tfirst commit - pism-exp-gsw - ice stream and sediment transport experiments | |
git clone git://src.adamsgaard.dk/pism-exp-gsw | |
Log | |
Files | |
Refs | |
README | |
LICENSE | |
--- | |
commit 67cc411b812c5b5294d00318345a3977068da6f5 | |
Author: Anders Damsgaard <[email protected]> | |
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 | |
t@@ -0,0 +1,681 @@ | |
+The Python scripts in this repository are derived from PISM examples, | |
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diff --git a/MISMIP.py b/MISMIP.py | |
t@@ -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, experi… | |
+ | |
+ 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, experi… | |
+ | |
+ 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 *… | |
+ | |
+ 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… | |
+ 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(… | |
+ - theta * s * b_x / h_f | |
+ - A(experiment, step) * (rho_g * (1.0 - r) / 4.0) ** n() * h_f ** … | |
+ | |
+ | |
+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 calcula… | |
+ 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(ex… | |
+ | |
+ # 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, … | |
+ | |
+ # 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() … | |
+ * ((q_0 + a() * (x_floating - xg)) ** (n() + 1) - q_0 ** (n() + 1)) / … | |
+ 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… | |
+ | |
+ 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… | |
+ parser.add_option("-e", "--experiment", dest="experiment", type="string", | |
+ default='1a', | |
+ help="MISMIP experiments (one of '1a', '1b', '2a', '2b',… | |
+ 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 | |
t@@ -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 | |
t@@ -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=Fa… | |
+ """ | |
+ 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_ty… | |
+ """ | |
+ 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=a… | |
+ 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 | |
t@@ -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 <[email protected]> | |
+ | |
+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 | |
t@@ -0,0 +1,139 @@ | |
+MISMIP in PISM | |
+============== | |
+ | |
+This directory contains scripts that can be used to run MISMIP experiments usi… | |
+ | |
+Older PISM versions included C++ code managing MISMIP experiments. With the ad… | |
+ | |
+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.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… | |
+`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 be… | |
+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/`, how… | |
+ | |
+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 mete… | |
+ | |
+The MISMIP parameter C corresponds to `tauc` in PISM. It can be set using `-yi… | |
+ | |
+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, … | |
+ | |
+Note that PISM does not at this time implement the stopping criteria described… | |
+ | |
+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 th… | |
+ | |
+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 … | |
+ | |
+ ./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… | |
+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 t… | |
+grounding line. | |
diff --git a/flowlineslab.py b/flowlineslab.py | |
t@@ -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 | |
t@@ -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 … | |
+ | |
+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… | |
+# 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=fillv… | |
+ 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 -… | |
diff --git a/plot.py b/plot.py | |
t@@ -0,0 +1,236 @@ | |
+#!/usr/bin/env python3 | |
+ | |
+import MISMIP | |
+ | |
+from pylab import figure, subplot, plot, xlabel, ylabel, title, axis, vlines, … | |
+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 fro… | |
+ 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", de… | |
+ help="Plot ice flux only") | |
+ parser.add_option("-p", "--profile", dest="flux", action="store_false", de… | |
+ 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… | |
+ 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, gr… | |
+ 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 … | |
+ 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 | |
t@@ -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) … | |
+ | |
+ 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_profil… | |
+ | |
+ # 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.si… | |
+ | |
+ 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=T… | |
+ import PISMNC | |
+ | |
+ xx = x(mode, N) | |
+ yy = y(xx) | |
+ | |
+ bed_elevation = bed_topography(experiment, xx) | |
+ ice_thickness = thickness(experiment, step, xx, calving_front, semianalyti… | |
+ 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 balanc… | |
+ 'standard_name': 'land_ice_surface_specific_mass… | |
+ 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 tempera… | |
+ 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 exte… | |
+ 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', … | |
+ 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", def… | |
+ 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 %… | |
+ 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 | |
t@@ -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, semianalyt… | |
+ 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… | |
+ #"-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 max… | |
+ #"-config_override %s" % config_filename, | |
+ #"-ssa_method fd", | |
+ #"-cfbc", # calving front boundary conditions | |
+ #"-part_grid", # sub-grid front motion parameteri… | |
+ #"-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 maxi… | |
+ "-config_override %s" % config_filename, | |
+ #"-ssa_method fd", | |
+ "-cfbc", # PIK: calving fron… | |
+ "-part_grid", # PIK: sub-grid front motion p… | |
+ "-kill_icebergs", # PIK: https://pism-docs.org/sphin… | |
+ "-subgl", # PIK: https://pism-docs.o… | |
+ #"-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 … | |
+ "-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… | |
+ "-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 parameteri… | |
+ #"-front_retreat_file %s" % input_file, # prescribe the max… | |
+ #"-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 se… | |
+ #]) | |
+ | |
+ | |
+ 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 … | |
+ ''' | |
+ | |
+ 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.experi… | |
+ "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.m… | |
+ | |
+ import prepare | |
+ prepare.pism_bootstrap_file(boot_filename, self.experiment, step, self… | |
+ 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,h… | |
+ "-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, … | |
+ | |
+ def options(self, step, input_file=None): | |
+ '''Generates a string of PISM options corresponding to a MISMIP experi… | |
+ | |
+ 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"… | |
+ # 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',… | |
+ 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 wa… | |
+ 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() |