def optimize_pm6(name, examples, param_string, starting_params, queue=None):
from scipy.optimize import minimize
examples = [structures.Struct(name=example, atoms=atoms(example))
for example in examples]
for e in examples:
e.bonds = [(b.atoms[0].index - 1, b.atoms[1].index - 1)
for b in geometry.get_bonds(e.atoms)]
n_bonds = sum([len(e.bonds) for e in examples])
counter = [0]
def pm6_error(params):
# Run Gaussian jobs with new parameters
for i, example in enumerate(examples):
running_jobs = [job('%s-%d-%d' % (name, counter[0], i),
'PM6=(Input,Print) Opt=Loose',
example.atoms,
extra_section=param_string % tuple(params),
queue=queue,
force=True)]
# Wait for all jobs to finish
for j in running_jobs:
j.wait()
# Get forces and energies resulting from new parameters
geom_error = 0.0
for i, example in enumerate(examples):
try:
new_energy, new_atoms = parse_atoms(
'%s-%d-%d' % (name, counter[0], i),
check_convergence=False)
except:
print '%s-%d-%d' % (name, counter[0], i), 'has no data'
exit()
if parse_atoms('%s-%d-%d' % (name, counter[0], i)) is None:
print '%s-%d-%d' % (name, counter[0], i),\
'did not converge fully'
# Compare results
for b in example.bonds:
d1 = geometry.dist(example.atoms[b[0]], example.atoms[b[1]])
d2 = geometry.dist(new_atoms[b[0]], new_atoms[b[1]])
geom_error += (d1 - d2)**2
error = geom_error / n_bonds
print error**0.5, params
counter[0] += 1
return error
minimize(pm6_error,
starting_params,
method='Nelder-Mead',
options={'disp': True})
def __init__(self, name, global_system=None, queue=None, procs=1, mem=1000,
priority=100, xhosts=None):
self.task_list = {}
self.task_order = []
self.name = name
self.global_system = global_system
self.queue = queue
self.procs = procs
self.mem = mem
self.priority = priority
self.xhosts = xhosts
self.parameters = structures.Struct()
self.data = None
Cl_, Cl = 21, 344
Pb_, Pb = 111, 907
Cs_, Cs = 72, 352
Si_, Si = 112, 908
O_, O = 113, 909
H_ = 54
N_ = 53
HN = 233
tersoff_atoms = [Pb, Cl, Cs]
extra_Pb = {
Pb: structures.Struct(index=Pb,
index2=Pb_,
element_name='Pb',
element=82,
mass=207.2,
charge=0.4,
vdw_e=10.1,
vdw_r=3.0),
}
extra_Si = {
Si: structures.Struct(index=Si,
index2=Si_,
element_name='Si',
element=14,
mass=28.0855,
charge=4,
vdw_e=10.1,
vdw_r=3.3),
}
"DMF":{"density":0.95, "dielectric":36.7},
"DMSO":{"density":1.0, "dielectric":46.7},
"NMP":{"density":1.1, "dielectric":32.3},
"ACETONE":{"density":0.78, "dielectric":20.7},
"METHACROLEIN":{"density":0.85, "dielectric":10.9},
"NITROMETHANE":{"density":1.14, "dielectric":35.9}}
for key in solvent.keys():
solvent[key.lower()] = solvent[key]
extra = { #(47, 3, 46):(85.00, 120.00), (47, 47, 3, 46):(0.0, 14.0, 0.0, 0.0),
#Pb: utils.Struct(index=Pb, index2=Pb_, element_name='Pb', element=82, mass=207.2, charge=2.0, vdw_e=0., vdw_r=4.0),
#Cl: utils.Struct(index=Cl, index2=Cl_, element_name='Cl', element=17, mass=35.45, charge=-0.0, vdw_e=0.01, vdw_r=4.0),
}
default_angles = {"type":structures.Struct(),
"angle":110.7,
"style":"harmonic",
"e":37.5,
"index2s":(13, 13, 46)}
# For debugging
#default_routes = ["! HF SV ECP{def2-TZVP}",
# "! OPT HF SV ECP{def2-TZVP} LooseOpt",
# "! OPT B97-D3 SV GCP(DFT/TZ) ECP{def2-TZVP} Grid7 SlowConv LooseOpt",
# "! OPT B97-D3 SV GCP(DFT/TZ) ECP{def2-TZVP} Grid7 SlowConv LooseOpt"]
# For actual use
default_routes = ["! OPT B97-D3 SV GCP(DFT/TZ) ECP{def2-TZVP} Grid7 SlowConv LooseOpt",
"! OPT B97-D3 def2-TZVP GCP(DFT/TZ) ECP{def2-TZVP} Grid7 SlowConv",
"! OPT PW6B95 def2-TZVP GCP(DFT/TZ) ECP{def2-TZVP} Grid7 SlowConv"]
def run_lammps(system, systems_by_composition, tersoff_atoms, lj_params,
atom_list, tersoff_params, run_name):
"""
Run a single step calculation using the given parameters.
