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)