def AmanziResults(input_filename,subtests,obs_slices,overwrite=False):
import run_amanzi_standard
# Create emtpy dictionaries
obs_scatter={}
obs_data={}
obs_xml={}
try:
for st in subtests:
# modify file content
old_content = open(input_filename).read()
new_content = old_content.replace("explicit first-order", subtests[st]['parameters'])
tmp_filename = "tmp.xml"
f = open(tmp_filename, 'w')
f.write(new_content)
f.flush()
f.close()
run_amanzi_standard.run_amanzi(tmp_filename, 8,
["amanzi_dispersion_45_point_2d.exo",tmp_filename],
subtests[st]['directory'])
obs_xml[st]=loadInputXML(input_filename)
obs_data[st]=loadDataFile(obs_xml[st],subtests[st]['directory'])
# Collect observations to plot
obs_scatter[st]=CollectObservations(obs_xml[st], obs_data[st], obs_slices)
finally:
pass
return obs_xml, obs_data, obs_scatter
'bo',
label='Amanzi: r=100m')
axes1.legend(loc='lower right')
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = os.path.join("amanzi_boundedDomain_2d.xml")
CWD = os.getcwd()
try:
run_amanzi_standard.run_amanzi(input_file, 16, [input_file])
obs_data = load_amanzi_obs()
obsdata = []
obstimes = []
for obs in obs_data.observations.itervalues():
obsdata.append(obs.data)
obstimes.append(obs.times)
obsdata = numpy.transpose(numpy.array(obsdata))
obstimes = numpy.transpose(numpy.array(obstimes))
obstimes[:] = obstimes[:] / 24. / 3600.
ana_data = load_ana_solution()
# note: in analytical solution the drawdown (m) was given at time in days
x_crunchflow, c_crunchflow = GetXY_CrunchFlow_1D(path_to_crunchflow,root,times_CF,comp,ignore)
# crunchflow OS3D
path_to_crunchflow = "crunchflow/os3d"
x_crunchOS3D, c_crunchOS3D = GetXY_CrunchFlow_1D(path_to_crunchflow,root,times_CF,comp,ignore)
CWD = os.getcwd()
local_path = ""
# amanziU
try:
comp = 'total_component_concentration.cell.tracer conc'
input_file = os.path.join("amanzi-u-1d-"+root+"-alq-pflo.xml")
path_to_amanzi = "output-u-alq-pflo"
run_amanzi_standard.run_amanzi(input_file, 1, ["1d-"+root+".in",root+".dat",input_file], path_to_amanzi)
x_amanzi_alquimia, c_amanzi_alquimia = GetXY_AmanziU_1D(path_to_amanzi,root,comp,1)
alq = len(x_amanzi_alquimia)
except:
alq = 0
try:
comp = 'total_component_concentration.cell.tracer conc'
input_file = os.path.join("amanzi-u-1d-"+root+"-alq-crunch.xml")
path_to_amanzi = "output-u-alq-crunch"
run_amanzi_standard.run_amanzi(input_file, 1, ["1d-"+root+"-crunch.in",root+".dbs",input_file], path_to_amanzi)
x_amanzi_alquimia_crunch, c_amanzi_alquimia_crunch = GetXY_AmanziU_1D(path_to_amanzi,root,comp,1)
alq_crunch = len(x_amanzi_alquimia_crunch)
except:
# root name for problem
root = "non_grid_aligned"
nodesx = 121
nodesy = 101
local_path = ""
# subplots
plt.subplots(1, figsize=(11, 8))
# Amanzi + Native chemistry
try:
input_file = os.path.join("non_grid_aligned-u.xml")
path_to_amanzi = "output-u"
run_amanzi_standard.run_amanzi(input_file, 1,
["calcite_dbs.bgd", input_file],
path_to_amanzi)
comp = 'mineral_volume_fractions.cell.Calcite vol frac'
x_native, y_native, z_native = GetXYZ_Amanzi(path_to_amanzi,
root,
comp,
nodesx=nodesx,
nodesy=nodesy)
except Exception:
pass
extent = [0.0, 0.60, 0.0, 0.50]
# plot adjustments
for i, time in enumerate(times_CF):
x_crunchflow, c_crunchflow = GetXY_CrunchFlow(path_to_crunchflow, root,
time, comp, ignore)
VF_crunchOS3D = VF_crunchOS3D + [c_crunchflow / 100.0]
CWD = os.getcwd()
local_path = ""
# subplots
fig, ax = plt.subplots(3, sharex=True, figsize=(8, 10))
try:
# Amanzi native chemistry
input_filename = os.path.join("amanzi-u-1d-calcite.xml")
