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fdata.py
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"""Class for FEHM data"""
"""
Copyright 2013.
Los Alamos National Security, LLC.
This material was produced under U.S. Government contract DE-AC52-06NA25396 for
Los Alamos National Laboratory (LANL), which is operated by Los Alamos National
Security, LLC for the U.S. Department of Energy. The U.S. Government has rights
to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS
ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES
ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce
derivative works, such modified software should be clearly marked, so as not to
confuse it with the version available from LANL.
Additionally, this library is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by the
Free Software Foundation; either version 2.1 of the License, or (at your option)
any later version. Accordingly, this library 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 Lesser General
Public License for more details.
"""
import numpy as np
from copy import copy, deepcopy
import os,time,platform,shutil,sys
from subprocess import Popen, PIPE
from time import sleep
from collections import Counter
from matplotlib.patches import Rectangle
try: import ctypes; has_ctypes = True
except: has_ctypes = False
try:
from matplotlib import pyplot as plt
#plt.ion()
from mpl_toolkits.mplot3d import axes3d
from matplotlib import cm
from matplotlib.pylab import subplots,close
except ImportError:
'placeholder'
from fgrid import*
from fvars import*
from fpost import*
from fdflt import*
from fhelp import*
dflt = fdflt()
WINDOWS = platform.system()=='Windows'
if not WINDOWS: has_ctypes = False
# list of macros that might be encountered
fdata_sections = ['cont','pres','zonn','zone','cond','time','ctrl','iter','rock','perm',
'boun','flow','strs','text','sol','nfin','hist','node','carb','rlp','grad','nobr',
'flxz','rlpm','hflx','trac','vcon','ppor','vapl','adif','ngas','flxo','head','flxn','air','airwater']
# list of potential CONTOUR output variables
contour_variables=[['strain','stress'],
['co2'],
['vapor','dp','grid','capillary','density','displacement','fhydrate','flux','permeability','porosity','source','velocity','wt','zid'],
['formatted','material','liquid','geo','nodit','concentration','head','pressure','saturation','temperature','xyz','zone']]
# list of potential HISTORY output variables
history_variables=['deg','temperature','mpa','pressure','head','meters','feet','saturation','wco','flow','kgs',
'enthalpy','efl','mjs','density','humidity','viscosity','zflux','concentration','wt','co2s',
'co2sl','co2sg','co2m','co2mt','co2mf','co2md','cfluxz','displacements','disx','disy','disz',
'stress','strsx','strsy','strsz','strsxy','strsxz','strsyz','strain','rel','global']
# dictionary of perm model parameters, indexed by perm model number, ORDER OF LIST MUST EQUAL ORDER OF INPUT
permDicts = dict((
(1,[]),
(21,['nx','ny','nz','frict_coef','cohesion','pore_press_factor','tau_ex_ramp_range',
'yngs_mod_mult_x','yngs_mod_mult_y','yngs_mod_mult_z','perm_mult_x','perm_mult_y','perm_mult_z']),
(22,['frict_coef','cohesion','pore_press_factor','tau_ex_ramp_range','yngs_mod_mult_x','yngs_mod_mult_y',
'yngs_mod_mult_z','perm_mult_x','perm_mult_y','perm_mult_z','por_mult','perm_incremental','tau_ex_init']),
(24,['shear_frac_tough','static_frict_coef','dynamic_frict_coef','frac_num','onset_disp',
'disp_interval','max_perm_change','frac_cohesion','frac_dens']),
(25,['shear_frac_tough',
'static_frict_coef','dynamic_frict_coef','frac_num','onset_disp','disp_interval','max_perm_change',
'frac_cohesion']),
(100,['perm_mult_x','perm_mult_y','perm_mult_z','ramp_range']),
))
# dictionary of plastic model parameters, indexed by plastic model number, ORDER OF LIST MUST EQUAL ORDER OF INPUT
plasticDicts = dict((
(3,['youngs_modulus','poissons_ratio','eta_drucker','zeta_drucker','c_drucker']),
))
# dictionary of perm model units, indexed by perm model number, ORDER OF LIST MUST EQUAL ORDER OF INPUT
permUnits = dict((
(1,[]),
(21,['','','','','MPa','','MPa','','','','','','']),
(22,['','MPa','','MPa','','','','','','','','','MPa']),
(24,['MPa/m','','','','m','m','log(m^2)','MPa','']),
(25,['MPa/m','','','','m','m','log(m^2)','MPa']),
(100,['','','','MPa']),
))
# dictionary of relative permeability model parameters, indexed by model number, ORDER OF LIST MUST EQUAL ORDER OF INPUT
rlpDicts = dict((
(-1,['liq_rel_perm','vap_rel_perm','cap_pres_zero_sat','sat_zero_cap_pres']),
(1,['resid_liq_sat','resid_vap_sat','max_liq_sat','max_vap_sat','cap_pres_zero_sat','sat_zero_cap_pres']),
(2,['resid_liq_sat','resid_vap_sat','cap_pres_zero_sat','sat_zero_cap_pres']),
(3,['resid_liq_sat','resid_vap_sat','inv_air_entry_head','power_exponent',
'low_sat_fit_param','cutoff_sat']),
(16,['resid_water_sat','max_water_sat','water_exp','resid_co2_sat','max_co2_sat','co2_exp',
'co2_water_Pc_exp','co2_water_Pc_max']),
(17,['resid_water_sat','max_water_sat','water_exp','resid_co2liq_sat','max_co2liq_sat','co2liq_exp',
'co2gasliq_exp','resid_co2gas_sat','max_co2gas_sat','co2gas_exp','co2liq_water_Pc_exp','co2liq_water_Pc_max',
'co2liq_co2gas_Pc_exp','co2liq_co2gas_Pc_max']),
))
adsorptionDicts = dict((
(0,['alpha1','alpha2','beta']), # conservative solute
(1,['alpha1','alpha2','beta']), # linear sorption isotherm
(2,['alpha1','alpha2','beta']), # Freundlich sorption isotherm
(3,['alpha1','alpha2','beta']), # Modified Freundlich sorption isotherm
(4,['alpha1','alpha2','beta']), # Langmuir sorption isotherm
))
diffusionDicts = dict((
(0,['diffusion','dispersion_x','dispersion_y','dispersion_z']), # molecular diffusion coefficient is constant
