Commit a936b7b2 authored by sjplimp's avatar sjplimp Committed by GitHub
Browse files

Merge pull request #419 from rbberger/python_fixes 

Library interface fixes, Python example fixes and better Python 3 compatibility
parents a91b851f cda82138

python/examples/matplotlib_plot.py

0 → 100755
+93 −0
Original line number Diff line number Diff line 
#!/usr/bin/env python -i

# preceding line should have path for Python on your machine



# matplotlib_plot.py

# Purpose: plot Temp of running LAMMPS simulation via matplotlib

# 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)



from __future__ import print_function

import sys

sys.path.append("./pizza")

import matplotlib

matplotlib.use('tkagg')

import matplotlib.pyplot as plt



# 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]



# create matplotlib plot

# just proc 0 handles plotting



if me == 0:

  fig = plt.figure()

  line, = plt.plot(xaxis, yaxis)

  plt.xlim([0, nsteps])

  plt.title(compute)

  plt.xlabel("Timestep")

  plt.ylabel("Temperature")

  plt.show(block=False)



# run nfreq steps at a time w/out pre/post, query compute, refresh plot

import time



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:

    line.set_xdata(xaxis)

    line.set_ydata(yaxis)

    ax = plt.gca()

    ax.relim()

    ax.autoscale_view(True, True, True)

    fig.canvas.draw()



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()



if sys.version_info[0] == 3:

    input("Press Enter to exit...")

else:

    raw_input("Press Enter to exit...")

python/examples/pizza/dump.py

+33 −33
Original line number Diff line number Diff line
@@ -146,6 +146,8 @@ d.extra(data) extract bond/tri/line list from data 
# History

#   8/05, Steve Plimpton (SNL): original version

#   12/09, David Hart (SNL): allow use of NumPy or Numeric

#   03/17, Richard Berger (Temple U): improve Python 3 compatibility,

#                                     simplify read_snapshot by using reshape



# ToDo list

#   try to optimize this line in read_snap: words += f.readline().split()
@@ -224,7 +226,7 @@ class dump: 
    self.flist = []

    for word in words: self.flist += glob.glob(word)

    if len(self.flist) == 0 and len(list) == 1:

      raise StandardError("no dump file specified")

      raise Exception("no dump file specified")

    

    if len(list) == 1:

      self.increment = 0
@@ -299,7 +301,7 @@ class dump: 


  def next(self):



    if not self.increment: raise StandardError("cannot read incrementally")

    if not self.increment: raise Exception("cannot read incrementally")



    # read next snapshot in current file using eof as pointer

    # if fail, try next file
@@ -344,13 +346,13 @@ class dump: 
    try:

      snap = Snap()

      item = f.readline()

      snap.time = int(f.readline().split()[0])    # just grab 1st field

      snap.time = int(f.readline().decode().split()[0])    # just grab 1st field

      item = f.readline()

      snap.natoms = int(f.readline())

      snap.natoms = int(f.readline().decode())



      snap.aselect = np.zeros(snap.natoms)



      item = f.readline()

      item = f.readline().decode()

      words = f.readline().split()

      snap.xlo,snap.xhi = float(words[0]),float(words[1])

      words = f.readline().split()
@@ -358,7 +360,7 @@ class dump: 
      words = f.readline().split()

      snap.zlo,snap.zhi = float(words[0]),float(words[1])



      item = f.readline()

      item = f.readline().decode()

      if len(self.names) == 0:

        words = item.split()[2:]

        if len(words):
@@ -372,24 +374,22 @@ class dump: 
            else: self.names[words[i]] = i



      if snap.natoms:

        words = f.readline().split()

        words = f.readline().decode().split()

        ncol = len(words)

        for i in range(1,snap.natoms):

          words += f.readline().split()

          words += f.readline().decode().split()

        floats = map(float,words)

        if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)

        else: atoms = np.zeros((snap.natoms,ncol),np.float)

        start = 0

        stop = ncol

        for i in range(snap.natoms):

          atoms[i] = floats[start:stop]

          start = stop

          stop += ncol

      else: atoms = None

      snap.atoms = atoms

        if oldnumeric:

          atom_data = np.array(list(floats),np.Float)

        else:

          atom_data = np.array(list(floats),np.float)



        snap.atoms = atom_data.reshape((snap.natoms, ncol))

      else:

        snap.atoms = None

      return snap

    except:

      return 0

      return None



  # --------------------------------------------------------------------

  # decide if snapshot i is scaled/unscaled from coords of first and last atom
@@ -417,7 +417,7 @@ class dump: 
  

  def map(self,*pairs):

    if len(pairs) % 2 != 0:

      raise StandardError("dump map() requires pairs of mappings")

      raise Exception("dump map() requires pairs of mappings")

    for i in range(0,len(pairs),2):

      j = i + 1

      self.names[pairs[j]] = pairs[i]-1
@@ -734,7 +734,7 @@ class dump: 
    for snap in self.snaps:

