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Changes from v0.7 to v1.0

This document lists notable changes from PISM v0.7 to v1.0.

Summary

  • New mass transport code makes it easier to "balance the books".
  • PISM's grids are no longer transposed ( (y,x) versus (x,y) ).
  • Adds an optimized implementation of the GPBLD flow law for the Glen n=3 case.
  • Adds von Mises calving (see Morlighem et al, Modeling of Store Gletscher's calving dynamics, West Greenland, in response to ocean thermal forcing, 2016)
  • Adds more diagnostic quantities (127 spatially-variable fields and 38 scalar variables in total)
  • Better code, better documentation, more regression and verification tests.

Please run git log v0.7..v1.0 for the full list.

See files in the doc/ sub-directory for changes from v0.6 to v0.7, etc.

Installation

  • Remove Pism_BUILD_TYPE and use CMAKE_BUILD_TYPE instead.

Prerequisites

  • Require CMake 3.1 and compilers supporting C++11.
  • Require PETSc built with PetscScalar as double. Stop if PetscScalar is complex. See issue 237.
  • Drop Subversion support. Please use Git to download PISM source code.
  • PETSc < 3.5 is not supported; use PETSc 3.5 and newer (PETSc 3.6.0 is not supported due to a bug).

Library and directory structure

  • Install PISM headers in include/pism, skipping 3rd party headers and empty directories (see issue 166.)
  • Link all of PISM into one single library.
  • Install all Python scripts in util/. Fixes issue 346.
  • Fix the directory structure created by make install.

Other

  • Remove all simpleXXX executables. See issue 343. Use Python wrappers to access exact solutions used in PISM's verification tests.
  • Remove pismo (use pismr -regional).

Documentation

Computational domain and grid

  • Add options -x_range, -y_range, which specify domain extent in the x and y direction during bootstrapping. These can be used to extract a subset of a grid for a regional run.
  • De-couple grid periodicity from grid registration and add the grid.registration parameter. This changes the interpretation of -Lx and -Ly during bootstrapping. See issue 347.
  • Support EPSG:26710, EPSG:3413, and EPSG:3031. When an input file contains the global attribute proj4 containing the string "+init=epsg:XXXX" where XXXX is one of these codes PISM will create a CF-conforming mapping variable with projection parameters corresponding to the selected mapping. See issue 350.
  • Write PROJ.4 parameters to mapping:proj4_params (for CDO).

Ice rheology

  • Add gpbld3, the n==3 optimized flow law.

    This is an optimized (vectorized) implementation of the Glen-Paterson-Budd-Lliboutry-Duval flow law with the fixed Glen exponent of 3.

    On modern (2011 and on) CPUs this flow law implementation is almost 4 times faster than the default one. This significantly reduces the cost of high-resolution runs.

    The implementation uses exp() from VDT, a vectorized math library developed at CERN. To reduce the number of external dependencies a copy of VDT (v0.3.6) is included in PISM's source tree.

Stress balance

  • SSAFD KSP solver: use the initial residual norm.

    This prevents the SSAFD solver from failing when the solver has no work to do.

  • Make the SSAFD solver a little more robust by replacing zero diagonal matrix entries with large beta, effectively "disabling" sliding at these locations. See issue 349.

  • Remove SIA_Sliding, EISMINT II tests G and H, verification test E.

  • Add stress_balance.vertical_velocity_approximation. I.e. (optionally) use first-order upwinding to compute u_x and v_y in the vertical velocity computation.

  • Add enhancement factors for interglacial periods (See Ralf Greve, Application of a polythermal three-dimensional ice sheet model to the Greenland ice sheet: Response to steady-state and transient climate scenarios, 1997.)

    Use the following configuration parameters to control this:

    • stress_balance.sia.enhancement_factor_interglacial
    • stress_balance.ssa.enhancement_factor_interglacial
    • time.eemian_start
    • time.eemian_end
    • time.holocene_start

Geometry and mass transport

  • Completely redesign and re-implement the mass transport code. The new code is well-isolated and extensible, designed to make "balancing the books" easier, and can be tested in isolation. See also issue 201.
  • Add the class Geometry that can be used to provide geometry information to PISM's sub-models. This improves interfaces of PISM's sub-models, reducing undesirable "tight" coupling.
  • Option -part_grid implies -part_redist.

Calving

  • Generalize eigen-calving code and add von Mises calving.
  • Implement calving front retreat due to frontal melting.
  • Rename -cfl_eigen_calving to -calving_cfl.
  • Make it possible to disable float_kill near grounding lines. See -float_kill_calve_near_grounding_line.
  • Add option -float_kill_margin_only. See issue 340.
  • Allow using spatially-variable calving at thickness thresholds.
  • Add -calving_wrap_around for synthetic geometry setups.

Energy conservation

  • BedThermalUnit ensures that computed bedrock temperatures exceed zero Kelvin. See issue 313.

  • PISM no longer ignores horizontal enthalpy advection and strain heating near ice margins. See issue 292.

  • Following a re-interpretation of Aschwanden et al, An enthalpy formulation for glaciers and ice sheets, 2012 we require that dH/dp=0.

    Assuming that specific heat capacities of ice and water do not depend on temperature, this gives

    L(p) = (T_m(p) - T_m(p_air)) (c_w - c_i) + L_0, where

    T_m

    melting temperature

    c_w

    specific heat capacity of water

    c_i

    specific heat capacity of ice

    L_0

    latent heat of fusion at air pressure

    p_air

    air (atmospheric) pressure

    Note that this form of the latent heat of fusion L(p) also follows from Kirchhoff's law of thermochemistry. See EnthalpyConverter::L(T_pm) for details. See issue 334.