path_to_amanzi = "amanzi-native-output"
run_amanzi_standard.run_amanzi(input_filename, 1, ["calcite.bgd"],
path_to_amanzi)
comp = 'total_component_concentration.cell.Ca++ conc'
Ca_amanzi_native = []
for i, time in enumerate(times):
x_amanzi_native, c_amanzi_native = GetXY_Amanzi(
path_to_amanzi, root, comp)
Ca_amanzi_native = Ca_amanzi_native + [c_amanzi_native]
comp = 'free_ion_species.cell.H+'
pH_amanzi_native = []
for i, time in enumerate(times):
x_amanzi_native, c_amanzi_native = GetXY_Amanzi(
path_to_amanzi, root, comp)
pH_amanzi_native = pH_amanzi_native + [-np.log10(c_amanzi_native)]
# mineral volume fraction
w_pflotran = [[] for x in range(len(vfpflo))]
for j, vf in enumerate(vfpflo):
x_pflotran, c_pflotran = GetXY_PFloTran_1D(path_to_pflotran,
root_pflotran, time, vf)
w_pflotran[j] = c_pflotran
CWD = os.getcwd()
local_path = ""
# Amanzi + Native chemistry
try:
input_file = os.path.join("amanzi-u-1d-" + root + ".xml")
path_to_amanzi = "output-u"
run_amanzi_standard.run_amanzi(input_file, 1,
[root + ".bgd", input_file],
path_to_amanzi)
time = timesama[0]
# tot conc
u_amanzi_native = [[] for x in range(len(totcama))]
for j, comp in enumerate(totcama):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(
path_to_amanzi, 'plot', comp, 1)
u_amanzi_native[j] = c_amanzi_native
# sorb conc
v_amanzi_native = [[] for x in range(len(sorbama))]
for j, sorb in enumerate(sorbama):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(
if os.path.exists("table_values.txt"):
os.remove("table_values.txt")
table_file = open("table_values.txt", "w+")
table_file.write(x.get_string())
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_filename = "amanzi_linear_materials_serial_1d-isv2.xml"
try:
run_amanzi_standard.run_amanzi(input_filename, 1)
obs_xml = loadInputXML(input_filename)
obs_data = loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([.15, .15, .80, .80])
cmap = plotTestObservations(obs_xml, obs_data, axes1)
plotTestModel(input_filename, cmap, axes1, obs_xml, obs_data)
# plt.show()
MakeTable(obs_data, obs_xml, input_filename)
finally:
pass
# crunchflow OS3D
path_to_crunchflow = "crunchflow/os3d"
x_crunchOS3D, c_crunchOS3D = GetXY_CrunchFlow(path_to_crunchflow, root,
times_CF, comp, ignore)
CWD = os.getcwd()
local_path = ""
# amanziU - native
try:
comp = 'total_component_concentration.cell.tracer conc'
input_filename = os.path.join("amanzi-u-1d-" + root + ".xml")
path_to_amanzi = "amanzi-u-native-output"
run_amanzi_standard.run_amanzi(input_filename, 1, [], path_to_amanzi)
x_amanzi_native, c_amanzi_native = GetXY_AmanziU(
path_to_amanzi, root, comp)
native = len(x_amanzi_native)
except:
native = 0
# amanziU - alquimia pflotran
try:
comp = 'total_component_concentration.cell.tracer conc'
input_filename = os.path.join("amanzi-u-1d-" + root + "-alq-pflo.xml")
path_to_amanzi = "amanzi-u-alq-pflo-output"
run_amanzi_standard.run_amanzi(input_filename, 1,
["1d-" + root + ".in", root + ".dat"],
for i, time in enumerate(times_CF_pH):
y_crunchflow, c_crunchflow = GetXY_CrunchFlow_1D(path_to_crunch,root,time,comp,ignore)
pH_crunchflow[i] = c_crunchflow
crunch = True
except:
crunch = False
# AmanziU + Native chemistry --->
try:
input_file = os.path.join("amanzi-u-1d-"+root+".xml")
path_to_amanzi = "output-u"
run_amanzi_standard.run_amanzi(input_file, 1,
[root+".bgd",input_file],
path_to_amanzi)
u_amanzi_native = [[[] for x in range(len(amanzi_totc))] for x in range(len(times))]
for i, time in enumerate(times):
for j, comp in enumerate(amanzi_totc):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(path_to_amanzi,root,comp,1)
