diff --git a/README.md b/README.md index affe4f5a3d1a995e5f78011fb1564f3e40760a4c..bcef6a27a6d2ebb070f8098c59934bcc9fc73a43 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,19 @@ def final_integrate(i): After defining the methods, it is necessary to setup the P4IRS simulations: ```python +dt = 0.005 +cutoff_radius = 2.5 +skin = 0.3 +ntypes = 4 +sigma = 1.0 +epsilon = 1.0 +sigma6 = sigma ** 6 +nx = 32 +ny = 32 +nz = 32 +rho = 0.8442 +temp = 1.44 + # Simulation setup psim = pairs.simulation( "md", # Simulation identifier @@ -52,20 +65,16 @@ psim.add_property('force', pairs.vector(), volatile=True) # Features and their properties psim.add_feature('type', ntypes) -psim.add_feature_property('type', 'epsilon', pairs.real(), [...]) -psim.add_feature_property('type', 'sigma6', pairs.real(), [...]) - -# Simulation domain -psim.set_domain([xmin, ymin, zmin, xmax, ymax, zmax]) +psim.add_feature_property('type', 'epsilon', pairs.real(), [epsilon for i in range(ntypes * ntypes)]) +psim.add_feature_property('type', 'sigma6', pairs.real(), [sigma6 for i in range(ntypes * ntypes)]) -# Initial state -psim.read_particle_data( - "data/copper_fcc_lattice.input", - ['type', 'mass', 'position', 'velocity'], - pairs.point_mass()) +# Simulation domain and initial state +psim.copper_fcc_lattice(nx, ny, nz, rho, temp, ntypes) +psim.set_domain_partitioner(pairs.regular_domain_partitioner()) +psim.compute_thermo(100) ``` -Then the optimization strategies and visualization settings to use: +Then, define the optimization strategies and visualization settings to use: ```python # Optimization settings