def create_random(N, phi_p=None, name="A", min_dist=0.7, box=None, seed=1, dimensions=3): R""" Generates N randomly positioned particles of the same type. Args: N (int): Number of particles to create. phi_p (float): Packing fraction of particles in the simulation box (unitless). name (str): Name of the particle type to create. min_dist (float): Minimum distance particles will be separated by (in distance units). box (:py:class:`hoomd.data.boxdim`): Simulation box dimensions. seed (int): Random seed. dimensions (int): The number of dimensions in the simulation. .. deprecated:: 2.0 Random initialization is best left to specific methods tailored by the user for their work. Either *phi_p* or *box* must be specified. If *phi_p* is provided, it overrides the value of *box*. Examples:: init.create_random(N=2400, phi_p=0.20) init.create_random(N=2400, phi_p=0.40, min_dist=0.5) system = init.create_random(N=2400, box=data.boxdim(L=20)) When *phi_p* is set, the dimensions of the created box are such that the packing fraction of particles in the box is *phi_p*. The number density \e n is related to the packing fraction by :math:`n = 2d/\pi \cdot \phi_P`, where *d* is the dimension, and assumes the particles have a radius of 0.5. All particles are created with the same type, given by *name*. The result of :py:func:`hoomd.deprecated.init.create_random` can be saved in a variable and later used to read and/or change particle properties later in the script. See :py:mod:`hoomd.data` for more information. """ hoomd.util.print_status_line(); hoomd.context._verify_init(); # check if initialization has already occurred if hoomd.init.is_initialized(): hoomd.context.msg.error("Cannot initialize more than once\n"); raise RuntimeError("Error initializing"); # check that dimensions are appropriate if dimensions not in (2,3): raise ValueError('dimensions must be 2 or 3') # abuse the polymer generator to generate single particles if phi_p is not None: # calculate the box size L = math.pow(math.pi/(2.0*dimensions)*N / phi_p, 1.0/dimensions); box = hoomd.data.boxdim(L=L, dimensions=dimensions); if box is None: raise RuntimeError('box or phi_p must be specified'); if not isinstance(box, hoomd.data.boxdim): hoomd.context.msg.error('box must be a data.boxdim object'); raise TypeError('box must be a data.boxdim object'); # create the generator generator = _deprecated.RandomGenerator(hoomd.context.exec_conf, box._getBoxDim(), seed, box.dimensions); # build type list type_vector = _hoomd.std_vector_string(); type_vector.append(name); # empty bond lists for single particles bond_ab = _hoomd.std_vector_uint(); bond_type = _hoomd.std_vector_string(); # create the generator generator.addGenerator(int(N), _deprecated.PolymerParticleGenerator(hoomd.context.exec_conf, 1.0, type_vector, bond_ab, bond_ab, bond_type, 100, box.dimensions)); # set the separation radius generator.setSeparationRadius(name, min_dist/2.0); # generate the particles generator.generate(); # initialize snapshot snapshot = generator.getSnapshot() my_domain_decomposition = hoomd.init._create_domain_decomposition(snapshot._global_box); if my_domain_decomposition is not None: hoomd.context.current.system_definition = _hoomd.SystemDefinition(snapshot, hoomd.context.exec_conf, my_domain_decomposition); else: hoomd.context.current.system_definition = _hoomd.SystemDefinition(snapshot, hoomd.context.exec_conf); # initialize the system hoomd.context.current.system = _hoomd.System(hoomd.context.current.system_definition, 0); hoomd.init._perform_common_init_tasks(); return hoomd.data.system_data(hoomd.context.current.system_definition);
def create_random_polymers(box, polymers, separation, seed=1): R""" Generates any number of randomly positioned polymers of configurable types. Args: box (:py:class:`hoomd.data.boxdim`): Simulation box dimensions polymers (list): Specification for the different polymers to create (see below) separation (dict): Separation radii for different particle types (see below) seed (int): Random seed to use .. deprecated:: 2.0 Random initialization is best left to specific methods tailored by the user for their work. Any number of polymers can be generated, of the same or different types, as specified in the argument *polymers*. Parameters for each polymer include bond length, particle type