<commit_before>import simtk.openmm as mm
from torsionfit import TorsionScanSet as ScanSet
import torsionfit.TorsionFitModel as Model
from torsionfit import sqlite_plus
from pymc import MCMC
from parmed.charmm import CharmmParameterSet

param = CharmmParameterSet('../../../../param/top_all36_cgenff.rtf',
                           '../../../../../data/charmm_ff/par_all36_cgenff.prm')
structure = '../../../../structure/butane_charge_off.psf'
scan = '../../../../torsion_scans/DFT_b3lyp/butane_scan_b3lyp_360.log'
butane_scan = ScanSet.parse_psi4(scan, structure)

platform = mm.Platform.getPlatformByName('Reference')

model = Model.TorsionFitModelEliminatePhase(param, butane_scan, platform=platform, decouple_n=True,
                                            param_to_opt=[('CG331', 'CG321', 'CG321', 'CG331'),
                                                          ('HGA3', 'CG331', 'CG321', 'HGA2'),
                                                          ('HGA3', 'CG331', 'CG321', 'CG321'),
                                                          ('HGA2', 'CG321', 'CG321', 'HGA2'),
                                                          ('CG331', 'CG321', 'CG321', 'HGA2')],
                                            decouple_n=True)

sampler = MCMC(model.pymc_parameters, db=sqlite_plus, dbname='butane_360_all_mult_off_charge_on.db', verbose=5)
sampler.sample(1000000)<commit_msg>fixed sampling script<commit_after>import simtk.openmm as mm
from torsionfit import TorsionScanSet as ScanSet
import torsionfit.TorsionFitModel as Model
from torsionfit import sqlite_plus
from pymc import MCMC
from parmed.charmm import CharmmParameterSet

param = CharmmParameterSet('../../../../param/top_all36_cgenff.rtf',
                           '../../../../../data/charmm_ff/par_all36_cgenff.prm')
structure = '../../../../structure/butane_charge_off.psf'
scan = '../../../../torsion_scans/DFT_b3lyp/butane_scan_b3lyp_360.log'
butane_scan = ScanSet.parse_psi4(scan, structure)

platform = mm.Platform.getPlatformByName('Reference')

model = Model.TorsionFitModelEliminatePhase(param, butane_scan, platform=platform, decouple_n=True,
                                            param_to_opt=[('CG331', 'CG321', 'CG321', 'CG331')])

sampler = MCMC(model.pymc_parameters, db=sqlite_plus, dbname='butane_360_4_mult_off_charge_on.db', verbose=5)
sampler.sample(1000000)
{'fraction_non_alphanumeric': 0.1379890618426588, 'fraction_numerical': 0.04333193100546908, 'mean_word_length': 2.368271954674221, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 14, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3637495', 'n_tokens_mistral': 810, 'n_tokens_neox': 731, 'n_words': 124}