forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5201 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
b63b44e274
commit
453aba29e5
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This directory contains Python code which wraps LAMMPS as a library
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and allows the library interface to be invoked from a Python, either
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from a script or interactively.
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Details on how to build and use this Python interface are given in
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doc/Section_python.html.
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Basically you have to extend the Python on your box to include the
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LAMMPS wrappers:
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python setup_serial.py build # for serial LAMMPS and Python
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sudo python setup_serial.py install
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python setup.py build # for parallel LAMMPS and Python
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sudo python setuppy install
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but there are several issues to be aware of, as discussed in the doc
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pages.
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-------------------------------------------------------------------
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Once you have successfully built and tested the wrappers, you can run
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the Python scripts in the examples sub-directory:
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trivial.py read/run a LAMMPS input script thru Python
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demo.py invoke various LAMMPS library interface routines
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simple.py mimic operation of couple/simple/simple.cpp in Python
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gui.py GUI go/stop/temperature-slider to control LAMMPS
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plot.py real-time temeperature plot with GnuPlot via Pizza.py
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viz.py real-time viz from GL tool in Pizza.py
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vizplotgui.py combination of viz.py and plot.py and gui.py
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Run them with the following input scripts and arguments:
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trivial.py in.trivial
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demo.py
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simple.py in.simple
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gui.py in.gui 100
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plot.py in.plot 10 1000 thermo_temp
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viz.py in.viz 100 5000
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vizplotgui.py in.viz 100 thermo_temp
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You can un-comment the Pypar calls if you want to run these in
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parallel.
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Each script has more documentation at the top of the file that
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explains how to use it.
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#!/usr/local/bin/python -i
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# preceeding line should have path for Python on your machine
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# demo.py
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# Purpose: illustrate use of many library interface commands
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# Syntax: demo.py
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# uses in.demo as LAMMPS input script
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import sys
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# parse command line
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argv = sys.argv
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if len(argv) != 1:
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print "Syntax: demo.py"
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sys.exit()
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me = 0
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# uncomment if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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#nprocs = pypar.size()
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from lammps import lammps
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from lammps import LMPINT as INT
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from lammps import LMPDOUBLE as DOUBLE
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from lammps import LMPIPTR as IPTR
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from lammps import LMPDPTR as DPTR
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from lammps import LMPDPTRPTR as DPTRPTR
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lmp = lammps()
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# test out various library functions after running in.demo
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lmp.file("in.demo")
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if me == 0: print "\nPython output:"
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natoms = lmp.extract_global("natoms",DOUBLE)
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mass = lmp.extract_atom("mass",DPTR)
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x = lmp.extract_atom("x",DPTRPTR)
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print "Natoms, mass, x[0][0] coord =",natoms,mass[1],x[0][0]
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temp = lmp.extract_compute("thermo_temp",0,0)
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print "Temperature from compute =",temp
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eng = lmp.extract_variable("eng",None,0)
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print "Energy from equal-style variable =",eng
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vy = lmp.extract_variable("vy","all",1)
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print "Velocity component from atom-style variable =",vy[1]
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natoms = lmp.get_natoms()
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print "Natoms from get_natoms =",natoms
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xc = lmp.get_coords()
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print "Global coords from get_coords =",xc[0],xc[1],xc[31]
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xc[0] = xc[0] + 1.0
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lmp.put_coords(xc)
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print "Changed x[0][0] via put_coords =",x[0][0]
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# uncomment if running in parallel via Pypar
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#print "Proc %d out of %d procs has" % (me,nprocs), lmp
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#pypar.finalize()
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#!/usr/local/bin/python -i
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# preceeding line should have path for Python on your machine
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# gui.py
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# Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI
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# Syntax: gui.py in.lammps Nfreq
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# in.lammps = LAMMPS input script
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# Nfreq = query GUI every this many steps
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import sys,time
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# methods called by GUI
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def go():
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global runflag
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runflag = 1
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def stop():
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global runflag
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runflag = 0
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def settemp(value):
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global temptarget
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temptarget = slider.get()
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def quit():
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global breakflag
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breakflag = 1
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# parse command line
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argv = sys.argv
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if len(argv) != 3:
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print "Syntax: gui.py in.lammps Nfreq"
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sys.exit()
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infile = sys.argv[1]
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nfreq = int(sys.argv[2])
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me = 0
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# uncomment if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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#nprocs = pypar.size()
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from lammps import lammps
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lmp = lammps()
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# run infile all at once
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# assumed to have no run command in it
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lmp.file(infile)
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lmp.command("thermo %d" % nfreq)
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# display GUI with go/stop/quit buttons and slider for temperature
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# just proc 0 handles GUI
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breakflag = 0
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runflag = 0
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temptarget = 1.0
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if me == 0:
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from Tkinter import *
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tkroot = Tk()
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tkroot.withdraw()
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root = Toplevel(tkroot)
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root.title("LAMMPS GUI")
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frame = Frame(root)
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Button(frame,text="Go",command=go).pack(side=LEFT)
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Button(frame,text="Stop",command=stop).pack(side=LEFT)
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slider = Scale(frame,from_=0.0,to=5.0,resolution=0.1,
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orient=HORIZONTAL,label="Temperature")
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slider.bind('<ButtonRelease-1>',settemp)
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slider.set(temptarget)
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slider.pack(side=LEFT)
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Button(frame,text="Quit",command=quit).pack(side=RIGHT)
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frame.pack()
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tkroot.update()
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# endless loop, checking status of GUI settings every Nfreq steps
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# run with pre yes/no and post yes/no depending on go/stop status
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# re-invoke fix langevin with new seed when temperature slider changes
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# after re-invoke of fix langevin, run with pre yes
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running = 0
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temp = temptarget
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seed = 12345
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lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))
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while 1:
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if me == 0: tkroot.update()
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if temp != temptarget:
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temp = temptarget
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seed += me+1
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lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))
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running = 0
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if runflag and running:
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lmp.command("run %d pre no post no" % nfreq)
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elif runflag and not running:
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lmp.command("run %d pre yes post no" % nfreq)
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elif not runflag and running:
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lmp.command("run %d pre no post yes" % nfreq)
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if breakflag: break
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if runflag: running = 1
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else: running = 0
