commit 67cc411b812c5b5294d00318345a3977068da6f5
Author: Anders Damsgaard <anders@adamsgaard.dk>
Date: Fri, 19 Nov 2021 08:53:57 +0100
first commit
Diffstat:
| A | LICENSE | | | 681 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | MISMIP.py | | | 312 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | Makefile | | | 49 | +++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | PISMNC.py | | | 178 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | README | | | 15 | +++++++++++++++ |
| A | README.md | | | 139 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | flowlineslab.py | | | 43 | +++++++++++++++++++++++++++++++++++++++++++ |
| A | pism_python.py | | | 100 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | plot.py | | | 236 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | prepare.py | | | 171 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | run.py | | | 392 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
11 files changed, 2316 insertions(+), 0 deletions(-)
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,681 @@
+The Python scripts in this repository are derived from PISM examples,
+see https://github.com/pism/pism for AUTHOR information.
+
+Like the PISM original source, all files in this repository are subject
+to the GNU Public License v. 3, included in full below.
+
+
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+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
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+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program 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 General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/MISMIP.py b/MISMIP.py
@@ -0,0 +1,312 @@
+#!/usr/bin/env python3
+import numpy as np
+
+"""This module contains MISMIP constants and parameters, as well as functions
+computing theoretical steady state profiles corresponding to various MISMIP
+experiments.
+
+It should not be cluttered with plotting or NetCDF output code.
+"""
+
+
+def secpera():
+ "Number of seconds per year."
+ return 3.15569259747e7
+
+
+def L():
+ "The length of the MISMIP domain."
+ return 1800e3
+
+
+def N(mode):
+ "Number of grid spaces corresponding to a MISMIP 'mode.'"
+ if mode == 1:
+ return 150
+
+ if mode == 2:
+ return 1500
+
+ raise ValueError("invalid mode (%s)" % mode)
+
+
+def A(experiment, step):
+ """Ice softness parameter for given experiment and step."""
+ A1 = np.array([4.6416e-24, 2.1544e-24, 1.0e-24,
+ 4.6416e-25, 2.1544e-25, 1.0e-25,
+ 4.6416e-26, 2.1544e-26, 1.0e-26])
+ # Values of A to be used in experiments 1 and 2.
+
+ A3a = np.array([3.0e-25, 2.5e-25, 2.0e-25,
+ 1.5e-25, 1.0e-25, 5.0e-26,
+ 2.5e-26, 5.0e-26, 1.0e-25,
+ 1.5e-25, 2.0e-25, 2.5e-25,
+ 3.0e-25])
+ # Values of A to be used in experiment 3a.
+
+ A3b = np.array([1.6e-24, 1.4e-24, 1.2e-24,
+ 1.0e-24, 8.0e-25, 6.0e-25,
+ 4.0e-25, 2.0e-25, 4.0e-25,
+ 6.0e-25, 8.0e-25, 1.0e-24,
+ 1.2e-24, 1.4e-24, 1.6e-24])
+ # Values of A to be used in experiment 3b.
+
+ try:
+ if experiment in ("1a", "1b", "2a", "2b"):
+ return A1[step - 1]
+
+ if experiment == "3a":
+ return A3a[step - 1]
+
+ if experiment == "3b":
+ return A3b[step - 1]
+ except:
+ raise ValueError("invalid step (%s) for experiment %s" % (step, experiment))
+
+ raise ValueError("invalid experiment (%s)" % experiment)
+
+
+def run_length(experiment, step):
+ """Returns the time interval for an experiment 3 step."""
+ T3a = np.array([3.0e4, 1.5e4, 1.5e4,
+ 1.5e4, 1.5e4, 3.0e4,
+ 3.0e4, 1.5e4, 1.5e4,
+ 3.0e4, 3.0e4, 3.0e4,
+ 1.5e4])
+ # Time intervals to be used in experiment 3a.
+
+ T3b = np.array([3.0e4, 1.5e4, 1.5e4,
+ 1.5e4, 1.5e4, 1.5e4,
+ 1.5e4, 3.0e4, 1.5e4,
+ 1.5e4, 1.5e4, 1.5e4,
+ 1.5e4, 3.0e4, 1.5e4])
+ # Time intervals to be used in experiment 3b.
+
+ try:
+ if experiment == "3a":
+ return T3a[step - 1]
+
+ if experiment == "3b":
+ return T3b[step - 1]
+ except:
+ raise ValueError("invalid step (%s) for experiment %s" % (step, experiment))
+
+ return 3e4
+
+
+def rho_i():
+ "Ice density"
+ return 900.0
+
+
+def rho_w():
+ "Water density"
+ return 1000.0
+
+
+def g():
+ """Acceleration due to gravity. (Table 2 on page 19 of mismip_4.pdf
+ uses this value, i.e. g = 9.8 m s-2.)"""
+ return 9.8
+
+
+def n():
+ "Glen exponent"
+ return 3.0
+
+
+def a():
+ "Accumulation rate (m/s)"
+ return 0.3 / secpera()
+
+
+def m(experiment):
+ "Sliding law exponent"
+ if experiment in ("1a", "2a", "3a"):
+ return 1 / 3.0
+
+ if experiment in ("1b", "2b", "3b"):
+ return 1.0
+
+ raise ValueError("invalid experiment (%s)" % experiment)
+
+
+def C(experiment):
+ "Sliding law coefficient"
+ if experiment in ("1a", "2a", "3a"):
+ return 7.624e6
+
+ if experiment in ("1b", "2b", "3b"):
+ return 7.2082e10
+
+ raise ValueError("invalid experiment (%s)" % experiment)
+
+
+def b(experiment, x):
+ "Bed depth below sea level. (-b(x) = topg(x))"
+
+ if experiment in ("1a", "1b", "2a", "2b"):
+ return -720. + 778.5 * (x / 7.5e5)
+
+ if experiment in ("3a", "3b"):
+ xx = x / 7.5e5
+ return -(729. - 2184.8 * xx ** 2. + 1031.72 * xx ** 4. - 151.72 * xx ** 6.)
+
+ raise ValueError("invalid experiment (%s)" % experiment)
+
+
+def b_slope(experiment, x):
+ """The x-derivative of b(experiment, x)."""
+
+ if experiment in ("1a", "1b", "2a", "2b"):
+ return 778.5 / 7.5e5
+
+ if experiment in ("3a", "3b"):
+ xx = x / 7.5e5
+ return -(- 2184.8 * (2. / 7.5e5) * xx
+ + 1031.72 * (4. / 7.5e5) * xx ** 3.
+ - 151.72 * (6. / 7.5e5) * xx ** 5.)
+
+ raise ValueError("invalid experiment (%s)" % experiment)
+
+
+def cold_function(experiment, step, x, theta=0.0):
+ """Evaluates function whose zeros define x_g in 'cold' steady marine sheet problem."""
+ r = rho_i() / rho_w()
+ h_f = r ** (-1.) * b(experiment, x)
+ b_x = b_slope(experiment, x)
+ s = a() * x
+ rho_g = rho_i() * g()
+ return (theta * a()
+ + C(experiment) * s ** (m(experiment) + 1.0) / (rho_g * h_f ** (m(experiment) + 2.))
+ - theta * s * b_x / h_f
+ - A(experiment, step) * (rho_g * (1.0 - r) / 4.0) ** n() * h_f ** (n() + 1.0))
+
+
+def x_g(experiment, step, theta=0.0):
+ """Computes the theoretical grounding line location using Newton's method."""
