kin = 0.5*np.sum(v**2) / n
print("{:40}{:15.6f}".format('Kinetic energy',kin) )
if np.fabs(delta_rho) < tol and np.fabs(delta_kin) < tol:
print('No changes requested')
else:
if np.fabs(delta_rho) > tol:
assert rho+delta_rho > 0.0, 'New requested density would be negative'
scale = ( rho / (rho+delta_rho) )**(1.0/3.0)
box = box * scale
r = r * scale
rho = n / box**3
print("{:40}{:15.6f}".format('Density',rho) )
if np.fabs(delta_kin) > tol:
assert kin+delta_kin > 0.0, 'New requested kinetic energy would be negative'
scale = np.sqrt ( (kin+delta_kin) / kin )
v = v * scale
kin = 0.5*np.sum(v**2) / n
print("{:40}{:15.6f}".format('New kinetic energy',kin) )
if atomic:
if velocities:
write_cnf_atoms ( filename, n, box, r, v )
else:
write_cnf_atoms ( filename, n, box, r )
else:
if velocities:
write_cnf_mols ( filename, n, box, r, e, v, w )
else:
write_cnf_mols ( filename, n, box, r, e )
zeta = 2.0 * zeta - 1.0 # Now in range (-1,+1)
box_scale = np.exp(zeta *
db_max) # Sampling log(box) and log(vol) uniformly
box_new = box * box_scale # New box (in sigma units)
den_scale = 1.0 / box_scale**3 # Density scaling factor
if not overlap(box_new, r,
e): # Test for non-overlapping configuration
delta = pressure * (box_new**3 - box**3
) # PV term (temperature = 1.0 )
delta = delta + (n + 1) * np.log(
den_scale) # Factor (n+1) consistent with log(box) sampling
if metropolis(delta): # Accept Metropolis test
box = box_new # Update box
v_ratio = 1.0 # Set move counter
blk_add(calc_variables())
blk_end(blk) # Output block averages
sav_tag = str(blk).zfill(
3) if blk < 1000 else 'sav' # Number configuration by block
write_cnf_mols(cnf_prefix + sav_tag, n, box, r * box,
e) # Save configuration
run_end(calc_variables())
assert not overlap(box, r, e), 'Overlap in final configuration'
write_cnf_mols(cnf_prefix + out_tag, n, box, r * box, e) # Save configuration
conclusion()