import argparse
parser = argparse.ArgumentParser(epilog=__doc__)
group = parser.add_mutually_exclusive_group()
group.add_argument('--ft', action='store_true', help='Use FT approximation')
group.add_argument('--fts', action='store_true', help='Use FTS approximation')
args = parser.parse_args()
if args.ft:
print("Using FT approximation method")
sd_method = "ft"
else:
print("Using FTS approximation method")
sd_method = "fts"
espressomd.assert_features("STOKESIAN_DYNAMICS")
system = espressomd.System(box_l=[10, 10, 10])
system.time_step = 1.5
system.cell_system.skin = 0.4
system.periodicity = [False, False, False]
system.integrator.set_stokesian_dynamics(viscosity=1.0,
radii={0: 1.0},
approximation_method=sd_method)
system.part.add(pos=[-5, 0, 0], rotation=[1, 1, 1])
system.part.add(pos=[0, 0, 0], rotation=[1, 1, 1])
system.part.add(pos=[7, 0, 0], rotation=[1, 1, 1])
gravity = espressomd.constraints.Gravity(g=[0, -1, 0])
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
Client part of the Gibbs ensemble simulation. This script handles the
simulation boxes and communicates the energies to the host. The Monte-Carlo
part of the simulation is done by the :file:`gibbs_ensemble_socket.py` script.
"""
import espressomd
import socket
import numpy as np
import pickle
import struct
import argparse
espressomd.assert_features("LENNARD_JONES")
seed = None
init_box_l = None
particle_number = None
lj_epsilon = None
lj_sigma = None
lj_cutoff = None
lj_shift = None
HOST = 'localhost'
PORT = 31415
# Message identifiers
MSG_START = 0
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import espressomd
from espressomd import assert_features, electrostatics, electrostatic_extensions
from espressomd.shapes import Wall
from espressomd.minimize_energy import steepest_descent
from espressomd import visualization_opengl
import numpy
from threading import Thread
assert_features(["ELECTROSTATICS", "MASS", "LENNARD_JONES"])
system = espressomd.System(box_l=[1.0, 1.0, 1.0])
numpy.random.seed(seed=42)
print("\n--->Setup system")
# System parameters
n_part = 1000
n_ionpairs = n_part / 2
density = 1.1138
time_step = 0.001823
temp = 1198.3
gamma = 50
#l_bjerrum = 0.885^2 * e^2/(4*pi*epsilon_0*k_B*T)
l_bjerrum = 130878.0 / temp
################################################################################
# #
# Active Matter: Swimmer Flow Field Tutorial #
# #
##########################################################################
from __future__ import print_function
import numpy as np
import os
import sys
import espressomd
from espressomd import assert_features, lb
assert_features(["ENGINE", "LB_GPU", "MASS", "ROTATION", "ROTATIONAL_INERTIA"])
# Read in the hydrodynamic type (pusher/puller) and position
if len(sys.argv) != 3:
print("Usage:", sys.argv[0], "<type> <pos>")
exit()
mode = sys.argv[1]
pos = float(sys.argv[2])
##########################################################################
outdir = "./RESULTS_FLOW_FIELD/T_{}_P_{}/".format(mode, pos)
try:
os.makedirs(outdir)
# (at your option) any later version. # # ESPResSo is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. import logging import numpy as np logging.basicConfig(level=logging.INFO) import espressomd espressomd.assert_features(['LENNARD_JONES']) import espressomd.accumulators import espressomd.observables import espressomd.polymer # Setup constant TIME_STEP = 0.01 LOOPS = 5000 STEPS = 100 # System setup system = espressomd.System(box_l=[32.0, 32.0, 32.0]) system.cell_system.skin = 0.4 # Lennard-Jones interaction system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1.0,
################################################################################
# #
# Active Matter: Rectification System Setup #
# #
##########################################################################
from __future__ import print_function
from math import cos, pi, sin
import numpy as np
import os
import sys
import espressomd
espressomd.assert_features(["LB_GPU", "LB_BOUNDARIES_GPU"])
from espressomd import lb
from espressomd.lbboundaries import LBBoundary
from espressomd.shapes import Cylinder, Wall, HollowCone
# Setup constants
outdir = "./RESULTS_RECTIFICATION"
try:
os.makedirs(outdir)
except:
print("INFO: Directory \"{}\" exists".format(outdir))
