def data(i):
lmp1 = lammps()
polymer = PyLammps(ptr=lmp1)
x = 60
y = 30
z = 30
t = 1
polymer.units("lj")
polymer.dimension(3)
polymer.atom_style("bond")
polymer.bond_style("harmonic")
polymer.pair_style("lj/cut", 3)
polymer.read_data("data.polymer")
polymer.region("void cylinder x", 15, 15, 2, 29, 31)
polymer.pair_coeff(1, 2, 2.5, 3)
polymer.pair_coeff(1, 3, 2.5, 1.12)
polymer.pair_coeff(2, 3, 2.5, 1.12)
polymer.velocity("all create", t, 97287)
polymer.group("polymer type", 1, 2)
polymer.group("first type", 1)
polymer.region("box block", 0, x, 0, y, 0, z)
polymer.region("spherein sphere", 29, 15, 15, 2)
polymer.region("boxin block", 27, 29, 13, 17, 13, 17)
polymer.region("hemiin intersect", 2, "boxin spherein")
x0 = polymer.atoms[0].position[0]
y0 = polymer.atoms[0].position[1]
z0 = polymer.atoms[0].position[2]
r = lambda x0, y0, z0: np.sqrt((x0 - 29)**2 + (y0 - 15)**2 + (z0 - 15)**2)
fx = lambda x0, y0, z0: 5 * (x0 - 29) / r(x0, y0, z0)
fy = lambda x0, y0, z0: 5 * (y0 - 15) / r(x0, y0, z0)
fz = lambda x0, y0, z0: 5 * (z0 - 15) / r(x0, y0, z0)
polymer.fix(1, "polymer nve")
polymer.fix(2, "polymer langevin", t, t, 1.5,
np.random.randint(2, high=200000))
polymer.fix(3, "polymer spring tether", 10, i, "NULL NULL", 0)
polymer.timestep(0.01)
polymer.compute("com polymer com")
polymer.variable("ftotal equal fcm(polymer,x)")
polymer.variable("c equal c_com[1]")
polymer.thermo_style("custom v_ftotal v_c")
polymer.thermo(1)
polymer.run(500000)
l = polymer.runs[0][0][1][20000:] + [i]
u = [np.mean(polymer.runs[0][0][0][20000:]), i]
np.savetxt("trial%dmean.txt" % i, u)
np.savetxt("trial%dall.txt" % i, l)
return u
class LammpsKernel(IGMKernel):
def __init__(self, model, cfg, runid):
self.cfg = cfg
self.model = model
self.runid = runid
self.tmp_dir = self.cfg.tmpdir('optimization')
self.randseed = int(self.cfg["optimization/kernel_opts/lammps/seed"])
self.initLammps()
self.setupSimulationBox()
self.setupParticles()
self.setCoordinates()
self.setRadii()
self.setupNeighbor()
def initLammps(self):
"""
setup lammps python interface, log file
"""
if self.cfg["optimization/kernel_opts/lammps/keep_logs"]:
self.Lmp = PyLammps(cmdargs=["-log",os.path.join(self.tmp_dir, self.runid+".log")])
else:
self.Lmp = PyLammps(cmdargs=["-log","none"])
self.Lmp.atom_style("bond")
self.Lmp.boundary('s','s','s')
def setupSimulationBox(self):
"""
setup lammps simulation box
"""
atom_types = 1
bond_types = 0
bond_per_atom = 0
for Res in self.model.restraints:
atom_types += Res.extra_atom_types
bond_types += Res.extra_bond_types
bond_per_atom += Res.extra_bond_per_atom
if res.type == "Envelope":
xx , yy, zz = Res.a*1.2, Res.b*1.2, Res.c*1.2
self.Lmp.region("IGMBOX", "block", -xx, xx, -yy, yy, -zz, zz)
self.Lmp.create_box(1, "IGMBOX", "bond/types", bond_types, "extra/bond/per/atom", bond_per_atom)
def setupParticles(self):
"""
initialize particles with random position
"""
#add user define per-atom property: radius(double)
self.Lmp.fix("UserProperty","all","property/atom","d_radius")
#number of particles
self.nbead = len(self.model.particles)
self.atom_style_index = 1
self.Lmp.create_atoms(1, "random", self.nbead, self.randseed, "IGMBOX")
#set particle mass 1.0
self.Lmp.mass('*', 1.0)
#group particle NORMAL
self.lmp_group_NORMAL = "NORMAL"
self.Lmp.group(self.lmp_group_NORMAL, "type", 1)
#get numpy view of per atom array
self.particle_id = self.Lmp.lmp.numpy.extract_atom_iarray('id', n, 1)
self._coordinates = self.Lmp.lmp.numpy.extract_atom_darray('x', n, 3)
self._radii = self.lmp.lmp.numpy.extract_atom_darray('d_radius', n, 1)
def indexMapping(self):
"""
particle mapping from lammps index to original index
"""
return np.argsort( self.particle_id[:, 0] )
def setCoordinates(self, crd = None):
"""
assign xyz values to lammps
"""
if crd:
self.coordinates[self.indexMapping(), :] = crd[:]
else:
self.coordinates[self.indexMapping(), :] = self.model.particles.coordinates[:]
def setRadii(self, radii = None):
"""
assign radius values to lammps
"""
if radii:
self.radii[self.indexMapping(), :] = radii[:]
else:
self.radii[self.indexMapping(), :] = self.model.particles.radii[:]
self.maxrad = max(self.radii)
def setupNeighbor(self):
"""
setup neighbor list rules
"""
if hasattr(self, "maxrad"):
self.Lmp.neighbor(self.maxrad, 'bin')
else:
raise RuntimeError("Radii not set before setupNeighbor()")
max_neighbor = int(self.cfg["optimization/kernel_opts/lammps/max_neigh"])
self.Lmp.neigh_modify('every',1,'check','yes')
self.Lmp.neigh_modify("one", max_neighbor, 'page', 20*max_neighbor)
def addRestraints(self):
"""
add restraints to lammps one by one
"""
#lammps bond style definition
bond_styles = set()
n = 1
for Res in self.model.restraints:
if hasattr(Res, "bond_style"):
bond_styles.add(Res.bond_style)
#give_bond_id
Res.setBondId(n)
n += 1
if len(bond_styles) == 1:
self.Lmp.bond_style(bond_styles.pop())
elif len(bond_styles) > 1:
cmd = ["bond_style", "hybrid"]
while bond_styles:
cmd.append(bond_styles.pop())
self.Lmp.command(" ".join(cmd))
#define variable for fast communication/avoid input string parsing
self.Lmp.variable("batoms","string","EMPTY")
bond_variable = "batoms"
#loop all restraints and apply lammps code
for Res in self.model.restraints:
Res.Lammps(self.Lmp, runid = self.runid,
tmp_dir = self.tmp_dir,
randseed = self.randseed,
normal_group = self.lmp_group_NORMAL,
bond_variable = bond_variable)