u_amanzi_native[i][j] = c_amanzi_native
v_amanzi_native = [[[] for x in range(len(amanzi_sorb))] for x in range(len(times))]
for i, time in enumerate(times):
for j, comp in enumerate(amanzi_sorb):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(path_to_amanzi,root,comp,1)
v_amanzi_native[i][j] = c_amanzi_native
pH_amanzi_native = [ [] for x in range(len(times)) ]
axes1.plot(numpy.log10(obstimes[1:ntime3,0]), obsdata[1:ntime3,0], 'ro', label='Amanzi: Obs1')
axes1.plot(numpy.log10(ana_data[ntime1+1:ntime2,0]), ana_data[ntime1+1:ntime2,1], '-b', label='Butler Pod Solution: Obs2')
axes1.plot(numpy.log10(obstimes[1:ntime4,1]), obsdata[1:ntime4,1], 'bo', label='Amanzi: Obs2')
axes1.legend(loc='upper left')
if __name__ == "__main__":
import os
import run_amanzi_standard
input_filename =os.path.join("amanzi_butler_pod_2d.xml")
cwd = os.getcwd()
try:
run_amanzi_standard.run_amanzi(input_filename, 10, {"mesh_cylinder.exo"})
obs_xml = loadInputXML(input_filename)
obs_data = load_amanzi_obs()
obsdata = []
obstimes = []
for obs in obs_data.observations.itervalues():
obsdata.append(obs.data)
obstimes.append(obs.times)
obsdata = numpy.transpose(numpy.array(obsdata))
obstimes = numpy.transpose(numpy.array(obstimes))
obstimes[:] = obstimes[:]/24./3600.
ana_data=load_ana_solution()
ana_data[:,0] = ana_data[:,0]/24./3600.
x_crunchflow, c_crunchflow = GetXY_CrunchFlow_1D(
path_to_crunchflow, root, time, comp, ignore)
VF_crunchOS3D = VF_crunchOS3D + [c_crunchflow]
CWD = os.getcwd()
local_path = ""
# subplots
fig, ax = plt.subplots(3, sharex=True, figsize=(8, 10))
try:
# Amanzi native chemistry
input_file = os.path.join("amanzi-u-1d-calcite.xml")
path_to_amanzi = "output-u"
run_amanzi_standard.run_amanzi(input_file, 1,
["calcite.bgd", input_file],
path_to_amanzi)
comp = 'total_component_concentration.cell.Ca++ conc'
Ca_amanzi_native = []
for i, time in enumerate(times):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(
path_to_amanzi, root, comp, 1)
Ca_amanzi_native = Ca_amanzi_native + [c_amanzi_native]
comp = 'free_ion_species.cell.H+'
pH_amanzi_native = []
for i, time in enumerate(times):
x_amanzi_native, c_amanzi_native = GetXY_AmanziU_1D(
path_to_amanzi, root, comp, 1)
pH_amanzi_native = pH_amanzi_native + [-np.log10(c_amanzi_native)]
table_file = open("table_values.txt", "w+")
table_file.write('.. tabularcolumns:: ' + '|R|C|C|C|' + '\n\n')
table_file.write(x.get_string(sortby="x [m]"))
table_file.write('\n')
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_filename = "amanzi_linear_head_head_1d-isv2.xml"
try:
max_np = 1
run_amanzi_standard.run_amanzi(input_filename, max_np)
obs_xml = loadInputXML(input_filename)
obs_data = loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([.15, .15, .80, .80])
MakeTable(obs_data, obs_xml, input_filename)
cmap = plotTestObservations(obs_xml, obs_data, axes1)
plotTestModel(input_filename, cmap, axes1, obs_xml, obs_data)
# plt.show()
finally:
pass
obsdata[1:ntime3, 0],
'bo',
label='Amanzi: r=100m')
axes1.legend(loc='lower right')
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = os.path.join("amanzi_hantush_anisotropic_2d-u.xml")
try:
run_amanzi_standard.run_amanzi(input_file, 1,
["porflow4_6.exo", input_file])
obs_data = load_amanzi_obs()
obsdata = []
obstimes = []
for obs in obs_data.observations.itervalues():
obsdata.append(obs.data)
obstimes.append(obs.times)
obsdata = numpy.transpose(numpy.array(obsdata))
obstimes = numpy.transpose(numpy.array(obstimes))
obstimes[:] = obstimes[:] / 24. / 3600.