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time.sleep(0.01)
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# uncomment if running in parallel via Pypar
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#print "Proc %d out of %d procs has" % (me,nprocs), lmp
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#pypar.finalize()
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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atom_modify map hash
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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variable eng equal pe
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variable vy atom vy
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run 100
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# 3d Lennard-Jones melt
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units lj
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dimension 2
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atom_style atomic
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lattice sq2 0.8442
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region box block 0 30 0 15 -0.5 0.5
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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timestep 0.003
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fix 1 all nve
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fix 3 all enforce2d
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# 3d Lennard-Jones melt
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units lj
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dimension 2
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atom_style atomic
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lattice sq2 0.8442
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region box block 0 30 0 15 -0.5 0.5
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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timestep 0.003
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fix 1 all nve
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fix 3 all enforce2d
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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atom_modify map array
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lattice fcc 0.8442
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 10
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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# 3d Lennard-Jones melt
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units lj
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dimension 2
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atom_style atomic
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lattice sq2 0.8442
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region box block 0 30 0 15 -0.5 0.5
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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timestep 0.003
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fix 1 all nve
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fix 3 all enforce2d
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@ -0,0 +1,906 @@
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LAMMPS (31 Oct 2010)
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# 3d Lennard-Jones melt
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units lj
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dimension 2
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atom_style atomic
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lattice sq2 0.8442
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Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
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region box block 0 30 0 15 -0.5 0.5
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create_box 1 box
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Created orthogonal box = (0 0 -0.769595) to (46.1757 23.0879 0.769595)
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1 by 1 by 1 processor grid
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create_atoms 1 box
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Created 900 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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timestep 0.003
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fix 1 all nve
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fix 3 all enforce2d
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thermo 100
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fix 2 all langevin 1 1 0.1 12345
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run 100 pre yes post no
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Memory usage per processor = 1.67412 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -2.6248859 0 -1.1864859 2.0176244
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100 0.99023288 -2.0005395 0 -1.0114069 5.9914427
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Loop time of 0.04617 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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100 0.99023288 -2.0005395 0 -1.0114069 5.9914427
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200 1.0641026 -2.126693 0 -1.0637727 5.3834133
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Loop time of 0.045666 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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200 1.0641026 -2.126693 0 -1.0637727 5.3834133
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300 1.0404544 -2.1182885 0 -1.0789901 5.4751694
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Loop time of 0.0448651 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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300 1.0404544 -2.1182885 0 -1.0789901 5.4751694
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400 0.9940782 -2.0913772 0 -1.0984035 5.7006406
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Loop time of 0.044888 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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400 0.9940782 -2.0913772 0 -1.0984035 5.7006406
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500 1.0533477 -2.1766862 0 -1.1245089 5.1818937
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Loop time of 0.0443962 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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500 1.0533477 -2.1766862 0 -1.1245089 5.1818937
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600 1.0371191 -2.1708671 0 -1.1349004 5.2128526
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Loop time of 0.0447521 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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600 1.0371191 -2.1708671 0 -1.1349004 5.2128526
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700 1.0178469 -2.1795112 0 -1.1627952 5.0714199
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Loop time of 0.0448291 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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700 1.0178469 -2.1795112 0 -1.1627952 5.0714199
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||||
800 1.0220115 -2.1753909 0 -1.1545149 5.1482844
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||||
Loop time of 0.044615 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
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Step Temp E_pair E_mol TotEng Press
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800 1.0220115 -2.1753909 0 -1.1545149 5.1482844
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900 1.0029029 -2.1674923 0 -1.1657037 5.1338534
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Loop time of 0.0446992 on 1 procs for 100 steps with 900 atoms
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run 100 pre no post no
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||||
Step Temp E_pair E_mol TotEng Press
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||||
900 1.0029029 -2.1674923 0 -1.1657037 5.1338534
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||||
1000 1.0400785 -2.1739867 0 -1.1350638 5.1279779
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Loop time of 0.0448501 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
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||||
Step Temp E_pair E_mol TotEng Press
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1000 1.0400785 -2.1739867 0 -1.1350638 5.1279779
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||||
1100 1.0248051 -2.1763751 0 -1.1527087 5.125636
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||||
Loop time of 0.0447941 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
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||||
Step Temp E_pair E_mol TotEng Press
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||||
1100 1.0248051 -2.1763751 0 -1.1527087 5.125636
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||||
1200 1.0129247 -2.1960205 0 -1.1842213 4.9280331
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||||
Loop time of 0.0442801 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1200 1.0129247 -2.1960205 0 -1.1842213 4.9280331
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||||
1300 1.0445891 -2.138322 0 -1.0948936 5.358069
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||||
Loop time of 0.044374 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1300 1.0445891 -2.138322 0 -1.0948936 5.358069
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||||
1400 1.0262085 -2.1210161 0 -1.0959478 5.5887816
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||||
Loop time of 0.044693 on 1 procs for 100 steps with 900 atoms
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||||
run 100 pre no post no
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||||
Step Temp E_pair E_mol TotEng Press
|
||||
1400 1.0262085 -2.1210161 0 -1.0959478 5.5887816
|
||||
1500 0.9862776 -2.1287449 0 -1.1435631 5.4408715
|
||||
Loop time of 0.0446811 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1500 0.9862776 -2.1287449 0 -1.1435631 5.4408715
|
||||
1600 1.0008092 -2.1637199 0 -1.1640227 5.2714443
|
||||
Loop time of 0.0442421 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1600 1.0008092 -2.1637199 0 -1.1640227 5.2714443
|
||||
1700 1.0258515 -2.1288392 0 -1.1041276 5.4565262
|
||||
Loop time of 0.0446551 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1700 1.0258515 -2.1288392 0 -1.1041276 5.4565262
|
||||
1800 0.99606403 -2.1881474 0 -1.1931901 5.0145909
|
||||
Loop time of 0.0446119 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1800 0.99606403 -2.1881474 0 -1.1931901 5.0145909
|
||||
1900 0.98665733 -2.1993707 0 -1.2138096 4.9672864
|
||||
Loop time of 0.044836 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1900 0.98665733 -2.1993707 0 -1.2138096 4.9672864
|
||||
2000 1.0155716 -2.1239518 0 -1.1095086 5.4592445
|
||||
Loop time of 0.044791 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2000 1.0155716 -2.1239518 0 -1.1095086 5.4592445
|
||||
2100 0.9688746 -2.1712503 0 -1.2034522 5.1417376
|
||||
Loop time of 0.0446949 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2100 0.9688746 -2.1712503 0 -1.2034522 5.1417376
|
||||
2200 1.0162371 -2.1732231 0 -1.1581152 5.1108471
|
||||
Loop time of 0.0448599 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2200 1.0162371 -2.1732231 0 -1.1581152 5.1108471
|
||||
2300 1.0245646 -2.1552369 0 -1.1318107 5.3316927
|
||||
Loop time of 0.0446439 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2300 1.0245646 -2.1552369 0 -1.1318107 5.3316927
|
||||
2400 1.0532627 -2.168732 0 -1.1166396 5.2318175
|
||||
Loop time of 0.044234 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2400 1.0532627 -2.168732 0 -1.1166396 5.2318175
|
||||
2500 1.0110981 -2.1283041 0 -1.1183294 5.470307
|
||||
Loop time of 0.044275 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 1.0110981 -2.1283041 0 -1.1183294 5.470307
|
||||
2600 0.99966902 -2.1728149 0 -1.1742566 5.1412453
|
||||
Loop time of 0.044683 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2600 0.99966902 -2.1728149 0 -1.1742566 5.1412453
|
||||
2700 0.99239191 -2.1637551 0 -1.1724659 5.2165707
|
||||
Loop time of 0.0447261 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2700 0.99239191 -2.1637551 0 -1.1724659 5.2165707
|
||||
2800 1.0301978 -2.1548308 0 -1.1257777 5.2638595
|
||||
Loop time of 0.044596 on 1 procs for 100 steps with 900 atoms
|
||||
fix 2 all langevin 5 5 0.1 12346
|
||||
run 100 pre yes post no
|
||||
Memory usage per processor = 1.67412 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2800 1.0227564 -2.1548308 0 -1.1332108 5.2575845
|
||||
2900 5.0485455 -0.28277455 0 4.7601615 20.746781
|
||||
Loop time of 0.0470662 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2900 5.0485455 -0.28277455 0 4.7601615 20.746781
|
||||
3000 4.8862233 -0.017789501 0 4.8630047 22.592756
|
||||
Loop time of 0.048033 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3000 4.8862233 -0.017789501 0 4.8630047 22.592756
|
||||
3100 4.9044567 -0.47959211 0 4.4194152 19.583353
|
||||
Loop time of 0.0480561 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3100 4.9044567 -0.47959211 0 4.4194152 19.583353
|
||||
3200 5.0879915 -0.14346616 0 4.938872 21.75943
|
||||
Loop time of 0.047853 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3200 5.0879915 -0.14346616 0 4.938872 21.75943
|
||||
3300 4.8191113 -0.12521782 0 4.688539 21.66605
|
||||
Loop time of 0.0484211 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3300 4.8191113 -0.12521782 0 4.688539 21.66605
|
||||
3400 5.1800461 -0.14238575 0 5.0319048 21.79606
|
||||
Loop time of 0.0481231 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3400 5.1800461 -0.14238575 0 5.0319048 21.79606
|
||||
3500 5.0607641 -0.16081652 0 4.8943245 21.486658
|
||||
Loop time of 0.0485091 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3500 5.0607641 -0.16081652 0 4.8943245 21.486658
|
||||
3600 5.3373422 -0.41828575 0 4.9131261 20.14676
|
||||
Loop time of 0.0482152 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3600 5.3373422 -0.41828575 0 4.9131261 20.14676
