# Production run
# In case, we need a thermostat:
params["Temperature"] = 300.0
params["Q"] = 100.0
params["thermostat_type"] = "Nose-Hoover"
params["nu_therm"] = 0.001
params["NHC_size"] = 5
params["sigma"] = 2.0
params["epsilon"] = 0.01
# Annealing
params["dt"] = 10.0
params["nsteps"] = 50
for i in xrange(10):
Q, P = run_nve(ndof, ntraj, q, p, iM, compute_model, params)
# Reset velocities
q = MATRIX(Q[-1])
lattice_p(p, Nx, Ny, Nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, rnd)
params["out_energy"] = "_output.txt"
params["out_phase_space"] = "_phase_space.txt"
params["out_positions"] = "_pos_space.txt"
params["trajectory_filename"] = "_traj.xyz"
params["dt"] = 10.0
params["nsteps"] = 2000
lattice_p(p, Nx, Ny, Nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, rnd)
Q, P, Etot = run_nvt(ndof, ntraj, q, p, iM, compute_model, params)
def run(T):
# ===== Define the system ==========
Nx, Ny, Nz = 3, 3, 3
nnucl = Nx * Ny * Nz
ndof, ntraj = 3*nnucl, 5
# Dynamical variables and system-specific properties
dx, dy, dz = 2.0, 2.0, 2.0
sx, sy, sz = 0.1, 0.1, 0.1
px, py, pz = 0.0, 0.0, 0.0
spx, spy, spz = 0.1, 0.1, 0.1
rnd = Random()
q = MATRIX(ndof,ntraj); lattice(q, Nx,Ny,Nz, dx, dy, dz, sx, sy, sz, rnd)
p = MATRIX(ndof,ntraj); lattice_p(p, Nx,Ny,Nz, px, py, pz, spx, spy, spz, rnd)
iM = MATRIX(ndof,1);
for i in xrange(ndof):
iM.set(i,0, 1.0/2000.0)
# ===== Define the simulation parameters ==========
# Model parameters
params = {}
# Simulation and output parameters
params["nsteps"] = 1000
params["out_energy"] = "_output-anneal.txt"
params["out_phase_space"] = "_phase_space-anneal.txt"
params["out_positions"] = "_pos_space-anneal.txt"
params["label"] = ["H"]*nnucl
params["trajectory_index"] = 0
params["trajectory_filename"] = "_traj-anneal.xyz"
# Production run
# In case, we need a thermostat:
params["Temperature"] = T
params["Q"] = 100.0
params["thermostat_type"] = "Nose-Hoover"
params["nu_therm"] = 0.001
params["NHC_size"] = 5
params["sigma"] = 2.0
params["epsilon"] = 0.01
# Annealing
params["dt"] = 10.0
params["nsteps"] = 50
for i in xrange(10):
Q, P = run_nve(ndof, ntraj, q, p, iM, compute_model, params)
# Reset velocities
q = MATRIX(Q[-1])
lattice_p(p, Nx,Ny,Nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, rnd)
params["out_energy"] = "_output.txt"
params["out_phase_space"] = "_phase_space.txt"
params["out_positions"] = "_pos_space.txt"
params["trajectory_filename"] = "_traj.xyz"
params["dt"] = 20.0
params["nsteps"] = 5000
lattice_p(p, Nx,Ny,Nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, rnd)
Q, P, Etot = run_nvt(ndof, ntraj, q, p, iM, compute_model, params)
params["start_step"] = 2000
cv = compute_cv(Etot, params["start_step"], params["dt"], "_cv.txt")
cv = cv / (kb * params["Temperature"] * params["Temperature"])
return cv