Repository: debeshmandal/starpolymers (language: python)

Issue:
Implement Outputting LAMMPS conf files in bond or angle atom_types
[Description can be found here](https://docs.lammps.org/atom_style.html)

In short, add options to include or not include the following bits of information:

- bonds
- angles
- dihedrals
- charge


Discussion / hints:

Fix patch:
diff --git a/.gitignore b/.gitignore
index fa9f3bc..8ff52e5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,4 +4,7 @@
 __pycache__
 test/configs/*/test_config.dat
 .pytest_cache
-**.bak
\ No newline at end of file
+**.bak
+
+lammps.test.conf
+log.lammps
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..bb8bcfc
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,2 @@
+include versioneer.py
+include starpolymers/_version.py
diff --git a/protocols/assemble-gel/main.py b/protocols/assemble-gel/main.py
new file mode 100644
index 0000000..02ecf71
--- /dev/null
+++ b/protocols/assemble-gel/main.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+"""Combines the generate-many and squeeze protocols to create a system
+that contains a high density of two different and opposite-ly charged
+molecule types, and then simulates them to equilibrium
+"""
+from softnanotools.logger import Logger
+logger = Logger('MAIN')
+
+def main(*args, **kwargs):
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    main(**vars(parser.parse_args()))
diff --git a/protocols/generate-many/config.py b/protocols/generate-many/config.py
new file mode 100644
index 0000000..3d264b6
--- /dev/null
+++ b/protocols/generate-many/config.py
@@ -0,0 +1,111 @@
+#!/usr/bin/env python
+"""Storing template configurations
+"""
+import json
+from typing import List
+import random
+
+from softnanotools.logger import Logger
+from starpolymers import molecules
+logger = Logger("CONFIG")
+
+from starpolymers.generators import System
+from starpolymers.io.configuration import ConfigFile
+from starpolymers.molecules import MoleculeFactory
+
+class ConfigurationContainer:
+    star = {
+        'molecule': 'star',
+        'kap': 10,
+        'lam': 3,
+        'charge' : {
+            'max': 0,
+            'style': 'all'
+        },
+        'central' : 'all',
+        'counterions': False,
+        'atom_type': 1,
+    }
+
+    dna = {
+        'molecule': 'dna',
+        'lam': 2,
+        'charge' : {
+            'max': 0,
+            'style': 'all'
+        },
+        'central' : 'all',
+        'counterions': False,
+        'atom_type': 2,
+    }
+
+    salt = {
+        'molecule': 'salt',
+        'anion': 1,
+        'cation': 1,
+        'concentration': 10,
+        'box': 20.0
+    }
+
+    def __init__(self, system: System):
+        self.system = system
+        self.items = []
+
+    def add_stars(
+        self,
+        N: int,
+        lam: int,
+        kap: int,
+    ):
+
+        for i in range(N):
+            item = ConfigurationContainer.star
+            item['kap'] = kap
+            item['lam'] = lam
+            self.items.append(item)
+        return
+
+    def add_dna(
+        self,
+        N: int
+    ):
+        for i in range(N):
+            self.items.append(ConfigurationContainer.dna)
+
+    def initialise(self):
+        random.shuffle(self.items)
+        factory = MoleculeFactory(item_list=self.items, box=self.system._box)
+        self.system.add_molecules(factory.molecules, distribute=True)
+        return
+
+
+def main(
+    stars: int = 5,
+    dna: int = 5,
+    box: float = 20.0,
+    lam: int = 5,
+    kap: int = 4,
+):
+    system = System(
+        box,
+        atom_masses=[1, 1, 1, 1, 1],
+        bond_types=2,
+        angle_types=0
+    )
+    container = ConfigurationContainer(system)
+    container.add_stars(stars, lam, kap)
+    container.add_dna(dna)
+    container.initialise()
+    config_file = ConfigFile(container.system, comment='Test', include_angles=False)
+    config_file.write('lammps.test.conf')
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument('stars', type=int)
+    parser.add_argument('dna', type=int)
+    parser.add_argument('-b', '--box', default=20.0, type=float)
+    parser.add_argument('-l', '--lam', default=5, type=int)
+    parser.add_argument('-k', '--kap', default=4, type=int)
+    main(**vars(parser.parse_args()))
\ No newline at end of file
diff --git a/protocols/generate-many/main.py b/protocols/generate-many/main.py
new file mode 100644
index 0000000..d4a7375
--- /dev/null
+++ b/protocols/generate-many/main.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+"""Example script for generating a LAMMPS system with many of the same
+topology with no overlaps.
+"""
+from starpolymers import generators
+import subprocess
+
+from starpolymers.io.configuration import ConfigFile
+from starpolymers.generators.system import System
+from starpolymers.molecules import MoleculeFactory
+from softnanotools.logger import Logger
+logger = Logger('MAIN')
+
+import config
+
+def generate(n: int, box: float, fname: str = 'lammps.test.conf'):
+    molecule_list = [config.ConfigurationContainer.star] * n
+    molecule_list.append(
+        config.ConfigurationContainer.salt
+    )
+    molecules = MoleculeFactory(molecule_list, box=box).molecules
+    system = System(box, molecules=molecules)
+    config_file = ConfigFile(
+        system,
+        comment=f"Example system with {n} star polymers"
+    )
+    config_file.write(fname=fname, angles=False)
+    return
+
+def run(lammps: str, input_file: str = 'lammps.test.in'):
+    cmd = lammps.split() + ['-i', input_file]
+    subprocess.check_output(cmd)
+    return
+
+def main(**kwargs):
+    generate(5, 50.0)
+    run('mpirun -np 2 /home/debesh/programs/lammps/build/lmp -sf gpu -pk gpu 1')
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    main(**vars(parser.parse_args()))
diff --git a/protocols/squeeze/main.py b/protocols/squeeze/main.py
new file mode 100644
index 0000000..17a878c
--- /dev/null
+++ b/protocols/squeeze/main.py
@@ -0,0 +1,205 @@
+#!/usr/bin/env python
+"""Example script for generating a single topology within a geometry
+with a given shape and size e.g. a sphere with radius=5, a cube with
+side=5 etc.
+"""
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+from mpl_toolkits.mplot3d import Axes3D
+from numpy.core.fromnumeric import squeeze
+from starpolymers.molecules import (
+    MoleculeFactory,
+    StarPolyelectrolyte,
+    LinearPolyelectrolyte,
+    AbstractMolecule
+)
+
+from itertools import product, combinations
+
+from softnanotools.logger import Logger
+logger = Logger('MAIN')
+
+class SqueezeGeometry:
+    __valid_geometries__ = {
+        'cube': {'L'},
+        'sphere': {'R'}
+    }
+
+    def __init__(
+        self,
+        kind: str = 'cube',
+        molecule: AbstractMolecule = None,
+        spacing: float = 1.0,
+        **kwargs
+    ):
+        assert kind in SqueezeGeometry.__valid_geometries__
+        #assert set(kwargs.keys()) == SqueezeGeometry.__valid_geometries__.values()
+        self.kind = kind
+        self.spacing = spacing
+
+        self._molecule = molecule
+        self._bound = 0.0
+
+    @property
+    def bound(self):
+        return self._bound
+
+    @property
+    def molecule(self):
+        return self._molecule
+
+    @molecule.setter
+    def molecule(self, obj: AbstractMolecule):
+        assert isinstance(obj, AbstractMolecule)
+        self._molecule = obj
+
+    def initialise(self, obj: AbstractMolecule):
+        self.molecule = obj
+        return
+
+    def build(
+        self,
+        strategy: str = 'zig-zag'
+    ):
+        """Takes a Molecule's parameters and rebuilds it to ensure that it is
+        centered (by its COM) in the centre of the geometry, and that
+        all of the atoms are within the bounds of the geometry"""
+
+        if strategy == 'zig-zag':
+            spacing = self.spacing
+            # we need to calculate the min and max angle
+
+            # the min angle is the minimum angle needed to avoid the
+            # next-but-one particle in a sequence
+            maximum_angle = np.deg2rad(60.0)
+
+            # the max angle is a maximum angle needed to avoid the edge
+            # of the box
+
+            # the min angle is given by the value of ((0.5 * lambda) / box)
+            # times the spacing, the ratio gives the
+            minimum_angle = float()
+
+            # vertical spacing = hypotenuse
+            # the other two sides = spacing
+
+            # therefore the angle = cosine of (spacing / (0.5 * vertical))
+            vertical = 2.0 * min([self.bound / self.molecule.lam, spacing])
+            print(vertical)
+            minimum_angle = np.arccos(spacing / 0.5 * vertical)
+
+            print(np.degrees(maximum_angle), np.degrees(minimum_angle))
+
+            assert maximum_angle >= minimum_angle, \
+                f"{maximum_angle} not greater than {minimum_angle}"
+
+            deviation = minimum_angle
+
+        else:
+            raise NotImplementedError
+
+        print(f"Deviation Angle is {deviation}")
+
+        return deviation
+
+class SqueezeCube(SqueezeGeometry):
+    def __init__(self, length: float):
+        super().__init__('cube', L=length)
+        self._bound = length
+
+    def add_to_ax(self, ax: plt.Axes):
+        # draw cube
+        r = np.array([-1, 1]) * self._bound
+        for s, e in combinations(np.array(list(product(r, r, r))), 2):
+            if np.sum(np.abs(s-e)) == r[1]-r[0]:
+                ax.plot3D(*zip(s, e), color="b", alpha=0.2)
+
+class SqueezeSphere(SqueezeGeometry):
+    def __init__(self, radius: float):
+        super().__init__('sphere', R=radius)
+        self._bound = radius
+
+    def add_to_ax(self, ax: plt.Axes):
+        # draw sphere
+        u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]
+        x = self._bound * np.cos(u)*np.sin(v)
+        y = self._bound * np.sin(u)*np.sin(v)
+        z = self._bound * np.cos(v)
+        ax.plot_wireframe(x, y, z, color="r", alpha=0.2)
+
+class SqueezedStarPolyelectrolyte(StarPolyelectrolyte):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+    def generate_atoms(self, squeeze: SqueezeGeometry = None):
+        if squeeze:
+            squeeze.initialise(self)
+            squeeze.build()
+
+        spacing = self.settings['spacing']
+        direction = self.settings['direction']
+        mol_length = self.lam * spacing
+        x = []
+        y = []
+        z = []
+        for i in range(self.kap):
+            for j in range(self.lam):
+                x.append((mol_length-(j*spacing))*direction[i][0])
+                y.append((mol_length-(j*spacing))*direction[i][1])
+                z.append((mol_length-(j*spacing))*direction[i][2])
+
+        x.append(0.0)
+        y.append(0.0)
+        z.append(0.0)
+
+        data = pd.DataFrame({
+                'mol' : len(x) * [self.mol],
+                'type' : len(x) * [self.types['atom']],
+                'x' : x,
+                'y' : y,
+                'z' : z,
+                'q' : self.generate_charges(x)
+            })
+
+        return data
+
+star = {
+        'molecule': 'star',
+        'kap': 4,
+        'lam': 10,
+        'charge' : {
+            'max': 1,
+            'style': 'all'
+        },
+        'central' : 'all',
+        'counterions': False,
+        'angle_type': 1
+    }
+
+def visualise(molecule: AbstractMolecule, squeeze: SqueezeGeometry):
+
+    fig = plt.figure()
+    ax = fig.gca(projection='3d')
+    ax.set_aspect("auto")
+    squeeze.add_to_ax(ax)
+    positions = molecule.generate_atoms(squeeze=squeeze)[['x', 'y', 'z']]
+    positions = positions.to_numpy()
+    ax.scatter(positions[:, 0], positions[:, 1], positions[:, 2], 'o')
+    fig.savefig('squeeze.png')
+    pass
+
+
+def main(*args, **kwargs):
+    box = 20
+    molecule = SqueezedStarPolyelectrolyte(star)
+    squeeze = SqueezeSphere(8.0)
+    #print(molecule._atoms)
+    visualise(molecule, squeeze)
+    #print(molecule.generate_atoms())
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    main(**vars(parser.parse_args()))
diff --git a/protocols/yukawa/README.md b/protocols/yukawa/README.md
new file mode 100644
index 0000000..930bf91
--- /dev/null
+++ b/protocols/yukawa/README.md
@@ -0,0 +1,8 @@
+# Yukawa
+
+## Summary
+
+In this section we present a method for simulating systems of polyelectrolytes using
+implicit-solvent, implicit-salt, screened-electrostatics models, which use a Lennard-Jones
+potential for excluded volume simulations, a Yukawa potential to simulate screened electrostatics,
+and a harmonic potential to approximate the energy of covalent bonds between bonded particles.
\ No newline at end of file
diff --git a/protocols/yukawa/config.py b/protocols/yukawa/config.py
new file mode 100644
index 0000000..4a8a830
--- /dev/null
+++ b/protocols/yukawa/config.py
@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+"""config.py - auto-generated by softnanotools"""
+from softnanotools.logger import Logger
+logger = Logger('CONFIG')
+
+def main(**kwargs):
+    logger.info('Running config...')
+    # insert code here
+    logger.info('Done!')
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser(description='config.py - auto-generated by softnanotools')
+    main(**vars(parser.parse_args()))
+
diff --git a/protocols/yukawa/lammps.main.conf b/protocols/yukawa/lammps.main.conf
new file mode 100644
index 0000000..616c24d
--- /dev/null
+++ b/protocols/yukawa/lammps.main.conf
@@ -0,0 +1,149 @@
+# LAMMPS config file [2020-05-22 18:31:45]
+# Neutral Linear Polyelectrolyte
+
+42 atoms
+40 bonds
+38 angles
+
+3 atom types
+1 bond types
+1 angle types
+
+-15.0 15.0 xlo xhi
+-15.0 15.0 ylo yhi
+-15.0 15.0 zlo zhi
+
+Masses
+
+1 1.0
+2 1.0
+3 1.0
+
+Atoms
+
+1 1 1 1.0 1.0 1.0
+2 1 1 2.0 1.0 1.0
+3 1 1 3.0 1.0 1.0
+4 1 1 4.0 1.0 1.0
+5 1 1 5.0 1.0 1.0
+6 1 1 6.0 1.0 1.0
+7 1 1 7.0 1.0 1.0
+8 1 1 8.0 1.0 1.0
+9 1 1 9.0 1.0 1.0
+10 1 1 10.0 1.0 1.0
+11 1 2 11.0 1.0 1.0
+12 1 2 12.0 1.0 1.0
+13 1 2 13.0 1.0 1.0
+14 1 2 14.0 1.0 1.0
+15 1 2 15.0 1.0 1.0
+16 1 2 16.0 1.0 1.0
+17 1 2 17.0 1.0 1.0
+18 1 3 18.0 1.0 1.0
+19 1 3 19.0 1.0 1.0
+20 1 3 20.0 1.0 1.0
+21 1 3 21.0 1.0 1.0
+22 2 1 1.0 1.0 5.0
+23 2 1 2.0 1.0 5.0
+24 2 1 3.0 1.0 5.0
+25 2 1 4.0 1.0 5.0
+26 2 1 5.0 1.0 5.0
+27 2 1 6.0 1.0 5.0
+28 2 1 7.0 1.0 5.0
+29 2 1 8.0 1.0 5.0
+30 2 1 9.0 1.0 5.0
+31 2 1 10.0 1.0 5.0
+32 2 2 11.0 1.0 5.0
+33 2 2 12.0 1.0 5.0
+34 2 2 13.0 1.0 5.0
+35 2 2 14.0 1.0 5.0
+36 2 2 15.0 1.0 5.0
+37 2 2 16.0 1.0 5.0
+38 2 2 17.0 1.0 5.0
+39 2 3 18.0 1.0 5.0
+40 2 3 19.0 1.0 5.0
+41 2 3 20.0 1.0 5.0
+42 2 3 21.0 1.0 5.0
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 13 14
+14 1 14 15
+15 1 15 16
+16 1 16 17
+17 1 17 18
+18 1 18 19
+19 1 19 20
+20 1 20 21
+21 1 22 23
+22 1 23 24
+23 1 24 25
+24 1 25 26
+25 1 26 27
+26 1 27 28
+27 1 28 29
+28 1 29 30
+29 1 30 31
+30 1 31 32
+31 1 32 33
+32 1 33 34
+33 1 34 35
+34 1 35 36
+35 1 36 37
+36 1 37 38
+37 1 38 39
+38 1 39 40
+39 1 40 41
+40 1 41 42
+
+Angles
+
+1 1 1 2 3
+2 1 2 3 4
+3 1 3 4 5
+4 1 4 5 6
+5 1 5 6 7
+6 1 6 7 8
+7 1 7 8 9
+8 1 8 9 10
+9 1 9 10 11
+10 1 10 11 12
+11 1 11 12 13
+12 1 12 13 14
+13 1 13 14 15
+14 1 14 15 16
+15 1 15 16 17
+16 1 16 17 18
+17 1 17 18 19
+18 1 18 19 20
+19 1 19 20 21
+20 1 22 23 24
+21 1 23 24 25
+22 1 24 25 26
+23 1 25 26 27
+24 1 26 27 28
+25 1 27 28 29
+26 1 28 29 30
+27 1 29 30 31
+28 1 30 31 32
+29 1 31 32 33
+30 1 32 33 34
+31 1 33 34 35
+32 1 34 35 36
+33 1 35 36 37
+34 1 36 37 38
+35 1 37 38 39
+36 1 38 39 40
+37 1 39 40 41
+38 1 40 41 42
diff --git a/protocols/yukawa/lammps.main.in b/protocols/yukawa/lammps.main.in
new file mode 100644
index 0000000..47be2ef
--- /dev/null
+++ b/protocols/yukawa/lammps.main.in
@@ -0,0 +1,39 @@
+# Harmonic beadspring benchmark, with yukawa potential
+
+units		lj
+atom_style	angle
+special_bonds lj 1.0 1.0 1.0
+
+read_data	lammps.main.conf
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style  harmonic
+bond_coeff	1 5.0 2.0
+
+#angle_style harmonic
+#angle_coeff 1 5.0 120
+
+pair_style	hybrid/overlay lj/cut 1.12 yukawa 5.0 10.0
+
+# lj/cut
+pair_modify pair lj/cut shift yes
+pair_coeff	* * lj/cut 1.0 1.0 1.12
+
+# yukawa
+pair_coeff * * yukawa 0.0
+pair_coeff 1 1 yukawa 1.0
+pair_coeff 1 3 yukawa -1.0
+pair_coeff 3 3 yukawa 1.0
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 1.0 904297
+
+thermo  10000
+dump 1 all atom 10000 dump/dump.*
+timestep	0.0012
+
+minimize 0.0 1.0e-8 1000 100000
+
+run		1000000
diff --git a/protocols/yukawa/log.lammps b/protocols/yukawa/log.lammps
new file mode 100644
index 0000000..66dd3b3
--- /dev/null
+++ b/protocols/yukawa/log.lammps
@@ -0,0 +1,259 @@
+LAMMPS (10 Feb 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# Harmonic beadspring benchmark, with yukawa potential
+
+units		lj
+atom_style	angle
+special_bonds lj 1.0 1.0 1.0
+
+read_data	lammps.main.conf
+Reading data file ...
+  orthogonal box = (-15.000000 -15.000000 -15.000000) to (15.000000 15.000000 15.000000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  42 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  40 bonds
+  reading angles ...
+  38 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    1        1        1       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.002 seconds
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style  harmonic
+bond_coeff	1 5.0 2.0
+
+#angle_style harmonic
+#angle_coeff 1 5.0 120
+
+pair_style	hybrid/overlay lj/cut 1.12 yukawa 5.0 10.0
+
+# lj/cut
+pair_modify pair lj/cut shift yes
+pair_coeff	* * lj/cut 1.0 1.0 1.12
+
+# yukawa
+pair_coeff * * yukawa 0.0
+pair_coeff 1 1 yukawa 1.0
+pair_coeff 1 3 yukawa -1.0
+pair_coeff 3 3 yukawa 1.0
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 1.0 904297
+
+thermo  10000
+dump 1 all atom 10000 dump/dump.*
+timestep	0.0012
+
+minimize 0.0 1.0e-8 1000 100000
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
+WARNING: Angles are defined but no angle style is set (src/force.cpp:206)
+WARNING: Likewise 1-3 special neighbor interactions != 1.0 (src/force.cpp:208)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.4
+  ghost atom cutoff = 10.4
+  binsize = 5.2, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair yukawa, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.700 | 7.700 | 7.700 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   0.95607455    4.7619048    5.7179793  0.016802164 
+      94            0 -0.00014330923 1.7453841e-07 -0.00014313469 -2.0284159e-07 
+Loop time of 0.00854897 on 1 procs for 94 steps with 42 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = linesearch alpha is zero
+  Energy initial, next-to-last, final = 
+      5.71797930706399 -0.000143134694575733 -0.000143134694575733
+  Force two-norm initial, final = 68.081154 0.048646867
+  Force max component initial, final = 34.040553 0.024753296
+  Final line search alpha, max atom move = 0.00024414062 6.0432853e-06
+  Iterations, force evaluations = 94 268
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0068839  | 0.0068839  | 0.0068839  |   0.0 | 80.52
+Bond    | 0.00023699 | 0.00023699 | 0.00023699 |   0.0 |  2.77
+Neigh   | 0.00058079 | 0.00058079 | 0.00058079 |   0.0 |  6.79
+Comm    | 0.00018048 | 0.00018048 | 0.00018048 |   0.0 |  2.11
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0006669  |            |       |  7.80
+
+Nlocal:        42.0000 ave          42 max          42 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        53.0000 ave          53 max          53 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        563.000 ave         563 max         563 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 563
+Ave neighs/atom = 13.404762
+Ave special neighs/atom = 5.4285714
+Neighbor list builds = 24
+Dangerous builds = 0
+
+run		1000000
+WARNING: Angles are defined but no angle style is set (src/force.cpp:206)
+WARNING: Likewise 1-3 special neighbor interactions != 1.0 (src/force.cpp:208)
+Per MPI rank memory allocation (min/avg/max) = 6.575 | 6.575 | 6.575 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+      94            0 -0.00014330923 1.7453841e-07 -0.00014313469 -2.0284159e-07 
+   10000    1.1462631 5.7842903e-05   0.51327984    2.1917943 0.00048181745 
+   20000   0.98285455 0.00047480314   0.47637311    1.9160278 -0.00015631273 
+   30000    1.1227838  8.29448e-05   0.67523931    2.3193986 -0.00039396965 
+   40000   0.99374454 6.5853042e-05   0.61488376    2.0700755 -0.00090846742 
+   50000   0.75358594 0.00084046358   0.57195248    1.6762581 -0.00053871608 
+   60000   0.71431832 4.8055262e-05   0.47470554    1.5207197 -0.0012573722 
+   70000     1.149685 0.0073688962   0.48358923    2.1744255 0.00072942624 
+   80000    1.1269927 2.9412752e-05   0.40810792    2.0583766 0.00021281591 
+   90000    0.9417947 0.0059085002   0.41345384    1.7984189 -0.00029006741 
+  100000   0.94637132 0.0017819297   0.54188341    1.9294233 6.2645037e-05 
+  110000    1.0736307 0.00087891441   0.45517746    2.0281584 0.00092277681 
+  120000    1.0253087 -2.1235534e-05   0.46115948    1.9624831 8.5602296e-05 
+  130000   0.89330395 0.0091324104   0.64576476    1.9629494 0.00040842239 
+  140000   0.99157911 0.0048310535   0.38617644    1.8429626 0.00029629943 
+  150000   0.85956604 0.00018348273   0.63334873    1.8921825 -0.00077306618 
+  160000    1.1024819 0.00022174075   0.53419492    2.1487652 5.6650838e-05 
+  170000   0.98883936 3.262117e-05   0.62697456    2.0749505 -0.001310114 
+  180000    1.0363726 0.0065568721   0.36343213    1.8875346  0.001513373 
+  190000    1.0486589  0.028305548   0.46014952    2.0239913 0.0007459676 
+  200000    1.1801872 0.00011502969   0.60954897    2.3377952 -0.00020949634 
+  210000    1.0902987 4.001813e-05   0.49733587    2.0938847 -0.00015838474 
+  220000   0.96178539 0.00015169345   0.76817672     2.176657 -0.0016375065 
+  230000    0.7886369  0.069715377   0.42384246    1.6483476 0.00051314102 
+  240000   0.97574255 2.7198149e-05   0.53320546    1.9619985 -0.00052767077 
+  250000    1.0635868 0.00015068849   0.47706923    2.0346149 0.00034724426 
+  260000   0.93091759 7.999423e-05    0.6570437     2.020253 -0.0021713475 
+  270000    1.0426365 0.00010303931   0.36278844    1.8896092 0.00052617732 
+  280000    1.1176872 0.00011055802   0.41524606      2.05197 0.00058952953 
+  290000    1.0950597 0.0076414577   0.55851324     2.169635 -0.00035066456 
+  300000    1.1015042 0.00028232933   0.49413374     2.107333 0.00034635423 
+  310000    1.0004292 4.517369e-05   0.31768848    1.7826479 0.00092761902 
+  320000    1.0509088 0.0025007768   0.41147158    1.9528032  0.001036808 
+  330000    1.2986756 3.5804065e-05   0.48115278    2.3828207 0.00060892335 
+  340000    1.1299933 9.2130526e-05   0.44417016    2.0988953 1.9828464e-06 
+  350000   0.82577923 0.0071735949   0.60155315    1.8179035 -0.00019462744 
+  360000    1.0425239 3.557105e-05   0.57649458     2.103083 -0.00085046871 
+  370000   0.98873937 0.0013426592   0.45808351    1.9072231 -3.7254307e-05 
+  380000   0.86430881 0.00013666319   0.62711997    1.8928517 -0.0013841533 
+  390000    1.1592427 3.4453381e-05   0.55186579    2.2493628 0.00014885223 
+  400000     1.037789 1.4976711e-05    0.4443973    1.9640319 -0.00025270538 
+  410000     1.021272 0.0001938716   0.47199521    1.9676231 0.0016422915 
+  420000   0.81315084 0.0076870113   0.51327783      1.71165 -0.00042239785 
+  430000   0.94043423 0.00048343155    0.7013742     2.078922 -0.00094107825 
+  440000    1.1096466   0.03876733   0.48334717    2.1469542 0.0010707089 
+  450000   0.70338048 0.00090654675   0.56366067    1.5945172 -0.00049374484 
+  460000   0.91104251 0.00013133624   0.45119129    1.7853492 -0.00051006277 
+  470000   0.96751155  0.030505762   0.61103714    2.0582562 0.00024554612 
+  480000   0.88083762  0.001156848   0.53700662    1.8279614 -0.00033451696 
+  490000    1.0668012 0.00010317114   0.57023915    2.1324441 6.2025521e-05 
+  500000    1.0137845 0.00012482508   0.59270694    2.0773019 -0.00032384736 
+  510000    1.0858168  0.018190281   0.71387661     2.322013 -0.00093021647 
+  520000    1.0630412 5.1434232e-05    0.6447498    2.2013973 -0.00064676445 
+  530000   0.84134966  0.010425932   0.34206983     1.584472 0.00010747126 
+  540000    1.1285189 0.00014296727   0.48959385     2.142211 2.9779253e-05 
+  550000    1.1133122 6.7293218e-05   0.71425191    2.3445264 -0.00080015305 
+  560000   0.86193994 9.1676488e-05   0.42752976    1.6897478 -0.00057607359 
+  570000    1.1937479 0.00075236348   0.65008783    2.3988281 0.00027176891 
+  580000   0.81810724 0.00016262038    0.4835365    1.6816419 -0.00031942468 
+  590000   0.94734293  0.028238377   0.67513916    2.0905582 -2.9316015e-05 
+  600000   0.98403454 2.8763711e-05   0.41661671    1.8575532 0.00015469798 
+  610000     1.088453 0.0001587111   0.50174247    2.0957073 0.00083974672 
+  620000    1.2968282 0.00012359951   0.47741123    2.3764619 0.00024533461 
+  630000    0.8179274 0.00043109098   0.61061915    1.8087297 -0.00080479023 
+  640000   0.93032338 0.0027157962   0.40943269    1.7744077 -0.00033806645 
+  650000    1.0601593 0.00016587784   0.55176542    2.1043074 0.00040137433 
+  660000    1.3189111   0.01304718   0.32552865    2.2698386 0.00074302672 
+  670000    1.2256607  0.052721825   0.74372223    2.5911615 -0.00030618609 
+  680000   0.80071989  0.041720997   0.66303084    1.8772345 -0.00097412994 
+  690000   0.95364509  0.036790512   0.51297554    1.9461749 0.00063540493 
+  700000   0.79731071 8.0623143e-05    0.4016484    1.5692197 -9.9027361e-06 
+  710000   0.89071934 0.00046399879   0.42087009    1.7256017 0.00041293412 
+  720000   0.95665692 0.0089555992   0.47238546    1.8821601 0.00056031128 
+  730000    1.1676467  0.020763338   0.50774158    2.2382733 0.0005075967 
+  740000   0.82741878 0.0090855872   0.38013065    1.6007937 0.00041865552 
+  750000    1.0080857  0.004731246   0.56025695    2.0411136 -0.00078350694 
+  760000   0.82702404 0.00015291663   0.46977313    1.6809255 -0.000820905 
+  770000   0.96391648 0.0013411274   0.60417827    2.0169685 -0.00051956373 
+  780000   0.97528532 0.0028410074   0.51110293    1.9420403 -0.00051762185 
+  790000   0.78582539 0.00014368726   0.48396785    1.6347844 -0.0005262384 
+  800000    1.1482334 0.0060664637   0.51461303    2.2020212 0.00061909959 
+  810000   0.97882137 0.0066405353   0.64670125    2.0866159 0.00018788314 
+  820000    1.2317391 0.00056565713   0.56221964    2.3664033 3.0818488e-05 
+  830000    1.2564498 0.00013237183   0.58542169    2.4253556 6.5635002e-05 
+  840000    1.1027131  0.064946055   0.58579155    2.2654246 5.3564737e-05 
+  850000   0.87641564  0.022664286   0.46957842    1.7755656 -7.7430743e-05 
+  860000   0.87009387 0.00011914161   0.46083289    1.7350181 0.00066066729 
+  870000   0.94953883 4.1557498e-05   0.43840292    1.8288406 0.00021541861 
+  880000    1.1087456 0.0039510655   0.33703983    1.9645112 0.00050410223 
+  890000    1.0562433 0.00012170508   0.66953279    2.2162965 -0.00046789575 
+  900000    1.0072998  0.011128926   0.64044647    2.1265501 -0.0008122421 
+  910000    1.1081698 0.0058118881   0.39686724    2.0253564 0.00070757328 
+  920000    1.0861105 0.00013435198   0.37542079    1.9659312 -0.00014243232 
+  930000    1.1237137 0.0039054941   0.45194116    2.1012846 0.00068601302 
+  940000    1.0917986 0.0002795543    0.4568898    2.0558745 0.00077213776 
+  950000   0.89542416 9.7223127e-05   0.70809365    2.0193477 -0.00080469826 
+  960000    1.1085226 0.0040694572   0.59589006    2.2231534 5.1072758e-05 
+  970000    1.2086448  0.016049678   0.54070735    2.3265583 0.00049708203 
+  980000    1.0891058 4.7795772e-05   0.53389572    2.1287056 -0.00076089985 
+  990000    0.9278773 0.0063742976   0.44211313    1.8071649 -0.00032156668 
+ 1000000    1.0253641 6.2993788e-05   0.69841023    2.1998992 -0.0017040317 
+ 1000094    1.0018359   0.02523756   0.61766897    2.1098805 -0.0011299612 
+Loop time of 21.0352 on 1 procs for 1000000 steps with 42 atoms
+
+Performance: 4928882.091 tau/day, 47539.372 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 15.768     | 15.768     | 15.768     |   0.0 | 74.96
+Bond    | 0.64757    | 0.64757    | 0.64757    |   0.0 |  3.08
+Neigh   | 0.58841    | 0.58841    | 0.58841    |   0.0 |  2.80
+Comm    | 0.93264    | 0.93264    | 0.93264    |   0.0 |  4.43
+Output  | 0.02342    | 0.02342    | 0.02342    |   0.0 |  0.11
+Modify  | 2.6148     | 2.6148     | 2.6148     |   0.0 | 12.43
+Other   |            | 0.4604     |            |       |  2.19
+
+Nlocal:        42.0000 ave          42 max          42 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        258.000 ave         258 max         258 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        507.000 ave         507 max         507 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 507
+Ave neighs/atom = 12.071429
+Ave special neighs/atom = 5.4285714
+Neighbor list builds = 19068
+Dangerous builds = 0
+Total wall time: 0:00:21
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..5b9cea9
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,29 @@
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = starpolymers/_version.py
+versionfile_build = starpolymers/_version.py
+tag_prefix = v
+
+# .coveragerc to control coverage.py
+[coverage:run]
+branch = True
+omit = *test*, *_version.py
+
+[coverage:report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
\ No newline at end of file
diff --git a/setup.py b/setup.py
index c5a7655..a6ec338 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,11 @@
 import setuptools
+import versioneer
 
