haranjackson/pypde

A Python library for solving any system of hyperbolic or parabolic Partial Differential Equations. The PDEs can have stiff source terms and non-conservative components.

pypde's Issues

Scalar field becomes filled with NaN s

Hi,
I'm trying to solve the Swift-Hohenbeg model's PDE as such:

l = 3
k_c = 0.5

grid = pde.CartesianGrid([[0, 100], [0, 100]], [100, 100])
field = pde.ScalarField.random_normal(grid, mean=10)

storage = pde.MemoryStorage()
eq = pde.PDE({"u": f"u -{l}*u**3 -laplace(laplace(u)) -{k_c**4}*u - 2*{k_c**2}*laplace(u)"})
result = eq.solve(field, t_range=100, dt=1e-2, tracker=["progress", storage.tracker(1)])
result.plot()

But for many values of l and k_c, The final result becomes a scalar field filled with NaN.

The current values causes this error.
Thanks

2D Navie-Stokes example code produces an error

TypingError Traceback (most recent call last)
Cell In [12], line 6
2 from numpy import linspace
4 from pypde import pde_solver
----> 6 out = pde_solver(u,
7 tf,
8 L,
9 F=F,
10 cfl=0.9,
11 order=2,
12 boundaryTypes='periodic')
14 x = linspace(0, L[0], nx)
15 y = linspace(0, L[1], ny)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/pypde/solvers.py:200, in pde_solver(Q0, tf, L, F, B, S, boundaryTypes, cfl, order, ndt, flux, stiff, nThreads)
196 secondOrder = nargs(F) == 3
198 print('compiling functions...')
--> 200 _F, _B, _S = generate_cfuncs(F, B, S, ndim, V)
202 solver = create_solver()
204 ret = zeros(ndt * Q0.size)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/pypde/cfuncs.py:37, in generate_cfuncs(F, B, S, ndim, V)
33 nBargs = nargs(B)
35 Fsig, Bsig, Ssig = generate_signatures(nFargs, nBargs)
---> 37 Fjit = njit(Fsig)(F)
38 Bjit = njit(Bsig)(B)
39 Sjit = njit(Ssig)(S)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/decorators.py:219, in _jit..wrapper(func)
217 with typeinfer.register_dispatcher(disp):
218 for sig in sigs:
--> 219 disp.compile(sig)
220 disp.disable_compile()
221 return disp

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/dispatcher.py:965, in Dispatcher.compile(self, sig)
963 with ev.trigger_event("numba:compile", data=ev_details):
964 try:
--> 965 cres = self._compiler.compile(args, return_type)
966 except errors.ForceLiteralArg as e:
967 def folded(args, kws):

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/dispatcher.py:129, in _FunctionCompiler.compile(self, args, return_type)
127 return retval
128 else:
--> 129 raise retval

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/dispatcher.py:139, in _FunctionCompiler._compile_cached(self, args, return_type)
136 pass
138 try:
--> 139 retval = self._compile_core(args, return_type)
140 except errors.TypingError as e:
141 self._failed_cache[key] = e

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/dispatcher.py:152, in _FunctionCompiler._compile_core(self, args, return_type)
149 flags = self._customize_flags(flags)
151 impl = self._get_implementation(args, {})
--> 152 cres = compiler.compile_extra(self.targetdescr.typing_context,
153 self.targetdescr.target_context,
154 impl,
155 args=args, return_type=return_type,
156 flags=flags, locals=self.locals,
157 pipeline_class=self.pipeline_class)
158 # Check typing error if object mode is used
159 if cres.typing_error is not None and not flags.enable_pyobject:

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler.py:716, in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
692 """Compiler entry point
693
694 Parameter
(...)
712 compiler pipeline
713 """
714 pipeline = pipeline_class(typingctx, targetctx, library,
715 args, return_type, flags, locals)
--> 716 return pipeline.compile_extra(func)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler.py:452, in CompilerBase.compile_extra(self, func)
450 self.state.lifted = ()
451 self.state.lifted_from = None
--> 452 return self._compile_bytecode()

