def myCalcs(self, D ):
if self.args['vectors']: D.foldMovieToUC(self.args['vectors'])
self.countBins(D.frame_data, D.frame_seed)
if self.missedLocations:
data = {'coords':self.missedLocations,'atoms':['N' for i in self.missedLocations]}
xyz(self.args['path'] + '/'+ self.feed +'/'+ 'gridMissedLocs.xyz', data)
self.output_results()
def makegrid():
numBins = tuple([600, 600, 1])
abc = tuple([60.066, 59.697, 13.383]) # unit cell dimensions
labels = np.chararray(shape=numBins, unicode=True, itemsize=5)
data = {'atoms': [], 'coords': []}
print('bin size = ',
[abc[0] / numBins[0], abc[1] / numBins[1], abc[2] / numBins[2]])
for i in range(numBins[0]):
for j in range(numBins[1]):
for k in range(numBins[2]):
coords = [
i * abc[0] / numBins[0], j * abc[1] / numBins[1],
k * abc[2] / numBins[2]
]
if micropore(coords):
data['atoms'].append('D')
elif mesopore(coords):
data['atoms'].append('F')
elif surface(coords):
data['atoms'].append('H')
data['coords'].append(coords)
xyz('/home/siepmann/josep180/Work/OFS/SPP/SPPgridcheck7.xyz', data)
def makegrid():
numBins = tuple([1, 500, 1])
abc = tuple([40.106, 100.0, 40.145]) # unit cell dimensions
labels = np.chararray(shape=numBins, unicode=True, itemsize=5)
data = {'atoms': [], 'coords': []}
print('bin size = ',
[abc[0] / numBins[0], abc[1] / numBins[1], abc[2] / numBins[2]])
for i in range(numBins[0]):
for j in range(numBins[1]):
for k in range(numBins[2]):
coords = [
i * abc[0] / numBins[0], j * abc[1] / numBins[1],
k * abc[2] / numBins[2]
]
if micropore(coords):
data['atoms'].append('D')
elif mesopore(coords):
data['atoms'].append('F')
elif surface(coords):
data['atoms'].append('H')
data['coords'].append(coords)
xyz('/home/siepmann/josep180/Work/BTX/MFI-nanogrid.xyz', data)
def myCalcs(self, D):
if self.args['vectors']: D.foldMovieToUC(self.args['vectors'])
self.countBins(D.frame_data, D.frame_seed)
if self.missedLocations:
data = {
'coords': self.missedLocations,
'atoms': ['N' for i in self.missedLocations]
}
xyz(
self.args['path'] + '/' + self.feed + '/' +
'gridMissedLocs.xyz', data)
# print(Regions)
# sys.stdout.write(repr(Regions))
# flag=''
# if self.filter_function:
# flag = '_filtered'
# xyz('%s/%s/movie_coords_mol%s_box%s%s_sim%s_%s.xyz'%(self.args['path'], self.feed,
# mol_num, self.args['box'],flag, ''.join(map(str,self.args['indep'])),
# '-'.join(self.args['bead'])), xyz_data)
outputDB(self.args['path'], [self.feed], self.args['type'],
{self.args['name']: self})
# pbc_coords = [[x[i],y[i]] for i in pbc_coords]
# coords = fold_coords(pbc_coords,[a,b])
# my_ax.plot(coords[:,0],coords[:,1],'-.',color='red')
from MCFlow.file_formatting import reader, writer
from MCFlow.calc_tools import calculate_distance, pbc, fold_coords
import numpy as np
import pprint
rcut = 5.0 / 2.
a, b, c = [20.022, 19.899, 13.383]
center = [10.011, 4.9748, 0.]
x, y, z = center
sphere = [[x, y, z], [a / 2 - x, b / 2 + y, c / 2 + z], [x, b / 2 - y, z],
[a / 2 + x, y, c / 2 - z], [a - x, b - y, c - z],
[a / 2 + x, b / 2 - y, c / 2 - z], [a - x, b / 2 + y, c - z],
[a / 2 - x, b - y, c / 2 + z]]
if __name__ == '__main__':
new_data = {'atoms': [], 'coords': []}
old_data = reader.xyz('energy_grid_114_O_merged1.5.xyz')
for atom, xyz in zip(old_data['atoms'], old_data['coords']):
for my_center in sphere:
if calculate_distance(xyz, my_center, [a, b, c]) < rcut:
atom = 'H'
new_data['atoms'].append(atom)
new_data['coords'].append(xyz)
writer.xyz('new_channels.xyz', new_data)