list, bond list, and count. The syntax is best shown by example. The below line specifies that 600 block copolymers A6B7A6 with a bond length of 1.2 be generated:: polymer1 = dict(bond_len=1.2, type=['A']*6 + ['B']*7 + ['A']*6, bond="linear", count=600) Here is an example for a second polymer, specifying just 100 polymers made of 5 B beads bonded in a branched pattern:: polymer2 = dict(bond_len=1.2, type=['B']*5, bond=[(0, 1), (1,2), (1,3), (3,4)] , count=100) The *polymers* argument can be given a list of any number of polymer types specified as above. *count* randomly generated polymers of each type in the list will be generated in the system. In detail: - bond_len defines the bond length of the generated polymers. This should not necessarily be set to the equilibrium bond length! The generator is dumb and doesn't know that bonded particles can be placed closer together than the separation (see below). Thus bond_len must be at a minimum set at twice the value of the largest separation radius. An error will be generated if this is not the case. - type is a python list of strings. Each string names a particle type in the order that they will be created in generating the polymer. - bond can be specified as "linear" in which case the generator connects all particles together with bonds to form a linear chain. bond can also be given a list if python tuples (see example above). - Each tuple in the form of \c (a,b) specifies that particle \c a of the polymer be bonded to particle \c b. These bonds are given the default type name of 'polymer' to be used when specifying parameters to bond forces such as bond.harmonic. - A tuple with three elements (a,b,type) can be used as above, but with a custom name for the bond. For example, a simple branched polymer with different bond types on each branch could be defined like so:: bond=[(0,1), (1,2), (2,3,'branchA'), (3,4,'branchA), (2,5,'branchB'), (5,6,'branchB')] separation must contain one entry for each particle type specified in polymers ('A' and 'B' in the examples above). The value given is the separation radius of each particle of that type. The generated polymer system will have no two overlapping particles. Examples:: init.create_random_polymers(box=data.boxdim(L=35), polymers=[polymer1, polymer2], separation=dict(A=0.35, B=0.35)); init.create_random_polymers(box=data.boxdim(L=31), polymers=[polymer1], separation=dict(A=0.35, B=0.35), seed=52); # create polymers in an orthorhombic box init.create_random_polymers(box=data.boxdim(Lx=18,Ly=10,Lz=25), polymers=[polymer2], separation=dict(A=0.35, B=0.35), seed=12345); # create a triclinic box with tilt factors xy=0.1 xz=0.2 yz=0.3 init.create_random_polymers(box=data.boxdim(L=18, xy=0.1, xz=0.2, yz=0.3), polymers=[polymer2], separation=dict(A=0.35, B=0.35)); With all other parameters the same, create_random_polymers will always create the same system if seed is the same. Set a different seed (any integer) to create a different random system with the same parameters. Note that different versions of HOOMD \e may generate different systems even with the same seed due to programming changes. Note: For relatively dense systems (packing fraction 0.4 and higher) the simple random generation algorithm may fail to find room for all the particles and print an error message. There are two methods to solve this. First, you can lower the separation radii allowing particles to be placed closer together. Then setup integrate.nve with the limit option set to a relatively small value. A few thousand time steps should relax the system so that the simulation can be continued without the limit or with a different integrator. For extremely troublesome systems, generate it at a very low density and shrink the box with the command update.box_resize to the desired final size. Note: The polymer generator always generates polymers as if there were linear chains. If you provide a non-linear bond topology, the bonds in the initial configuration will be stretched significantly. This normally doesn't pose a problem for harmonic bonds (bond.harmonic) as the system will simply relax over a few time steps, but can cause the system to blow up with FENE bonds (bond.fene). """ hoomd.util.print_status_line(); hoomd.context._verify_init(); # check if initialization has already occurred if hoomd.init.is_initialized(): hoomd.context.msg.error("Cannot initialize more than once\n"); raise RuntimeError("Error creating random polymers"); if len(polymers) == 0: hoomd.context.msg.error("Polymers list cannot be empty.