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler.py:520, in CompilerBase._compile_bytecode(self)
516 """
517 Populate and run pipeline for bytecode input
518 """
519 assert self.state.func_ir is None
--> 520 return self._compile_core()

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler.py:499, in CompilerBase._compile_core(self)
497 self.state.status.fail_reason = e
498 if is_final_pipeline:
--> 499 raise e
500 else:
501 raise CompilerError("All available pipelines exhausted")

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler.py:486, in CompilerBase._compile_core(self)
484 res = None
485 try:
--> 486 pm.run(self.state)
487 if self.state.cr is not None:
488 break

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler_machinery.py:368, in PassManager.run(self, state)
365 msg = "Failed in %s mode pipeline (step: %s)" %
366 (self.pipeline_name, pass_desc)
367 patched_exception = self._patch_error(msg, e)
--> 368 raise patched_exception

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler_machinery.py:356, in PassManager.run(self, state)
354 pass_inst = _pass_registry.get(pss).pass_inst
355 if isinstance(pass_inst, CompilerPass):
--> 356 self._runPass(idx, pass_inst, state)
357 else:
358 raise BaseException("Legacy pass in use")

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler_lock.py:35, in _CompilerLock.call.._acquire_compile_lock(*args, **kwargs)
32 @functools.wraps(func)
33 def _acquire_compile_lock(*args, **kwargs):
34 with self:
---> 35 return func(*args, **kwargs)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler_machinery.py:311, in PassManager._runPass(self, index, pss, internal_state)
309 mutated |= check(pss.run_initialization, internal_state)
310 with SimpleTimer() as pass_time:
--> 311 mutated |= check(pss.run_pass, internal_state)
312 with SimpleTimer() as finalize_time:
313 mutated |= check(pss.run_finalizer, internal_state)

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/compiler_machinery.py:273, in PassManager._runPass..check(func, compiler_state)
272 def check(func, compiler_state):
--> 273 mangled = func(compiler_state)
274 if mangled not in (True, False):
275 msg = ("CompilerPass implementations should return True/False. "
276 "CompilerPass with name '%s' did not.")

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/typed_passes.py:105, in BaseTypeInference.run_pass(self, state)
99 """
100 Type inference and legalization
101 """
102 with fallback_context(state, 'Function "%s" failed type inference'
103 % (state.func_id.func_name,)):
104 # Type inference
--> 105 typemap, return_type, calltypes, errs = type_inference_stage(
106 state.typingctx,
107 state.targetctx,
108 state.func_ir,
109 state.args,
110 state.return_type,
111 state.locals,
112 raise_errors=self._raise_errors)
113 state.typemap = typemap
114 # save errors in case of partial typing

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/typed_passes.py:83, in type_inference_stage(typingctx, targetctx, interp, args, return_type, locals, raise_errors)
81 infer.build_constraint()
82 # return errors in case of partial typing
---> 83 errs = infer.propagate(raise_errors=raise_errors)
84 typemap, restype, calltypes = infer.unify(raise_errors=raise_errors)
86 # Output all Numba warnings

File ~/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/typeinfer.py:1086, in TypeInferer.propagate(self, raise_errors)
1083 force_lit_args = [e for e in errors
1084 if isinstance(e, ForceLiteralArg)]
1085 if not force_lit_args:
-> 1086 raise errors[0]
1087 else:
1088 raise reduce(operator.or_, force_lit_args)

TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Failed in nopython mode pipeline (step: nopython frontend)
No implementation of function Function(<function dot at 0x7faf3c155940>) found for signature:

dot(array(float64, 1d, C), array(float64, 1d, C))

There are 4 candidate implementations:

• Of which 4 did not match due to:
  Overload in function '_OverloadWrapper._build..ol_generated': File: numba/core/overload_glue.py: Line 129.
  With argument(s): '(array(float64, 1d, C), array(float64, 1d, C))':
  Rejected as the implementation raised a specific error:
  LoweringError: Failed in nopython mode pipeline (step: native lowering)
  scipy 0.16+ is required for linear algebra