      if not snap.tselect: continue

      if snap.nselect != len(vec):

        raise StandardError("vec length does not match # of selected atoms")

        raise Exception("vec length does not match # of selected atoms")

      atoms = snap.atoms

      m = 0

      for i in range(snap.natoms):
@@ -800,7 +800,7 @@ class dump: 


  def atom(self,n,*list):

    if len(list) == 0:

      raise StandardError("no columns specified")

      raise Exception("no columns specified")

    columns = []

    values = []

    for name in list:
@@ -816,7 +816,7 @@ class dump: 
      for i in range(snap.natoms):

        if atoms[i][id] == n: break

      if atoms[i][id] != n:

        raise StandardError("could not find atom ID in snapshot")

        raise Exception("could not find atom ID in snapshot")

      for j in range(ncol):

        values[j][m] = atoms[i][columns[j]]

      m += 1
@@ -831,7 +831,7 @@ class dump: 
    snap = self.snaps[self.findtime(n)]

    

    if len(list) == 0:

      raise StandardError("no columns specified")

      raise Exception("no columns specified")

    columns = []

    values = []

    for name in list:
@@ -957,9 +957,9 @@ class dump: 
  # --------------------------------------------------------------------



  def findtime(self,n):

    for i in range(self.nsnaps):

      if self.snaps[i].time == n: return i

    raise StandardError("no step %d exists" % n)

    for i, snap in enumerate(self.snaps):

      if snap.time == n: return i

    raise Exception("no step %d exists" % n)



  # --------------------------------------------------------------------

  # return maximum box size across all selected snapshots
@@ -1008,7 +1008,7 @@ class dump: 
        nbonds = int(f.readline())

        item = f.readline()

        if not re.search("BONDS",item):

          raise StandardError("could not read bonds from dump file")

          raise Exception("could not read bonds from dump file")



        words = f.readline().split()

        ncol = len(words)
@@ -1031,7 +1031,7 @@ class dump: 
          self.bondflag = 1

          self.bondlist = bondlist

      except:

        raise StandardError("could not read from bond dump file")

        raise Exception("could not read from bond dump file")

      

    # request bonds from data object
@@ -1047,7 +1047,7 @@ class dump: 
          self.bondflag = 1

          self.bondlist = bondlist

      except:

        raise StandardError("could not extract bonds from data object")

        raise Exception("could not extract bonds from data object")



    # request tris/lines from cdata object
@@ -1061,7 +1061,7 @@ class dump: 
          self.lineflag = 1

          self.linelist = lines

      except:

        raise StandardError("could not extract tris/lines from cdata object")

        raise Exception("could not extract tris/lines from cdata object")



    # request tris from mdump object
@@ -1070,10 +1070,10 @@ class dump: 
        self.triflag = 2

        self.triobj = arg

      except:

        raise StandardError("could not extract tris from mdump object")

        raise Exception("could not extract tris from mdump object")



    else:

      raise StandardError("unrecognized argument to dump.extra()")

      raise Exception("unrecognized argument to dump.extra()")

      

  # --------------------------------------------------------------------

python/examples/pizza/pdbfile.py

+8 −1
Original line number Diff line number Diff line
@@ -54,6 +54,7 @@ index,time,flag = p.iterator(1) 


# History

#   8/05, Steve Plimpton (SNL): original version

#   3/17, Richard Berger (Temple U): improve Python 3 compatibility



# ToDo list

#   for generic PDB file (no template) from a LJ unit system,
@@ -68,6 +69,12 @@ index,time,flag = p.iterator(1) 
# Imports and external programs



import sys, types, glob, urllib

PY3 = sys.version_info[0] == 3



if PY3:

    string_types = str,

else:

    string_types = basestring



# Class definition
@@ -77,7 +84,7 @@ class pdbfile: 


  def __init__(self,*args):

    if len(args) == 1:

      if type(args[0]) is types.StringType:

      if type(args[0]) is string_types:

        filestr = args[0]

        self.data = None

      else:

python/examples/viz_atomeye.py

+1 −1
Original line number Diff line number Diff line
@@ -42,7 +42,7 @@ lmp = lammps() 


lmp.file(infile)

lmp.command("thermo %d" % nfreq)

lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % nfreq)

lmp.command("dump python all cfg %d tmp.cfg.* mass type xs ys zs id" % nfreq)



# initial 0-step run to generate dump file and image

python/examples/vizplotgui_atomeye.py

+1 −1
Original line number Diff line number Diff line
@@ -73,7 +73,7 @@ lmp = lammps() 


lmp.file(infile)

lmp.command("thermo %d" % nfreq)

lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % nfreq)

lmp.command("dump python all cfg %d tmp.cfg.* mass type xs ys zs id" % nfreq)



# initial 0-step run to generate initial 1-point plot, dump file, and image

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