(1,['diffusion','dispersion_x','dispersion_y','dispersion_z']), # Millington Quark diffusion model
(2,['diffusion','dispersion_x','dispersion_y','dispersion_z']), # Conca Wright diffusion model
(3,['diffusion','dispersion_x','dispersion_y','dispersion_z']), # calculated from adif
))
vconDicts = dict((
(1,['T_ref','cond_ref','dcond_dT']), # linear variation of thermal conductivity with temperature
(2,['cond_s1','cond_s0']), # square root variation of thermal conductivity with liquid saturation
(3,['T_ref','cond_ref','exponent']), # intact salt
(4,['T_ref','cond_ref','coeff_phi4','coeff_phi3','coeff_phi2','coeff_phi1','coeff_phi0','exponent']), # crushed salt
))
pporDicts = dict((
(1,['compressibility']), # aquifer compressibility
(-1,['specific_storage']), # specific storage
(-2,['exponent','Px']), # gangi model
(7,['param1','param2','param3','param4']), # unknown - salt
))
model_list = dict((('permmodel',permDicts),
('plasticmodel',plasticDicts),
('rlp',rlpDicts),
('vcon',vconDicts),
('ppor',pporDicts),
('adsorption',adsorptionDicts),
('diffusion',diffusionDicts)))
model_titles = dict((('rlp','RELATIVE PERMEABILITY'),
('permmodel',''),
('plasticmodel',''),
('vcon','VARIABLE THERMAL CONDUCTIVITY'),
('ppor','VARIABLE POROSITY'),
('dispersion',''),
('adsorption',''),
))
# list of macros
fpres = (('pressure',None),('temperature',None),('saturation',None))
fperm = (('kx',None),('ky',None),('kz',None))
fcond = (('cond_x',None),('cond_y',None),('cond_z',None))
fflow = (('rate',None),('energy',None),('impedance',None))
frock = (('density',None),('specific_heat',None),('porosity',None))
fgrad = (('reference_coord',None),('direction',None),('variable',None),('reference_value',None),('gradient',None))
fbiot = (('thermal_expansion',None),('pressure_coupling',None))
felastic = (('youngs_modulus',None),('poissons_ratio',None))
fbodyforce = (('fx',None),('fy',None),('fz',None))
fco2frac = (('water_rich_sat',None),('co2_rich_sat',None),('co2_mass_frac',None),('init_salt_conc',None),('override_flag',None))
fco2flow = (('rate',None),('energy',None),('impedance',None),('bc_flag',None))
fco2diff = (('diffusion',None),('tortuosity',None))
fco2pres = (('pressure',None),('temperature',None),('phase',None))
fstressboun = (('value',None),('direction',None))
fhflx = (('heat_flow',None),('multiplier',None))
ftpor = (('tracer_porosity',None),)
macro_list = dict((('pres',fpres),('perm',fperm),('cond',fcond),('flow',fflow),('rock',frock),
('biot',fbiot),('elastic',felastic),('bodyforce',fbodyforce),('co2frac',fco2frac),('co2flow',fco2flow),
('co2pres',fco2pres),('co2diff',fco2diff),
('stressboun',fstressboun),('grad',fgrad),('hflx',fhflx),('tpor',ftpor)))
# potential nodal properties
node_props = ('kx','ky','kz','cond_x','cond_y','cond_z','density','specific_heat','porosity','thermal_expansion','pressure_coupling',
'youngs_modulus','poissons_ratio')
node_gen = ('rate','energy','impedance')
macro_titles = dict((('pres','INITIAL TEMPERATURE AND PRESSURE'),
('perm','PERMEABILITY'),
('cond','ROCK CONDUCTIVITY'),
('flow','GENERATORS'),
('hflx',''),
('rock','MATERIAL PARAMETERS'),
('grad','INITIAL VARIABLE GRADIENTS'),
('elastic',''),
('biot',''),
('bodyforce',''),
('co2flow',''),
('co2frac',''),
('co2pres',''),
('co2diff',''),
('stressboun',''),
('rlpm','RELATIVE PERMEABILITY'),
('tpor',''),))
macro_descriptor = dict((
('pres','Initial conditions'),
('perm','Permeability'),
('cond','Thermal conductivity properties'),
('flow','Source or sink'),
('rock','Material properties'),
('grad','Initial condition gradients'),
('elastic','Elastic properties'),
('bodyforce','Body force at node'),
('biot','Fluid-stress coupling properties'),
('co2flow','CO2 source of sink'),
('co2frac','CO2 fraction'),
('co2pres','CO2 initial conditions'),
('co2diff','CO2 diffusion properties'),
('stressboun','Stress boundary condition'),
('permmodel','Stress permeability relationship'),
('plasticmodel','Plasticity relationship'),
('rlp','Relative permeablity relationship'),
('hflx','Heat flux boundary condition'),
('tpor','Tracer porosity'),)
)
rlpm_dicts=dict((
('constant',{}),
('linear',(('minimum_saturation',0),('maximum_saturation',1))),
('exponential',(('minimum_saturation',0),('maximum_saturation',1),('exponent',1),('maximum_relperm',1))),
('corey',(('minimum_saturation',0),('maximum_saturation',1))),
('brooks-corey',(('minimum_saturation',0),('maximum_saturation',1),('exponent',1))),
('vg',(('minimum_saturation',0),('maximum_saturation',1),('air_entry_head',1),('exponent',1))),
('linear_cap',(('cap_at_zero_sat',None),('sat_at_zero_cap',None))),
('brooks-corey_cap',(('minimum_saturation',0),('maximum_saturation',1),('exponent',1),('capillary_entry_presure',0.01),
('low_saturation_fitting',None),('cutoff_saturation',None))),
('vg_cap',(('minimum_saturation',0),('maximum_saturation',1),('air_entry_head',1),('exponent',1),
('low_saturation_fitting',None),('cutoff_saturation',None))),
))
rlpm_cap1 = dict((('vg_cap','vg_cap'),('brooks-corey_cap','brooks-corey'),('linear_cap','linear_for')))
rlpm_cap2 = dict((('vg_cap','vg_cap'),('brooks-corey','brooks-corey_cap'),('linear_for','linear_cap')))
rlpm_phases = ['water','air','co2_liquid','co2_gas','vapor']
buildWarnings = []
def _buildWarnings(s):
global buildWarnings
buildWarnings.append(s)
def _title_string(s,n): #prepends headers to sections of FEHM input file
if not n: return
ws = '# '
pad = int(np.floor((n - len(s) - 2)/2))
for i in range(pad): ws+='-'
ws+=s
for i in range(pad): ws+='-'
ws+='\n'
return ws
def _zone_ind(indStr): return abs(int(indStr))-(int(indStr)+abs(int(indStr)))/2
class fzone(object): #FEHM zone object.
