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arekpaterakarekpaterak
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Adjust the tolerance in the comparison between methods
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‎examples/PyMPDATA_examples/comparisons_against_pypde/diffusion_equation_with_spatial_dependence/diffusion_equation_with_spatial_dependence.ipynb‎

Lines changed: 68 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -25,29 +25,37 @@
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 3,
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"id": "46e47a0b",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"The autoreload extension is already loaded. To reload it, use:\n",
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" %reload_ext autoreload\n"
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]
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}
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],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 4,
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"id": "c91b4ebc",
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"metadata": {},
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"outputs": [],
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"source": [
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"import logging\n",
54+
"import time\n",
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"\n",
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"import numpy as np\n",
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"import pde as py_pde\n",
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"from IPython.display import display\n",
49-
"import time\n",
50-
"\n",
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"from PyMPDATA_examples.comparisons_against_pypde.diffusion_equation_with_spatial_dependence import (\n",
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" solutions,\n",
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")\n",
@@ -71,12 +79,14 @@
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"id": "76f14b27",
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"metadata": {},
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"source": [
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"## Original example from the *py-pde* library"
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"## Original example from the *py-pde* library\n",
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"\n",
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"We use the almost identical code as in the original example from the *py-pde* library, which is available [here](https://py-pde.readthedocs.io/en/latest/examples_gallery/simple_pdes/pde_heterogeneous_diffusion.html)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"id": "209d79d2",
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"metadata": {},
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"outputs": [
@@ -85,15 +95,15 @@
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"output_type": "stream",
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"text": [
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"INFO:pde.tools.numba:Compile `dot_compiled` with parallel=True\n",
88-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
89-
"INFO:pde.tools.numba:Compile `laplace` with parallel=True\n",
98+
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
99+
"INFO:pde.tools.numba:Compile `gradient` with parallel=True\n",
90100
"INFO:pde.tools.numba:Compile `set_valid` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `set_valid_bcs` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `apply_op_compiled` with parallel=True\n",
95-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
96-
"INFO:pde.tools.numba:Compile `gradient` with parallel=True\n",
105+
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
106+
"INFO:pde.tools.numba:Compile `laplace` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `set_valid` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
@@ -105,8 +115,8 @@
105115
"INFO:pde.tools.expressions.ScalarExpression:Parse sympy expression `(tanh(x) + 1.01)*laplace(c, none, bc_args) + dot(gradient(tanh(x) + 1.01, none, bc_args), gradient(c, none, bc_args))`\n",
106116
"INFO:pde.tools.numba:Compile `_lambdifygenerated` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `rhs_func` with parallel=True\n",
108-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
109118
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
119+
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
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"INFO:pde.pdes.PDE:RHS for `c` has signature ('c', 't', 'none', 'bc_args', 'x')\n",
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"INFO:pde.tools.expressions.ScalarExpression:Parse sympy expression `(tanh(x) + 1.01)*laplace(c, none, bc_args) + dot(gradient(tanh(x) + 1.01, none, bc_args), gradient(c, none, bc_args))`\n",
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"INFO:pde.solvers.ExplicitSolver:Init explicit Euler stepper with dt=0.001\n",
@@ -126,10 +136,10 @@
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{
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"data": {
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"text/plain": [
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"<pde.tools.plotting.PlotReference at 0x29102b96c40>"
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"<pde.tools.plotting.PlotReference at 0x12a29a66d00>"
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]
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},
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"execution_count": 3,
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -140,7 +150,6 @@
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"term_2 = f\"dot(gradient({diffusivity}), gradient(c))\"\n",
141151
"eq = py_pde.PDE({\"c\": f\"{term_1} + {term_2}\"}, bc={\"value\": 0})\n",
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"\n",
143-
"\n",
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"grid = py_pde.CartesianGrid([[-5, 5]], 64)\n",
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"field = py_pde.ScalarField(grid, 1)\n",
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"\n",
@@ -160,7 +169,33 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 8,
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"id": "1c5bf44b",
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"metadata": {},
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"outputs": [],
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"source": [
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"class Timer:\n",
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" \"\"\"A simple timer class to measure elapsed time.\"\"\"\n",
179+
"\n",
180+
" def __init__(self):\n",
181+
" self._start = None\n",
182+
" self._time = None\n",
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"\n",
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" @property\n",
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" def time(self):\n",
186+
" return self._time\n",
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"\n",
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" def __enter__(self):\n",
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" self._start = time.perf_counter()\n",
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" return self\n",
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"\n",
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" def __exit__(self, *args):\n",
