def read_and_calc(self, target):
uobj = UDFManager(target)
time = []
g = []
temp = []
# データ読み込み
prev_g = 0.
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
time.append(uobj.get("Time"))
temp.append(uobj.get('Statistics_Data.Temperature.Batch_Average'))
#
if self.mode == 'elong':
stress = uobj.get("Statistics_Data.Stress.Total.Batch_Average")
tmp_g = (stress[2] -
(stress[0] + stress[1]) / 2.) / (self.deform**2 -
1 / self.deform)
elif self.mode == 'shear':
tmp_stress = uobj.get(
'Statistics_Data.Stress.Total.Batch_Average.xy'
) - self.ave_xy
tmp_g = tmp_stress / self.deform
if tmp_g <= 0:
tmp_g = prev_g
g.append(tmp_g)
prev_g = tmp_g
# smoothing
mod_g = signal.savgol_filter(g, 11, 3)
# pack up
data = np.stack([time, g, temp], 1)
data_mod = np.stack([time, mod_g, temp], 1)
return data, data_mod
def read_and_calc(self, target, c_strain):
uobj = UDFManager(target)
time = []
temp = []
stress = []
strain = []
# データ読み込み
prev_stress = 0.
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
time.append(uobj.get("Time"))
temp.append(uobj.get('Statistics_Data.Temperature.Batch_Average'))
#
if self.mode == 'elong':
strs = uobj.get("Statistics_Data.Stress.Total.Batch_Average")
tmp_stress = strs[2] - (strs[0] + strs[1]) / 2.
elif self.mode == 'shear':
tmp_stress = uobj.get(
'Statistics_Data.Stress.Total.Batch_Average.xy'
) #- self.ave_xy
if tmp_stress <= 0:
tmp_stress = prev_stress
#
stress.append(tmp_stress)
strain.append(c_strain)
prev_stress = tmp_stress
#
stress_part = np.stack([time, stress, temp], 1)
strain_part = np.stack([time, strain, temp], 1)
return stress_part, strain_part
def make_base_udf(self, t_udf):
if self.calc_mode == 'cycle':
lamd_str = str(self.cycle_lamd).replace('.', '_')
rate_str = str("{0:4.0e}".format(self.rate)).replace('.', '_')
calc_dir = 'Hysteresis_' + self.calc_mode + '_rate_' + rate_str + '_lambda_' + lamd_str
if os.path.exists(calc_dir):
print("Use existing dir of ", calc_dir)
else:
print("Make new dir of ", calc_dir)
os.makedirs(calc_dir)
#
base = os.path.join(calc_dir, self.base_udf)
print("Readin file = ", t_udf)
udf = UDFManager(t_udf)
self.mod_base_udf(udf)
udf.write(base)
return base, calc_dir
def calc_init(self, target):
uobj = UDFManager(target)
uobj.jump(0)
#
cell = uobj.get("Structure.Unit_Cell.Cell_Size")
area_init = cell[0] * cell[1]
z_init = cell[2]
#
uobj.jump(1)
vol = uobj.get("Statistics_Data.Volume.Batch_Average")
return area_init, z_init
def read_and_calc(target, c_strain, mode):
# low = 1e-5
uobj = UDFManager(target)
time = []
temp = []
stress = []
strain = []
gt = []
# データ読み込み
prev_stress = 0.
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
time.append(uobj.get("Time"))
temp.append(uobj.get('Statistics_Data.Temperature.Batch_Average'))
#
if mode == 'elong':
strs = uobj.get("Statistics_Data.Stress.Total.Batch_Average")
tmp_stress = strs[2] - (strs[0] + strs[1]) / 2.
if tmp_stress <= 0.05 * prev_stress:
tmp_stress = 4 * prev_stress / 5
if tmp_stress < 1e-4:
tmp_stress = 1e-4
tmp_gt = tmp_stress / c_strain / 3.
