||||
itype += 1
|
||||
print >>fp
|
||||
print >>fp,itype,nx,ny
|
||||
print(file=fp)
|
||||
print(itype,nx,ny, file=fp)
|
||||
for ix in range(nx):
|
||||
for iy in range(ny):
|
||||
xgrid,ygrid,value = array[ix][iy]
|
||||
print >>fp," ",xgrid,ygrid,value
|
||||
print(" ",xgrid,ygrid,value, file=fp)
|
||||
fp.close()
|
||||
|
||||
lines = []
|
||||
@ -1624,21 +1625,21 @@ d.write(datafile)
|
||||
|
||||
# print stats to screen
|
||||
|
||||
print "Natoms =",natoms
|
||||
print "Ntypes =",ntypes
|
||||
print "Tinker XYZ types =",len(tink2lmp)
|
||||
print "Tinker PRM types =",prm.ntypes
|
||||
print("Natoms =",natoms)
|
||||
print("Ntypes =",ntypes)
|
||||
print("Tinker XYZ types =",len(tink2lmp))
|
||||
print("Tinker PRM types =",prm.ntypes)
|
||||
#print "Tinker groups =",ngroups
|
||||
print "Nmol =",nmol
|
||||
print "Nbonds =",nbonds
|
||||
print "Nangles =",nangles
|
||||
print "Ndihedrals =",ndihedrals
|
||||
print "Nimpropers =",nimpropers
|
||||
print "Npitorsions =",npitorsions
|
||||
print "Nbitorsions =",nbitorsions
|
||||
print "Nbondtypes =",len(bparams)
|
||||
print "Nangletypes =",len(aparams)
|
||||
print "Ndihedraltypes =",len(dparams)
|
||||
print "Nimpropertypes =",len(oparams)
|
||||
print "Npitorsiontypes =",len(pitorsionparams)
|
||||
print "Nbitorsiontypes =",len(bitorsionparams)
|
||||
print("Nmol =",nmol)
|
||||
print("Nbonds =",nbonds)
|
||||
print("Nangles =",nangles)
|
||||
print("Ndihedrals =",ndihedrals)
|
||||
print("Nimpropers =",nimpropers)
|
||||
print("Npitorsions =",npitorsions)
|
||||
print("Nbitorsions =",nbitorsions)
|
||||
print("Nbondtypes =",len(bparams))
|
||||
print("Nangletypes =",len(aparams))
|
||||
print("Ndihedraltypes =",len(dparams))
|
||||
print("Nimpropertypes =",len(oparams))
|
||||
print("Npitorsiontypes =",len(pitorsionparams))
|
||||
print("Nbitorsiontypes =",len(bitorsionparams))
|
||||
|
||||
Reference in New Issue
Block a user