def test_constraint():
box = Box()
assert (box.is_inside([0.5, 0.5, 0.5]))
assert (not box.is_inside([0.5, 0.5, 1.5]))
assert (not box.is_inside([0.5, 1.5, 0.5]))
assert (not box.is_inside([1.5, 0.5, 0.5]))
def test_constraint():
box = Box()
assert (box.is_inside([0.5,0.5,0.5]))
assert ( not box.is_inside([0.5,0.5,1.5]))
assert ( not box.is_inside([0.5,1.5,0.5]))
assert ( not box.is_inside([1.5,0.5,0.5]))
def test_constrain_box_on_polymer():
box = Box([0, 0, 0], [10, 10, 10])
coords, bonds, type_beads, ids = one_polymer(N=200,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
gconstrain=[box])
for p in coords:
assert (box.is_inside(p))
def test_lammps_angle():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
liaison = {"1-1":[1,1]}
angle_def = {"1-1-1":[20,1]}
P1 = Polymer(N=20,type_bead=1,liaison=liaison,angle_bond=True,angle_def=angle_def,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add_box(box)
for idl,value in liaison.iteritems():
R0,idbond = value
idpair1,idpair2=map(int,idl.split("-"))
Simu.add_bond(typeb="harmonic",idbond=idbond,K=80,R0=R0)
Simu.add_pair(typep="lj/cut",idpair1=idpair1,idpair2=idpair2,epsilon=1,sigma=R0,cutoff1=1.15)
for idl,value in angle_def.iteritems():
K,idangle = value
idpair1,idpair2,idpair3=map(int,idl.split("-"))
Simu.add_angle(typea="harmonic",idangle=idangle,K=K,theta=180)
Simu.generate_xyz("test/lp.xyz",Mass="one")
Simu.generate_interactions("test/ainteractions")
Simu.generate_pdb("test/lp.pdb")
Simu.generate_script("test/lp.txt",run_length=10000,samplingrate=10,initconf="test/lp.xyz",
outtraj="test/lp.dcd",outfile="test/lp.xyz",interactions="test/ainteractions",particle="1 2")
Simu.run(script="test/lp.txt")
def test_generate_interaction():
Simu = LSimu()
Simu.create_polymers(NP=10,N=100,box=Box([0,0,0],[10,10,10]))
Simu.add_bond(typeb="harmonic",idbond=1,K=80,R0=1)
Simu.add_pair(typep="lj/cut",idpair1=1,idpair2=1,epsilon=1,sigma=1,cutoff1=1.12)
Simu.generate_interactions("test/interaction")
def test_constrain_on_polymer_start():
start = Point(index=0, position=[0.2, 0.2, 0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0, 0, 0], [10, 10, 10])
coords, bonds, type_beads, ids = one_polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[start],
gconstrain=[box])
assert (norm(coords[0] - np.array([0.2, 0.2, 0.2])) < 0.01)
def test_constrain_on_polymer_end():
end = Point(index=19, position=[0.2, 0.2, 0.2])
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([0, 0, 0], [20, 20, 20])
coords, bonds, type_beads, ids = one_polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[end],
gconstrain=[box],
max_trial=1000)
print norm(coords[-2] - np.array([0.2, 0.2, 0.2]))
assert (norm(coords[-2] - np.array([0.2, 0.2, 0.2])) < 3)
def test_lammps_from_hand_mix_interactions():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
liaison = {"1-1":[1,1],"1-2":[1,2],"2-2":[1,3]}
P1 = Polymer(N=20,type_bead=[1]*10+[2]*10,liaison=liaison,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add_box(box)
for idl,value in liaison.iteritems():
R0,idbond = value
idpair1,idpair2=map(int,idl.split("-"))
Simu.add_bond(typeb="harmonic",idbond=idbond,K=350,R0=R0)
Simu.add_pair(typep="lj/cut",idpair1=idpair1,idpair2=idpair2,epsilon=1,sigma=R0,cutoff1=1.15)
Simu.generate_xyz("test/mix.xyz",Mass="one")
Simu.generate_interactions("test/softinteractions")
Simu.generate_pdb("test/mix.pdb")
Simu.generate_script("test/basic.txt",run_length=10000,samplingrate=100,initconf="test/mix.xyz",outtraj="test/out.dcd",