"""FEHM Zone object.
"""
__slots__ = ['_index','_type','_points','_file','_name','_parent','_nodelist','_file','_permeability',
'_conductivity','_density','_specific_heat','_porosity','_youngs_modulus','_poissons_ratio',
'_thermal_expansion','_pressure_coupling','_Pi','_Ti','_Si','_fixedT','_fixedP','_updateFlag','_silent']
def __init__(self,index=None,type='',points=[],nodelist=[],file='',name = ''):
self._index=None
self._silent = dflt.silent
if index != None: self._index = index
self._type=''
if type: self._type = type
self._points=[]
if points: self._points=points
self._file = ''
self._name = ''
self._parent = None
if name: self._name = name
self._nodelist=[]
if (self.type == 'nnum' or self.type == 'list') and nodelist:
self._nodelist = nodelist
if file: self._file = file
# material properties
self._permeability = None
self._conductivity = None
self._density = None
self._specific_heat = None
self._porosity = None
self._youngs_modulus = None
self._poissons_ratio = None
self._thermal_expansion = None
self._pressure_coupling = None
self._Pi = None
self._Ti = None
self._Si = None
self._fixedT = None
self._fixedP = None
self._updateFlag = True
def __repr__(self): return 'zn'+str(self.index)
def __getstate__(self):
return dict((k, getattr(self, k)) for k in self.__slots__)
def __setstate__(self, data_dict):
for (name, value) in data_dict.items():
setattr(self, name, value)
def _get_index(self): return self._index
def _set_index(self,value): self._index = value
index = property(_get_index,_set_index) #: (*int*) Integer number denoting the zone.
def _get_type(self): return self._type
def _set_type(self,value):
oldtype = self._type
self._type = value
if self._type != oldtype:
self._points = []
type = property(_get_type,_set_type) #: (*str*) String denoting the zone type. Default is 'rect', alternatives are 'list', 'nnum'
def _get_name(self): return self._name
def _set_name(self,value): self._name = value
name = property(_get_name,_set_name) #: (*str*) Name of the zone. Will appear commented beside the zone definition in the input file. Can be used to index the ``fdata.zone`` attribute.
def _get_file(self): return self._file
def _set_file(self,value): self._file=value
file = property(_get_file,_set_file) #: (*str*) File name if zone data is or is to be contained in a separate file. If file does not exist, it will be created and written to when the FEHM input file is being written out.
def rect(self,p1,p2): #generates a rectangular zone based on corner coordinates
"""Create a rectangular zone corresponding to the bounding box delimited by p1 and p2.
:param p1: coordinate of first corner of the bounding box.
:type p1: ndarray
:param p2: coordinate of the second corner of the bounding box.
:type p2: ndarray
"""
self.type='rect'
if len(p1) == 2:
xmax,xmin = np.max([p1[0],p2[0]]),np.min([p1[0],p2[0]])
ymax,ymin = np.max([p1[1],p2[1]]),np.min([p1[1],p2[1]])
self.points=[[xmin,xmax,xmax,xmin],
[ymax,ymax,ymin,ymin],
#[0., 0., 0., 0., 0., 0., 0., 0.]
]
elif len(p1) == 3:
xmax,xmin = np.max([p1[0],p2[0]]),np.min([p1[0],p2[0]])
ymax,ymin = np.max([p1[1],p2[1]]),np.min([p1[1],p2[1]])
zmax,zmin = np.max([p1[2],p2[2]]),np.min([p1[2],p2[2]])
self.points=[[xmin,xmax,xmax,xmin,xmin,xmax,xmax,xmin],
[ymax,ymax,ymin,ymin,ymax,ymax,ymin,ymin],
[zmax,zmax,zmax,zmax,zmin,zmin,zmin,zmin]]
def fix_temperature(self,T,multiplier=1.e10,file=None):
''' Fixes temperatures at nodes within this zone. Temperatures fixed by adding an HFLX macro with high
heat flow multiplier.
:param T: Temperature to fix.
:type T: fl64
:param multiplier: Multiplier for HFLX macro (default = 1.e10)
:type multiplier: fl64
:param file: Name of auxiliary file to save macro.
:type file: str
'''
if not self._parent:
pyfehm_print('fix_temperature() only available if zone associated with fdata() object',self._silent)
return
self._parent.add(fmacro('hflx',zone=self,param=(('heat_flow',T),('multiplier',multiplier)),file=file))
self._fixedT = T
def fix_pressure(self,P=0, T=30., impedance=1.e6, file = None):
''' Fixes pressures at nodes within this zone. Pressures fixed by adding a FLOW macro with high
impedance.
:param P: Pressure to fix. Default is 0, corresponding to fixing initial pressure.
:type P: fl64
:param T: Temperature to fix (default = 30 degC).
:type T: fl64
:param impedance: Impedance for FLOW macro (default = 1.e6)
:type impedance: fl64
:param file: Name of auxiliary file to save macro.
:type file: str
'''
if not self._parent:
pyfehm_print('fix_pressure() only available if zone associated with fdata() object',self._silent)
return
self._parent.add(fmacro('flow',zone=self,param=(('rate',P),('energy',-T),('impedance',impedance)),file=file))
self._fixedP = [P,T]
def fix_displacement(self,direction,displacement,file=None):
''' Fixes displacement at nodes within this zone. Displacements fixed by adding a STRESSBOUN macro.
:param direction: Direction in which displacement is fixed. Specify as string or integer, e.g., 1 = 'x', 2 = 'y', 3 = 'z'.
:type direction: str, int
:param displacement: Fixed displacement
:type displacement: fl64
:param file: Name of auxiliary file to save macro.
