def myExtension_initygrad():
####################################
#set fixed parameter values first
####################################
mu = 1.0
Wi = 1.2
beta = 1. / (2 * Wi)
xorigin = -1.0
xextent = 2.0
yorigin = -4.0
yextent = 8.0
origin = (xorigin, yorigin)
U = 2.0 / Wi
#set time parameters, save data every numskip time steps (default is every time step)
#note that I do not control the time step in the solver!!
# my time step only determines the maximum time step allowed
t0 = 0
totalTime = 3.0
dt = 5.e-2
eps_grid = 0.2
myVelocity = bgvels_Viscoelasticity.Extension
veldocstring = 'Purely extensional flow near hyperbolic stagnation point: bgvels_Viscoelasticity.Extension'
# solver options for viscoelastic flow
stressflag = 1
regridding = 0
rtol = 1.e-3
fnamestart = 'ext_initygrad_PtinC_noregrid_rtol%02d' % int(
np.abs(np.log10(rtol)))
####################################
#choose a directory for saving files
####################################
basedir = os.path.expanduser('~/VEsims/ExactExtensionalFlow/')
if not os.path.exists(basedir):
basedir = '/Volumes/ExtMacBree/VEsims/ExactExtensionalFlow/'
if not os.path.exists(basedir):
basedir = '/scratch03/bcummins/mydata/ve/ExactExtensionalFlow/'
if not os.path.exists(basedir):
print('Choose a different directory for saving files')
raise (SystemExit)
Nlist = [20] #,40,80]
for N in Nlist:
gridspc = xextent / N
M = int(np.ceil(yextent / gridspc))
####################################
#Put parameters into dictionaries...
####################################
pdict = dict(N=N,
M=M,
U=U,
gridspc=gridspc,
origin=origin,
mu=mu,
Wi=Wi,
beta=beta,
eps_grid=eps_grid,
veldocstring=veldocstring)
wdict = dict(pdict=pdict, myVelocity=myVelocity)
pdict = None #to avoid heisenbugs during refactor
#make the grid
l0 = mygrids.makeGridCenter(N, M, gridspc, origin)
P0 = np.zeros((N, M, 2, 2))
P0[:, :, 0,
0] = (1.0 + l0[:, :, 1]**2)**(1.0 / (2 * Wi * U) -
1.0) + 1.0 / (1.0 - 2 * Wi * U)
P0[:, :, 1, 1] = 1.0
print(P0.shape)
y0 = np.append(l0.flatten(), P0.flatten())
#Viscoelastic run
print('Extensional flow, initial y gradient, N = %02d' % N)
StateSave = eVE.mySolver(eVE.viscoElasticUpdater_bgvel,
y0,
t0,
dt,
totalTime,
wdict,
stressflag,
regridding,
rtol=rtol)
#save the output
StateSave['pdict'] = wdict['pdict']
StateSave['dt'] = dt
fname = basedir + fnamestart
F = open(
fname + '_eps%03d_N%03d_Wi%02d_Time%02d.pickle' %
(int(round(eps_grid * 1000)), N, int(
round(Wi)), int(round(totalTime))), 'w')
Pickler(F).dump(StateSave)
F.close()
def mySwimmer_sine():
####################################
#set fixed parameter values first
####################################
mu = 1.0
xorigin = 0.0
xextent = 1.6
yorigin = 0.1
yextent = 0.8
origin = (xorigin, yorigin)
#set time parameters, save data every time step
#note that I do not control the time step in the solver!!
# my time step only tells me where I will save data
t0 = 0
totalTime = 5.0
dt = 5.e-2
initTime = 1.0 #need this to be a full swimmer cycle -- see curvature forces in code
#make swimmer
a = 0.16
w = 2 * np.pi #swimmer period is 1
lam = 2.5 * np.pi
Np = 20
L = 0.78
h = L / (Np - 1)
K = 40.0
xr = np.array([h])
forcedict = dict(a=a,
w=w,
t=0,
Kcurv=0.01,
lam=lam,
Np=Np,
h=h,
L=L,
K=K,
xr=xr)
eps_obj = 2 * h
myForces = forces_Viscoelasticity.calcForcesSwimmer
forcedocstring = 'Swimmer curvature forces according to linearly increasing sine wave: forces_Viscoelasticity.calcForcesSwimmer'
# solver options for viscoelastic flow
stressflag = 1
regridding = 1
regriddict = dict(timecrit=1.0,
edgecrit=None,
detcrit=None,
scalefactor=2,
addpts=0)
vfname = 'visco_PtinC_fixedregrid010_scalefactor2_addpts0_'
####################################
#Put parameters into dictionaries...