|
||||
3700 5.3202661 -0.30023033 0 5.0141243 20.855754
|
||||
Loop time of 0.0481288 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3700 5.3202661 -0.30023033 0 5.0141243 20.855754
|
||||
3800 4.8588585 -0.10399834 0 4.7494614 21.771522
|
||||
Loop time of 0.0481648 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3800 4.8588585 -0.10399834 0 4.7494614 21.771522
|
||||
3900 4.9193657 0.060661037 0 4.9745608 22.688265
|
||||
Loop time of 0.0485899 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
3900 4.9193657 0.060661037 0 4.9745608 22.688265
|
||||
4000 4.9689317 -0.135649 0 4.8277616 21.630946
|
||||
Loop time of 0.0486522 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4000 4.9689317 -0.135649 0 4.8277616 21.630946
|
||||
4100 5.0796995 -0.42489129 0 4.6491641 19.912881
|
||||
Loop time of 0.047446 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4100 5.0796995 -0.42489129 0 4.6491641 19.912881
|
||||
4200 4.9121803 -0.26921478 0 4.6375075 20.682997
|
||||
Loop time of 0.047961 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4200 4.9121803 -0.26921478 0 4.6375075 20.682997
|
||||
4300 5.2480878 -0.25203366 0 4.9902229 21.055825
|
||||
Loop time of 0.048105 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4300 5.2480878 -0.25203366 0 4.9902229 21.055825
|
||||
4400 5.1754321 -0.1379211 0 5.0317606 21.721423
|
||||
Loop time of 0.0476389 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4400 5.1754321 -0.1379211 0 5.0317606 21.721423
|
||||
4500 4.8163772 -0.13665697 0 4.6743687 21.338168
|
||||
Loop time of 0.048456 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4500 4.8163772 -0.13665697 0 4.6743687 21.338168
|
||||
4600 5.1321419 -0.30134093 0 4.8250986 20.640859
|
||||
Loop time of 0.048126 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4600 5.1321419 -0.30134093 0 4.8250986 20.640859
|
||||
4700 5.054895 -0.11869342 0 4.930585 21.525844
|
||||
Loop time of 0.0480442 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4700 5.054895 -0.11869342 0 4.930585 21.525844
|
||||
4800 4.7735419 -0.28788546 0 4.4803525 20.241875
|
||||
Loop time of 0.048465 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4800 4.7735419 -0.28788546 0 4.4803525 20.241875
|
||||
4900 5.1590733 -0.36928517 0 4.7840559 19.906086
|
||||
Loop time of 0.0482421 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
4900 5.1590733 -0.36928517 0 4.7840559 19.906086
|
||||
5000 5.172434 -0.21783749 0 4.9488493 21.017977
|
||||
Loop time of 0.0482352 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5000 5.172434 -0.21783749 0 4.9488493 21.017977
|
||||
5100 5.3222066 -0.28431917 0 5.0319738 20.654341
|
||||
Loop time of 0.0479338 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5100 5.3222066 -0.28431917 0 5.0319738 20.654341
|
||||
5200 5.2269814 -0.24120657 0 4.9799671 20.863157
|
||||
Loop time of 0.0479622 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5200 5.2269814 -0.24120657 0 4.9799671 20.863157
|
||||
5300 4.9617285 -0.25596507 0 4.7002504 20.508874
|
||||
Loop time of 0.047616 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5300 4.9617285 -0.25596507 0 4.7002504 20.508874
|
||||
5400 5.1034361 -0.23375901 0 4.8640066 20.874041
|
||||
Loop time of 0.048399 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5400 5.1034361 -0.23375901 0 4.8640066 20.874041
|
||||
5500 5.1033392 -0.023852659 0 5.0738162 21.959054
|
||||
Loop time of 0.0481031 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5500 5.1033392 -0.023852659 0 5.0738162 21.959054
|
||||
5600 4.9693008 -0.3822577 0 4.5815217 19.745578
|
||||
Loop time of 0.0481269 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5600 4.9693008 -0.3822577 0 4.5815217 19.745578
|
||||
5700 4.9504059 -0.16971504 0 4.7751904 20.984851
|
||||
Loop time of 0.047688 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5700 4.9504059 -0.16971504 0 4.7751904 20.984851
|
||||
5800 5.4859652 -0.12581898 0 5.3540507 21.643131
|
||||
Loop time of 0.0482688 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5800 5.4859652 -0.12581898 0 5.3540507 21.643131
|
||||
5900 5.1041625 -0.24499773 0 4.8534935 20.550919
|
||||
Loop time of 0.0485001 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
5900 5.1041625 -0.24499773 0 4.8534935 20.550919
|
||||
6000 4.7912324 -0.23215106 0 4.5537577 20.385388
|
||||
Loop time of 0.0481 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6000 4.7912324 -0.23215106 0 4.5537577 20.385388
|
||||
6100 4.8687128 -0.36715522 0 4.4961479 19.616564
|
||||
Loop time of 0.047904 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6100 4.8687128 -0.36715522 0 4.4961479 19.616564
|
||||
6200 5.1633792 -0.42749917 0 4.7301429 19.411301
|
||||
Loop time of 0.0479479 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6200 5.1633792 -0.42749917 0 4.7301429 19.411301
|
||||
6300 5.0233319 0.019274316 0 5.0370247 22.144843
|
||||
Loop time of 0.048382 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6300 5.0233319 0.019274316 0 5.0370247 22.144843
|
||||
6400 4.9283818 -0.080911928 0 4.8419939 21.398618
|
||||
Loop time of 0.048492 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6400 4.9283818 -0.080911928 0 4.8419939 21.398618
|
||||
6500 5.0852451 -0.29922243 0 4.7803724 20.191962
|
||||
Loop time of 0.0481842 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6500 5.0852451 -0.29922243 0 4.7803724 20.191962
|
||||
6600 4.9084541 -0.25046783 0 4.6525324 20.294621
|
||||
Loop time of 0.048028 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6600 4.9084541 -0.25046783 0 4.6525324 20.294621
|
||||
6700 5.158646 -0.24156185 0 4.9113523 20.674148
|
||||
Loop time of 0.048152 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6700 5.158646 -0.24156185 0 4.9113523 20.674148
|
||||
6800 5.0800581 -0.26396878 0 4.8104448 20.254552
|
||||
Loop time of 0.0481989 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6800 5.0800581 -0.26396878 0 4.8104448 20.254552
|
||||
6900 5.0775502 -0.39390401 0 4.6780045 19.376358
|
||||
Loop time of 0.0482252 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
6900 5.0775502 -0.39390401 0 4.6780045 19.376358
|
||||
7000 4.9478484 -0.14828675 0 4.7940641 20.564728
|
||||
Loop time of 0.0481858 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7000 4.9478484 -0.14828675 0 4.7940641 20.564728
|
||||
7100 5.1059459 -0.097059214 0 5.0032134 21.193873
|
||||
Loop time of 0.0478609 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7100 5.1059459 -0.097059214 0 5.0032134 21.193873
|
||||
7200 5.1752568 -0.37658971 0 4.7929168 19.495134
|
||||
Loop time of 0.04796 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7200 5.1752568 -0.37658971 0 4.7929168 19.495134
|
||||
7300 5.0979223 -0.059859304 0 5.0323987 21.118636
|
||||
Loop time of 0.0480049 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7300 5.0979223 -0.059859304 0 5.0323987 21.118636
|
||||
7400 4.980172 -0.27439819 0 4.7002403 19.959942
|
||||
Loop time of 0.047915 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7400 4.980172 -0.27439819 0 4.7002403 19.959942
|
||||
7500 5.0625014 -0.1884279 0 4.8684485 20.652757
|
||||
Loop time of 0.0479548 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7500 5.0625014 -0.1884279 0 4.8684485 20.652757
|
||||
7600 4.950022 -0.38785668 0 4.5566653 19.255054
|
||||
Loop time of 0.047981 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7600 4.950022 -0.38785668 0 4.5566653 19.255054
|
||||
7700 5.038467 0.010501622 0 5.0433703 21.612637
|
||||
Loop time of 0.0483868 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7700 5.038467 0.010501622 0 5.0433703 21.612637
|
||||
7800 5.0722091 -0.23929391 0 4.8272794 20.163109
|
||||
Loop time of 0.0484369 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7800 5.0722091 -0.23929391 0 4.8272794 20.163109
|
||||
7900 4.8266996 -0.26738065 0 4.5539559 19.950113
|
||||
Loop time of 0.0484252 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
7900 4.8266996 -0.26738065 0 4.5539559 19.950113
|
||||
8000 5.228568 -0.22189741 0 5.0008611 20.340648
|
||||
Loop time of 0.0480399 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8000 5.228568 -0.22189741 0 5.0008611 20.340648
|
||||
8100 5.0226139 -0.32338281 0 4.6936504 19.597461
|
||||
Loop time of 0.0477419 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8100 5.0226139 -0.32338281 0 4.6936504 19.597461
|
||||
8200 4.9067102 -0.1492661 0 4.7519922 20.325845
|
||||
Loop time of 0.0479119 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8200 4.9067102 -0.1492661 0 4.7519922 20.325845
|
||||
8300 5.1266856 -0.22929386 0 4.8916954 20.201339
|
||||
Loop time of 0.0479472 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8300 5.1266856 -0.22929386 0 4.8916954 20.201339
|
||||
8400 5.0589881 -0.45921427 0 4.5941528 18.70978
|
||||
Loop time of 0.048357 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8400 5.0589881 -0.45921427 0 4.5941528 18.70978
|
||||
8500 4.8413482 -0.19493887 0 4.64103 19.954031
|
||||
Loop time of 0.0475209 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8500 4.8413482 -0.19493887 0 4.64103 19.954031
|
||||
8600 5.0908293 -0.54321499 0 4.5419579 18.109321
|
||||
Loop time of 0.0483789 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8600 5.0908293 -0.54321499 0 4.5419579 18.109321
|
||||
8700 5.1796752 -0.2916707 0 4.8822493 19.664654
|
||||
Loop time of 0.048032 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8700 5.1796752 -0.2916707 0 4.8822493 19.664654
|
||||
8800 5.2539084 -0.45997392 0 4.7880968 18.655485
|
||||
Loop time of 0.0482469 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8800 5.2539084 -0.45997392 0 4.7880968 18.655485
|
||||
8900 5.1024558 -0.23247495 0 4.8643114 19.86178
|
||||
Loop time of 0.0481958 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
8900 5.1024558 -0.23247495 0 4.8643114 19.86178
|
||||
9000 5.1823165 -0.39916589 0 4.7773924 18.971835
|
||||
Loop time of 0.0481231 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9000 5.1823165 -0.39916589 0 4.7773924 18.971835
|
||||
9100 4.8447578 -0.36539964 0 4.4739751 18.749222
|
||||
Loop time of 0.0482869 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9100 4.8447578 -0.36539964 0 4.4739751 18.749222
|
||||
9200 4.7762145 -0.41137254 0 4.3595351 18.283329
|
||||
Loop time of 0.0483339 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9200 4.7762145 -0.41137254 0 4.3595351 18.283329
|
||||
9300 5.0833877 -0.32352098 0 4.7542185 19.215267
|
||||
Loop time of 0.0479991 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9300 5.0833877 -0.32352098 0 4.7542185 19.215267
|
||||
9400 5.0177659 -0.28646064 0 4.72573 19.284236
|
||||
Loop time of 0.048521 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9400 5.0177659 -0.28646064 0 4.72573 19.284236
|
||||
9500 5.094124 -0.2545962 0 4.8338677 19.49513
|
||||
Loop time of 0.0480311 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9500 5.094124 -0.2545962 0 4.8338677 19.49513
|
||||
9600 5.0240503 -0.35703989 0 4.6614281 18.851793
|
||||
Loop time of 0.048084 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9600 5.0240503 -0.35703989 0 4.6614281 18.851793
|
||||
9700 4.7489492 -0.25367959 0 4.489993 19.113672
|
||||
Loop time of 0.047981 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9700 4.7489492 -0.25367959 0 4.489993 19.113672
|
||||
9800 4.9909149 -0.34688365 0 4.6384858 18.781061
|
||||
Loop time of 0.0480509 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9800 4.9909149 -0.34688365 0 4.6384858 18.781061
|
||||
9900 5.2358495 -0.20088636 0 5.0291455 19.968679
|
||||
Loop time of 0.0480289 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
9900 5.2358495 -0.20088636 0 5.0291455 19.968679
|
||||
10000 5.0336433 -0.30070619 0 4.7273442 19.288936
|
||||
Loop time of 0.0481491 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10000 5.0336433 -0.30070619 0 4.7273442 19.288936
|
||||
10100 4.7368529 -0.43300505 0 4.2985846 18.223831
|
||||
Loop time of 0.047874 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10100 4.7368529 -0.43300505 0 4.2985846 18.223831
|
||||
10200 5.1921737 -0.39013066 0 4.796274 18.671159
|
||||
Loop time of 0.0475681 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10200 5.1921737 -0.39013066 0 4.796274 18.671159
|
||||
10300 4.8489929 -0.26376235 0 4.5798428 19.1258
|
||||
Loop time of 0.04794 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10300 4.8489929 -0.26376235 0 4.5798428 19.1258
|
||||
10400 4.8344238 -0.39563076 0 4.4334214 18.406798
|
||||
Loop time of 0.0483451 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10400 4.8344238 -0.39563076 0 4.4334214 18.406798
|
||||
10500 4.7947329 -0.30412973 0 4.4852757 18.895224
|
||||
Loop time of 0.047621 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10500 4.7947329 -0.30412973 0 4.4852757 18.895224
|
||||
10600 5.1411793 -0.14227144 0 4.9931954 19.939056
|
||||
Loop time of 0.048378 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10600 5.1411793 -0.14227144 0 4.9931954 19.939056
|
||||
10700 4.6126242 -0.35662101 0 4.250878 18.178539
|
||||
Loop time of 0.0480251 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10700 4.6126242 -0.35662101 0 4.250878 18.178539
|
||||
10800 5.218192 -0.26093796 0 4.9514561 19.419601
|
||||
Loop time of 0.0479641 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10800 5.218192 -0.26093796 0 4.9514561 19.419601
|
||||
10900 4.9434504 -0.45628696 0 4.4816707 18.016015
|
||||
Loop time of 0.048048 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10900 4.9434504 -0.45628696 0 4.4816707 18.016015
|
||||
11000 5.2502606 -0.29191121 0 4.9525157 19.228121
|
||||
Loop time of 0.0480599 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11000 5.2502606 -0.29191121 0 4.9525157 19.228121
|
||||
11100 4.7598343 -0.37412706 0 4.3804185 18.317182
|
||||
Loop time of 0.048358 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11100 4.7598343 -0.37412706 0 4.3804185 18.317182
|
||||
11200 5.323248 -0.21800357 0 5.0993297 19.810405
|
||||
Loop time of 0.04793 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11200 5.323248 -0.21800357 0 5.0993297 19.810405
|
||||