**Parameters**
system:
systems_by_composition:
tersoff_atoms:
lj_params:
atom_list:
tersoff_params:
run_name:
**Returns**
Stuff.
"""
# Ensure cwd/lammps/run_name exists
directory_to_work = '%s/lammps/%s' % (os.getcwd(), run_name)
directory_to_work = directory_to_work.split("/")
for i, d in enumerate(directory_to_work):
if d.strip() == "":
continue
if not os.path.isdir("/".join(directory_to_work[:i + 1])):
os.mkdir("/".join(directory_to_work[:i + 1]))
directory_to_work = "/".join(directory_to_work)
os.chdir(directory_to_work)
system.name = run_name
# Make a file that has all the names of the systems we are using here
files.write_lammps_data(system)
# Begin code for the LAMMPS input file
commands = ('''
units real
atom_style full
pair_style hybrid/overlay lj/cut/coul/inout 0.2 3.5 15 tersoff
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
boundary f f f
read_data ''' + run_name + '''.data
''').splitlines()
# Indices of OPLS parameters
tersoff_types = [t for t in system.atom_types if t.index in tersoff_atoms]
charges = lj_params[0]
lj_sigma = lj_params[1]
lj_epsilon = lj_params[2]
# This is how we are reading in the 104 tersoff parameters
# (i.e. m,gamma,N,D...etc)
tersoff_strings, i, j = [], 0, 0
# Concatenate the atom names and params
while i < (len(tersoff_params) - 1):
tmp = atom_list[j].split(",")
for param in tersoff_params[i:i + 14]:
tmp.append(str(param))
tersoff_strings.append(tmp)
i += 14
j += 1
# R and D are the distances from the center of the first atom, so this is
# how we get the cutoff distance between those
inner_cutoffs = {}
for type_i in tersoff_types:
for type_j in tersoff_types:
for s in tersoff_strings:
types = s[:3]
R, D = float(s[13]), float(s[14])
if types == (type_i.element_name, type_j.element_name,
type_j.element_name):
inner_cutoffs[(type_i, type_j)] = R + D
index = 0
for t in system.atom_types:
if t in tersoff_types:
t.charge = charges[index]
t.vdw_e = lj_epsilon[index]
t.vdw_r = lj_sigma[index]
index += 1
# Write to the lammps file the atom types and vdw radii
for i in range(len(system.atom_types)):
for j in range(i, len(system.atom_types)):
type_i = system.atom_types[i]
type_j = system.atom_types[j]
commands.append(
'pair_coeff %d %d lj/cut/coul/inout %f %f %f' %
(i + 1, j + 1, (type_i.vdw_e * type_j.vdw_e)**0.5,
(type_i.vdw_r * type_j.vdw_r)**0.5, inner_cutoffs[(i, j)] if
(i, j) in inner_cutoffs else 0.0))
commands.append('set type %d charge %f' % (i + 1, type_i.charge))
# Generate a lmp object to make the LAMMPS input file
lmp = structures.Struct()
lmp.file = open(run_name + '.in', 'w')
def writeline(line):
lmp.file.write(line + '\n')
lmp.command = writeline
for line in commands:
lmp.command(line)
# Write the pair_coeff command
mcsmrff_files.write_params(lj_params,
atom_list,
tersoff_params,
run_name,
append="_input")
mcsmrff_files.write_system_and_training_data(run_name, system,
systems_by_composition)
lmp.command('pair_coeff * * tersoff ' + run_name + '_input.tersoff ' +
(' '.join([(t.element_name if t in tersoff_types else 'NULL')
for t in system.atom_types])))
for t in system.bond_types:
lmp.command('bond_coeff %d %f %f' % (t.lammps_type, t.e, t.r))
for t in system.angle_types:
lmp.command('angle_coeff %d %f %f' % (t.lammps_type, t.e, t.angle))
for t in system.dihedral_types:
lmp.command('dihedral_coeff %d %f %f %f %f' %
((t.lammps_type, ) + t.e))
commands = '''
compute atom_pe all pe/atom
compute sum_pe all reduce sum c_atom_pe
neigh_modify once yes
dump 2 all xyz 1 ''' + run_name + '''.xyz
dump 1 all custom 1 ''' + run_name + '''.dump id type x y z fx fy fz c_atom_pe
fix temp all nvt temp 10.0 10.0 100.0
run 0
undump 1
'''
for line in commands.splitlines():
lmp.command(line)
lmp.file.close()
# Run the simulation the change directory back to the parent one
os.system('%s -in %s.in -log %s.log >> out.log' %
