def serve_md(nuclear_charges, coordinates, calculator=None, temp=None):
"""
"""
if calculator is None:
parameters = {}
parameters["offset"] = -97084.83100465109
parameters["sigma"] = 10.0
alphas = np.load(FILENAME_ALPHAS)
X = np.load(FILENAME_REPRESENTATIONS)
Q = np.load(FILENAME_CHARGES, allow_pickle=True)
alphas = np.array(alphas, order="F")
X = np.array(X, order="F")
calculator = QMLCalculator(parameters, X, Q, alphas)
# SET MOLECULE
molecule = ase.Atoms(nuclear_charges, coordinates)
molecule.set_calculator(calculator)
# SET ASE MD
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(molecule, 200 * units.kB)
time = 0.5
if temp is None:
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(molecule, time * units.fs) # 1 fs time step.
else:
dyn = NVTBerendsen(molecule, time*units.fs, temp, time*units.fs, fixcm=False)
# SET AND SERVE NARUPA MD
imd = ASEImdServer(dyn)
while True:
imd.run(10)
print("")
dump_xyz(molecule, tmpdir + "snapshot.xyz")
return
def md_run(
parent_dataset,
dft_calculator,
starting_image,
temp,
dt,
count,
label,
ensemble="NVE",
):
slab = starting_image.copy()
slab.set_calculator(AMPOnlineCalc(parent_dataset, dft_calculator, 3))
# MaxwellBoltzmannDistribution(slab, temp * units.kB)
if ensemble == "nvtberendsen":
dyn = NVTBerendsen(slab,
dt * ase.units.fs,
temp,
taut=300 * ase.units.fs)
traj = ase.io.Trajectory(label + ".traj", "w", slab)
dyn.attach(traj.write, interval=1)
dyn.run(count - 1)
# Parameters for the Morse potential for Cu
D = 0.3429
r0 = 2.866
alpha = 1.3588
atoms = read('hexagonal_lattice.xyz')
atoms.set_calculator(MorsePotential(D=D, alpha=alpha, r0=r0))
vel = np.zeros((len(atoms), 3))
# initialize velocities with uniform random numbers between [-0.005, 0.005]
# gives random initial velocity
vel[:, 0] = (np.random.rand(len(atoms)) - 0.5) * 1e-2
vel[:, 1] = (np.random.rand(len(atoms)) - 0.5) * 1e-2
atoms.set_velocities(vel)
open('berendsen.log', 'w').close()
dyn = NVTBerendsen(atoms,
timestep=1 * units.fs,
temperature=600,
taut=100 * units.fs,
logfile='berendsen.log',
trajectory='berendsen.traj')
# Note that the temperature in NVTBerendsen is given in K
# taut = relaxtation time
dyn.run(1000)
write('berendsen.xyz', read('berendsen.traj@:'))
from ase.units import fs
from run_opt import read_incar, write_contcar, get_ele_dict
import os, sys
calc = GAP(rcut=6.0)
nsw, pstress, tebeg, potim, _ = read_incar()
my_atoms = read('POSCAR', format='vasp')
my_atoms.set_calculator(calc)
"""
for NVT
"""
#print(tebeg,'tebeg')
dyn = NVTBerendsen(my_atoms,
timestep=potim * fs,
temperature=tebeg,
taut=0.5 * 1000 * fs,
trajectory='ase.traj')
dyn.attach(MDLogger(dyn,
my_atoms,
'OUTCAR',
header=True,
stress=True,
pstress=pstress,
peratom=False,
mode="w"),
interval=1)
dyn.run(steps=nsw)
atoms_lat = my_atoms.cell
atoms_pos = my_atoms.positions
def ribs(params, voidcount, voidrad, frame_count=1000):
calc = IdealBrittleSolid(rc=params.rc,
k=params.k,
a=params.a,
beta=params.beta)
x_dimer = np.linspace(params.a - (params.rc - params.a),
params.a + 1.1 * (params.rc - params.a), 51)
dimers = [
Atoms('Si2', [(0, 0, 0), (x, 0, 0)], cell=[10., 10., 10.], pbc=True)
for x in x_dimer
]
calc.set_reference_crystal(dimers[0])
e_dimer = []
f_dimer = []
f_num = []
for d in dimers:
d.set_calculator(calc)
e_dimer.append(d.get_potential_energy())
f_dimer.append(d.get_forces())
f_num.append(calc.calculate_numerical_forces(d))
e_dimer = np.array(e_dimer)
f_dimer = np.array(f_dimer)
f_num = np.array(f_num)
assert abs(f_dimer - f_num).max() < 0.1
#! crystal is created here, the length and height can be modified here as well
#! edit 3N changed to different values to test
crystal = triangular_lattice_slab(params.a, params.lm * params.N, params.N)
calc.set_reference_crystal(crystal)
crystal.set_calculator(calc)
e0 = crystal.get_potential_energy()
l = crystal.cell[0, 0]
h = crystal.cell[1, 1]
print('l=', l, 'h=', h)
# compute surface (Griffith) energy
b = crystal.copy()
b.set_calculator(calc)
shift = calc.parameters['rc'] * 2
y = crystal.positions[:, 1]
b.positions[y > h / 2, 1] += shift
b.cell[1, 1] += shift
e1 = b.get_potential_energy()
E_G = (e1 - e0) / l
print('Griffith energy', E_G)
# compute Griffith strain
eps = 0.0 # initial strain is zero
eps_max = 2 / np.sqrt(3) * (params.rc - params.a) * np.sqrt(
params.N - 1) / h # Griffith strain assuming harmonic energy
deps = eps_max / 100. # strain increment
e_over_l = 0.0 # initial energy per unit length is zero