:type file: str
'''
if not self._parent:
pyfehm_print('fix_displacement() only available if zone associated with fdata() object',self._silent)
return
if direction == 'x': direction = 1
elif direction == 'y': direction = 2
elif direction == 'z': direction = 3
elif direction in [1,2,3]: pass
else:
pyfehm_print('direction must be specified as either 1, 2, 3, \'x\', \'y\', \'z\'.',self._silent)
return
self._parent.add(fmacro('stressboun',zone=self,param=(('direction',direction),('value',displacement)),file=file))
def fix_stress(self,direction,stress,file=None):
''' Fixes displacement at nodes within this zone. Displacements fixed by adding a STRESSBOUN macro.
:param direction: Direction in which stress is fixed. Specify as string or integer, e.g., 1 = 'x', 2 = 'y', 3 = 'z'.
:type direction: str, int
:param stress: Fixed stress
:type stress: fl64
:param file: Name of auxiliary file to save macro.
:type file: str
'''
if not self._parent:
pyfehm_print('fix_stress() only available if zone associated with fdata() object',self._silent)
return
if direction == 'x': direction = 1
elif direction == 'y': direction = 2
elif direction == 'z': direction = 3
elif abs(direction) in [1,2,3]: pass
else:
pyfehm_print('direction must be specified as either 1, 2, 3, \'x\', \'y\', \'z\'.',self._silent)
return
self._parent.add(fmacro('stressboun',zone=self,param=(('direction',-abs(direction)),('value',stress)),file=file))
def roller(self,direction=None,file=None):
''' Assigns a roller boundary condition to the zone (zero displacement in normal direction).
:param direction: Normal of roller. Specify as string or integer, e.g., 1 = 'x', 2 = 'y', 3 = 'z'. Defaults to zone normal for 'XMIN', 'ZMAX' etc.
:type direction: str, int
'''
if direction is None:
if self.name in ['XMIN','XMAX']: direction = 1
elif self.name in ['YMIN','YMAX']: direction = 2
elif self.name in ['ZMIN','ZMAX']: direction = 3
else:
pyfehm_print('no direction specified',self._silent)
return
self.fix_displacement(direction=direction,displacement=0,file=file)
def free_surface(self,direction=None,file=None):
''' Assigns a free surface boundary condition to the zone (zero stress in normal direction).
:param direction: Normal of free surface. Specify as string or integer, e.g., 1 = 'x', 2 = 'y', 3 = 'z'. Defaults to zone normal for 'XMIN', 'ZMAX' etc.
:type direction: str, int
'''
if direction is None:
if self.name in ['XMIN','XMAX']: direction = -1
elif self.name in ['YMIN','YMAX']: direction = -2
elif self.name in ['ZMIN','ZMAX']: direction = -3
else:
pyfehm_print('no direction specified',self._silent)
return
self.fix_stress(direction=direction,stress=0,file=file)
def extract(self, rate, zoneflux_output=True):
''' convenience method for adding extraction
:param rate: If float, interpreted as constant extraction rate, otherwise a two column array denoting variable extraction rate over time.
:type rate: float, array-like
:param zoneflux_output: Flag indicating whether output should be generated for this source term.
:type displacement: bool
'''
# check if array-like
try:
[_ for _ in rate]
variable_extraction=True
rate = np.array(rate)
assert any(np.array(rate.shape) == 2)
if rate.shape[1] != 2: rate = rate.T
except TypeError:
rate = float(rate)
variable_extraction=False
if variable_extraction:
flow = fboun('ti_linear', self.index, times=rate[:,0], variable=[['dsw'+list(rate[:,1])],])
else:
flow = fmacro('flow',self.index,(('rate',rate),('energy',50),('impedance',0)))
self._parent.add(flow)
if zoneflux_output:
self._parent.hist.zoneflux.append(self)
self._parent.hist.variables = list(set(self._parent.hist.variables+['flow','zflux']))
if len(self._parent.hist.nodelist) == 0:
self._parent.hist.nodelist.append(self.nodelist[0])
def copy_from(self,from_zone=None,grid_new=None,method = 'nearest',grid_old=None):
'''Transfer zone information from one grid to another.
:param from_zone: Zone object to convert.
:type from_zone: fzone
:param method: Method for node to node transfer of zone. Options are 'nearest', 'volume'.
:type method: str
'''
if grid_new: self.grid = grid_new
if grid_old: from_zone.grid = grid_old
if not self.index: self.index = from_zone.index
if not from_zone: pyfehm_print('No zone supplied',self._silent); return
if from_zone.type == 'rect': # if rectangular zone, copy across bounding box
self.type = 'rect'
self.points = from_zone.points
else: # zone comprises a list of nodes
if not from_zone.grid or not from_zone.nodelist:
pyfehm_print('Supplied zone does not contain grid information.',self._silent)
return
from_nodes = from_zone.nodelist
if method == 'nearest':
ndinds = np.unique([self.grid.node_nearest_point(nd.position) for nd in from_nodes])
ndinds = [nd.index for nd in ndinds if nd != None]
elif method == 'volume':
raise
if not self.type: self.type = from_zone.type
self.nodelist = [self.grid.node[ndind] for ndind in ndinds]
def plot(self,save='',angle=[45,45],color='k',connections=False,equal_axes=True,
xlabel='x / m',ylabel='y / m',zlabel='z / m',title='',font_size='small'): #generates a 3-D plot of the zone.
'''Generates and saves a 3-D plot of the zone.
:param save: Name of saved zone image.
:type save: str
:param angle: View angle of zone. First number is azimuth angle in degrees, second number is tilt. Alternatively, if angle is 'x', 'y', 'z', view is aligned along the corresponding axis.
:type angle: [fl64,fl64], str
:param color: Colour of zone.
:type color: str, [fl64,fl64,fl64]
:param connections: Plot connections. If ``True`` all connections plotted. If between 0 and 1, random proportion plotted. If greater than 1, specified number plotted.
:type connections: bool
:param equal_axes: Force plotting with equal aspect ratios for all axes.
:type equal_axes: bool
:param xlabel: Label on x-axis.
:type xlabel: str
:param ylabel: Label on y-axis.
:type ylabel: str
:param zlabel: Label on z-axis.
:type zlabel: str
:param title: Title of plot.
:type title: str
:param font_size: Size of text on plot.