11300 4.7219543 -0.50822681 0 4.2084808 17.364301
|
||||
Loop time of 0.0486059 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11300 4.7219543 -0.50822681 0 4.2084808 17.364301
|
||||
11400 5.2261295 -0.41060675 0 4.8097159 18.184162
|
||||
Loop time of 0.0475581 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11400 5.2261295 -0.41060675 0 4.8097159 18.184162
|
||||
11500 5.4192661 -0.41967268 0 4.993572 18.44905
|
||||
Loop time of 0.048496 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11500 5.4192661 -0.41967268 0 4.993572 18.44905
|
||||
11600 4.9327793 -0.29827109 0 4.6290273 18.678345
|
||||
Loop time of 0.0480838 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11600 4.9327793 -0.29827109 0 4.6290273 18.678345
|
||||
11700 4.9061719 -0.40278149 0 4.4979391 18.015662
|
||||
Loop time of 0.0484679 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11700 4.9061719 -0.40278149 0 4.4979391 18.015662
|
||||
11800 5.1217904 -0.38967412 0 4.7264254 18.297707
|
||||
Loop time of 0.047833 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11800 5.1217904 -0.38967412 0 4.7264254 18.297707
|
||||
11900 4.898336 -0.52304599 0 4.3698475 17.482045
|
||||
Loop time of 0.0480511 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
11900 4.898336 -0.52304599 0 4.3698475 17.482045
|
||||
12000 5.0463402 -0.34458395 0 4.6961492 18.259663
|
||||
Loop time of 0.048959 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12000 5.0463402 -0.34458395 0 4.6961492 18.259663
|
||||
12100 5.2244507 -0.48448431 0 4.7341614 17.921372
|
||||
Loop time of 0.0479109 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12100 5.2244507 -0.48448431 0 4.7341614 17.921372
|
||||
12200 4.9182331 -0.38972269 0 4.5230457 18.065869
|
||||
Loop time of 0.047838 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12200 4.9182331 -0.38972269 0 4.5230457 18.065869
|
||||
12300 5.1236535 -0.50804995 0 4.6099106 17.491542
|
||||
Loop time of 0.0480042 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12300 5.1236535 -0.50804995 0 4.6099106 17.491542
|
||||
12400 4.9892711 -0.35640526 0 4.6273222 18.09428
|
||||
Loop time of 0.04794 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12400 4.9892711 -0.35640526 0 4.6273222 18.09428
|
||||
12500 4.9708898 -0.47291494 0 4.4924516 17.463457
|
||||
Loop time of 0.0483761 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12500 4.9708898 -0.47291494 0 4.4924516 17.463457
|
||||
12600 4.9060868 -0.42653866 0 4.4740969 17.831651
|
||||
Loop time of 0.047663 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12600 4.9060868 -0.42653866 0 4.4740969 17.831651
|
||||
12700 5.0407771 -0.44712314 0 4.5880531 17.595615
|
||||
Loop time of 0.0484769 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12700 5.0407771 -0.44712314 0 4.5880531 17.595615
|
||||
12800 5.0365185 -0.55979777 0 4.4711246 16.934523
|
||||
Loop time of 0.048032 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12800 5.0365185 -0.55979777 0 4.4711246 16.934523
|
||||
12900 5.2486399 -0.34366283 0 4.8991453 18.510825
|
||||
Loop time of 0.0479882 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
12900 5.2486399 -0.34366283 0 4.8991453 18.510825
|
||||
13000 5.1541271 -0.40831419 0 4.7400861 17.984905
|
||||
Loop time of 0.0485048 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13000 5.1541271 -0.40831419 0 4.7400861 17.984905
|
||||
13100 4.9252416 -0.37543615 0 4.544333 18.047342
|
||||
Loop time of 0.0478559 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13100 4.9252416 -0.37543615 0 4.544333 18.047342
|
||||
13200 4.7618949 -0.57797993 0 4.178624 16.678145
|
||||
Loop time of 0.047977 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13200 4.7618949 -0.57797993 0 4.178624 16.678145
|
||||
13300 5.0754762 -0.494503 0 4.5753338 17.274009
|
||||
Loop time of 0.04761 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13300 5.0754762 -0.494503 0 4.5753338 17.274009
|
||||
13400 4.7373562 -0.26050743 0 4.471585 18.244677
|
||||
Loop time of 0.048439 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13400 4.7373562 -0.26050743 0 4.471585 18.244677
|
||||
13500 5.2850198 -0.52753121 0 4.7516163 17.30467
|
||||
Loop time of 0.0479879 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13500 5.2850198 -0.52753121 0 4.7516163 17.30467
|
||||
13600 4.962689 -0.43162132 0 4.5255536 17.440072
|
||||
Loop time of 0.048393 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13600 4.962689 -0.43162132 0 4.5255536 17.440072
|
||||
13700 5.0155844 -0.51839355 0 4.491618 16.999978
|
||||
Loop time of 0.048249 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13700 5.0155844 -0.51839355 0 4.491618 16.999978
|
||||
13800 5.1030716 -0.54350825 0 4.5538933 17.135096
|
||||
Loop time of 0.047961 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13800 5.1030716 -0.54350825 0 4.5538933 17.135096
|
||||
13900 4.9484073 -0.32896034 0 4.6139487 17.994498
|
||||
Loop time of 0.0479271 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
13900 4.9484073 -0.32896034 0 4.6139487 17.994498
|
||||
14000 5.1556711 -0.39450883 0 4.7554337 18.024111
|
||||
Loop time of 0.0485859 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14000 5.1556711 -0.39450883 0 4.7554337 18.024111
|
||||
14100 5.3411027 -0.33237876 0 5.0027894 18.189551
|
||||
Loop time of 0.047961 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14100 5.3411027 -0.33237876 0 5.0027894 18.189551
|
||||
14200 5.2775385 -0.20079896 0 5.0708756 18.794478
|
||||
Loop time of 0.0479829 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14200 5.2775385 -0.20079896 0 5.0708756 18.794478
|
||||
14300 4.9698674 -0.54120662 0 4.4231387 16.769686
|
||||
Loop time of 0.048353 on 1 procs for 100 steps with 900 atoms
|
||||
fix 2 all langevin 3 3 0.1 12347
|
||||
run 100 pre yes post no
|
||||
Memory usage per processor = 1.67412 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14300 4.9315283 -0.54120662 0 4.3848423 16.737356
|
||||
14400 3.0737982 -1.157576 0 1.9128069 11.390762
|
||||
Loop time of 0.0469351 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14400 3.0737982 -1.157576 0 1.9128069 11.390762
|
||||
14500 3.0997503 -1.1613569 0 1.9349492 11.746787
|
||||
Loop time of 0.046298 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14500 3.0997503 -1.1613569 0 1.9349492 11.746787
|
||||
14600 3.0089981 -1.2950599 0 1.7105948 10.694304
|
||||
Loop time of 0.0462 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14600 3.0089981 -1.2950599 0 1.7105948 10.694304
|
||||
14700 3.0731576 -1.1944523 0 1.8752907 11.177629
|
||||
Loop time of 0.0471361 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14700 3.0731576 -1.1944523 0 1.8752907 11.177629
|
||||
14800 3.0790691 -1.2454277 0 1.8302202 11.050986
|
||||
Loop time of 0.0467501 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14800 3.0790691 -1.2454277 0 1.8302202 11.050986
|
||||
14900 2.9875216 -1.2120329 0 1.7721692 11.196195
|
||||
Loop time of 0.046731 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
14900 2.9875216 -1.2120329 0 1.7721692 11.196195
|
||||
15000 3.0023895 -1.1473321 0 1.8517215 11.450509
|
||||
Loop time of 0.046834 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15000 3.0023895 -1.1473321 0 1.8517215 11.450509
|
||||
15100 3.1095672 -1.186375 0 1.9197372 11.392239
|
||||
Loop time of 0.046701 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15100 3.1095672 -1.186375 0 1.9197372 11.392239
|
||||
15200 3.0788594 -1.1581741 0 1.9172643 11.434699
|
||||
Loop time of 0.0466931 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15200 3.0788594 -1.1581741 0 1.9172643 11.434699
|
||||
15300 3.097962 -1.2142726 0 1.8802473 11.060786
|
||||
Loop time of 0.0467482 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15300 3.097962 -1.2142726 0 1.8802473 11.060786
|
||||
15400 3.0085051 -1.2068705 0 1.7982919 11.125663
|
||||
Loop time of 0.046351 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15400 3.0085051 -1.2068705 0 1.7982919 11.125663
|
||||
15500 2.91789 -1.2471287 0 1.6675192 10.908068
|
||||
Loop time of 0.0467601 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15500 2.91789 -1.2471287 0 1.6675192 10.908068
|
||||
15600 3.1592422 -1.320622 0 1.83511 10.315596
|
||||
Loop time of 0.0463359 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15600 3.1592422 -1.320622 0 1.83511 10.315596
|
||||
15700 3.1361836 -1.16244 0 1.9702589 11.474858
|
||||
Loop time of 0.0472879 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15700 3.1361836 -1.16244 0 1.9702589 11.474858
|
||||
15800 3.0412387 -1.2445264 0 1.7933331 10.828289
|
||||
Loop time of 0.0468159 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15800 3.0412387 -1.2445264 0 1.7933331 10.828289
|
||||
15900 3.1318652 -1.1349315 0 1.9934539 11.506448
|
||||
Loop time of 0.04685 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
15900 3.1318652 -1.1349315 0 1.9934539 11.506448
|
||||
16000 3.1012109 -1.2285496 0 1.8692155 11.001584
|
||||
Loop time of 0.0467439 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16000 3.1012109 -1.2285496 0 1.8692155 11.001584
|
||||
16100 3.0508387 -1.2590515 0 1.7883974 10.774791
|
||||
Loop time of 0.046726 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16100 3.0508387 -1.2590515 0 1.7883974 10.774791
|
||||
16200 3.1900114 -1.3779639 0 1.8085031 10.051609
|
||||
Loop time of 0.047003 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16200 3.1900114 -1.3779639 0 1.8085031 10.051609
|
||||
16300 2.9418317 -1.2584583 0 1.6801047 10.537777
|
||||
Loop time of 0.0466199 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16300 2.9418317 -1.2584583 0 1.6801047 10.537777
|
||||
16400 2.9386319 -1.2427586 0 1.6926082 10.643756
|
||||
Loop time of 0.0467391 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16400 2.9386319 -1.2427586 0 1.6926082 10.643756
|
||||
16500 2.9129152 -1.0821846 0 1.8274941 11.598824
|
||||
Loop time of 0.046731 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16500 2.9129152 -1.0821846 0 1.8274941 11.598824
|
||||
16600 3.09857 -1.1510317 0 1.9440954 11.235013
|
||||
Loop time of 0.046741 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16600 3.09857 -1.1510317 0 1.9440954 11.235013
|
||||
16700 2.8592356 -1.2474647 0 1.6085939 10.595499
|
||||
Loop time of 0.046757 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16700 2.8592356 -1.2474647 0 1.6085939 10.595499
|
||||
16800 2.930352 -1.2310556 0 1.6960404 10.789207
|
||||
Loop time of 0.04637 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16800 2.930352 -1.2310556 0 1.6960404 10.789207
|
||||
16900 2.9631052 -1.2091634 0 1.7506495 10.861427
|
||||
Loop time of 0.046385 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
16900 2.9631052 -1.2091634 0 1.7506495 10.861427
|
||||
17000 2.9507403 -1.0775066 0 1.8699552 11.496194
|
||||
Loop time of 0.0468409 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
17000 2.9507403 -1.0775066 0 1.8699552 11.496194
|
||||
17100 3.1429056 -1.1518542 0 1.9875593 11.382163
|
||||
Loop time of 0.0466008 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
17100 3.1429056 -1.1518542 0 1.9875593 11.382163
|
||||
17200 3.0175223 -1.2168934 0 1.7972761 10.888517
|
||||
Loop time of 0.0468168 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
17200 3.0175223 -1.2168934 0 1.7972761 10.888517
|
||||
17300 3.0849889 -1.2641589 0 1.8174022 10.561238
|
||||
Loop time of 0.0463462 on 1 procs for 100 steps with 900 atoms
|
||||
run 100 pre no post no
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
17300 3.0849889 -1.2641589 0 1.8174022 10.561238
|
||||
17400 2.9622086 -1.2777097 0 1.6812076 10.441674
|
||||
Loop time of 0.0466161 on 1 procs for 100 steps with 900 atoms
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,383 @@
|
|||
# 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.
|
||||
|
||||
# gnu tool
|
||||
|
||||
oneline = "Create plots via GnuPlot plotting program"
|
||||
|
||||
docstr = """
|
||||
g = gnu() start up GnuPlot
|
||||
g.stop() shut down GnuPlot process
|
||||
|
||||
g.plot(a) plot vector A against linear index
|
||||
g.plot(a,b) plot B against A
|
||||
g.plot(a,b,c,d,...) plot B against A, D against C, etc
|
||||
g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
|
||||
|
||||
each plot argument can be a tuple, list, or Numeric/NumPy vector
|
||||
mplot loops over range(M,N,S) and create one plot per iteration
|
||||
last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
|
||||
each plot is made from a portion of the vectors, depending on loop index i
|
||||
Ith plot is of b[0:i] vs a[0:i], etc
|
||||
series of plots saved as file0000.eps, file0001.eps, etc
|
||||
if use xrange(),yrange() then plot axes will be same for all plots
|
||||
|
||||
g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
|
||||
|
||||
g.enter() enter GnuPlot shell
|
||||
gnuplot> plot sin(x) with lines type commands directly to GnuPlot
|
||||
gnuplot> exit, quit exit GnuPlot shell
|
||||
|
||||
g.export("data",range(100),a,...) create file with columns of numbers
|
||||
|
||||
all vectors must be of equal length
|
||||
could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
|
||||
|
||||
g.select(N) figure N becomes the current plot
|
||||
|
||||
subsequent commands apply to this plot
|
||||
|
||||
g.hide(N) delete window for figure N
|
||||
g.save("file") save current plot as file.eps
|
||||
|
||||
Set attributes for current plot:
|
||||
|
||||
g.erase() reset all attributes to default values
|
||||
g.aspect(1.3) aspect ratio
|
||||
g.xtitle("Time") x axis text
|
||||
g.ytitle("Energy") y axis text
|
||||
g.title("My Plot") title text
|
||||
g.title("title","x","y") title, x axis, y axis text
|
||||
g.xrange(xmin,xmax) x axis range
|
||||
g.xrange() default x axis range
|
||||
g.yrange(ymin,ymax) y axis range
|
||||
g.yrange() default y axis range
|
||||
g.xlog() toggle x axis between linear and log
|
||||
g.ylog() toggle y axis between linear and log
|
||||
g.label(x,y,"text") place label at x,y coords
|
||||
g.curve(N,'r') set color of curve N
|
||||
|
||||
colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue
|
||||
'm' = magenta, 'c' = cyan, 'y' = yellow
|
||||
"""