+
+ # set the initial guess
+ if experiment in ("3a", "3b"):
+ x = 800.0e3
+ else:
+ x = 1270.0e3
+
+ delta_x = 10. # Finite difference step size (metres) for gradient calculation
+ tolf = 1.e-4 # Tolerance for finding zeros
+ eps = np.finfo(float).eps
+ normf = tolf + eps
+ toldelta = 1.e1 # Newton step size tolerance
+ dx = toldelta + 1.0
+
+ # this is just a shortcut
+ def F(x):
+ return cold_function(experiment, step, x, theta)
+
+ while (normf > tolf) or (abs(dx) > toldelta):
+ f = F(x)
+ normf = abs(f)
+ grad = (F(x + delta_x) - f) / delta_x
+ dx = -f / grad
+ x = x + dx
+
+ return x
+
+
+def thickness(experiment, step, x, theta=0.0):
+ """Compute ice thickness for x > 0.
+ """
+ # compute the grounding line position
+ xg = x_g(experiment, step, theta)
+
+ def surface(h, x):
+ b_x = b_slope(experiment, x)
+ rho_g = rho_i() * g()
+ s = a() * np.abs(x)
+ return b_x - (C(experiment) / rho_g) * s ** m(experiment) / h ** (m(experiment) + 1)
+
+ # extract the grounded part of the grid
+ x_grounded = x[x < xg]
+
+ # We will integrate from the grounding line inland. odeint requires that
+ # the first point in x_grid be the one corresponding to the initial
+ # condition; append it and reverse the order.
+ x_grid = np.append(xg, x_grounded[::-1])
+
+ # use thickness at the grounding line as the initial condition
+ h_f = b(experiment, xg) * rho_w() / rho_i()
+
+ import scipy.integrate
+ thk_grounded = scipy.integrate.odeint(surface, [h_f], x_grid, atol=1.e-9, rtol=1.e-9)
+
+ # now 'result' contains thickness in reverse order, including the grounding
+ # line point (which is not on the grid); discard it and reverse the order.
+ thk_grounded = np.squeeze(thk_grounded)[:0:-1]
+
+ # extract the floating part of the grid
+ x_floating = x[x >= xg]
+
+ # compute the flux through the grounding line
+ q_0 = a() * xg
+
+ # Calculate ice thickness for shelf from van der Veen (1986)
+ r = rho_i() / rho_w()
+ rho_g = rho_i() * g()
+ numer = h_f * (q_0 + a() * (x_floating - xg))
+ base = q_0 ** (n() + 1) + h_f ** (n() + 1) * ((1 - r) * rho_g / 4) ** n() * A(experiment, step) \
+ * ((q_0 + a() * (x_floating - xg)) ** (n() + 1) - q_0 ** (n() + 1)) / a()
+ thk_floating = numer / (base ** (1.0 / (n() + 1)))
+
+ return np.r_[thk_grounded, thk_floating]
+
+
+def plot_profile(experiment, step, out_file):
+ from pylab import figure, subplot, hold, plot, xlabel, ylabel, text, title, axis, vlines, savefig
+
+ if out_file is None:
+ out_file = "MISMIP_%s_A%d.pdf" % (experiment, step)
+
+ xg = x_g(experiment, step)
+
+ x = np.linspace(0, L(), N(2) + 1)
+ thk = thickness(experiment, step, x)
+ x_grounded, thk_grounded = x[x < xg], thk[x < xg]
+ x_floating, thk_floating = x[x >= xg], thk[x >= xg]
+
+ figure(1)
+ ax = subplot(111)
+ hold(True)
+ plot(x / 1e3, np.zeros_like(x), ls='dotted', color='red')
+ plot(x / 1e3, -b(experiment, x), color='black')
+ plot(x / 1e3, np.r_[thk_grounded - b(experiment, x_grounded),
+ thk_floating * (1 - rho_i() / rho_w())],
+ color='blue')
+ plot(x_floating / 1e3, -thk_floating * (rho_i() / rho_w()), color='blue')
+ _, _, ymin, ymax = axis(xmin=0, xmax=x.max() / 1e3)
+ vlines(xg / 1e3, ymin, ymax, linestyles='dashed', color='black')
+
+ xlabel('distance from the summit, km')
+ ylabel('elevation, m')
+ text(0.6, 0.9, "$x_g$ (theory) = %4.0f km" % (xg / 1e3),
+ color='black', transform=ax.transAxes)
+ title("MISMIP experiment %s, step %d" % (experiment, step))
+ savefig(out_file)
+
+
+if __name__ == "__main__":
+ from optparse import OptionParser
+
+ parser = OptionParser()
+
+ parser.usage = "%prog [options]"
+ parser.description = "Plots the theoretical geometry profile corresponding to MISMIP experiment and step."
+ parser.add_option("-e", "--experiment", dest="experiment", type="string",
+ default='1a',
+ help="MISMIP experiments (one of '1a', '1b', '2a', '2b', '3a', '3b')")
+ parser.add_option("-s", "--step", dest="step", type="int", default=1,
+ help="MISMIP step number")
+ parser.add_option("-o", dest="out_file", help="output file name")
+
+ (opts, args) = parser.parse_args()
+
+ plot_profile(opts.experiment, opts.step, opts.out_file)
diff --git a/Makefile b/Makefile
@@ -0,0 +1,48 @@
+NPROC != awk '/^cpu cores/ {print $$4; exit}' /proc/cpuinfo
+
+all: \
+ ABC1_1a_M1_A1-flux.pdf\
+ ABC1_1a_M3_A1-flux.pdf\
+ ABC1_3a_M1_A1-flux.pdf\
+ ABC1_3a_M3_A1-flux.pdf\
+
+ABC1_1a_M1_A1-flux.pdf: ABC1_1a_M1_A1.nc plot.py
+ ./plot.py ABC1_1a_M1_A1.nc
+
+ABC1_1a_M3_A1-flux.pdf: ABC1_1a_M3_A1.nc plot.py
+ ./plot.py ABC1_1a_M3_A1.nc
+
+ABC1_3a_M1_A1-flux.pdf: ABC1_3a_M1_A1.nc plot.py
+ ./plot.py ABC1_3a_M1_A1.nc
+
+ABC1_3a_M3_A1-flux.pdf: ABC1_3a_M3_A1.nc plot.py
+ ./plot.py ABC1_3a_M3_A1.nc
+
+ABC1_1a_M1_A1.nc: experiment-1a-mode-1.sh
+ time sh experiment-1a-mode-1.sh ${NPROC} | tee out.1a-mode-1
+
+ABC1_1a_M3_A1.nc: experiment-1a-mode-3.sh
+ time sh experiment-1a-mode-3.sh ${NPROC} | tee out.1a-mode-3
+
+ABC1_3a_M1_A1.nc: experiment-3a-mode-1.sh
+ time sh experiment-3a-mode-1.sh ${NPROC} | tee out.3a-mode-1
+
+ABC1_3a_M3_A1.nc: experiment-3a-mode-3.sh
+ time sh experiment-3a-mode-3.sh ${NPROC} | tee out.3a-mode-3
+
+experiment-3a-mode-1.sh: run.py
+ ./run.py -e 3a --mode=1 > $@
+
+experiment-3a-mode-3.sh: run.py
+ ./run.py -e 3a --mode=3 --Mx=1201 > $@
+
+experiment-1a-mode-1.sh: run.py
+ ./run.py -e 1a --mode=1 > $@
+
+experiment-1a-mode-3.sh: run.py
+ ./run.py -e 1a --mode=3 --Mx=1201 > $@
+
+clean:
+ rm -f out.* experiment-*.sh *.nc *.pdf
+
+.PHONY: all clean+
\ No newline at end of file
diff --git a/PISMNC.py b/PISMNC.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python3
+
+try:
+ import netCDF4 as netCDF
+except:
+ print("netCDF4 is not installed!")