File "", line 3:

During: lowering "$8call_function.3 = call $2load_global.0(a, b, func=$2load_global.0, args=[Var(a, :3), Var(b, :3)], kws=(), vararg=None, varkwarg=None, target=None)" at (3)
raised from /home/valentin/anaconda3/envs/pdesolve/lib/python3.8/site-packages/numba/core/errors.py:837

During: resolving callee type: Function(<function dot at 0x7faf3c155940>)
During: typing of call at /tmp/ipykernel_14609/274012429.py (16)

File "../../tmp/ipykernel_14609/274012429.py", line 16:

During: resolving callee type: type(CPUDispatcher(<function pressure at 0x7faf13aac670>))
During: typing of call at /tmp/ipykernel_14609/274012429.py (34)

During: resolving callee type: type(CPUDispatcher(<function pressure at 0x7faf13aac670>))
During: typing of call at /tmp/ipykernel_14609/274012429.py (34)

File "../../tmp/ipykernel_14609/274012429.py", line 34:

matplotlib broke compatibility with get_cmap in new release (3.9)

matplotlib broke compatibility with get_cmap in new release (3.9)

When executing the base example on a newly installed version of py-pde:

import pde

grid = pde.UnitGrid([32,32])
state = pde.ScalarField.random_uniform(grid, -1, 1)

eq = pde.DiffusionPDE(diffusivity=0.1)
result = eq.solve(state, t_range=1, dt=0.01)
result.plot()

I receive the following traceback, which was subsequently solved by performing the command pip install --force-reinstall "matplotlib==3.8.3", which downgrades matplotlib to 3.8.3.

Other packages seem to be having the same issue (atarashansky/SAMap#148).

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
File ~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:21
     [20](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:20) try:
---> [21](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:21)     from matplotlib.colormaps import get_cmap
     [22](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:22) except ImportError:

ModuleNotFoundError: No module named 'matplotlib.colormaps'

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
Cell In[3], [line 1](vscode-notebook-cell:?execution_count=3&line=1)
----> [1](vscode-notebook-cell:?execution_count=3&line=1) import pde
      [3](vscode-notebook-cell:?execution_count=3&line=3) grid = pde.UnitGrid
      [4](vscode-notebook-cell:?execution_count=3&line=4) state = pde.ScalarField.random_uniform(grid)

File ~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:28
     [25](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:25) del Config  # clean name space
     [27](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:27) # import all other modules that should occupy the main name space
---> [28](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:28) from .fields import *  # @UnusedWildImport
     [29](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:29) from .grids import *  # @UnusedWildImport
     [30](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/__init__.py:30) from .pdes import *  # @UnusedWildImport

File ~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:26
      [1](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:1) """
      [2](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:2) Defines fields, which contain the actual data stored on a discrete grid.
      [3](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:3) 
   (...)
     [22](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:22) .. codeauthor:: David Zwicker <[email protected]>
     [23](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:23) """
     [25](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:25) from .base import FieldBase
---> [26](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:26) from .collection import FieldCollection
     [27](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:27) from .scalar import ScalarField
     [28](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/__init__.py:28) from .tensorial import Tensor2Field

File ~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:23
     [21](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:21)     from matplotlib.colormaps import get_cmap
     [22](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:22) except ImportError:
---> [23](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:23)     from matplotlib.cm import get_cmap
     [25](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:25) from ..grids.base import GridBase
     [26](https://file+.vscode-resource.vscode-cdn.net/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/~/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/pde/fields/collection.py:26) from ..tools.docstrings import fill_in_docstring

ImportError: cannot import name 'get_cmap' from 'matplotlib.cm' (/Users/tmroyal/Documents/composition/opuses2024/coding_projects/pde_play/.venv/lib/python3.11/site-packages/matplotlib/cm.py)