Python compute_trajectoryの例

コード例 #1

ファイル: full_test.py プロジェクト: suttond/GeometricMD

def butane_single_process():

    try:
        start_point = read('test_files/x0.xyz')
        start_point.set_calculator(EMT())
        end_point = read('test_files/xN.xyz')

        traj = Curve(start_point, end_point, 12, 1E+03)

        compute_trajectory(traj, 9, 1E+03, 0.003, 'Butane', {'processes': 1})

        return True

    except:

        return False

コード例 #2

ファイル: butane_single_process.py プロジェクト: suttond/GeometricMD

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
from ase.io import read
from ase.calculators.emt import EMT


start_point = read('x0.xyz')
start_point.set_calculator(EMT())
end_point = read('xN.xyz')

traj = Curve(start_point, end_point, 12, 1E+03)

compute_trajectory(traj, 9, 1E+03, 0.001, 'Butane', {'processes': 1})

コード例 #3

ファイル: single_process2.py プロジェクト: Yuanpengli/GeometricMD_without_molecular

__author__ = 'liyuanpeng'

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
import numpy as np
import time
start = time.clock()

start_point = np.asarray([2.0,5.5,3.3])
end_point = np.asarray([100.0,99.0,98.0])
global_number_node=30
traj = Curve(start_point, end_point, global_number_node)
tol=10

compute_trajectory(traj, 9, tol, {'processes': 1})

print traj.points

f=open("geodesic.txt",'w')
for i in range(global_number_node):
    t=traj.points[i]
    f.write(str(t)+ "\n")
f.close()

spent_time= (time.clock()-start)

print spent_time

コード例 #4

ファイル: single_process.py プロジェクト: Yuanpengli/geometricmd_quasi_potential

__author__ = 'liyuanpeng'
from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
from ase.io import read
from ase.calculators.emt import EMT


start_point = read('x0.xyz')
start_point.set_calculator(EMT())
end_point = read('xN.xyz')

traj = Curve(start_point, end_point, 12, 1E+03)

compute_trajectory(traj, 9, 0.001, {'processes': 1})

コード例 #5

ファイル: multiple_process.py プロジェクト: Yuanpengli/GeometricMD_without_molecular

__author__ = "liyuanpeng"

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
import numpy as np
import time
from multiprocessing import cpu_count

start = time.clock()

start_point = np.asarray([2.0, 5.5, 3.3])
end_point = np.asarray([100.0, 99.0, 98.0])
global_number_node = 30
traj = Curve(start_point, end_point, global_number_node)
tol = 10

compute_trajectory(traj, 9, tol, {"processes": (cpu_count() - 1)})

print traj.points

f = open("geodesic.txt", "w")
for i in range(global_number_node):
    t = traj.points[i]
    f.write(str(t) + "\n")
f.close()

spent_time = time.clock() - start

print spent_time

コード例 #6

ファイル: butane_multi_process.py プロジェクト: suttond/GeometricMD

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
from ase.io import read
from ase.calculators.emt import EMT
from multiprocessing import cpu_count

start_point = read('x0.xyz')
start_point.set_calculator(EMT())
end_point = read('xN.xyz')

traj = Curve(start_point, end_point, 12, 1E+03)

compute_trajectory(traj, 9, 1E+03, 0.001, 'Butane', {'processes': (cpu_count()-1)})

コード例 #7

__author__ = 'liyuanpeng'

from geometricmd.curve_shorten import compute_trajectory
from geometricmd.geometry import Curve
import numpy as np
import time
start = time.clock()

start_point = np.asarray([2.0, 5.5, 3.3])
end_point = np.asarray([100.0, 99.0, 98.0])
global_number_node = 30
traj = Curve(start_point, end_point, global_number_node)
tol = 10

compute_trajectory(traj, 9, tol, {'processes': 1})

print traj.points

f = open("geodesic.txt", 'w')
for i in range(global_number_node):
    t = traj.points[i]
    f.write(str(t) + "\n")
f.close()

spent_time = (time.clock() - start)

print spent_time