energy = []
strain = []
while e_over_l < E_G:
c = crystal.copy()
c.set_calculator(calc)
c.positions[:, 1] *= (1.0 + eps)
c.cell[1, 1] *= (1.0 + eps)
e_over_l = c.get_potential_energy() / l
energy.append(e_over_l)
strain.append(eps)
eps += deps
energy = np.array(energy)
eps_of_e = interp1d(energy, strain, kind='linear')
eps_G = eps_of_e(E_G)
print('Griffith strain', eps_G)
c = crystal.copy()
c.info['E_G'] = E_G
c.info['eps_G'] = eps_G
# open up the cell along x and y by introducing some vaccum
orig_cell_width = c.cell[0, 0]
orig_cell_height = c.cell[1, 1]
c.center(params.vacuum, axis=0)
c.center(params.vacuum, axis=1)
# centre the slab on the origin
c.positions[:, 0] -= c.positions[:, 0].mean()
c.positions[:, 1] -= c.positions[:, 1].mean()
c.info['cell_origin'] = [-c.cell[0, 0] / 2, -c.cell[1, 1] / 2, 0.0]
ase.io.write('crack_1.xyz', c, format='extxyz')
width = (c.positions[:, 0].max() - c.positions[:, 0].min())
height = (c.positions[:, 1].max() - c.positions[:, 1].min())
c.info['OrigHeight'] = height
print((
'Made slab with %d atoms, original width and height: %.1f x %.1f A^2' %
(len(c), width, height)))
top = c.positions[:, 1].max()
bottom = c.positions[:, 1].min()
left = c.positions[:, 0].min()
right = c.positions[:, 0].max()
crack_seed_length = 0.2 * width
strain_ramp_length = 8.0 * params.a # make this bigger until crack looks nicer
delta_strain = params.strain_rate * params.dt
# fix top and bottom rows, and setup Stokes damping mask
# initial use constant strain
set_constraints(c, params.a)
# apply initial displacment field
c.positions[:, 1] += thin_strip_displacement_y(
c.positions[:, 0], c.positions[:, 1], params.delta * eps_G,
left + crack_seed_length,
left + crack_seed_length + strain_ramp_length)
print('Applied initial load: delta=%.2f strain=%.4f' %
(params.delta, params.delta * eps_G))
ase.io.write('crack_2.xyz', c, format='extxyz')
c.set_calculator(calc)
cl, cs, cr = calc.get_wave_speeds(c)
print("rayleigh speed = %f" % cr)
# relax initial structure
# opt = FIRE(c)
# opt.run(fmax=1e-3)
ase.io.write('crack_3.xyz', c, format='extxyz')
#length and height of the slab is defined here
L = params.N * params.lm
H = params.N * 2
#Atomic Void Simulations
#😵------------------------------------------------------------------------------
#the following lines of code were written to convert 1D positions into a 2D array
#so as to make manipulation of slab easier
if True:
#void parameters are defined here.
#around a max of [0.3--1.7] recommended
y_offset = 0.1
#y offset is a fraction of distance from the end of the slab
x_offset = 0.4
rad = voidrad
#this reference code is for 160x40 slab
#in steps of 40 i.e. the height, create a list upto the length of slab
#row0 = range(0,6400,40)
row0 = range(0, len(c), H)
#the 2D array will be held in slab
slab = []
for col in range(H):
row = []
for r in row0:
i = col + r
row.append(c.positions[i])
slab.append(row)
slab = np.array(slab)
#all items in the array reversed, needed because the salb is built from bottom left up
#in other words, reflected in x axis
slab = slab[::-1]
# print(slab[0])
# slab[modifiers.mask(h=H,w=L, center=[int(L*x_offset),int((H - 1)*y_offset)], radius=rad)] = 0
#multiple voids if need be
if True:
for i in range(voidcount):
y_offset = rand.uniform(0.1, 0.9)
x_offset = rand.uniform(0.3, 0.95)
slab[modifiers.mask(
h=H,
w=L,
center=[int(L * x_offset),
int((H - 1) * y_offset)],
radius=rad)] = 0
#reversed the slab back again here
slab = slab[::-1]
# # this is a useful text-array representation of the slab, for debugging purposes
# mtext = open('masktest.txt','w')
# for row in slab:
# mtext.write(str(row).replace("\n",",")+"\n")
# mtext.close
slab_1d = []
for col in range(L):
for row in range(H):
slab_1d.append(slab[row, col])
slab_1d = np.array(slab_1d)
todel = []
for i in range(len(c)):
if slab_1d[i][2] == 0:
todel.append(i)
print(todel)
del c[todel]
# return
#End of Void Simulation
#-------------------------------------------------------------------------------
#Grain Boundary Simulations
#-------------------------------------------------------------------------------
if False:
hi = 2
#-------------------------------------------------------------------------------
#! replaced velcityVerlet with Lagevin to add temperature parameter
if params.v_verlet:
dyn = VelocityVerlet(c, params.dt * units.fs, logfile=None)
# set_initial_velocities(dyn.atoms)
else:
print("Using NVT!")