+ sys.exit(1)
+
+
+class PISMDataset(netCDF.Dataset):
+
+ def create_time(self, use_bounds=False, length=None, units=None):
+ self.createDimension('time', size=length)
+ t_var = self.createVariable('time', 'f8', ('time',))
+
+ t_var.axis = "T"
+ t_var.long_name = "time"
+ if not units:
+ t_var.units = "seconds since 1-1-1" # just a default
+ else:
+ t_var.units = units
+
+ if use_bounds:
+ self.createDimension('n_bounds', 2)
+ self.createVariable("time_bounds", 'f8', ('time', 'n_bounds'))
+ t_var.bounds = "time_bounds"
+
+ def create_dimensions(self, x, y, time_dependent=False, use_time_bounds=False):
+ """
+ Create PISM-compatible dimensions in a NetCDF file.
+ """
+
+ if time_dependent and not 'time' in list(self.variables.keys()):
+ self.create_time(use_time_bounds)
+
+ self.createDimension('x', x.size)
+ self.createDimension('y', y.size)
+
+ x_var = self.createVariable('x', 'f8', ('x',))
+ x_var[:] = x
+
+ y_var = self.createVariable('y', 'f8', ('y',))
+ y_var[:] = y
+
+ x_var.axis = "X"
+ x_var.long_name = "X-coordinate in Cartesian system"
+ x_var.units = "m"
+ x_var.standard_name = "projection_x_coordinate"
+
+ y_var.axis = "Y"
+ y_var.long_name = "Y-coordinate in Cartesian system"
+ y_var.units = "m"
+ y_var.standard_name = "projection_y_coordinate"
+
+ self.sync()
+
+ def append_time(self, value, bounds=None):
+ if 'time' in list(self.dimensions.keys()):
+ time = self.variables['time']
+ N = time.size
+ time[N] = value
+
+ if bounds:
+ self.variables['time_bounds'][N, :] = bounds
+
+ def set_attrs(self, var_name, attrs):
+ """attrs should be a list of (name, value) tuples."""
+ if not attrs:
+ return
+
+ for (name, value) in attrs.items():
+ if name == "_FillValue":
+ continue
+ setattr(self.variables[var_name], name, value)
+
+ def define_2d_field(self, var_name, time_dependent=False, dims=None, nc_type='f8', attrs=None):
+ """
+ time_dependent: boolean
+
+ dims: an optional list of dimension names. use this to override the
+ default order ('time', 'y', 'x')
+
+ attrs: a dictionary of attributes
+ """
+ if not dims:
+ if time_dependent:
+ dims = ('time', 'y', 'x')
+ else:
+ dims = ('y', 'x')
+
+ try:
+ var = self.variables[var_name]
+ except:
+ if attrs is not None and '_FillValue' in list(attrs.keys()):
+ var = self.createVariable(var_name, nc_type, dims,
+ fill_value=attrs['_FillValue'])
+ else:
+ var = self.createVariable(var_name, nc_type, dims)
+
+ self.set_attrs(var_name, attrs)
+
+ return var
+
+ def define_timeseries(self, var_name, attrs=None):
+ try:
+ if attrs is not None and '_FillValue' in list(attrs.keys()):
+ var = self.createVariable(var_name, 'f8', ('time',),
+ fill_value=attrs['_FillValue'])
+ else:
+ var = self.createVariable(var_name, 'f8', ('time',))
+ except:
+ var = self.variables[var_name]
+
+ self.set_attrs(var_name, attrs)
+
+ return var
+
+ def write(self, var_name, data, time_dependent=False, attrs=None):
+ """
+ Write time-series or a 2D field to a file.
+ """
+
+ if data.ndim == 1:
+ return self.write_timeseries(var_name, data, attrs=attrs)
+ elif data.ndim == 2:
+ return self.write_2d_field(var_name, data, time_dependent, attrs=attrs)
+ else:
+ return None
+
+ def write_2d_field(self, var_name, data, time_dependent=False, attrs=None):
+ """
+ Write a 2D numpy array to a file in a format PISM can read.
+ """
+
+ var = self.define_2d_field(var_name, time_dependent, attrs=attrs)
+
+ if time_dependent:
+ last_record = self.variables['time'].size - 1
+ var[last_record, :, :] = data
+ else:
+ var[:] = data
+
+ return var
+
+ def write_timeseries(self, var_name, data, attrs=None):
+ """Write a 1D (time-series) array to a file."""
+
+ var = self.define_timeseries(var_name, attrs=attrs)
+ var[:] = data
+
+ return var
+
+
+if __name__ == "__main__":
+ # produce a NetCDF file for testing
+ from numpy import linspace, meshgrid
+
+ nc = PISMDataset("foo.nc", 'w')
+
+ x = linspace(-100, 100, 101)
+ y = linspace(-100, 100, 201)
+
+ xx, yy = meshgrid(x, y)
+
+ nc.create_dimensions(x, y, time_dependent=True, use_time_bounds=True)
+
+ nc.define_2d_field("xx", time_dependent=True,
+ attrs={"long_name": "xx",
+ "comment": "test variable",
+ "valid_range": (-200.0, 200.0)})
+
+ for t in [0, 1, 2, 3]:
+ nc.append_time(t, (t - 1, t))
+
+ nc.write("xx", xx + t, time_dependent=True)
+ nc.write("yy", yy + 2 * t, time_dependent=True)
+
+ nc.close()
diff --git a/README b/README
@@ -0,0 +1,14 @@
+This repository is hosted at [0] and includes a modified version of the
+PISM[1] MISMIP example. All scripts here should be run with a modified
+version of PISM[2] that supports modeling of subglacial till advection.
+
+Author:
+Anders Damsgaard <anders@adamsgaard.dk>
+
+License:
+See LICENSE
+
+References:
+0: https://src.adamsgaard.dk/pism-exp-gsw
+1: https://github.com/pism/pism
+2: https://src.adamsgaard.dk/pism (tillflux branch)+
\ No newline at end of file
diff --git a/README.md b/README.md
@@ -0,0 +1,139 @@
+MISMIP in PISM
+==============
+
+This directory contains scripts that can be used to run MISMIP experiments using PISM. To understand the intent of these experiments, please see the MISMIP website at http://homepages.ulb.ac.be/~fpattyn/mismip/, and download the intercomparison description PDF from that site.
+
+Older PISM versions included C++ code managing MISMIP experiments. With the addition of more sophisticated reporting code that old code became unnecessary. Here all MISMIP-specific code is in Python scripts.
+
+Step by step instructions
+-------------------------
+
+First of all, you will need to copy or symlink `util/PISMNC.py` into the
+current directory to make sure that Python will be able to import it.
+
+The script `run.py` is used to generate a `bash` scripts performing MISMIP
+experiments. Running `run.py --help` produces the following:
+
+ Usage: run.py [options]
+
+ Creates a script running MISMIP experiments.
+
+ Options:
+ -h, --help show this help message and exit
+ --initials=INITIALS Initials (3 letters)
+ -e EXPERIMENT, --experiment=EXPERIMENT
+ MISMIP experiments (one of '1a', '1b', '2a', '2b',
+ '3a', '3b')
+ -s STEP, --step=STEP MISMIP step number
+ -u, --uniform_thickness
+ Use uniform 10 m ice thickness
+ -a, --all Run all experiments
+ -m MODE, --mode=MODE MISMIP grid mode
+ --Mx=MX Custom grid size; use with --mode=3
+ --model=MODEL Models: 1 - SSA only; 2 - SIA+SSA
+ --executable=EXECUTABLE
+ Executable to run, e.g. 'mpiexec -n 4 pismr'
+
+For example, to set up MISMIP experiment `1a` using grid mode 1, a 12 km grid, run
+
+ ./run.py -e 1a --mode=1 > experiment-1a-mode-1.sh
+
+This will create `experiment-1a-mode-1.sh` as well as the bootstrapping file
+`MISMIP_boot_1a_M1_A1.nc` and configuration files corresponding to each "step"
+in the experiment.