:type font_size: str, int
*Example:*
``zn.plot(save='myzone.png', angle = [45,45], xlabel = 'x / m', font_size = 'small', color = 'r')``
'''
save = os_path(save)
if isinstance(angle,str):
if angle == 'x': angle = [0,0]
elif angle == 'y': angle = [0,90]
elif angle == 'z': angle = [90,90]
else: return
plotBoundingBox = False
plotZoneBox = False
if self._parent: plotBoundingBox = True
if self.type == 'rect': plotZoneBox = True
# plot bounding box
plt.clf()
fig = plt.figure(figsize=[8.275,11.7])
ax = plt.axes(projection='3d')
ax.set_aspect('auto', 'datalim')
ax.set_xlabel(xlabel,size=font_size)
ax.set_ylabel(ylabel,size=font_size)
ax.set_zlabel(zlabel,size=font_size)
ax.set_title(title,size=font_size)
for t in ax.get_xticklabels():
t.set_fontsize(font_size)
for t in ax.get_yticklabels():
t.set_fontsize(font_size)
for t in ax.get_zticklabels():
t.set_fontsize(font_size)
xmin,xmax = self._parent.grid.xmin, self._parent.grid.xmax
ymin,ymax = self._parent.grid.ymin, self._parent.grid.ymax
zmin,zmax = self._parent.grid.zmin, self._parent.grid.zmax
if equal_axes:
MAX = np.max([xmax-xmin,ymax-ymin,zmax-zmin])/2
C = np.array([xmin+xmax,ymin+ymax,zmin+zmax])/2
for direction in (-1, 1):
for point in np.diag(direction * MAX * np.array([1,1,1])):
ax.plot([point[0]+C[0]], [point[1]+C[1]], [point[2]+C[2]], 'w')
ax.view_init(angle[0],angle[1])
if plotBoundingBox:
# x lines
ax.plot([xmin,xmax],[ymin,ymin],[zmin,zmin],'k--')
ax.plot([xmin,xmax],[ymax,ymax],[zmin,zmin],'k--')
ax.plot([xmin,xmax],[ymax,ymax],[zmax,zmax],'k--')
ax.plot([xmin,xmax],[ymin,ymin],[zmax,zmax],'k--')
# y lines
ax.plot([xmin,xmin],[ymin,ymax],[zmin,zmin],'k--')
ax.plot([xmax,xmax],[ymin,ymax],[zmin,zmin],'k--')
ax.plot([xmax,xmax],[ymin,ymax],[zmax,zmax],'k--')
ax.plot([xmin,xmin],[ymin,ymax],[zmax,zmax],'k--')
# z lines
ax.plot([xmin,xmin],[ymin,ymin],[zmin,zmax],'k--')
ax.plot([xmin,xmin],[ymax,ymax],[zmin,zmax],'k--')
ax.plot([xmax,xmax],[ymax,ymax],[zmin,zmax],'k--')
ax.plot([xmax,xmax],[ymin,ymin],[zmin,zmax],'k--')
# plot node connections
if connections:
conns = []
for node in self.nodelist:
for nb in node.connected_nodes:
if nb in self.nodelist:
p1 = node.position
p2 = nb.position
conns.append((p1,p2))
if not isinstance(connections,bool): # plot all connections
if connections>0 and connections<1: # plot proportion of connections
connections = int(len(conns)*connections)
connections = np.min([connections,len(conns)])
import random
random.shuffle(conns)
conns = conns[:connections]
for p1,p2 in conns:
ax.plot([p1[0],p2[0]],[p1[1],p2[1]],[p1[2],p2[2]],color=color, linestyle = '-', linewidth = 0.5) # plot some connections
# plot nodes
for node in self.nodelist:
ax.plot([node.position[0],],[node.position[1],],[node.position[2],],
markerfacecolor=color,marker='o',markersize=3,markeredgecolor=color)
if plotZoneBox:
xmax,xmin = np.max(self.points[0]),np.min(self.points[0])
ymax,ymin = np.max(self.points[1]),np.min(self.points[1])
zmax,zmin = np.max(self.points[2]),np.min(self.points[2])
# x lines
ax.plot([xmin,xmax],[ymin,ymin],[zmin,zmin],color=color,linestyle='-')
ax.plot([xmin,xmax],[ymax,ymax],[zmin,zmin],color=color,linestyle='-')
ax.plot([xmin,xmax],[ymax,ymax],[zmax,zmax],color=color,linestyle='-')
ax.plot([xmin,xmax],[ymin,ymin],[zmax,zmax],color=color,linestyle='-')
# y lines
ax.plot([xmin,xmin],[ymin,ymax],[zmin,zmin],color=color,linestyle='-')
ax.plot([xmax,xmax],[ymin,ymax],[zmin,zmin],color=color,linestyle='-')
ax.plot([xmax,xmax],[ymin,ymax],[zmax,zmax],color=color,linestyle='-')
ax.plot([xmin,xmin],[ymin,ymax],[zmax,zmax],color=color,linestyle='-')
# z lines
ax.plot([xmin,xmin],[ymin,ymin],[zmin,zmax],color=color,linestyle='-')
ax.plot([xmin,xmin],[ymax,ymax],[zmin,zmax],color=color,linestyle='-')
ax.plot([xmax,xmax],[ymax,ymax],[zmin,zmax],color=color,linestyle='-')
ax.plot([xmax,xmax],[ymin,ymin],[zmin,zmax],color=color,linestyle='-')
extension, save_fname, pdf = save_name(save,variable='zone'+str(self.index),time=1)
plt.savefig(save_fname, dpi=200, facecolor='w', edgecolor='w',orientation='portrait',
format=extension,transparent=True, bbox_inches=None, pad_inches=0.1)
if pdf:
os.system('epstopdf ' + save_fname)
os.remove(save_fname)
def topo(self,save='',cbar=True,equal_axes=True, method = 'nearest', divisions=[30,30], xlims=[],
ylims=[], clims=[], levels=10,clabel='',
xlabel='x / m',ylabel='y / m',zlabel='z / m',title='',font_size='small'): #generates a 2-D topographical plot of the zone.
'''Returns a contour plot of the top surface of the zone.
:param divisions: Resolution to supply mesh data.
:type divisions: [int,int]
:param method: Method of interpolation, options are 'nearest', 'linear'.
:type method: str
:param levels: Contour levels to plot. Can specify specific levels in list form, or a single integer indicating automatic assignment of levels.
:type levels: lst[fl64], int
:param cbar: Add colour bar to plot.
:param type: bool
:param xlims: Plot limits on x-axis.