# mbd(c, 20 * units.kB, force_temp = True)
# dyn = Langevin(c,params.dt*units.fs,params.T*units.kB, 5)
dyn = NVTBerendsen(c,
params.dt * units.fs,
params.T,
taut=0.5 * 1000 * units.fs)
#dyn.atoms.rattle(1e-3) # non-deterministic simulations - adjust to suit
#!simulation outputs numbered, avoids deleting exisiting results
iterFile = open("simIteration.txt", 'r+')
iteration = int(iterFile.readlines()[0]) + 1
if params.overwrite_output:
iteration -= 1
iterFile.seek(0, 0)
iterFile.write(str(iteration))
iterFile.close()
dir = "./.simout/void/sim_" + str(iteration) + "_" + str(
params.keep_test).lower() + "_" + params.desc + "/"
cf.createFolder(dir)
#!Saving parameter values for each iteration of the simulation
logFile = open(dir + "params_log.txt", 'w')
for p, value in params.compose_params().iteritems():
logFile.write(p + " ==> " + str(value) + "\n")
logFile.close
crack_pos = []
if params.keep_test:
traj = NetCDFTrajectory(dir + 'traj' + str(iteration) + '.nc', 'w', c)
dyn.attach(traj.write, 10, dyn.atoms, arrays=['stokes', 'momenta'])
# #! isolating crack tip_x for saving
# crack_tip_file2 = open(dir+'tip_x.txt','w')
# crack_tip_file2.close()
tip_x_file = open(dir + 'tip_x.txt', 'a')
console_output = open(dir + 'console_output.txt', 'a')
coord_file = open(dir + 'coordinates.csv', 'a')
coordinates = []
distances = []
dyn.attach(find_crack_tip,
10,
dyn.atoms,
tipxfile=tip_x_file,
cout=console_output,
coord=coordinates,
d=distances,
dt=params.dt * 10,
store=True,
results=crack_pos)
# run for 2000 time steps to reach steady state at initial load
# for i in range(10):
# dyn.run(250)
# if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
# set_constraints(dyn.atoms, params.a)
# start decreasing strain
#set_constraints(dyn.atoms, params.a, delta_strain=delta_strain)
# strain_atoms = ConstantStrainRate(dyn.atoms.info['OrigHeight'],
# delta_strain)
# dyn.attach(strain_atoms.apply_strain, 1, dyn. atoms )
# for i in range(50):
# dyn.run(100)
# if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
# set_constraints(dyn.atoms, params.a)
# #cleardel dyn.observers[-1] # stop increasing the strain
# for i in range(1000):
# dyn.run(100)
# if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
# set_constraints(dyn.atoms, params.a)
dyn.run(int(1 * frame_count) * 10 + 10)
# print("\n\n\n\n\n -----Adding Temperature------\n\n\n\n\n")
# # mbd(c, 2*params.T * units.kB, force_temp = True)
# dyn.set_temperature(params.T*units.kB)
# dyn.run(int(0.5*frame_count)*10+10)
for c in coordinates:
coord_file.write(str(c[0]) + ',' + str(c[1]) + '\n')
coord_file.close()
if params.keep_test:
traj.close()
tip_x_file.close()
console_output.close()
si.set_calculator(calc)
# geometry optimization
si = optimize(si, box=True)
print('equlirum cell para: ', si.get_cell()[0][0])
print('equlirum energy: ', si.get_potential_energy())
print('equlirum stress', -si.get_stress() / units.GPa)
# Build the 2*2*2 supercell
atoms = si * 2
atoms.set_calculator(calc)
print(atoms)
# NVT MD simulation
dyn = NVTBerendsen(atoms,
p.time_step * units.fs,
p.temperature,
taut=p.taut * units.fs)
MaxwellBoltzmannDistribution(atoms, p.temperature * units.kB)
dyn.attach(MDLogger(dyn,
atoms,
'md.log',
header=True,
stress=False,
mode="w"),
interval=p.save_interval)
traj = Trajectory('md.traj', 'w', atoms)
dyn.attach(traj.write, interval=p.save_interval)
dyn.run(p.run_step)