+
+Run in the backround with 2 cores and saving output to a text file this way:
+
+ bash experiment-1a-mode-1.sh 2 >& out.1a-mode-1 &
+
+You can also copy the script (along with
+`MISMIP_boot_1a_M1_A1.nc` and `MISMIP_conf_1a_A*.nc`) to a supercomputer to
+do the run later. For such application, the script helpfully uses environment variables `PISM_DO`,
+`PISM_BIN` and `PISM_MPIDO`. For example, on some Cray machines you might do
+
+ PISM_MPIDO="aprun -n " bash experiment-1a-mode-1.sh 32
+
+will use `aprun` on 32 cores. Alternatively, you can use
+
+ ./run.py -e 1a --mode=1 --executable="aprun -n 32 pismr"
+
+or similar to skip the "preamble" handling environment variables and get "raw"
+commands.
+
+
+Refined grid runs
+-----------------
+
+The above "grid mode 1" runs use 150 grid spaces in the MISMIP modeling domain,
+which is 301 grid points in PISM's (doubled) domain. The domain is doubled because
+PISM is easiest configure as a whole ice sheet model with ice free ocean at the
+edge of the computation domain. (Compare the example in `examples/jako/`, however.)
+
+To run a higher resolution 3 km grid, with somewhat-improved grounding line
+performance, ask the `run.py` script to put option `-Mx 1201` into the bash
+script:
+
+ ./run.py -e 1a --mode=3 --Mx=1201 > experiment-1a-mode-3.sh
+
+Then this is a 4 core run:
+
+ bash experiment-1a-mode-3.sh 4 >& out.1a-mode-3 &
+
+
+Technical details
+-----------------
+
+The script `MISMIP.py` contains MISMIP parameters and the code needed to
+compute the semi-analytic grounding line location and the corresponding
+thickness profile for each experiment.
+
+The script `prepare.py` contains functions using `MISMIP.py` to generate
+PISM-readable NetCDF files with semi-analytic ice thickness profiles, and
+the prescribed accumulation map. It can be imported as a module or run
+as a script to generate PISM bootstrapping files.
+
+The script `run.py` generates `bash` scripts performing MISMIP runs using
+`MISMIP.py` and `prepare.py`.
+
+Implementation details
+----------------------
+
+We can turn PISM's default sliding law into MISMIP's power law by setting the
+threshold speed to 1 meter per second, which will make it inactive.
+
+The `-pseudo_plastic_uthreshold` command-line option takes an argument in meters per year, so we use `-pseudo_plastic_uthreshold 3.15569259747e7`, where `3.15569259747e7` is the number of seconds in a year.
+
+The MISMIP parameter C corresponds to `tauc` in PISM. It can be set using `-yield_stress constant -tauc C`.
+
+The MISMIP power law exponent `m` corresponds to `-pseudo_plastic_q` in PISM.
+
+We use the `-config_override` option to set other MISMIP-specific parameters, such as ice softness, ice density and others.
+
+Note that PISM does not at this time implement the stopping criteria described in the MISMIP specification. Instead we use the maximum run lengths that are provided as an alternative. On the other hand, PISM's output files contain all the information necessary to compute the rate of change of the grounding line position and the thickness rate of change during post-processing.
+
+Post-processing
+---------------
+
+Converting PISM output files to ASCII files following MISMIP
+specifications is left as an exercise.
+
+However, we do provide the `plot.py` script for visualization.
+
+It plots modeled ice flux as a function of the distance from the divide and the geometry profile.
+
+We see a discontinuity in the flux at the grounding
+line. This is an issue in PISM that needs to be addressed to improve its
+handling of the grounding line motion. For example, try
+
+ ./plot.py ABC1_1a_M1_A1.nc -f -o flux.png
+
+Run `plot.py --help` for a list of command-line options. You can also produce plots for several PISM output files at once. For example,
+
+ ./plot.py ABC*.nc
+
+will create geometry profile *and* ice flux plots for all matched files.
+
+Also, note that the variable `ice_area_glacierized_grounded` in `ts_ABC1_1a_M1_A1.nc` and similar
+allows one to see time-dependent changes in the grounding line location
+because grounded ice area is proportional to the distance from the divide to the
+grounding line.
diff --git a/flowlineslab.py b/flowlineslab.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+
+# creates an example flowline data set "slab.nc" which can be used with
+# flowline.py to show how to run PISM in flow-line mode
+
+# see the "Using PISM for flow-line modeling" subsection of the Users Manual
+
+# We recommend creating more metadata-rich datasets than is done here.
+# Here we generate the bare minimum to work with flowline.py and PISM.
+
+from numpy import linspace, minimum, maximum, abs
+import netCDF4
+
+Lx = 1000e3 # 1000 km
+Mx = 501
+topg_slope = -1e-4
+thk_0 = 1e3 # meters
+climatic_mass_balance_0 = 0 # kg m-2 s-1
+ice_surface_temp_0 = -10 # Celsius
+
+nc = netCDF4.Dataset("slab.nc", 'w')
+nc.createDimension('x', Mx)
+
+x = nc.createVariable('x', 'f4', ('x',))
+topg = nc.createVariable('topg', 'f4', ('x',))
+thk = nc.createVariable('thk', 'f4', ('x',))
+climatic_mass_balance = nc.createVariable('climatic_mass_balance', 'f4', ('x',))
+ice_surface_temp = nc.createVariable('ice_surface_temp', 'f4', ('x',))
+
+x[:] = linspace(-Lx, Lx, Mx)
+x.units = "m"
+topg[:] = topg_slope * (x[:] - Lx)
+topg.units = "m"
+
+thk[:] = maximum(minimum(5e3 - abs(x[:]) * 0.01, thk_0), 0)
+thk.units = "m"
+
+climatic_mass_balance[:] = climatic_mass_balance_0
+climatic_mass_balance.units = "kg m-2 s-1"
+ice_surface_temp[:] = ice_surface_temp_0
+ice_surface_temp.units = "Celsius"
+
+nc.close()
diff --git a/pism_python.py b/pism_python.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+
+# Copyright (C) 2009-2015, 2018 the PISM Authors
+
+# @package pism_python
+# \author the PISM authors
+# \brief Creates "from scratch" a boring dataset with the right format
+# to use as a PISM bootstrapping file.
+# \details Example use of Python for this purpose.
+#
+# Usage, including a minimal PISM call to bootstrap from this file:
+#
+# \verbatim $ pism_python.py # creates foo.nc \endverbatim
+# \verbatim $ pismr -i foo.nc -bootstrap -Mx 41 -My 41 -Mz 21 -Lz 4000 -Mbz 5 -Lbz 500 -y 1 \endverbatim
+
+import sys
+import time
+import numpy as np
+
+# try different netCDF modules
+try:
+ from netCDF4 import Dataset as CDF
+except:
+ print("netCDF4 is not installed!")
+ sys.exit(1)
+
+# set up the grid:
+Lx = 1e6
+Ly = 1e6
+Mx = 51
+My = 71
+x = np.linspace(-Lx, Lx, Mx)
+y = np.linspace(-Ly, Ly, My)
+
+# create dummy fields
+[xx, yy] = np.meshgrid(x, y) # if there were "ndgrid" in numpy we would use it
+acab = np.zeros((Mx, My))
+artm = np.zeros((Mx, My)) + 273.15 + 10.0 # 10 degrees Celsius
+topg = 1000.0 + 200.0 * (xx + yy) / max(Lx, Ly) # change "1000.0" to "0.0" to test
+# flotation criterion, etc.