# Setup the box (we pad the diameter to ensure that the LB boundaries
# and therefore the constraints, are away from the edge of the box)
# ESPResSo is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ Demonstrates the construction of a rigid object by means of the VIRTUAL_SITES_RELATIVE feature. """ from __future__ import print_function import espressomd espressomd.assert_features(["VIRTUAL_SITES_RELATIVE"]) from espressomd import thermostat from espressomd import integrate from espressomd.virtual_sites import VirtualSitesRelative import numpy as np required_features = ["VIRTUAL_SITES_RELATIVE", "MASS", "ROTATIONAL_INERTIA"] espressomd.assert_features(required_features) box_l = 100 system = espressomd.System(box_l=[box_l, box_l, box_l]) system.set_random_state_PRNG() system.seed = system.cell_system.get_state()['n_nodes'] * [1234] system.time_step = 0.01
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
################################################################################
# #
# Active Matter: Swimmer Flow Field Tutorial #
# #
##########################################################################
import numpy as np
import os
import sys
import espressomd
from espressomd import assert_features, lb
assert_features(["ENGINE", "CUDA", "MASS", "ROTATION", "ROTATIONAL_INERTIA"])
# Read in the hydrodynamic type (pusher/puller) and position
if len(sys.argv) != 3:
print("Usage:", sys.argv[0], "<type> <pos>")
exit()
mode = sys.argv[1]
pos = float(sys.argv[2])
##########################################################################
outdir = "./RESULTS_FLOW_FIELD/T_{}_P_{}/".format(mode, pos)
try:
os.makedirs(outdir)
except:
# #
##########################################################################
from __future__ import print_function
from math import cos, pi, sin
import numpy as np
import os
import sys
import espressomd
from espressomd import assert_features
from espressomd.shapes import Cylinder, Wall, HollowCone
assert_features(["ENGINE", "CONSTRAINTS", "LENNARD_JONES", "ROTATION", "MASS"])
# Quaternion procedure
def a2quat(phi, theta):
q1w = cos(theta / 2.0)
q1x = 0
q1y = sin(theta / 2.0)
q1z = 0
q2w = cos(phi / 2.0)
q2x = 0
q2y = 0
q2z = sin(phi / 2.0)
phase diagram differ from the long range uncut LJ-potential. The phase diagram
of the used potential can be found in 'B. Smit, J. Chem. Phys. 96 (11), 1992,
Phase diagrams of Lennard-Jones fluids'.
"""
import socket
import numpy as np
import pickle
import subprocess
import struct
import random
import matplotlib.pyplot as plt
import argparse
from espressomd import assert_features
assert_features("LENNARD_JONES")
parser = argparse.ArgumentParser()
parser.add_argument('-s', '--seed', type=int, nargs=1)
parser.add_argument('-S', '--steps', type=int, nargs=1)
parser.add_argument('-w', '--warm_up_steps', type=int, nargs=1)
parser.add_argument('-E', '--espresso-executable', nargs=1)
parser.add_argument('-C', '--client-script', nargs=1)
parser.add_argument('-n', '--number-of-particles', type=int, nargs=1)
parser.add_argument('-l', '--box-length', type=float, nargs=1)
parser.add_argument('-T', '--temperature', type=float, nargs=1)
args = parser.parse_args()
# system parameters
seed = None
# Active Matter: Enhanced Diffusion Tutorial
#
##########################################################################
import numpy as np
import os
import sys
import argparse
import time
import espressomd
from espressomd import assert_features
from espressomd.observables import ParticlePositions, ParticleVelocities, ParticleAngularVelocities
from espressomd.accumulators import Correlator
espressomd.assert_features(
["ENGINE", "ROTATION", "MASS", "ROTATIONAL_INERTIA"])
# create an output folder
outdir = "./RESULTS_ENHANCED_DIFFUSION/"
os.makedirs(outdir, exist_ok=True)
##########################################################################
# Read in the active velocity from the command prompt
parser = argparse.ArgumentParser()
parser.add_argument('vel', type=float, help='Velocity of active particle.')
args = parser.parse_args()
vel = args.vel
import random
import os
import numpy as np
from itertools import product
from espressomd.io.writer import vtf
from espressomd.virtual_sites import VirtualSitesRelative
from espressomd import lb
from espressomd import interactions
import espressomd
espressomd.assert_features([
"ROTATION", "ROTATIONAL_INERTIA", "EXTERNAL_FORCES", "MASS",
"VIRTUAL_SITES_RELATIVE", "LENNARD_JONES"
])
# System parameters
#############################################################
box_l = 40. # size of the simulation box
skin = 3 # Skin parameter for the Verlet lists
time_step = 0.001
eq_tstep = 0.001
n_cycle = 1000 # 100
integ_steps = 150
# Interaction parameters (Lennard-Jones for raspberry)
#############################################################
# the subscript c is for colloid and s is for salt (also used for the surface beads)
agrid = 1
eps_ss = 1 # LJ epsilon between the colloid's surface particles.