elif mode == 'shear':
tmp_stress = uobj.get(
'Statistics_Data.Stress.Total.Batch_Average.xy'
) #- self.ave_xy
if tmp_stress <= 0.05 * prev_stress:
tmp_stress = 4 * prev_stress / 5
if tmp_stress < 1e-4:
tmp_stress = 1e-4
tmp_gt = tmp_stress / c_strain
# tmp_stress = low
#
stress.append(tmp_stress)
strain.append(c_strain)
gt.append(tmp_gt)
prev_stress = tmp_stress
#
mod_stress = signal.savgol_filter(stress, 5, 3)
stress_part = np.stack([time, mod_stress, temp], 1)
strain_part = np.stack([time, strain, temp], 1)
gt_part = np.stack([time, gt, temp], 1)
return stress_part, strain_part, gt_part
def make_base_udf(self, t_udf):
if os.path.exists(self.calc_dir):
print("Use existing dir of ", self.calc_dir)
else:
print("Make new dir of ", self.calc_dir)
os.makedirs(self.calc_dir)
#
base = os.path.join(self.calc_dir, self.base_udf)
print("Readin file = ", t_udf)
u = UDFManager(t_udf)
u.jump(1)
u.eraseRecord(record_pos=-999,record_num=-999)
u.write(base)
return base
def read_and_calc(target):
uobj = UDFManager(target)
data = []
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
stress = uobj.get('Statistics_Data.Stress.Total.Batch_Average.xy')
#
strain = uobj.get('Structure.Unit_Cell.Shear_Strain')
#
data.append([strain, stress])
return data
def make_base_udf(self, t_udf):
if os.path.exists(self.calc_dir):
print("Use existing dir of ", self.calc_dir)
else:
print("Make new dir of ", self.calc_dir)
os.makedirs(self.calc_dir)
#
base = os.path.join(self.calc_dir, self.base_udf)
print("Readin file = ", t_udf)
u = UDFManager(t_udf)
# u.jump(u.totalRecord() - 1)
# ave_xy = u.get('Statistics_Data.Stress.Total.Total_Average.xy')
u.eraseRecord(0, u.totalRecord() - 2)
u.write(base)
return base
def mod_udf(self, udf_in, rate):
if self.def_mode == 'elong':
time_1_step = int(self.res/self.time_div/rate)
time_total = time_1_step*(self.deform_max - 1)/self.res
elif self.def_mode == 'shear':
deform_time = self.deform_max/rate
time_total = round(deform_time/self.time_div)
time_1_step = int(self.res/self.time_div/rate)
#
u = UDFManager(udf_in)
# goto global data
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(self.time_div, p + 'Time.delta_T')
u.put(time_total, p + 'Time.Total_Steps')
u.put(time_1_step, p + 'Time.Output_Interval_Steps')
u.put(1.0, p + 'Temperature.Temperature')
u.put(0, p + 'Temperature.Interval_of_Scale_Temp')
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
if self.def_mode == 'elong':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
elif self.def_mode == 'shear':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Lees_Edwards', p + 'Method')
u.put('Steady', p + 'Lees_Edwards.Method')
u.put(rate, p + 'Lees_Edwards.Steady.Shear_Rate')
# Output_Flags
u.put([1, 1, 1], 'Simulation_Conditions.Output_Flags.Structure')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put(['', -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put(['', -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(udf_in)
return
import math
from numpy import *
from UDFManager import *
uobj=UDFManager("./output.udf")
Ns=len(uobj.get("object_type.spherical_particle.Particle_spec[]"))
Nc=uobj.get("object_type.spherical_particle.Particle_spec[].Particle_number")
N1=0
for i in range(Ns):
N1=N1+Nc[i]
print Ns, Nc, N1
nx=uobj.get("mesh.NPX")
ny=uobj.get("mesh.NPY")
nz=uobj.get("mesh.NPZ")
lx=2**nx
ly=2**ny
lz=2**nz
pi2=3.14159265358979*2.0
dia=uobj.get("A")*2.0
print "#",N1,lx,ly,lz,dia
f_sk = open('sk.dat','w')
mxk=100000
k01=arange(0,mxk)
k02=arange(0,mxk)
k03=arange(0,mxk)
n1 = 10
n2 = 10
delk = pi2/float(50)
nnk = 0
iz = 0
iy = 0
for ix in range(1, n1):
def mod_udf(self, uin, pre, direction, lamd):
time_1_step = round(self.resol/self.time_div/self.rate, -2)
time_total = round(time_1_step*(lamd - 1)/self.resol, -2)
#
udf = UDFManager(uin)
udf.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
udf.put(time_total, p + 'Time.Total_Steps')
udf.put(time_1_step, p + 'Time.Output_Interval_Steps')
if direction == 'backward':
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
srate = udf.get(p + 'Cell_Deformation.Simple_Elongation.Deformation_Speed.Speed')
udf.put(-1*srate, p + 'Cell_Deformation.Simple_Elongation.Deformation_Speed.Speed')