|
||||
|
||||
# History
|
||||
# 8/05, Matt Jones (BYU): original version
|
||||
# 9/05, Steve Plimpton: added mplot() method
|
||||
|
||||
# ToDo list
|
||||
# allow choice of JPG or PNG or GIF when saving ?
|
||||
# can this be done from GnuPlot or have to do via ImageMagick convert ?
|
||||
# way to trim EPS plot that is created ?
|
||||
# hide does not work on Mac aqua
|
||||
# select does not pop window to front on Mac aqua
|
||||
|
||||
# Variables
|
||||
# current = index of current figure (1-N)
|
||||
# figures = list of figure objects with each plot's attributes
|
||||
# so they aren't lost between replots
|
||||
|
||||
# Imports and external programs
|
||||
|
||||
import types, os
|
||||
|
||||
try: from DEFAULTS import PIZZA_GNUPLOT
|
||||
except: PIZZA_GNUPLOT = "gnuplot"
|
||||
try: from DEFAULTS import PIZZA_GNUTERM
|
||||
except: PIZZA_GNUTERM = "x11"
|
||||
|
||||
# Class definition
|
||||
|
||||
class gnu:
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __init__(self):
|
||||
self.GNUPLOT = os.popen(PIZZA_GNUPLOT,'w')
|
||||
self.file = "tmp.gnu"
|
||||
self.figures = []
|
||||
self.select(1)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def stop(self):
|
||||
self.__call__("quit")
|
||||
del self.GNUPLOT
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __call__(self,command):
|
||||
self.GNUPLOT.write(command + '\n')
|
||||
self.GNUPLOT.flush()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def enter(self):
|
||||
while 1:
|
||||
command = raw_input("gnuplot> ")
|
||||
if command == "quit" or command == "exit": return
|
||||
self.__call__(command)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write plot vectors to files and plot them
|
||||
|
||||
def plot(self,*vectors):
|
||||
if len(vectors) == 1:
|
||||
file = self.file + ".%d.1" % self.current
|
||||
linear = range(len(vectors[0]))
|
||||
self.export(file,linear,vectors[0])
|
||||
self.figures[self.current-1].ncurves = 1
|
||||
else:
|
||||
if len(vectors) % 2: raise StandardError,"vectors must come in pairs"
|
||||
for i in range(0,len(vectors),2):
|
||||
file = self.file + ".%d.%d" % (self.current,i/2+1)
|
||||
self.export(file,vectors[i],vectors[i+1])
|
||||
self.figures[self.current-1].ncurves = len(vectors)/2
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# create multiple plots from growing vectors, save to numbered files
|
||||
# don't plot empty vector, create a [0] instead
|
||||
|
||||
def mplot(self,start,stop,skip,file,*vectors):
|
||||
n = 0
|
||||
for i in range(start,stop,skip):
|
||||
partial_vecs = []
|
||||
for vec in vectors:
|
||||
if i: partial_vecs.append(vec[:i])
|
||||
else: partial_vecs.append([0])
|
||||
self.plot(*partial_vecs)
|
||||
|
||||
if n < 10: newfile = file + "000" + str(n)
|
||||
elif n < 100: newfile = file + "00" + str(n)
|
||||
elif n < 1000: newfile = file + "0" + str(n)
|
||||
else: newfile = file + str(n)
|
||||
|
||||
self.save(newfile)
|
||||
n += 1
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write list of equal-length vectors to filename
|
||||
|
||||
def export(self,filename,*vectors):
|
||||
n = len(vectors[0])
|
||||
for vector in vectors:
|
||||
if len(vector) != n: raise StandardError,"vectors must be same length"
|
||||
f = open(filename,'w')
|
||||
nvec = len(vectors)
|
||||
for i in xrange(n):
|
||||
for j in xrange(nvec):
|
||||
print >>f,vectors[j][i],
|
||||
print >>f
|
||||
f.close()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# select plot N as current plot
|
||||
|
||||
def select(self,n):
|
||||
self.current = n
|
||||
if len(self.figures) < n:
|
||||
for i in range(n - len(self.figures)):
|
||||
self.figures.append(figure())
|
||||
cmd = "set term " + PIZZA_GNUTERM + ' ' + str(n)
|
||||
self.__call__(cmd)
|
||||
if self.figures[n-1].ncurves: self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# delete window for plot N
|
||||
|
||||
def hide(self,n):
|
||||
cmd = "set term %s close %d" % (PIZZA_GNUTERM,n)
|
||||
self.__call__(cmd)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# save plot to file.eps
|
||||
# final re-select will reset terminal
|
||||
# do not continue until plot file is written out
|
||||
# else script could go forward and change data file
|
||||
# use tmp.done as semaphore to indicate plot is finished
|
||||
|
||||
def save(self,file):
|
||||
self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
|
||||
cmd = "set output '%s.eps'" % file
|
||||
self.__call__(cmd)
|
||||
if os.path.exists("tmp.done"): os.remove("tmp.done")
|
||||
self.draw()
|
||||
self.__call__("!touch tmp.done")
|
||||
while not os.path.exists("tmp.done"): continue
|
||||
self.__call__("set output")
|
||||
self.select(self.current)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# restore default attributes by creating a new fig object
|
||||
|
||||
def erase(self):
|
||||
fig = figure()
|
||||
fig.ncurves = self.figures[self.current-1].ncurves
|
||||
self.figures[self.current-1] = fig
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def aspect(self,value):
|
||||
self.figures[self.current-1].aspect = value
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xrange(self,*values):
|
||||
if len(values) == 0:
|
||||
self.figures[self.current-1].xlimit = 0
|
||||
else:
|
||||
self.figures[self.current-1].xlimit = (values[0],values[1])
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def yrange(self,*values):
|
||||
if len(values) == 0:
|
||||
self.figures[self.current-1].ylimit = 0
|
||||
else:
|
||||
self.figures[self.current-1].ylimit = (values[0],values[1])
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def label(self,x,y,text):
|
||||
self.figures[self.current-1].labels.append((x,y,text))
|
||||
self.figures[self.current-1].nlabels += 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def nolabels(self):
|
||||
self.figures[self.current-1].nlabel = 0
|
||||
self.figures[self.current-1].labels = []
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def title(self,*strings):
|
||||
if len(strings) == 1:
|
||||
self.figures[self.current-1].title = strings[0]
|
||||
else:
|
||||
self.figures[self.current-1].title = strings[0]
|
||||
self.figures[self.current-1].xtitle = strings[1]
|
||||
self.figures[self.current-1].ytitle = strings[2]
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xtitle(self,label):
|
||||
self.figures[self.current-1].xtitle = label
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def ytitle(self,label):
|
||||
self.figures[self.current-1].ytitle = label
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xlog(self):
|
||||
if self.figures[self.current-1].xlog:
|
||||
self.figures[self.current-1].xlog = 0
|
||||
else:
|
||||
self.figures[self.current-1].xlog = 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def ylog(self):
|
||||
if self.figures[self.current-1].ylog:
|
||||
self.figures[self.current-1].ylog = 0
|
||||
else:
|
||||
self.figures[self.current-1].ylog = 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def curve(self,num,color):
|
||||
fig = self.figures[self.current-1]
|
||||
while len(fig.colors) < num: fig.colors.append(0)
|
||||
fig.colors[num-1] = colormap[color]
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# draw a plot with all its settings
|
||||
# just return if no files of vectors defined yet
|
||||
|
||||
def draw(self):
|
||||
fig = self.figures[self.current-1]
|
||||
if not fig.ncurves: return
|
||||
|
||||
cmd = 'set size ratio ' + str(1.0/float(fig.aspect))
|
||||
self.__call__(cmd)
|
||||
|
||||
cmd = 'set title ' + '"' + fig.title + '"'
|
||||
self.__call__(cmd)
|
||||
cmd = 'set xlabel ' + '"' + fig.xtitle + '"'
|
||||
self.__call__(cmd)
|
||||
cmd = 'set ylabel ' + '"' + fig.ytitle + '"'
|
||||
self.__call__(cmd)
|
||||
|
||||
if fig.xlog: self.__call__("set logscale x")
|
||||
else: self.__call__("unset logscale x")
|
||||
if fig.ylog: self.__call__("set logscale y")
|
||||
else: self.__call__("unset logscale y")
|
||||
if fig.xlimit:
|
||||
cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
|
||||
self.__call__(cmd)
|
||||
else: self.__call__("set xr [*:*]")
|
||||
if fig.ylimit:
|
||||
cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
|
||||
self.__call__(cmd)
|
||||
else: self.__call__("set yr [*:*]")
|
||||
|
||||
self.__call__("set nolabel")
|
||||
for i in range(fig.nlabels):
|
||||
x = fig.labels[i][0]
|
||||
y = fig.labels[i][1]
|
||||
text = fig.labels[i][2]
|
||||
cmd = 'set label ' + '\"' + text + '\" at ' + str(x) + ',' + str(y)
|
||||
self.__call__(cmd)
|
||||
|
||||
self.__call__("set key off")
|
||||
cmd = 'plot '
|
||||
for i in range(fig.ncurves):
|
||||
file = self.file + ".%d.%d" % (self.current,i+1)
|
||||
if len(fig.colors) > i and fig.colors[i]:
|
||||
cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]
|
||||
else:
|
||||
cmd += "'" + file + "' using 1:2 with lines, "
|
||||
self.__call__(cmd[:-2])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# class to store settings for a single plot
|
||||
|
||||
class figure:
|
||||
|
||||
def __init__(self):
|
||||
self.ncurves = 0
|
||||
self.colors = []
|
||||
self.title = ""
|
||||
self.xtitle = ""
|
||||
self.ytitle = ""
|
||||
self.aspect = 1.3
|
||||
self.xlimit = 0
|
||||
self.ylimit = 0
|
||||
self.xlog = 0
|
||||
self.ylog = 0
|
||||
self.nlabels = 0
|
||||
self.labels = []
