import unittest
import pytraj as pt
from array import array
import numpy as np
from pytraj import Frame
from pytraj.base import *
from pytraj.math import Vec3
from pytraj.testing import aa_eq
N_ATOMS = 10
FRAME = Frame(N_ATOMS)
arr = np.arange(3 * N_ATOMS)
FRAME.xyz[:] = arr.reshape(N_ATOMS, 3)
FRAME_orig = FRAME.copy()
class TestFrame(unittest.TestCase):
def test_fit(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajnew = pt.iterload("./data/md1_prod.fit_to_first.Tc5b.x",
"./data/Tc5b.top")
# make sure 0-th frame does not change
frame0 = traj[0]
frame0new = trajnew[0]
frame1 = traj[1]
frame1new = trajnew[1]
# try do-fitting from Python
import unittest
import pytraj as pt
from utils import fn
from array import array
import numpy as np
from pytraj import Frame
from pytraj.testing import aa_eq
from pytraj import *
N_ATOMS = 10
FRAME = Frame(N_ATOMS)
arr = np.arange(3 * N_ATOMS)
FRAME.xyz[:] = arr.reshape(N_ATOMS, 3)
FRAME_orig = FRAME.copy()
class TestFrame(unittest.TestCase):
def test_fit(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
trajnew = pt.iterload(fn('md1_prod.fit_to_first.Tc5b.x'),
fn('Tc5b.top'))
# make sure 0-th frame does not change
frame0 = traj[0]
trajnew[0]
frame1 = traj[1]
frame1new = trajnew[1]
# try do-fitting from Python
if rank == 0:
ref = traj[0]
ref_xyz = np.asarray(ref.xyz, dtype=np.float64)
else:
ref = None
ref_xyz = np.empty((n_atoms, 3), dtype=np.float64)
# broadcast ref_xyz to other cores from master
comm.Bcast([ref_xyz, MPI.DOUBLE])
if rank != 0:
# need to reconstruct ref
ref = Frame()
ref.append_xyz(ref_xyz)
_ref = ref.copy()
def rmsd_mpi(traj, _ref):
arr0 = pyca.calc_rmsd("@CA", traj, traj.top, _ref)
return arr0
arr0 = rmsd_mpi(traj, _ref)
if rank == 0:
data = np.empty(size * traj.n_frames, dtype=np.float64)
else:
data = None
data = comm.gather(arr0, root=0)