def setUp(self): self.lamb = 1 # Dipolar coupling constant: mu0*m^2/ (2 * pi * d^3 * K * T) self.r_cut = 15 # interaction cut-off self.diameter = 1 # particles diameter # interaction between point dipoles self.dipole_dipole = """ float rsq = dot(r_ij, r_ij); float r_cut = {0}; if (rsq < r_cut*r_cut) {{ float lambda = {1}; float r = fast::sqrt(rsq); float r3inv = 1.0 / rsq / r; vec3<float> t = r_ij / r; vec3<float> pi_o(1,0,0); vec3<float> pj_o(1,0,0); rotmat3<float> Ai(q_i); rotmat3<float> Aj(q_j); vec3<float> pi = Ai * pi_o; vec3<float> pj = Aj * pj_o; float Udd = (lambda*r3inv/2)*( dot(pi,pj) - 3 * dot(pi,t) * dot(pj,t)); return Udd; }} else return 0.0f; """.format(self.r_cut, self.lamb) self.snapshot = data.make_snapshot(N=2, box=data.boxdim(L=2 * self.r_cut, dimensions=3), particle_types=['A'])
def setUp(self): lennard_jones = """ float rsq = dot(r_ij, r_ij); float rcut = alpha_iso[0]; if (rsq <= rcut*rcut) {{ float sigma = alpha_iso[1]; float eps = alpha_iso[2]; float sigmasq = sigma*sigma; float rsqinv = sigmasq / rsq; float r6inv = rsqinv*rsqinv*rsqinv; return 4.0f*eps*r6inv*(r6inv-1.0f); }} else {{ return 0.0f; }} """ self.dist = 2.0 # distance between test particles snapshot = data.make_snapshot(N=2, box=data.boxdim(L=10, dimensions=3), particle_types=['A']) snapshot.particles.position[0, :] = (0, 0, 0) snapshot.particles.position[1, :] = (self.dist, 0, 0) system = init.read_snapshot(snapshot) mc = hpmc.integrate.sphere(seed=1, d=0) mc.shape_param.set('A', diameter=0) self.patch = jit.patch.user(mc=mc, r_cut=2.5, array_size=3, code=lennard_jones) self.logger = analyze.log(filename=None, quantities=["hpmc_patch_energy"], period=1)
def initialize_snap(syst, params={}): syst["np"] = sum( syst["len_polymers"]) * (1 + syst["excess_DNA"]) + syst["ndiff"] syst["nbond"] = sum(syst["len_polymers"]) - len(syst["len_polymers"]) if syst["cohesin_real"]: syst["np"] += syst["n_cohesin"] * syst["particule_per_cohesin"] syst["nbond"] += syst["n_cohesin"] * syst["particule_per_cohesin"] syst["Rf"] = (sum(syst["len_polymers"]) * 0.5**3 / syst['density'])**0.33 print("Radius of the cell", syst["Rf"]) R = syst["Rf"] + 1 snapshot = data.make_snapshot(N=syst["np"], box=data.boxdim(L=2 * R), bond_types=['polymer']) syst["bond_list"] = ['DNA', 'cohesin', "fFactor", "weak"] syst["plist"] = [ "DNA", "uDNA", "pDNA", "fFactor", 'cohesine', "rDNA", "fDNA", "tDNA" ] # uDNA unreplicated DNA # rDNA replicated DNA # fDNA freshly replicated DNA # tDNA template replicated DNA return snapshot, syst
def setUp(self): snap = data.make_snapshot(3, data.boxdim(Lx = 3.5, Ly = 1.5, Lz = 1.5)) #Setup a set of positions which we can easily see the overlaps for snap.particles.position[0] = [-.9, 0.0, 0.0] snap.particles.position[1] = [0.0, 0.0, 0.0] snap.particles.position[2] = [1.0, 0.25, 0.0] self.system = init.read_snapshot(snap) self.mc = hpmc.integrate.sphere(seed=123)
def setUp(self): snap = data.make_snapshot(3, data.boxdim(Lx=3.5, Ly=1.5, Lz=1.5)) #Setup a set of positions which we can easily see the overlaps for snap.particles.position[0] = [-.9, 0.0, 0.0] snap.particles.position[1] = [0.0, 0.0, 0.0] snap.particles.position[2] = [1.0, 0.25, 0.0] self.system = init.read_snapshot(snap) self.mc = hpmc.integrate.sphere(seed=123)
def setUp(self): # square well attraction on constituent spheres square_well = """float rsq = dot(r_ij, r_ij); float r_cut = alpha_union[0]; if (rsq < r_cut*r_cut) return alpha_union[1]; else return 0.0f; """ # soft repulsion between centers of unions soft_repulsion = """float rsq = dot(r_ij, r_ij); float r_cut = alpha_iso[0]; if (rsq < r_cut*r_cut) return alpha_iso[1]; else return 0.0f; """ diameter = 1.0 snapshot = data.make_snapshot(N=2, box=data.boxdim(L=10, dimensions=3), particle_types=['A']) snapshot.particles.position[0, :] = (0, 0, 0) snapshot.particles.position[1, :] = (diameter, 0, 0) system = init.read_snapshot(snapshot) mc = hpmc.integrate.sphere_union(d=0, a=0, seed=1) mc.shape_param.set('A', diameters=[diameter] * 2, centers=[(0, 0, -diameter / 2), (0, 0, diameter / 2)], overlap=[0] * 2) self.patch = jit.patch.user_union(mc=mc, r_cut=2.5, array_size=2, r_cut_iso=2.5, array_size_iso=2, \ code=square_well, code_iso=soft_repulsion) self.patch.set_params('A', positions=[(0, 0, -diameter / 2), (0, 0, diameter / 2)], typeids=[0, 0]) self.logger = analyze.log(filename=None, quantities=["hpmc_patch_energy"], period=1)
def to_hoomd_snapshot(self, snapshot=None): "Copy this frame to a HOOMD-blue snapshot." self.load() if snapshot is None: try: from hoomd import data except ImportError: try: # Try importing from hoomd 1.x from hoomd_script import data except ImportError: raise ImportError('hoomd') box = data.boxdim( Lx=self.box.Lx, Ly=self.box.Ly, Lz=self.box.Lz, xy=self.box.xy, xz=self.box.xz, yz=self.box.yz, dimensions=self.box.dimensions, ) snapshot = data.make_snapshot( N=len(self), box=box, particle_types=self.types, ) np.copyto( snapshot.particles.typeid, np.array(self.typeid, dtype=snapshot.particles.typeid.dtype)) for prop in PARTICLE_PROPERTIES: try: np.copyto(getattr(snapshot.particles, prop), getattr(self, prop)) except AttributeError: pass return snapshot
def create_empty(**kwargs): snap = data.make_snapshot(**kwargs); return init.read_snapshot(snap);
def test_access(self): N = 2 L = 10 context.initialize() self.snapshot = data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=2), particle_types=['A']) # sphere diam = 1.125 self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphere(seed=2398, d=0.0) self.mc.shape_param.set('A', diameter=diam) self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam) del self.mc del self.system context.initialize() # ellipsoid a = 1.125 b = 0.238 c = 2.25 self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0) self.mc.shape_param.set('A', a=a, b=b, c=c) self.assertAlmostEqual(self.mc.shape_param['A'].a, a) self.assertAlmostEqual(self.mc.shape_param['A'].b, b) self.assertAlmostEqual(self.mc.shape_param['A'].c, c) del self.mc del self.system context.initialize() # convex_polygon v = [(-1, -1), (1, -1), (1, 1), (-1, 1)] self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) del self.mc del self.system context.initialize() # convex_spheropolygon v = [(-1, -1), (1, -1), (1, 