####################################
pdict = dict(mu=mu,
forcedict=forcedict,
eps_obj=eps_obj,
forcedocstring=forcedocstring)
wdict = dict(pdict=pdict, myForces=myForces)
pdict = None #to avoid heisenbugs during refactor
####################################
#choose a directory for saving files
####################################
basedir = os.path.expanduser('~/VEsims/SwimmerRefactored/SineWave/')
if not os.path.exists(basedir):
basedir = '/Volumes/ExtMacBree/VEsims/SwimmerRefactored/SineWave/'
if not os.path.exists(basedir):
basedir = '/scratch03/bcummins/mydata/ve/SwimmerRefactored/SineWave/'
if not os.path.exists(basedir):
print('Choose a different directory for saving files')
raise (SystemExit)
####################################
#Stokes flow reference run...
####################################
#Set up initial conditions for flat swimmer
y00 = 0.5 * np.ones((2 * Np, ))
v = np.arange(0.3, 0.3 + L + h / 2, h)
y00[:-1:2] = v
#Initialize flat swimmer in Stokes flow (ramp up to emergent swimming shape)
print('Initialize swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater, y00, t0, dt, initTime,
wdict)
inits = np.asarray(StateSave['fpts'])[-1, :]
#run the ode solver for Stokes flow
print('Swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater, inits, initTime, dt,
totalTime + initTime, wdict)
#save the output
StateSave['pdict'] = wdict['pdict']
F = open(
basedir + 'stokes_epsobj%03d_Time%02d.pickle' %
(int(round(eps_obj * 1000)), int(totalTime + initTime)), 'w')
Pickler(F).dump(StateSave)
F.close()
####################################
#now for viscoelastic simulations....
####################################
Wilist = [
0.25
] #, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75]#, 2.0, 2.5, 3.0]#[0.1,0.08,0.06,0.04,0.02]
Nlist = [41] #[20,40,80,160]
for N in Nlist:
gridspc = xextent / N
eps_grid = eps_obj #2*gridspc
M = int(np.ceil(yextent / gridspc))
#make the grid
l0 = mygrids.makeGridCenter(N, M, gridspc, origin)
P0 = np.zeros((N, M, 2, 2))
P0[:, :, 0, 0] = 1.0
P0[:, :, 1, 1] = 1.0
# set initial conditions for VE simulations
y0 = np.append(np.append(inits, l0.flatten()), P0.flatten())
for Wi in Wilist:
#assign and record VE params
beta = 1. / (2 * Wi)
wdict['pdict']['N'] = N
wdict['pdict']['M'] = M
wdict['pdict']['gridspc'] = gridspc
wdict['pdict']['origin'] = origin
wdict['pdict']['Wi'] = Wi
wdict['pdict']['beta'] = beta
wdict['pdict']['eps_grid'] = eps_grid
#Viscoelastic run
print('Swimmer in VE flow, N = %02d, Wi = %f' % (N, Wi))
StateSave = eVE.mySolver(eVE.viscoElasticUpdater_force, y0,
initTime, dt, totalTime + initTime, wdict,
stressflag, regridding, regriddict)
#save the output
StateSave['pdict'] = wdict['pdict']
StateSave['regriddict'] = regriddict
F = open(
basedir + vfname +
'epsobj%03d_epsgrid%03d_N%03d_Wi%04d_Time%02d.pickle' %
(int(round(eps_obj * 1000)), int(round(eps_grid * 1000)), N,
int(round(Wi * 100)), int(totalTime + initTime)), 'w')
Pickler(F).dump(StateSave)
F.close()
def mySwimmer_TeranFauciShelley():
####################################
#set fixed parameter values first
####################################
mu = 1.0
xorigin = 0.0
xextent = 1.3
yorigin = 0.05
yextent = 0.9
origin = (xorigin,yorigin)
#set time parameters, save data every time step
#note that I do not control the time step in the solver!!
