import numpy as np
import time
import sys
import os
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 90.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=10)
dmp = 100
scft_calc = True
t1 = time.time()
box.interactions.newType("a", 0.5, (1.0, 1.0, 1.5))
box.interactions.newType("b", 0.55, (1.0, 0.5, 1.5), ('a,b', (0.1, 0.2, 1.5)))
if scft_calc == True:
box.meanfield.parameters(
"test",
[10, 10, 10],
25.0,
'cubic',
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
scft = False
print("NANOPOLY SIMULATION")
box_size = 80.0
cellnums = 70
t0 = time.time()
box = PolyLattice(box_size, cellnums)
t1 = time.time()
box.interactions.newType("a", 0.5, (0.1, 1.0, 1.5, (1, 1.0, 0.1)))
box.interactions.newType("b", 1.0, (0.1, 0.5, 1.5, (1, 1.0, 0.1)),
('a,b', (0.1, 0.2, 1.5, (1, 1.0, 0.1))))
b_frac = 0.8
a_frac = (1 - b_frac) / 2
if scft == True:
box.meanfield.parameters(
"test",
[int(0.5 * cellnums),
int(0.5 * cellnums),
import time
import sys
sys.path.insert(0, '../../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check, Percolation
print("NANOPOLY SIMULATION")
pair_cutoff = 1.5
pair_sigma = 0.3 # lennard jones potential length, pair potential information
pair_epsilon = 0.05
box_size = 4.0
t0 = time.time()
box = PolyLattice(box_size, pair_cutoff, pair_sigma, pair_epsilon)
t1 = time.time()
print(f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}")
# types of atom in box-----------------------------------------------------------------------
# key = types, entry = masses
types={"a" : 1.0,
"b" : 1.0,
"c" : 1.0}
# RANDOM WALKS ------------------------------------------------------------------------------
nums = 10 # number of random walks
size = 20 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.0
rw_epsilon = 0.05
rw_sigma = 0.4
import random
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
double = False
print("NANOPOLY SIMULATION")
box_size = 17.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=12)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 1.0, (1.0, 0.2, 1.5))
box.interactions.newType("b", 0.5, (1.0, 1.0, 1.5), ('a,b', (1.0, 0.2, 1.5)))
size = 100 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.5
rw_epsilon = 1.0
import numpy as np
import time
import random
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 17.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=12)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 1.0, (1.0, 0.2, 1.5))
box.interactions.newType("b", 0.5, (1.0, 1.0, 1.5), ('a,b', (1.0, 0.2, 1.5)))
size = 100 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.5
rw_epsilon = 1.0
# Author: Aravinthen Rajkumar
# Description: recreation of parker-rottler simulation
import numpy as np
import time
import sys
sys.path.insert(0, '../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check
print("NANOPOLY SIMULATION")
box_size = 200.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=100)
t1 = time.time()
simname = "parker_rottler"
dmp = 1000
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Order of properties: Sigma, energy, cutoff
box.interactions.newType("a", 1.0, (1.0, 1.0, 1.5))
box.interactions.newType("b", 0.5, (1.0, 0.5, 1.5), ('a,b', (1.0, 0.2, 1.5)))
# following values determine the bonding of the random walks
num_walks = 600
# Program Name: interactions.py
# Author: Aravinthen Rajkumar
# Description: Example of the interactions class
import numpy as np
import time
import sys
sys.path.insert(0, '../../../main')
from mdsim import MDSim
from poly import PolyLattice
# polylattice object
box = PolyLattice(50, 30)
dmp = 100
def print_type():
print(box.interactions.types)
print(box.interactions.type_matrix)
print(box.interactions.sigma_matrix)
print(box.interactions.energy_matrix)
print(box.interactions.cutoff_matrix)
print(box.interactions.n_matrix)
print(box.interactions.alpha_matrix)
print(box.interactions.lmbda_matrix)
box.interactions.newType("mainbead", 0.5,
(0.1, 0.2, 1.5))
box.interactions.newType("subbead", 1.0,
(0.1, 0.5, 1.5),
('mainbead,subbead', (0.1, 0.2, 1.5)))
import numpy as np
import time
import sys
sys.path.insert(0, '../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 10.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=10)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 0.5, (0.2, 2, 1))
box.interactions.newType("b", 1.0, (0.3, 3, 1), ('a,b', (0.3, 4, 2)))
box.interactions.newType("c", 1.0, (0.3, 3, 1), ('c,a', (0.2, 4, 3)),
('c,b', (0.2, 4, 2)))
box.interactions.newType("d", 1.0, (0.24, 3, 1), ('d,a', (0.1, 4, 2)),
import numpy as np
import time
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 70.0
t0 = time.time()
cellnums = 70
box = PolyLattice(box_size, cellnums)
dmp = 100
scft_calc = True
t1 = time.time()