:type xlims: [fl64, fl64]
:param ylims: Plot limits on y-axis.
:type ylims: [fl64, fl64]
:param clims: Colour limits.
:type clims: [fl64,fl64]
:param save: Name to save plot. Format specified extension (default .png if none give). Supported extensions: .png, .eps, .pdf.
:type save: str
:param xlabel: Label on x-axis.
:type xlabel: str
:param ylabel: Label on y-axis.
:type ylabel: str
:param title: Plot title.
:type title: str
:param font_size: Specify text size, either as an integer or string, e.g., 10, 'small', 'x-large'.
:type font_size: str, int
:param equal_axes: Specify equal scales on axes.
:type equal_axes: bool
*Example:*
``dat.zone[2].topo('zoneDEMtopo.png',method = 'linear')``
'''
save = os_path(save)
if not self.nodelist:
pyfehm_print('ERROR: No node information, aborting...',self._silent)
return
if not title:
title = 'Topographic plot of zone ' +str(self.index)
if self.name: title += ': '+self.name
# assemble data
xs = np.unique([nd.position[0] for nd in self.nodelist])
ys = np.unique([nd.position[1] for nd in self.nodelist])
xmin = np.min(xs); xmax = np.max(xs)
ymin = np.min(ys); ymax = np.max(ys)
xrange = np.linspace(xmin,xmax,divisions[0])
yrange = np.linspace(ymin,ymax,divisions[1])
XI,YI = np.meshgrid(xs,ys)
X,Y = np.meshgrid(xrange,yrange)
ZI = np.ones((len(ys),len(xs)))*self._parent.grid.zmin-1
for nd in self.nodelist:
i = np.where(xs==nd.position[0])[0][0]
j = np.where(ys==nd.position[1])[0][0]
ZI[j,i] = np.max([ZI[j,i],nd.position[2]])
pts = np.transpose(np.reshape((X,Y),(2,X.size)))
ptsI = np.transpose(np.reshape((XI,YI,ZI),(3,XI.size)))
from scipy.interpolate import griddata
vals = griddata(ptsI[:,:2],ptsI[:,2],pts,method=method)
vals = np.reshape(vals,(X.shape[0],X.shape[1]))
# plot topo
plt.clf()
fig = plt.figure(figsize=[8.275,11.7])
ax = plt.axes([0.15,0.15,0.7,0.7])
if xlims: ax.set_xlim(xlims)
if ylims: ax.set_ylim(ylims)
if equal_axes: ax.set_aspect('auto', 'datalim')
CS = plt.contourf(X,Y,vals,levels)
if clims: CS.vmin=clims[0]; CS.vmax=clims[1]
if xlabel: plt.xlabel(xlabel,size=font_size)
if ylabel: plt.ylabel(ylabel,size=font_size)
if title: plt.title(title,size=font_size)
if cbar:
cbar=plt.colorbar(CS)
for t in cbar.ax.get_yticklabels():
t.set_fontsize(font_size)
for t in ax.get_xticklabels():
t.set_fontsize(font_size)
for t in ax.get_yticklabels():
t.set_fontsize(font_size)
ax.set_aspect('auto', 'datalim')
extension, save_fname, pdf = save_name(save,variable='zone_topo'+str(self.index),time=1)
plt.savefig(save_fname, dpi=200, facecolor='w', edgecolor='w',orientation='portrait',
format=extension,transparent=True, bbox_inches=None, pad_inches=0.1)
def _get_info(self):
"""Print details of the zone to the screen."""
ws = 'Zone '+str(self.index)+'\n'
ws+='\nGeometric properties.......\n'
if self.type == 'rect':
ws += ' Type: rectangular box\n'
if self.nodelist: ws += ' Contains '+str(len(self.nodelist))+' nodes\n'
pts = np.array(self.points)
if np.size(pts)==24: pts=pts.reshape(3,8)
else: pts = pts.reshape(2,4)
xmin, xmax = np.min(pts[0,:]), np.max(pts[0,:])
ymin, ymax = np.min(pts[1,:]), np.max(pts[1,:])
if pts.shape[1] == 3:
zmin, zmax = np.min(pts[2,:]), np.max(pts[2,:])
dx,dy,dz = [xmax-xmin,ymax-ymin,zmax-zmin]
ws += ' dimensions: ['+str(dx)+', '+str(dy)+', '+str(dz)+']'
if 100*dz<dx and 100*dz<dy: ws += ' (plane at z = '+str((zmin+zmax)/2)+')'
elif 100*dx<dy and 100*dx<dz: ws += ' (plane at x = '+str((xmin+xmax)/2)+')'
elif 100*dy<dz and 100*dy<dz: ws += ' (plane at y = '+str((ymin+ymax)/2)+')'
elif 100*dz<dx and 100*dy<dx: ws += ' (column at x = '+str((xmin+xmax)/2)+')'
elif 100*dx<dy and 100*dz<dy: ws += ' (column at y = '+str((ymin+ymax)/2)+')'
elif 100*dx<dz and 100*dy<dz: ws += ' (column at z = '+str((zmin+zmax)/2)+')'
ws += '\n'
ws += ' x-range: '+str(xmin)+' - '+str(xmax)+'\n'
ws += ' y-range: '+str(ymin)+' - '+str(ymax)+'\n'
if pts.shape[1] == 3:
ws += ' z-range: '+str(zmin)+' - '+str(zmax)+'\n'
ws += ' mid-point: ['+str((xmin+xmax)/2.)+', '+str((ymin+ymax)/2.)+', '+str((zmin+zmax)/2.)+']\n'
elif pts.shape[1] ==1:
ws += ' mid-point: ['+str((xmin+xmax)/2.)+', '+str((ymin+ymax)/2.)+']\n'
elif self.type == 'list':
#ws = 'Zone '+str(self.index)+'\n'
#ws+='\nGeometric properties.......\n'
ws += ' Type: list\n'
ws += ' Contains '+str(len(self.nodelist))+' nodes\n'
pts=np.array(self.points)
ws += ' x-range: '+str(np.min(pts[:,0]))+' - '+str(np.max(pts[:,0]))+'\n'
ws += ' y-range: '+str(np.min(pts[:,1]))+' - '+str(np.max(pts[:,1]))+'\n'
ws += ' z-range: '+str(np.min(pts[:,2]))+' - '+str(np.max(pts[:,2]))+'\n'
ws += ' mid-point: ['+str(np.mean(pts[:,0]))+', '+str(np.mean(pts[:,1]))+', '+str(np.mean(pts[:,2]))+']\n'
if pts.shape[0]<20:
ws+=' points: ['+str(self.points[0][0])+', '+str(self.points[0][1])+', '+str(self.points[0][2])+']\n'
for pt in self.points[1:]:
ws+=' ['+str(pt[0])+', '+str(pt[1])+', '+str(pt[2])+']\n'
elif self.type == 'nnum':
ws += ' Type: nnum (list of nodes)\n'
ws += ' Contains '+str(len(self.nodelist))+' nodes\n'
elif not self.index:
ws += ' Background zone (denoted 1 0 0), encompassing all nodes.\n'
else: return
ws += '\nMaterial properties........\n'
if self._permeability != None: ws += ' permeability...... '+str(self._permeability)+'\n'