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" self._time = time.perf_counter() - self._start"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ba25763a",
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"metadata": {},
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"outputs": [
@@ -169,15 +204,15 @@
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"output_type": "stream",
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"text": [
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"INFO:pde.tools.numba:Compile `dot_compiled` with parallel=True\n",
172-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
173-
"INFO:pde.tools.numba:Compile `laplace` with parallel=True\n",
207+
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
208+
"INFO:pde.tools.numba:Compile `gradient` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `set_valid` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `set_valid_bcs` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `apply_op_compiled` with parallel=True\n",
179-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
180-
"INFO:pde.tools.numba:Compile `gradient` with parallel=True\n",
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"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
215+
"INFO:pde.tools.numba:Compile `laplace` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `set_valid` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `virtual_point` with parallel=True\n",
@@ -189,8 +224,8 @@
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"INFO:pde.tools.expressions.ScalarExpression:Parse sympy expression `(tanh(x) + 1.01)*laplace(c, none, bc_args) + dot(gradient(tanh(x) + 1.01, none, bc_args), gradient(c, none, bc_args))`\n",
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"INFO:pde.tools.numba:Compile `_lambdifygenerated` with parallel=True\n",
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"INFO:pde.tools.numba:Compile `rhs_func` with parallel=True\n",
192-
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
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"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `gradient` in PDE for `c`\n",
228+
"INFO:pde.pdes.PDE:Using boundary condition `{'value': 0}` for operator `laplace` in PDE for `c`\n",
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"INFO:pde.pdes.PDE:RHS for `c` has signature ('c', 't', 'none', 'bc_args', 'x')\n",
195230
"INFO:pde.tools.expressions.ScalarExpression:Parse sympy expression `(tanh(x) + 1.01)*laplace(c, none, bc_args) + dot(gradient(tanh(x) + 1.01, none, bc_args), gradient(c, none, bc_args))`\n",
196231
"INFO:pde.solvers.ExplicitSolver:Init explicit Euler stepper with dt=0.001\n",
@@ -199,9 +234,9 @@
199234
}
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],
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"source": [
202-
"start_time = time.perf_counter()\n",
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"py_pde_result = solutions.py_pde_solution(simulation_args)\n",
204-
"py_pde_time = time.perf_counter() - start_time"
237+
"with Timer() as timer:\n",
238+
" py_pde_result = solutions.py_pde_solution(simulation_args)\n",
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"py_pde_time = timer.time"
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]
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},
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{
@@ -214,7 +249,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 7,
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"id": "42c6278f",
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"metadata": {},
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"outputs": [],
@@ -269,7 +304,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"id": "51c60e1d",
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"metadata": {},
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"outputs": [
@@ -281,26 +316,15 @@
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"INFO:root:Using native PyMPDATA implementation (should be ~3x faster than Strang splitting)\n",
282317
"INFO:root:Diffusivity range: 0.010 to 2.010\n",
283318
"INFO:root:Using balanced mu coefficient: 0.050000\n",
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"INFO:root:At step 10000/100000\n",
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"INFO:root:At step 20000/100000\n",
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"INFO:root:At step 30000/100000\n",
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"INFO:root:At step 40000/100000\n",
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"INFO:root:At step 50000/100000\n",
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"INFO:root:At step 60000/100000\n",
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"INFO:root:At step 70000/100000\n",
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"INFO:root:At step 80000/100000\n",
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"INFO:root:At step 90000/100000\n",
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"INFO:root:At step 100000/100000\n",
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"INFO:root:Simulation completed!\n",
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"INFO:root:Mass conservation: initial=64.000000, final=4.440033\n",
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"INFO:root:Relative mass change: 9.31e+01%\n"
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"INFO:root:At step 10000/100000\n"
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]
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}
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],
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"source": [
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"start_time = time.perf_counter()\n",
302-
"pympdata_result = solutions.pympdata_solution(simulation_args)\n",
303-
"pympdata_time = time.perf_counter() - start_time"
324+
"with Timer() as timer:\n",
325+
" pympdata_result = solutions.pympdata_solution(simulation_args)\n",
326+
" \n",
327+
"pympdata_time = timer.time"
304328
]
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},
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{
@@ -390,13 +414,13 @@
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": null,
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"id": "f2ac8a37",
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"metadata": {},
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"outputs": [],
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"source": [
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"assert np.allclose(\n",
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" pympdata_result.kymograph_result, py_pde_result.kymograph_result, atol=5*1e-1\n",
423+
" pympdata_result.kymograph_result, py_pde_result.kymograph_result, atol=0.2\n",
400424
"), \"Kymograph results do not match.\""
401425
]
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},

‎tests/smoke_tests/comparison_against_pypde/diffusion_equation_with_spatial_dependence/test_similarity.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -38,5 +38,5 @@ def test_similarity():
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pympdata_result.kymograph_result.shape == py_pde_result.kymograph_result.shape
3939
), "Kymograph results from both implementations should have the same shape."
4040
assert np.allclose(
41-
pympdata_result.kymograph_result, py_pde_result.kymograph_result, atol=5 * 1e-1
41+
pympdata_result.kymograph_result, py_pde_result.kymograph_result, atol=0.2
4242
), "Kymograph results from both implementations should be similar within the tolerance."

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