box.interactions.newType("a", 0.5, (0.0, 1.0, 1.5))
box.interactions.newType("b", 0.55, (0.0, 0.5, 1.5), ('a,b', (0.0, 0.2, 1.5)))
if scft_calc == True:
box.meanfield.parameters(f"test", [35, 35, 35],
25.0,
'cubic',
1.0e-2,
'I m -3 m', [[("a", 1.0, 0.25),
("b", 1.0, 0.75)]],
cell_param=1.923202,
cl_values = [100]
number_of_samples = 10
for i in cl_values:
for sample in range(number_of_samples):
print(
"--------------------------------------------------------------------------------------"
)
print(
f" MOLECULAR DYNAMICS SIMULATION WITH {i} CROSSLINKERS"
)
print(f" SAMPLE NUMBER: {sample}")
print(
"--------------------------------------------------------------------------------------"
)
box = PolyLattice(celllen, cellnums, pair_cutoff, pair_sigma,
pair_epsilon)
t0 = time.time()
for j in range(num_walks):
current_walks = box.num_walks
while True:
try:
box.random_walk(j,
size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_types=types)
if box.num_walks == current_walks + 1:
print(
f"Simulation {i}_{sample}: Random walk {j} complete"
# Program Name: interactions.py
# Author: Aravinthen Rajkumar
# Description: Example of the interactions class
import numpy as np
import time
import sys
sys.path.insert(0, '../../../main')
from mdsim import MDSim
from poly import PolyLattice
# polylattice object
box = PolyLattice(22.0, 40)
dmp = 100
def print_type():
print(box.interactions.types)
print(box.interactions.type_matrix)
print(box.interactions.sigma_matrix)
print(box.interactions.energy_matrix)
print(box.interactions.cutoff_matrix)
print(box.interactions.n_matrix)
print(box.interactions.alpha_matrix)
print(box.interactions.lmbda_matrix)
box.interactions.newType("mainbead", 0.5, (0.1, 0.2, 1.5, (1, 1.0, 0.3)))
box.interactions.newType("subbead", 1.0, (0.1, 0.5, 1.5, (1, 1.0, 0.3)),
('mainbead,subbead', (0.1, 0.2, 1.5, (1, 1.0, 0.3))))
# Author: Aravinthen Rajkumar
# Description: nanopoly configuration that runs random walks and unbonded crosslink beads
import numpy as np
import time
import sys
sys.path.insert(0, '../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check
print("NANOPOLY SIMULATION")
box_size = 10.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=10)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 0.5, (0.2, 2, 1))
box.interactions.newType("b", 1.0, (0.3, 3, 1), ('a,b', (0.3, 4, 2)))
box.interactions.newType("c", 1.0, (0.3, 3, 1), ('c,a', (0.2, 4, 3)),
('c,b', (0.2, 4, 2)))
box.interactions.newType("d", 1.0, (0.24, 3, 1), ('d,a', (0.1, 4, 2)),
import numpy as np
import time
import random
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 10.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=5)
t1 = time.time()
print(f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}")
# Atom interactions
# TYPES
box.interactions.newType("a", 1.0,
(1.0, 0.2, 1.5))
box.interactions.newType("b", 0.5,
(1.0, 1.0, 1.5),
('a,b', (1.0, 0.2, 1.5)))
numwalks = 12
size = 30 # size of the chain
rw_kval = 30.0
import numpy as np
import time
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 50.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=40)
t1 = time.time()
simname = "walks_example"
dmp = 100
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
#----------------------------------------------------------------------------------------
# INTERACTION ASSIGNMENTS
#----------------------------------------------------------------------------------------
# Order of properties: Sigma, energy, cutoff
box.interactions.newType("a", 1.0, (0.01, 0.2, 1.5))
box.interactions.newType("b", 0.5, (0.01, 1.0, 1.5), ('a,b', (0.01, 0.2, 1.5)))
import time
import sys
sys.path.insert(0, '../../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check, Percolation
print("NANOPOLY SIMULATION")
pair_cutoff = 1.5
pair_sigma = 0.3 # lennard jones potential length, pair potential information
pair_epsilon = 0.05
box_size = 4.0
t0 = time.time()
box = PolyLattice(box_size, pair_cutoff, pair_sigma, pair_epsilon)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# types of atom in box-----------------------------------------------------------------------
# key = types, entry = masses
types = {"a": 1.0, "b": 1.0, "c": 1.0}
# RANDOM WALKS ------------------------------------------------------------------------------
nums = 10 # number of random walks
size = 20 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.0
rw_epsilon = 0.05
# Description: nanopoly configuration that just runs the random walks
import numpy as np
import time
import random
import sys
sys.path.insert(0, '../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check
print("NANOPOLY SIMULATION")
box_size = 10.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=8)
t1 = time.time()
