git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5231 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -22,26 +22,60 @@ pages.
|
||||
Once you have successfully built and tested the wrappers, you can run
|
||||
the Python scripts in the examples sub-directory:
|
||||
|
||||
trivial.py read/run a LAMMPS input script thru Python
|
||||
demo.py invoke various LAMMPS library interface routines
|
||||
simple.py mimic operation of couple/simple/simple.cpp in Python
|
||||
gui.py GUI go/stop/temperature-slider to control LAMMPS
|
||||
plot.py real-time temeperature plot with GnuPlot via Pizza.py
|
||||
viz.py real-time viz from GL tool in Pizza.py
|
||||
vizplotgui.py combination of viz.py and plot.py and gui.py
|
||||
trivial.py read/run a LAMMPS input script thru Python
|
||||
demo.py invoke various LAMMPS library interface routines
|
||||
simple.py mimic operation of couple/simple/simple.cpp in Python
|
||||
gui.py GUI go/stop/temperature-slider to control LAMMPS
|
||||
plot.py real-time temeperature plot with GnuPlot via Pizza.py
|
||||
viz_tool.py real-time viz from GL tool in Pizza.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
|
||||
demo.py
|
||||
simple.py in.simple
|
||||
gui.py in.gui 100
|
||||
plot.py in.plot 10 1000 thermo_temp
|
||||
viz.py in.viz 100 5000
|
||||
vizplotgui.py in.viz 100 thermo_temp
|
||||
viz_tool.py in.viz 100 5000
|
||||
vizplotgui_tool.py in.viz 100 thermo_temp
|
||||
|
||||
You can un-comment the Pypar calls if you want to run these in
|
||||
parallel.
|
||||
|
||||
Each script has more documentation at the top of the file that
|
||||
explains how to use it.
|
||||
Each script has more documentation in the file that explains how to
|
||||
use it and what it is doing.
|
||||
|
||||
289
python/examples/pizza/pdbfile.py
Normal file
289
python/examples/pizza/pdbfile.py
Normal file
@ -0,0 +1,289 @@
|
||||
# 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
|
||||
Reference in New Issue
Block a user