# my time step only tells me where I will save data
t0 = 0; totalTime = 10.0; dt = 5.e-2;
initTime=1.0 #need this to be a full swimmer cycle -- see curvature forces in code
#make swimmer
a = 0.16
w = -2*np.pi #swimmer period is 1
lam = 2.5*np.pi
L = 0.6
myForces = forces_Viscoelasticity.calcForcesSwimmerTFS
forcedocstring = 'Swimmer curvature forces according to Teran, Fauci, and Shelley: forces_Viscoelasticity.calcForcesSwimmerTFS'
forcedict = dict(a=a, w=w, t=0, lam=lam, L=L)
# solver options for viscoelastic flow
stressflag=1
regridding=1
regriddict = dict(timecrit=0.4,edgecrit=None,detcrit=None,scalefactor=2,addpts=0)
vfname = 'visco_PtinC_changingNp_fixedregrid004_scalefactor2_addpts0_'
####################################
#Set up dictionaries for parameters...
####################################
pdict = dict( mu=mu, forcedocstring=forcedocstring)
wdict = dict(pdict=pdict,myForces=myForces)
pdict = None #to avoid heisenbugs during refactor
####################################
#choose a directory for saving files
####################################
basedir = os.path.expanduser('~/VEsims/SwimmerRefactored/TFS_FinalParams/')
if not os.path.exists(basedir):
basedir = '/Volumes/LCD/VEsims/SwimmerRefactored/TFS_FinalParams/'
if not os.path.exists(basedir):
basedir = '/scratch03/bcummins/mydata/ve/SwimmerRefactored/TFS_FinalParams/'
if not os.path.exists(basedir):
print('Choose a different directory for saving files')
raise(SystemExit)
####################################
#loop over parameters
####################################
Wilist = [1.0]#[0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75]#, 2.0, 2.5, 3.0]#[0.1,0.08,0.06,0.04,0.02]
Nlist = [54,108, 216]#[20,40,80,160]
Nplist = [26]#[26, 50, 98]
Np = Nplist[0]
h = L/(Np-1)
Kcurvlist = [0.2]#[0.2, 0.2/3, 0.2/4]
Kcurv = Kcurvlist[0]
Klist = [40.] #[40.,20.,10.]
K = Klist[0]
xr = np.array([h])
forcedict['h'] = h
forcedict['xr'] = xr
forcedict['Np'] = Np
forcedict['Kcurv'] = Kcurv
forcedict['K'] = K
eps_obj = 1.5*h
wdict['pdict']['forcedict'] = forcedict
wdict['pdict']['eps_obj'] = eps_obj
####################################
#Stokes flow reference run...
####################################
#Set up initial conditions for flat swimmer
y00 = 0.5*np.ones((2*Np,))
v = np.arange(0.3,0.3+L+h/2,h)
y00[:-1:2] = v
#Initialize flat swimmer in Stokes flow (ramp up to emergent swimming shape)
print('Initialize swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater,y00,t0,dt,initTime,wdict)
inits = np.asarray(StateSave['fpts'])[-1,:]
#run the ode solver for Stokes flow
print('Swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater,inits,initTime,dt,totalTime+initTime,wdict)
#save the output
StateSave['pdict']=wdict['pdict']
F = open( basedir+'stokes_Kcurv%03d_K%03d_epsobj%03d_Time%02d.pickle' % (int(round(forcedict['Kcurv']*100)),int(round(forcedict['K'])),int(round(eps_obj*1000)),int(totalTime+initTime)), 'w' )
Pickler(F).dump(StateSave)
F.close()
for k in range(len(Nlist)):
print(h,xextent/Nlist[k])
####################################
#Oldroyd-B flow reference run...
####################################
#assign and record parameters
N = Nlist[k]
gridspc = xextent/N
eps_grid = eps_obj#2*gridspc
M = int(np.ceil(yextent/gridspc))
wdict['pdict']['N'] = N
wdict['pdict']['M'] = M
wdict['pdict']['gridspc'] = gridspc
wdict['pdict']['origin'] = origin
wdict['pdict']['eps_grid'] = eps_grid
#make the initial grid
l0 = mygrids.makeGridCenter(N,M,gridspc,origin)
P0 = np.zeros((N,M,2,2))
P0[:,:,0,0] = 1.0
P0[:,:,1,1] = 1.0
# set initial conditions for VE simulations
y0 = np.append(np.append(inits, l0.flatten()),P0.flatten())
for Wi in Wilist:
#assign and record params
beta = 1./(2*Wi)
wdict['pdict']['Wi'] = Wi
wdict['pdict']['beta'] = beta
#Viscoelastic run
print('Swimmer in VE flow, N = %02d, Wi = %f' % (N,Wi))
StateSave = eVE.mySolver(eVE.viscoElasticUpdater_force,y0,initTime,dt,totalTime+initTime,wdict,stressflag,regridding,regriddict)
#save the output
StateSave['pdict']=wdict['pdict']
StateSave['regriddict']=regriddict
F = open(basedir+vfname+'Kcurv%03d_K%03d_epsobj%03d_epsgrid%03d_N%03d_Wi%04d_Time%02d.pickle' % (int(round(forcedict['Kcurv']*100)),int(round(forcedict['K'])),int(round(eps_obj*1000)),int(round(eps_grid*1000)),N,int(round(Wi*100)),int(totalTime+initTime)), 'w' )
Pickler(F).dump(StateSave)
F.close()
def myExtension_initygrad():
####################################
#set fixed parameter values first
####################################
mu = 1.0
Wi = 1.2
beta = 1. / (2*Wi)
xorigin = -1.0
xextent = 2.0
yorigin = -4.0
yextent = 8.0
origin = (xorigin,yorigin)
U = 2.0/Wi
#set time parameters, save data every numskip time steps (default is every time step)
#note that I do not control the time step in the solver!!
# my time step only determines the maximum time step allowed
t0 = 0; totalTime = 3.0; dt = 5.e-2
myVelocity = bgvels_Viscoelasticity.Extension
veldocstring = 'Purely extensional flow near hyperbolic stagnation point: bgvels_Viscoelasticity.Extension'
# solver options for viscoelastic flow
stressflag=1
regridding=0
####################################
#choose a directory for saving files
####################################
basedir = os.path.expanduser('~/VEsims/ExactExtensionalFlow/')
if not os.path.exists(basedir):
basedir = '/Volumes/LCD/VEsims/ExactExtensionalFlow/'
if not os.path.exists(basedir):
basedir = '/scratch03/bcummins/mydata/ve/ExactExtensionalFlow/'
if not os.path.exists(basedir):
print('Choose a different directory for saving files')
raise(SystemExit)
for rtol in [1.e-3,1.e-4,1.e-5,1.e-6]:
fnamestart = 'ext_initygrad_PtinC_noregrid_rtol%02d' % int(np.abs(np.log10(rtol)))
Nlist = [20]#,40,80]
for N in Nlist:
gridspc = xextent/N
eps_grid = 2*gridspc
M = int(np.ceil(yextent/gridspc))
####################################
#Put parameters into dictionaries...
####################################
pdict = dict( N = N, M = M, U=U, gridspc = gridspc, origin = origin, mu = mu, Wi = Wi, beta=beta, eps_grid=eps_grid, veldocstring=veldocstring)
wdict = dict(pdict=pdict,myVelocity=myVelocity)
pdict = None #to avoid heisenbugs during refactor
#make the grid
l0 = mygrids.makeGridCenter(N,M,gridspc,origin)
P0 = np.zeros((N,M,2,2))
P0[:,:,0,0] = (1.0 +l0[:,:,1]**2)**(1.0/(2*Wi*U) - 1.0) + 1.0/(1.0-2*Wi*U)
P0[:,:,1,1] = 1.0
print(P0.shape)
y0 = np.append(l0.flatten(),P0.flatten())
#Viscoelastic run
print('Extensional flow, initial y gradient, N = %02d' % N)
StateSave = eVE.mySolver(eVE.viscoElasticUpdater_bgvel,y0,t0,dt,totalTime,wdict,stressflag,regridding,rtol=rtol)
#save the output
StateSave['pdict']=wdict['pdict']
StateSave['dt']=dt
fname = basedir + fnamestart
F = open( fname+'_eps%03d_N%03d_Wi%02d_Time%02d.pickle' % (int(round(eps_grid*1000)),N,int(round(Wi)),int(round(totalTime))), 'w' )
Pickler(F).dump(StateSave)
F.close()
def mySwimmer_sine():
####################################
#set fixed parameter values first
####################################
mu = 1.0
xorigin = 0.0
xextent = 1.6
yorigin = 0.1
yextent = 0.8
origin = (xorigin,yorigin)
#set time parameters, save data every time step
#note that I do not control the time step in the solver!!
# my time step only tells me where I will save data
t0 = 0; totalTime = 5.0; dt = 5.e-2;
initTime=1.0 #need this to be a full swimmer cycle -- see curvature forces in code
#make swimmer
a = 0.16
w = 2*np.pi #swimmer period is 1
lam = 2.5*np.pi
Np = 20
L = 0.78
h = L/(Np-1)
K =40.0
xr = np.array([h])
forcedict = dict(a=a, w=w, t=0, Kcurv=0.01, lam=lam, Np=Np, h=h, L=L, K=K, xr=xr)
eps_obj = 2*h
myForces = forces_Viscoelasticity.calcForcesSwimmer
forcedocstring = 'Swimmer curvature forces according to linearly increasing sine wave: forces_Viscoelasticity.calcForcesSwimmer'
# solver options for viscoelastic flow
stressflag=1
regridding=1
regriddict = dict(timecrit=1.0,edgecrit=None,detcrit=None,scalefactor=2,addpts=0)
vfname = 'visco_PtinC_fixedregrid010_scalefactor2_addpts0_'
####################################
#Put parameters into dictionaries...
####################################
pdict = dict( mu=mu, forcedict=forcedict, eps_obj=eps_obj, forcedocstring=forcedocstring)
wdict = dict(pdict=pdict,myForces=myForces)
pdict = None #to avoid heisenbugs during refactor
####################################
#choose a directory for saving files
####################################
basedir = os.path.expanduser('~/VEsims/SwimmerRefactored/SineWave/')
if not os.path.exists(basedir):
basedir = '/Volumes/LCD/VEsims/SwimmerRefactored/SineWave/'
if not os.path.exists(basedir):
basedir = '/scratch03/bcummins/mydata/ve/SwimmerRefactored/SineWave/'
if not os.path.exists(basedir):
print('Choose a different directory for saving files')
raise(SystemExit)
####################################
#Stokes flow reference run...
####################################
#Set up initial conditions for flat swimmer
y00 = 0.5*np.ones((2*Np,))
v = np.arange(0.3,0.3+L+h/2,h)
y00[:-1:2] = v
#Initialize flat swimmer in Stokes flow (ramp up to emergent swimming shape)
print('Initialize swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater,y00,t0,dt,initTime,wdict)
inits = np.asarray(StateSave['fpts'])[-1,:]
#run the ode solver for Stokes flow
print('Swimmer in Stokes flow...')
StateSave = eVE.mySolver(eVE.stokesFlowUpdater,inits,initTime,dt,totalTime+initTime,wdict)
#save the output
StateSave['pdict']=wdict['pdict']
F = open( basedir+'stokes_epsobj%03d_Time%02d.pickle' % (int(round(eps_obj*1000)),int(totalTime+initTime)), 'w' )
Pickler(F).dump(StateSave)
F.close()
####################################
#now for viscoelastic simulations....
####################################
Wilist = [0.25]#, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75]#, 2.0, 2.5, 3.0]#[0.1,0.08,0.06,0.04,0.02]
Nlist = [41] #[20,40,80,160]
for N in Nlist:
gridspc = xextent/N
eps_grid = eps_obj#2*gridspc
M = int(np.ceil(yextent/gridspc))
#make the grid
l0 = mygrids.makeGridCenter(N,M,gridspc,origin)
P0 = np.zeros((N,M,2,2))
P0[:,:,0,0] = 1.0
P0[:,:,1,1] = 1.0
# set initial conditions for VE simulations
y0 = np.append(np.append(inits, l0.flatten()),P0.flatten())
for Wi in Wilist:
#assign and record VE params
beta = 1./(2*Wi)
wdict['pdict']['N'] = N
wdict['pdict']['M'] = M
wdict['pdict']['gridspc'] = gridspc
wdict['pdict']['origin'] = origin
wdict['pdict']['Wi'] = Wi
wdict['pdict']['beta'] = beta
wdict['pdict']['eps_grid'] = eps_grid
#Viscoelastic run
print('Swimmer in VE flow, N = %02d, Wi = %f' % (N,Wi))
StateSave = eVE.mySolver(eVE.viscoElasticUpdater_force,y0,initTime,dt,totalTime+initTime,wdict,stressflag,regridding,regriddict)
#save the output
StateSave['pdict']=wdict['pdict']
StateSave['regriddict']=regriddict
F = open(basedir+vfname+'epsobj%03d_epsgrid%03d_N%03d_Wi%04d_Time%02d.pickle' % (int(round(eps_obj*1000)),int(round(eps_grid*1000)),N,int(round(Wi*100)),int(totalTime+initTime)), 'w' )
Pickler(F).dump(StateSave)
F.close()
