def run_nvt(_nnucl, _ntraj, _q, _p, iM, model, params):
"""
model - setup the Hamiltonian
outname - the name of the output file
"""
Q, P = [], []
ndia, nadi, nnucl, ntraj = 1, 1, _nnucl, _ntraj
q = MATRIX(_q)
p = MATRIX(_p)
# ======= Hierarchy of Hamiltonians =======
ham = nHamiltonian(ndia, nadi, nnucl)
ham.init_all(2)
ham1 = []
for tr in xrange(ntraj):
ham1.append(nHamiltonian(ndia, nadi, nnucl))
ham1[tr].init_all(2)
ham.add_child(ham1[tr])
# Set up the models and compute internal variables
# Initial calculations
ham.compute_diabatic(compute_model, q, params, 1)
ham.compute_adiabatic(1, 1)
therms = Thermostat(params)
therms.set_Nf_t(nnucl * ntraj)
therms.set_Nf_r(0)
therms.set_Nf_b(0)
therms.init_nhc()
Ebath = therms.energy()
therms.show_info()
# sys.exit()
Ekin, Epot, Etot = compute_etot(ham, p, iM)
out1 = open(params["out_energy"], "w")
out1.close()
out2 = open(params["out_phase_space"], "w")
out2.close()
out3 = open(params["out_positions"], "w")
out3.close()
dt = params["dt"]
Q.append(MATRIX(q))
P.append(MATRIX(p))
f = open(params["trajectory_filename"], "w")
f.close()
# Do the propagation
for i in xrange(params["nsteps"]):
print_xyz(params["label"], q, params["trajectory_index"],
params["trajectory_filename"], i)
Verlet1_nvt(dt, q, p, iM, ham, compute_model, params, 0, therms)
Q.append(MATRIX(q))
P.append(MATRIX(p))
#=========== Properties ==========
Ekin, Epot, Etot = compute_etot(ham, p, iM)
Ebath = therms.energy() / float(ntraj)
Tcurr = 2.0 * Ekin / (nnucl * kb)
# Print the ensemble average - kinetic, potential, and total energies
# Print the tunneling information. Here, we count each trajectory across the barrier.
out1 = open(params["out_energy"], "a")
out1.write(" %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %8.5f\n" %
(i * dt, Ekin, Epot, Etot, Ebath, Etot + Ebath, Tcurr))
out1.close()
# Print the phase space information
out2 = open(params["out_phase_space"], "a")
for j in range(ntraj):
out2.write(" %8.5f %8.5f" % (q.get(0, j), p.get(0, j))),
out2.write("\n")
out2.close()
# Print the position versus time infromation
out3 = open(params["out_positions"], "a")
out3.write(" %8.5f" % (i * dt)),
for j in range(ntraj):
out3.write(" %8.5f" % (q.get(0, j)))
out3.write("\n")
out3.close()
return Q, P
def run_nve(_nnucl, _ntraj, _q, _p, iM, model, params):
"""
model - setup the Hamiltonian
outname - the name of the output file
"""
ndia, nadi, nnucl, ntraj = 1, 1, _nnucl, _ntraj
q = MATRIX(_q)
p = MATRIX(_p)
# ======= Hierarchy of Hamiltonians =======
ham = nHamiltonian(ndia, nadi, nnucl)
ham.init_all(2)
ham1 = []
for tr in xrange(ntraj):
ham1.append(nHamiltonian(ndia, nadi, nnucl))
ham1[tr].init_all(2)
ham.add_child(ham1[tr])
# Set up the models and compute internal variables
# Initial calculations
ham.compute_diabatic(compute_model, q, params, 1)
ham.compute_adiabatic(1, 1)
Ekin, Epot, Etot = compute_etot(ham, p, iM)
out1 = open(params["out_energy"], "w")
out1.close()
out2 = open(params["out_phase_space"], "w")
out2.close()
out3 = open(params["out_positions"], "w")
out3.close()
dt = params["dt"]
Q, P = [], []
Q.append(MATRIX(q))
P.append(MATRIX(p))
f = open(params["trajectory_filename"], "w")
f.close()
for i in xrange(params["nsteps"]):
print_xyz(params["label"], q, params["trajectory_index"],
params["trajectory_filename"], i)
Verlet1(dt, q, p, iM, ham, compute_model, params, 0)
# sys.exit(0)
"""
if params["is_periodic"] == 1:
for dof in xrange(nnucl):
print dof
for tr in xrange(ntraj):
if(q.get(dof, tr) > TV):
pass #q.add(dof, tr, -1.0*TV)
elif(q.get(dof, tr) < 0.0):
pass #q.add(dof, tr, TV)
sys.exit(0)
"""
Q.append(MATRIX(q))
P.append(MATRIX(p))
#=========== Properties ==========
Ekin, Epot, Etot = compute_etot(ham, p, iM)
Tcurr = 2.0 * Ekin / (nnucl * kb)