if self._conductivity != None: ws += ' conductivity...... '+str(self._conductivity)+'\n'
if self._density: ws += ' density........... '+str(self._density)+'\n'
if self._specific_heat: ws += ' specific heat..... '+str(self._specific_heat)+'\n'
if self._porosity: ws += ' porosity.......... '+str(self._porosity)+'\n'
if self._youngs_modulus: ws += ' Youngs modulus.... '+str(self._youngs_modulus)+'\n'
if self._poissons_ratio: ws += ' Poissons ratio.... '+str(self._poissons_ratio)+'\n'
if self._thermal_expansion: ws += ' thermal expansion. '+str(self._thermal_expansion)+'\n'
if self._pressure_coupling: ws += ' pressure coupling. '+str(self._pressure_coupling)+'\n'
ws += '\nInitial conditions.........\n'
if self._Pi: ws += ' pressure.......... '+str(self._Pi)+'\n'
if self._Ti: ws += ' temperature....... '+str(self._Ti)+'\n'
if self._Si: ws += ' saturation........ '+str(self._Si)+'\n'
ws += '\nBoundary conditions........\n'
if self._fixedT: ws += ' fixed temperature.... '+str(self._fixedT)+'\n'
if self._fixedP:
ws += ' fixed pressure....... '+str(self._fixedP[0])+'\n'
ws += ' inflow temperature. '+str(self._fixedP[1])+'\n'
print(ws)
what = property(_get_info) #: Print to screen information about the zone.
def _get_nodes(self):
"""Assemble a list of fnode objects contained in the zone."""
nds = []
if self.type == 'rect':
if not self._parent.grid: self._nodelist = nds; return self._nodelist
xmax,xmin = np.max(self.points[0]),np.min(self.points[0])
ymax,ymin = np.max(self.points[1]),np.min(self.points[1])
if self._parent._grid.dimensions == 3:
zmax,zmin = np.max(self.points[2]),np.min(self.points[2])
else:
zmax,zmin = self._parent._grid.zmax+.01,self._parent._grid.zmin-.01
x,y,z = np.array([nd._position for nd in self._parent._grid._nodelist]).T
inds = np.where((x<=xmax)&(x>=xmin)&(y<=ymax)&(y>=ymin)&(z<=zmax)&(z>=zmin))
self._nodelist = [self._parent._grid._nodelist[i] for i in inds[0]]
if self._index == 0: self._nodelist = self._parent._grid._nodelist
return self._nodelist
def _set_nodes(self,value):
if self.type == 'rect':
pyfehm_print('ERROR: nodelist for zone defined by content of points.',self._silent)
return
self._nodelist = value
nodelist = property(_get_nodes,_set_nodes) #: (*lst[fnode]*) List of nodes contained within the zone.
def _get_node(self): return dict([(nd.index,nd) for nd in self.nodelist])
node = property(_get_node) #: (*dict[fnode]*) Dictionary of nodes contained within the zone, indexed by node number.
def _get_points(self):
"""Assemble spatial data as it would appear in an FEHM input file."""
pts=[]
if self.type in ['nnum','list']:
if not self._parent.grid: self._points = pts; return self._points
row = []
if self.type == 'nnum': row.append(len(self.nodelist))
for nd in self.nodelist:
if isinstance(nd,int): nd = self._parent.grid.node[nd]
if self.type == 'list': pts.append(nd.position)
elif self.type == 'nnum': row.append(nd.index)
if len(row) == 10: pts.append(row); row = []
if row != []: pts.append(row)
self._points = pts
return self._points
def _set_points(self,value):
if self.type in ['list','nnum']:
pyfehm_print('ERROR: points defined by content of nodelist.',self._silent)
return
self._points = value
points = property(_get_points,_set_points)#: (*lst[fl64]*) Spatial data defining the zone.
def _get_permeability(self): return self._permeability
def _set_permeability(self,value):
self._permeability = value
# set commands
if not self._parent: _buildWarnings('Zone not associated with input file, no macro changes made.'); return
if isinstance(value,(int,float)): kx = value; ky = value; kz = value
elif isinstance(value,(list,tuple,np.ndarray)) and len(value)==3: kx,ky,kz = value
if self.index in list(self._parent.perm.keys()):
if self._updateFlag:
self._parent.perm[self.index].param['kx']=kx
self._parent.perm[self.index].param['ky']=ky
self._parent.perm[self.index].param['kz']=kz
else:
self._parent.add(fmacro('perm',zone=self.index,param=(('kx',kx),('ky',ky),('kz',kz))))
if self._parent:
for nd in self.nodelist:
if not (nd.permeability is not None and self.index == 0):
nd._permeability = np.array([kx,ky,kz])
permeability = property(_get_permeability, _set_permeability) #: (*fl64*,*lst*) Permeability properties of zone.
def _get_conductivity(self): return self._conductivity
def _set_conductivity(self,value):
self._conductivity = value
# set commands
if not self._parent: _buildWarnings('Zone not associated with input file, no macro changes made.'); return
if isinstance(value,(int,float)): kx = value; ky = value; kz = value
elif isinstance(value,(list,tuple,np.ndarray)) and len(value)==3: kx,ky,kz = value
if self.index in list(self._parent.cond.keys()):
if self._updateFlag:
self._parent.cond[self.index].param['cond_x']=kx
self._parent.cond[self.index].param['cond_y']=ky
self._parent.cond[self.index].param['cond_z']=kz
else:
self._parent.add(fmacro('cond',zone=self.index,param=(('cond_x',kx),('cond_y',ky),('cond_z',kz))))
if self._parent:
for nd in self.nodelist:
if not (nd.conductivity is not None and self.index == 0):
nd._conductivity = np.array([kx,ky,kz])
conductivity = property(_get_conductivity, _set_conductivity) #: (*fl64*,*lst*) Conductivity properties of zone.
