from pygmin.potentials.maxneib_blj import MaxNeibsBLJ, MaxNeibsBLJSystem
from pygmin.gui import run_gui
natoms = 20
ntypeA = natoms/2
max_neibs = 4.5
system = MaxNeibsBLJSystem(natoms, ntypeA=ntypeA, max_neibs=max_neibs, rneib=1.7,
epsneibs=12., epsAB=1., epsB=0.01, epsA=0.01,
neib_crossover=.05)
dbname = "blj_N%d_NA%d_n%d.db" %(natoms, ntypeA, max_neibs)
run_gui(system)#, db=dbname)
system = MaxNeibsBLJSystem(natoms, ntypeA=ntypeA, max_neibs=max_neibs,
neib_crossover=.3,
rneib=rneib,
epsneibs=6., epsAB=1., epsB=0.01, epsA=0.01,
sigB=1.,
# sigA=1.3, sigB=1.3, sigAB=1.,
boxl=boxl,
only_AB_neibs=only_AB_neibs)
#system.params.basinhopping.outstream = None
if only_AB_neibs:
onlyAB = "_onlyAB"
else:
onlyAB = ""
if periodic:
textboxl = "_boxl%.2f" % boxl
else:
textboxl = ""
dbname = "blj_N%d_NA%d_n%d%s%s_rneib%.2f.db" %(natoms, ntypeA, max_neibs, textboxl, onlyAB, rneib)
print dbname
gui = True
if gui:
run_gui(system, db=dbname)
else:
db=system.create_database(dbname)
bh = system.get_basinhopping(database=db)
bh.run(1000000)
from pygmin.potentials.maxneib_blj import MaxNeibsBLJ, MaxNeibsBLJSystem
from pygmin.gui import run_gui
natoms = 20
ntypeA = natoms / 2
max_neibs = 4.5
system = MaxNeibsBLJSystem(natoms,
ntypeA=ntypeA,
max_neibs=max_neibs,
rneib=1.7,
epsneibs=12.,
epsAB=1.,
epsB=0.01,
epsA=0.01,
neib_crossover=.05)
dbname = "blj_N%d_NA%d_n%d.db" % (natoms, ntypeA, max_neibs)
run_gui(system) #, db=dbname)
super(MagneticColloidSystem, self).__init__(natoms)
self.natoms = natoms
self.box = box
def get_potential(self):
return MagneticColloidPotential(self.natoms, self.box)
def get_compare_exact(self, **kwargs):
raise NotImplementedError
def get_mindist(self, **kwargs):
raise NotImplementedError
if __name__ == "__main__":
natoms = 10
box = np.array([10.,10.,10.])
pot = MagneticColloidPotential(natoms, box)
coords = np.random.uniform(0, 1, 3*natoms) * 2.
print "starting potential"
e, grad = pot.getEnergyGradient(coords)
print "finished potential"
print e
pot.test_potential(coords)
system = MagneticColloidSystem(natoms, box)
from pygmin.gui import run_gui
run_gui(system)
super(MagneticColloidSystem, self).__init__(natoms)
self.natoms = natoms
self.box = box
def get_potential(self):
return MagneticColloidPotential(self.natoms, self.box)
def get_compare_exact(self, **kwargs):
raise NotImplementedError
def get_mindist(self, **kwargs):
raise NotImplementedError
if __name__ == "__main__":
natoms = 10
box = np.array([10., 10., 10.])
pot = MagneticColloidPotential(natoms, box)
coords = np.random.uniform(0, 1, 3 * natoms) * 2.
print "starting potential"
e, grad = pot.getEnergyGradient(coords)
print "finished potential"
print e
pot.test_potential(coords)
system = MagneticColloidSystem(natoms, box)
from pygmin.gui import run_gui
run_gui(system)