  • To allow for better code optimization, EnthalpyConverter no longer uses virtual methods. ColdEnthalpyConverter used in temperature-based verification tests sets ice melting temperature to 1e6 Kelvin to ensure that all ice is considered "cold." varcEnthalpyConverter, which implemented linear-in-temperature specific heat capacity of ice, is removed.

  • Code solving the enthalpy equation within an ice column supports both Dirichlet and Neumann boundary conditions at the top surface.

    Only the Dirichlet condition is used in modeling runs; Neumann B.C. code is there to simplify testing.

  • Documented the discretization of the enthalpy column system. Added simple verification tests for the enthalpy solver within an ice column (pure advection and pure diffusion with different boundary conditions).

  • To simplify model initialization and testing energy balance models are isolated. The rest of PISM uses the interface class EnergyModel. The old "cold mode" temperature-based energy balance model is in TemperatureModel. The enthalpy-based model is in EnthalpyModel.

Input and output

  • Remove the HDF5-based parallel I/O code.

  • Remove -o_format quilt and pismmerge.

  • Implement reading string attributes from NetCDF-4 files.

  • Add detailed I/O (writing) reporting with -verbose 3.

  • Add pism::StringLogger, a logger that prints to a string.

  • Add an option -profile to write detailed profiling information.

  • Add ice thickness thresholds for reporting and stress balance.

    This makes it easier to track changes corresponding to "glacierized" areas while excluding the seasonal cover.

    See output.ice_free_thickness_standard and stress_balance.ice_free_thickness_standard.

  • Write run statistics to extra and time-series files. (See issue 324, issue 330.)

  • New option: -save_force_output_times.

  • Avoid re-writing metadata that does not change during the run.

Diagnostics

  • Add numerous new diagnostic quantities, including sets of diagnostics needed to "balance the books" when accounting for mass changes (conservation).
  • Add scalar diagnostics using the new (higher) thickness threshold used to determine if a cell ice "ice-free". These diagnostics have the "_glacierized" suffix and can be interpreted as tracking changes in glacierized areas (ignoring the seasonal cover).
  • Rates of change reported by PISM are mean rates of change over reporting intervals computed using finite differences.
  • Better feedback on missing (or renamed) diagnostics. If a requested diagnostic is not available PISM will stop with an error message listing available diagnostics.

Bed deformation

  • Add a new command-line option: -uplift_file. Use it to specify the name of a file containing the variable dbdt to use when initializing the Lingle-Clark bed deformation model. See issue 390.

  • Add -topg_delta_file topg_delta.nc.

    With this option PISM tries to read "topg_delta" from a specified file and sets bed topography at the beginning of a run to

    bed_elevation = topg + topg_delta.

    Here topg is read from an input file (-i), topg_delta -- from topg_delta.nc.

  • Lingle-Clark bed deformation model: save the viscous bed displacement on the extended grid so that stopping and re-starting the model does not affect results. This also makes it possible to refine computational grids in runs using the model. See issue 370.

  • Bed deformation models can be used and tested in isolation (see issue 181).

Subglacial hydrology

  • Re-implement lateral till water diffusion as in Bueler and Brown, 2009.

Climate forcing

  • Apply lapse rate corrections throughout the domain.

    Previously it was used in icy areas only.

  • Remove old PDD code.

  • -atmosphere: use "kg m-2 second-1" precipitation units.

  • Add ocean_frac_SMB, a modifier scaling shelf-base mass flux

  • Atmosphere and ocean modifiers save "effective" fields.

  • Add an option and config. parameter surface.force_to_thickness.start_time to allow delaying the nudging effect.

Bug fixes

(This is an incomplete list.)

  • Fix issue 328 (diagnostic computation of wvelsurf).
  • Fix a bug in pism::ocean::Constant (-shelf_base_melt_rate was ignored).
  • Fix issue 351 (duplicate history in -extra_files).
  • Fix a bug in the code implementing -save_file with -save_split (see issue 325).
  • Fix issue 323 (fix EISMINT II settings so v0.7 conforms).
  • Fix issue 321: Sea level affects margin stress B.C. in the "dry simulation" mode.
  • Fix interpolation weights and add a test. See issue 326.

Miscellaneous

  • Undo the "fundamental transpose": now PISM uses the (y,x) order in files and memory.

    This simplifies pre-processing of input files and post-processing and analysis of modeling results.

  • Allow extrapolation during regridding to simplify restarting in runs where ice thickness exceeded the height of the computational domain and to extend the domain in continental ice sheet simulations. See issue 302.

  • Save the model state if the ice thickness exceeds the height of the computational domain.

  • The age model was moved to AgeModel.

  • Add the ability to add "hooks" to RuntimeError.

    Added to allow custom actions (such as printing a traceback) when an error is detected.

  • Improve PISM's version information

    • Add committer's name and date to the version string.
    • pismr -version prints versions of
      • PISM
      • PETSc (including configuration options)
      • MPI
      • NetCDF
      • FFTW
      • GSL
      • PROJ.4
      • SWIG (if Python bindings are enabled)

  • Add support for coverage testing using lcov.

    Set Pism_CODE_COVERAGE to enable, use make coverage_report to generate a report and and make coverage_reset to reset coverage data.

  • Add .clang-format to the top level directory

    clang-format makes it much easier to use consistent code formatting throughout. To re-format a file, commit it to the repository, then run

    clang-format -i filename.cc

    (Here -i tells clang-format to edit files "in place." Note that editing in place is safe because you added it to the repository.)

  • Re-organize configuration parameters: all parameters have new names that reflect their places within the model hierarchy.

  • Improve processing of boolean command-line options

    -foo yes
-foo on
-foo true
-foo True
-foo (no argument)

    set the boolean flag to "true."

    -foo no
-foo false
-foo False
-no_foo (for backward compatibility)

    set the flag to "false."

  • Add numerous regression tests.