(mcsmrff_constants.lammps_mcsmrff, run_name, run_name))
os.chdir("../../")
def run_mcsmrff(run_name, system, parameters, tersoff_atoms,
queue=None, procs=1, email=None,
pair_coeffs_included=True, hybrid_pair=False,
hybrid_angle=False, TIP4P=False, seed=None):
if seed is None:
seed = str(int(md5(run_name).hexdigest(), 16) % (2**16))
else:
seed = str(seed)
system.name = run_name
# Begin generating string to hold LAMMPS input
commands = ('''units real
atom_style full
pair_style hybrid/overlay lj/cut/coul/inout 0.2 3.5 15 tersoff
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
boundary p p p
read_data ''' + run_name + '''.data
''').splitlines()
# Removed HN for no H3 input types
tersoff_types = [t for t in system.atom_types
if t.index in tersoff_atoms]
elems_by_index = [(t.lammps_type, t.element) for t in system.atom_types]
elems_by_index = sorted(elems_by_index, key=lambda x: [0])
elems_by_index = ' '.join([units.elem_i2s(e[1]) for e in elems_by_index])
# Grab the parameters. Could in theory just use "parameters" variable,
# but too lazy to change code
for line in open('%s.tersoff' % run_name):
if line.startswith('# Charges:'):
charges = [float(x) for x in line.split()[2:]]
if line.startswith('# LJ-sigma:'):
lj_sigma = [float(x) for x in line.split()[2:]]
if line.startswith('# LJ-epsilon:'):
lj_epsilon = [float(x) for x in line.split()[2:]]
tersoff_strings = findall('\n' +
('(\S+) +' * 9)[:-2] +
' *\n +' +
('(\S+) +' * 8)[:-2],
open(run_name + '.tersoff').read())
inner_cutoffs = {}
for type_i in tersoff_types:
for type_j in tersoff_types:
for s in tersoff_strings:
types = s[:3]
R, D = float(s[13]), float(s[14])
if types == (type_i.element_name,
type_j.element_name,
type_j.element_name):
inner_cutoffs[(type_i, type_j)] = R + D
index = 0
for t in system.atom_types:
if t in tersoff_types:
t.charge = charges[index]
t.vdw_e = lj_epsilon[index]
t.vdw_r = lj_sigma[index]
index += 1
# Write out parameters to LAMMPS input string
for i in range(len(system.atom_types)):
for j in range(i, len(system.atom_types)):
type_i = system.atom_types[i]
type_j = system.atom_types[j]
commands.append('pair_coeff %d %d lj/cut/coul/inout %f %f %f' %
(i + 1, j + 1,
(type_i.vdw_e * type_j.vdw_e)**0.5,
(type_i.vdw_r * type_j.vdw_r)**0.5,
inner_cutoffs[(i, j)]
if (i, j) in inner_cutoffs else 0.0))
commands.append('set type %d charge %f' % (i + 1, type_i.charge))
# Generate a LAMMPS structure for an input file
lmp = structures.Struct()
lmp.file = open(run_name + '.in', 'w')
def writeline(line):
lmp.file.write(line + '\n')
lmp.command = writeline
for line in commands:
lmp.command(line)
commands.append('pair_coeff * * tersoff ' + run_name + '.tersoff ' +
(' '.join([(t.element_name
if t in tersoff_types else 'NULL')
for t in system.atom_types])))
for t in system.bond_types:
commands.append('bond_coeff %d %f %f' % (t.lammps_type, t.e, t.r))
for t in system.angle_types:
commands.append('angle_coeff %d %f %f' % (t.lammps_type, t.e, t.angle))
for t in system.dihedral_types:
commands.append('dihedral_coeff %d %f %f %f %f' %
((t.lammps_type,) + t.e))
commands.append('''
neigh_modify every 1 check yes delay 0
dump 1 all xyz 100 ''' + run_name + '''.xyz
dump_modify 1 element ''' + elems_by_index + '''
dump 2 all custom 100 ''' + run_name + '''2.dump type xu yu zu
thermo_style custom step temp press ke pe epair emol vol
thermo 1000
group mobile id > 0
velocity all create 10.0 ''' + seed + ''' rot yes dist gaussian
timestep 0.01
fix press all npt temp 10.0 10.0 10.0 iso 0.0 0.0 100.0
run 50000
unfix press
fix motion all nvt temp 10.0 300.0 100.0
run 200000
''')
# job(run_name, commands, system, queue=None, hybrid_angle=False)
J = job(run_name, "\n".join(commands), system, parameters, queue=queue,
procs=procs, email=email,
pair_coeffs_included=pair_coeffs_included,
hybrid_pair=hybrid_pair, hybrid_angle=hybrid_angle, TIP4P=TIP4P)
return J