# Print the ensemble average - kinetic, potential, and total energies
# Print the tunneling information. Here, we count each trajectory across the barrier.
out1 = open(params["out_energy"], "a")
out1.write(" %8.5f %8.5f %8.5f %8.5f %8.5f\n" %
(i * dt, Ekin, Epot, Etot, Tcurr))
out1.close()
# Print the phase space information
out2 = open(params["out_phase_space"], "a")
for j in range(ntraj):
out2.write(" %8.5f %8.5f" % (q.get(0, j), p.get(0, j))),
out2.write("\n")
out2.close()
# Print the position versus time infromation
out3 = open(params["out_positions"], "a")
out3.write(" %8.5f" % (i * dt)),
for j in range(ntraj):
out3.write(" %8.5f" % (q.get(0, j)))
out3.write("\n")
out3.close()
return Q, P
def run_nve(_nnucl, _ntraj, _q, _p, iM, model, params):
"""
model - setup the Hamiltonian
outname - the name of the output file
"""
ndia, nadi, nnucl, ntraj = 1, 1, _nnucl, _ntraj
q = MATRIX(_q)
p = MATRIX(_p)
# ======= Hierarchy of Hamiltonians =======
ham = nHamiltonian(ndia, nadi, nnucl)
ham.init_all(2)
ham1 = []
for tr in xrange(ntraj):
ham1.append(nHamiltonian(ndia, nadi, nnucl))
ham1[tr].init_all(2)
ham.add_child(ham1[tr])
# Set up the models and compute internal variables
# Initial calculations
ham.compute_diabatic(compute_model, q, params, 1)
ham.compute_adiabatic(1, 1)
Ekin, Epot, Etot = compute_etot(ham, p, iM)
out1 = open(params["out_energy"], "w")
out1.close()
out2 = open(params["out_phase_space"], "w")
out2.close()
out3 = open(params["out_positions"], "w")
out3.close()
dt = params["dt"]
Q, P = [], []
Q.append(MATRIX(q))
P.append(MATRIX(p))
# Do the propagation
for i in xrange(params["nsteps"]):
Verlet1(dt, q, p, iM, ham, compute_model, params, 0)
Q.append(MATRIX(q))
P.append(MATRIX(p))
#=========== Properties ==========
Ekin, Epot, Etot = compute_etot(ham, p, iM)
# Print the ensemble average - kinetic, potential, and total energies
# Print the tunneling information. Here, we count each trajectory across the barrier.
out1 = open(params["out_energy"], "a")
out1.write(" %8.5f %8.5f %8.5f %8.5f\n" %
(i * dt, Ekin, Epot, Etot))
out1.close()
# Print the phase space information
out2 = open(params["out_phase_space"], "a")
for j in range(ntraj):
out2.write(" %8.5f %8.5f" % (q.get(0, j), p.get(0, j))),
out2.write("\n")
out2.close()
# Print the position versus time infromation
out3 = open(params["out_positions"], "a")
out3.write(" %8.5f" % (i * dt)),
for j in range(ntraj):
out3.write(" %8.5f" % (q.get(0, j)))
out3.write("\n")
out3.close()
return Q, P