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python/README
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Once you have successfully built and tested the wrappers, you can run Once you have successfully built and tested the wrappers, you can run
the Python scripts in the examples sub-directory: the Python scripts in the examples sub-directory:
trivial.py read/run a LAMMPS input script thru Python trivial.py read/run a LAMMPS input script thru Python
demo.py invoke various LAMMPS library interface routines demo.py invoke various LAMMPS library interface routines
simple.py mimic operation of couple/simple/simple.cpp in Python simple.py mimic operation of couple/simple/simple.cpp in Python
gui.py GUI go/stop/temperature-slider to control LAMMPS gui.py GUI go/stop/temperature-slider to control LAMMPS
plot.py real-time temeperature plot with GnuPlot via Pizza.py plot.py real-time temeperature plot with GnuPlot via Pizza.py
viz.py real-time viz from GL tool in Pizza.py viz_tool.py real-time viz from GL tool in Pizza.py
vizplotgui.py combination of viz.py and plot.py and gui.py vizplotgui_tool.py combination of viz.py and plot.py and gui.py
Run them with the following input scripts and arguments: For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol", depending on what visualization
package you have installed. We hope to add a VMD option soon.
Note that for GL, you need to be able to run the Pizza.py GL tool,
which is included in the pizza sub-directory. See the Pizza.py doc
pages for more info:
http://www.sandia.gov/~sjplimp/pizza.html
Note that for AtomEye, you need version 3, and their is a line in the
scripts that specifies the path and name of the executable. See
the AtomEye WWW pages for more details:
http://mt.seas.upenn.edu/Archive/Graphics/A/
http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
Note that for PyMol, you need to have built and installed the
open-source version of PyMol in your Python, so that you can import it
from a Python script. See the AtomEye WWW pages for more details:
http://www.pymol.org/
http://sourceforge.net/scm/?type=svn&group_id=4546
The latter link is to the open-source version.
You can run a particular script in either of the following ways:
% trivial.py in.trivial
% python -i trivial.py in.trivial
The former assumes that you have changed the first line of the script
to point to the Python installed on your box.
Run the Python scripts with the following LAMMPS input scripts and arguments:
trivial.py in.trivial trivial.py in.trivial
demo.py demo.py
simple.py in.simple simple.py in.simple
gui.py in.gui 100 gui.py in.gui 100
plot.py in.plot 10 1000 thermo_temp plot.py in.plot 10 1000 thermo_temp
viz.py in.viz 100 5000 viz_tool.py in.viz 100 5000
vizplotgui.py in.viz 100 thermo_temp vizplotgui_tool.py in.viz 100 thermo_temp
You can un-comment the Pypar calls if you want to run these in You can un-comment the Pypar calls if you want to run these in
parallel. parallel.
Each script has more documentation at the top of the file that Each script has more documentation in the file that explains how to
explains how to use it. use it and what it is doing.

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python/examples/pizza/pdbfile.py Normal file
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# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# pdb tool
oneline = "Read, write PDB files in combo with LAMMPS snapshots"
docstr = """
p = pdbfile("3CRO") create pdb object from PDB file or WWW
p = pdbfile("pep1 pep2") read in multiple PDB files
p = pdbfile("pep*") can use wildcards
p = pdbfile(d) read in snapshot data with no PDB file
p = pdbfile("3CRO",d) read in single PDB file with snapshot data
string arg contains one or more PDB files
don't need .pdb suffix except wildcard must expand to file.pdb
if only one 4-char file specified and it is not found,
it will be downloaded from http://www.rcsb.org as 3CRO.pdb
d arg is object with atom coordinates (dump, data)
p.one() write all output as one big PDB file to tmp.pdb
p.one("mine") write to mine.pdb
p.many() write one PDB file per snapshot: tmp0000.pdb, ...
p.many("mine") write as mine0000.pdb, mine0001.pdb, ...
