def compute_energy(template, i):
potpath = os.path.join(os.environ['LAMMPS_POTENTIALS'], 'Au_u3.eam')
potential = ClassicalPotential(path=potpath, ptype='eam', element=["Au"])
runpath = Dir(path=os.path.join(
os.environ['WORKDIR'],
"final_project/Au110_reconstructed/test6_cubic/", str(i)))
natoms, struc = make_struc(i=i)
output_file = lammps_run(struc=struc,
runpath=runpath,
potential=potential,
intemplate=template,
inparam={})
energy, lattice = get_lammps_energy(outfile=output_file)
print('lattice is', lattice)
surface_area = 1 / (math.sqrt(2)) * lattice * lattice
print(natoms)
energy_per_atom = energy / natoms
surface_energy = []
surface_energy = ((1 / (2 * surface_area)) * (energy - (natoms) *
(-3.930000000176775)))
return energy, lattice, energy_per_atom, surface_energy
def compute_dynamics(size, timestep, nsteps, temperature):
"""
Make an input template and select potential and structure, and input parameters.
Return a pair of output file and RDF file written to the runpath directory.
"""
intemplate = """
# ---------- Initialize simulation ---------------------
units metal
atom_style atomic
dimension 3
boundary p p p
read_data $DATAINPUT
pair_style eam/alloy
pair_coeff * * $POTENTIAL Al
velocity all create $TEMPERATURE 87287 dist gaussian
# ---------- Describe computed properties------------------
compute msdall all msd
thermo_style custom step pe ke etotal temp press density c_msdall[4]
thermo $TOUTPUT
# ---------- Specify ensemble ---------------------
fix 1 all nve
#fix 1 all nvt temp $TEMPERATURE $TEMPERATURE $TDAMP
# --------- Compute RDF ---------------
compute rdfall all rdf 100 1 1
fix 2 all ave/time 1 $RDFFRAME $RDFFRAME c_rdfall[*] file $RDFFILE mode vector
# --------- Run -------------
timestep $TIMESTEP
run $NSTEPS
"""
potential = ClassicalPotential(ptype='eam',
element='Al',
name='Al_zhou.eam.alloy')
runpath = Dir(
path=os.path.join(os.environ['WORKDIR'], "Lab4/Problem1", "size_" +
str(size)))
struc = make_struc(size=size)
inparam = {
'TEMPERATURE': temperature,
'NSTEPS': nsteps,
'TIMESTEP': timestep,
'TOUTPUT': 100, # how often to write thermo output
'TDAMP': 50 * timestep, # thermostat damping time scale
'RDFFRAME': int(nsteps / 4), # frames for radial distribution function
}
outfile = lammps_run(struc=struc,
runpath=runpath,
potential=potential,
intemplate=intemplate,
inparam=inparam)
output = parse_lammps_thermo(outfile=outfile)
rdffile = get_rdf(runpath=runpath)
rdfs = parse_lammps_rdf(rdffile=rdffile)
return output, rdfs
def compute_energy(alat, template):
"""
Make an input template and select potential and structure, and the path where to run
"""
potpath = os.path.join(os.environ['LAMMPS_POTENTIALS'],
'Al_zhou.eam.alloy')
potential = ClassicalPotential(path=potpath, ptype='eam', element=["Al"])
runpath = Dir(path=os.path.join(os.environ['WORKDIR'], "Lab1", str(alat)))
struc = make_struc(alat=alat)
output_file = lammps_run(struc=struc,
runpath=runpath,
potential=potential,
intemplate=template,
inparam={})
energy, lattice = get_lammps_energy(outfile=output_file)
return energy, lattice
def compute_energy(alat, template):
"""
Make an input template and select potential and structure, and the path where to run
"""
potpath = os.path.join(os.environ['LAMMPS_POTENTIALS'], 'Au_u3.eam')
potential = ClassicalPotential(path=potpath, ptype='eam', element=["Au"])
runpath = Dir(path=os.path.join(
os.environ['WORKDIR'],
"final_project/bulk_cohesive_energy/test10_relaxed_cubic_a_and_b/",
str(alat)))
struc = make_struc(alat=alat)
output_file = lammps_run(struc=struc,
runpath=runpath,
potential=potential,
intemplate=template,
inparam={})
energy, lattice = get_lammps_energy(outfile=output_file)
return energy, lattice
def compute_AgI_dynamics(size, timestep, nsteps, temperature, ncpu):
"""
Make an input template and select potential and structure, and input parameters.
Return a pair of output file and RDF file written to the runpath directory.
"""
potential = ClassicalPotential(ptype='eam',
element='Al',
name='Al_zhou.eam.alloy')
runpath = Dir(
path=os.path.join(os.environ['WORKDIR'], "Lab4/Problem2", "temp_" +
str(temperature)))
struc = make_struc(size=size)
inparam = {
'TEMPERATURE': temperature,
'NSTEPS': nsteps,
'TIMESTEP': timestep,
'TOUTPUT': 100, # how often to write thermo output
'TDAMP': 50 * timestep, # thermostat damping time scale
'RDFFRAME': int(nsteps / 4), # frames for radial distribution function
}
outfile = lammps_run(struc=struc,
runpath=runpath,
potential=potential,
intemplate=intemplate,
inparam=inparam,
ncpu=ncpu,
triclinic=True)
output = parse_lammps_thermo(outfile=outfile)
rdfAgFile = File(path=os.path.join(runpath.path, 'lammps.rdf.Ag'))
rdfIFile = File(path=os.path.join(runpath.path, 'lammps.rdf.I'))
rdfAgIFile = File(path=os.path.join(runpath.path, 'lammps.rdf.AgI'))
rdfsAg = parse_lammps_rdf(rdffile=rdfAgFile)
rdfsI = parse_lammps_rdf(rdffile=rdfIFile)
rdfsAgI = parse_lammps_rdf(rdffile=rdfAgIFile)
return output, rdfsAg, rdfsI, rdfsAgI