 with open("README.md", "r") as f:
     long_description = f.read()
 
 setuptools.setup(
     name="starpolymers",
-    version="2.1.0",
     author="Debesh Mandal",
     description="Package for creating polymers for simulation",
     long_description=long_description,
@@ -18,6 +18,8 @@
         "Operating System :: OS Independent",
     ],
     python_requires=">=3.5",
-    package_data = {'starpolymers' : ['generators/input_files/*.in']},
-    include_package_data=True
+    package_data = {'starpolymers' : ['io/input_files/*.in']},
+    include_package_data=True,
+    version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
 )
diff --git a/starpolymers/__init__.py b/starpolymers/__init__.py
index f256c09..50cb1ba 100644
--- a/starpolymers/__init__.py
+++ b/starpolymers/__init__.py
@@ -1,2 +1,7 @@
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions
+
 from .molecules import MoleculeFactory
-from .generators import System, ConfigFile
+from .generators import System
+from .io import ConfigFile
diff --git a/starpolymers/_version.py b/starpolymers/_version.py
new file mode 100644
index 0000000..84a8b30
--- /dev/null
+++ b/starpolymers/_version.py
@@ -0,0 +1,520 @@
+
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "$Format:%d$"
+    git_full = "$Format:%H$"
+    git_date = "$Format:%ci$"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "pep440"
+    cfg.tag_prefix = "v"
+    cfg.parentdir_prefix = "None"
+    cfg.versionfile_source = "softnanotools/_version.py"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r'\d', r)])
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            if verbose:
+                print("picking %s" % r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
+                                          "--always", "--long",
+                                          "--match", "%s*" % tag_prefix],
+                                   cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for i in cfg.versionfile_source.split('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}
diff --git a/starpolymers/generators/__init__.py b/starpolymers/generators/__init__.py
index 4226df3..f10f0e7 100644
--- a/starpolymers/generators/__init__.py
+++ b/starpolymers/generators/__init__.py
@@ -1,2 +1,1 @@
-from .system import System
-from .configuration import ConfigFile
\ No newline at end of file
+from .system import System
\ No newline at end of file
diff --git a/starpolymers/generators/configuration.py b/starpolymers/generators/configuration.py
deleted file mode 100644
index 169d93e..0000000
--- a/starpolymers/generators/configuration.py
+++ /dev/null
@@ -1,163 +0,0 @@
-from .system import System
-import datetime
-
-import pandas as pd
-
-class ConfigFile():
-    def __init__(self, system, comment=''):
-        self._system = system
-        self.comment = comment
-
-    def write(self, fname='config.dat'):
-        with open(fname, 'w') as f:
-            f.write(self.comments)
-            f.write(self.header)
-            f.write(self.masses)
-            f.write(self.atoms)
-            f.write(self.bonds)
-            f.write(self.angles)
-
-    @property
-    def comments(self):
-        first_line = 'LAMMPS config file [{}]'.format(
-            str(datetime.datetime.today()).split('.')[0]
-        )
-        second_line = self.comment
-        comments = '# {}\n# {}\n\n'.format(first_line, second_line)
-        return comments
-
-    @property
-    def header(self):
-        box = self._system.box
-        header = ''
-        header += str("{} atoms\n".format(self._system.n['atoms']))
-        header += str("{} bonds\n".format(self._system.n['bonds']))
-        header += str("{} angles\n".format(self._system.n['angles']))
-        header += "\n"
-        header += str("{} atom types\n".format(self._system.types['atom']))
-        header += str("{} bond types\n".format(self._system.types['bond']))
-        header += str("{} angle types\n".format(self._system.types['angle']))
-        header += "\n"
-        header += str("{} {} xlo xhi\n".format(box['xlo'], box['xhi']))
-        header += str("{} {} ylo yhi\n".format(box['ylo'], box['yhi']))
-        header += str("{} {} zlo zhi\n".format(box['zlo'], box['zhi']))
-        return header
-    
-    @property
-    def masses(self):
-        masses = '\nMasses\n\n'
-        for i, mass in enumerate(self._system._masses):
-            masses += "{} {}\n".format(i + 1, mass)
-        return masses
-
-    @property
-    def atoms(self):
-        atoms = '\nAtoms\n\n' 
-        table = self._system.atoms
-        for i in range(len(table)):
-            atoms += "{} {} {} {} {} {} {}\n".format(
-                i + 1,
-                table['mol'][i],
-                table['type'][i],
-                table['q'][i],
-                table['x'][i],
-                table['y'][i],
-                table['z'][i]
-            )
-        return atoms
-
-    @property
-    def bonds(self):
-        bonds = '\nBonds\n\n' 
-        table = self._system.bonds
-        for i in range(len(table)):
-            bonds += "{} {} {} {}\n".format(
-                i + 1,
-                table['type'][i],
-                int(table['atom_1'][i]),
-                int(table['atom_2'][i])
-            )
-        return bonds
-
-    @property
-    def angles(self):
-        angles = '\nAngles\n\n' 
-        table = self._system.angles
-        for i in range(len(table)):
-            angles += "{} {} {} {} {}\n".format(
-                i + 1,
-                table['type'][i],
-                table['atom_1'][i],
-                table['atom_2'][i],
-                table['atom_3'][i]
-            )
-        return angles
-
-    @staticmethod
-    def stats(fname):
-        stats = {}
-
-        with open(fname, 'r') as f:
-            [f.readline() for i in range(3)]
-            stats['n_atoms'] = int(f.readline().split()[0])
-            stats['n_bonds'] = int(f.readline().split()[0])
-            stats['n_angles'] = int(f.readline().split()[0])
-            f.readline()
-            stats['atom_types'] = int(f.readline().split()[0])
-            stats['bond_types'] = int(f.readline().split()[0])
-            stats['angle_types'] = int(f.readline().split()[0])
-
-        skip_atoms = 21+stats['atom_types']
-        skip_bonds = 24+stats['atom_types']+stats['n_atoms']
-        skip_angles = 26+stats['atom_types']+stats['n_atoms']+stats['n_bonds']
-
-        stats['atoms'] = pd.read_csv(
-                fname, 
-                delim_whitespace=True, 
-                header=None, 
-                skiprows=skip_atoms,
-                nrows=stats['n_atoms']
-            )
-
-        stats['bonds'] = pd.read_csv(
-                fname, 
-                delim_whitespace=True, 
-                header=None, 
-                skiprows=skip_bonds,
-                nrows=stats['n_bonds']
-            )
-
-        stats['angles'] = pd.read_csv(
-                fname, 
-                delim_whitespace=True, 
-                header=None, 
-                skiprows=skip_angles,
-                nrows=stats['n_angles']
-            )
-
-        return stats
-
-    @staticmethod
-    def validate(fname):
-        stats = ConfigFile.stats(fname)
-        for name in ['atom', 'bond', 'angle']:
-            header_n = stats['n_{}s'.format(name)]
-            length_n = len(stats['{}s'.format(name)])
-            if header_n != length_n:
-                return False
-        return True
-
-    @staticmethod
-    def compare(fname_1, fname_2):
-        stats_1 = ConfigFile.stats(fname_1)
-        stats_2 = ConfigFile.stats(fname_2)
-        for key, value in list(stats_1.items()):
-            try:
-                if stats_2[key] != value:
-                    return False
-            except ValueError:
-                if isinstance(value, pd.DataFrame):
-                    continue
-                else:
-                    raise ValueError
-        return True
\ No newline at end of file
diff --git a/starpolymers/generators/system.py b/starpolymers/generators/system.py
index 64591b2..1ed3ef3 100644
--- a/starpolymers/generators/system.py
+++ b/starpolymers/generators/system.py
@@ -1,14 +1,28 @@
 import numpy as np
 import pandas as pd
 