outfile="test/final.xyz",interactions="test/softinteractions",particle="1 2")
Simu.run(script="test/basic.txt")
box = Box([0,0,0],[10,10,10])
Simu.add_box(box)
Simu.clean_interactions()
for idl,value in liaison.iteritems():
R0,idbond = value
idpair1,idpair2=map(int,idl.split("-"))
Simu.add_bond(typeb="fene",idbond=idbond,K=80,R0=R0,epsilon=1.2,sigma=1)
Simu.add_pair(typep="lj/cut",idpair1=idpair1,idpair2=idpair2,epsilon=1,sigma=R0,cutoff1=1.15)
Simu.generate_xyz("test/mix2.xyz",Mass="one",from_lammps_xyz="test/final.xyz")
Simu.generate_interactions("test/interactions")
Simu.generate_script("test/basic_rest.txt",template_name="./template/basic.txt",
run_length=1000,samplingrate=10,initconf="test/mix2.xyz",outtraj="test/out2.dcd",outfile="test/out2.xyz",
interactions="test/interactions",particle="1 2")
Simu.run(script="test/basic_rest.txt")
def test_lammps_from_hand():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
P1 = Polymer(N=20,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add_box(box)
Simu.add_bond(typeb="harmonic",idbond=1,K=80,R0=1)
Simu.add_pair(typep="lj/cut",idpair1=1,idpair2=1,epsilon=1,sigma=1,cutoff1=1.12)
Simu.generate_xyz("test/mixh.xyz",Mass="one")
Simu.generate_interactions("test/interactionsh")
Simu.generate_pdb("test/mixh.pdb")
Simu.generate_script("test/basich.txt",run_length=1000,samplingrate=10,initconf="test/mixh.xyz",
outtraj="test/out.dcd",outfile="test/out.xyz",interactions="test/interactionsh",particle="1")
Simu.run(script="test/basich.txt")
def test_bond_size():
box = Box([-100, -100, -100], [400, 400, 400])
coords, bonds, type_beads, ids = one_polymer(N=400,
type_bead=1,
liaison={"1-1": [2.0, 1]},
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[],
gconstrain=[box],
max_trial=300000,
rc=0.5,
virtual_lp=None,
rigid_constrain=True)
bonds = np.mean(np.sqrt(np.sum((coords[1:] - coords[:-1])**2, axis=1)))
assert (abs(bonds - 2) < 0.1)
def test_unwrap():
l = 10
box = Box([0, 0, 0], [l, l, l])
P1 = Polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[],
gconstrain=[box])
for i in range(20):
P1.coords[i][0] = i
if P1.coords[i][0] > l:
P1.coords[i][0] -= l
print P1.coords
P1.unwrap(ref=[0, 0, 0], box=box)
print P1.coords
assert np.sum(P1.coords[::, 0] - np.array(range(20))) < 1e-9
def test_crash():
PS = [0.2, 0.2, 0.2]
PM = [10, 10.2, 0.2]
PE = [0.2, 199, 19]
start = Point(index=0, position=PS)
middle = Point(index=39, position=PM)
end = Point(index=399, position=PE)
#end = Point(index=199,position=[0.2,0.2,0.2])
box = Box([-10, -10, -10], [400, 400, 400])
coords_lp, bonds, type_beads, ids = one_polymer(
N=400,
type_bead=1,
liaison={"1-1": [1.0, 1]},
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[start, middle, end],
gconstrain=[box],
max_trial=500000,
rc=0.5,
virtual_lp=3,
rigid_constrain=True)
def test_constrain_box_on_polymer():
box = Box([0,0,0],[10,10,10])
coords,bonds,type_beads,ids = one_polymer(N=200,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,gconstrain=[box])
for p in coords:
assert(box.is_inside(p))
def test_lammps_poly_add_onep():
Simu = LSimu()
Simu.create_polymers(NP=10,N=100,box=Box([0,0,0],[10,10,10]))
Simu.add(Polymer(N=1))
Simu.generate_xyz("test/mix.xyz",Mass="one")
Simu.generate_pdb("test/mix.pdb")
def test_lammps_poly_simu():
Simu = LSimu()
Simu.create_polymers(NP=10,N=100,box=Box([0,0,0],[10,10,10]))
Simu.generate_xyz("test/mix.xyz",Mass="one")