Clean up inital configuration python script

.gitignore

@@ -1,7 +1,10 @@
-
+# LAMMPS files
 morse_input*
 log.lammps
 *.xyz
 *.gz
 *.thermo
+
+# Python files
 .idea/
+/venv

gel_setup/README.md

@@ -0,0 +1,17 @@
+# Creating polydisperse gel configurations
+
+This script provides a way to create starting configurations of a polydisperse gel described by a Morse potential. This seven component gel is the same mixture used in Griifiths et al. 2017 (https://aip.scitation.org/doi/10.1063/1.4973351)
+
+Since we want to use the gel as part of a molecular dynamics simulation in LAMMPS (https://lammps.sandia.gov/), it would be convenient to define the gel in a LAMMPS input script. However, the LAMMPS input language is hard to work with so instead we do the heavy lifting in Python and create a LAMMPS dump file which defines an initial configuration which is then read in at the start of the simulation.
+
+The script produces a configuration with overlapping particles so it is important that at the start of the simulation a short energy minimisation is conducted to remove the overlaps before starting the time stepping.
+
+The script creates a cubic simulation box, the side length set by the specified number density of the particles.
+
+The script takes the parameters:
+* Epsilon - the Morse well depth
+* Number density - used to set the size of the simulation box relative to the number of particles
+* Rho_0 - the Morse interaction distance
+* Number of particles - the number of particles to put in the simulation box
+
+By default the script sets the morse interaction cutoff to 1.4

gel_setup/gel_setup.py

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+# October 2018
+# Writing a LAMMPS input file for a system with Morse interaction and gaussian polydispersity
+
+import numpy as np
+from scipy.stats import norm
+import sys
+
+
+def main(epsilon: float = 5, number_density: float = 0.2, rho: float = 33,
+         num_particles: int = 1000):
+    """Main function
+    :param epsilon: Morse potential well depth.
+    :param number_density: Density of particles.
+    :param rho: Morse interaction distance.
+    :param num_particles: Number of particles in simulation box.
+    """
+    r_cut_coeff = 1.4               # Morse cutoff
+    pd = 0.04                       # Polydispersity gaussian sigma
+    num_types = 7                   # Number of different particle species in polydisperse mixture
+    # If turned on, "dpd_thermostat" will add "Morse" to the interaction potential to allow use
+    # of the hybrid/overlay style
+    dpd_thermostat = True
+
+    box_volume = num_particles/number_density
+    side_len = box_volume ** (1/3)
+
+    # Set up the particle diameters
+    half_num_types = np.floor(num_types/2)
+    bin_edges = np.arange(1 - (half_num_types * pd), 1 + (half_num_types * pd) + pd, pd) - pd / 2.
+    bin_centers = (np.arange(-half_num_types, half_num_types + 1) * pd) + 1
+
+    # Set up the Gaussian from which particle species are drawn
+    cumulative = norm.cdf(bin_edges, 1, pd)
+    # Set the limits of the Gaussian to be 0 and 1.
+    cumulative[0] = 0
+    cumulative[-1] = 1
+
+    # Determine the particle species
+    random_num = np.random.rand(num_particles)
+    # Return the indices of the bins to which each value in random_num belongs
+    particle_species = np.digitize(random_num, cumulative)
+
+    # Create random particle coordinates
+    x = np.random.uniform(0, side_len, size=num_particles)
+    y = np.random.uniform(0, side_len, size=num_particles)
+    z = np.random.uniform(0, side_len, size=num_particles)
+
+    packing = 0
+    for i in range(num_particles):
+        packing += np.pi / 6 * (bin_centers[particle_species[i] - 1] ** 3) / box_volume
+
+    print(f"* The packing fraction is {packing:.4f}")
+
+    filename = "morse_input_phi%.4f.lmp" % packing
+
+    with open(filename, 'w') as ouptut_file:
+        # Write the LAMMPS file header
+        ouptut_file.write("LAMMPS Description\n\n")
+        ouptut_file.write("{} atoms\n\n".format(num_particles))
+
+        # Write the box size
+        ouptut_file.write("{} atom types\n".format(num_types))
+        ouptut_file.write("0 {:.6f} xlo xhi\n"
+                          "0 {:.6f} ylo yhi\n"
+                          "0 {:.6f} zlo zhi\n\n".format(side_len, side_len, side_len))
+
+        # Write the particle masses, the particle types all have mass density = 1
+        ouptut_file.write("Masses\n\n")
+        for i in range(num_types):
+            ouptut_file.write("%d %g\n" % (i + 1, np.pi / 6 * bin_centers[i] ** 3))
+        ouptut_file.write("\n")
+
+        # If the hybrid/overlay command is used, need to specify the type of the potential
+        if dpd_thermostat:
+            keyword = " morse "
+        else:
+            keyword = ""
+
+        # Specify the interaction coefficient for the Morse potential:
+        # in LAMMPS's documentation they are: d0 alpha r0 cutoff
+        ouptut_file.write("PairIJ Coeffs\n\n")
+        for type_1 in range(num_types):
+            for type_2 in range(type_1, num_types):
+                diam_i = bin_centers[type_1]
+                diam_j = bin_centers[type_2]
+                mixed_diam = 0.5 * (diam_i + diam_j)
+                ouptut_file.write(f"{type_1 + 1:d} {type_2 + 1:d}{keyword:s}{epsilon:g} {rho:g} "
+                                  f"{mixed_diam:g} {r_cut_coeff * mixed_diam:g}\n")
+
+        # Write coordinates
+        ouptut_file.write("\nAtoms\n\n")
+        for i in range(num_particles):
+            ouptut_file.write(f"{i + 1:d} {particle_species[i]:d} {x[i]:g} {y[i]:g} {z[i]:g}\n")
+
+
+if __name__ == '__main__':
+    args = sys.argv
+    if len(args) != 5:
+        raise SyntaxError("Incorrect syntax.\nUse python gel_setup.py epsilon number_density "
+                          "rho_0 num_particles")
+    epsilon = float(sys.argv[1])
+    number_density = float(sys.argv[2])
+    rho_0 = float(sys.argv[3])
+    num_particles = int(sys.argv[4])
+    main(epsilon, number_density, rho_0, num_particles)