+from typing import List
+
 from scipy.spatial.distance import cdist
 from starpolymers.molecules import Salt
 from starpolymers.molecules._common import registry, AbstractMolecule
 
 
 class System():
-    def __init__(self, box, molecules=[], atom_masses=[1.0], bond_types=1, angle_types=1, threshold=0.01):
-
+    def __init__(
+        self,
+        box,
+        molecules=[],
+        atom_masses=[1.0],
+        bond_types=1,
+        angle_types=1,
+        threshold=0.01,
+        allow_unbalanced_charges: bool = False
+    ):
+        # initial setting to account for unbalanced charges
+        self.allow_unbalanced_charges = allow_unbalanced_charges
+
+        # initialise tables
         self._atom_ID_shift = 0
         self._molecules = int(0)
         self._box = float(box)
@@ -27,16 +41,58 @@ def __init__(self, box, molecules=[], atom_masses=[1.0], bond_types=1, angle_typ
         self._angles = pd.DataFrame(
             columns = registry.columns['angles']
         )
-        
+
         self.add_molecules(molecules)
         self.assert_neutral()
         self.fix_overlap(threshold)
 
-    def add_molecules(self, molecules):
+    def add_molecules(self, molecules: List[AbstractMolecule], distribute: bool = False):
+        """Adds a list of molecules stored as a list of AbstractMolecule to
+        the system, if the keyword argument distribute is set to True, then
+        the molecules will dynamically by placed in a grid throughout the
+        box
+
+        Parameters:
+        -----------
+            molecules: a list of items stored as AbstractMolecule
+            distribute:
+                if True, dynamically translates the molecules to fit
+                in the space
+
+        Raises:
+        -------
+            AssertionError:
+                if the system is not neutral in charge after adding
+                the molecules to the system
+
+        """
+        N = len(molecules)
+        if distribute:
+            positions = []
+            row_size = np.ceil(np.cbrt(N))
+            grid_space = (self._box) / (row_size + 1)
+            for i in range(N):
+                a = (i // row_size) - 1
+                b = (i % row_size) - 1
+                c = (i // (row_size ** 2)) - 1
+
+                a -= (c + 1) * row_size
+                com = np.array([a, b, c]) * grid_space
+                positions.append(com)
 
         for i, molecule in enumerate(molecules):
             if molecule._item['molecule'] == 'salt':
                 mol, salt = i, molecule
+
+            if distribute:
+                com = molecule._atoms[['x', 'y', 'z']].mean(axis=0).to_numpy()
+                x = (positions[i][0] - com[0])
+                y = (positions[i][1] - com[1])
+                z = (positions[i][2] - com[2])
+                molecule._atoms['x'] = molecule._atoms['x'] + x
+                molecule._atoms['y'] = molecule._atoms['y'] + y
+                molecule._atoms['z'] = molecule._atoms['z'] + z
+
             self.add_molecule(molecule)
 
         try:
@@ -65,10 +121,9 @@ def fix_overlap(self, threshold):
                 raise StopIteration("Trying to fix overlaps but reached iteration limit of 25.")
         return
 
-
-
     def assert_neutral(self):
-        assert self.charge == 0
+        if not self.allow_unbalanced_charges:
+            assert self.charge == 0
 
     @property
     def atoms(self):
@@ -81,7 +136,7 @@ def bonds(self):
     @property
     def angles(self):
         return self._angles
-    
+
     @property
     def box(self):
         return {
@@ -107,7 +162,7 @@ def charge(self):
         _charge = sum(self._atoms['q'].values)
         return _charge
 
-    def add_molecule(self, molecule):
+    def add_molecule(self, molecule: AbstractMolecule, auto_translate: bool = False):
         #if not isinstance(molecule, AbstractMolecule):
         #    raise TypeError(
         #        'A molecule that is not an '
@@ -115,9 +170,10 @@ def add_molecule(self, molecule):
         def _atoms():
             _temp = molecule._atoms.copy()
             _temp['mol'] = self._molecules + 1
-            _temp['x'] = _temp['x'].values + registry.start[self._molecules, 0] * self.box['xhi']
-            _temp['y'] = _temp['y'].values + registry.start[self._molecules, 1] * self.box['yhi']
-            _temp['z'] = _temp['z'].values + registry.start[self._molecules, 2] * self.box['zhi']
+            if auto_translate:
+                _temp['x'] = _temp['x'].values + registry.start[self._molecules, 0] * self.box['xhi']
+                _temp['y'] = _temp['y'].values + registry.start[self._molecules, 1] * self.box['yhi']
+                _temp['z'] = _temp['z'].values + registry.start[self._molecules, 2] * self.box['zhi']
             self._atoms = pd.concat([self._atoms, _temp], sort=False).reset_index(drop=True)
 
         def _bonds():
@@ -132,7 +188,7 @@ def _angles():
             _temp['atom_2'] = _temp['atom_2'] + self._atom_ID_shift
             _temp['atom_3'] = _temp['atom_3'] + self._atom_ID_shift
             self._angles = pd.concat([self._angles, _temp], sort=False).reset_index(drop=True)
-        
+
         _atoms()
         _bonds()
         _angles()
@@ -153,7 +209,7 @@ def difference(_delta, n_anions, anion, n_cations, cation):
         if delta < 0:
             n_cations = abs( delta // abs(int(salt.cation)) )
             n_anions = 0
-            
+
         if delta > 0:
             n_anions = abs( delta // abs(int(salt.anion)))
             n_cations = 0
@@ -171,12 +227,12 @@ def difference(_delta, n_anions, anion, n_cations, cation):
             i+=1
             if i > 20:
                 raise StopIteration
-            
+
         n = int(n_cations + n_anions)
 
         if mol == None:
             mol = self._molecules
-        
+
         self._atoms = pd.concat([self._atoms,
             pd.DataFrame({
                     'mol' : n * [mol],
@@ -187,7 +243,7 @@ def difference(_delta, n_anions, anion, n_cations, cation):
                     'q' : [salt.cation] * int(n_cations) + [-salt.anion] * int(n_anions)
                 })
             ], sort=True).reset_index(drop=True)
-        
+
         self.assert_neutral()
         return
 
diff --git a/starpolymers/io/__init__.py b/starpolymers/io/__init__.py
new file mode 100644
index 0000000..03beb5b
--- /dev/null
+++ b/starpolymers/io/__init__.py
@@ -0,0 +1,3 @@
+from .colvars import Colvars
+from .input_file import InputFile
+from .configuration import ConfigFile
diff --git a/starpolymers/generators/colvars.py b/starpolymers/io/colvars.py
similarity index 100%
rename from starpolymers/generators/colvars.py
rename to starpolymers/io/colvars.py
diff --git a/starpolymers/io/configuration.py b/starpolymers/io/configuration.py
new file mode 100644
index 0000000..66f1a2e
--- /dev/null
+++ b/starpolymers/io/configuration.py
@@ -0,0 +1,295 @@
+from ..generators.system import System
+import datetime
+import time
+
+import pandas as pd
+
+STYLES = [
+    'atomic',
+    'bond',
+    'angle',
+    'dihedral',
+    'full',
+    'molecular',
+    'charge',
+]
+
+class ConfigFile():
+    def __init__(
+        self,
+        system: System,
+        comment: str = '',
+        style: str = 'full',
+        include_bonds: bool = True,
+        include_angles: bool = True,
+        include_dihedrals: bool = False,
+        include_charges: bool = False,
+    ):
+        # important attributes
+        self._system = system
+        self.comment = comment
+        self.style = style
+
+        # list of things to include
+        # note that style will dynamically EXCLUDE some of these
+        self.include_bonds = include_bonds
+        self.include_angles = include_angles
+        self.include_dihedrals = include_dihedrals
+        self.include_charges = include_charges
+
+        self.implement_style()
+
+    def implement_style(self, style: str = None):
+        """Changes all obj.include_* boolean storage units to ensure
+        only the proper parts of the system are included"""
+        if style:
+            self.style = style
+
+        def atomic():
+            self.include_bonds = False
+            self.include_angles = False
+            self.include_dihedrals = False
+            self.include_charges = False
+            return
+
+        def bond():
+            # skip bonds - defined in class
+            self.include_angles = False
+            self.include_dihedrals = False
+            self.include_charges = False
+            return
+
+        def angle():
+            # skip bonds - defined in class
+            # skip angles - defined in class
+            self.include_dihedrals = False
+            self.include_charges = False
+            return
+
+        def molecular():
+            # skip bonds - defined in class
+            # skip angles - defined in class
+            # skip dihedrals - defined in class
+            self.include_charges = False
+            return
+
+        def dihedral():
+            # skip bonds - defined in class
+            # skip angles - defined in class
+            # skip dihedrals - defined in class
+            self.include_charges = False
+            raise NotImplementedError
+            return
+
+        def full():
+            # skip bonds - defined in class
+            # skip angles - defined in class
+            # skip dihedrals - defined in class
+            self.include_charges = True
+            return
+
+        def charge():
+            self.include_bonds = False
+            self.include_angles = False
+            self.include_dihedrals = False
+            self.include_charges = True
+            return
+
+        # create hash-table of style functions
+        style_functions = {
+            'atomic': atomic,
+            'bond': bond,
+            'angle': angle,
+            'dihedral': dihedral,
+            'full': full,
+            'molecular': molecular,
+            'charge': charge
+        }
+
+        # choose function and call
+        style_functions[self.style]()
+
+        return
+
+    def write(
+        self,
+        fname='lammps.main.conf',
+        bonds: bool = None,
+        angles: bool = None,
+        dihedrals: bool = None,
+        style: str = None,
+    ):
+
+        if style:
+            self.implement_style(style=style)
+
+        with open(fname, 'w') as f:
+            f.write(self.comments)
+            f.write(self.header)
+            f.write(self.masses)
+            f.write(self.atoms)
+            if bonds or self.include_bonds:
+                f.write(self.bonds)
+            if angles or self.include_angles:
+                f.write(self.angles)
+            if dihedrals or self.include_dihedrals:
+                raise NotImplementedError
+
+
+    @property
+    def comments(self):
+        first_line = 'LAMMPS config file [{}]'.format(
+            str(datetime.datetime.today()).split('.')[0]
+        )
+        second_line = self.comment
+        comments = '# {}\n# {}\n\n'.format(first_line, second_line)
+        return comments
+
+    @property
+    def header(self):
+        box = self._system.box
+        header = ''
+        header += str("{} atoms\n".format(self._system.n['atoms']))
+        header += str("{} bonds\n".format(self._system.n['bonds']))
+        if self.include_angles:
+            header += str("{} angles\n".format(self._system.n['angles']))
+        header += "\n"
+        header += str("{} atom types\n".format(self._system.types['atom']))
+        header += str("{} bond types\n".format(self._system.types['bond']))
+        if self.include_angles:
+            header += str("{} angle types\n".format(self._system.types['angle']))
+        header += "\n"
+        header += str("{} {} xlo xhi\n".format(box['xlo'], box['xhi']))
+        header += str("{} {} ylo yhi\n".format(box['ylo'], box['yhi']))
+        header += str("{} {} zlo zhi\n".format(box['zlo'], box['zhi']))
+        return header
+
+    @property
+    def masses(self):
+        masses = '\nMasses\n\n'
+        for i, mass in enumerate(self._system._masses):
+            masses += "{} {}\n".format(i + 1, mass)
+        return masses
+
+    @property
+    def atoms(self):
+        atoms = '\nAtoms\n\n'
+        table = self._system.atoms
+        for i in range(len(table)):
+            if self.include_charges:
+                atoms += "{} {} {} {} {} {} {}\n".format(
+                    i + 1,
+                    table['mol'][i],
+                    table['type'][i],
+                    table['q'][i],
+                    table['x'][i],
+                    table['y'][i],
+                    table['z'][i]
+                )
+            else:
+                atoms += "{} {} {} {} {} {}\n".format(
+                    i + 1,
+                    table['mol'][i],
+                    table['type'][i],
+                    table['x'][i],
+                    table['y'][i],
+                    table['z'][i]
+                )
+
+        return atoms
+
+    @property
+    def bonds(self):
+        bonds = '\nBonds\n\n'
+        table = self._system.bonds
+        for i in range(len(table)):
+            bonds += "{} {} {} {}\n".format(
+                i + 1,
+                table['type'][i],
+                int(table['atom_1'][i]),
+                int(table['atom_2'][i])
+            )
+        return bonds
+
+    @property
+    def angles(self):
+        angles = '\nAngles\n\n'
+        table = self._system.angles
+        for i in range(len(table)):
+            angles += "{} {} {} {} {}\n".format(
+                i + 1,
+                table['type'][i],
+                table['atom_1'][i],
+                table['atom_2'][i],
+                table['atom_3'][i]
+            )
+        return angles
+
+    @staticmethod
+    def stats(fname):
+        stats = {}
+
+        with open(fname, 'r') as f:
+            [f.readline() for i in range(3)]
+            stats['n_atoms'] = int(f.readline().split()[0])
+            stats['n_bonds'] = int(f.readline().split()[0])
+            stats['n_angles'] = int(f.readline().split()[0])
+            f.readline()
+            stats['atom_types'] = int(f.readline().split()[0])
+            stats['bond_types'] = int(f.readline().split()[0])
+            stats['angle_types'] = int(f.readline().split()[0])
+
+        skip_atoms = 21+stats['atom_types']
+        skip_bonds = 24+stats['atom_types']+stats['n_atoms']
+        skip_angles = 26+stats['atom_types']+stats['n_atoms']+stats['n_bonds']
+
+        stats['atoms'] = pd.read_csv(
+                fname,
+                delim_whitespace=True,
+                header=None,
+                skiprows=skip_atoms,
+                nrows=stats['n_atoms']
+            )
+
+        stats['bonds'] = pd.read_csv(
+                fname,
+                delim_whitespace=True,
+                header=None,
+                skiprows=skip_bonds,
+                nrows=stats['n_bonds']
+            )
+
+        stats['angles'] = pd.read_csv(
+                fname,
+                delim_whitespace=True,
+                header=None,
+                skiprows=skip_angles,
+                nrows=stats['n_angles']
+            )
+
+        return stats
+
+    @staticmethod
+    def validate(fname):
+        stats = ConfigFile.stats(fname)
+        for name in ['atom', 'bond', 'angle']:
+            header_n = stats['n_{}s'.format(name)]
+            length_n = len(stats['{}s'.format(name)])
+            if header_n != length_n:
+                return False
+        return True
+
+    @staticmethod
+    def compare(fname_1, fname_2):
+        stats_1 = ConfigFile.stats(fname_1)
+        stats_2 = ConfigFile.stats(fname_2)
+        for key, value in list(stats_1.items()):
+            try:
+                if stats_2[key] != value:
+                    return False
+            except ValueError:
+                if isinstance(value, pd.DataFrame):
+                    continue
+                else:
+                    raise ValueError
+        return True
\ No newline at end of file
diff --git a/starpolymers/generators/input_file.py b/starpolymers/io/input_file.py
similarity index 100%
rename from starpolymers/generators/input_file.py
rename to starpolymers/io/input_file.py
diff --git a/starpolymers/generators/input_files/_01_master.in b/starpolymers/io/input_files/_01_master.in
similarity index 100%
rename from starpolymers/generators/input_files/_01_master.in
rename to starpolymers/io/input_files/_01_master.in
diff --git a/starpolymers/molecules/__init__.py b/starpolymers/molecules/__init__.py
index 9c578df..69a8b6a 100644
--- a/starpolymers/molecules/__init__.py
+++ b/starpolymers/molecules/__init__.py
@@ -1,7 +1,7 @@
 from .polyelectrolyte import StarPolyelectrolyte, LinearPolyelectrolyte
 from .salt import Salt
 import json
-from ._common import registry
+from ._common import AbstractMolecule, registry
 