1), (-1, 1)] r = 0.1234 self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r) del self.mc del self.system context.initialize() #simple_polygon v = [(-1, -1), (1, -1), (1, 1), (-1, 1)] self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) del self.mc del self.system context.initialize() # polyhedron import math v = [(-0.5, -0.5, 0), (-0.5, 0.5, 0), (0.5, -0.5, 0), (0.5, 0.5, 0), (0, 0, 1.0 / math.sqrt(2)), (0, 0, -1.0 / math.sqrt(2))] f = [(0, 4, 1), (1, 4, 2), (2, 4, 3), (3, 4, 0), (0, 5, 1), (1, 5, 2), (2, 5, 3), (3, 5, 0)] r = 0.0 self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.polyhedron(seed=10) self.mc.shape_param.set('A', vertices=v, faces=f, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r) del self.mc del self.system context.initialize() # convex_polyhedron v = [(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1), (1, -1, -1), (-1, -1, -1), (-1, 1, -1)] self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) del self.mc del self.system context.initialize() # convex_spheropolyhedron v = [(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1), (1, -1, -1), (-1, -1, -1), (-1, 1, -1)] r = 0.1234 self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r) del self.mc del self.system context.initialize() # faceted_sphere v = [(-1, -1, -1), (-1, -1, 1), (-1, 1, -1), (-1, 1, 1), (1, -1, -1), (1, -1, 1), (1, 1, -1), (1, 1, 1)] offs = [-1] * 6 norms = [(-1, 0, 0), (1, 0, 0), ( 0, 1, 0, ), (0, -1, 0), (0, 0, 1), (0, 0, -1)] diam = 2 orig = (0, 0, 0) self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.faceted_sphere(seed=10) self.mc.shape_param.set('A', normals=norms, offsets=offs, vertices=v, diameter=diam, origin=orig) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(offs) - np.array(self.mc.shape_param['A'].offsets)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(norms) - np.array(self.mc.shape_param['A'].normals)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(orig) - np.array(self.mc.shape_param['A'].origin)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam) del self.mc del self.system context.initialize() # sphinx # GPU Sphinx is not built on most the time if not hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled(): cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)] diams = [2, -2.2, -2.2] self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphinx(seed=10) self.mc.shape_param.set('A', diameters=diams, centers=cent) diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(diams) - np.array(self.mc.shape_param['A'].diameters)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) del self.mc del self.system context.initialize() # sphere_union cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)] diams = [2, 2.2, 1.75] self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphere_union(seed=10) self.mc.shape_param.set('A', diameters=diams, centers=cent) diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) for i, m in enumerate(self.mc.shape_param['A'].members): self.assertAlmostEqual(m.diameter, diams[i]) del self.mc del self.system del self.snapshot context.initialize()
def setUp(self): snap = data.make_snapshot(N=0,box=data.boxdim(Lx = 10, Ly = 10, Lz = 10)) self.system = init.read_snapshot(snap) self.mc = hpmc.integrate.convex_polyhedron(seed=123)
def simulate(traj_filename): with open(traj_filename, "r") as f: traj = json.load(f) seed = traj["seed"] len_chrom = traj["len_chrom"] Cent = traj["Cent"] p_ribo = traj["p_ribo"] R = traj["R"] micron = traj["micron"] data_folder = traj["data_folder"] # Diffusing elements N_diffu = traj["N_diffu"] cut_off_inte = traj["cut_off_inte"] p_inte = traj["p_inte"] dt = traj["dt"] p_origins = traj["p_origins"] # Yeast case spb = traj["spb"] nucleole = traj["nucleole"] telomere = traj["telomere"] microtubule_length = traj["microtubule_length"] * micron diameter_nuc = traj["diameter_nuc"] * micron special_start = traj["special_start"] Activ_Origins = traj["Activ_Origins"] visu = traj["visu"] dump_hic = traj["dump_hic"] # Scenari diff_alone = traj["diff_alone"] diff_bind_when_free = traj["diff_bind_when_free"] diff_bind_when_on_DNA = traj["diff_bind_when_on_DNA"] replicate_DNA = traj["replicate_DNA"] np.random.seed(seed) hoomd.context.initialize("--mode=cpu") if diff_alone: # Check assert (diff_bind_when_free is False) assert (diff_bind_when_on_DNA is False) # End of parameter ########################################## ######################################### # Define polymer bonding and positions Np = len(len_chrom) assert (len(len_chrom) == len(Cent) == len(p_ribo)) if special_start: Sim = create_init_conf_yeast(len_chrom=len_chrom, dist_centro=Cent, p_ribo=p_ribo, Radius=R, Mt=microtubule_length) else: Sim = [] spbp = 0 if not spb else 1 Total_particle = sum(len_chrom) + N_diffu * 2 + spbp list_nuc = [ list(range(start, start + size)) if size != 0 else [] for start, size in p_ribo ] # print(list_nuc) # exit() snapshot = data.make_snapshot(N=Total_particle, box=data.boxdim(L=2 * R), bond_types=['polymer']) spbb = Np if spb else 0 if visu: spbb = 0 bond_diffu = 0 if diff_bind_when_free: bond_diffu = N_diffu snapshot.bonds.resize(sum(len_chrom) - len(len_chrom) + bond_diffu + spbb) bond_list = ['Mono_Mono', 'Diff_Diff', 'Mono_Diff'] if spb: bond_list += ["Spb_Cen"] if nucleole: bond_list += ["Mono_Nuc", "Nuc_Nuc"] snapshot.bonds.types = bond_list plist = ['Mono', 'Ori', 'Diff', 'A_Ori', 'P_Ori', 'S_Diff', 'F_Diff'] if spb: plist.append("Spb") if nucleole: plist += ['Nuc', 'A_Nuc', 'P_Nuc'] if telomere: plist += ["Telo"] snapshot.particles.types = plist offset_bond = 0 offset_particle = 0 lPolymers = [] ################################################ # Polymer chains Cen_pos = [] for i in range(Np): found_cen = False npp = len_chrom[i] # Number of particles # Position of origin of replication pos_origins = p_origins[i] if Sim == []: initp = 2 * np.random.rand(3) - 1 else: # print(i) initp = Sim.molecules[i].coords[0] for p in range(npp - 1): inuc = 0 if nucleole: if p in list_nuc[i]: inuc += 1 if p + 1 in list_nuc[i]: inuc += 1 snapshot.bonds.group[offset_bond + p] = [ offset_particle + p, offset_particle + p + 1 ] if inuc == 0: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Mono_Mono') # polymer_A if inuc == 1: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Mono_Nuc') # polymer_A if inuc == 2: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Nuc_Nuc') # polymer_A offset_bond += npp - 1 for p in range(npp): # print(offset_bond, offset_bond + p) if Sim == []: new = 2 * (2 * np.random.rand(3) - 1) while linalg.norm(initp + new) > R - 1: new = 2 * (2 * np.random.rand(3) - 1) initp += new else: initp = Sim.molecules[i].coords[p] snapshot.particles.position[offset_particle + p] = initp if p in pos_origins: snapshot.particles.typeid[offset_particle + p] = plist.index( 'Ori') # Ori else: snapshot.particles.typeid[offset_particle + p] = plist.index( 'Mono') # A if spb and p == Cent[i]: Cen_pos.append(offset_particle + p) found_cen = True if nucleole and p in list_nuc[i]: snapshot.particles.typeid[offset_particle + p] = plist.index('Nuc') if telomere and (p == 0 or p == npp - 1): snapshot.particles.typeid[offset_particle + p] = plist.index('Telo') lPolymers.append( Polymer(i, offset_particle, offset_particle + npp - 1, [po + offset_particle for po in pos_origins])) offset_particle += npp assert (found_cen == spb) phic = 0 if dump_hic: phic = 0 + offset_particle - 1 ################################################### # SPD if spb: tag_spb = 0 + offset_particle # print(tag_spb) # print(snapshot.particles[offset_particle]) snapshot.particles.position[offset_particle] = [-R + 0.1, 0, 0] snapshot.particles.typeid[offset_particle] = plist.index('Spb') offset_particle += 1 if not visu: for i in range(Np): # print(offset_particle - 1, Cen_pos[i]) snapshot.bonds.group[offset_bond] = [ offset_particle - 1, Cen_pos[i] ] snapshot.bonds.typeid[offset_bond] = bond_list.index( 'Spb_Cen') # polymer_A offset_bond += 1 ############################################################ # Diffusing elements # Defining useful classes # Defining particles and bonds for the simulation for i in range(N_diffu): npp = 2 # Number of particles initp = (R - 2) * (2 * np.random.rand(3) - 1) while linalg.norm(initp) > R - 1: initp = (R - 2) * (2 * np.random.rand(3) - 1) if diff_bind_when_free: for p in range(npp - 1): snapshot.bonds.group[offset_bond + p] = [ offset_particle + p, offset_particle + p + 1 ] snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Diff_Diff') # Diff_Diff offset_bond += npp - 1 for p in range(npp): # print(offset_bond, offset_bond + p) if diff_bind_when_free: new = 2 * (2 * np.random.rand(3) - 1) while linalg.norm(initp + new) > R - 1: new = 2 * (2 * np.random.rand(3) - 1) # print(initp,new,R,linalg.norm(initp + new)) # exit() initp += new else: initp = (R - 1) * (2 * np.random.rand(3) - 1) snapshot.particles.position[offset_particle + p] = initp snapshot.particles.typeid[offset_particle + p] = plist.index( "Diff") # Diffu offset_particle += npp # Load the configuration for i, p in enumerate(snapshot.bonds.group): if p[0] == p[1]: print(i, p) system = init.read_snapshot(snapshot) for i, p in enumerate(system.particles): # print(p) # exit() assert p.tag == i for i, b in enumerate(system.bonds): if b.a == b.b: print(b.a, b.b) raise # print(p) # exit() assert b.tag == i ############################################### ############################################### # Defining force field: harmonic = md.bond.harmonic() harmonic.bond_coeff.set(bond_list, k=330.0, r0=1) harmonic.bond_coeff.set('Mono_Diff', k=10.0, r0=1) if spb: harmonic.bond_coeff.set('Spb_Cen', k=1000.0, r0=microtubule_length) if nucleole: harmonic.bond_coeff.set('Nuc_Nuc', k=330, r0=diameter_nuc) harmonic.bond_coeff.set('Mono_Nuc', k=330, r0=diameter_nuc / 2. + 1. / 2) nl = md.nlist.tree(r_buff=0.4, check_period=1) # Potential for warmup gauss = md.pair.gauss(r_cut=3.0, nlist=nl) gauss.pair_coeff.set(plist, plist, epsilon=1.0, sigma=1.0) if nucleole: for ip1, p1 in enumerate(plist): for p2 in plist[ip1:]: inuc = 0 if "Nuc" in p1: inuc += 1 if "Nuc" in p2: inuc += 1 if inuc == 1: gauss.pair_coeff.set(p1, p2, epsilon=.5, sigma=0.5 + diameter_nuc / 2., r_cut=(0.5 + diameter_nuc / 2.) * 3) if inuc == 2: gauss.pair_coeff.set(p1, p2, epsilon=1.0, sigma=diameter_nuc, r_cut=3 * diameter_nuc) # gauss.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0) # gauss.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0) # Spherical confinement sphere = md.wall.group() sphere.add_sphere(r=R, origin=(0.0, 0.0, 0.0), inside=True) wall_force_slj = md.wall.slj(sphere, r_cut=3.0) wall_force_slj.force_coeff.set(plist, epsilon=1.0, sigma=1.0, r_cut=1.12) if nucleole: wall_force_slj.force_coeff.set('Nuc', epsilon=1.0, sigma=diameter_nuc, r_cut=diameter_nuc * 1.12) if telomere: wall_force_slj.force_coeff.set(plist, epsilon=2.0, sigma=1.5, r_cut=3) # Group; all_beads = group.all() if spb: Spb_g = group.tag_list(name="Spb", tags=[tag_spb]) pspb = [p.position for p in Spb_g] print(pspb) all_move = group.difference(name="move", a=all_beads, b=Spb_g) else: all_move = all_beads # Log logger = analyze.log(filename=data_folder + 'mylog.log', period=1000, quantities=[ 'temperature', 'potential_energy', 'kinetic_energy', 'volume', 'pressure' ], overwrite=True) # Warmup converged = False dt = 0.005 while not converged and not visu: try: method = md.integrate.mode_minimize_fire(group=all_move, dt=dt) while not (method.has_converged()): if spb: pspb = [p.position for p in Spb_g] """ print(pspb) for cen in Cen_pos: cent_tmp = system.particles[cen] print(cent_tmp.position) print(linalg.norm(np.array(pspb[0])-np.array(cent_tmp.position))) print(R * microtubule_length) """ # exit() hoomd.run(100) converged = True except: converged = False dt /= 2. print(dt) # Restore positions for ip, p in enumerate(snapshot.particles.position): system.particles[ip].position = p """ gauss.disable() slj=md.pair.slj(r_cut=2, nlist=nl) slj.pair_coeff.set(plist,plist,sigma=1,epsilon=1,r_cut=1.12) print("Second minimizing") method=md.integrate.mode_minimize_fire(group=all_beads,dt=0.05) while not(method.has_converged()): hoomd.run(100) """ # hoomd.run(1000000) # method.disable() # Dumping if visu: xml = deprecated.dump.xml(filename=data_folder + "atoms.hoomdxml", period=None, group=all_beads, vis=True) exit() # gsd = dump.gsd(filename=data_folder + "atoms.gsd",period=None,group=all_beads) dcd = dump.dcd(filename=data_folder + 