def initialize(self):
rc = self.rc.config['west', 'system']
# pcoord parameters
self.pcoord_ndim = 2
self.pcoord_len = 2
self.pcoord_dtype = pcoord_dtype
self.target_count = rc.get('target_count')
self.nbins = rc.get('nbins')
y = np.linspace(0.05, 0.95, self.nbins)
centers = np.zeros((self.nbins, self.pcoord_ndim),
dtype=self.pcoord_dtype)
centers[:, 1] = y
self.bin_mapper = VoronoiBinMapper(dfunc, centers)
self.bin_target_counts = np.zeros((self.bin_mapper.nbins, ),
dtype=np.int_)
self.bin_target_counts[...] = self.target_count
# string method parameters
self.sm_params = {
'slen': [self.nbins],
'kappa': 0.01,
'fixed_ends': False,
'isperiodic': np.array([0, 1], dtype=np.int),
'boxsize': np.array([1.0e8, 1.0]),
'sciflag': True
}
def initialize(self):
rc = self.rc.config['west', 'system']
self.pcoord_ndim = 3
self.pcoord_len = 2
self.pcoord_dtype = pcoord_dtype
self.target_count = rc.get('target_count')
self.nbins = rc.get('nbins')
slen = self.nbins // 2
x = np.linspace(-3.0, 3.0, slen)
centers = np.zeros((self.nbins, self.pcoord_ndim), dtype=self.pcoord_dtype)
centers[:slen, 0] = x
centers[slen:, 0] = x[::-1]
centers[:slen, 2] = 0.0
centers[slen:, 2] = 1.0
self.bin_mapper = VoronoiBinMapper(dfunc, centers)
self.bin_target_counts = np.zeros((self.bin_mapper.nbins,), dtype=np.int_)
self.bin_target_counts[...] = self.target_count
slen = self.nbins // 2
self.sm_params = {'slen': [slen, slen],
'kappa': 0.001,
'dtau': 0.15,
'fixed_ends': False,
'sciflag': True,
'mpairs': [[0, self.nbins - 1], [slen - 1, slen]],
'slabels': [2],
'fourierflag': True,
'fourier_P': 2}
def update_bin_mapper(self):
'''Update the bin_mapper using the current set of voronoi centers'''
westpa.rc.pstatus('westext.adaptvoronoi: Updating bin mapper\n')
westpa.rc.pflush()
# self.mapper_func = plugin_config.get('mapper_func', False)
try:
dfargs = getattr(self.system, 'dfargs', None)
dfkwargs = getattr(self.system, 'dfkwargs', None)
if self.mapper_func:
# The mapper should take in 1) distance function,
# 2) centers, 3) dfargs, 4) dfkwargs and return
# the mapper we want
self.system.bin_mapper = self.mapper_func(self.dfunc,
self.centers,
dfargs=dfargs,
dfkwargs=dfkwargs)
else:
self.system.bin_mapper = VoronoiBinMapper(self.dfunc,
self.centers,
dfargs=dfargs,
dfkwargs=dfkwargs)
self.ncenters = self.system.bin_mapper.nbins
new_target_counts = np.empty((self.ncenters, ), np.int)
new_target_counts[...] = self.walk_count
self.system.bin_target_counts = new_target_counts
except (ValueError, TypeError) as e:
log.error('AdaptiveVoronoiDriver Error: \
Failed updating the bin mapper: {}'.format(e))
raise
def initialize(self):
self.pcoord_ndim = 2
self.pcoord_dtype = pcoord_dtype
self.pcoord_len = pcoord_len
nbins = 1
self.nbins = nbins
centers = np.zeros((self.nbins,self.pcoord_ndim),dtype=self.pcoord_dtype)
centers[:,:] = 1
self.bin_mapper = VoronoiBinMapper(dfunc, centers)
self.bin_target_counts = np.empty((self.bin_mapper.nbins,), np.int)
self.bin_target_counts[...] = 10
def update_bin_mapper(self):
'''Update the bin_mapper using the current string'''
westpa.rc.pstatus('westext.stringmethod: Updating bin mapper\n')
westpa.rc.pflush()
try:
dfargs = getattr(self.system, 'dfargs', None)
dfkwargs = getattr(self.system, 'dfkwargs', None)
self.system.bin_mapper = VoronoiBinMapper(self.dfunc, self.strings.centers,
dfargs=dfargs,
dfkwargs=dfkwargs)
except (ValueError, TypeError) as e:
log.error('StringDriver Error: Failed updating the bin mapper: {}'.format(e))
raise
def initialize(self):
self.pcoord_ndim = 8
self.pcoord_len = 2
self.pcoord_dtype = np.float32
self.nbins = 1
centers = np.zeros((self.nbins, self.pcoord_ndim),
dtype=self.pcoord_dtype)
# Using the values from the inital point
centers[0, 0] = 4.0
centers[0, 1] = 18.0
centers[0, 4] = 1.0
centers[0, 6] = 1.0
self.bin_mapper = VoronoiBinMapper(dfunc, centers)
self.bin_target_counts = np.empty((self.bin_mapper.nbins, ), np.int)
self.bin_target_counts[...] = 10
def initialize(self):
rc = self.rc.config
# pcoord parameters
ff_data = np.load(rc.require(['west', 'elasticnetwork', 'ff_data']))
self.pcoord_ndim = 2 * ff_data['coordsA'].size
self.pcoord_len = rc.require(
['west', 'elasticnetwork', 'blocks_per_iteration'])
self.pcoord_dtype = pcoord_dtype
self.target_count = rc.require(['west', 'system', 'target_count'])
self.nbins = rc.require(['west', 'system', 'nbins'])
# string method parameters
self.cpos = self.pcoord_ndim // 2
self.natoms = ff_data['coordsA'].shape[0]
self.sm_params = {
'slen': [self.nbins],
'dtau':
0.1,
'kappa':
0.2,
'fixed_ends':
rc.require(['west', 'plugins', 1, 'fixed_ends'], type_=bool),
'slabels':
range(self.cpos, self.pcoord_ndim)
}
self.init_pos = {}
self.init_pos['coordsA'] = ff_data['coordsA']
self.init_pos['coordsB'] = ff_data['coordsB']
try:
self.init_str_ends = np.load(
rc.get(['west', 'plugins', 1, 'init_string_ends'], None))
except:
self.init_str_ends = np.vstack((self.init_pos['coordsA'].ravel(),
self.init_pos['coordsB'].ravel()))
confA = self.init_str_ends[0]
confB = self.init_str_ends[1]
# Check and reshape coordinates
assert confA.shape == confB.shape
if len(confA.shape) == 1:
confA = confA.reshape((self.cpos // 3, 3))
if len(confB.shape) == 1:
confB = confB.reshape((self.cpos // 3, 3))
assert confA.shape == confB.shape == (self.cpos // 3, 3)
# Build initial string
centers = str_utils.interpolate_conformations(confA, confB, self.nbins)
# Add dummy progress coordinates for velocities
centers = np.hstack(
(centers, np.zeros_like(centers))).astype(pcoord_dtype)
self.bin_mapper = VoronoiBinMapper(dfunc, centers)
self.bin_target_counts = np.zeros((self.bin_mapper.nbins, ),
dtype=np.int_)
self.bin_target_counts[...] = self.target_count