 class MoleculeFactory():
     def __init__(self, item_list, box=None):
diff --git a/starpolymers/molecules/polyelectrolyte.py b/starpolymers/molecules/polyelectrolyte.py
index 168d6bf..2d103aa 100644
--- a/starpolymers/molecules/polyelectrolyte.py
+++ b/starpolymers/molecules/polyelectrolyte.py
@@ -61,9 +61,11 @@ def generate_angles(self):
 
     def generate_charges(self, positions):
 
-        charge = float(self._item['charge']['max'])
+        # store length in a variable
         length = len(positions)
 
+        # define the generation functions
+
         def _all():
             return [charge] * length
 
@@ -82,13 +84,24 @@ def _random():
         def _diblock():
             return [charge] * length
 
+        # store the functions in a hash table
         functions = {
-            'all' : _all,
-            'random' : _random,
-            'diblock-regular' : _diblock
-        }
+                'all' : _all,
+                'random' : _random,
+                'diblock-regular' : _diblock
+            }
+
+        # manage charges if they exist
+        charge = 0
+        _c = self._item.get('charge', False)
+        if _c:
+            charge += _c['max']
+            return functions[self._item['charge'].get('style', 'all')]()
+
+        # default should be charge is zero of all the particle
+        else:
+            return functions['all']()
 
-        return functions[self._item['charge'].get('style', 'all')]()
 
 class StarPolyelectrolyte(Molecule):
     def __init__(self, item, **kwargs):
@@ -137,12 +150,12 @@ def generate_bonds(self):
             'atom_1' : [],
             'atom_2' : []
         }
-            
+
         for i in range(m_bonds):
             atom_1 = i+1
-            
-            if (i+1) % self.lam == 0:      
-                atom_2 = self.n['atoms']                       
+
+            if (i+1) % self.lam == 0:
+                atom_2 = self.n['atoms']
             else:
                 atom_2 = i+2
 
@@ -191,7 +204,7 @@ def generate_angles(self):
         return pd.DataFrame(data)
 
     def generate_charges(self, positions):
-        
+
         charge = float(self._item['charge']['max'])
         length = len(positions)
 
@@ -225,10 +238,10 @@ def _diblock():
 
             # the PEs tail is where the 0th index is
             if position == 'core':
-                arm_list[:n_charges_per_arm] = 0.0
+                arm_list[:-n_charges_per_arm] = 0.0
             elif position == 'tail':
                 arm_list[n_charges_per_arm:] = 0.0
-        
+
             arm_list = np.concatenate([arm_list] * self.kap)
             arm_list = np.concatenate([arm_list, np.array([params.get('central', q)])])
             assert len(arm_list) == len(positions)
diff --git a/starpolymers/molecules/salt.py b/starpolymers/molecules/salt.py
index b57e60c..2a2db31 100644
--- a/starpolymers/molecules/salt.py
+++ b/starpolymers/molecules/salt.py
@@ -2,6 +2,9 @@
 import numpy as np
 import pandas as pd
 
+from softnanotools.logger import Logger
+logger = Logger(__name__)
+
 class Salt(ParticleArray):
     def __init__(self, item, **kwargs):
         ParticleArray.__init__(self, item, **kwargs)
@@ -9,7 +12,7 @@ def __init__(self, item, **kwargs):
         self.anion = float(self._item['anion'])
         self.cation = float(self._item['cation'])
         self._atoms = self.generate_atoms()
-    
+
     def generate_atoms(self):
         """
         Returns dataframe with the following columns
@@ -17,6 +20,8 @@ def generate_atoms(self):
 
         q = self.generate_charges()
 
+        logger.debug(f'Generated charges for Salt object:\n{q}')
+
         positions \
             = np.random.uniform(size=(q.shape[0], 3)) \
             * self._kwargs['box']
@@ -31,7 +36,7 @@ def generate_atoms(self):
         })
 
         return data
-    
+
     def generate_charges(self):
 