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
udf.put('Restart', p + 'Method')
udf.put([pre, -1, 1, 0], p + 'Restart')
#--- Write UDF ---
udf.write(uin)
return
def mod_udf(self, udf_in, rate):
time_1_step = int(self.res/self.time_div/rate)
time_total = time_1_step*(self.Lamd_max - 1)/self.res
#
u = UDFManager(udf_in)
# goto global data
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(self.time_div, p + 'Time.delta_T')
u.put(time_total, p + 'Time.Total_Steps')
u.put(time_1_step, p + 'Time.Output_Interval_Steps')
u.put(1.0, p + 'Temperature.Temperature')
u.put(0, p + 'Temperature.Interval_of_Scale_Temp')
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put([self.base_udf, -1, 1, 0], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(udf_in)
return
def read_and_calc(area_init, z_init, target):
uobj = UDFManager(target)
data = []
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
cell = uobj.get("Structure.Unit_Cell.Cell_Size")
#
stress = uobj.get("Statistics_Data.Stress.Total.Batch_Average")
t_stress = calc_stress(cell, stress, area_init)
#
bond_stress = uobj.get("Statistics_Data.Stress.Bond.Batch_Average")
bond = calc_stress(cell, bond_stress, area_init)
#
non_bond_stress = uobj.get(
"Statistics_Data.Stress.Non_Bond.Batch_Average")
non_bond = calc_stress(cell, non_bond_stress, area_init)
#
strain = uobj.get("Structure.Unit_Cell.Cell_Size.c") / z_init
#
temp = uobj.get("Statistics_Data.Temperature.Batch_Average")
#
data.append([strain, t_stress, non_bond, bond, temp])
return data
def step_elong(self, base, udf_in, time_temp):
u = UDFManager(base)
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(time_temp[0], p + 'Time.delta_T')
u.put(time_temp[1], p + 'Time.Total_Steps')
u.put(time_temp[2], p + 'Time.Output_Interval_Steps')
#
u.put(1.0, p + 'Temperature.Temperature')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
#
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(self.step_rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put([self.base_udf, -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(os.path.join(self.calc_dir, udf_in))
return
def step_deform(self, base, axis, udf_in, time_temp, target_dir):
u = UDFManager(base)
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(time_temp[0], p + 'Time.delta_T')
u.put(time_temp[1], p + 'Time.Total_Steps')
u.put(time_temp[2], p + 'Time.Output_Interval_Steps')
#
u.put(1.0, p + 'Temperature.Temperature')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
#
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
if self.mode == 'elong':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate',
p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(
self.step_rate, p +
'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
elif self.mode == 'shear':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Lees_Edwards', p + 'Method')
u.put('Steady', p + 'Lees_Edwards.Method')
u.put(self.step_rate, p + 'Lees_Edwards.Steady.Shear_Rate')
# Output_Flags
u.put([1, 1, 1], 'Simulation_Conditions.Output_Flags.Structure')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put(['', -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put(['', -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
# Rotate system
self.rotate_position(u, axis)
#--- Write UDF ---
u.write(os.path.join(target_dir, udf_in))
return
def read_step_stress(self, t_udf):
print("Readin file = ", t_udf)
area_init, z_init = self.calc_init(t_udf)
uobj = UDFManager(t_udf)
time = []
strain = []
g = []
stress = []
temp = []
# データ読み込み
prev_stress = 0.
prev_g = 0.
for rec in range(uobj.totalRecord()):
print("Reading Rec.=", rec)
uobj.jump(rec)
#
time.append(uobj.get("Time"))
if self.mode == 'elong':
tmp_strain = uobj.get(
"Structure.Unit_Cell.Cell_Size.c") / z_init
elif self.mode == 'shear':
tmp_strain = uobj.get('Structure.Unit_Cell.Shear_Strain')
strain.append(tmp_strain)
#
if rec == 0:
tmp_stress = prev_stress
tmp_g = prev_g
temp.append(1.)
else:
temp.append(
uobj.get('Statistics_Data.Temperature.Batch_Average'))
if self.mode == 'elong':
stress_list = uobj.get(
"Statistics_Data.Stress.Total.Batch_Average")
tmp_stress = stress_list[2] - (stress_list[0] +
stress_list[1]) / 2.
