def test_from_dict():
# Define a new potential, the format is python dictionary or json
spec = {
"nonbonded" : {"Na" : {"q" : 1, "sigma": 0.2, "eps": 0.3, "type": "Na"},
"Cl" : {"q" : -1, "sigma": 0.2, "eps": 0.3, "type": "Cl"},
"OW" : {"q" : 1, "sigma": 0.2, "eps": 0.3, "type": "O"},
"HW1" : {"q" : 1, "sigma": 0.2, "eps": 0.3, "type": "H"},
"HW2" : {"q" : 1, "sigma": 0.2, "eps": 0.3, "type": "H"}},
"bonded" : {'SOL' : { 'particles': ['OW', 'HW1', 'HW2'],
'bonds': [{ 'between': (0, 1), 'r' : 0.2, 'k': 0.1 },
{ 'between': (0, 1), 'r' : 0.2, 'k': 0.1 }],
'angles': [{'between': (1, 0, 2), 'theta' : 90, 'k': 0.1}]
},
'NA' : { 'particles' : ['Na'] },
'CL' : { 'particles' : ['Cl'] },
}
}
na = Molecule.from_arrays(type_array=['Na'], molecule_name='NA')
cl = Molecule.from_arrays(type_array=['Cl'], molecule_name='CL')
water = Molecule.from_arrays(type_array=['O', 'H', 'H'],
molecule_name='SOL',
bonds=[[0, 1], [0, 2]])
s = System([na, na, cl, cl, water, water])
p = ForceGenerator(spec)
print to_top(s, p)
def make_gromacs(simulation, directory, clean=False):
"""Create gromacs directory structure"""
if clean is False and os.path.exists(directory):
raise ValueError(
'Cannot override {}, use option clean=True'.format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Check custom simulation potential
if simulation.potential.intermolecular.type == 'custom':
for pair in simulation.potential.intermolecular.special_pairs:
table = to_table(
simulation.potential.intermolecular.pair_interaction(*pair),
simulation.cutoff)
fname1 = os.path.join(directory,
'table_{}_{}.xvg'.format(pair[0], pair[1]))
fname2 = os.path.join(directory,
'table_{}_{}.xvg'.format(pair[1], pair[0]))
with open(fname1, 'w') as fd:
fd.write(table)
with open(fname2, 'w') as fd:
fd.write(table)
ndx = {'System': np.arange(simulation.system.n_atoms, dtype='int')}
for particle in simulation.potential.intermolecular.particles:
idx = simulation.system.where(
atom_name=particle)['atom'].nonzero()[0]
ndx[particle] = idx
with open(os.path.join(directory, 'index.ndx'), 'w') as fd:
fd.write(to_ndx(ndx))
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, 'grompp.mdp'), 'w') as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, 'topol.top'), 'w') as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, 'conf.gro'),
'w').write('system', simulation.system)
return directory
def make_gromacs(simulation, directory, clean=False):
"""Create gromacs directory structure"""
if clean is False and os.path.exists(directory):
raise ValueError("Cannot override {}, use option clean=True".format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Check custom simulation potential
if simulation.potential.intermolecular.type == "custom":
for pair in simulation.potential.intermolecular.special_pairs:
table = to_table(simulation.potential.intermolecular.pair_interaction(*pair), simulation.cutoff)
fname1 = os.path.join(directory, "table_{}_{}.xvg".format(pair[0], pair[1]))
fname2 = os.path.join(directory, "table_{}_{}.xvg".format(pair[1], pair[0]))
with open(fname1, "w") as fd:
fd.write(table)
with open(fname2, "w") as fd:
fd.write(table)
ndx = {"System": np.arange(simulation.system.n_atoms, dtype="int")}
for particle in simulation.potential.intermolecular.particles:
idx = simulation.system.where(atom_name=particle)["atom"].nonzero()[0]
ndx[particle] = idx
with open(os.path.join(directory, "index.ndx"), "w") as fd:
fd.write(to_ndx(ndx))
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, "grompp.mdp"), "w") as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, "topol.top"), "w") as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, "conf.gro"), "w").write("system", simulation.system)
return directory
def run_gromacs(simulation, directory, clean=False):
if clean is False and os.path.exists(directory):
raise ValueError(
'Cannot override {}, use option clean=True'.format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, 'grompp.mdp'), 'w') as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, 'topol.top'), 'w') as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, 'conf.gro'),
'w').write('system', simulation.system)
process = subprocess.Popen(
'cd {} && grompp_d && exec mdrun_d -v'.format(directory),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
output_box = Textarea()
output_box.height = '200px'
output_box.font_family = 'monospace'
output_box.color = '#AAAAAA'
output_box.background_color = 'black'
output_box.width = '800px'
display(output_box)
def output_function(text, output_box=output_box):
output_box.value += text.decode('utf8')
output_box.scroll_to_bottom()
return AsyncCalculation(process, simulation, directory, output_function)
def run_gromacs(simulation, directory, clean=False):
if clean is False and os.path.exists(directory):
raise ValueError("Cannot override {}, use option clean=True".format(directory))
else:
shutil.rmtree(directory, ignore_errors=True)
os.mkdir(directory)
# Parameter file
mdpfile = to_mdp(simulation)
with open(os.path.join(directory, "grompp.mdp"), "w") as fd:
fd.write(mdpfile)
# Topology file
topfile = to_top(simulation.system, simulation.potential)
with open(os.path.join(directory, "topol.top"), "w") as fd:
fd.write(topfile)
# Simulation file
datafile(os.path.join(directory, "conf.gro"), "w").write("system", simulation.system)
process = subprocess.Popen(
"cd {} && grompp_d && exec mdrun_d -v".format(directory),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
)
output_box = Textarea()
output_box.height = "200px"
output_box.font_family = "monospace"
output_box.color = "#AAAAAA"
output_box.background_color = "black"
output_box.width = "800px"
display(output_box)
def output_function(text, output_box=output_box):
output_box.value += text.decode("utf8")
output_box.scroll_to_bottom()
return AsyncCalculation(process, simulation, directory, output_function)
