rmatsum836

<ForceField>
  <AtomTypes>
    <Type name="lopes_010" class="" element="N" mass="14.00672" def="[N;X3;r5]1[C;X3;r5][N;X3;r5][C;X3;r5][C;X3;r5]1" overrides="" desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_011" class="" element="C" mass="12.01078" def="[C;X3;r5]1[N;%lopes_010][C;X3;r5][C;X3;r5][N;%lopes_010]1" overrides="" desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_012" class="" element="C" mass="12.01078" def="[C;X3;r5]1[C;X3;r5][N;%lopes_010][C;X3;r5][N;%lopes_010]1" overrides="" desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_013" class="" element="H" mass="1.007947" def="H[C;%lopes_011,%lopes_012]" overrides="" desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_014" class="" element="C" mass="12.01078" def="[C;X4][N;%lopes_010]" overrides="," desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_015" class="" element="H" mass="1.007947" def="H[C;%lopes_014]" overrides="" desc="" doi="10.1021/jp0362133"/>
    <Type name="lopes_017" class="" element="C" mass="12.01078" de

rmatsum836

 def apply_multiple_forcefields(compound, residue_dict):
     """
     Applies multiple forcefields to a mb.Compound
 
     Parameters
     ----------
     compound: mb.Compound
     residue_dict: dict
         Dictionary containing residues (key) and foyer Forcefields (value) pairs
 

rmatsum836

<ForceField>
    <AtomTypes>
        <Type name="CH3" class="CT" element="C" mass="12.01100" def="[C;X4](C)(H)(H)H" desc="alkane CH3" doi="10.1021/ja9621760"/>
        <Type name="CH2" class="CT" element="C" mass="12.01100" def="[C;X4](C)(C)(H)H" desc="alkane CH2" doi="10.1021/ja9621760"/>
        <Type name="CH" class="CT" element="C" mass="12.01100" def="[C;X4](C)(C)(C)H" desc="alkane CH" doi="10.1021/ja9621760"/>
        <Type name="CH4" class="CT" element="C" mass="12.01100" def="[C;X4](H)(H)(H)H" desc="alkane CH4" doi="10.1021/ja9621760"/>
        <Type name="C" class="CT" element="C" mass="12.01100" def="[C;X4](C)(C)(C)C" desc="alkane C" doi="10.1021/ja9621760"/>
        <Type name="HC" class="HC" element="H" mass="1.00800"  def="H[C;X4]" desc="alkane H" doi="10.1021/ja9621760"/>
    </AtomTypes>
    <HarmonicBondForce>

rmatsum836

import mbuild as mb
import foyer
from foyer import Forcefield

butane = mb.load('CCCC', smiles=True)
gomc = Forcefield('opls_gomc.xml')

typed = gomc.apply(butane, assert_dihedral_params=False)
typed.save('butane.top', overwrite=True)

rmatsum836

dimension           3
units               real
boundary            p p p

atom_style          full
pair_style          lj/cut/coul/long 7.0
bond_style          harmonic
angle_style         harmonic
box                 tilt large
read_data           data.water

rmatsum836

il = mb.Compound()
solvent = mb.Compound()
for child in system.children:
    if child.name in ['bmim', 'tf2n']:
        il.add(mb.clone(child))
    elif child.name == 'acn':
        sollvent.add(mb.clone(child))
        
 opls = Forcefield(name='oplsaa')
 lopes = Forcefield('kpl.xml')

rmatsum836

import mbuild as mb
import matplotlib.pyplot as plt
import time
import foyer

def build_mbuild():
    from mbuild.formats.lammpsdata import write_lammpsdata
    from foyer import Forcefield
    
    water = mb.load("files/tip3p.mol2")

rmatsum836

import mdtraj as md
import numpy as np
import matplotlib.pyplot as plt
from scattering.scattering import structure_factor

# Load trajectory with MDTraj
trj = md.load('sample.trr', top='sample.gro')
il = trj.topology.select('resid 0')
trj_il = trj.atom_slice(il)

rmatsum836

import signac
import os

project = signac.get_project()

for job in project.find_jobs():
  sq = os.path.join(job.workspace(), 'sq.txt')

rmatsum836

project = signac.get_project()
for job in project.find_jobs():  
    fig, ax = plt.subplots()
    if os.path.isfile(os.path.join(job.workspace(), 'all-reducs.pkl')):
     with open(os.path.join(job.workspace(), 'all-reducs.pkl'), 'rb') as f:
         reduc = pickle.load(f)
     c = deepcopy(reduc)
     cluster_sizes = []
     for proc in c:
         for matrix in proc: