def __init__(self, eqn, domain, domain_params, bc_params, solver_params,
settings):
'''
Reactive transport class for carbonation
A Lattice Boltzmann method based reactive transport model \
where reactions are computed using geochemical solver PHREEQC
'''
if (settings['diffusivity']['type'] == 'fixed'):
print("newMlvl")
eqn = 'MultilevelAdvectionDiffusion2'
#solver_params['tauref'] = 1
#domain_params['Deref'] = settings['diffusivity']['D_border']
#solver_params['tauref'] = 0.5*np.max(settings['Dref'])/domain_params['Deref']+0.5#5.5 for 1e-10
self.auto_time_step = solver_params.get('auto_time_step', True)
self.phrqc = Phrqc(domain, domain_params, bc_params, solver_params)
components = self.phrqc.components
bc = self.phrqc.boundary_conditions
init_c = self.phrqc.initial_conditions
for name in components:
if name not in domain_params:
domain_params[name] = {}
domain_params[name]['c'] = init_c[name]
for name in bc:
for comp in components:
if comp not in bc_params:
bc_params[comp] = {}
bc_params[comp][name] = ['c', bc[name][comp]]
self.fluid = Multicomponent(eqn, components, domain, domain_params,
bc_params, solver_params)
self.solid = Solid(domain, domain_params, solver_params)
self.ptype = 'CSH' if hasattr(self.fluid, 'Si') else 'CH'
self.app_tort_degree = settings['app_tort']['degree']
self.update_solid_params()
self.nodetype = deepcopy(domain.nodetype)
self.apply_settings(settings)
self.update_nodetype()
self.update_border_and_interface(self.nodetype)
#self.fluid.call("_set_relaxation_params")
self.solid.prev_border = deepcopy(self.solid.border)
self.Dref = settings['Dref']
def __init__(self, eqn, domain, domain_params, bc_params, solver_params,
settings):
'''
Reactive transport class for carbonation
A Lattice Boltzmann method based reactive transport model \
where reactions are computed using geochemical solver PHREEQC
'''
self.auto_time_step = solver_params.get('auto_time_step', True)
self.phrqc = phrqc.CarbonationPhrqc(domain, domain_params, bc_params,
solver_params)
components = self.phrqc.components
bc = self.phrqc.boundary_conditions
init_c = self.phrqc.initial_conditions
for name in components:
if name not in domain_params:
domain_params[name] = {}
domain_params[name]['c'] = init_c[name]
for name in bc:
for comp in components:
if comp not in bc_params:
bc_params[comp] = {}
bc_params[comp][name] = ['c', bc[name][comp]]
self.fluid = Multicomponent(eqn, components, domain, domain_params,
bc_params, solver_params)
self.solid = Solid(domain, domain_params, solver_params)
self.ptype = 'CSH' if hasattr(self.fluid, 'Si') else 'CH'
self.nodetype = deepcopy(domain.nodetype)
self.apply_settings(settings)
self.update_volume()
self.update_porosity()
self.update_app_tort()
self.update_init_phrqc()
self.update_bc(settings)
self.update_phases()
self.update_nodetype()
self.update_target_SI()
class CarbonationRT(PhrqcReactiveTransport):
def __init__(self, eqn, domain, domain_params, bc_params, solver_params,
settings):
'''
Reactive transport class for carbonation
A Lattice Boltzmann method based reactive transport model \
where reactions are computed using geochemical solver PHREEQC
'''
self.auto_time_step = solver_params.get('auto_time_step', True)
self.phrqc = phrqc.CarbonationPhrqc(domain, domain_params, bc_params,
solver_params)
components = self.phrqc.components
bc = self.phrqc.boundary_conditions
init_c = self.phrqc.initial_conditions
for name in components:
if name not in domain_params:
domain_params[name] = {}
domain_params[name]['c'] = init_c[name]
for name in bc:
for comp in components:
if comp not in bc_params:
bc_params[comp] = {}
bc_params[comp][name] = ['c', bc[name][comp]]
self.fluid = Multicomponent(eqn, components, domain, domain_params,
bc_params, solver_params)
self.solid = Solid(domain, domain_params, solver_params)
self.ptype = 'CSH' if hasattr(self.fluid, 'Si') else 'CH'
self.nodetype = deepcopy(domain.nodetype)
self.apply_settings(settings)
self.update_volume()
self.update_porosity()
self.update_app_tort()
self.update_init_phrqc()
self.update_bc(settings)
self.update_phases()
self.update_nodetype()
self.update_target_SI()
def advance(self):
self.update_diffusivity()
print(self.iters, self.dt)
print('self.fluid.Ca.D0[1,:]', self.fluid.Ca.D0[1, :])
print('solid mass calcite', self.solid.phaseqty[0][1, :])
print('solid mass CH', self.solid.phaseqty[1][1, :])
print(self.fluid.Ca.cphi)
print('self.solid.poros[1,:]', self.solid.poros[1, :])
print('self.solid.tort[1,:]', self.solid.app_tort[1, :])
print('tau[1,:]', self.fluid.Ca.tau[1, :])
print("self.iters=:", self.iters)
print("befor LB [Ca]:", self.fluid.Ca.c[1, :])
print("before LB [C]:", self.fluid.C.c[1, :])
print("ss[Ca]:", self.fluid.Ca.ss[1, :])
print("----------------------------------")
self.fluid.call('advance')
self.update_target_SI()
self.update_source()
self.update_phases()
self.update_velocity()
self.update_nodetype()
#%% UPDATES
def update_volume(self):
vol = np.zeros(self.solid.shape)
phase_list = deepcopy(self.solid.diffusive_phase_list)
for num, phase in enumerate(phase_list, start=1):
val = getattr(self.solid, phase)
vol += val.c * self.solid.mvol[num - 1]
self.solid.vol = vol
def update_porosity(self):
self.solid.poros = 1. - self.solid.vol / self.solid.voxel_vol
if np.any(self.solid.poros <= 1e-10):
sys.exit('Negative or zero porosity')
def update_app_tort(self, ):
self.solid.app_tort = 1. * self.solid.poros**self.solid.app_tort_degree
def update_boundary_cells(self):
nodes = np.zeros(np.shape(self.nodetype))
nodes[0, :] = ct.Type.SOLID
nodes[-1, :] = ct.Type.SOLID
nodes[:, 0] = ct.Type.SOLID
nodes[:, -1] = ct.Type.SOLID
return nodes
def update_bc(self, settings):
ptype = self.ptype
for key in self.phrqc.boundary_solution_labels:
self.fluid.Ca.bc[key] = ['flux', 0.0]
self.fluid.Ca._bc[key + 'bc'] = 'flux'
if (settings['bc']['type'] == 'pco2'):
self.fluid.C.bc[key] = ['flux', 0.0]
self.fluid.C._bc[key + 'bc'] = 'flux'
self.fluid.H.bc[key] = ['flux', 0.0]
self.fluid.H._bc[key + 'bc'] = 'flux'
self.fluid.O.bc[key] = ['flux', 0.0]
self.fluid.O._bc[key + 'bc'] = 'flux'
if (ptype == 'CSH'):
self.fluid.Si.bc[key] = ['flux', 0.0]
self.fluid.Si._bc[key + 'bc'] = 'flux'
def update_init_phrqc(self):
self.phrqc.boundcells = self.update_boundary_cells()
if 'portlandite' in self.solid.diffusive_phase_list:
self.phrqc.init_port = self.solid.portlandite.c > 0
if self.ptype == 'CSH':
self.phrqc.init_csh = np.logical_or(
np.logical_or(self.solid.CSHQ_TobD.c > 0,
self.solid.CSHQ_TobH.c > 0),
np.logical_or(self.solid.CSHQ_JenD.c > 0,
self.solid.CSHQ_JenH.c > 0))
if 'calcite' in self.solid.diffusive_phase_list:
self.phrqc.is_calc = self.solid.calcite.c > 0
self.phrqc._target_SI = np.zeros(self.solid.shape)
self.phrqc.nodetype = deepcopy(self.nodetype)
if self.solid.nphases > 0:
phaseqty = self.solid.phaseqty_for_phrqc()
self.phrqc.modify_solid_phases(phaseqty)
def update_phrqc(self):
self.phrqc.poros = deepcopy(self.solid.poros)
self.phrqc.is_calc = self.solid.calcite.c > 0 #TODO check if necessary - move to update phrqc function
if (self.phrqc.precipitation == 'interface'):
if (self.phrqc.active != 'interface'):
self.phrqc.nodetype = deepcopy(self.nodetype)
def apply_settings(self, settings):
self.settings = settings
self.Dref = settings['Dref']
self.dx = settings['dx']
self.solid.app_tort_degree = settings['app_tort']['degree']
self.phrqc.pinput = settings['bc']
self.phrqc.active = settings['active_nodes']
self.phrqc.precipitation = settings['precipitation']
self.phrqc.pcs = settings['pcs_mode']['pcs']
self.phrqc.phrqc_flags['only_mineral'] = False
self.phrqc.phrqc_flags['only_interface'] = False
self.phrqc.phrqc_flags['only_fluid'] = False
self.phrqc.phrqc_flags['smart_run'] = False
if (settings['active_nodes'] == 'all'):
self.phrqc.nodetype = deepcopy(self.nodetype)
elif (settings['active_nodes'] == 'interface'):
self.phrqc.phrqc_flags['only_interface'] = True
elif (settings['active_nodes'] == 'smart'):
self.phrqc.phrqc_flags['smart_run'] = True
elif (settings['active_nodes'] == 'mineral'):
self.phrqc.phrqc_flags['only_mineral'] = True
elif (settings['active_nodes'] == 'fluid'):
self.phrqc.phrqc_flags['only_fluid'] = True
else:
sys.exit()
if ('pco2' in settings) and (settings['bc']['type'] == 'pco2'):
self.phrqc.ppt = settings['pco2']
else:
self.phrqc.ppt = False
def update_source(self):
c = deepcopy(self.fluid.get_attr('c'))
phaseqty = self.solid.phaseqty_for_phrqc()
phase_list = deepcopy(self.solid.diffusive_phase_list)
for num, phase in enumerate(phase_list, start=1):
phaseqty[phase] = deepcopy(self.solid._diffusive_phaseqty[num - 1])
if (self.settings['dissolution'] == 'subgrid'):
phaseqty['portlandite'][np.where(self.solid.border)] = 0
#phaseqty['portlandite'] = np.zeros(phaseqty['portlandite'].shape)
print("self.phrqc.iters=", self.phrqc.iters)
print("after LB [Ca]:", self.fluid.Ca.c[1, :])
print("after LB [C]:", self.fluid.C.c[1, :])
print("^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
self.phrqc.modify_solid_phases(phaseqty)
ss = self.phrqc.modify_solution(c, self.dt, self.solid.nodetype)
print(ss.keys())
print("after reaction self.phrqc.selected_out()['poros'][1,:]",
self.phrqc.selected_output()['poros'][1, :])
print("after reaction self.phrqc.selected_out()['Ca'][1,:]",
self.phrqc.selected_output()['Ca'][1, :])
print("after reaction self.phrqc.selected_out()['CH'][1,:]",
self.phrqc.selected_output()['portlandite'][1, :])
print("after reaction self.phrqc.selected_out()['C'][1,:]",
self.phrqc.selected_output()['C'][1, :])
print("after reaction self.phrqc.selected_out()['CC'][1,:]",
self.phrqc.selected_output()['calcite'][1, :])
print("+++++++++++++++++++++++++++++++++++++++++")
if (self.settings['dissolution'] == 'multilevel'):
pqty = self.solid.update(self.phrqc.dphases)
else:
if self.iters > 1: pqty = self.solid.update(self.phrqc.dphases)
self.update_solid_params()
ss = self.update_border_solution(c, ss)
self.update_solid_params()
self.update_target_SI()
self.update_phrqc()
ss = self.update_no_flux(ss)
self.fluid.set_attr('ss', ss)
print("at last self.phrqc.selected_out()['Ca'][1,:]",
self.phrqc.selected_output()['Ca'][1, :])
print("at last self.phrqc.selected_out()['CH'][1,:]",
self.phrqc.selected_output()['portlandite'][1, :])
print("at last self.phrqc.selected_out()['C'][1,:]",
self.phrqc.selected_output()['C'][1, :])
print("at last self.phrqc.selected_out()['CC'][1,:]",
self.phrqc.selected_output()['calcite'][1, :])
def update_border_solution(self, c, ss):
#poros = self.solid.poros#
phrqc_poros = self.solid.poros #self.phrqc.selected_output()['poros'] #
fraction = self.settings['subgrid']['fraction']
result = {}
by = np.where(self.solid.border)[0]
bx = np.where(self.solid.border)[1]
bf = np.where(self.solid.border.flatten())[0]
for i in np.arange(0, np.sum(self.solid.border)):
if fraction > 0:
cell_m = bf[i] + 1
result = self.update_equilibrium(
result, cell_m, self.solid.portlandite.c[by[i], bx[i]],
phrqc_poros[by[i], bx[i]], fraction)
print('border changing results:', result)
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (result[str(cell_m)][name] -
c[name][by[i], bx[i]]) / self.dt
ssnew[name] *= phrqc_poros[by[i], bx[i]]
ss[name][by[i], bx[i]] = ssnew[name]
for i in np.arange(0, np.sum(self.solid.border)):
self.solid.portlandite.c[by[i],
bx[i]] = result[str(bf[i] +
1)]['portlandite_m']
#self.solid.calcite.c[by[i], bx[i]] = result[str(bf[i]+1)]['calcite_m']
return ss
def update_equilibrium(self, result, n_ch, m_ch, porosity, fraction=1):
print("now we are in border mixing!!!!!!!!!!!!!!!")
print(fraction)
ncell = 123456
fract = fraction / porosity
if fract > 1: fract = 1
#print(fract)
modify_str = []
modify_str.append("EQUILIBRIUM_PHASES %i" % ncell)
modify_str.append("Portlandite 0 %.20e dissolve only" % (m_ch))
modify_str.append("END")
modify_str.append('MIX %i' % ncell)
modify_str.append('%i %.20e' %
(n_ch, fract)) #modify_str.append('%i 1' %n_int)
modify_str.append('SAVE solution %i' % ncell)
modify_str.append("END")
modify_str.append('USE solution %i' % ncell)
modify_str.append('USE equilibrium_phase %i' % ncell)
modify_str.append('SAVE solution %i' % ncell)
modify_str.append("END")
modify_str.append("END")
modify_str = '\n'.join(modify_str)
self.phrqc.IPhreeqc.RunString(modify_str)
output = self.phrqc.IPhreeqc.GetSelectedOutputArray()
#print(modify_str)
#print(output)
print('1st mixing', output)
port = output[2][10]
modify_str = []
modify_str.append("EQUILIBRIUM_PHASES %i" % n_ch)
modify_str.append("Portlandite 0 %.20e" % (0)) # dissolve only
modify_str.append("END")
modify_str.append('USE equilibrium_phase %i' % n_ch)
modify_str.append('MIX %i' % ncell)
modify_str.append('%i 1' % ncell)
modify_str.append(
'%i %.20e' % (n_ch, 1. - fract)) #modify_str.append('%i 0' %n_int)
modify_str.append('SAVE solution %i' % (n_ch))
modify_str.append('SAVE equilibrium_phase %i' % (n_ch))
modify_str.append("END")
modify_str = '\n'.join(modify_str)
self.phrqc.IPhreeqc.RunString(modify_str)
output = self.phrqc.IPhreeqc.GetSelectedOutputArray()
print('2nd mixing', output)
#print(modify_str)
#print(output)
comp = {}
comp['portlandite_m'] = port
comp['C'] = output[1][6]
comp['Ca'] = output[1][7]
comp['H'] = (output[1][8] - self.phrqc.H_norm)
comp['O'] = (output[1][9] - self.phrqc.O_norm)
result[str(n_ch)] = comp
return (result)
def update_solid_params(self):
'''
Calculates porosity, apparent tortuosity,
volume and change in volume last time step
'''
self.solid.prev_vol = deepcopy(self.solid.vol)
self.update_volume()
self.update_porosity()
self.update_app_tort()
if (self.settings['velocity'] == True):
self.solid.dvol = self.solid.vol - self.solid.prev_vol
self.fluid.call(
'update_transport_params',
self.solid.poros, #move to solid params function
self.solid.app_tort,
self.auto_time_step)
def update_phases(self, thres=1.0e-3):
ch = self.solid.portlandite.c * self.solid.portlandite.mvol
cc = self.solid.calcite.c * self.solid.calcite.mvol
tot = cc + ch
is_cl = (self.nodetype == 1) #clinker
is_liq = (tot < thres) * ((self.nodetype == -2) +
(self.nodetype == -1))
phases = is_cl * 2 + is_liq * (-1)
if (self.ptype == 'CH'):
is_cc = (cc == np.maximum.reduce([cc, ch])) * ~is_liq * ~is_cl
is_ch = (ch == np.maximum.reduce([cc, ch])) * ~is_liq * ~is_cl
phases += is_ch * (-10) + is_cc * (-15)
if (self.ptype == 'CSH'):
csh = self.solid.CSHQ_TobH.c * self.solid.CSHQ_TobH.mvol + \
self.solid.CSHQ_TobD.c * self.solid.CSHQ_TobH.mvol + \
self.solid.CSHQ_JenH.c * self.solid.CSHQ_TobH.mvol + \
self.solid.CSHQ_JenD.c * self.solid.CSHQ_TobH.mvol
tot += csh
is_cc = (cc == np.maximum.reduce([cc, ch, csh])) * ~is_liq * ~is_cl
is_ch = (ch == np.maximum.reduce([cc, ch, csh])) * ~is_liq * ~is_cl
is_csh = (csh == np.maximum.reduce([cc, ch, csh
])) * ~is_liq * ~is_cl
phases += is_csh * (-5) + is_ch * (-10) + is_cc * (-15)
self.solid.csh = csh
self.solid.phases = phases
#self.c = []
self.solid.prev_calc = deepcopy(self.solid.calcite.c > 1e-4)
self.solid.prev_port = deepcopy(self.solid.portlandite.c > 0)
def update_nodetype(self):
'''
find neighbous of the multilevel cells
'''
prev_nodetype = deepcopy(self.nodetype)
is_port = (self.solid.portlandite.c > 0)
is_calc = (self.solid.calcite.c > 0)
#is_clinker = self.solid.nodetype == ct.Type.CLINKER
is_solid = self.solid.nodetype == ct.Type.SOLID
is_critical = np.zeros(np.shape(is_port))
is_interface = np.zeros(np.shape(is_port))
#calc_c = self.phrqc.solid_phase_conc['calcite']
if self.ptype == 'CH':
is_liquid = (~is_port)
if (self.iters > 1):
is_critical = (self.solid.pore_size <=
self.solid.threshold_pore_size) & is_calc & (
~is_port)
is_liquid = (~is_critical) & (~is_port) & (~is_solid) & (
~is_calc) #&((prev_nodetype==-1)|(prev_nodetype==-2))
is_interface = (~is_critical) & (~is_port) & (~is_solid) & (
~is_liquid)
self.solid.nodetype = ct.Type.LIQUID * is_liquid + \
ct.Type.MULTILEVEL * is_critical + \
ct.Type.MULTILEVEL * is_port +\
ct.Type.INTERFACE * is_interface + \
ct.Type.SOLID * is_solid
if self.ptype == 'CSH':
is_csh= (self.solid.CSHQ_JenD.c>0) | (self.solid.CSHQ_JenH.c>0) | \
(self.solid.CSHQ_TobD.c>0) |(self.solid.CSHQ_TobH.c>0) &(~is_port)
is_liquid = (~is_port) & (~is_csh)
if (self.iters > 1):
is_critical = (self.solid.pore_size <=
self.solid.threshold_pore_size) & is_calc & (
~is_port)
is_liquid = (~is_critical) & (~is_port) & (~is_solid) & (
~is_calc) & (~is_csh
) #&((prev_nodetype==-1)|(prev_nodetype==-2))
is_interface = (~is_critical) & (~is_port) & (~is_solid) & (
~is_liquid) & (~is_csh)
self.solid.nodetype = ct.Type.LIQUID * is_liquid + \
ct.Type.MULTILEVEL * is_critical + \
ct.Type.MULTILEVEL * is_port +\
ct.Type.MULTILEVEL * is_csh +\
ct.Type.INTERFACE * is_interface + \
ct.Type.SOLID * is_solid
yantra._solvers.update2d.reassign_mlvl(self.solid.nodetype)
self.solid.nodetype[prev_nodetype == ct.Type.SOLID] = ct.Type.SOLID
yantra._solvers.update2d.reassign_mlvl_solid(self.solid.nodetype)
self.solid.prev_calc_c = deepcopy(
self.phrqc.solid_phase_conc['calcite'])
self.nodetype = self.solid.nodetype
self.update_border()
self.fluid.set_attr('nodetype',
self.solid.nodetype,
component_dict=False)
def update_diffusivity(self):
Dref = self.Dref
cc = self.settings['diffusivity']['CC']
ch = self.settings['diffusivity']['CH']
D_border = self.Dref
if ('border' in self.settings['diffusivity']):
D_border = self.settings['diffusivity']['border']
is_border = self.solid.border
is_port = (self.solid.portlandite.c > 0) & (~is_border)
is_calc = np.logical_and(self.solid.calcite.c > 0, ~is_port)
#is_calc = np.logical_and(is_calc,~is_border)
is_liquid = np.logical_and(~is_port, ~is_calc)
is_liquid = np.logical_and(is_liquid, ~is_border)
D_archie = Dref * self.solid.poros * self.solid.app_tort
D_CC = D_archie
D_CH = D_archie
if (cc[0] == 'const'):
D_CC = cc[1] * np.ones(D_CC.shape)
elif (cc[0] == 'inverse'):
mineral = self.solid.calcite.c * self.solid.calcite.mvol
#D_CC =np.nan_to_num(1./((1-mineral)/Dref/self.solid.poros/self.solid.app_tort + mineral/cc[1]), Dref)
D_CC = np.nan_to_num(1. / ((1 - mineral) / Dref + mineral / cc[1]),
Dref)
if (ch[0] == 'const'):
D_CH = ch[1] * np.ones(D_CH.shape)
elif (ch[0] == 'inverse'):
mineral = self.solid.vol
D_CH = np.nan_to_num(
1. / ((1 - mineral) / Dref / self.solid.poros /
self.solid.app_tort + mineral / ch[1]), Dref)
De = D_CH * is_port + D_CC * is_calc + D_CC * is_border + Dref * is_liquid
self.fluid.set_attr('D0', De, component_dict=False)
self.fluid.set_attr('Deref', np.max(De), component_dict=False)
self.fluid.call("_set_relaxation_params")
def update_velocity(self):
if (self.settings['velocity']):
is_solid = self.solid.nodetype >= 1
not_solid = ~is_solid
neighbors = np.roll(not_solid, shift = 1, axis= 1).astype(int) + \
np.roll(not_solid, shift = -1, axis= 1).astype(int) +\
np.roll(not_solid, shift = 1, axis= 0).astype(int) +\
np.roll(not_solid, shift = -1, axis= 0).astype(int)
self.fluid.u = self.solid.dvol / (
neighbors + 1 *
(neighbors == 0)) * not_solid * self.solid.poros
ux = (np.roll(self.fluid.u,1,1) - np.roll(self.fluid.u,-1,1))* \
not_solid
uy = (np.roll(self.fluid.u,1,0) - np.roll(self.fluid.u,-1,0))* \
not_solid
velocity = np.array((uy, ux))
velocity = {}
for name in self.fluid.components:
velocity[name] = np.array((ux, uy))
self.fluid.set_attr('u', velocity)
else:
pass
def update_target_SI(self):
self.solid.vol_ch = self.volume_CH()
self.solid.vol_cc = self.volume_CC()
if (self.settings['pcs_mode']['pores'] == 'cylinder'):
#TODO check this case
if (self.iters <= 1):
self.solid.threshold_pore_size = self.settings['pcs_mode'][
'crystal_size']
self.solid.pore_length = self.settings['pcs_mode'][
'crystal_size']
self.solid.pore_amount = self.pore_amount()
self.solid.free_vol_cc = (self.solid.voxel_vol - self.solid.vol_ch
) * self.dx**3 #self.free_volume()
self.solid.pore_size = self.pore_size()
self.solid.pore_volume_cc = self.pore_volume_CC()
elif (self.settings['pcs_mode']['pores'] == 'block'):
if (self.iters < 1):
self.solid.threshold_crystal = self.settings['pcs_mode'][
'crystal_size'] #default crystal size
self.solid.threshold_pore_size = self.settings['pcs_mode'][
'pore_size']
self.solid.threshold_distance = self.solid.threshold_pore_size * 2
self.solid.block_size = self.block_size()
self.solid.free_vol_cc = (
self.solid.voxel_vol - self.solid.vol_ch
) * self.dx**3 #self.solid._poros * self.dx**3#self.get_pore_volume(self)
self.solid.ncrystals = self.block_amount()
self.solid.crystal_size = self.crystal_size()
self.solid.distance = self.distance()
self.solid.pore_size = self.pore_size()
else:
pass
self.solid.target_SI = self.target_SI()
self.phrqc._target_SI = self.solid.target_SI
def update_no_flux(self, ss):
ss['Ca'] = ss['Ca'] * (self.phrqc.boundcells
== 0) + 0 * (self.phrqc.boundcells == 1)
if (self.ptype == 'CSH'):
ss['Si'] = ss['Si'] * (self.phrqc.boundcells
== 0) + 0 * (self.phrqc.boundcells == 1)
return (ss)
def update_border(self):
is_port = (self.solid.portlandite.c > 0)
is_mineral = is_port | (self.solid.nodetype == ct.Type.SOLID)
val = -16
temp = deepcopy(self.solid.nodetype)
temp = temp * (~is_mineral) + val * is_mineral
rolled = np.roll(temp, -1, axis = 1)/4+np.roll(temp, 1, axis = 1)/4 +\
np.roll(temp, -1, axis = 0)/4+np.roll(temp, 1, axis = 0)/4
border = (rolled != val) & is_port
self.solid.border = border
#%% VOLUMES
def volume_CH(self):
CH_vol = self.solid.portlandite.c * self.solid.portlandite.mvol
return CH_vol
def volume_CC(self):
CC_vol = self.solid.calcite.c * self.solid.calcite.mvol
return CC_vol
def volume_CSH(self):
CSH_vol = self.solid.CSHQ_JenD.c * self.solid.CSHQ_JenD.mvol +\
self.solid.CSHQ_JenH.c * self.solid.CSHQ_JenH.mvol +\
self.solid.CSHQ_TobD.c * self.solid.CSHQ_TobD.mvol +\
self.solid.CSHQ_TobH.c * self.solid.CSHQ_TobH.mvol
return CSH_vol
def pore_volume_CC(self):
v = 0
if (self.settings['pcs_mode']['pores'] == 'cylinder'):
v = self.solid.pore_amount * np.pi * self.solid.pore_size**2 * \
self.solid.pore_length #*2
else:
v = self.free_volume()
return v
def free_volume(self):
v = self.solid.voxel_vol - self.solid.vol_ch
return v
#%% PORE PROPERTIES
def pore_amount(self, ptype='CH'):
'''
Return matrix of pore amounts per each cell
'''
vol = self.free_volume()
n = self.settings['pcs_mode'][
'pore_density'] * vol #* np.ones(np.shape(pore_vol))
n[n < 1] = 1
return n
@staticmethod
def get_cylinder_radius(pore_vol, pore_num, pore_length, dx):
'''
Formula for cylinder pore radius
Pore volume is total free volume or porosity
'''
r = (pore_vol * dx**3 / (pore_num * np.pi * pore_length))**(1. / 2.)
return r
def pore_size(self):
'''
Return matrix of pore radiuses per each cell
'''
pore_size = np.ones(np.shape(self.solid.shape))
if (self.settings['pcs_mode']['pores'] == 'cylinder'):
pore_size = self.get_cylinder_radius(
self.solid.poros,
self.solid.pore_amount, #self.settings['pcs']['pore_density']
self.solid.pore_length,
self.dx)
#pore_size[pore_size>self.solid.threshold_pore_size ] = self.solid.threshold_pore_size
else:
pore_size = self.solid.distance / 2.
return pore_size
def threshold_pore_size(self):
si = self.settings['pcs_mode']['threshold_SI']
omega = 10.**si
ps = (-1) * self.settings['si_params']['mvol'] *\
np.cos(np.pi*self.settings['si_params']['angle'])*2*\
self.settings['pcs_mode']['iene'] /\
self.settings['pcs_mode']['R'] /\
self.settings['pcs_mode']['T'] / np.log(omega)
return ps
def block_size(self):
return self.solid.threshold_crystal + self.solid.threshold_distance
def block_amount(self):
v_cp = (self.solid.threshold_crystal +
self.solid.threshold_distance)**3
N = self.solid.free_vol_cc / v_cp
return N
def crystal_size(self):
return (self.solid.vol_cc / self.solid.ncrystals)**(1. / 3.) * self.dx
def distance(self):
return (self.solid.block_size - self.solid.crystal_size)
def block_porosity(self):
v_cp = ((self.solid.crystal_size + self.solid.distance) / self.dx)**3
v_c = (self.solid.crystal_size + self.dx)**3
p = 1 - v_c / v_cp
return p
#%% SATURATION INDEX
def target_SI(self):
pore_size = self.solid.pore_size
si = self.saturation_index(pore_size)
#is_port = (self.solid.vol_ch >0)
not_critical = (pore_size >= self.solid.threshold_pore_size
) #rt.solid.radius_max
#si[np.logical_or(is_port, not_critical)]= 0
si[not_critical] = 0
return si
@staticmethod
def saturation_ratio(r,
int_energy=0.094,
angle=np.pi,
mvol=3.69e-5,
gas_c=8.314,
temp_kelv=298.3):
'''
Saturation ratio for pore-size controlled solubility
'''
omega = np.exp(-1 * mvol * np.cos(angle) * 2 * int_energy /
(gas_c * temp_kelv * r))
return omega
def saturation_index(self, size):
'''
Saturation index
'''
params = self.settings['pcs_mode']
omega = self.saturation_ratio(size, params.get('int_energy'), df.ANGLE,
df.MVOL_CC, df.GAS_CONSTANT,
df.TEMPERATURE)
si = np.log10(omega)
return si
#%% PROPERTIES
def csh_conc(self):
csh = self.solid.CSHQ_TobH.c+ self.solid.CSHQ_TobD.c +\
self.solid.CSHQ_JenH.c + self.solid.CSHQ_JenD.c
return csh
class LeachingRT(PhrqcReactiveTransport):
def __init__(self, eqn, domain, domain_params, bc_params, solver_params,
settings):
'''
Reactive transport class for carbonation
A Lattice Boltzmann method based reactive transport model \
where reactions are computed using geochemical solver PHREEQC
'''
if (settings['diffusivity']['type'] == 'fixed'):
print("newMlvl")
eqn = 'MultilevelAdvectionDiffusion2'
#solver_params['tauref'] = 1
#domain_params['Deref'] = settings['diffusivity']['D_border']
#solver_params['tauref'] = 0.5*np.max(settings['Dref'])/domain_params['Deref']+0.5#5.5 for 1e-10
self.auto_time_step = solver_params.get('auto_time_step', True)
self.phrqc = Phrqc(domain, domain_params, bc_params, solver_params)
components = self.phrqc.components
bc = self.phrqc.boundary_conditions
init_c = self.phrqc.initial_conditions
for name in components:
if name not in domain_params:
domain_params[name] = {}
domain_params[name]['c'] = init_c[name]
for name in bc:
for comp in components:
if comp not in bc_params:
bc_params[comp] = {}
bc_params[comp][name] = ['c', bc[name][comp]]
self.fluid = Multicomponent(eqn, components, domain, domain_params,
bc_params, solver_params)
self.solid = Solid(domain, domain_params, solver_params)
self.ptype = 'CSH' if hasattr(self.fluid, 'Si') else 'CH'
self.app_tort_degree = settings['app_tort']['degree']
self.update_solid_params()
self.nodetype = deepcopy(domain.nodetype)
self.apply_settings(settings)
self.update_nodetype()
self.update_border_and_interface(self.nodetype)
#self.fluid.call("_set_relaxation_params")
self.solid.prev_border = deepcopy(self.solid.border)
self.Dref = settings['Dref']
def advance(self):
#print(self.iters)
self.update_border_and_interface(self.nodetype)
if (~np.all(self.solid.border == self.solid.prev_border)):
print("update")
self.update_diffusivity()
self.solid.prev_border = deepcopy(self.solid.border)
self.fluid.call('advance')
if ('Multilevel'
in self.fluid.eqn) and (self.solid.n_diffusive_phases > 0):
self.fluid.call('update_transport_params', self.solid.poros,
self.solid.app_tort, self.auto_time_step)
self.phrqc.poros = deepcopy(self.solid.poros)
c = deepcopy(self.fluid.get_attr('c'))
phaseqty = self.solid.phaseqty_for_phrqc()
phase_list = deepcopy(self.solid.diffusive_phase_list)
for num, phase in enumerate(phase_list, start=1):
phaseqty[phase] = deepcopy(self.solid._diffusive_phaseqty[num - 1])
#if self.iters ==0:
# self.phrqc.modify_solid_phases(phaseqty)
#self.modify_eq(phaseqty)
ss = self.phrqc.modify_solution(c, self.dt, self.solid.nodetype)
if self.iters > 1: pqty = self.solid.update(self.phrqc.dphases)
ss = self.update_portlandite_eq(c, ss)
#if(self.settings['dissolution']=='subgrid'):
#ss=self.update_border_solution(c,ss)
self.set_volume()
self.set_porosity()
self.set_app_tort()
self.update_nodetype()
self.fluid.set_attr('nodetype',
self.solid.nodetype,
component_dict=False)
self.fluid.set_attr('ss', ss)
#self.fluid.call("_set_relaxation_params")
def modify_eq(self, phaseqty):
"""
modifies the phaseqty in phreeqc
Parameters
----------
phaseqty: dict
dictionary containing an ndarray of new quantities of equilibrium phases
"""
phaseqty = self.phrqc.flatten_dict(phaseqty)
modifystr = []
bord = np.where(self.solid.border.flatten())[0] + 1
for cell in range(self.phrqc.startcell, self.phrqc.stopcell + 1, 1):
if (cell not in bord):
modifystr.append("EQUILIBRIUM_PHASES_MODIFY %d" % cell)
for key in phaseqty.keys():
modifystr.append("\t -component %s" % (key))
modifystr.append("\t\t%s\t%.20e" %
('-moles', phaseqty[key][cell - 1]))
#modifystr.append("\t\t%s\t%.20e" %('-si', 2))
modifystr.append("end")
modifystr = '\n'.join(modifystr)
#print(modifystr)
self.phrqc.IPhreeqc.RunString(modifystr)
#%% SETTINGS
def set_volume(self):
self.solid.vol = np.zeros(self.solid.shape)
phase_list = deepcopy(self.solid.diffusive_phase_list)
for num, phase in enumerate(phase_list, start=1):
val = getattr(self.solid, phase)
self.solid.vol += val.c * self.solid.mvol[num - 1]
def set_porosity(self):
self.solid.poros = 1. - self.solid.vol / self.solid.voxel_vol
if np.any(self.solid.poros <= 1e-10):
sys.exit('Negative or zero porosity')
def set_app_tort(self):
d = self.app_tort_degree
self.solid.app_tort = 1. * self.solid.poros**d
def set_boundary_cells(self):
nodes = np.zeros(np.shape(self.nodetype))
nodes[0, :] = ct.Type.SOLID
nodes[-1, :] = ct.Type.SOLID
nodes[:, 0] = ct.Type.SOLID
nodes[:, -1] = ct.Type.SOLID
return nodes
def apply_settings(self, settings):
self.settings = settings
self.dx = settings['dx']
#%% UPDATES
def update_diffusivity(self):
Dref = self.Dref
D_border = self.Dref
if ('D_border' in self.settings['diffusivity']):
D_border = self.settings['diffusivity']['D_border']
if ('D_CH' in self.settings['diffusivity']):
D_CH = self.settings['diffusivity']['D_CH']
is_border = self.solid.border
is_port = (self.solid.portlandite.c > 0) & (~is_border)
is_liquid = np.logical_and(~is_port, ~is_border)
#Dnew_lb = Dref*np.ones(np.shape(self.nodetype))
De = D_CH * is_port + D_border * is_border + Dref * is_liquid
#print(De[1,:])
#Dnew_lb = De/self.solid.poros/self.solid.app_tort
#(Dnew_lb[1,:])
self.fluid.set_attr('D0', De, component_dict=False)
self.fluid.set_attr('Deref', np.max(De), component_dict=False)
self.fluid.call("_set_relaxation_params")
def update_solid_params(self):
'''
Calculates porosity, apparent tortuosity,
volume and change in volume last time step
'''
self.set_volume()
self.set_porosity()
self.set_app_tort()
def update_nodetype(self):
prev_nodetype = self.nodetype
is_port = (self.solid.portlandite.c > 0)
is_solid = self.solid.nodetype == ct.Type.SOLID
is_interface = np.zeros(np.shape(is_port))
#calc_c = self.phrqc.solid_phase_conc['calcite']
if self.ptype == 'CH':
is_liquid = (~is_port)
if (self.iters > 1):
is_liquid = (~is_port) & (~is_solid)
self.solid.nodetype = ct.Type.LIQUID * is_liquid + \
ct.Type.MULTILEVEL * is_port +\
ct.Type.INTERFACE * is_interface + \
ct.Type.SOLID * is_solid
if self.ptype == 'CSH':
pass
yantra._solvers.update2d.reassign_mlvl(self.solid.nodetype)
self.solid.nodetype[prev_nodetype == ct.Type.SOLID] = ct.Type.SOLID
yantra._solvers.update2d.reassign_mlvl_solid(self.solid.nodetype)
self.fluid.set_attr('nodetype',
self.solid.nodetype,
component_dict=False)
self.nodetype = self.solid.nodetype
def update_no_flux(self, ss):
ss['Ca'] = ss['Ca'] * (self.phrqc.boundcells
== 0) + 0 * (self.phrqc.boundcells == 1)
return (ss)
def update_border_and_interface(self, nodetype):
is_port = (self.solid.portlandite.c > 0)
is_mineral = is_port | (nodetype == ct.Type.SOLID)
val = -16
temp = deepcopy(nodetype)
temp = temp * (~is_mineral) + val * is_mineral
border = self.get_border(temp, val, is_port)
interface = self.get_interfaces(border, temp, val)
self.solid.border = border
self.solid.interface = interface
def get_border(self, nt, val, is_port):
rolled = np.roll(nt, -1, axis = 1)/4+np.roll(nt, 1, axis = 1)/4 +\
np.roll(nt, -1, axis = 0)/4+np.roll(nt, 1, axis = 0)/4
is_border = (rolled != val) & is_port
return (is_border)
def get_interfaces(self, is_border, nt, val):
down = is_border & (np.roll(nt, 1, axis=0) != val)
up = is_border & (np.roll(nt, -1, axis=0) != val)
left = is_border & (np.roll(nt, 1, axis=1) != val)
right = is_border & (np.roll(nt, -1, axis=1) != val)
interfaces = {
'left': left,
'right': right,
'up': up,
'down': down,
'sum': 1 * down + 1 * up + 1 * left + 1 * right
}
return interfaces
def update_border_solution(self, c, ss):
phrqc_poros = self.phrqc.selected_output()['poros']
fr = np.zeros(phrqc_poros.shape)
fraction = self.settings['subgrid']['fraction']
result = {}
by = np.where(self.solid.border)[0]
bx = np.where(self.solid.border)[1]
bf = np.where(self.solid.border.flatten())[0]
lx = self.nodetype.shape[1]
for i in np.arange(0, np.sum(self.solid.border)):
if fraction is None:
fraction = 1 - phrqc_poros[by[i], bx[i]]
else:
if (self.settings['subgrid']['poros']):
fraction = fraction - phrqc_poros[by[i], bx[i]]
#print(fraction)
if fraction > 0:
fr[by[i], bx[i]] = fraction
if (self.solid.interface['down'][by[i], bx[i]]):
cell_i = bf[i] + 1 - lx
cell_m = bf[i] + 1
result = self.update_neighbour_solution(
result, cell_i, cell_m,
self.solid.portlandite.c[by[i], bx[i]], fraction)
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (
result[str(cell_m) + ' ' + str(cell_i)][name] -
c[name][by[i] - 1, bx[i]]) / self.dt
ssnew[name] *= phrqc_poros[by[i] - 1, bx[i]]
ss[name][by[i] - 1, bx[i]] = ssnew[name]
if (self.solid.interface['up'][by[i], bx[i]]):
cell_i = bf[i] + 1 + lx
cell_m = bf[i] + 1
