def data(i):
lmp1 = lammps()
polymer = PyLammps(ptr=lmp1)
x = 60
y = 30
z = 30
t = 1
polymer.units("lj")
polymer.dimension(3)
polymer.atom_style("bond")
polymer.bond_style("harmonic")
polymer.pair_style("lj/cut", 3)
polymer.read_data("data.polymer")
polymer.region("void cylinder x", 15, 15, 2, 29, 31)
polymer.pair_coeff(1, 2, 2.5, 3)
polymer.pair_coeff(1, 3, 2.5, 1.12)
polymer.pair_coeff(2, 3, 2.5, 1.12)
polymer.velocity("all create", t, 97287)
polymer.group("polymer type", 1, 2)
polymer.group("first type", 1)
polymer.region("box block", 0, x, 0, y, 0, z)
polymer.region("spherein sphere", 29, 15, 15, 2)
polymer.region("boxin block", 27, 29, 13, 17, 13, 17)
polymer.region("hemiin intersect", 2, "boxin spherein")
x0 = polymer.atoms[0].position[0]
y0 = polymer.atoms[0].position[1]
z0 = polymer.atoms[0].position[2]
r = lambda x0, y0, z0: np.sqrt((x0 - 29)**2 + (y0 - 15)**2 + (z0 - 15)**2)
fx = lambda x0, y0, z0: 5 * (x0 - 29) / r(x0, y0, z0)
fy = lambda x0, y0, z0: 5 * (y0 - 15) / r(x0, y0, z0)
fz = lambda x0, y0, z0: 5 * (z0 - 15) / r(x0, y0, z0)
polymer.fix(1, "polymer nve")
polymer.fix(2, "polymer langevin", t, t, 1.5,
np.random.randint(2, high=200000))
polymer.fix(3, "polymer spring tether", 10, i, "NULL NULL", 0)
polymer.timestep(0.01)
polymer.compute("com polymer com")
polymer.variable("ftotal equal fcm(polymer,x)")
polymer.variable("c equal c_com[1]")
polymer.thermo_style("custom v_ftotal v_c")
polymer.thermo(1)
polymer.run(500000)
l = polymer.runs[0][0][1][20000:] + [i]
u = [np.mean(polymer.runs[0][0][0][20000:]), i]
np.savetxt("trial%dmean.txt" % i, u)
np.savetxt("trial%dall.txt" % i, l)
return u
# L.pair_coeff("* * eam Au_u3.eam")
# L.pair_coeff(1,2,"lj/cut",epsAuC,sigAuC,10.0)
# L.pair_coeff("* * tersoff SiC.tersoff NULL C")
(nPart1, nPart2, nPartsub, coords1, coords2, coordssub, indices1, indices2,
indicessub) = getcoords()
print("no. of atoms in the system: {} Au, {} Ni, {} C".format(
nPart1, nPart2, nPartsub))
scaleF = nPart1 * cdf1[-1] / (nPart2 * cdf2[-1])
print(scaleF)
L.minimize(1e-6, 1e-7, 5000, 50000)
print("initial minimization completed.")