         # lowest common multiple
diff --git a/versioneer.py b/versioneer.py
new file mode 100644
index 0000000..64fea1c
--- /dev/null
+++ b/versioneer.py
@@ -0,0 +1,1822 @@
+
+# Version: 0.18
+
+"""The Versioneer - like a rocketeer, but for versions.
+
+The Versioneer
+==============
+
+* like a rocketeer, but for versions!
+* https://github.com/warner/python-versioneer
+* Brian Warner
+* License: Public Domain
+* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
+* [![Latest Version]
+(https://pypip.in/version/versioneer/badge.svg?style=flat)
+](https://pypi.python.org/pypi/versioneer/)
+* [![Build Status]
+(https://travis-ci.org/warner/python-versioneer.png?branch=master)
+](https://travis-ci.org/warner/python-versioneer)
+
+This is a tool for managing a recorded version number in distutils-based
+python projects. The goal is to remove the tedious and error-prone "update
+the embedded version string" step from your release process. Making a new
+release should be as easy as recording a new tag in your version-control
+system, and maybe making new tarballs.
+
+
+## Quick Install
+
+* `pip install versioneer` to somewhere to your $PATH
+* add a `[versioneer]` section to your setup.cfg (see below)
+* run `versioneer install` in your source tree, commit the results
+
+## Version Identifiers
+
+Source trees come from a variety of places:
+
+* a version-control system checkout (mostly used by developers)
+* a nightly tarball, produced by build automation
+* a snapshot tarball, produced by a web-based VCS browser, like github's
+  "tarball from tag" feature
+* a release tarball, produced by "setup.py sdist", distributed through PyPI
+
+Within each source tree, the version identifier (either a string or a number,
+this tool is format-agnostic) can come from a variety of places:
+
+* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows
+  about recent "tags" and an absolute revision-id
+* the name of the directory into which the tarball was unpacked
+* an expanded VCS keyword ($Id$, etc)
+* a `_version.py` created by some earlier build step
+
+For released software, the version identifier is closely related to a VCS
+tag. Some projects use tag names that include more than just the version
+string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool
+needs to strip the tag prefix to extract the version identifier. For
+unreleased software (between tags), the version identifier should provide
+enough information to help developers recreate the same tree, while also
+giving them an idea of roughly how old the tree is (after version 1.2, before
+version 1.3). Many VCS systems can report a description that captures this,
+for example `git describe --tags --dirty --always` reports things like
+"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
+0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
+uncommitted changes.
+
+The version identifier is used for multiple purposes:
+
+* to allow the module to self-identify its version: `myproject.__version__`
+* to choose a name and prefix for a 'setup.py sdist' tarball
+
+## Theory of Operation
+
+Versioneer works by adding a special `_version.py` file into your source
+tree, where your `__init__.py` can import it. This `_version.py` knows how to
+dynamically ask the VCS tool for version information at import time.
+
+`_version.py` also contains `$Revision$` markers, and the installation
+process marks `_version.py` to have this marker rewritten with a tag name
+during the `git archive` command. As a result, generated tarballs will
+contain enough information to get the proper version.
+
+To allow `setup.py` to compute a version too, a `versioneer.py` is added to
+the top level of your source tree, next to `setup.py` and the `setup.cfg`
+that configures it. This overrides several distutils/setuptools commands to
+compute the version when invoked, and changes `setup.py build` and `setup.py
+sdist` to replace `_version.py` with a small static file that contains just
+the generated version data.
+
+## Installation
+
+See [INSTALL.md](./INSTALL.md) for detailed installation instructions.
+
+## Version-String Flavors
+
+Code which uses Versioneer can learn about its version string at runtime by
+importing `_version` from your main `__init__.py` file and running the
+`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can
+import the top-level `versioneer.py` and run `get_versions()`.
+
+Both functions return a dictionary with different flavors of version
+information:
+
+* `['version']`: A condensed version string, rendered using the selected
+  style. This is the most commonly used value for the project's version
+  string. The default "pep440" style yields strings like `0.11`,
+  `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section
+  below for alternative styles.
+
+* `['full-revisionid']`: detailed revision identifier. For Git, this is the
+  full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac".
+
+* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the
+  commit date in ISO 8601 format. This will be None if the date is not
+  available.
+
+* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that
+  this is only accurate if run in a VCS checkout, otherwise it is likely to
+  be False or None
+
+* `['error']`: if the version string could not be computed, this will be set
+  to a string describing the problem, otherwise it will be None. It may be
+  useful to throw an exception in setup.py if this is set, to avoid e.g.
+  creating tarballs with a version string of "unknown".
+
+Some variants are more useful than others. Including `full-revisionid` in a
+bug report should allow developers to reconstruct the exact code being tested
+(or indicate the presence of local changes that should be shared with the
+developers). `version` is suitable for display in an "about" box or a CLI
+`--version` output: it can be easily compared against release notes and lists
+of bugs fixed in various releases.
+
+The installer adds the following text to your `__init__.py` to place a basic
+version in `YOURPROJECT.__version__`:
+
+    from ._version import get_versions
+    __version__ = get_versions()['version']
+    del get_versions
+
+## Styles
+
+The setup.cfg `style=` configuration controls how the VCS information is
+rendered into a version string.
+
+The default style, "pep440", produces a PEP440-compliant string, equal to the
+un-prefixed tag name for actual releases, and containing an additional "local
+version" section with more detail for in-between builds. For Git, this is
+TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags
+--dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the
+tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and
+that this commit is two revisions ("+2") beyond the "0.11" tag. For released
+software (exactly equal to a known tag), the identifier will only contain the
+stripped tag, e.g. "0.11".
+
+Other styles are available. See [details.md](details.md) in the Versioneer
+source tree for descriptions.
+
+## Debugging
+
+Versioneer tries to avoid fatal errors: if something goes wrong, it will tend
+to return a version of "0+unknown". To investigate the problem, run `setup.py
+version`, which will run the version-lookup code in a verbose mode, and will
+display the full contents of `get_versions()` (including the `error` string,
+which may help identify what went wrong).
+
+## Known Limitations
+
+Some situations are known to cause problems for Versioneer. This details the
+most significant ones. More can be found on Github
+[issues page](https://github.com/warner/python-versioneer/issues).
+
+### Subprojects
+
+Versioneer has limited support for source trees in which `setup.py` is not in
+the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are
+two common reasons why `setup.py` might not be in the root:
+
+* Source trees which contain multiple subprojects, such as
+  [Buildbot](https://github.com/buildbot/buildbot), which contains both
+  "master" and "slave" subprojects, each with their own `setup.py`,
+  `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
+  distributions (and upload multiple independently-installable tarballs).
+* Source trees whose main purpose is to contain a C library, but which also
+  provide bindings to Python (and perhaps other langauges) in subdirectories.
+
+Versioneer will look for `.git` in parent directories, and most operations
+should get the right version string. However `pip` and `setuptools` have bugs
+and implementation details which frequently cause `pip install .` from a
+subproject directory to fail to find a correct version string (so it usually
+defaults to `0+unknown`).
+
+`pip install --editable .` should work correctly. `setup.py install` might
+work too.
+
+Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
+some later version.
+
+[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
+this issue. The discussion in
+[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
+issue from the Versioneer side in more detail.
+[pip PR#3176](https://github.com/pypa/pip/pull/3176) and
+[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
+pip to let Versioneer work correctly.
+
+Versioneer-0.16 and earlier only looked for a `.git` directory next to the
+`setup.cfg`, so subprojects were completely unsupported with those releases.
+
+### Editable installs with setuptools <= 18.5
+
+`setup.py develop` and `pip install --editable .` allow you to install a
+project into a virtualenv once, then continue editing the source code (and
+test) without re-installing after every change.
+
+"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a
+convenient way to specify executable scripts that should be installed along
+with the python package.
+
+These both work as expected when using modern setuptools. When using
+setuptools-18.5 or earlier, however, certain operations will cause
+`pkg_resources.DistributionNotFound` errors when running the entrypoint
+script, which must be resolved by re-installing the package. This happens
+when the install happens with one version, then the egg_info data is
+regenerated while a different version is checked out. Many setup.py commands
+cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
+a different virtualenv), so this can be surprising.
+
+[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
+this one, but upgrading to a newer version of setuptools should probably
+resolve it.
+
+### Unicode version strings
+
+While Versioneer works (and is continually tested) with both Python 2 and
+Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
+Newer releases probably generate unicode version strings on py2. It's not
+clear that this is wrong, but it may be surprising for applications when then
+write these strings to a network connection or include them in bytes-oriented
+APIs like cryptographic checksums.
+
+[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
+this question.
+
+
+## Updating Versioneer
+
+To upgrade your project to a new release of Versioneer, do the following:
+
+* install the new Versioneer (`pip install -U versioneer` or equivalent)
+* edit `setup.cfg`, if necessary, to include any new configuration settings
+  indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details.
+* re-run `versioneer install` in your source tree, to replace
+  `SRC/_version.py`
+* commit any changed files
+
+## Future Directions
+
+This tool is designed to make it easily extended to other version-control
+systems: all VCS-specific components are in separate directories like
+src/git/ . The top-level `versioneer.py` script is assembled from these
+components by running make-versioneer.py . In the future, make-versioneer.py
+will take a VCS name as an argument, and will construct a version of
+`versioneer.py` that is specific to the given VCS. It might also take the
+configuration arguments that are currently provided manually during
+installation by editing setup.py . Alternatively, it might go the other
+direction and include code from all supported VCS systems, reducing the
+number of intermediate scripts.
+
+
+## License
+
+To make Versioneer easier to embed, all its code is dedicated to the public
+domain. The `_version.py` that it creates is also in the public domain.
+Specifically, both are released under the Creative Commons "Public Domain
+Dedication" license (CC0-1.0), as described in
+https://creativecommons.org/publicdomain/zero/1.0/ .
+
+"""
+
+from __future__ import print_function
+try:
+    import configparser
+except ImportError:
+    import ConfigParser as configparser
+import errno
+import json
+import os
+import re
+import subprocess
+import sys
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_root():
+    """Get the project root directory.
+
+    We require that all commands are run from the project root, i.e. the
+    directory that contains setup.py, setup.cfg, and versioneer.py .
+    """
+    root = os.path.realpath(os.path.abspath(os.getcwd()))
+    setup_py = os.path.join(root, "setup.py")
+    versioneer_py = os.path.join(root, "versioneer.py")
+    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+        # allow 'python path/to/setup.py COMMAND'
+        root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
+        setup_py = os.path.join(root, "setup.py")
+        versioneer_py = os.path.join(root, "versioneer.py")
+    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+        err = ("Versioneer was unable to run the project root directory. "
+               "Versioneer requires setup.py to be executed from "
+               "its immediate directory (like 'python setup.py COMMAND'), "
+               "or in a way that lets it use sys.argv[0] to find the root "
+               "(like 'python path/to/setup.py COMMAND').")
+        raise VersioneerBadRootError(err)
+    try:
+        # Certain runtime workflows (setup.py install/develop in a setuptools
+        # tree) execute all dependencies in a single python process, so
+        # "versioneer" may be imported multiple times, and python's shared
+        # module-import table will cache the first one. So we can't use
+        # os.path.dirname(__file__), as that will find whichever
+        # versioneer.py was first imported, even in later projects.
+        me = os.path.realpath(os.path.abspath(__file__))
+        me_dir = os.path.normcase(os.path.splitext(me)[0])
+        vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
+        if me_dir != vsr_dir:
+            print("Warning: build in %s is using versioneer.py from %s"
+                  % (os.path.dirname(me), versioneer_py))
+    except NameError:
+        pass
+    return root
+
+
+def get_config_from_root(root):
+    """Read the project setup.cfg file to determine Versioneer config."""
+    # This might raise EnvironmentError (if setup.cfg is missing), or
+    # configparser.NoSectionError (if it lacks a [versioneer] section), or
+    # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+    # the top of versioneer.py for instructions on writing your setup.cfg .
+    setup_cfg = os.path.join(root, "setup.cfg")
+    parser = configparser.SafeConfigParser()
+    with open(setup_cfg, "r") as f:
+        parser.readfp(f)
+    VCS = parser.get("versioneer", "VCS")  # mandatory
+
+    def get(parser, name):
+        if parser.has_option("versioneer", name):
+            return parser.get("versioneer", name)
+        return None
+    cfg = VersioneerConfig()
+    cfg.VCS = VCS
+    cfg.style = get(parser, "style") or ""
+    cfg.versionfile_source = get(parser, "versionfile_source")
+    cfg.versionfile_build = get(parser, "versionfile_build")
+    cfg.tag_prefix = get(parser, "tag_prefix")
+    if cfg.tag_prefix in ("''", '""'):
+        cfg.tag_prefix = ""
+    cfg.parentdir_prefix = get(parser, "parentdir_prefix")
+    cfg.verbose = get(parser, "verbose")
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+# these dictionaries contain VCS-specific tools
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %s" % dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %s" % (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %s (error)" % dispcmd)
+            print("stdout was %s" % stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+LONG_VERSION_PY['git'] = '''
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.18 (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+
+def get_keywords():
+    """Get the keywords needed to look up the version information."""
+    # these strings will be replaced by git during git-archive.
+    # setup.py/versioneer.py will grep for the variable names, so they must
+    # each be defined on a line of their own. _version.py will just call
+    # get_keywords().
+    git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
+    git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
+    git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s"
+    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
+    return keywords
+
+
+class VersioneerConfig:
+    """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+    """Create, populate and return the VersioneerConfig() object."""
+    # these strings are filled in when 'setup.py versioneer' creates
+    # _version.py
+    cfg = VersioneerConfig()
+    cfg.VCS = "git"
+    cfg.style = "%(STYLE)s"
+    cfg.tag_prefix = "%(TAG_PREFIX)s"
+    cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s"
+    cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s"
+    cfg.verbose = False
+    return cfg
+
+
+class NotThisMethod(Exception):
+    """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method):  # decorator
+    """Decorator to mark a method as the handler for a particular VCS."""
+    def decorate(f):
+        """Store f in HANDLERS[vcs][method]."""
+        if vcs not in HANDLERS:
+            HANDLERS[vcs] = {}
+        HANDLERS[vcs][method] = f
+        return f
+    return decorate
+
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
+                env=None):
+    """Call the given command(s)."""
+    assert isinstance(commands, list)
+    p = None
+    for c in commands:
+        try:
+            dispcmd = str([c] + args)
+            # remember shell=False, so use git.cmd on windows, not just git
+            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
+                                 stdout=subprocess.PIPE,
+                                 stderr=(subprocess.PIPE if hide_stderr
+                                         else None))
+            break
+        except EnvironmentError:
+            e = sys.exc_info()[1]
+            if e.errno == errno.ENOENT:
+                continue
+            if verbose:
+                print("unable to run %%s" %% dispcmd)
+                print(e)
+            return None, None
+    else:
+        if verbose:
+            print("unable to find command, tried %%s" %% (commands,))
+        return None, None
+    stdout = p.communicate()[0].strip()
+    if sys.version_info[0] >= 3:
+        stdout = stdout.decode()
+    if p.returncode != 0:
+        if verbose:
+            print("unable to run %%s (error)" %% dispcmd)
+            print("stdout was %%s" %% stdout)
+        return None, p.returncode
+    return stdout, p.returncode
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %%s but none started with prefix %%s" %%
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %%d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r'\d', r)])
+        if verbose:
+            print("discarding '%%s', no digits" %% ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %%s" %% ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            if verbose:
+                print("picking %%s" %% r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %%s not under git control" %% root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
+                                          "--always", "--long",
+                                          "--match", "%%s*" %% tag_prefix],
+                                   cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%%s'"
+                               %% describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%%s' doesn't start with prefix '%%s'"
+                print(fmt %% (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'"
+                               %% (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%%d" %% pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%%d" %% pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%%s" %% pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%%s" %% pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%%s'" %% style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+def get_versions():
+    """Get version information or return default if unable to do so."""
+    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+    # __file__, we can work backwards from there to the root. Some
+    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+    # case we can only use expanded keywords.
+
+    cfg = get_config()
+    verbose = cfg.verbose
+
+    try:
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
+    except NotThisMethod:
+        pass
+
+    try:
+        root = os.path.realpath(__file__)
+        # versionfile_source is the relative path from the top of the source
+        # tree (where the .git directory might live) to this file. Invert
+        # this to find the root from __file__.
+        for i in cfg.versionfile_source.split('/'):
+            root = os.path.dirname(root)
+    except NameError:
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
+
+    try:
+        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+        return render(pieces, cfg.style)
+    except NotThisMethod:
+        pass
+
+    try:
+        if cfg.parentdir_prefix:
+            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+    except NotThisMethod:
+        pass
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}
+'''
+
+
+@register_vcs_handler("git", "get_keywords")
+def git_get_keywords(versionfile_abs):
+    """Extract version information from the given file."""
+    # the code embedded in _version.py can just fetch the value of these
+    # keywords. When used from setup.py, we don't want to import _version.py,
+    # so we do it with a regexp instead. This function is not used from
+    # _version.py.
+    keywords = {}
+    try:
+        f = open(versionfile_abs, "r")
+        for line in f.readlines():
+            if line.strip().startswith("git_refnames ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["refnames"] = mo.group(1)
+            if line.strip().startswith("git_full ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["full"] = mo.group(1)
+            if line.strip().startswith("git_date ="):
+                mo = re.search(r'=\s*"(.*)"', line)
+                if mo:
+                    keywords["date"] = mo.group(1)
+        f.close()
+    except EnvironmentError:
+        pass
+    return keywords
+
+
+@register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+    """Get version information from git keywords."""
+    if not keywords:
+        raise NotThisMethod("no keywords at all, weird")
+    date = keywords.get("date")
+    if date is not None:
+        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
+        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
+        # -like" string, which we must then edit to make compliant), because
+        # it's been around since git-1.5.3, and it's too difficult to
+        # discover which version we're using, or to work around using an
+        # older one.
+        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+    refnames = keywords["refnames"].strip()
+    if refnames.startswith("$Format"):
+        if verbose:
+            print("keywords are unexpanded, not using")
+        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
+    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+    TAG = "tag: "
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    if not tags:
+        # Either we're using git < 1.8.3, or there really are no tags. We use
+        # a heuristic: assume all version tags have a digit. The old git %d
+        # expansion behaves like git log --decorate=short and strips out the
+        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+        # between branches and tags. By ignoring refnames without digits, we
+        # filter out many common branch names like "release" and
+        # "stabilization", as well as "HEAD" and "master".
+        tags = set([r for r in refs if re.search(r'\d', r)])
+        if verbose:
+            print("discarding '%s', no digits" % ",".join(refs - tags))
+    if verbose:
+        print("likely tags: %s" % ",".join(sorted(tags)))
+    for ref in sorted(tags):
+        # sorting will prefer e.g. "2.0" over "2.0rc1"
+        if ref.startswith(tag_prefix):