result = self.update_neighbour_solution(
result, cell_i, cell_m,
self.solid.portlandite.c[by[i], bx[i]],
fraction) #self.solid.poros[1,1])
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (
result[str(cell_m) + ' ' + str(cell_i)][name] -
c[name][by[i] + 1, bx[i]]) / self.dt
ssnew[name] *= phrqc_poros[by[i] + 1, bx[i]]
ss[name][by[i] + 1, bx[i]] = ssnew[name]
if (self.solid.interface['left'][by[i], bx[i]]):
cell_i = bf[i]
cell_m = bf[i] + 1
result = self.update_neighbour_solution(
result, cell_i, cell_m,
self.solid.portlandite.c[by[i], bx[i]], fraction)
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (
result[str(cell_m) + ' ' + str(cell_i)][name] -
c[name][by[i], bx[i] - 1]) / self.dt
ssnew[name] *= phrqc_poros[by[i], bx[i] - 1]
ss[name][by[i], bx[i] - 1] = ssnew[name]
if (self.solid.interface['right'][by[i], bx[i]]):
cell_i = bf[i] + 2
cell_m = bf[i] + 1
result = self.update_neighbour_solution(
result, cell_i, cell_m,
self.solid.portlandite.c[by[i], bx[i]], fraction)
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (
result[str(cell_m) + ' ' + str(cell_i)][name] -
c[name][by[i], bx[i] + 1]) / self.dt
ssnew[name] *= phrqc_poros[by[i], bx[i] + 1]
ss[name][by[i], bx[i] + 1] = ssnew[name]
for i in np.arange(0, np.sum(self.solid.border)):
if (self.solid.interface['down'][by[i], bx[i]]
and fr[by[i], bx[i]] > 0):
self.solid.portlandite.c[by[i], bx[i]] = result[
str(bf[i] + 1) + ' ' +
str(bf[i] - lx + 1)]['portlandite_m']
if (self.solid.interface['up'][by[i], bx[i]]
and fr[by[i], bx[i]] > 0):
self.solid.portlandite.c[by[i], bx[i]] = result[
str(bf[i] + 1) + ' ' +
str(bf[i] + lx + 1)]['portlandite_m']
if (self.solid.interface['left'][by[i], bx[i]]
and fr[by[i], bx[i]] > 0):
self.solid.portlandite.c[by[i], bx[i]] = result[
str(bf[i] + 1) + ' ' + str(bf[i])]['portlandite_m']
if (self.solid.interface['right'][by[i], bx[i]]
and fr[by[i], bx[i]] > 0):
self.solid.portlandite.c[by[i], bx[i]] = result[
str(bf[i] + 1) + ' ' + str(bf[i] + 2)]['portlandite_m']
return ss
def update_portlandite_eq(self, c, ss):
phrqc_poros = self.phrqc.selected_output()['poros']
fr = np.zeros(phrqc_poros.shape)
fraction = self.settings['subgrid']['fraction']
result = {}
by = np.where(self.solid.border)[0]
bx = np.where(self.solid.border)[1]
bf = np.where(self.solid.border.flatten())[0]
for i in np.arange(0, np.sum(self.solid.border)):
if fraction > 0:
fr[by[i], bx[i]] = fraction
cell_m = bf[i] + 1
result = self.update_equilibrium(
result, cell_m, self.solid.portlandite.c[by[i], bx[i]],
phrqc_poros[by[i], bx[i]], fraction)
ssnew = {}
for name in self.phrqc.components:
ssnew[name] = (result[str(cell_m)][name] -
c[name][by[i], bx[i]]) / self.dt
ssnew[name] *= phrqc_poros[by[i], bx[i]]
ss[name][by[i], bx[i]] = ssnew[name]
for i in np.arange(0, np.sum(self.solid.border)):
self.solid.portlandite.c[by[i],
bx[i]] = result[str(bf[i] +
1)]['portlandite_m']
return ss
def update_equilibrium(self, result, n_ch, m_ch, porosity, fraction=1):
ncell = 123456
fract = fraction / porosity
if fract > 1: fract = 1
#print(fract)
modify_str = []
modify_str.append("EQUILIBRIUM_PHASES %i" % ncell)
modify_str.append("Portlandite 0 %.20e dissolve only" % (m_ch))
modify_str.append("END")
modify_str.append('MIX %i' % ncell)
modify_str.append('%i %.20e' %
(n_ch, fract)) #modify_str.append('%i 1' %n_int)
modify_str.append('SAVE solution %i' % ncell)
modify_str.append("END")
modify_str.append('USE solution %i' % ncell)
modify_str.append('USE equilibrium_phase %i' % ncell)
modify_str.append('SAVE solution %i' % ncell)
modify_str.append("END")
modify_str.append("END")
modify_str = '\n'.join(modify_str)
self.phrqc.IPhreeqc.RunString(modify_str)
output = self.phrqc.IPhreeqc.GetSelectedOutputArray()
#print(modify_str)
#print(output)
port = output[2][9]
modify_str = []
modify_str.append("EQUILIBRIUM_PHASES %i" % n_ch)
modify_str.append("Portlandite 0 %.20e" % (0)) # dissolve only
modify_str.append("END")
modify_str.append('USE equilibrium_phase %i' % n_ch)
modify_str.append('MIX %i' % ncell)
modify_str.append('%i 1' % ncell)
modify_str.append(
'%i %.20e' % (n_ch, 1. - fract)) #modify_str.append('%i 0' %n_int)
modify_str.append('SAVE solution %i' % (n_ch))
#modify_str.append('SAVE equilibrium_phase %i' %(n_ch))
modify_str.append("END")
modify_str = '\n'.join(modify_str)
self.phrqc.IPhreeqc.RunString(modify_str)
output = self.phrqc.IPhreeqc.GetSelectedOutputArray()
#print(modify_str)
#print(output)
comp = {}
comp['portlandite_m'] = port
comp['Ca'] = output[1][6]
comp['H'] = (output[1][7] - self.phrqc.H_norm)
comp['O'] = (output[1][8] - self.phrqc.O_norm)
result[str(n_ch)] = comp
return (result)
#%% PROPERIES
def volume_CH(self):
CH_vol = self.solid.portlandite.c * self.solid.portlandite.mvol
return CH_vol
def volume_CSH(self):
CSH_vol = self.solid.CSHQ_JenD.c * self.solid.CSHQ_JenD.mvol +\
self.solid.CSHQ_JenH.c * self.solid.CSHQ_JenH.mvol +\
self.solid.CSHQ_TobD.c * self.solid.CSHQ_TobD.mvol +\
self.solid.CSHQ_TobH.c * self.solid.CSHQ_TobH.mvol
return CSH_vol
def free_volume(self):
v = self.solid.voxel_vol - self.solid.vol_ch
return v
def csh_conc(self):
csh = self.solid.CSHQ_TobH.c+ self.solid.CSHQ_TobD.c +\
self.solid.CSHQ_JenH.c + self.solid.CSHQ_JenD.c
return csh