+thk = 3000.0 * (1.0 - 3.0 * (xx ** 2 + yy ** 2) / Lx ** 2)
+thk[thk < 0.0] = 0.0
+
+# Output filename
+ncfile = 'foo.nc'
+
+# Write the data:
+nc = CDF(ncfile, "w", format='NETCDF3_CLASSIC') # for netCDF4 module
+
+# Create dimensions x and y
+nc.createDimension("x", size=Mx)
+nc.createDimension("y", size=My)
+
+x_var = nc.createVariable("x", 'f4', dimensions=("x",))
+x_var.units = "m"
+x_var.long_name = "easting"
+x_var.standard_name = "projection_x_coordinate"
+x_var[:] = x
+
+y_var = nc.createVariable("y", 'f4', dimensions=("y",))
+y_var.units = "m"
+y_var.long_name = "northing"
+y_var.standard_name = "projection_y_coordinate"
+y_var[:] = y
+
+fill_value = np.nan
+
+
+def def_var(nc, name, units, fillvalue):
+ # dimension transpose is standard: "float thk(y, x)" in NetCDF file
+ var = nc.createVariable(name, 'f', dimensions=("y", "x"), fill_value=fillvalue)
+ var.units = units
+ return var
+
+
+bed_var = def_var(nc, "topg", "m", fill_value)
+bed_var.standard_name = "bedrock_altitude"
+bed_var[:] = topg
+
+thk_var = def_var(nc, "thk", "m", fill_value)
+thk_var.standard_name = "land_ice_thickness"
+thk_var[:] = thk
+
+acab_var = def_var(nc, "climatic_mass_balance", "m year-1", fill_value)
+acab_var.standard_name = "land_ice_surface_specific_mass_balance"
+acab_var[:] = acab
+
+artm_var = def_var(nc, "ice_surface_temp", "K", fill_value)
+artm_var[:] = artm
+
+# set global attributes
+nc.Conventions = "CF-1.4"
+historysep = ' '
+historystr = time.asctime() + ': ' + historysep.join(sys.argv) + '\n'
+setattr(nc, 'history', historystr)
+
+nc.close()
+print(' PISM-bootable NetCDF file %s written' % ncfile)
+print(' for example, run:')
+print(' $ pismr -i foo.nc -bootstrap -Mx 41 -My 41 -Mz 21 -Lz 4000 -Mbz 5 -Lbz 500 -y 1')
diff --git a/plot.py b/plot.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python3
+
+import MISMIP
+
+from pylab import figure, subplot, plot, xlabel, ylabel, title, axis, vlines, savefig, text, tight_layout
+from sys import exit
+
+import numpy as np
+from optparse import OptionParser
+import os.path
+
+try:
+ from netCDF4 import Dataset as NC
+except:
+ print("netCDF4 is not installed!")
+ sys.exit(1)
+
+
+def parse_filename(filename, opts):
+ "Get MISMIP info from a file name."
+ tokens = filename.split('_')
+ if tokens[0] == "ex":
+ tokens = tokens[1:]
+
+ try:
+ model = tokens[0]
+ experiment = tokens[1]
+ mode = int(tokens[2][1])
+ step = int(tokens[3][1])
+
+ except:
+ if opts.experiment is None:
+ print("Please specify the experiment name (e.g. '-e 1a').")
+ exit(0)
+ else:
+ experiment = opts.experiment
+
+ if opts.step is None:
+ print("Please specify the step (e.g. '-s 1').")
+ exit(0)
+ else:
+ step = opts.step
+
+ if opts.model is None:
+ print("Please specify the model name (e.g. '-m ABC1').")
+ exit(0)
+ else:
+ model = opts.model
+
+ try:
+ nc = NC(filename)
+ x = nc.variables['x'][:]
+ N = (x.size - 1) / 2
+ if N == 150:
+ mode = 1
+ elif N == 1500:
+ mode = 2
+ else:
+ mode = 3
+ except:
+ mode = 3
+
+ return model, experiment, mode, step
+
+
+def process_options():
+ "Process command-line options and arguments."
+ parser = OptionParser()
+ parser.usage = "%prog <input files> [options]"
+ parser.description = "Plots the ice flux as a function of the distance from the divide."
+ parser.add_option("-o", "--output", dest="output", type="string",
+ help="Output image file name (e.g. -o foo.png)")
+ parser.add_option("-e", "--experiment", dest="experiment", type="string",
+ help="MISMIP experiment: 1a,1b,2a,2b,3a,3b (e.g. -e 1a)")
+ parser.add_option("-s", "--step", dest="step", type="int",
+ help="MISMIP step: 1,2,3,... (e.g. -s 1)")
+ parser.add_option("-m", "--model", dest="model", type="string",
+ help="MISMIP model (e.g. -M ABC1)")
+ parser.add_option("-f", "--flux", dest="profile", action="store_false", default=True,
+ help="Plot ice flux only")
+ parser.add_option("-p", "--profile", dest="flux", action="store_false", default=True,
+ help="Plot geometry profile only")
+
+ opts, args = parser.parse_args()
+
+ if len(args) == 0:
+ print("ERROR: An input file is requied.")
+ exit(0)
+
+ if len(args) > 1 and opts.output:
+ print("More than one input file given. Ignoring the -o option...\n")
+ opts.output = None
+
+ if opts.output and opts.profile and opts.flux:
+ print("Please choose between flux (-f) and profile (-p) plots.")
+ exit(0)
+
+ return args, opts.output, opts
+
+
+def read(filename, name):
+ "Read a variable and extract the middle row."
+ nc = NC(filename)
+
+ try:
+ var = nc.variables[name][:]
+ except:
+ print("ERROR: Variable '%s' not present in '%s'" % (name, filename))
+ exit(1)
+
+ N = len(var.shape)
+ if N == 1:
+ return var[:] # a coordinate variable ('x')
+ elif N == 2:
+ return var[1] # get the middle row
+ elif N == 3:
+ return var[-1, 1] # get the middle row of the last record
+ else:
+ raise Exception("Can't read %s. (It's %d-dimensional.)" % (name, N))
+
+
+def find_grounding_line(x, topg, thk, mask):
+ "Find the modeled grounding line position."
+ # "positive" parts of x, topg, thk, mask
+ topg = topg[x > 0]
+ thk = thk[x > 0]
+ mask = mask[x > 0]
+ x = x[x > 0] # this should go last
+
+ def f(j):
+ "See equation (7) in Pattyn et al, 'Role of transition zones in marine ice sheet dynamics', 2005."