'poly.dcd', period=100, overwrite=True) # Dynamics t0 = time.time() md.integrate.mode_standard(dt=0.01) method = md.integrate.langevin(group=all_move, kT=1, seed=seed) snp = system # .take_snapshot() def Change_type(typep, particle_list, snp, msg=""): # print(particle_list) for p in particle_list: snp.particles[p].type = typep if particle_list != [] and msg != "": print(msg) def Bind(typeb, bondlist, snp): btags = [] for b1, b2 in bondlist: btags.append(snp.bonds.add(typeb, b1, b2)) return btags def Release(btags, snp): for bt in btags: snp.bonds.remove(bt) def AddParticle(position, type): snp.particles.add(type) snp.particles[-1].position = position def Shift(bonds, snp): for tag, new in bonds: b = snp.bonds.get(tag) btype = "" + b.type fork = b.b + 0 snp.bonds.remove(tag) # print(b.type) snp.bonds.add(btype, new, fork) # print(new,b) # print(dir(snp.bonds)) # b.a = new group_diffu = group.type(name="Diff", type='Diff') if Activ_Origins != []: group_origin = group.type(name="Activ_Ori", type=Activ_Origins[0]) if len(Activ_Origins) > 1: for t in Activ_Origins[1:]: group_origin = group.union(name="Activ_origin", a=group_origin, b=group.type(name="tmp", type=t)) r_hic = [] if dump_hic: group_hic = group.tags(name="hic", tag_min=0, tag_max=phic) # nl.tune(warmup=1,steps=1000) for i in range(100): # Chek that the microtubule length is correct if spb: for cen in Cen_pos: cent_tmp = system.particles[cen] # print(cent_tmp.position) d = linalg.norm( np.array(pspb[0]) - np.array(cent_tmp.position)) if d > 2 * microtubule_length: print("MT too long", d) exit() # Dump the Hi-Cs # system.restore_snapshot(snp) hoomd.run(1000) if dump_hic: ph = np.array([p.position for p in group_hic]) D = cdist(ph, ph) D[D < 2] = 1 D[D >= 2] = 0 np.fill_diagonal(D, 0) if r_hic != []: r_hic += D else: r_hic = D np.save(data_folder + "/hic", r_hic) # snp = system.take_snapshot() # update the position of the monomer by updating bonds for iP, P in enumerate(lPolymers): verbose = False # if iP == 9: # verbose = True bind_diff, diff_diff, shifted_bonds, \ passivated_origin, to_release, alone = P.increment_time( 1, verbose) Change_type('P_Ori', passivated_origin, snp, msg="") # Passivated origin if not diff_alone: Shift(shifted_bonds, snp) # Bond tags to release (Alone particle) Release(to_release, snp) if diff_bind_when_free: # Pair of diffu to attach Bind("Diff_Diff", bind_diff, snp) # We cannot use the single diff anymore Change_type("S_Diff", alone, snp) # Change type for pair of diff diff Change_type("Diff", diff_diff, snp) group_diffu.force_update() group_origin.force_update() # Update Type because of (Ori to passivated) # Update group # Find new interacting particles # First check if Dimer are close from one origin p_diffu = np.array([p.position for p in group_diffu]) tag_diffu = [p.tag for p in group_diffu] p_origin = np.array([p.position for p in group_origin]) tag_origin = [p.tag for p in group_origin] if tag_diffu != [] and tag_origin != []: distances = cdist(p_diffu, p_origin) print(distances.shape) # Reorder the distances with the dimer tags Indexes = [] PTags = [] # t0 = time.time() Btags = [] # Groups Diff-Diff by bond to compute the distances if diff_bind_when_free: for b in system.bonds: if b.type == 'Diff_Diff' and system.particles[ b.a].type == 'Diff': Indexes.append(tag_diffu.index(b.a)) Indexes.append(tag_diffu.index(b.b)) Btags.append(b.tag) PTags.append([b.a, b.b]) # print(time.time() -t0) d2 = distances[Indexes][::2] / 2 + distances[Indexes][1::2] / 2 else: n_diffu = len(tag_diffu) Indexes = list(range(n_diffu)) Btags = [None] * n_diffu PTags = [[t] for t in tag_diffu] d2 = distances[Indexes] activated = [] for iD, (btag, ptags) in enumerate(zip(Btags, PTags)): # print(d2.shape) # print(d2[iD]) for iorigin, di in enumerate(d2[iD]): if iorigin in activated: # Needed because we don't want an origin to be activated # twice continue if di > cut_off_inte: continue if np.random.rand() > p_inte: continue for P in lPolymers: if not P.has_origin(tag_origin[iorigin]): continue if diff_bind_when_free and \ not diff_bind_when_on_DNA: Release([btag], snp) # Break the dimer btag = None # We need btag only in the case where they stays attached if not diff_alone: # Or attached separatly or already bound: if diff_bind_when_free: # We are sure they are two and we can # start Change_type('F_Diff', ptags, snp) # Diffusive element attached particular_origin = tag_origin[iorigin] new_btags = Bind( "Mono_Diff", [[particular_origin, ptags[0]], [particular_origin, ptags[1]]], snp) Change_type('A_Ori', [particular_origin], snp) activated.append(iorigin) P.add_fork(ptags, particular_origin, new_btags, btag) else: Change_type('F_Diff', ptags, snp) # Diffusive element attached particular_origin = tag_origin[iorigin] new_btags = Bind( "Mono_Diff", [[particular_origin, ptags[0]]], snp) start = P.attach_one_diff( ptags[0], particular_origin, new_btags[0]) if start: # get particles involves p1, p2 = P.get_diff_at_origin( particular_origin) if diff_bind_when_on_DNA: btag = Bind("Diff_Diff", [[p1[0], p2[0]]], snp)[0] Change_type('A_Ori', [particular_origin], snp) P.add_fork([p1[0], p2[0]], particular_origin, [p1[1], p2[1]], btag) else: # start when touched and release particular_origin = tag_origin[iorigin] activated.append(iorigin) Change_type('A_Ori', [particular_origin], snp) P.add_fork([None, None], particular_origin, [None, None], None) break # If we arrive there it means that one interaction has beeen # found break # t0 = time.time() with open(data_folder + "polymer_timing.dat", "wb") as f: cPickle.dump(lPolymers, f) # print(time.time() -t0) # Then if it is the case attach them according to p law to the origin print(gauss.get_energy(all_beads), wall_force_slj.get_energy(all_beads)) print(time.time() - t0)