# analytic solution is not available yet
ana_data = load_ana_solution()
table_file = open("table_values.txt", "w+")
table_file.write('.. tabularcolumns:: ' + '|R|C|C|C|' + '\n\n')
table_file.write(x.get_string(sortby="x [m]"))
table_file.write('\n')
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = "amanzi_linear_head_head_1d-u.xml"
try:
max_np = 1
run_amanzi_standard.run_amanzi(input_file, max_np, [input_file])
obs_xml = loadInputXML(input_file)
obs_data = loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([.15, .15, .80, .80])
MakeTable(obs_data, obs_xml, input_file)
cmap = plotTestObservations(obs_xml, obs_data, axes1)
plotTestModel(input_file, cmap, axes1, obs_xml, obs_data)
# plt.show()
finally:
pass
'bo',
label='Amanzi: Obs2')
axes1.legend(loc='upper left')
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = os.path.join("amanzi_butler_pod_2d.xml")
cwd = os.getcwd()
try:
run_amanzi_standard.run_amanzi(input_file, 10,
["mesh_cylinder.exo", input_file])
obs_xml = loadInputXML(input_file)
obs_data = load_amanzi_obs()
obsdata = []
obstimes = []
for obs in obs_data.observations.itervalues():
obsdata.append(obs.data)
obstimes.append(obs.times)
obsdata = numpy.transpose(numpy.array(obsdata))
obstimes = numpy.transpose(numpy.array(obstimes))
obstimes[:] = obstimes[:] / 24. / 3600.
ana_data = load_ana_solution()
ana_data[:, 0] = ana_data[:, 0] / 24. / 3600.
os.remove("table_values.txt")
table_file = open("table_values.txt", "w+")
table_file.write('.. tabularcolumns:: ' + '|R|C|C|C|' + '\n\n')
table_file.write(x.get_string(sortby="x [m]"))
table_file.write('\n')
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_filename = "amanzi_unconfined_seepage_1d-isv2.xml"
try:
run_amanzi_standard.run_amanzi(input_filename, 1, ["porflow4_4.exo"])
obs_xml=loadInputXML(input_filename)
obs_data=loadDataFile(obs_xml)
fig1 = plt.figure()
axes1=fig1.add_axes([.15,.15,.80,.80])
MakeTable(obs_data,obs_xml,input_filename)
cmap = plotTestObservations(obs_xml,obs_data,axes1)
plotTestModel(input_filename,cmap,axes1,obs_xml,obs_data)
# plt.show()
finally:
pass
table_file = open("table_values.txt", "w+")
table_file.write('.. tabularcolumns:: ' + '|R|C|C|C|' + '\n\n')
table_file.write(x.get_string(sortby="x [m]"))
table_file.write('\n')
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = "amanzi_linear_flux_head_1d-u.xml"
run_dir = "amanzi-output"
try:
run_amanzi_standard.run_amanzi(input_file, 2, [input_file], run_dir)
obs_xml = loadInputXML(input_file)
obs_data = loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([.15, .15, .80, .80])
MakeTable(obs_data, obs_xml, input_file)
cmap = plotTestObservations(obs_xml, obs_data, axes1)
plotTestModel(input_file, cmap, axes1, obs_xml, obs_data)
# plt.show()
finally:
pass
if legend == "Amanzi" :
axes1.scatter(obs.times, numpy.log10(obs.data), marker='o', s=25, c=color, label=legend)
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = os.path.join("amanzi_single_fracture.xml")
path_to_amanzi = "amanzi-output"
cwd = os.getcwd()
try:
max_np = 1
run_amanzi_standard.run_amanzi(input_file, max_np,
["single_fracture.exo", input_file], path_to_amanzi)
obs_xml=loadInputXML(input_file)
obs_data=loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([0.12,0.1,0.86,0.84])
plotSingleFractureObservations(obs_xml,obs_data,axes1)
# first benchmark (2 figures are planned for future)
data = []
data = open("benchmark/UiB_RT0.txt").read().split();
for i in range(0, len(data)):
data[i] = data[i].split(',')