+            r = ref[len(tag_prefix):]
+            if verbose:
+                print("picking %s" % r)
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
+    # no suitable tags, so version is "0+unknown", but full hex is still there
+    if verbose:
+        print("no suitable tags, using unknown + full revision id")
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
+
+
+@register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+    """Get version from 'git describe' in the root of the source tree.
+
+    This only gets called if the git-archive 'subst' keywords were *not*
+    expanded, and _version.py hasn't already been rewritten with a short
+    version string, meaning we're inside a checked out source tree.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                          hide_stderr=True)
+    if rc != 0:
+        if verbose:
+            print("Directory %s not under git control" % root)
+        raise NotThisMethod("'git rev-parse --git-dir' returned error")
+
+    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+    # if there isn't one, this yields HEX[-dirty] (no NUM)
+    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
+                                          "--always", "--long",
+                                          "--match", "%s*" % tag_prefix],
+                                   cwd=root)
+    # --long was added in git-1.5.5
+    if describe_out is None:
+        raise NotThisMethod("'git describe' failed")
+    describe_out = describe_out.strip()
+    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    if full_out is None:
+        raise NotThisMethod("'git rev-parse' failed")
+    full_out = full_out.strip()
+
+    pieces = {}
+    pieces["long"] = full_out
+    pieces["short"] = full_out[:7]  # maybe improved later
+    pieces["error"] = None
+
+    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+    # TAG might have hyphens.
+    git_describe = describe_out
+
+    # look for -dirty suffix
+    dirty = git_describe.endswith("-dirty")
+    pieces["dirty"] = dirty
+    if dirty:
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
+
+    # now we have TAG-NUM-gHEX or HEX
+
+    if "-" in git_describe:
+        # TAG-NUM-gHEX
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        if not mo:
+            # unparseable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
+            return pieces
+
+        # tag
+        full_tag = mo.group(1)
+        if not full_tag.startswith(tag_prefix):
+            if verbose:
+                fmt = "tag '%s' doesn't start with prefix '%s'"
+                print(fmt % (full_tag, tag_prefix))
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
+            return pieces
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+        # distance: number of commits since tag
+        pieces["distance"] = int(mo.group(2))
+
+        # commit: short hex revision ID
+        pieces["short"] = mo.group(3)
+
+    else:
+        # HEX: no tags
+        pieces["closest-tag"] = None
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
+                                    cwd=root)
+        pieces["distance"] = int(count_out)  # total number of commits
+
+    # commit date: see ISO-8601 comment in git_versions_from_keywords()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
+                       cwd=root)[0].strip()
+    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
+
+    return pieces
+
+
+def do_vcs_install(manifest_in, versionfile_source, ipy):
+    """Git-specific installation logic for Versioneer.
+
+    For Git, this means creating/changing .gitattributes to mark _version.py
+    for export-subst keyword substitution.
+    """
+    GITS = ["git"]
+    if sys.platform == "win32":
+        GITS = ["git.cmd", "git.exe"]
+    files = [manifest_in, versionfile_source]
+    if ipy:
+        files.append(ipy)
+    try:
+        me = __file__
+        if me.endswith(".pyc") or me.endswith(".pyo"):
+            me = os.path.splitext(me)[0] + ".py"
+        versioneer_file = os.path.relpath(me)
+    except NameError:
+        versioneer_file = "versioneer.py"
+    files.append(versioneer_file)
+    present = False
+    try:
+        f = open(".gitattributes", "r")
+        for line in f.readlines():
+            if line.strip().startswith(versionfile_source):
+                if "export-subst" in line.strip().split()[1:]:
+                    present = True
+        f.close()
+    except EnvironmentError:
+        pass
+    if not present:
+        f = open(".gitattributes", "a+")
+        f.write("%s export-subst\n" % versionfile_source)
+        f.close()
+        files.append(".gitattributes")
+    run_command(GITS, ["add", "--"] + files)
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+    """Try to determine the version from the parent directory name.
+
+    Source tarballs conventionally unpack into a directory that includes both
+    the project name and a version string. We will also support searching up
+    two directory levels for an appropriately named parent directory
+    """
+    rootdirs = []
+
+    for i in range(3):
+        dirname = os.path.basename(root)
+        if dirname.startswith(parentdir_prefix):
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        else:
+            rootdirs.append(root)
+            root = os.path.dirname(root)  # up a level
+
+    if verbose:
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
+    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+
+
+SHORT_VERSION_PY = """
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+%s
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)
+"""
+
+
+def versions_from_file(filename):
+    """Try to determine the version from _version.py if present."""
+    try:
+        with open(filename) as f:
+            contents = f.read()
+    except EnvironmentError:
+        raise NotThisMethod("unable to read _version.py")
+    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
+                   contents, re.M | re.S)
+    if not mo:
+        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
+                       contents, re.M | re.S)
+    if not mo:
+        raise NotThisMethod("no version_json in _version.py")
+    return json.loads(mo.group(1))
+
+
+def write_to_version_file(filename, versions):
+    """Write the given version number to the given _version.py file."""
+    os.unlink(filename)
+    contents = json.dumps(versions, sort_keys=True,
+                          indent=1, separators=(",", ": "))
+    with open(filename, "w") as f:
+        f.write(SHORT_VERSION_PY % contents)
+
+    print("set %s to '%s'" % (filename, versions["version"]))
+
+
+def plus_or_dot(pieces):
+    """Return a + if we don't already have one, else return a ."""
+    if "+" in pieces.get("closest-tag", ""):
+        return "."
+    return "+"
+
+
+def render_pep440(pieces):
+    """Build up version string, with post-release "local version identifier".
+
+    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+    Exceptions:
+    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_pre(pieces):
+    """TAG[.post.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += ".post.dev%d" % pieces["distance"]
+    else:
+        # exception #1
+        rendered = "0.post.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces):
+    """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+    The ".dev0" means dirty. Note that .dev0 sorts backwards
+    (a dirty tree will appear "older" than the corresponding clean one),
+    but you shouldn't be releasing software with -dirty anyways.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+    return rendered
+
+
+def render_pep440_old(pieces):
+    """TAG[.postDISTANCE[.dev0]] .
+
+    The ".dev0" means dirty.
+
+    Eexceptions:
+    1: no tags. 0.postDISTANCE[.dev0]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["dirty"]:
+                rendered += ".dev0"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["dirty"]:
+            rendered += ".dev0"
+    return rendered
+
+
+def render_git_describe(pieces):
+    """TAG[-DISTANCE-gHEX][-dirty].
+
+    Like 'git describe --tags --dirty --always'.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"]:
+            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render_git_describe_long(pieces):
+    """TAG-DISTANCE-gHEX[-dirty].
+
+    Like 'git describe --tags --dirty --always -long'.
+    The distance/hash is unconditional.
+
+    Exceptions:
+    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+    else:
+        # exception #1
+        rendered = pieces["short"]
+    if pieces["dirty"]:
+        rendered += "-dirty"
+    return rendered
+
+
+def render(pieces, style):
+    """Render the given version pieces into the requested style."""
+    if pieces["error"]:
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
+
+    if not style or style == "default":
+        style = "pep440"  # the default
+
+    if style == "pep440":
+        rendered = render_pep440(pieces)
+    elif style == "pep440-pre":
+        rendered = render_pep440_pre(pieces)
+    elif style == "pep440-post":
+        rendered = render_pep440_post(pieces)
+    elif style == "pep440-old":
+        rendered = render_pep440_old(pieces)
+    elif style == "git-describe":
+        rendered = render_git_describe(pieces)
+    elif style == "git-describe-long":
+        rendered = render_git_describe_long(pieces)
+    else:
+        raise ValueError("unknown style '%s'" % style)
+
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
+
+
+class VersioneerBadRootError(Exception):
+    """The project root directory is unknown or missing key files."""
+
+
+def get_versions(verbose=False):
+    """Get the project version from whatever source is available.
+
+    Returns dict with two keys: 'version' and 'full'.
+    """
+    if "versioneer" in sys.modules:
+        # see the discussion in cmdclass.py:get_cmdclass()
+        del sys.modules["versioneer"]
+
+    root = get_root()
+    cfg = get_config_from_root(root)
+
+    assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
+    handlers = HANDLERS.get(cfg.VCS)
+    assert handlers, "unrecognized VCS '%s'" % cfg.VCS
+    verbose = verbose or cfg.verbose
+    assert cfg.versionfile_source is not None, \
+        "please set versioneer.versionfile_source"
+    assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
+
+    versionfile_abs = os.path.join(root, cfg.versionfile_source)
+
+    # extract version from first of: _version.py, VCS command (e.g. 'git
+    # describe'), parentdir. This is meant to work for developers using a
+    # source checkout, for users of a tarball created by 'setup.py sdist',
+    # and for users of a tarball/zipball created by 'git archive' or github's
+    # download-from-tag feature or the equivalent in other VCSes.
+
+    get_keywords_f = handlers.get("get_keywords")
+    from_keywords_f = handlers.get("keywords")
+    if get_keywords_f and from_keywords_f:
+        try:
+            keywords = get_keywords_f(versionfile_abs)
+            ver = from_keywords_f(keywords, cfg.tag_prefix, verbose)
+            if verbose:
+                print("got version from expanded keyword %s" % ver)
+            return ver
+        except NotThisMethod:
+            pass
+
+    try:
+        ver = versions_from_file(versionfile_abs)
+        if verbose:
+            print("got version from file %s %s" % (versionfile_abs, ver))
+        return ver
+    except NotThisMethod:
+        pass
+
+    from_vcs_f = handlers.get("pieces_from_vcs")
+    if from_vcs_f:
+        try:
+            pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
+            ver = render(pieces, cfg.style)
+            if verbose:
+                print("got version from VCS %s" % ver)
+            return ver
+        except NotThisMethod:
+            pass
+
+    try:
+        if cfg.parentdir_prefix:
+            ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+            if verbose:
+                print("got version from parentdir %s" % ver)
+            return ver
+    except NotThisMethod:
+        pass
+
+    if verbose:
+        print("unable to compute version")
+
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None, "error": "unable to compute version",
+            "date": None}
+
+
+def get_version():
+    """Get the short version string for this project."""
+    return get_versions()["version"]
+
+
+def get_cmdclass():
+    """Get the custom setuptools/distutils subclasses used by Versioneer."""
+    if "versioneer" in sys.modules:
+        del sys.modules["versioneer"]
+        # this fixes the "python setup.py develop" case (also 'install' and
+        # 'easy_install .'), in which subdependencies of the main project are
+        # built (using setup.py bdist_egg) in the same python process. Assume
+        # a main project A and a dependency B, which use different versions
+        # of Versioneer. A's setup.py imports A's Versioneer, leaving it in
+        # sys.modules by the time B's setup.py is executed, causing B to run
+        # with the wrong versioneer. Setuptools wraps the sub-dep builds in a
+        # sandbox that restores sys.modules to it's pre-build state, so the
+        # parent is protected against the child's "import versioneer". By
+        # removing ourselves from sys.modules here, before the child build
+        # happens, we protect the child from the parent's versioneer too.
+        # Also see https://github.com/warner/python-versioneer/issues/52
+
+    cmds = {}
+
+    # we add "version" to both distutils and setuptools
+    from distutils.core import Command
+
+    class cmd_version(Command):
+        description = "report generated version string"
+        user_options = []
+        boolean_options = []
+
+        def initialize_options(self):
+            pass
+
+        def finalize_options(self):
+            pass
+
+        def run(self):
+            vers = get_versions(verbose=True)
+            print("Version: %s" % vers["version"])
+            print(" full-revisionid: %s" % vers.get("full-revisionid"))
+            print(" dirty: %s" % vers.get("dirty"))
+            print(" date: %s" % vers.get("date"))
+            if vers["error"]:
+                print(" error: %s" % vers["error"])
+    cmds["version"] = cmd_version
+
+    # we override "build_py" in both distutils and setuptools
+    #
+    # most invocation pathways end up running build_py:
+    #  distutils/build -> build_py
+    #  distutils/install -> distutils/build ->..
+    #  setuptools/bdist_wheel -> distutils/install ->..
+    #  setuptools/bdist_egg -> distutils/install_lib -> build_py
+    #  setuptools/install -> bdist_egg ->..
+    #  setuptools/develop -> ?
+    #  pip install:
+    #   copies source tree to a tempdir before running egg_info/etc
+    #   if .git isn't copied too, 'git describe' will fail
+    #   then does setup.py bdist_wheel, or sometimes setup.py install
+    #  setup.py egg_info -> ?
+
+    # we override different "build_py" commands for both environments
+    if "setuptools" in sys.modules:
+        from setuptools.command.build_py import build_py as _build_py
+    else:
+        from distutils.command.build_py import build_py as _build_py
+
+    class cmd_build_py(_build_py):
+        def run(self):
+            root = get_root()
+            cfg = get_config_from_root(root)
+            versions = get_versions()
+            _build_py.run(self)
+            # now locate _version.py in the new build/ directory and replace
+            # it with an updated value
+            if cfg.versionfile_build:
+                target_versionfile = os.path.join(self.build_lib,
+                                                  cfg.versionfile_build)
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+    cmds["build_py"] = cmd_build_py
+
+    if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
+        from cx_Freeze.dist import build_exe as _build_exe
+        # nczeczulin reports that py2exe won't like the pep440-style string
+        # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
+        # setup(console=[{
+        #   "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION
+        #   "product_version": versioneer.get_version(),
+        #   ...
+
+        class cmd_build_exe(_build_exe):
+            def run(self):
+                root = get_root()
+                cfg = get_config_from_root(root)
+                versions = get_versions()
+                target_versionfile = cfg.versionfile_source
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+
+                _build_exe.run(self)
+                os.unlink(target_versionfile)
+                with open(cfg.versionfile_source, "w") as f:
+                    LONG = LONG_VERSION_PY[cfg.VCS]
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
+        cmds["build_exe"] = cmd_build_exe
+        del cmds["build_py"]
+
+    if 'py2exe' in sys.modules:  # py2exe enabled?
+        try:
+            from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
+        except ImportError:
+            from py2exe.build_exe import py2exe as _py2exe  # py2
+
+        class cmd_py2exe(_py2exe):
+            def run(self):
+                root = get_root()
+                cfg = get_config_from_root(root)
+                versions = get_versions()
+                target_versionfile = cfg.versionfile_source
+                print("UPDATING %s" % target_versionfile)
+                write_to_version_file(target_versionfile, versions)
+
+                _py2exe.run(self)
+                os.unlink(target_versionfile)
+                with open(cfg.versionfile_source, "w") as f:
+                    LONG = LONG_VERSION_PY[cfg.VCS]
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
+        cmds["py2exe"] = cmd_py2exe
+
+    # we override different "sdist" commands for both environments
+    if "setuptools" in sys.modules:
+        from setuptools.command.sdist import sdist as _sdist
+    else:
+        from distutils.command.sdist import sdist as _sdist
+
+    class cmd_sdist(_sdist):
+        def run(self):
+            versions = get_versions()
+            self._versioneer_generated_versions = versions
+            # unless we update this, the command will keep using the old
+            # version
+            self.distribution.metadata.version = versions["version"]
+            return _sdist.run(self)
+
+        def make_release_tree(self, base_dir, files):
+            root = get_root()
+            cfg = get_config_from_root(root)
+            _sdist.make_release_tree(self, base_dir, files)
+            # now locate _version.py in the new base_dir directory
+            # (remembering that it may be a hardlink) and replace it with an
+            # updated value
+            target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
+            print("UPDATING %s" % target_versionfile)
+            write_to_version_file(target_versionfile,
+                                  self._versioneer_generated_versions)
+    cmds["sdist"] = cmd_sdist
+
+    return cmds
+
+
+CONFIG_ERROR = """
+setup.cfg is missing the necessary Versioneer configuration. You need
+a section like:
+
+ [versioneer]
+ VCS = git
+ style = pep440
+ versionfile_source = src/myproject/_version.py
+ versionfile_build = myproject/_version.py
+ tag_prefix =
+ parentdir_prefix = myproject-
+
+You will also need to edit your setup.py to use the results:
+
+ import versioneer
+ setup(version=versioneer.get_version(),
+       cmdclass=versioneer.get_cmdclass(), ...)
+
+Please read the docstring in ./versioneer.py for configuration instructions,
+edit setup.cfg, and re-run the installer or 'python versioneer.py setup'.
+"""
+
+SAMPLE_CONFIG = """
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+
+[versioneer]
+#VCS = git
+#style = pep440
+#versionfile_source =
+#versionfile_build =
+#tag_prefix =
+#parentdir_prefix =
+
+"""
+
+INIT_PY_SNIPPET = """
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions
+"""
+
+
+def do_setup():
+    """Main VCS-independent setup function for installing Versioneer."""
+    root = get_root()
+    try:
+        cfg = get_config_from_root(root)
+    except (EnvironmentError, configparser.NoSectionError,
+            configparser.NoOptionError) as e:
+        if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
+            print("Adding sample versioneer config to setup.cfg",
+                  file=sys.stderr)
+            with open(os.path.join(root, "setup.cfg"), "a") as f:
+                f.write(SAMPLE_CONFIG)
+        print(CONFIG_ERROR, file=sys.stderr)
+        return 1
+
+    print(" creating %s" % cfg.versionfile_source)
+    with open(cfg.versionfile_source, "w") as f:
+        LONG = LONG_VERSION_PY[cfg.VCS]
+        f.write(LONG % {"DOLLAR": "$",
+                        "STYLE": cfg.style,
+                        "TAG_PREFIX": cfg.tag_prefix,
+                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        })
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
+                       "__init__.py")
+    if os.path.exists(ipy):
+        try:
+            with open(ipy, "r") as f:
+                old = f.read()
+        except EnvironmentError:
+            old = ""
+        if INIT_PY_SNIPPET not in old:
+            print(" appending to %s" % ipy)
+            with open(ipy, "a") as f:
+                f.write(INIT_PY_SNIPPET)
+        else:
+            print(" %s unmodified" % ipy)
+    else:
+        print(" %s doesn't exist, ok" % ipy)
+        ipy = None
+
+    # Make sure both the top-level "versioneer.py" and versionfile_source
+    # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
+    # they'll be copied into source distributions. Pip won't be able to
+    # install the package without this.
+    manifest_in = os.path.join(root, "MANIFEST.in")
+    simple_includes = set()
+    try:
+        with open(manifest_in, "r") as f:
+            for line in f:
+                if line.startswith("include "):
+                    for include in line.split()[1:]:
+                        simple_includes.add(include)
+    except EnvironmentError:
+        pass
+    # That doesn't cover everything MANIFEST.in can do
+    # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
+    # it might give some false negatives. Appending redundant 'include'
+    # lines is safe, though.
+    if "versioneer.py" not in simple_includes:
+        print(" appending 'versioneer.py' to MANIFEST.in")
+        with open(manifest_in, "a") as f:
+            f.write("include versioneer.py\n")
+    else:
+        print(" 'versioneer.py' already in MANIFEST.in")
+    if cfg.versionfile_source not in simple_includes:
+        print(" appending versionfile_source ('%s') to MANIFEST.in" %
+              cfg.versionfile_source)
+        with open(manifest_in, "a") as f:
+            f.write("include %s\n" % cfg.versionfile_source)
+    else:
+        print(" versionfile_source already in MANIFEST.in")
+
+    # Make VCS-specific changes. For git, this means creating/changing
+    # .gitattributes to mark _version.py for export-subst keyword
+    # substitution.
+    do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
+    return 0
+
+
+def scan_setup_py():
+    """Validate the contents of setup.py against Versioneer's expectations."""
+    found = set()
+    setters = False
+    errors = 0
+    with open("setup.py", "r") as f:
+        for line in f.readlines():
+            if "import versioneer" in line:
+                found.add("import")
+            if "versioneer.get_cmdclass()" in line:
+                found.add("cmdclass")
+            if "versioneer.get_version()" in line:
+                found.add("get_version")
+            if "versioneer.VCS" in line:
+                setters = True
+            if "versioneer.versionfile_source" in line:
+                setters = True
+    if len(found) != 3:
+        print("")
+        print("Your setup.py appears to be missing some important items")
+        print("(but I might be wrong). Please make sure it has something")
+        print("roughly like the following:")
+        print("")
+        print(" import versioneer")
+        print(" setup( version=versioneer.get_version(),")
+        print("        cmdclass=versioneer.get_cmdclass(),  ...)")
+        print("")
+        errors += 1
+    if setters:
+        print("You should remove lines like 'versioneer.VCS = ' and")
+        print("'versioneer.versionfile_source = ' . This configuration")
+        print("now lives in setup.cfg, and should be removed from setup.py")
+        print("")
+        errors += 1
+    return errors
+
+
+if __name__ == "__main__":
+    cmd = sys.argv[1]
+    if cmd == "setup":
+        errors = do_setup()
+        errors += scan_setup_py()
+        if errors:
+            sys.exit(1)