def create_initial_configuration(traj): len_chrom = traj["len_chrom"] Cent = traj["Cent"] p_ribo = traj["p_ribo"] R = traj["R"] micron = traj["micron"] # Diffusing elements N_diffu = traj["N_diffu"] r_diffu = traj.get("diameter_diffu", 1) / 2 # exit() p_origins = traj["p_origins"] if type(len_chrom) != list: len_chrom, _ = load_lengths_and_centro(len_chrom, traj["coarse"]) if type(Cent) != list: _, Cent = load_lengths_and_centro(Cent, traj["coarse"]) if type(p_origins) != list: p_origins = load_ori_position(traj["p_origins"], traj["ori_type"], len_chrom, traj["coarse"]) p_ribo = [[int(position) // int(traj["coarse"] // 1000), length] for position, length in p_ribo] two_types = traj.get("two_types", False) p_second = traj.get("p_second", []) dstrength = traj.get("dstrength", 0) strengths = None if p_second != []: # Assign delta_strength if dstrength != 0: strengths = [] for bands, pos in zip(p_second, p_origins): strengths.append([]) for p in pos: found = False for Intervals in bands: if Intervals[0] < p < Intervals[1]: strengths[-1].append(dstrength) found = True break if not found: strengths[-1].append(1) ps = [] for ch in p_second: ps.append([]) for p1, p2 in ch: ps[-1] += range(p1, p2) p_second = ps boundaries = traj.get("boundaries", False) if boundaries: extra_boundaries = load_boundaries(coarse=traj["coarse"]) print("strengths", strengths) # Yeast case spb = traj["spb"] nucleole = traj["nucleole"] telomere = traj["telomere"] microtubule_length = traj["microtubule_length"] * micron special_start = traj["special_start"] visu = traj["visu"] dump_hic = traj["dump_hic"] # Scenari diff_bind_when_free = traj["diff_bind_when_free"] # Simulation parameters Np = len(len_chrom) assert (len(len_chrom) == len(Cent) == len(p_ribo)) if special_start: Sim = create_init_conf_yeast(len_chrom=len_chrom, dist_centro=Cent, p_ribo=p_ribo, Radius=R - 1, Mt=microtubule_length) else: Sim = [] spbp = 0 if not spb else 1 Total_particle = sum(len_chrom) + N_diffu * 2 + spbp list_nuc = [ list(range(start, start + size)) if size != 0 else [] for start, size in p_ribo ] # print(list_nuc) # exit() snapshot = data.make_snapshot(N=Total_particle, box=data.boxdim(L=2 * R), bond_types=['polymer']) spbb = Np if spb else 0 if visu: spbb = 0 bond_diffu = 0 if diff_bind_when_free: bond_diffu = N_diffu snapshot.bonds.resize(sum(len_chrom) - len(len_chrom) + bond_diffu + spbb) bond_list = ['Mono_Mono', 'Diff_Diff', 'Mono_Diff'] if spb: bond_list += ["Spb_Cen"] if nucleole: bond_list += ["Mono_Nuc", "Nuc_Nuc"] snapshot.bonds.types = bond_list plist = ['Mono', 'Ori', 'Diff', 'S_Diff', 'F_Diff', "I_Diff"] if two_types: plist.append("Mono1") if spb: plist.append("Spb") if visu: plist.append("Cen") if nucleole: plist += ['Nuc', 'A_Nuc', 'P_Nuc'] if telomere: plist += ["Telo"] snapshot.particles.types = plist offset_bond = 0 offset_particle = 0 lPolymers = [] ################################################ # Polymer chains Cen_pos = [] list_ori = [] for i in range(Np): found_cen = False npp = len_chrom[i] # Number of particles # Position of origin of replication pos_origins = p_origins[i] istrength = None if strengths is not None: istrength = strengths[i] if Sim == []: initp = 2 * np.random.rand(3) - 1 else: # print(i) initp = Sim.molecules[i].coords[0] for p in range(npp - 1): inuc = 0 if nucleole: if p in list_nuc[i]: inuc += 1 if p + 1 in list_nuc[i]: inuc += 1 snapshot.bonds.group[offset_bond + p] = [ offset_particle + p, offset_particle + p + 1 ] if inuc == 0: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Mono_Mono') # polymer_A if inuc == 1: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Mono_Nuc') # polymer_A if inuc == 2: snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Nuc_Nuc') # polymer_A offset_bond += npp - 1 for p in range(npp): # print(offset_bond, offset_bond + p) if Sim == []: new = 2 * (2 * np.random.rand(3) - 1) while linalg.norm(initp + new) > R - 1: new = 2 * (2 * np.random.rand(3) - 1) initp += new else: initp = Sim.molecules[i].coords[p] snapshot.particles.position[offset_particle + p] = initp # snapshot.particles.diameter[offset_particle + p] = 1 if p in pos_origins: list_ori.append(offset_particle + p) if visu and (p in pos_origins): snapshot.particles.typeid[offset_particle + p] = plist.index( 'Ori') # Ori else: snapshot.particles.typeid[offset_particle + p] = plist.index( 'Mono') # A if two_types and p in p_second[i]: snapshot.particles.typeid[offset_particle + p] = plist.index('Mono1') # A if spb and p == Cent[i]: Cen_pos.append(offset_particle + p) if visu: snapshot.particles.typeid[offset_particle + p] = plist.index('Cen') # A found_cen = True if nucleole and p in list_nuc[i]: snapshot.particles.typeid[offset_particle + p] = plist.index('Nuc') if telomere and (p == 0 or p == npp - 1): snapshot.particles.typeid[offset_particle + p] = plist.index('Telo') if boundaries and p in extra_boundaries[i]: snapshot.particles.typeid[offset_particle + p] = plist.index('Telo') lPolymers.append( Polymer(i, offset_particle, offset_particle + npp - 1, [po + offset_particle for po in pos_origins], strengths=istrength)) offset_particle += npp assert (found_cen == spb) phic = 0 if dump_hic: phic = 0 + offset_particle - 1 ################################################### # SPD tag_spb = None if spb: tag_spb = 0 + offset_particle # print(tag_spb) # print(snapshot.particles[offset_particle]) snapshot.particles.position[offset_particle] = [-R + 0.1, 0, 0] snapshot.particles.typeid[offset_particle] = plist.index('Spb') offset_particle += 1 if not visu: for i in range(Np): # print(offset_particle - 1, Cen_pos[i]) snapshot.bonds.group[offset_bond] = [ offset_particle - 1, Cen_pos[i] ] snapshot.bonds.typeid[offset_bond] = bond_list.index( 'Spb_Cen') # polymer_A offset_bond += 1 ############################################################ # Diffusing elements # Defining useful classes # Defining particles and bonds for the simulation p_tag_list = [] for i in range(N_diffu): npp = 2 # Number of particles initp = (R - 2) * (2 * np.random.rand(3) - 1) while linalg.norm(initp) > R - 1: initp = (R - 2) * (2 * np.random.rand(3) - 1) if diff_bind_when_free: for p in range(npp - 1): snapshot.bonds.group[offset_bond + p] = [ offset_particle + p, offset_particle + p + 1 ] snapshot.bonds.typeid[offset_bond + p] = bond_list.index( 'Diff_Diff') # Diff_Diff offset_bond += npp - 1 p_tag_list.append([]) for p in range(npp): # print(offset_bond, offset_bond + p) if diff_bind_when_free: new = 2 * (2 * np.random.rand(3) - 1) while linalg.norm(initp + new) > R - 1: new = 2 * (2 * np.random.rand(3) - 1) # print(initp,new,R,linalg.norm(initp + new)) # exit() initp += new else: initp = (R - 2) * (2 * np.random.rand(3) - 1) while linalg.norm(initp) > R - 1: initp = (R - 2) * (2 * np.random.rand(3) - 1) snapshot.particles.position[offset_particle + p] = initp # snapshot.particles.mass[offset_particle + p] = r_diffu**3 * 2**3 snapshot.particles.typeid[offset_particle + p] = plist.index( "Diff") # Diffu p_tag_list[-1].append(offset_particle + p) offset_particle += npp # Load the configuration for i, p in enumerate(snapshot.bonds.group): if p[0] == p[1]: print(i, p) return snapshot, phic, tag_spb, bond_list, plist, Cen_pos, lPolymers, list_ori, p_tag_list
