Add S(q) simulation scripts

examples/StaticStructureFactor-LJ/StaticStructureFactor-LJ.py

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+import itertools
+import math
+
+import gsd.hoomd
+import hoomd
+import numpy
+
+if __name__ == "__main__":
+    # create a particle lattice
+    m = 10
+    N_particles = m ** 3
+    spacing = 1.3
+    K = math.ceil(N_particles ** (1 / 3))
+    L = K * spacing
+    x = numpy.linspace(-L / 2, L / 2, K, endpoint=False)
+    position = list(itertools.product(x, repeat=3))
+
+    # create a Snapshot from the particle configuration
+    snapshot = gsd.hoomd.Snapshot()
+    snapshot.particles.N = N_particles
+    snapshot.particles.position = position[0:N_particles]
+    snapshot.particles.typeid = [0] * N_particles
+    snapshot.configuration.box = [L, L, L, 0, 0, 0]
+    snapshot.particles.types = ["A"]
+
+    # initialize a simulation from the snapshot
+    cpu = hoomd.device.CPU()
+    sim = hoomd.Simulation(device=cpu, seed=1)
+    sim.create_state_from_snapshot(snapshot)
+
+    # configure the integrator and LJ potential
+    integrator = hoomd.md.Integrator(dt=0.005)
+    cell = hoomd.md.nlist.Cell()
+    lj = hoomd.md.pair.LJ(nlist=cell)
+    lj.params[("A", "A")] = dict(epsilon=1, sigma=1)
+    lj.r_cut[("A", "A")] = 2.5
+    integrator.forces.append(lj)
+    nvt = hoomd.md.methods.NVT(kT=1.5, filter=hoomd.filter.All(), tau=1.0)
+    integrator.methods.append(nvt)
+
+    # link the integrator to the simulation, assign initial particle momenta
+    sim.operations.integrator = integrator
+    sim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.5)
+
+    # add a gsd writer, this will write 4 frames from the trajectory
+    gsd_writer = hoomd.write.GSD(
+        filename="../data/LJsampleTraj.gsd",
+        trigger=hoomd.trigger.Periodic(2500),
+        mode="wb",
+    )
+    sim.operations.writers.append(gsd_writer)
+
+    sim.run(10000)