# the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # ESPResSo is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. from __future__ import print_function import math import numpy as np import espressomd espressomd.assert_features(["MASS"]) import espressomd.shapes from espressomd.visualization_opengl import openGLLive box_l = 50 system = espressomd.System(box_l=[box_l, 15, box_l]) system.set_random_state_PRNG() #system.seed = system.cell_system.get_state()['n_nodes'] * [1234] np.random.seed(seed=system.seed) yoff = 3 # cup cup_top_circ = 21 cup_bot_circ = 15 cup_height = 6
##########################################################################
from __future__ import print_function
import numpy as np
import os
import sys
import time
import espressomd
from espressomd import assert_features
from espressomd.observables import ParticlePositions, ParticleVelocities, ParticleAngularVelocities
from espressomd.accumulators import Correlator
required_features = ["ENGINE", "ROTATION"]
assert_features(required_features)
# create an output folder
outdir = "./RESULTS_ENHANCED_DIFFUSION/"
try:
os.makedirs(outdir)
except:
print("INFO: Directory \"{}\" exists".format(outdir))
##########################################################################
# Read in the active velocity from the command prompt
if len(sys.argv) != 2:
print("Usage:", sys.argv[0], "<vel> (0 <= vel < 10.0)")
exit()
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import espressomd
from espressomd import assert_features, electrostatics
from espressomd.observables import RDF
from espressomd.accumulators import MeanVarianceCalculator
import numpy
assert_features(["ELECTROSTATICS", "WCA"])
print("\n--->Setup system")
# System parameters
n_part = 200
n_ionpairs = n_part / 2
density = 0.5
time_step = 0.01
temp = 1.0
gamma = 1.0
l_bjerrum = 7.0
num_steps_equilibration = 1000
num_configs = 100
integ_steps_per_config = 1000
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
This sample sets up a polymer and tests the available cell systems.
"""
from __future__ import print_function
import time
import numpy as np
import espressomd
espressomd.assert_features(["LENNARD_JONES"])
from espressomd import polymer
from espressomd import interactions
def profile():
cs.skin = skin
ti = time.time()
system.integrator.run(n_steps)
tf = time.time()
print("\t with skin={} ran {:d} steps in {:f} seconds. steps/sec:{:f} ".
format(skin, n_steps, tf - ti, n_steps * 1. / (tf - ti)))
system = espressomd.System(box_l=[100, 100, 100])
system.set_random_state_PRNG()
# Active Matter: Rectification System Setup #
# #
################################################################################
from __future__ import print_function
from math import cos, pi, sin
import numpy as np
import os
import sys
from espressomd import assert_features, lb
from espressomd.lbboundaries import LBBoundary
from espressomd.shapes import Cylinder, Wall, HollowCone
assert_features(["LB_GPU", "LB_BOUNDARIES_GPU"])
# Setup constants
outdir = "./RESULTS_RECTIFICATION_GEOMETRY/"
try:
os.makedirs(outdir)
except:
print("INFO: Directory \"{}\" exists".format(outdir))
# Setup the box (we pad the diameter to ensure that the LB boundaries
# and therefore the constraints, are away from the edge of the box)
length = 100
diameter = 20
dt = 0.01
# the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # ESPResSo is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # """ This sample sets up a diamond-structured polymer network. """ import espressomd espressomd.assert_features(["WCA"]) from espressomd import thermostat from espressomd import interactions from espressomd import diamond from espressomd.io.writer import vtf # pylint: disable=import-error import numpy as np # System parameters ############################################################# system = espressomd.System(box_l=[1.0, 1.0, 1.0]) system.set_random_state_PRNG() system.seed = system.cell_system.get_state()['n_nodes'] * [1234] np.seed = system.seed system.time_step = 0.01
# Active Matter: Enhanced Diffusion Tutorial #
# #
################################################################################
from __future__ import print_function
import numpy as np
import os
import sys
import time
from espressomd import assert_features
from espressomd.observables import ParticlePositions, ParticleVelocities, ParticleAngularVelocities
from espressomd.correlators import Correlator
assert_features(["ENGINE", "ROTATION"])
# create an output folder
outdir = "./RESULTS_ENHANCED_DIFFUSION/"
try:
os.makedirs(outdir)
except:
print("INFO: Directory \"{}\" exists".format(outdir))
################################################################################
# Read in the active velocity from the command prompt
if len(sys.argv) != 2:
print("Usage:", sys.argv[0], "<vel> (0 <= vel < 10.0)")