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# line color settings
|
||||
|
||||
colormap = {'k':-1, 'r':1, 'g':2, 'b':3, 'm':4, 'c':5, 'y':7}
|
||||
|
|
@ -0,0 +1,391 @@
|
|||
# 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.
|
||||
|
||||
# vizinfo class, not a top-level Pizza.py tool
|
||||
|
||||
# History
|
||||
# 8/05, Matt Jones (BYU): original version
|
||||
# 9/05, Steve Plimpton: added 140-color table
|
||||
|
||||
# ToDo list
|
||||
|
||||
# Variables
|
||||
|
||||
# Imports and external programs
|
||||
|
||||
import types
|
||||
|
||||
# Class definition
|
||||
|
||||
class vizinfo:
|
||||
"""
|
||||
Information holder for Pizza.py visualization tools
|
||||
|
||||
acolor,bcolor,tcolor,lcolor = RGB values for each atom/bond/tri/line type
|
||||
arad = radius of each atom type
|
||||
brad,lrad = thickness of each bond/line type
|
||||
tfill = fill flag for each triangle type
|
||||
|
||||
all of these arrays are indexed by object type which runs 1-Ntype
|
||||
nacolor,nbcolor,ntcolor,nlcolor,narad,nbrad,nlrad,ntfill
|
||||
are # of types each array holds
|
||||
actual length is nacolor+1 so that array can be indexed by 1-Ntype
|
||||
|
||||
setcolors() = set atom/bond/tri/line colors
|
||||
setradii() = set atom/bond/line radii/thickness
|
||||
setfill() = set triangle fill factor
|
||||
extend() = grow an array
|
||||
"""
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __init__(self):
|
||||
self.acolor = []
|
||||
self.arad = []
|
||||
self.bcolor = []
|
||||
self.brad = []
|
||||
self.tcolor = []
|
||||
self.tfill = []
|
||||
self.lcolor = []
|
||||
self.lrad = []
|
||||
self.nacolor = self.narad = 0
|
||||
self.nbcolor = self.nbrad = 0
|
||||
self.ntcolor = self.ntfill = 0
|
||||
self.nlcolor = self.nlrad = 0
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# set color RGB for which = atoms, bonds, triangles
|
||||
|
||||
def setcolors(self,which,ids,rgbs):
|
||||
|
||||
# convert args into lists if single values
|
||||
# if arg = 0, convert to full-range list
|
||||
|
||||
if type(ids) is types.IntType and ids == 0:
|
||||
if which == "atom": ids = range(self.nacolor)
|
||||
if which == "bond": ids = range(self.nbcolor)
|
||||
if which == "tri": ids = range(self.ntcolor)
|
||||
if which == "line": ids = range(self.nlcolor)
|
||||
if type(ids) is not types.ListType and type(ids) is not types.TupleType:
|
||||
ids = [ids]
|
||||
if type(rgbs) is not types.ListType and type(rgbs) is not types.TupleType:
|
||||
rgbs = [rgbs]
|
||||
|
||||
# if list of types has a 0, increment each type value
|
||||
|
||||
if 0 in ids:
|
||||
for i in xrange(len(ids)): ids[i] += 1
|
||||
|
||||
# extend storage list if necessary
|
||||
# extend other arrays for same "which" so that gl::make_atom_calllist
|
||||
# has valid arrays to work with
|
||||
|
||||
if which == "atom":
|
||||
if max(ids) > self.nacolor:
|
||||
self.nacolor = self.extend(self.acolor,max(ids))
|
||||
self.nacolor = self.extend(self.arad,max(ids))
|
||||
if which == "bond":
|
||||
if max(ids) > self.nbcolor:
|
||||
self.nbcolor = self.extend(self.bcolor,max(ids))
|
||||
self.nbcolor = self.extend(self.brad,max(ids))
|
||||
if which == "tri":
|
||||
if max(ids) > self.ntcolor:
|
||||
self.ntcolor = self.extend(self.tcolor,max(ids))
|
||||
self.ntcolor = self.extend(self.tfill,max(ids))
|
||||
if which == "line":
|
||||
if max(ids) > self.nlcolor:
|
||||
self.nlcolor = self.extend(self.lcolor,max(ids))
|
||||
self.nlcolor = self.extend(self.lrad,max(ids))
|
||||
|
||||
# set color for each type
|
||||
# if list lengths match, set directly, else interpolate
|
||||
# convert final color from 0-255 to 0.0-1.0
|
||||
|
||||
ntypes = len(ids)
|
||||
nrgbs = len(rgbs)
|
||||
|
||||
for i in xrange(ntypes):
|
||||
id = ids[i]
|
||||
|
||||
if rgbs[0] == "loop":
|
||||
list = colors.keys()
|
||||
red,green,blue = colors[list[i % len(colors)]]
|
||||
elif ntypes == nrgbs:
|
||||
red,green,blue = colors[rgbs[i]]
|
||||
else:
|
||||
r = i/float(ntypes-1) * float(nrgbs-1)
|
||||
jlo = int(r)
|
||||
jhi = jlo + 1
|
||||
if jhi == nrgbs: jhi = nrgbs - 1
|
||||
clo = colors[rgbs[jlo]]
|
||||
chi = colors[rgbs[jhi]]
|
||||
delta = r - jlo
|
||||
red = clo[0] + delta*(chi[0]-clo[0])
|
||||
green = clo[1] + delta*(chi[1]-clo[1])
|
||||
blue = clo[2] + delta*(chi[2]-clo[2])
|
||||
|
||||
color = [red/255.0,green/255.0,blue/255.0]
|
||||
|
||||
if which == "atom": self.acolor[id] = color
|
||||
if which == "bond": self.bcolor[id] = color
|
||||
if which == "tri": self.tcolor[id] = color
|
||||
if which == "line": self.lcolor[id] = color
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# set radii for which = atoms, bonds, lines
|
||||
|
||||
def setradii(self,which,ids,radii):
|
||||
|
||||
# convert args into lists if single values
|
||||
# if arg = 0, convert to full-range list
|
||||
|
||||
if type(ids) is types.IntType and ids == 0:
|
||||
if which == "atom": ids = range(self.narad)
|
||||
if which == "bond": ids = range(self.nbrad)
|
||||
if which == "line": ids = range(self.nlrad)
|
||||
if type(ids) is not types.ListType and type(ids) is not types.TupleType:
|
||||
ids = [ids]
|
||||
if type(radii) is not types.ListType and \
|
||||
type(radii) is not types.TupleType:
|
||||
radii = [radii]
|
||||
|
||||
# if list of types has a 0, increment each type value
|
||||
|
||||
if 0 in ids:
|
||||
for i in xrange(len(ids)): ids[i] += 1
|
||||
|
||||
# extend storage list if necessary
|
||||
# extend other arrays for same "which" so that gl::make_atom_calllist
|
||||
# has valid arrays to work with
|
||||
|
||||
if which == "atom":
|
||||
if max(ids) > self.narad:
|
||||
self.narad = self.extend(self.arad,max(ids))
|
||||
self.narad = self.extend(self.acolor,max(ids))
|
||||
if which == "bond":
|
||||
if max(ids) > self.nbrad:
|
||||
self.nbrad = self.extend(self.brad,max(ids))
|
||||
self.nbrad = self.extend(self.bcolor,max(ids))
|
||||
if which == "line":
|
||||
if max(ids) > self.nlrad:
|
||||
self.nlrad = self.extend(self.lrad,max(ids))
|
||||
self.nlrad = self.extend(self.lcolor,max(ids))
|
||||
|
||||
# set radius for each type
|
||||
# if list lengths match, set directly, else interpolate
|
||||
|
||||
ntypes = len(ids)
|
||||
nradii = len(radii)
|
||||
|
||||
for i in range(ntypes):
|
||||
id = ids[i]
|
||||
|
||||
if ntypes == nradii: rad = radii[i]
|
||||
else:
|
||||
r = i/float(ntypes-1) * float(nradii-1)
|
||||
jlo = int(r)
|
||||
jhi = jlo + 1
|
||||
if jhi == nradii: jhi = nradii - 1
|
||||
rlo = radii[jlo]
|
||||
rhi = radii[jhi]
|
||||
delta = r - jlo
|
||||
rad = rlo + delta*(rhi-rlo)
|
||||
|
||||
if which == "atom": self.arad[id] = rad
|
||||
if which == "bond": self.brad[id] = rad
|
||||
if which == "line": self.lrad[id] = rad
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# set triangle fill style
|
||||
# 0 = fill only, 1 = line only, 2 = fill and line
|
||||
|
||||
def setfills(self,which,ids,fills):
|
||||
|
||||
# convert args into lists if single values
|
||||
# if arg = 0, convert to full-range list
|
||||
|
||||
if type(ids) is types.IntType and ids == 0:
|
||||
ids = range(self.ntfill)
|
||||
if type(ids) is not types.ListType and type(ids) is not types.TupleType:
|
||||
ids = [ids]
|
||||
if type(fills) is not types.ListType and \
|
||||
type(fills) is not types.TupleType:
|
||||
fills = [fills]
|
||||
|
||||
# if list of types has a 0, increment each type value
|
||||
|
||||
if 0 in ids:
|
||||
for i in xrange(len(ids)): ids[i] += 1
|
||||
|
||||
# extend storage list if necessary
|
||||
# extend other arrays for same "which" so that gl::make_atom_calllist
|
||||
# has valid arrays to work with
|
||||
|
||||
if max(ids) > self.ntfill:
|
||||
self.ntfill = self.extend(self.tfill,max(ids))
|
||||
self.ntfill = self.extend(self.tcolor,max(ids))
|
||||
|
||||
# set fill flag for each type
|
||||
# if list lengths match, set directly, else set types to 1st fill value
|
||||
|
||||
if len(fills) == len(ids):
|
||||
for i in xrange(len(ids)): self.tfill[ids[i]] = int(fills[i])
|
||||
else:
|
||||
for id in ids: self.tfill[id] = int(fills[0])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def extend(self,array,n):
|
||||
for i in range(n-len(array)+1): array.append(0)
|
||||
return n
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# dictionary of 140 color names and associated RGB values
|
||||
|
||||
colors = {}
|
||||
|
||||
colors["aliceblue"] = [240, 248, 255]
|
||||
colors["antiquewhite"] = [250, 235, 215]
|
||||
colors["aqua"] = [0, 255, 255]
|
||||
colors["aquamarine"] = [127, 255, 212]
|
||||
colors["azure"] = [240, 255, 255]
|
||||
colors["beige"] = [245, 245, 220]
|
||||
colors["bisque"] = [255, 228, 196]
|
||||
colors["black"] = [0, 0, 0]
|
||||
colors["blanchedalmond"] = [255, 255, 205]
|
||||
colors["blue"] = [0, 0, 255]
|
||||
colors["blueviolet"] = [138, 43, 226]
|
||||
colors["brown"] = [165, 42, 42]
|
||||
colors["burlywood"] = [222, 184, 135]
|
||||
colors["cadetblue"] = [95, 158, 160]
|
||||
colors["chartreuse"] = [127, 255, 0]
|
||||
colors["chocolate"] = [210, 105, 30]
|
||||
colors["coral"] = [255, 127, 80]
|
||||
colors["cornflowerblue"] = [100, 149, 237]
|
||||
colors["cornsilk"] = [255, 248, 220]
|
||||
colors["crimson"] = [220, 20, 60]
|
||||
colors["cyan"] = [0, 255, 255]
|
||||
colors["darkblue"] = [0, 0, 139]
|
||||
colors["darkcyan"] = [0, 139, 139]
|
||||
colors["darkgoldenrod"] = [184, 134, 11]
|
||||
colors["darkgray"] = [169, 169, 169]
|
||||
colors["darkgreen"] = [0, 100, 0]
|
||||
colors["darkkhaki"] = [189, 183, 107]
|
||||
colors["darkmagenta"] = [139, 0, 139]
|
||||
colors["darkolivegreen"] = [85, 107, 47]
|
||||
colors["darkorange"] = [255, 140, 0]
|
||||
colors["darkorchid"] = [153, 50, 204]
|
||||
colors["darkred"] = [139, 0, 0]
|
||||
colors["darksalmon"] = [233, 150, 122]
|
||||
colors["darkseagreen"] = [143, 188, 143]
|
||||
colors["darkslateblue"] = [72, 61, 139]
|
||||
colors["darkslategray"] = [47, 79, 79]
|
||||
colors["darkturquoise"] = [0, 206, 209]
|
||||
colors["darkviolet"] = [148, 0, 211]
|
||||
colors["deeppink"] = [255, 20, 147]
|
||||
colors["deepskyblue"] = [0, 191, 255]
|
||||
colors["dimgray"] = [105, 105, 105]
|
||||
colors["dodgerblue"] = [30, 144, 255]
|
||||
colors["firebrick"] = [178, 34, 34]
|
||||
colors["floralwhite"] = [255, 250, 240]
|
||||
colors["forestgreen"] = [34, 139, 34]
|
||||
colors["fuchsia"] = [255, 0, 255]
|
||||
colors["gainsboro"] = [220, 220, 220]
|
||||
colors["ghostwhite"] = [248, 248, 255]
|
||||
colors["gold"] = [255, 215, 0]
|
||||
colors["goldenrod"] = [218, 165, 32]
|
||||
colors["gray"] = [128, 128, 128]
|
||||
colors["green"] = [0, 128, 0]
|
||||
colors["greenyellow"] = [173, 255, 47]
|
||||
colors["honeydew"] = [240, 255, 240]
|
||||
colors["hotpink"] = [255, 105, 180]
|
||||
colors["indianred"] = [205, 92, 92]
|
||||
colors["indigo"] = [75, 0, 130]
|
||||
colors["ivory"] = [255, 240, 240]
|
||||
colors["khaki"] = [240, 230, 140]
|
||||
colors["lavender"] = [230, 230, 250]
|
||||
colors["lavenderblush"] = [255, 240, 245]
|
||||
colors["lawngreen"] = [124, 252, 0]
|
||||
colors["lemonchiffon"] = [255, 250, 205]
|
||||
colors["lightblue"] = [173, 216, 230]
|
||||
colors["lightcoral"] = [240, 128, 128]
|
||||
colors["lightcyan"] = [224, 255, 255]
|
||||
colors["lightgoldenrodyellow"] = [250, 250, 210]
|
||||
colors["lightgreen"] = [144, 238, 144]
|
||||
colors["lightgrey"] = [211, 211, 211]
|
||||
colors["lightpink"] = [255, 182, 193]
|
||||
colors["lightsalmon"] = [255, 160, 122]
|
||||
colors["lightseagreen"] = [32, 178, 170]
|
||||
colors["lightskyblue"] = [135, 206, 250]
|
||||
colors["lightslategray"] = [119, 136, 153]
|
||||
colors["lightsteelblue"] = [176, 196, 222]
|
||||
colors["lightyellow"] = [255, 255, 224]
|
||||
colors["lime"] = [0, 255, 0]
|
||||
colors["limegreen"] = [50, 205, 50]
|
||||
colors["linen"] = [250, 240, 230]
|
||||
colors["magenta"] = [255, 0, 255]
|
||||
colors["maroon"] = [128, 0, 0]
|
||||
colors["mediumaquamarine"] = [102, 205, 170]
|
||||
colors["mediumblue"] = [0, 0, 205]
|
||||
colors["mediumorchid"] = [186, 85, 211]
|
||||
colors["mediumpurple"] = [147, 112, 219]
|
||||
colors["mediumseagreen"] = [60, 179, 113]
|
||||
colors["mediumslateblue"] = [123, 104, 238]
|
||||
colors["mediumspringgreen"] = [0, 250, 154]
|
||||
colors["mediumturquoise"] = [72, 209, 204]
|
||||
colors["mediumvioletred"] = [199, 21, 133]
|
||||
colors["midnightblue"] = [25, 25, 112]
|
||||
colors["mintcream"] = [245, 255, 250]
|
||||
colors["mistyrose"] = [255, 228, 225]
|
||||
colors["moccasin"] = [255, 228, 181]
|
||||
colors["navajowhite"] = [255, 222, 173]
|
||||
colors["navy"] = [0, 0, 128]
|
||||
colors["oldlace"] = [253, 245, 230]
|
||||
colors["olive"] = [128, 128, 0]
|
||||
colors["olivedrab"] = [107, 142, 35]
|
||||
colors["orange"] = [255, 165, 0]
|
||||
colors["orangered"] = [255, 69, 0]
|
||||
colors["orchid"] = [218, 112, 214]
|
||||
colors["palegoldenrod"] = [238, 232, 170]
|
||||
colors["palegreen"] = [152, 251, 152]
|
||||
colors["paleturquoise"] = [175, 238, 238]
|
||||
colors["palevioletred"] = [219, 112, 147]
|
||||
colors["papayawhip"] = [255, 239, 213]
|
||||
colors["peachpuff"] = [255, 239, 213]
|
||||
colors["peru"] = [205, 133, 63]
|
||||
colors["pink"] = [255, 192, 203]
|
||||
colors["plum"] = [221, 160, 221]
|
||||
colors["powderblue"] = [176, 224, 230]
|
||||
colors["purple"] = [128, 0, 128]
|
||||
colors["red"] = [255, 0, 0]
|
||||
colors["rosybrown"] = [188, 143, 143]
|
||||
colors["royalblue"] = [65, 105, 225]
|
||||
colors["saddlebrown"] = [139, 69, 19]
|
||||
colors["salmon"] = [250, 128, 114]
|
||||
colors["sandybrown"] = [244, 164, 96]
|
||||
colors["seagreen"] = [46, 139, 87]
|
||||
colors["seashell"] = [255, 245, 238]
|
||||
colors["sienna"] = [160, 82, 45]
|
||||
colors["silver"] = [192, 192, 192]
|
||||
colors["skyblue"] = [135, 206, 235]
|
||||
colors["slateblue"] = [106, 90, 205]
|
||||
colors["slategray"] = [112, 128, 144]
|
||||
colors["snow"] = [255, 250, 250]
|
||||
colors["springgreen"] = [0, 255, 127]
|
||||
colors["steelblue"] = [70, 130, 180]
|
||||
colors["tan"] = [210, 180, 140]
|
||||
colors["teal"] = [0, 128, 128]
|
||||
colors["thistle"] = [216, 191, 216]
|
||||
colors["tomato"] = [253, 99, 71]
|
||||
colors["turquoise"] = [64, 224, 208]
|
||||
colors["violet"] = [238, 130, 238]
|
||||
colors["wheat"] = [245, 222, 179]
|
||||
colors["white"] = [255, 255, 255]
|
||||
colors["whitesmoke"] = [245, 245, 245]
|
||||
colors["yellow"] = [255, 255, 0]
|
||||
colors["yellowgreen"] = [154, 205, 50]
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# plot.py
|
||||
# Purpose: plot Temp of running LAMMPS simulation via GnuPlot in Pizza.py
|
||||
# Syntax: plot.py in.lammps Nfreq Nsteps compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point every this many steps
|
||||
# Nsteps = run for this many steps
|
||||
# compute-ID = ID of compute that calculates temperature
|
||||
# (or any other scalar quantity)
|
||||
|
||||
import sys
|
||||
sys.path.append("./pizza")
|
||||
from gnu import gnu
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 5:
|
||||
print "Syntax: plot.py in.lammps Nfreq Nsteps compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
nfreq = int(sys.argv[2])
|
||||
nsteps = int(sys.argv[3])
|
||||
compute = sys.argv[4]
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile all at once
|
||||
# assumed to have no run command in it
|
||||
|
||||
lmp.file(infile)
|
||||
lmp.command("thermo %d" % nfreq)
|
||||
|
||||
# initial 0-step run to generate initial 1-point plot
|
||||
|
||||
lmp.command("run 0 pre yes post no")
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
ntimestep = 0
|
||||
xaxis = [ntimestep]
|
||||
yaxis = [value]
|
||||
|
||||
# wrapper on GnuPlot via Pizza.py gnu tool
|
||||
# just proc 0 handles plotting
|
||||
|
||||
if me == 0:
|
||||
gn = gnu()
|
||||
gn.plot(xaxis,yaxis)
|
||||
gn.xrange(0,nsteps)
|
||||
gn.title(compute,"Timestep","Temperature")
|
||||
|
||||
# run nfreq steps at a time w/out pre/post, query compute, refresh plot
|
||||
|
||||
while ntimestep < nsteps:
|
||||
lmp.command("run %d pre no post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
xaxis.append(ntimestep)
|
||||
yaxis.append(value)
|
||||
if me == 0: gn.plot(xaxis,yaxis)
|
||||
|
||||
lmp.command("run 0 pre no post yes")
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# simple.py
|
||||
# Purpose: mimic operation of couple/simple/simple.cpp via Python
|
||||
# Syntax: simple.py in.lammps
|
||||
# in.lammps = LAMMPS input script
|
||||
|
||||
import sys
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 2:
|
||||
print "Syntax: simple.py in.lammps"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile one line at a time
|
||||
|
||||
lines = open(infile,'r').readlines()
|
||||
for line in lines: lmp.command(line)
|
||||
|
||||
# run 10 more steps
|
||||
# get coords from LAMMPS
|
||||
# change coords of 1st atom
|
||||
# put coords back into LAMMPS
|
||||
# run a single step with changed coords
|
||||
|
||||
lmp.command("run 10")
|
||||
x = lmp.get_coords()
|
||||
epsilon = 0.1
|
||||
x[0] += epsilon
|
||||
lmp.put_coords(x)
|
||||
lmp.command("run 1");
|
||||
lmp.command("run 1")
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# trivial.py
|
||||
# Purpose: run a LAMMPS input script via Python
|
||||
# Syntax: trivial.py in.lammps
|
||||
# in.lammps = LAMMPS input script
|
||||
|
||||
import sys
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 2:
|
||||
print "Syntax: trivial.py in.lammps"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile all at once
|
||||
|
||||
lmp.file(infile)
|
||||
|
||||
# run infile one line at a time
|
||||
|
||||
#lines = open(infile,'r').readlines()
|
||||
#for line in lines: lmp.command(line)
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# viz.py
|
||||
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
|
||||
# Syntax: viz.py in.lammps Nfreq Nsteps
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = dump and viz shapshot every this many steps
|
||||
# Nsteps = run for this many steps
|
||||
|
||||
import sys
|
||||
sys.path.append("./pizza")
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: viz.py in.lammps Nfreq Nsteps"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
nfreq = int(sys.argv[2])
|
||||
nsteps = int(sys.argv[3])
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile all at once
|
||||
# assumed to have no run command in it
|
||||
|
||||
lmp.file(infile)
|
||||
lmp.command("thermo %d" % nfreq)
|
||||
lmp.command("dump python all atom %d tmp.dump" % nfreq)
|
||||
|
||||
# initial 0-step run to generate dump file and image
|
||||
|
||||
lmp.command("run 0 pre yes post no")
|
||||
ntimestep = 0
|
||||
|
||||
# wrapper on GL window via Pizza.py gl tool
|
||||
# just proc 0 handles reading of dump file and viz
|
||||
|
||||
if me == 0:
|
||||
import Tkinter
|
||||
tkroot = Tkinter.Tk()
|
||||
tkroot.withdraw()
|
||||
|
||||
from dump import dump
|
||||
from gl import gl
|
||||
|
||||
d = dump("tmp.dump",0)
|
||||
g = gl(d)
|
||||
d.next()
|
||||
d.unscale()
|
||||
g.zoom(1)
|
||||
g.shift(0,0)
|
||||
g.rotate(0,270)
|
||||
g.q(10)
|
||||
g.box(1)
|
||||
g.show(ntimestep)
|
||||
|
||||
# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
|
||||
|
||||
while ntimestep < nsteps:
|
||||
lmp.command("run %d pre no post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0:
|
||||
d.next()
|
||||
d.unscale()
|
||||
g.show(ntimestep)
|
||||
|
||||
lmp.command("run 0 pre no post yes")
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
|
|
@ -0,0 +1,171 @@
|
|||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# vizplotgui.py
|
||||
# Purpose: viz running LAMMPS simulation with plot and GUI
|
||||
# Syntax: vizplotgui.py in.lammps Nfreq compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point and viz shapshot every this many steps
|
||||
# compute-ID = ID of compute that calculates temperature
|
||||
# (or any other scalar quantity)
|
||||
|
||||
import sys,time
|
||||
sys.path.append("./pizza")
|
||||
|
||||
# methods called by GUI
|
||||
|
||||
def run():
|
||||
global runflag
|
||||
runflag = 1
|
||||
def stop():
|
||||
global runflag
|
||||
runflag = 0
|
||||
def settemp(value):
|
||||
global temptarget
|
||||
temptarget = slider.get()
|
||||
def quit():
|
||||
global breakflag
|
||||
breakflag = 1
|
||||
|
||||
# method called by timestep loop every Nfreq steps
|
||||
# read dump snapshot and viz it, update plot with compute value
|
||||
|
||||
def update(ntimestep):
|
||||
d.next()
|
||||
d.unscale()
|
||||
g.show(ntimestep)
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
xaxis.append(ntimestep)
|
||||
yaxis.append(value)
|
||||
gn.plot(xaxis,yaxis)
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
nfreq = int(sys.argv[2])
|
||||
compute = sys.argv[3]
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile all at once
|
||||
# assumed to have no run command in it
|
||||
|
||||
lmp.file(infile)
|
||||
lmp.command("thermo %d" % nfreq)
|
||||
lmp.command("dump python all atom %d tmp.dump" % nfreq)
|
||||
|
||||
# initial 0-step run to generate initial 1-point plot, dump file, and image
|
||||
|
||||
lmp.command("run 0 pre yes post no")
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
ntimestep = 0
|
||||
xaxis = [ntimestep]
|
||||
yaxis = [value]
|
||||
|
||||
# wrapper on GL window via Pizza.py gl tool
|
||||
# just proc 0 handles reading of dump file and viz
|
||||
|
||||
breakflag = 0
|
||||
runflag = 0
|
||||
temptarget = 1.0
|
||||
|
||||
if me == 0:
|
||||
from Tkinter import *
|
||||
tkroot = Tk()
|
||||
tkroot.withdraw()
|
||||
|
||||
from dump import dump
|
||||
from gl import gl
|
||||
|
||||
d = dump("tmp.dump",0)
|
||||
g = gl(d)
|
||||
d.next()
|
||||
d.unscale()
|
||||
g.zoom(1)
|
||||
g.shift(0,0)
|
||||
g.rotate(0,270)
|
||||
g.q(10)
|
||||
g.box(1)
|
||||
g.show(ntimestep)
|
||||
|
||||
# display GUI with run/stop buttons and slider for temperature
|
||||
|
||||
if me == 0:
|
||||
from Tkinter import *
|
||||
tkroot = Tk()
|
||||
tkroot.withdraw()
|
||||
root = Toplevel(tkroot)
|
||||
root.title("LAMMPS GUI")
|
||||
|
||||
frame = Frame(root)
|
||||
Button(frame,text="Run",command=run).pack(side=LEFT)
|
||||
Button(frame,text="Stop",command=stop).pack(side=LEFT)
|
||||
slider = Scale(frame,from_=0.0,to=5.0,resolution=0.1,
|
||||
orient=HORIZONTAL,label="Temperature")
|
||||
slider.bind('<ButtonRelease-1>',settemp)
|
||||
slider.set(temptarget)
|
||||
slider.pack(side=LEFT)
|
||||
Button(frame,text="Quit",command=quit).pack(side=RIGHT)
|
||||
frame.pack()
|
||||
tkroot.update()
|
||||
|
||||
# wrapper on GnuPlot via Pizza.py gnu tool
|
||||
|
||||
if me == 0:
|
||||
from gnu import gnu
|
||||
gn = gnu()
|
||||
gn.plot(xaxis,yaxis)
|
||||
gn.title(compute,"Timestep","Temperature")
|
||||
|
||||
# endless loop, checking status of GUI settings every Nfreq steps
|
||||
# run with pre yes/no and post yes/no depending on go/stop status
|
||||
# re-invoke fix langevin with new seed when temperature slider changes
|
||||
# after re-invoke of fix langevin, run with pre yes
|
||||
|
||||
running = 0
|
||||
temp = temptarget
|
||||
seed = 12345
|
||||
|
||||
lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))
|
||||
|
||||
while 1:
|
||||
if me == 0: tkroot.update()
|
||||
if temp != temptarget:
|
||||
temp = temptarget
|
||||
seed += me+1
|
||||
lmp.command("fix 2 all langevin %g %g 0.1 12345" % (temp,temp))
|
||||
running = 0
|
||||
if runflag and running:
|
||||
lmp.command("run %d pre no post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
elif runflag and not running:
|
||||
lmp.command("run %d pre yes post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
elif not runflag and running:
|
||||
lmp.command("run %d pre no post yes" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
if breakflag: break
|
||||
if runflag: running = 1
|
||||
else: running = 0
|
||||
time.sleep(0.01)
|
||||
|
||||
lmp.command("run 0 pre no post yes")
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
|
|
@ -0,0 +1,169 @@
|
|||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# Copyright (2003) 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.