simname = "condensed_relax2"
dmp = 100
print(f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}")
# Order of properties: Sigma, energy, cutoff
box.interactions.newType("a", 1.0,
(1.0, 1.0, 1.5))
box.interactions.newType("b", 0.5,
(1.0, 0.5, 1.5),
('a,b', (1.0, 0.2, 1.5)))
# following values determine the bonding of the random walks
# Author: Aravinthen Rajkumar
# Description: test of the chain grafting mechanism
import numpy as np
import time
import sys
sys.path.insert(0, '../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check
print("NANOPOLY SIMULATION")
box_size = 10.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=10)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 1.0, (0.3, 0.01, 1.5))
box.interactions.newType("b", 0.5, (0.3, 0.15, 1.5), ('a,b', (0.3, 0.01, 1.5)))
box.interactions.newType("c", 0.3, (0.2, 0.1, 1.5), ('c,a', (0.3, 0.01, 1.5)),
('c,b', (0.2, 0.01, 1.5)))
# following values determine the bonding of the random walks
import time
import sys
sys.path.insert(0, '../../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Check, Percolation
print("NANOPOLY SIMULATION")
pair_cutoff = 1.5
pair_sigma = 0.3 # lennard jones potential length, pair potential information
pair_epsilon = 0.05
box_size = 5.0
t0 = time.time()
box = PolyLattice(box_size, pair_cutoff, pair_sigma, pair_epsilon)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Parameters ------------------------------------------------------------------------------
# Random walks
nums = 20 # number of random walks
size = 10 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.0
rw_epsilon = 0.05
rw_sigma = 0.4
# Crosslinks
# Program Name: interactions.py
# Author: Aravinthen Rajkumar
# Description: Example of the interactions class
import numpy as np
import time
import sys
sys.path.insert(0, '../../main')
from simulation import Simulation
from poly import PolyLattice
# polylattice object
box = PolyLattice(20.0, 15)
dmp = 0
def print_type():
print(box.interactions.types)
print(box.interactions.type_matrix)
print(box.interactions.sigma_matrix)
print(box.interactions.energy_matrix)
print(box.interactions.cutoff_matrix)
print(box.interactions.n_matrix)
print(box.interactions.alpha_matrix)
print(box.interactions.lmbda_matrix)
box.interactions.newType("mainbead", 0.5, (0.1, 0.2, 1.5, (1, 1.0, 0.1)))
box.interactions.newType("subbead", 1.0, (0.1, 0.5, 1.5, (1, 1.0, 0.1)),
('mainbead,subbead', (0.1, 0.2, 1.5, (1, 1.0, 0.1))))
import numpy as np
import time
import sys
sys.path.insert(0, '../main')
from simulation import Simulation
from poly import PolyLattice
from analysis import Percolation
print("NANOPOLY SIMULATION")
pair_cutoff = 1.5
pair_sigma = 0.3 # lennard jones potential length, pair potential information
pair_epsilon = 0.05
box_size = 2.0
t0 = time.time()
box = PolyLattice(box_size, pair_cutoff, pair_sigma, pair_epsilon)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# types of atom in box-----------------------------------------------------------------------
# key = types, entry = masses
types = {1: 1.0, 2: 1.0, 3: 1.0}
nums = 2 # number of random walks
size = 10 # size of the chain
rw_kval = 30.0
rw_cutoff = 3.5
rw_epsilon = 0.05
import numpy as np
import time
import sys
import os
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 50.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=15)
dmp = 100
scft_calc = False
t1 = time.time()
box.interactions.newType("a", 0.5, (1.0, 1.0, 1.5))
box.interactions.newType("b", 0.55, (1.0, 0.5, 1.5), ('a,b', (0.1, 0.2, 1.5)))
if scft_calc == True:
box.meanfield.parameters(
"test",
[15, 15, 15],
25.0,
'cubic',
import sys
import os
import shutil
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 90.0
cellnums = 80
t0 = time.time()
box = PolyLattice(box_size, cellnums)
dmp = 1000
scft_calc = True
t1 = time.time()
print(f"Box initialised. Time taken: {t1-t0} seconds.")
box.interactions.newType("a", 0.5, (1.0, 1.0, 1.5))
box.interactions.newType("b", 0.51, (1.0, 0.5, 1.5), ('a,b', (1.0, 0.2, 1.5)))
bsize = 0.8
asize = (1 - bsize) / 2
t0 = time.time()
if scft_calc == True:
import numpy as np
import time
import random
import sys
sys.path.insert(0, '../../main')
from mdsim import MDSim
from poly import PolyLattice
from analysis import Check
from meanfield import MeanField
print("NANOPOLY SIMULATION")
box_size = 5.0
t0 = time.time()
box = PolyLattice(box_size, cellnums=3)
t1 = time.time()
print(
f"Box generated, with {len(box.Cells)} cells in total. Time taken: {t1 - t0}"
)
# Atom interactions
# TYPES
box.interactions.newType("a", 1.0, (1.0, 0.2, 1.5))
box.interactions.newType("b", 0.5, (1.0, 1.0, 1.5), ('a,b', (1.0, 0.2, 1.5)))
size = 20 # size of the chain
rw_kval = 30.0
rw_cutoff = 1.5
rw_epsilon = 1.0