+ z_sl = 0
+ return (z_sl - topg[j]) * MISMIP.rho_w() / (MISMIP.rho_i() * thk[j])
+
+ for j in range(x.size):
+ if mask[j] == 2 and mask[j + 1] == 3: # j is grounded, j+1 floating
+ nabla_f = (f(j + 1) - f(j)) / (x[j + 1] - x[j])
+
+ # See equation (8) in Pattyn et al
+ return (1.0 - f(j) + nabla_f * x[j]) / nabla_f
+
+ raise Exception("Can't find the grounding line")
+
+
+def plot_profile(in_file, out_file):
+ print("Reading %s to plot geometry profile for model %s, experiment %s, grid mode %s, step %s" % (
+ in_file, model, experiment, mode, step))
+
+ if out_file is None:
+ out_file = os.path.splitext(in_file)[0] + "-profile.pdf"
+
+ mask = read(in_file, 'mask')
+ usurf = read(in_file, 'usurf')
+ topg = read(in_file, 'topg')
+ thk = read(in_file, 'thk')
+ x = read(in_file, 'x')
+
+ # theoretical grounding line position
+ xg = MISMIP.x_g(experiment, step)
+ # modeled grounding line position
+ xg_PISM = find_grounding_line(x, topg, thk, mask)
+
+ # mask out ice-free areas
+ usurf = np.ma.array(usurf, mask=mask == 4)
+
+ # compute the lower surface elevation
+ lsrf = topg.copy()
+ lsrf[mask == 3] = -MISMIP.rho_i() / MISMIP.rho_w() * thk[mask == 3]
+ lsrf = np.ma.array(lsrf, mask=mask == 4)
+
+ # convert x to kilometers
+ x /= 1e3
+
+ figure(1)
+ ax = subplot(111)
+ plot(x, np.zeros_like(x), ls='dotted', color='red')
+ plot(x, topg, color='black')
+ plot(x, usurf, 'o', color='blue', markersize=4)
+ plot(x, lsrf, 'o', color='blue', markersize=4)
+ xlabel('distance from the divide, km')
+ ylabel('elevation, m')
+ title("MISMIP experiment %s, step %d" % (experiment, step))
+ text(0.6, 0.9, "$x_g$ (model) = %4.0f km" % (xg_PISM / 1e3), color='r',
+ transform=ax.transAxes)
+ text(0.6, 0.85, "$x_g$ (theory) = %4.0f km" % (xg / 1e3), color='black',
+ transform=ax.transAxes)
+
+ #_, _, ymin, ymax = axis(xmin=0, xmax=x.max())
+ _, _, ymin, ymax = axis(xmin=x.min(), xmax=x.max())
+
+ vlines(xg / 1e3, ymin, ymax, linestyles='dashed', color='black')
+ vlines(xg_PISM / 1e3, ymin, ymax, linestyles='dashed', color='red')
+
+ print("Saving '%s'...\n" % out_file)
+ savefig(out_file)
+
+
+def plot_flux(in_file, out_file):
+ print("Reading %s to plot ice flux for model %s, experiment %s, grid mode %s, step %s" % (
+ in_file, model, experiment, mode, step))
+
+ if out_file is None:
+ out_file = os.path.splitext(in_file)[0] + "-flux.pdf"
+
+ x = read(in_file, 'x')
+ flux_mag = read(in_file, 'flux_mag')
+
+ # plot positive xs only
+ flux_mag = flux_mag[x >= 0]
+ x = x[x >= 0]
+
+ figure(2)
+
+ plot(x / 1e3, flux_mag, 'k.-', markersize=10, linewidth=2)
+ plot(x / 1e3, x * MISMIP.a() * MISMIP.secpera(), 'r:', linewidth=1.5)
+
+ title("MISMIP experiment %s, step %d" % (experiment, step))
+ xlabel("x ($\mathrm{km}$)", size=14)
+ ylabel(r"flux ($\mathrm{m}^2\,\mathrm{a}^{-1}$)", size=14)
+
+ tight_layout()
+ print("Saving '%s'...\n" % out_file)
+ savefig(out_file, dpi=300, facecolor='w', edgecolor='w')
+
+
+if __name__ == "__main__":
+ args, out_file, opts = process_options()
+
+ for in_file in args:
+ model, experiment, mode, step = parse_filename(in_file, opts)
+
+ if opts.profile:
+ plot_profile(in_file, out_file)
+
+ if opts.flux:
+ plot_flux(in_file, out_file)
diff --git a/prepare.py b/prepare.py
@@ -0,0 +1,171 @@
+#!/usr/bin/env python3
+
+try:
+ from netCDF4 import Dataset as NC
+except:
+ print("netCDF4 is not installed!")
+ sys.exit(1)
+
+import MISMIP
+
+import numpy as np
+
+
+def bed_topography(experiment, x):
+ """Computes bed elevation as a function of x.
+ experiment can be '1a', '1b', '2a', '2b', '3a', '3b'.
+ """
+
+ return np.tile(-MISMIP.b(experiment, np.abs(x)), (3, 1))
+
+
+def surface_mass_balance(x):
+ """Computes the surface mass balance."""
+ return np.tile(np.zeros_like(x) + MISMIP.a(), (3, 1)) * MISMIP.rho_i()
+
+
+def ice_surface_temp(x):
+ """Computes the ice surface temperature (irrelevant)."""
+ return np.tile(np.zeros_like(x) + 273.15, (3, 1))
+
+
+def x(mismip_mode, N=None):
+ if mismip_mode in (1, 2):
+ return np.linspace(-MISMIP.L(), MISMIP.L(), 2 * MISMIP.N(mismip_mode) + 1)
+
+ return np.linspace(-MISMIP.L(), MISMIP.L(), N)
+
+
+def y(x):
+ """Computes y coordinates giving the 1:1 aspect ratio.
+ Takes cross-flow grid periodicity into account."""
+ dx = x[1] - x[0]
+ dy = dx
+ return np.array([-dy, 0, dy])
+
+
+def thickness(experiment, step, x, calving_front=1750e3, semianalytical_profile=True):
+
+ # we expect x to have an odd number of grid points so that one of them is
+ # at 0
+ if x.size % 2 != 1:
+ raise ValueError("x has to have an odd number of points, got %d", x.size)
+
+ x_nonnegative = x[x >= 0]
+ if not semianalytical_profile:
+ thk_nonnegative = np.zeros_like(x_nonnegative) + 10
+ else:
+ thk_nonnegative = MISMIP.thickness(experiment, step, x_nonnegative)
+
+ thk_nonnegative[x_nonnegative > calving_front] = 0
+
+ thk = np.zeros_like(x)
+ thk[x >= 0] = thk_nonnegative
+ thk[x < 0] = thk_nonnegative[:0:-1]
+
+ return np.tile(thk, (3, 1))
+
+
+def pism_bootstrap_file(filename, experiment, step, mode,
+ calving_front=1750e3, N=None, semianalytical_profile=True):
+ import PISMNC
+
+ xx = x(mode, N)
+ yy = y(xx)
+
+ bed_elevation = bed_topography(experiment, xx)
+ ice_thickness = thickness(experiment, step, xx, calving_front, semianalytical_profile)
+ ice_surface_mass_balance = surface_mass_balance(xx)
+ ice_surface_temperature = ice_surface_temp(xx)
+
+ ice_extent = np.zeros_like(ice_thickness)
+ ice_extent[ice_thickness > 0] = 1
+ ice_extent[bed_elevation > 0] = 1
+
+ nc = PISMNC.PISMDataset(filename, 'w', format="NETCDF3_CLASSIC")
+
+ nc.create_dimensions(xx, yy)
+
+ nc.define_2d_field('topg',
+ attrs={'units': 'm',
+ 'long_name': 'bedrock surface elevation',
+ 'standard_name': 'bedrock_altitude'})
+ nc.write('topg', bed_elevation)
+
+ nc.define_2d_field('thk',
+ attrs={'units': 'm',
+ 'long_name': 'ice thickness',
+ 'standard_name': 'land_ice_thickness'})
+ nc.write('thk', ice_thickness)
+
+ nc.define_2d_field('climatic_mass_balance',
+ attrs={'units': 'kg m-2 / s',
+ 'long_name': 'ice-equivalent surface mass balance (accumulation/ablation) rate',
+ 'standard_name': 'land_ice_surface_specific_mass_balance_flux'})
+ nc.write('climatic_mass_balance', ice_surface_mass_balance)
+
+ nc.define_2d_field('ice_surface_temp',
+ attrs={'units': 'Kelvin',
+ 'long_name': 'annual average ice surface temperature, below firn processes'})
+ nc.write('ice_surface_temp', ice_surface_temperature)
+
+ nc.define_2d_field('land_ice_area_fraction_retreat',
+ attrs={'units': '1',
+ 'long_name': 'mask defining the maximum ice extent'})
+ nc.write('land_ice_area_fraction_retreat', ice_extent)
+
+ nc.close()
+
+
+if __name__ == "__main__":
+
+ from optparse import OptionParser
+
+ parser = OptionParser()
+
+ parser.usage = "%prog [options]"
+ parser.description = "Creates a MISMIP boostrapping file for use with PISM."