Test patch:
diff --git a/protocols/generate-many/lammps.test.in b/protocols/generate-many/lammps.test.in
new file mode 100644
index 0000000..9988d95
--- /dev/null
+++ b/protocols/generate-many/lammps.test.in
@@ -0,0 +1,72 @@
+# LAMMPS input file
+# Star Polymer in solution
+
+# ----- Variables -----
+
+variable K equal 10.0
+variable R0 equal 5.0
+variable eps equal 0.5
+variable sig equal 1.10
+
+variable fconfig string lammps.test.conf
+variable step equal 10000
+variable dump_step equal 10000
+variable dt equal 0.00015
+variable runlength equal 5000000
+
+# ----- Initialisation -----
+
+units 			lj
+boundary 		p p p
+atom_style 		full
+timestep 		${dt}
+
+# ----- Atom Definition -----
+
+read_data 		${fconfig}
+special_bonds lj 1.0 1.0 1.0
+dielectric 0.417
+
+neigh_modify one 10000
+
+# ----- Force Fields -----
+
+bond_style  harmonic
+bond_coeff	* 5.0 2.0
+
+pair_style	hybrid/overlay lj/cut 1.12 yukawa 1.0 10.0
+
+# lj/cut
+pair_modify pair lj/cut shift yes
+pair_coeff	* * lj/cut 1.0 1.0 1.12
+
+# yukawa
+pair_coeff * * yukawa 0.0
+pair_coeff 1 1 yukawa 1.0
+pair_coeff 1 2 yukawa -3.0
+pair_coeff 2 2 yukawa 3.0
+
+# ----- Thermostats -----
+
+reset_timestep 	0
+fix 			1 all nve
+fix 			2 all langevin 1.2 1.2 1.0 6994
+
+min_style               cg
+minimize                1e-10 1e-10 500000 1000000
+run                     50000
+reset_timestep  0
+
+# ----- Run Minimization -----
+
+thermo 			${dump_step}
+thermo_style 	custom step pe ke etotal temp
+
+dump 			1 all custom ${dump_step} dump/dump.*.lammpstrj id type x y z q vx vy vz mol ix iy iz xu yu zu
+run ${runlength}
+
+# ----- Final Statement -----
+
+# Simulation Finished
+
+print 			"All Done"
diff --git a/starpolymers/generators/input_files/_00_test.in b/starpolymers/io/input_files/_00_test.in
similarity index 100%
rename from starpolymers/generators/input_files/_00_test.in
rename to starpolymers/io/input_files/_00_test.in
diff --git a/test/input_files/01/test_input_01.py b/test/input_files/01/test_input_01.py
index fbe3eb0..3abcfbf 100644
--- a/test/input_files/01/test_input_01.py
+++ b/test/input_files/01/test_input_01.py
@@ -1,4 +1,4 @@
-from starpolymers.generators.input_file import templates, Variable
+from starpolymers.io.input_file import templates, Variable
 import pandas as pd
 
