"""LAMMPS datasets.
"""
from os.path import dirname, join
from glob import glob
from .. import Bunch
[docs]
def load_benzene():
"""Load data set of benzene in water.
Returns
-------
data: Bunch
Dictionary-like object, the interesting attributes are:
- 'data' : the data files from lammps dump output
* "mbar": Files formatted for BAR or MBAR
* '1_coul-off': NPT removal of benzene's charges
* '2_vdw': NPT decoupling of vdw forces between benzene and water
* '3_coul-on': NVT in vacuum restoration of benzene's charges
* "ti"
* '1_coul-off': NPT removal of benzene's charges
* '2_vdw': NPT decoupling of vdw forces between benzene and water
* '3_coul-on': NVT in vacuum restoration of benzene's charges
- 'DESCR': the full description of the dataset
"""
module_path = dirname(__file__)
data = {
"mbar": {
'1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/mbar*.txt.bz2')),
'2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/mbar*.txt.bz2')),
'3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/mbar*.txt.bz2')),
},
"ti": {
'1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/ti*.txt.bz2')),
'2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/ti*.txt.bz2')),
'3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/ti*.txt.bz2')),
}
}
with open(join(module_path, 'benzene', 'descr.rst')) as rst_file:
fdescr = rst_file.read()
return Bunch(data=data,
DESCR=fdescr)
[docs]
def load_lj_dimer():
"""Load data set of LJ dimer in solvent.
Returns
-------
data: Bunch
Dictionary-like object, the interesting attributes are:
- 'data' : the data files from lammps dump output
- 'DESCR': the full description of the dataset
"""
module_path = dirname(__file__)
data = glob(join(module_path, 'lj_dimer/cross_epsilon/linear*.txt.bz2'))
with open(join(module_path, 'lj_dimer', 'descr.rst')) as rst_file:
fdescr = rst_file.read()
return Bunch(data=data,
DESCR=fdescr)