p.single(N) write timestamp N as tmp.pdb
p.single(N,"new") write as new.pdb
how new PDB files are created depends on constructor inputs:
if no d: one new PDB file for each file in string arg (just a copy)
if only d specified: one new PDB file per snapshot in generic format
if one file in str arg and d: one new PDB file per snapshot
using input PDB file as template
multiple input PDB files with a d is not allowed
index,time,flag = p.iterator(0)
index,time,flag = p.iterator(1)
iterator = loop over number of PDB files
call first time with arg = 0, thereafter with arg = 1
N = length = # of snapshots or # of input PDB files
index = index of snapshot or input PDB file (0 to N-1)
time = timestep value (time stamp for snapshot, index for multiple PDB)
flag = -1 when iteration is done, 1 otherwise
typically call p.single(time) in iterated loop to write out one PDB file
"""
# History
# 8/05, Steve Plimpton (SNL): original version
# ToDo list
# for generic PDB file (no template) from a LJ unit system,
# the atoms in PDB file are too close together
# Variables
# files = list of input PDB files
# data = data object (ccell,data,dump) to read snapshots from
# atomlines = dict of ATOM lines in original PDB file
# key = atom id, value = tuple of (beginning,end) of line
# Imports and external programs
import sys, types, glob, urllib
# Class definition
class pdbfile:
# --------------------------------------------------------------------
def __init__(self,*args):
if len(args) == 1:
if type(args[0]) is types.StringType:
filestr = args[0]
self.data = None
else:
filestr = None
self.data = args[0]
elif len(args) == 2:
filestr = args[0]
self.data = args[1]
else: raise StandardError, "invalid args for pdb()"
# flist = full list of all PDB input file names
# append .pdb if needed
if filestr:
list = filestr.split()
flist = []
for file in list:
if '*' in file: flist += glob.glob(file)
else: flist.append(file)
for i in xrange(len(flist)):
if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
if len(flist) == 0:
raise StandardError,"no PDB file specified"
self.files = flist
else: self.files = []
if len(self.files) > 1 and self.data:
raise StandardError, "cannot use multiple PDB files with data object"
if len(self.files) == 0 and not self.data:
raise StandardError, "no input PDB file(s)"
# grab PDB file from http://rcsb.org if not a local file
if len(self.files) == 1 and len(self.files[0]) == 8:
try:
open(self.files[0],'r').close()
except:
print "downloading %s from http://rcsb.org" % self.files[0]
fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
urllib.urlretrieve(fetchstr,self.files[0])
if self.data and len(self.files): self.read_template(self.files[0])
# --------------------------------------------------------------------
# write a single large PDB file for concatenating all input data or files
# if data exists:
# only selected atoms returned by extract
# atoms written in order they appear in snapshot
# atom only written if its tag is in PDB template file
# if no data:
# concatenate all input files to one output file
def one(self,*args):
if len(args) == 0: file = "tmp.pdb"
elif args[0][-4:] == ".pdb": file = args[0]
else: file = args[0] + ".pdb"
f = open(file,'w')
# use template PDB file with each snapshot
if self.data:
n = flag = 0
while 1:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
self.convert(f,which)
print >>f,"END"
print time,
sys.stdout.flush()
n += 1
else:
for file in self.files:
f.write(open(file,'r').read())
print >>f,"END"
print file,
sys.stdout.flush()
f.close()
print "\nwrote %d datasets to %s in PDB format" % (n,file)
# --------------------------------------------------------------------
# write series of numbered PDB files
# if data exists:
# only selected atoms returned by extract
# atoms written in order they appear in snapshot
# atom only written if its tag is in PDB template file
# if no data:
# just copy all input files to output files
def many(self,*args):
if len(args) == 0: root = "tmp"
else: root = args[0]
if self.data:
n = flag = 0
while 1:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
if n < 10:
file = root + "000" + str(n)
elif n < 100:
file = root + "00" + str(n)
elif n < 1000:
file = root + "0" + str(n)
else:
file = root + str(n)
file += ".pdb"
f = open(file,'w')
self.convert(f,which)
f.close()
print time,
sys.stdout.flush()
n += 1
else:
n = 0
for infile in self.files:
if n < 10:
file = root + "000" + str(n)
elif n < 100:
file = root + "00" + str(n)
elif n < 1000:
file = root + "0" + str(n)
else:
file = root + str(n)
file += ".pdb"
f = open(file,'w')
f.write(open(infile,'r').read())
f.close()
print file,
sys.stdout.flush()
n += 1
print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
# --------------------------------------------------------------------
# write a single PDB file
# if data exists:
# time is timestamp in snapshot
# only selected atoms returned by extract
# atoms written in order they appear in snapshot
# atom only written if its tag is in PDB template file
# if no data:
# time is index into list of input PDB files
# just copy one input file to output file
def single(self,time,*args):
if len(args) == 0: file = "tmp.pdb"
elif args[0][-4:] == ".pdb": file = args[0]
else: file = args[0] + ".pdb"
f = open(file,'w')
if self.data:
which = self.data.findtime(time)
self.convert(f,which)
else:
f.write(open(self.files[time],'r').read())
f.close()
# --------------------------------------------------------------------
# iterate over list of input files or selected snapshots
# latter is done via data objects iterator
def iterator(self,flag):
if not self.data:
if not flag: self.iterate = 0
else:
self.iterate += 1
if self.iterate > len(self.files): return 0,0,-1
return self.iterate,self.iterate,1
return self.data.iterator(flag)
# --------------------------------------------------------------------
# read a PDB file and store ATOM lines
def read_template(self,file):
lines = open(file,'r').readlines()
self.atomlines = {}
for line in lines:
if line.find("ATOM") == 0:
tag = int(line[4:11])
begin = line[:30]
end = line[54:]
self.atomlines[tag] = (begin,end)
# --------------------------------------------------------------------
# convert one set of atoms to PDB format and write to f
def convert(self,f,which):
time,box,atoms,bonds,tris,lines = self.data.viz(which)
if len(self.files):
for atom in atoms:
id = atom[0]
if self.atomlines.has_key(id):
(begin,end) = self.atomlines[id]
line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
print >>f,line,
else:
for atom in atoms:
begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
end = " 1.00 0.00 NONE"
print >>f,begin+middle+end