|
||||
#
|
||||
# See the README file in the top-level LAMMPS directory.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
# Python wrapper on LAMMPS library via ctypes
|
||||
|
||||
import types
|
||||
from ctypes import *
|
||||
|
||||
LMPINT = 0
|
||||
LMPDOUBLE = 1
|
||||
LMPIPTR = 2
|
||||
LMPDPTR = 3
|
||||
LMPDPTRPTR = 4
|
||||
|
||||
class lammps:
|
||||
def __init__(self,args=None):
|
||||
|
||||
# attempt to load parallel library first, serial library next
|
||||
# could provide caller a flag to choose which library to load
|
||||
|
||||
try:
|
||||
self.lib = CDLL("_lammps.so")
|
||||
except:
|
||||
try:
|
||||
self.lib = CDLL("_lammps_serial.so")
|
||||
except:
|
||||
raise StandardError,"Could not load LAMMPS dynamic library"
|
||||
|
||||
# create an instance of LAMMPS
|
||||
# don't know how to pass an MPI communicator from PyPar
|
||||
# no_mpi call lets LAMMPS use MPI_COMM_WORLD
|
||||
# cargs = array of C strings from args
|
||||
|
||||
if args:
|
||||
args.insert(0,"lammps.py")
|
||||
narg = len(args)
|
||||
cargs = (c_char_p*narg)(*args)
|
||||
self.lmp = c_void_p()
|
||||
self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
|
||||
else:
|
||||
self.lmp = c_void_p()
|
||||
self.lib.lammps_open_no_mpi(0,None,byref(self.lmp))
|
||||
# could use just this if LAMMPS lib interface supported it
|
||||
# self.lmp = self.lib.lammps_open_no_mpi(0,None)
|
||||
|
||||
def __del__(self):
|
||||
if self.lmp: self.lib.lammps_close(self.lmp)
|
||||
|
||||
def close(self):
|
||||
self.lib.lammps_close(self.lmp)
|
||||
self.lmp = None
|
||||
|
||||
def file(self,file):
|
||||
self.lib.lammps_file(self.lmp,file)
|
||||
|
||||
def command(self,cmd):
|
||||
self.lib.lammps_command(self.lmp,cmd)
|
||||
|
||||
def extract_global(self,name,type):
|
||||
if type == LMPDOUBLE:
|
||||
self.lib.lammps_extract_global.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_global(self.lmp,name)
|
||||
return ptr[0]
|
||||
if type == LMPINT:
|
||||
self.lib.lammps_extract_global.restype = POINTER(c_int)
|
||||
ptr = self.lib.lammps_extract_global(self.lmp,name)
|
||||
return ptr[0]
|
||||
return None
|
||||
|
||||
def extract_atom(self,name,type):
|
||||
if type == LMPDPTRPTR:
|
||||
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
|
||||
ptr = self.lib.lammps_extract_atom(self.lmp,name)
|
||||
return ptr
|
||||
if type == LMPDPTR:
|
||||
self.lib.lammps_extract_atom.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_atom(self.lmp,name)
|
||||
return ptr
|
||||
if type == LMPIPTR:
|
||||
self.lib.lammps_extract_atom.restype = POINTER(c_int)
|
||||
ptr = self.lib.lammps_extract_atom(self.lmp,name)
|
||||
return ptr
|
||||
return None
|
||||
|
||||
def extract_compute(self,id,style,type):
|
||||
if type == 0:
|
||||
if style > 0: return None
|
||||
self.lib.lammps_extract_compute.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
|
||||
return ptr[0]
|
||||
elif type == 1:
|
||||
self.lib.lammps_extract_compute.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
|
||||
return ptr
|
||||
elif type == 2:
|
||||
self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
|
||||
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
|
||||
return ptr
|
||||
return None
|
||||
|
||||
# in case of global datum, free memory for 1 double via lammps_free()
|
||||
# double was allocated by library interface function
|
||||
|
||||
def extract_fix(self,id,style,type,i=0,j=0):
|
||||
if type == 0:
|
||||
if style > 0: return None
|
||||
self.lib.lammps_extract_fix.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_bix(self.lmp,id,style,type,i,j)
|
||||
result = ptr[0]
|
||||
self.lib.lammps_free(ptr)
|
||||
return result
|
||||
elif type == 1:
|
||||
self.lib.lammps_extract_fix.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
|
||||
return ptr
|
||||
elif type == 2:
|
||||
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
|
||||
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
|
||||
return ptr
|
||||
return None
|
||||
|
||||
# free memory for 1 double or 1 vector of doubles via lammps_free()
|
||||
# for vector, must copy nlocal returned values to local c_double vector
|
||||
# memory was allocated by library interface function
|
||||
|
||||
def extract_variable(self,name,group,type):
|
||||
if type == 0:
|
||||
self.lib.lammps_extract_variable.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
|
||||
result = ptr[0]
|
||||
self.lib.lammps_free(ptr)
|
||||
return result
|
||||
if type == 1:
|
||||
self.lib.lammps_extract_global.restype = POINTER(c_int)
|
||||
nlocalptr = self.lib.lammps_extract_global(self.lmp,"nlocal")
|
||||
nlocal = nlocalptr[0]
|
||||
result = (c_double*nlocal)()
|
||||
self.lib.lammps_extract_variable.restype = POINTER(c_double)
|
||||
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
|
||||
for i in xrange(nlocal): result[i] = ptr[i]
|
||||
self.lib.lammps_free(ptr)
|
||||
return result
|
||||
return None
|
||||
|
||||
def get_natoms(self):
|
||||
return self.lib.lammps_get_natoms(self.lmp)
|
||||
|
||||
def get_coords(self):
|
||||
nlen = 3 * self.lib.lammps_get_natoms(self.lmp)
|
||||
coords = (c_double*nlen)()
|
||||
self.lib.lammps_get_coords(self.lmp,coords)
|
||||
return coords
|
||||
|
||||
# assume coords is an array of c_double, as created by get_coords()
|
||||
# could check if it is some other Python object and create c_double array?
|
||||
# constructor for c_double array can take an arg to use to fill it?
|
||||
|
||||
def put_coords(self,coords):
|
||||
self.lib.lammps_put_coords(self.lmp,coords)
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
#!/usr/local/bin/python
|
||||
|
||||
"""
|
||||
setup.py file for LAMMPS with system MPI library
|
||||
"""
|
||||
|
||||
from distutils.core import setup, Extension
|
||||
|
||||
import os, glob
|
||||
path = os.path.dirname(os.getcwd())
|
||||
|
||||
# list of src files for LAMMPS
|
||||
|
||||
libfiles = glob.glob("%s/src/*.cpp" % path)
|
||||
|
||||
lammps_library = Extension("_lammps",
|
||||
sources = libfiles,
|
||||
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
|
||||
("LAMMPS_GZIP",1),
|
||||
("FFT_NONE",1),],
|
||||
# src files for LAMMPS
|
||||
include_dirs = ["../src"],
|
||||
# additional libs for MPICH on Linux
|
||||
libraries = ["mpich","rt"],
|
||||
# where to find the MPICH lib on Linux
|
||||
library_dirs = ["/usr/local/lib"],
|
||||
# additional libs for MPI on Mac
|
||||
# libraries = ["mpi"],
|
||||
)
|
||||
|
||||
setup(name = "lammps",
|
||||
version = "26Oct10",
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = """LAMMPS molecular dynamics library - parallel""",
|
||||
py_modules = ["lammps"],
|
||||
ext_modules = [lammps_library]
|
||||
)
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
#!/usr/local/bin/python
|
||||
|
||||
"""
|
||||
setup_serial.py file for LAMMPS with dummy serial MPI library
|
||||
"""
|
||||
|
||||
from distutils.core import setup, Extension
|
||||
|
||||
import os, glob
|
||||
path = os.path.dirname(os.getcwd())
|
||||
|
||||
# list of src files for LAMMPS and MPI STUBS
|
||||
|
||||
libfiles = glob.glob("%s/src/*.cpp" % path) + \
|
||||
glob.glob("%s/src/STUBS/*.cpp" % path)
|
||||
|
||||
lammps_library = Extension("_lammps_serial",
|
||||
sources = libfiles,
|
||||
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
|
||||
("LAMMPS_GZIP",1),
|
||||
("FFT_NONE",1),],
|
||||
# src files for LAMMPS and MPI STUBS
|
||||
include_dirs = ["../src", "../src/STUBS"]
|
||||
)
|
||||
|
||||
setup(name = "lammps_serial",
|
||||
version = "26Oct10",
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = """LAMMPS molecular dynamics library - serial""",
|
||||
py_modules = ["lammps"],
|
||||
ext_modules = [lammps_library]
|
||||
)
|
||||
Loading…
Reference in New Issue