tmp_g = tmp_stress / (tmp_strain**2 - 1 / tmp_strain)
elif self.mode == 'shear':
tmp_stress = uobj.get(
'Statistics_Data.Stress.Total.Batch_Average.xy'
) - self.ave_xy
tmp_g = tmp_stress / tmp_strain
if tmp_stress <= 0:
tmp_stress = prev_stress
tmp_g = prev_g
stress.append(tmp_stress)
g.append(tmp_g)
#
prev_stress = tmp_stress
prev_g = tmp_g
#
mod_g = signal.savgol_filter(g, 11, 3)
#
gt_step_mod = np.stack([time, mod_g, temp], 1)
gt_step = np.stack([time, g, temp], 1)
ss_step = np.stack([strain, stress, temp], 1)
self.save_data(ss_step, 'ss_step.dat')
self.save_data(gt_step, 'gt_step.dat')
self.save_data(gt_step_mod, 'gt_step_mod.dat')
return gt_step, gt_step_mod
def eq_udf(self, template, read_udf, present_udf, time_temp):
u = UDFManager(os.path.join(self.calc_dir, template))
u.jump(-1)
#--- Simulation_Conditions ---
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(time_temp[0], p+'Time.delta_T')
u.put(time_temp[1], p+'Time.Total_Steps')
u.put(time_temp[2], p+'Time.Output_Interval_Steps')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('None', p + 'Method')
#--- Initial_Structure ---
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p+'Method')
u.put([read_udf, -1, 1, 1], p+'Restart')
#--- Write UDF ---
u.write(os.path.join(self.calc_dir, present_udf))
return
def read_and_calc(target):
if target.split('_')[0] == 'Cycle':
sim_type = target.split('_')[4]
else:
sim_type = target.split('_')[3]
uobj = UDFManager(target)
if sim_type == 'forward':
uobj.jump(0)
cell = uobj.get("Structure.Unit_Cell.Cell_Size")
area_init = cell[0] * cell[1]
z_init = cell[2]
data = [[1.0, 0, 0, 0]]
elif sim_type == 'backward':
uobj.jump(1)
vol = uobj.get("Statistics_Data.Volume.Batch_Average")
area_init = vol**(2. / 3.)
z_init = vol**(1. / 3.)
data = []
for i in range(1, uobj.totalRecord()):
print("Reading Rec.=", i)
uobj.jump(i)
#
cell = uobj.get("Structure.Unit_Cell.Cell_Size")
#
stress = uobj.get("Statistics_Data.Stress.Total.Batch_Average")
t_stress = calc_stress(cell, stress, area_init)
#
bond_stress = uobj.get("Statistics_Data.Stress.Bond.Batch_Average")
bond = calc_stress(cell, bond_stress, area_init)
#
non_bond_stress = uobj.get(
"Statistics_Data.Stress.Non_Bond.Batch_Average")
non_bond = calc_stress(cell, non_bond_stress, area_init)
#
strain = uobj.get("Structure.Unit_Cell.Cell_Size.c") / z_init
#
temp = uobj.get("Statistics_Data.Temperature.Batch_Average")
#
data.append([strain, t_stress, non_bond, bond, temp])
return data
def read_step_stress(self, t_udf):
print("Readin file = ", t_udf)
area_init, z_init = self.calc_init(t_udf)
uobj = UDFManager(t_udf)
time = []
strain = []
stress = []
temp = []
# データ読み込み
prev_stress = 0.
for rec in range(uobj.totalRecord()):
print("Reading Rec.=", rec)
uobj.jump(rec)
#
time.append(uobj.get("Time"))
if self.mode == 'elong':
tmp_strain = uobj.get(
"Structure.Unit_Cell.Cell_Size.c") / z_init
elif self.mode == 'shear':
tmp_strain = uobj.get('Structure.Unit_Cell.Shear_Strain')
strain.append(tmp_strain)
#
if rec == 0:
tmp_stress = prev_stress
temp.append(1.)
else:
temp.append(
uobj.get('Statistics_Data.Temperature.Batch_Average'))
if self.mode == 'elong':
stress_list = uobj.get(
"Statistics_Data.Stress.Total.Batch_Average")
tmp_stress = stress_list[2] - (stress_list[0] +
stress_list[1]) / 2.
elif self.mode == 'shear':
tmp_stress = uobj.get(
'Statistics_Data.Stress.Total.Batch_Average.xy'
) #- self.ave_xy
if tmp_stress <= 0:
tmp_stress = prev_stress
stress.append(tmp_stress)
#
prev_stress = tmp_stress
#
stress_step = np.stack([time, stress, temp], 1)
strain_step = np.stack([time, strain, temp], 1)
ss = np.stack([strain, stress, temp], 1)
self.plot(strain_step, 'strain_step.dat')
self.plot(stress_step, 'stress_step.dat')
self.plot(ss, 'ss.dat')
return stress_step, strain_step