def generate_interactions_o(self,
interaction_name,
bond="harmonic",
SPB=False,
radius=10,
cutoff=1.15,
reducedv_factor=1,
khun=1.):
if bond == "harmonic":
temp1 = "bond_style harmonic\n"
temp2 = "bond_coeff %i %.2f %.2f"
ene = 350
if bond == "fene":
if SPB:
temp1 = "bond_style hybrid harmonic fene\n"
temp2 = "bond_coeff %i fene %.2f %.2f %.2f %.2f"
else:
temp1 = "bond_style fene\n"
temp2 = "bond_coeff %i %.2f %.2f %.2f %.2f"
ene = 30 * 1
Bond = [temp1]
if bond == "fene":
Bond.append("special_bonds fene\n")
ene_ratio = 1 #.35
#Bond.append("special_bonds 0.0 1.0 1.0\n")
if SPB and False:
#print radius
Pair = [
"pair_style hybrid lj/cut 3.0 gauss/cut %.2f \n" %
(2 * radius) + "pair_modify shift yes\n"
]
else:
Pair = ["pair_style lj/cut 1.4 \n" + "pair_modify shift yes\n"]
Angle = ["angle_style cosine/delta\n"]
Angle = ["angle_style harmonic\n"]
keyl = range(1, len(self.natom) + 1)
for t1 in keyl:
for t2 in keyl:
if t2 >= t1:
if not self.liaison.has_key("%s-%s" % (t1, t2)):
print "Warning liaison between {0} and {1} not defined".format(
t1, t2)
dist, tybe_b = self.liaison["%s-%s" % (t1, t2)]
if cutoff is not None:
cut = dist * cutoff
else:
cut = dist * pow(2., 1 / 6.)
odist = copy.deepcopy(dist)
#dist=1
if bond == "fene":
Bond.append(
temp2 %
(tybe_b, ene_ratio * ene /
(dist * dist), 1.5 * dist, ene_ratio, dist) +
"\n")
else:
Bond.append(temp2 % (tybe_b, ene, dist) + "\n")
dist = odist
precise = ""
if SPB and False:
precise = "lj/cut"
reduced = 1
if t1 == t2 and t1 == 3:
reduced = 1
else:
reduced = reducedv_factor
Pair.append("""pair_coeff %s %s %s %.1f %.2f %.2f\n""" %
(t1, t2, precise, ene_ratio, dist * reduced,
cut * reduced))
if self.angle_def is not None and self.Angle != []:
for t3 in keyl:
if t3 >= t2:
dist, tybe_b = self.angle_def["%s-%s-%s" %
(t1, t2, t3)]
k = khun / 2. * dist # dist = 1 if no ribo involved else 0
Angle.append("angle_coeff %i %.3f 180.0\n" %
(tybe_b, k))
if SPB:
if bond == "fene":
Bond.append("bond_coeff %i harmonic 0 0 \n" %
(self.liaison["spb"][1]))
spbond = "bond_coeff %i harmonic %.1f %.1f\n" % (
self.liaison["spb"][1], 10, microtubule / realsigma)
else:
Bond.append("bond_coeff %i 0 0 \n" % (self.liaison["spb"][1]))
spbond = "bond_coeff %i %.1f %.1f\n" % (
self.liaison["spb"][1], 10, microtubule / realsigma)
n_i = len(diameter) / 2
for t1 in range(len(diameter)):
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n""" %
(t1 + 1, num_particle["spb"], precise, dist, cut))
Pair.append(
"""pair_coeff %i %i %s 0. %.2f %.2f\n""" %
(num_particle["spb"], num_particle["spb"], precise, dist, cut))
g = open(interaction_name, "w")
g.write("".join(Bond) + "\n")
g.write("".join(Pair) + "\n")
if self.Angle != []:
g.write("".join(Angle))
def generate_interactions_o(self,interaction_name,bond="harmonic",SPB=False,radius=10,cutoff=1.15,reducedv_factor=1,khun=1.):
if bond == "harmonic" :
temp1 = "bond_style harmonic\n"
temp2 = "bond_coeff %i %.2f %.2f"
ene = 350
if bond == "fene":
if SPB:
temp1 = "bond_style hybrid harmonic fene\n"
temp2 = "bond_coeff %i fene %.2f %.2f %.2f %.2f"
else:
temp1 = "bond_style fene\n"
temp2 = "bond_coeff %i %.2f %.2f %.2f %.2f"
ene = 30 * 1
Bond = [temp1]
if bond == "fene":
Bond.append("special_bonds fene\n")
ene_ratio=1#.35
#Bond.append("special_bonds 0.0 1.0 1.0\n")
if SPB and False:
#print radius
Pair = ["pair_style hybrid lj/cut 3.0 gauss/cut %.2f \n"%(2*radius) + "pair_modify shift yes\n"]
else:
Pair = ["pair_style lj/cut 1.4 \n" + "pair_modify shift yes\n"]
Angle = ["angle_style cosine/delta\n"]
Angle = ["angle_style harmonic\n"]
keyl = range(1,len(self.natom)+1)
for t1 in keyl:
for t2 in keyl:
if t2 >= t1:
if not self.liaison.has_key("%s-%s"%(t1,t2)):
print "Warning liaison between {0} and {1} not defined".format(t1,t2)
dist,tybe_b = self.liaison["%s-%s"%(t1,t2)]
if cutoff is not None:
cut = dist*cutoff
else:
cut = dist*pow(2.,1/6.)
odist = copy.deepcopy(dist)
#dist=1
if bond == "fene":
Bond.append(temp2 % (tybe_b,ene_ratio * ene/(dist*dist),1.5*dist,ene_ratio,dist) +"\n")
else:
Bond.append(temp2 % (tybe_b, ene,dist) +"\n")
dist = odist
precise =""
if SPB and False:
precise = "lj/cut"
reduced = 1
if t1 == t2 and t1 == 3:
reduced = 1
else:
reduced = reducedv_factor
Pair.append("""pair_coeff %s %s %s %.1f %.2f %.2f\n"""%(t1,t2,precise,ene_ratio,dist*reduced,cut*reduced))
if self.angle_def is not None and self.Angle != []:
for t3 in keyl:
if t3 >= t2:
dist,tybe_b = self.angle_def["%s-%s-%s"%(t1,t2,t3)]
k=khun/2. * dist # dist = 1 if no ribo involved else 0
Angle.append("angle_coeff %i %.3f 180.0\n"%(tybe_b,k))
if SPB:
if bond == "fene":
Bond.append("bond_coeff %i harmonic 0 0 \n"%(self.liaison["spb"][1]))
spbond = "bond_coeff %i harmonic %.1f %.1f\n"%(self.liaison["spb"][1],10,microtubule/realsigma)
else:
Bond.append("bond_coeff %i 0 0 \n"%(self.liaison["spb"][1]))
spbond = "bond_coeff %i %.1f %.1f\n"%(self.liaison["spb"][1],10,microtubule/realsigma)
n_i = len(diameter)/2
for t1 in range(len(diameter) ):
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n"""%(t1+1,num_particle["spb"],precise,dist,cut))
Pair.append("""pair_coeff %i %i %s 0. %.2f %.2f\n"""%(num_particle["spb"],num_particle["spb"],precise,dist,cut))
g = open(interaction_name,"w")
g.write("".join(Bond)+"\n")
g.write("".join(Pair)+"\n")
if self.Angle != []:
g.write("".join(Angle))