+ parser.add_option("-o", dest="output_filename",
+ help="output file")
+ parser.add_option("-e", "--experiment", dest="experiment", type="string",
+ help="MISMIP experiment (one of '1a', '1b', '2a', '2b', '3a', '3b')",
+ default="1a")
+ parser.add_option("-s", "--step", dest="step", type="int", default=1,
+ help="MISMIP step")
+ parser.add_option("-u", "--uniform_thickness",
+ action="store_false", dest="semianalytical_profile", default=True,
+ help="Use uniform 10 m ice thickness")
+ parser.add_option("-m", "--mode", dest="mode", type="int", default=2,
+ help="MISMIP grid mode")
+ parser.add_option("-N", dest="N", type="int", default=3601,
+ help="Custom grid size; use with --mode=3")
+ parser.add_option("-c", dest="calving_front", type="float", default=1600e3,
+ help="Calving front location, in meters (e.g. 1600e3)")
+
+ (opts, args) = parser.parse_args()
+
+ experiments = ('1a', '1b', '2a', '2b', '3a', '3b')
+ if opts.experiment not in experiments:
+ print("Invalid experiment %s. Has to be one of %s." % (
+ opts.experiment, experiments))
+ exit(1)
+
+ if not opts.output_filename:
+ output_filename = "MISMIP_%s_%d_%d.nc" % (opts.experiment,
+ opts.step,
+ opts.mode)
+ else:
+ output_filename = opts.output_filename
+
+ print("Creating MISMIP setup for experiment %s, step %s, grid mode %d in %s..." % (
+ opts.experiment, opts.step, opts.mode, output_filename))
+
+ pism_bootstrap_file(output_filename,
+ opts.experiment,
+ opts.step,
+ opts.mode,
+ calving_front=opts.calving_front,
+ N=opts.N,
+ semianalytical_profile=opts.semianalytical_profile)
+
+ print("done.")
diff --git a/run.py b/run.py
@@ -0,0 +1,392 @@
+#!/usr/bin/env python3
+import MISMIP
+
+# This scripts generates bash scripts that run MISMIP experiments and generates
+# all the necessary input files.
+#
+# Run run.py > my_new_mismip.sh and use that.
+
+try:
+ from netCDF4 import Dataset as NC
+except:
+ print("netCDF4 is not installed!")
+ sys.exit(1)
+
+import sys
+
+# The "standard" preamble used in many PISM scripts:
+preamble = '''
+if [ -n "${SCRIPTNAME:+1}" ] ; then
+ echo "[SCRIPTNAME=$SCRIPTNAME (already set)]"
+ echo ""
+else
+ SCRIPTNAME="#(mismip.sh)"
+fi
+
+echo
+echo "# =================================================================================="
+echo "# MISMIP experiments"
+echo "# =================================================================================="
+echo
+
+set -e # exit on error
+
+NN=2 # default number of processors
+if [ $# -gt 0 ] ; then # if user says "mismip.sh 8" then NN = 8
+ NN="$1"
+fi
+
+echo "$SCRIPTNAME NN = $NN"
+
+# set MPIDO if using different MPI execution command, for example:
+# $ export PISM_MPIDO="aprun -n "
+if [ -n "${PISM_MPIDO:+1}" ] ; then # check if env var is already set
+ echo "$SCRIPTNAME PISM_MPIDO = $PISM_MPIDO (already set)"
+else
+ PISM_MPIDO="mpiexec -n "
+ echo "$SCRIPTNAME PISM_MPIDO = $PISM_MPIDO"
+fi
+
+# check if env var PISM_DO was set (i.e. PISM_DO=echo for a 'dry' run)
+if [ -n "${PISM_DO:+1}" ] ; then # check if env var DO is already set
+ echo "$SCRIPTNAME PISM_DO = $PISM_DO (already set)"
+else
+ PISM_DO=""
+fi
+
+# prefix to pism (not to executables)
+if [ -n "${PISM_BIN:+1}" ] ; then # check if env var is already set
+ echo "$SCRIPTNAME PISM_BIN = $PISM_BIN (already set)"
+else
+ PISM_BIN="" # just a guess
+ echo "$SCRIPTNAME PISM_BIN = $PISM_BIN"
+fi
+'''
+
+
+class Experiment:
+
+ "A MISMIP experiment."
+ experiment = ""
+ mode = 1
+ model = 1
+ semianalytic = True
+ Mx = 151
+ My = 3
+ Mz = 15
+ initials = "ABC"
+ executable = "$PISM_DO $PISM_MPIDO $NN ${PISM_BIN}pismr"
+
+ def __init__(self, experiment, model=1, mode=1, Mx=None, Mz=15, semianalytic=True,
+ initials="ABC", executable=None):
+ self.model = model
+ self.mode = mode
+ self.experiment = experiment
+ self.initials = initials
+ self.semianalytic = semianalytic
+
+ if executable:
+ self.executable = executable
+
+ if mode == 3:
+ self.Mx = Mx
+ else:
+ self.Mx = 2 * MISMIP.N(self.mode) + 1
+
+ self.My = 3
+
+ if self.experiment == "2b":
+ self.Lz = 7000
+ else:
+ self.Lz = 6000
+ self.Lz *= 2.0
+
+ def physics_options(self, input_file, step):
+ "Options corresponding to modeling choices."
+ config_filename = self.config(step)
+
+ #options = ["-energy none", # isothermal setup; allows selecting cold-mode flow laws
+ #"-ssa_flow_law isothermal_glen", # isothermal setup
+ #"-yield_stress constant",
+ #"-tauc %e" % MISMIP.C(self.experiment),
+ #"-pseudo_plastic",
+ #"-gradient eta",
+ #"-pseudo_plastic_q %e" % MISMIP.m(self.experiment),
+ #"-pseudo_plastic_uthreshold %e" % MISMIP.secpera(),
+ #"-front_retreat_file %s" % input_file, # prescribe the maximum ice extent
+ #"-config_override %s" % config_filename,
+ #"-ssa_method fd",
+ #"-cfbc", # calving front boundary conditions
+ #"-part_grid", # sub-grid front motion parameterization
+ #"-ssafd_ksp_rtol 1e-7",
+ #"-ys 0",
+ #"-ye %d" % MISMIP.run_length(self.experiment, step),
+ #"-options_left",
+ #]
+
+
+ options = ["-stress_balance ssa+sia",
+ #"-ssa_flow_law isothermal_glen", # isothermal setup
+ #"-yield_stress constant",
+ #"-tauc %e" % MISMIP.C(self.experiment),
+ #"-pseudo_plastic",
+ "-gradient eta",
+ #"-pseudo_plastic_q %e" % MISMIP.m(self.experiment),
+ #"-pseudo_plastic_uthreshold %e" % MISMIP.secpera(),
+ #"-yield_stress mohr_coulomb",
+ #"-till_flux",
+ "-front_retreat_file %s" % input_file, # prescribe the maximum ice extent
+ "-config_override %s" % config_filename,
+ #"-ssa_method fd",
+ "-cfbc", # PIK: calving front boundary conditions
+ "-part_grid", # PIK: sub-grid front motion parameterization
+ "-kill_icebergs", # PIK: https://pism-docs.org/sphinx/manual/modeling-choices/marine/pik.html#iceberg-removal
+ "-subgl", # PIK: https://pism-docs.org/sphinx/manual/modeling-choices/marine/pik.html#sub-grid-treatment-of-the-grounding-line-position
+ #"-ssafd_ksp_rtol 1e-7",
+ "-ys 0",
+ "-ye 1e4",
+ "-options_left",
+ #"-hydrology routing",
+ "-plastic_phi 24", # Tulaczyk et al 2000
+ "-till_cohesion 0", # Tulaczyk et al 2000
+ #"-geothermal_flux 70e-3", # Feldmann and Levermann 2017
+ "-sia_e 4.5", # Martin et al 2010
+ "-ssa_e 0.512", # Martin et al 2010
+ "-bed_def lc", # Lingle and Clark 1985, Bueler et al 2007
+ "-stress_balance.sia.max_diffusivity 1e4",
+ ]
+
+
+ #options = [,
+ #"-yield_stress mohr_coulomb",
+ #"-Lz 1e4",
+ ##"-till_flux",
+ #"-cfbc", # calving front boundary conditions
+ #"-part_grid", # sub-grid front motion parameterization
+ #"-front_retreat_file %s" % input_file, # prescribe the maximum ice extent
+ #"-ys 0",
+ #"-ye %d" % MISMIP.run_length(self.experiment, step),
+ #"-options_left",
+ #]
+
+
+ #if self.model == 1:
+ #options.extend(["-stress_balance ssa"])
+ #else:
+ #options.extend(["-stress_balance ssa+sia",
+ #"-sia_flow_law isothermal_glen", # isothermal setup
+ #])
+
+
+ return options
+
+ def config(self, step):
+ '''Generates a config file containing flags and parameters
+ for a particular experiment and step.
