def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT * 3, box_vectors=np.eye(3) * bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT*3, box_vectors=np.eye(3)*bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def test_canonical():
'''test for Canonical Ensemble'''
# Liquid argon Near experimental density
sys = MonatomicSystem.spaced_lattice('Ar', 100, 5.0)
energies = []
pot = []
kin = []
times = []
display_system(sys)
gen = evolve_generator(sys, 100.0, 0.002)
count = 0
for sys, t in gen:
v = cenergy.lennard_jones(sys.r_array*1e-9, sys.type, periodic=sys.boxsize*1e-9)
m = typetomass['Ar'] * 1.660538921e-27
k = (0.5 * m * sys.varray * sys.varray * 1e6).sum()
count +=1
if (count % 1000) == 0:
pot.append(v)
kin.append(k)
energies.append((v + k))
times.append(t)
display_system(sys)
pl.plot(times, energies, label="H")
pl.plot(times, pot, label='V')
pl.plot(times, kin, label='K')
pl.legend()
pl.show()
def test_random():
'''Testing random made box'''
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = cdb.get("molecule", 'gromacs.spce')
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
display_system(s)
from chemlab.core import Atom, Molecule, crystal
from chemlab.graphics import display_system
# Molecule templates
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
s = crystal(
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], # Fractional Positions
[na, cl], # Molecules
225, # Space Group
cellpar=[.54, .54, .54, 90, 90, 90], # unit cell parameters
repetitions=[5, 5, 5]) # unit cell repetitions in each direction
display_system(s)