def test_lattice(self): N=128; latticeq = [[1,0,0,0] for i in range(N)]; k = 10.0; kalt = np.exp(15); dx2d = np.array([0.1, 0.1, 0.0]); theta = np.pi/6; eng_check2d = round(N*k*dx2d.dot(dx2d), 3); dx3d = np.array([0.1, 0.1, 0.1]); eng_check3d = round(N*k*dx3d.dot(dx3d), 3); dq = np.array([np.cos(theta/2.0),0.,0.,np.sin(theta/2)]) ddq = np.array([1.,0.,0.,0.]) - dq; eng_checkq = round(10.0*k*N*ddq.dot(ddq), 3); hexuc = hoomd.lattice.hex(a=2.0); self.system = init.read_snapshot(hexuc.get_snapshot()); self.system.replicate(nx=8, ny=8, nz=1); self.snapshot2d = self.system.take_snapshot(particles=True); #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A']) lattice2d = []; if hoomd.comm.get_rank() == 0: lattice2d = self.snapshot2d.particles.position[:]; self.snapshot2d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']); if hoomd.comm.get_rank() == 0: self.snapshot2d_s.particles.position[:] = self.snapshot2d.particles.position[:]+dx2d; self.snapshot2d_s.particles.orientation[:] = np.array([dq for _ in range(N)]); del self.system context.initialize(); bccuc = hoomd.lattice.bcc(a=2.0); self.system = init.read_snapshot(bccuc.get_snapshot()); self.system.replicate(nx=4, ny=4, nz=4); self.snapshot3d = self.system.take_snapshot(particles=True); #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A']) lattice3d = []; if hoomd.comm.get_rank() == 0: lattice3d = self.snapshot3d.particles.position[:]; self.snapshot3d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']); if hoomd.comm.get_rank() == 0: self.snapshot3d_s.particles.position[:] = self.snapshot3d.particles.position[:]+dx3d; self.snapshot3d_s.particles.orientation[:] = np.array([dq for _ in range(N)]); del self.system context.initialize(); # sphere print("****************************************") print("* sphere *") print("****************************************") # d = 0.0014284726343172743, p = 0.20123046875 uein = 1.5 # kT diam = 1.0; self.system = init.read_snapshot(self.snapshot3d) self.mc = hpmc.integrate.sphere(seed=2398, d=0.0) self.mc.shape_param.set('A', diameter=diam) self.run_test(latticep=lattice3d, latticeq=[], k=k, kalt=kalt, q=0, qalt=0, uein=1.5, snapshot_s=self.snapshot3d_s, eng_check=eng_check3d, d=0.001428 ); self.tear_down() # ellipsoid print("****************************************") print("* ellipsoid *") print("****************************************") # a = 0.00038920117896296716, p = 0.2035860456051452 # d = 0.0014225507698958867, p = 0.19295361127422195 a = 0.5; b = 0.54; c = 0.35; uein = 3.0 # kT self.system = init.read_snapshot(self.snapshot3d) self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', a=a, b=b, c=c) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq), a = 0.000389, d = 0.001423); self.tear_down() # convex_polygon print("****************************************") print("* convex_polygon *") print("****************************************") # a = 0.001957745443687172, p = 0.19863574351978172 # d = 0.0017185407622231329, p = 0.2004306126443531 self.system = init.read_snapshot(self.snapshot2d) v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]); self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=1.5, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq), a = 0.001958, d = 0.001719); self.tear_down() # convex_spheropolygon print("****************************************") print("* convex_spheropolygon *") print("****************************************") self.system = init.read_snapshot(self.snapshot2d) v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]); r = 0.1234; self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq)); self.tear_down() #simple_polygon print("****************************************") print("* simple_polygon *") print("****************************************") self.system = init.read_snapshot(self.snapshot2d) v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]); self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq)); self.tear_down() # polyhedron print("****************************************") print("* polyhedron *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33*np.array([(-0.5, -0.5, -0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, 0.5, 0.5), (0.5, -0.5, -0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, 0.5, 0.5)]); f = [(7, 3, 1, 5), (7, 5, 4, 6), (7, 6, 2, 3), (3, 2, 0, 1), (0, 2, 6, 4), (1, 0, 4, 5)]; r = 0.0; self.mc = hpmc.integrate.polyhedron(seed=10); self.mc.shape_param.set('A', vertices=v, faces =f, sweep_radius=r); diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r); del self.mc del self.system context.initialize() # convex_polyhedron print("****************************************") print("* convex_polyhedron *") print("****************************************") #a = 0.00038920117896296716, p = 0.2035860456051452 #d = 0.0014225507698958867, p = 0.19295361127422195 self.system = init.read_snapshot(self.snapshot3d) v = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]); self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq), a = 0.0003892, d = 0.00142255); self.tear_down() # convex_spheropolyhedron print("****************************************") print("* convex_spheropolyhedron *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]); r = 0.1234; self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq)); self.tear_down() # faceted_sphere print("****************************************") print("* faceted_sphere *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33*np.array([(-1,-1,-1),(-1,-1,1),(-1,1,-1),(-1,1,1),(1,-1,-1),(1,-1,1),(1,1,-1),(1,1,1)]); offs = [-1]*6; norms =[(-1,0,0), (1,0,0), (0,1,0,), (0,-1,0), (0,0,1), (0,0,-1)]; diam = 1.0; orig = (0,0,0); self.mc = hpmc.integrate.faceted_sphere(seed=10, d=0.0, a=0.0); self.mc.shape_param.set('A', normals=norms, offsets=offs, vertices=v, diameter=diam, origin=orig); self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq)); self.tear_down() # sphinx print("****************************************") print("* sphinx *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)] diams = [1,-1.2,-1.2]; self.mc = hpmc.integrate.sphinx(seed=10, d=0.0, a=0.0); self.mc.shape_param.set('A', diameters=diams, centers=cent); self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq)); self.tear_down() # sphere_union print("****************************************") print("* sphere_union *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) cent = [(0,0,0), (0,0,0.15), (0,0,-0.15)] diams = [1,1,1]; self.mc = hpmc.integrate.sphere_union(seed=10, d=0.0, a=0.0); self.mc.shape_param.set('A', diameters=diams, centers=cent); self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq)); self.tear_down()
def test_access(self): N=2 L=10 context.initialize() self.snapshot = data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=2), particle_types=['A']) # sphere diam = 1.125; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphere(seed=2398, d=0.0) self.mc.shape_param.set('A', diameter=diam) self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam); del self.mc del self.system context.initialize() # ellipsoid a = 1.125; b = 0.238; c = 2.25; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0) self.mc.shape_param.set('A', a=a, b=b, c=c) self.assertAlmostEqual(self.mc.shape_param['A'].a, a); self.assertAlmostEqual(self.mc.shape_param['A'].b, b); self.assertAlmostEqual(self.mc.shape_param['A'].c, c); del self.mc del self.system context.initialize() # convex_polygon v = [(-1,-1), (1,-1), (1,1), (-1,1)]; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); del self.mc del self.system context.initialize() # convex_spheropolygon v = [(-1,-1), (1,-1), (1,1), (-1,1)]; r = 0.1234; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r); del self.mc del self.system context.initialize() #simple_polygon v = [(-1,-1), (1,-1), (1,1), (-1,1)]; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); del self.mc del self.system context.initialize() # polyhedron import math v = [(-0.5, -0.5, 0), (-0.5, 0.5, 0), (0.5, -0.5, 0), (0.5, 0.5, 0), (0,0, 1.0/math.sqrt(2)),(0,0,-1.0/math.sqrt(2))]; f = [(0,4,1),(1,4,2),(2,4,3),(3,4,0),(0,5,1),(1,5,2),(2,5,3),(3,5,0)] r = 0.0; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.polyhedron(seed=10); self.mc.shape_param.set('A', vertices=v, faces =f, sweep_radius=r); diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r); del self.mc del self.system context.initialize() # convex_polyhedron v = [(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); del self.mc del self.system context.initialize() # convex_spheropolyhedron v = [(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]; r = 0.1234; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.1, a=0.1) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r); del self.mc del self.system context.initialize() # faceted_sphere v = [(-1,-1,-1),(-1,-1,1),(-1,1,-1),(-1,1,1),(1,-1,-1),(1,-1,1),(1,1,-1),(1,1,1)]; offs = [-1]*6; norms =[(-1,0,0), (1,0,0), (0,1,0,), (0,-1,0), (0,0,1), (0,0,-1)]; diam = 2; orig = (0,0,0); self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.faceted_sphere(seed=10); self.mc.shape_param.set('A', normals=norms, offsets=offs, vertices=v, diameter=diam, origin=orig); diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(offs) - np.array(self.mc.shape_param['A'].offsets)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(norms) - np.array(self.mc.shape_param['A'].normals)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(orig) - np.array(self.mc.shape_param['A'].origin)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam); del self.mc del self.system context.initialize() # sphinx # GPU Sphinx is not built on most the time if not hoomd.context.exec_conf.isCUDAEnabled(): cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)] diams = [2,-2.2,-2.2]; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphinx(seed=10); self.mc.shape_param.set('A', diameters=diams, centers=cent); diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); diff = (np.array(diams) - np.array(self.mc.shape_param['A'].diameters)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); del self.mc del self.system context.initialize() # sphere_union cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)] diams = [2,2.2,1.75]; self.system = init.read_snapshot(self.snapshot) self.mc = hpmc.integrate.sphere_union(seed=10); self.mc.shape_param.set('A', diameters=diams, centers=cent); diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten(); self.assertAlmostEqual(diff.dot(diff), 0); for i,m in enumerate(self.mc.shape_param['A'].members): self.assertAlmostEqual(m.diameter, diams[i]); del self.mc del self.system del self.snapshot context.initialize()
def test_lattice(self): N = 128 latticeq = [[1, 0, 0, 0] for i in range(N)] k = 10.0 kalt = np.exp(15) dx2d = np.array([0.1, 0.1, 0.0]) theta = np.pi / 6 eng_check2d = round(N * k * dx2d.dot(dx2d), 3) dx3d = np.array([0.1, 0.1, 0.1]) eng_check3d = round(N * k * dx3d.dot(dx3d), 3) dq = np.array([np.cos(theta / 2.0), 0., 0., np.sin(theta / 2)]) ddq = np.array([1., 0., 0., 0.]) - dq eng_checkq = round(10.0 * k * N * ddq.dot(ddq), 3) hexuc = hoomd.lattice.hex(a=2.0) self.system = init.read_snapshot(hexuc.get_snapshot()) self.system.replicate(nx=8, ny=8, nz=1) self.snapshot2d = self.system.take_snapshot(particles=True) #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A']) lattice2d = [] if hoomd.comm.get_rank() == 0: lattice2d = self.snapshot2d.particles.position[:] self.snapshot2d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']) if hoomd.comm.get_rank() == 0: self.snapshot2d_s.particles.position[:] = self.snapshot2d.particles.position[:] + dx2d self.snapshot2d_s.particles.orientation[:] = np.array( [dq for _ in range(N)]) del self.system context.initialize() bccuc = hoomd.lattice.bcc(a=2.0) self.system = init.read_snapshot(bccuc.get_snapshot()) self.system.replicate(nx=4, ny=4, nz=4) self.snapshot3d = self.system.take_snapshot(particles=True) #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A']) lattice3d = [] if hoomd.comm.get_rank() == 0: lattice3d = self.snapshot3d.particles.position[:] self.snapshot3d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']) if hoomd.comm.get_rank() == 0: self.snapshot3d_s.particles.position[:] = self.snapshot3d.particles.position[:] + dx3d self.snapshot3d_s.particles.orientation[:] = np.array( [dq for _ in range(N)]) del self.system context.initialize() # sphere print("****************************************") print("* sphere *") print("****************************************") # d = 0.0014284726343172743, p = 0.20123046875 uein = 1.5 # kT diam = 1.0 self.system = init.read_snapshot(self.snapshot3d) self.mc = hpmc.integrate.sphere(seed=2398, d=0.0) self.mc.shape_param.set('A', diameter=diam) self.run_test(latticep=lattice3d, latticeq=[], k=k, kalt=kalt, q=0, qalt=0, uein=1.5, snapshot_s=self.snapshot3d_s, eng_check=eng_check3d, d=0.001428) self.tear_down() # ellipsoid print("****************************************") print("* ellipsoid *") print("****************************************") # a = 0.00038920117896296716, p = 0.2035860456051452 # d = 0.0014225507698958867, p = 0.19295361127422195 a = 0.5 b = 0.54 c = 0.35 uein = 3.0 # kT self.system = init.read_snapshot(self.snapshot3d) self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', a=a, b=b, c=c) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq), a=0.000389, d=0.001423) self.tear_down() # convex_polygon print("****************************************") print("* convex_polygon *") print("****************************************") # a = 0.001957745443687172, p = 0.19863574351978172 # d = 0.0017185407622231329, p = 0.2004306126443531 self.system = init.read_snapshot(self.snapshot2d) v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)]) self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=1.5, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d + eng_checkq), a=0.001958, d=0.001719) self.tear_down() # convex_spheropolygon print("****************************************") print("* convex_spheropolygon *") print("****************************************") self.system = init.read_snapshot(self.snapshot2d) v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)]) r = 0.1234 self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d + eng_checkq)) self.tear_down() #simple_polygon print("****************************************") print("* simple_polygon *") print("****************************************") self.system = init.read_snapshot(self.snapshot2d) v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)]) self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d + eng_checkq)) self.tear_down() # polyhedron print("****************************************") print("* polyhedron *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33 * np.array([(-0.5, -0.5, -0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, 0.5, 0.5), (0.5, -0.5, -0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, 0.5, 0.5)]) f = [(7, 3, 1, 5), (7, 5, 4, 6), (7, 6, 2, 3), (3, 2, 0, 1), (0, 2, 6, 4), (1, 0, 4, 5)] r = 0.0 self.mc = hpmc.integrate.polyhedron(seed=10) self.mc.shape_param.set('A', vertices=v, faces=f, sweep_radius=r) diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten() self.assertAlmostEqual(diff.dot(diff), 0) self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r) del self.mc del self.system context.initialize() # convex_polyhedron print("****************************************") print("* convex_polyhedron *") print("****************************************") #a = 0.00038920117896296716, p = 0.2035860456051452 #d = 0.0014225507698958867, p = 0.19295361127422195 self.system = init.read_snapshot(self.snapshot3d) v = 0.33 * np.array([(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1), (1, -1, -1), (-1, -1, -1), (-1, 1, -1)]) self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq), a=0.0003892, d=0.00142255) self.tear_down() # convex_spheropolyhedron print("****************************************") print("* convex_spheropolyhedron *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33 * np.array([(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1), (1, -1, -1), (-1, -1, -1), (-1, 1, -1)]) r = 0.1234 self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.0, a=0.0) self.mc.shape_param.set('A', vertices=v, sweep_radius=r) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq)) self.tear_down() # faceted_sphere print("****************************************") print("* faceted_sphere *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) v = 0.33 * np.array([(-1, -1, -1), (-1, -1, 1), (-1, 1, -1), (-1, 1, 1), (1, -1, -1), (1, -1, 1), (1, 1, -1), (1, 1, 1)]) offs = [-1] * 6 norms = [(-1, 0, 0), (1, 0, 0), ( 0, 1, 0, ), (0, -1, 0), (0, 0, 1), (0, 0, -1)] diam = 1.0 orig = (0, 0, 0) self.mc = hpmc.integrate.faceted_sphere(seed=10, d=0.0, a=0.0) self.mc.shape_param.set('A', normals=norms, offsets=offs, vertices=v, diameter=diam, origin=orig) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq)) self.tear_down() # sphinx print("****************************************") print("* sphinx *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)] diams = [1, -1.2, -1.2] self.mc = hpmc.integrate.sphinx(seed=10, d=0.0, a=0.0) self.mc.shape_param.set('A', diameters=diams, centers=cent) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq)) self.tear_down() # sphere_union print("****************************************") print("* sphere_union *") print("****************************************") self.system = init.read_snapshot(self.snapshot3d) cent = [(0, 0, 0), (0, 0, 0.15), (0, 0, -0.15)] diams = [1, 1, 1] self.mc = hpmc.integrate.sphere_union(seed=10, d=0.0, a=0.0) self.mc.shape_param.set('A', diameters=diams, centers=cent) self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k * 10.0, qalt=kalt * 10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d + eng_checkq)) self.tear_down()
def create_empty(**kwargs): snap = data.make_snapshot(**kwargs) return init.read_snapshot(snap)
def setUp(self): snap = data.make_snapshot(N=0, box=data.boxdim(Lx=10, Ly=10, Lz=10)) self.system = init.read_snapshot(snap) self.mc = hpmc.integrate.convex_polyhedron(seed=123)