+
+ This takes care of flags and parameters that *cannot* be set using
+ command-line options. (We try to use command-line options whenever we can.)
+ '''
+
+ filename = "MISMIP_conf_%s_A%s.nc" % (self.experiment, step)
+
+ nc = NC(filename, 'w', format="NETCDF3_CLASSIC")
+
+ var = nc.createVariable("pism_overrides", 'i')
+
+ attrs = {"geometry.update.use_basal_melt_rate": "no",
+ "stress_balance.ssa.compute_surface_gradient_inward": "no",
+ "flow_law.isothermal_Glen.ice_softness": MISMIP.A(self.experiment, step),
+ "constants.ice.density": MISMIP.rho_i(),
+ "constants.sea_water.density": MISMIP.rho_w(),
+ "bootstrapping.defaults.geothermal_flux": 0.0,
+ "stress_balance.ssa.Glen_exponent": MISMIP.n(),
+ "constants.standard_gravity": MISMIP.g(),
+ "ocean.sub_shelf_heat_flux_into_ice": 0.0,
+ }
+
+ if self.model != 1:
+ attrs["stress_balance.sia.bed_smoother.range"] = 0.0
+
+ for name, value in attrs.items():
+ var.setncattr(name, value)
+
+ nc.close()
+
+ return filename
+
+ def bootstrap_options(self, step):
+ boot_filename = "MISMIP_boot_%s_M%s_A%s.nc" % (self.experiment, self.mode, step)
+
+ import prepare
+ prepare.pism_bootstrap_file(boot_filename, self.experiment, step, self.mode, N=self.Mx,
+ semianalytical_profile=self.semianalytic)
+
+ options = ["-i %s -bootstrap" % boot_filename,
+ "-Mx %d" % self.Mx,
+ "-My %d" % self.My,
+ "-Mz %d" % self.Mz,
+ "-Lz %d" % self.Lz]
+
+ return options, boot_filename
+
+ def output_options(self, step):
+ output_file = self.output_filename(self.experiment, step)
+ extra_file = "ex_" + output_file
+ ts_file = "ts_" + output_file
+
+ options = ["-extra_file %s" % extra_file,
+ "-extra_times 0:50:3e4",
+ "-extra_vars thk,topg,velbar_mag,flux_mag,mask,dHdt,usurf,hardav,velbase_mag,nuH,tauc,taud,taub,flux_divergence,cell_grounded_fraction",
+ "-ts_file %s" % ts_file,
+ "-ts_times 0:50:3e4",
+ #"-backup_size big",
+ "-backup_size big_2d",
+ "-o %s" % output_file,
+ "-o_order zyx",
+ ]
+
+ return output_file, options
+
+ def output_filename(self, experiment, step):
+ return "%s%s_%s_M%s_A%s.nc" % (self.initials, self.model, experiment, self.mode, step)
+
+ def options(self, step, input_file=None):
+ '''Generates a string of PISM options corresponding to a MISMIP experiment.'''
+
+ if input_file is None:
+ input_options, input_file = self.bootstrap_options(step)
+ else:
+ input_options = ["-i %s" % input_file]
+
+ physics = self.physics_options(input_file, step)
+
+ output_file, output_options = self.output_options(step)
+
+ return output_file, (input_options + physics + output_options)
+
+ def run_step(self, step, input_file=None):
+ out, opts = self.options(step, input_file)
+ print('echo "# Step %s-%s"' % (self.experiment, step))
+ print("%s %s" % (self.executable, ' '.join(opts)))
+ print('echo "Done."\n')
+
+ return out
+
+ def run(self, step=None):
+ print('echo "# Experiment %s"' % self.experiment)
+
+ if self.experiment in ('1a', '1b'):
+ # bootstrap
+ input_file = None
+ # steps 1 to 9
+ steps = list(range(1, 10))
+
+ if self.experiment in ('2a', '2b'):
+ # start from step 9 of the corresponding experiment 1
+ input_file = self.output_filename(self.experiment.replace("2", "1"), 9)
+ # steps 8 to 1
+ steps = list(range(8, 0, -1))
+
+ if self.experiment == '3a':
+ # bootstrap
+ input_file = None
+ # steps 1 to 13
+ steps = list(range(1, 14))
+
+ if self.experiment == '3b':
+ # bootstrap
+ input_file = None
+ # steps 1 to 15
+ steps = list(range(1, 16))
+
+ if step is not None:
+ input_file = None
+ steps = [step]
+
+ for step in steps:
+ input_file = self.run_step(step, input_file)
+
+
+def run_mismip(initials, executable, semianalytic):
+ Mx = 601
+ models = (1, 2)
+ modes = (1, 2, 3)
+ experiments = ('1a', '1b', '2a', '2b', '3a', '3b')
+
+ print(preamble)
+
+ for model in models:
+ for mode in modes:
+ for experiment in experiments:
+ e = Experiment(experiment,
+ initials=initials,
+ executable=executable,
+ model=model, mode=mode, Mx=Mx,
+ semianalytic=semianalytic)
+ e.run()
+
+
+if __name__ == "__main__":
+ from optparse import OptionParser
+
+ parser = OptionParser()
+
+ parser.usage = "%prog [options]"
+ parser.description = "Creates a script running MISMIP experiments."
+ parser.add_option("--initials", dest="initials", type="string",
+ help="Initials (3 letters)", default="ABC")
+ parser.add_option("-e", "--experiment", dest="experiment", type="string",
+ default='1a',
+ help="MISMIP experiments (one of '1a', '1b', '2a', '2b', '3a', '3b')")
+ parser.add_option("-s", "--step", dest="step", type="int",
+ help="MISMIP step number")
+ parser.add_option("-u", "--uniform_thickness",
+ action="store_false", dest="semianalytic", default=True,
+ help="Use uniform 10 m ice thickness")
+ parser.add_option("-a", "--all",
+ action="store_true", dest="all", default=False,
+ help="Run all experiments")
+ parser.add_option("-m", "--mode", dest="mode", type="int", default=1,
+ help="MISMIP grid mode")
+ parser.add_option("--Mx", dest="Mx", type="int", default=601,
+ help="Custom grid size; use with --mode=3")
+ parser.add_option("--model", dest="model", type="int", default=1,
+ help="Models: 1 - SSA only; 2 - SIA+SSA")
+ parser.add_option("--executable", dest="executable", type="string",
+ help="Executable to run, e.g. 'mpiexec -n 4 pismr'")
+
+ (opts, args) = parser.parse_args()
+
+ if opts.all:
+ run_mismip(opts.initials, opts.executable, opts.semianalytic)
+ exit(0)
+
+ def escape(arg):
+ if arg.find(" ") >= 0:
+ parts = arg.split("=")
+ return "%s=\"%s\"" % (parts[0], ' '.join(parts[1:]))
+ else:
+ return arg
+
+ arg_list = [escape(a) for a in sys.argv]
+
+ print("#!/bin/bash")
+ print("# This script was created by examples/mismip/run.py. The command was:")
+ print("# %s" % (' '.join(arg_list)))
+
+ if opts.executable is None:
+ print(preamble)
+
+ e = Experiment(opts.experiment,
+ initials=opts.initials,
+ executable=opts.executable,
+ model=opts.model,
+ mode=opts.mode,
+ Mx=opts.Mx,
+ semianalytic=opts.semianalytic)
+
+ if opts.step is not None:
+ e.run(opts.step)
+ else:
+ e.run()