def _set_property(self,value,prop0,props,macro):
self.__setattr__(prop0,value)
if not self._parent:
pyfehm_print('Zone not associated with input file, no macro changes made.',self._silent)
return
# macro creation/modification
ks = list(self._parent.__getattribute__(macro).keys())
if self.index in ks:
if self._updateFlag:
self._parent.__getattribute__(macro)[self.index].param[prop0[1:]]=value
else:
params = [(prop0[1:],value)]
for prop in props:
params.append((prop[1:],dflt.__getattribute__(prop[1:])))
self._parent.add(fmacro(macro,zone=self.index,param=tuple(params)))
warn_string = 'WARNING: Assigning default '
for prop in props:
warn_string += prop[1:]+' (%6.1f'%dflt.__getattribute__(prop[1:])+'), '
warn_string = warn_string[:-2] + ' to zone '+str(self.index)+'.'
_buildWarnings(warn_string)
for prop in props:
self.__setattr__(prop[1:],dflt.__getattribute__(prop[1:]))
# node association
if self._parent:
for nd in self._nodelist:
if isinstance(nd,int): nd = self._parent.grid.node[nd]
if len(set([zn.index for zn in nd.zonelist])-set([994,995,996,997,998,999]))==0:
nd.__setattr__(prop0,value)
elif len([zn.index for zn in nd.zonelist if zn.index in ks])==0:
nd.__setattr__(prop0,value)
elif self.index == np.max([zn.index for zn in nd.zonelist if zn.index in ks]):
nd.__setattr__(prop0,value)
def _get_density(self): return self._density
def _set_density(self,value):
self._set_property(value,'_density',['_specific_heat','_porosity'],'rock')
density = property(_get_density, _set_density) #: (*fl64*) Density of zone.
def _get_specific_heat(self): return self._specific_heat
def _set_specific_heat(self,value):
self._set_property(value,'_specific_heat',['_density','_porosity'],'rock')
specific_heat = property(_get_specific_heat, _set_specific_heat) #: (*fl64*) Specific heat of zone.
def _get_porosity(self): return self._porosity
def _set_porosity(self,value):
self._set_property(value,'_porosity',['_density','_specific_heat'],'rock')
porosity = property(_get_porosity, _set_porosity) #: (*fl64*) Porosity of zone.
def _get_youngs_modulus(self): return self._youngs_modulus
def _set_youngs_modulus(self,value):
self._set_property(value,'_youngs_modulus',['_poissons_ratio'],'elastic')
youngs_modulus = property(_get_youngs_modulus, _set_youngs_modulus) #: (*fl64*) Young's modulus of zone.
def _get_poissons_ratio(self): return self._poissons_ratio
def _set_poissons_ratio(self,value):
self._set_property(value,'_poissons_ratio',['_youngs_modulus'],'elastic')
poissons_ratio = property(_get_poissons_ratio, _set_poissons_ratio) #: (*fl64*) Poisson's ratio of zone.
def _get_thermal_expansion(self): return self._thermal_expansion
def _set_thermal_expansion(self,value):
self._set_property(value,'_thermal_expansion',['_pressure_coupling'],'biot')
thermal_expansion = property(_get_thermal_expansion, _set_thermal_expansion) #: (*fl64*) Coefficient of thermal expansion of zone.
def _get_pressure_coupling(self): return self._pressure_coupling
def _set_pressure_coupling(self,value):
self._set_property(value,'_pressure_coupling',['_thermal_expansion'],'biot')
pressure_coupling = property(_get_pressure_coupling, _set_pressure_coupling) #: (*fl64*) Pressure coupling term of zone.
def _get_Pi(self): return self._Pi
def _set_Pi(self,value):
self._Pi = value
# set commands
if not self._parent:
pyfehm_print('Zone not associated with input file, no macro changes made.',self._silent)
return
if self.index in list(self._parent.pres.keys()):
if self._updateFlag:
self._parent.pres[self.index].param['pressure']=value
else:
self._parent.add(fmacro('pres',zone=self.index,param=(('pressure',value),('temperature',dflt.Ti),('saturation',1))))
_buildWarnings('WARNING: Assigning default initial temperature (%4.1f'%dflt.Ti+' degC, fully saturated liquid) to zone '+str(self.index)+'.')
self.Ti = dflt.Ti
if self.Ti is not None:
if self.Ti > tsat(self.Pi)[0]:
self._parent.pres[self.index].param['saturation']=3
self.Si = 0.
else:
self._parent.pres[self.index].param['saturation']=1
self.Si = 1.
if self._parent:
for nd in self.nodelist:
if not (nd.Pi is not None and self.index == 0):
nd._Pi = value
Pi = property(_get_Pi, _set_Pi) #: (*fl64*) Initial pressure in zone.
def _get_Ti(self): return self._Ti
def _set_Ti(self,value):
self._Ti = value
# set commands
if not self._parent:
pyfehm_print('Zone not associated with input file, no macro changes made.',self._silent)
return
if self.index in list(self._parent.pres.keys()):
if self._updateFlag:
self._parent.pres[self.index].param['temperature']=value
else:
self._parent.add(fmacro('pres',zone=self.index,param=(('pressure',dflt.Pi),('temperature',value),('saturation',1))))
_buildWarnings('WARNING: Assigning default initial pressure (%4.1f'%dflt.Pi+' MPa, fully saturated liquid) to zone '+str(self.index)+'.')
self._Pi = dflt.Pi
if self._Ti > tsat(self._Pi)[0]:
self._parent.pres[self.index].param['saturation']=3
self._Si = 0.
else:
self._parent.pres[self.index].param['saturation']=1
self._Si = 1.
if self._parent:
for nd in self.nodelist:
if not (nd.Ti is not None and self.index == 0):
nd._Ti = value
Ti = property(_get_Ti, _set_Ti) #: (*fl64*) Initial temperature in zone.