L.compute("K", "all", "ke/atom")
L.compute("P", "all", "pe/atom")
L.compute(
"coordno", "all", "coord/atom", "cutoff", NNthresh
) # calculate coordination no between all atoms of type 1 or 2 (exclude substrate atoms (type 3)
#L.dump("d1","all","xyz",1000,"output.xyz")
#L.dump("d1","all","custom",1000,"output.out", "id", "type","x","y","z","vx","vy","vz","c_K","c_P","c_coordno")
#L.dump("d1","xtc","atom",100,"T" + str(Temp) + "_Fulltrajectories.xtc",100) # last value gives precision, a value of 100 means that coordinates are stored to 1/100 nanometer accuracy
#L.dump_modify("d1","element","Au","Ni","C")
#L.dump_modify("d1","pbc","yes") # remap atoms via periodic boundary conditions
#L.dump("trajectory","all","atom",100, "T" + str(Temp) + "_Fulltrajectories.lammpstrj")
# Set thermo output to log file
L.thermo_style("custom", "step", "atoms", "temp", "etotal", "pe", "ke",
"dt")
# GROUPS & COMPUTES
if hasattr(run_args, 'label_micelles'):
micelle_group = 'sol_tips'
sol_tip_bead_type = model.state_structures[0][0][-1]
py_lmp.variable(micelle_group, 'atom',
'"type == {:d}"'.format(sol_tip_bead_type))
py_lmp.group(micelle_group, 'dynamic', simulation.rods_group, 'var',
micelle_group, 'every', out_freq)
micelle_compute = "micelle_ID"
if hasattr(run_args, 'micelle_cutoff'):
micelle_cutoff = run_args.micelle_cutoff
else:
SS_tip_int_key = model.eps[(sol_tip_bead_type, sol_tip_bead_type)][1]
SS_tip_int_range = model.int_types[SS_tip_int_key][1]
micelle_cutoff = 2 * model.rod_radius + SS_tip_int_range
py_lmp.compute(micelle_compute, micelle_group, 'aggregate/atom',
micelle_cutoff)
# OUTPUT
dump_elems = "id x y z type mol"
try:
dump_elems += " c_" + micelle_compute
except:
pass
py_lmp.dump("dump_cmd", "all", "custom", out_freq, '"' + dump_path + '"',
dump_elems)
py_lmp.dump_modify("dump_cmd", "sort id")
py_lmp.thermo_style("custom", "step atoms", "pe temp")
py_lmp.thermo(out_freq)
# RUN ...
py_lmp.run(args.simlen)
# GROUPS & COMPUTES
if hasattr(run_args, 'label_micelles'):
micelle_group = 'sol_tips'
sol_tip_bead_type = model.state_structures[0][0][-1]
py_lmp.variable(micelle_group, 'atom',
'"type == {:d}"'.format(sol_tip_bead_type))
py_lmp.group(micelle_group, 'dynamic', simulation.rods_group, 'var',
micelle_group, 'every', out_freq)
micelle_compute = "micelle_ID"
if hasattr(run_args, 'micelle_cutoff'):
micelle_cutoff = run_args.micelle_cutoff
else:
SS_tip_int_key = model.eps[(sol_tip_bead_type, sol_tip_bead_type)][1]
SS_tip_int_range = model.int_types[SS_tip_int_key][1]
micelle_cutoff = 2 * model.rod_radius + SS_tip_int_range
py_lmp.compute(micelle_compute, micelle_group, 'aggregate/atom',
micelle_cutoff)
#TODO label_fibrils ??
# FIXES & DYNAMICS
thermo_fix = 'thermostat'
py_lmp.fix(thermo_fix, 'all', 'langevin', run_args.temp, run_args.temp,
run_args.damp, seed) #, "zero yes")
simulation.set_rod_dynamics('nve', opt=['mol', model.rod_states[0]])
py_lmp.region('gcmc_init', 'block', membrane.xmin + model.rod_length / 2,
membrane.xmax - model.rod_length / 2,
membrane.ymin + model.rod_length / 2,
membrane.ymax - model.rod_length / 2, 0.0 + model.rod_length / 2,
run_args.Lz - model.rod_length / 2)
else:
fibril_cutoff = 0
i = -1
for t1 in beta_active_patch_types:
i += 1
for t2 in beta_active_patch_types[i:]:
try:
int_key = model.eps[(t1, t2)][1]
except:
continue
int_range = model.int_types[int_key][1]
cutoff = model.bead_radii[t1] + model.bead_radii[
t2] + int_range * 2 / 3
if cutoff > fibril_cutoff:
fibril_cutoff = cutoff
py_lmp.compute(fibril_compute, fibril_group, 'aggregate/atom',
fibril_cutoff)
# OUTPUT
py_lmp.thermo_style("custom", "step atoms", "pe temp")
dump_elems = "id x y z type mol"
try:
dump_elems += " c_" + fibril_compute
except:
pass
py_lmp.dump("dump_cmd", "all", "custom", out_freq, dump_path, dump_elems)
py_lmp.dump_modify("dump_cmd", "sort id")
py_lmp.thermo(out_freq)
# RUN...
if model.num_states == 1 or run_args.mc_moves == 0:
raise Exception(
