def __init__(self, filename, quantities, period, header_prefix='', overwrite=False, phase=0):
hoomd.util.print_status_line();
# initialize base class
_analyzer.__init__(self);
if filename is None or filename == "":
filename = "";
period = 1;
# create the c++ mirror class
self.cpp_analyzer = _hoomd.LogPlainTXT(hoomd.context.current.system_definition, filename, header_prefix, overwrite);
self.setupAnalyzer(period, phase);
# set the logged quantities
quantity_list = _hoomd.std_vector_string();
for item in quantities:
quantity_list.append(str(item));
self.cpp_analyzer.setLoggedQuantities(quantity_list);
# add the logger to the list of loggers
hoomd.context.current.loggers.append(self);
# store metadata
self.metadata_fields = ['filename','period']
self.filename = filename
self.period = period
def set_params(self, quantities=None, delimiter=None):
R""" Change the parameters of the log.
Args:
quantities (list): New list of quantities to log (if specified)
delimiter (str): New delimiter between columns in the output file (if specified)
Examples::
logger.set_params(quantities=['bond_harmonic_energy'])
logger.set_params(delimiter=',');
logger.set_params(quantities=['bond_harmonic_energy'], delimiter=',');
"""
hoomd.util.print_status_line();
if quantities is not None:
# set the logged quantities
quantity_list = _hoomd.std_vector_string();
for item in quantities:
quantity_list.append(str(item));
self.cpp_analyzer.setLoggedQuantities(quantity_list);
if delimiter:
self.cpp_analyzer.setDelimiter(delimiter);
def set_params(self, quantities=None, delimiter=None):
R""" Change the parameters of the log.
Args:
quantities (list): New list of quantities to log (if specified)
delimiter (str): New delimiter between columns in the output file (if specified)
Examples::
logger.set_params(quantities=['bond_harmonic_energy'])
logger.set_params(delimiter=',');
logger.set_params(quantities=['bond_harmonic_energy'], delimiter=',');
"""
hoomd.util.print_status_line();
if quantities is not None:
# set the logged quantities
quantity_list = _hoomd.std_vector_string();
for item in quantities:
quantity_list.append(str(item));
self.cpp_analyzer.setLoggedQuantities(quantity_list);
if delimiter:
self.cpp_analyzer.setDelimiter(delimiter);
def __init__(self, filename, quantities, period, header_prefix='', overwrite=False, phase=0):
hoomd.util.print_status_line();
# initialize base class
_analyzer.__init__(self);
if filename is None or filename == "":
filename = "";
period = 1;
# create the c++ mirror class
self.cpp_analyzer = _hoomd.LogPlainTXT(hoomd.context.current.system_definition, filename, header_prefix, overwrite);
self.setupAnalyzer(period, phase);
# set the logged quantities
quantity_list = _hoomd.std_vector_string();
for item in quantities:
quantity_list.append(str(item));
self.cpp_analyzer.setLoggedQuantities(quantity_list);
# add the logger to the list of loggers
hoomd.context.current.loggers.append(self);
# store metadata
self.metadata_fields = ['filename','period']
self.filename = filename
self.period = period
def __init__(self,
quantities,
filename="autocorrelate.log",
period=1,
eval_period=0):
hoomd.util.print_status_line()
# initialize base class
hoomd.analyze._analyzer.__init__(self)
# hoomd.analyze._correlate.__init__(self)
# convert quantities to a HOOMD vector string
quantity_list = _hoomd.std_vector_string()
for item in quantities:
quantity_list.append(str(item))
# initialize the reflected c++ class
self.cpp_analyzer = _correlator.Correlator(
hoomd.context.current.system_definition,
filename,
quantity_list,
period,
eval_period,
)
self.cpp_analyzer.setLoggedQuantities(quantity_list)
self.setupAnalyzer(period)
# add the correlator to the list of loggers
hoomd.context.current.loggers.append(self)
def set_params(self, quantities=None, matrix_quantities=None):
R""" Change the parameters of the log.
Warning:
Do not change the number or order of logged non-matrix quantities compared to values stored in the file.
"""
if quantities is not None:
# set the logged quantities
quantity_list = _hoomd.std_vector_string()
for item in quantities:
quantity_list.append(str(item))
self.cpp_analyzer.setLoggedQuantities(quantity_list)
if matrix_quantities is not None:
# set the logged quantities
matrix_quantity_list = _hoomd.std_vector_string()
for item in matrix_quantities:
matrix_quantity_list.append(str(item))
self.cpp_analyzer.setLoggedMatrixQuantities(matrix_quantity_list)
def set_params(self, quantities=None, matrix_quantities=None):
R""" Change the parameters of the log.
Warning:
Do not change the number or order of logged non-matrix quantities compared to values stored in the file.
"""
hoomd.util.print_status_line()
if quantities is not None:
# set the logged quantities
quantity_list = _hoomd.std_vector_string()
for item in quantities:
quantity_list.append(str(item))
self.cpp_analyzer.setLoggedQuantities(quantity_list)
if matrix_quantities is not None:
# set the logged quantities
matrix_quantity_list = _hoomd.std_vector_string()
for item in matrix_quantities:
matrix_quantity_list.append(str(item))
self.cpp_analyzer.setLoggedMatrixQuantities(matrix_quantity_list)
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);