data = numpy.array(data, dtype=numpy.double)
import matplotlib
from matplotlib import pyplot as plt
import run_amanzi_standard
from compare_field_results import GetXY_AmanziU_1D
from compare_field_results import GetXY_AmanziS_1D
if __name__ == "__main__":
# Amanzi: unstructured
try:
input_file = "amanzi_infiltration_sand_loam_1d-u.xml"
path_to_amanzi = "output_2b-u"
root_amanzi = 'case_2b_plot'
run_amanzi_standard.run_amanzi(input_file, 1, [input_file],
path_to_amanzi)
comp = 'pressure.cell.0'
x_amanziU, c_amanziU = GetXY_AmanziU_1D(path_to_amanzi, root_amanzi,
comp, 3)
unstruct = len(x_amanziU)
except:
unstruct = 0
# Amanzi: structured
try:
input_file = "amanzi_infiltration_sand_loam_1d-s.xml"
path_to_amanzi = "output_2b-s"
root_amanzi = "plot"
run_amanzi_standard.run_amanzi(input_file, 1, [input_file],
table_file.write('.. tabularcolumns:: ' + '|R|C|C|C|' + '\n\n')
table_file.write(x.get_string(sortby="x [m]"))
table_file.write('\n')
table_file.close()
if __name__ == "__main__":
import os
import run_amanzi_standard
input_file = "amanzi_unconfined_seepage_1d-u.xml"
run_dir = "amanzi-output"
try:
run_amanzi_standard.run_amanzi(input_file, 1,
["porflow4_4.exo", input_file], run_dir)
obs_xml = loadInputXML(input_file)
obs_data = loadDataFile(obs_xml)
fig1 = plt.figure()
axes1 = fig1.add_axes([.15, .15, .80, .80])
MakeTable(obs_data, obs_xml, input_file)
cmap = plotTestObservations(obs_xml, obs_data, axes1)
plotTestModel(input_file, cmap, axes1, obs_xml, obs_data)
plt.savefig('unconfined_seepage_1d.png')
# plt.show()
finally:
x_crunchflow, c_crunchflow = GetXY_CrunchFlow(path_to_crunchflow, root,
times_CF, comp, ignore)
CWD = os.getcwd()
local_path = ""
# subplots
fig, ax = plt.subplots()
# AmanziS + Alqumia + PFlotran chemistry
try:
input_file = os.path.join("amanzi-s-1d-" + root + "-alq-pflo.xml")
path_to_amanzi = "output-s-alq-pflo"
run_amanzi_standard.run_amanzi(
input_file, 1,
["1d-" + root + "-trim.in", root + ".dat", input_file],
path_to_amanzi)
root_amanzi = "plt00037"
comp = "Tritium_water_Concentration"
x_amanziS, c_amanziS = GetXY_AmanziS(path_to_amanzi, root_amanzi, comp)
struct = len(x_amanziS)
except:
struct = 0
# AmanziS + Alqumia + CrunchFlow chemistry
try:
input_file = os.path.join("amanzi-s-1d-" + root + "-alq-crunch.xml")
path_to_amanzi = "output-s-alq-crunch"
run_amanzi_standard.run_amanzi(input_file, 1, [
"1d-" + root + "-crunch.in", root + ".dbs", "aqueous.dbs",
input_file
'total_sorbed.cell.3']
amanzi_compS = ['Na+_Aqueous_Concentration', \
'Ca++_Aqueous_Concentration', \
'Mg++_Aqueous_Concentration', \
'Cl-_Aqueous_Concentration']
amanzi_sorbS = ['Na+_Sorbed_Concentration', \
'Ca++_Sorbed_Concentration', \
'Mg++_Sorbed_Concentration', \
'Cl-_Sorbed_Concentration']
try:
# Amanzi native chemistry
input_filename = os.path.join("amanzi-u-1d-"+root+".xml")
path_to_amanzi = "amanzi-native-output"
run_amanzi_standard.run_amanzi(input_filename, 1, [root+".bgd"], path_to_amanzi)
u_amanzi_native = [[[] for x in range(len(amanzi_components))] for x in range(len(times))]
for i, time in enumerate(times):
for j, comp in enumerate(amanzi_components):
x_amanzi_native, c_amanzi_native = GetXY_Amanzi(path_to_amanzi,root,comp)
u_amanzi_native[i][j] = c_amanzi_native
v_amanzi_native = [[[] for x in range(len(amanzi_sorbed))] for x in range(len(times))]
for i, time in enumerate(times):
for j, comp in enumerate(amanzi_sorbed):
x_amanzi_native, c_amanzi_native = GetXY_Amanzi(path_to_amanzi,root,comp)
v_amanzi_native[i][j] = c_amanzi_native
native = True