\n"); raise RuntimeError("Error creating random polymers"); if len(separation) == 0: hoomd.context.msg.error("Separation dict cannot be empty.\n"); raise RuntimeError("Error creating random polymers"); if not isinstance(box, hoomd.data.boxdim): hoomd.context.msg.error('Box must be a data.boxdim object\n'); raise TypeError('box must be a data.boxdim object'); # create the generator generator = _deprecated.RandomGenerator(hoomd.context.exec_conf,box._getBoxDim(), seed, box.dimensions); # make a list of types used for an eventual check vs the types in separation for completeness types_used = []; # track the minimum bond length min_bond_len = None; # build the polymer generators for poly in polymers: type_list = []; # check that all fields are specified if not 'bond_len' in poly: hoomd.context.msg.error('Polymer specification missing bond_len\n'); raise RuntimeError("Error creating random polymers"); if min_bond_len is None: min_bond_len = poly['bond_len']; else: min_bond_len = min(min_bond_len, poly['bond_len']); if not 'type' in poly: hoomd.context.msg.error('Polymer specification missing type\n'); raise RuntimeError("Error creating random polymers"); if not 'count' in poly: hoomd.context.msg.error('Polymer specification missing count\n'); raise RuntimeError("Error creating random polymers"); if not 'bond' in poly: hoomd.context.msg.error('Polymer specification missing bond\n'); raise RuntimeError("Error creating random polymers"); # build type list type_vector = _hoomd.std_vector_string(); for t in poly['type']: type_vector.append(t); if not t in types_used: types_used.append(t); # build bond list bond_a = _hoomd.std_vector_uint(); bond_b = _hoomd.std_vector_uint(); bond_name = _hoomd.std_vector_string(); # if the bond setting is 'linear' create a default set of bonds if poly['bond'] == 'linear': for i in range(0,len(poly['type'])-1): bond_a.append(i); bond_b.append(i+1); bond_name.append('polymer') #if it is a list, parse the user custom bonds elif type(poly['bond']) == type([]): for t in poly['bond']: # a 2-tuple gets the default 'polymer' name for the bond if len(t) == 2: a,b = t; name = 'polymer'; # and a 3-tuple specifies the name directly elif len(t) == 3: a,b,name = t; else: hoomd.context.msg.error('Custom bond ' + str(t) + ' must have either two or three elements\n'); raise RuntimeError("Error creating random polymers"); bond_a.append(a); bond_b.append(b); bond_name.append(name); else: hoomd.context.msg.error('Unexpected argument value for polymer bond\n'); raise RuntimeError("Error creating random polymers"); # create the generator generator.addGenerator(int(poly['count']), _deprecated.PolymerParticleGenerator(hoomd.context.exec_conf, poly['bond_len'], type_vector, bond_a, bond_b, bond_name, 100, box.dimensions)); # check that all used types are in the separation list for t in types_used: if not t in separation: hoomd.context.msg.error("No separation radius specified for type " + str(t) + "\n"); raise RuntimeError("Error creating random polymers"); # set the separation radii, checking that it is within the minimum bond length for t,r in separation.items(): generator.setSeparationRadius(t, r); if 2*r >= min_bond_len: hoomd.context.msg.error("Separation radius " + str(r) + " is too big for the minimum bond length of " + str(min_bond_len) + " specified\n"); raise RuntimeError("Error creating random polymers"); # generate the particles generator.generate(); # copy over data to snapshot snapshot = generator.getSnapshot() my_domain_decomposition = hoomd.init._create_domain_decomposition(snapshot._global_box); if my_domain_decomposition is not None: hoomd.context.current.system_definition = _hoomd.SystemDefinition(snapshot, hoomd.context.exec_conf, my_domain_decomposition); else: hoomd.context.current.system_definition = _hoomd.SystemDefinition(snapshot, hoomd.context.exec_conf); # initialize the system hoomd.context.current.system = _hoomd.System(hoomd.context.current.system_definition, 0); hoomd.init._perform_common_init_tasks(); return hoomd.data.system_data(hoomd.context.current.system_definition);