Commit 349ed48d authored by Richard Berger's avatar Richard Berger
Browse files

Start process of converting Pizza.py into standard Python package

parent 602672ec

.gitignore

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+1 −0
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__pycache__

pizza/__init__.py

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+0 −0

Empty file added.

src/log.py→pizza/log.py

+4 −7
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@@ -126,7 +126,7 @@ class log: 


    m = []

    for key in keys:

      if self.ptr.has_key(key):

      if key in self.ptr:

        m.append(self.ptr[key])

      else:

        count = 0
@@ -154,7 +154,7 @@ class log: 
    if len(keys):

      m = []

      for key in keys:

        if self.ptr.has_key(key):

        if key in self.ptr:

          m.append(self.ptr[key])

        else:

          count = 0
@@ -169,12 +169,9 @@ class log: 
    else:

      m = list(range(self.nvec))



    f = open(filename,"w")

    with open(filename,"w") as f:

      for i in range(self.nlen):

      for x in m:

        print(self.data[i][x], end='', file=f)

      print(file=f)

    f.close()

        print(' '.join(map(str, [self.data[i][x] for x in m])), file=f)



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

setup.py

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#!/usr/bin/env python



from distutils.core import setup



setup(name='Pizza.py',

      version='1.0',

      description='Pizza.py is a loosely integrated collection of tools written in Python, many of which provide pre- '

                  'and post-processing capability for the LAMMPS molecular dynamics package. There are tools to create '

                  'input files, convert between file formats, process log and dump files, create plots, and visualize '

                  'and animate simulation snapshots.',

      author='Steve Plimpton',

      author_email='sjplimp@sandia.gov',

      url='http://pizza.sandia.gov/',

      packages=['pizza'],

     )
 
 No newline at end of file

tests/test_log.py

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import unittest

import csv

import os

from pizza.log import log





class TestLog(unittest.TestCase):

    EXAMPLE_FILE = "../examples/files/log.obstacle"



    def test_read_log(self):

        lg = log(TestLog.EXAMPLE_FILE)

        self.assertEqual(lg.nvec, 7)

        self.assertEqual(lg.nlen, 26)

        self.assertListEqual(lg.names, ["Step", "Temperature", "E_pair", "E_bond", "E_total", "Pressure", "Volume"])



    def test_log_get(self):

        lg = log(TestLog.EXAMPLE_FILE)

        time, temp, press = lg.get("Step", "Temp", "Press")

        self.assertEqual(len(time), 26)

        self.assertEqual(len(temp), 26)

        self.assertEqual(len(press), 26)



    def test_write_all(self):

        tmp_file = "/tmp/tmp.log"

        lg = log(TestLog.EXAMPLE_FILE)

        lg.write(tmp_file)

        self.assertTrue(os.path.exists(tmp_file))



        with open(tmp_file, 'rt') as csvfile:

            lines = list(csv.reader(csvfile, delimiter=' '))

            self.assertEqual(len(lines), 26)

            self.assertEqual(len(lines[0]), 7)



    def test_write_columns(self):

        tmp_file = "/tmp/tmp.log.two"

        lg = log(TestLog.EXAMPLE_FILE)

        lg.write(tmp_file, "Step", "E_pair")

        self.assertTrue(os.path.exists(tmp_file))



        with open(tmp_file, 'rt') as csvfile:

            lines = list(csv.reader(csvfile, delimiter=' '))

            self.assertEqual(len(lines), 26)

            self.assertEqual(len(lines[0]), 2)