 def test_01():
diff --git a/test/io/test_colvars.py b/test/io/test_colvars.py
new file mode 100644
index 0000000..34960fa
--- /dev/null
+++ b/test/io/test_colvars.py
@@ -0,0 +1,7 @@
+import starpolymers.io.colvars as colvars
+
+def test_create():
+    return
+
+if __name__ == '__main__':
+    test_create()
\ No newline at end of file
diff --git a/test/io/test_configuration.py b/test/io/test_configuration.py
new file mode 100644
index 0000000..8fdac63
--- /dev/null
+++ b/test/io/test_configuration.py
@@ -0,0 +1,38 @@
+from pathlib import Path
+
+from starpolymers.io.configuration import *
+
+from starpolymers import ConfigFile
+from starpolymers import System
+
+from starpolymers.molecules import LinearPolyelectrolyte
+
+FOLDER = Path(__file__).parent
+
+def test_configuration(delete: bool = True):
+    item = {
+        'molecule': 'dna',
+        'lam': 10
+    }
+    molecule = LinearPolyelectrolyte(item)
+    system = System(10., molecules=[molecule])
+
+    # try all styles except dihedral
+    for style in STYLES:
+        if style == 'dihedral': continue
+        config_file = ConfigFile(system, style=style)
+
+        OUT = FOLDER / f'lammps.{style}.conf'
+        OUT.unlink(missing_ok=True)
+        config_file.write(OUT)
+
+        if delete:
+            OUT.unlink()
+
+    return
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--delete', action='store_true')
+    test_configuration(parser.parse_args().delete)
\ No newline at end of file
diff --git a/test/io/test_input_file.py b/test/io/test_input_file.py
new file mode 100644
index 0000000..ab4d577
--- /dev/null
+++ b/test/io/test_input_file.py
@@ -0,0 +1,4 @@
+import starpolymers.io.input_file
+
+def test_input_file():
+    return
diff --git a/test/test_generators.py b/test/test_generators.py
index b12a30f..e28b8fd 100644
--- a/test/test_generators.py
+++ b/test/test_generators.py
@@ -1,16 +1,10 @@
-from starpolymers.generators.configuration import *
-from starpolymers.generators.input_file import *
-from starpolymers.generators.colvars import *
 import starpolymers.generators.system as system
 
-def test_colvars():
-    assert True
-
-def test_configuration():
-    assert True
-
 def test_input_file():
     assert True
 
 def test_system():
-    system.System(100)
\ No newline at end of file
+    system.System(100)
+
+if __name__ == '__main__':
+    test_system()
\ No newline at end of file