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Merged
srmnitc merged 6 commits into from
Jul 9, 2025
Merged

example 7 bug fix and tests/test_ex07 inclusion #173

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c57ed70
bug fix
Jul 7, 2025
260ae1d
testing helpers
Jul 7, 2025
e730796
tested bug fix
Varun-nair1997 Jul 9, 2025
ba4a57d
cleaned up tested bug fix
Varun-nair1997 Jul 9, 2025
ea1da55
testing bug fix
Jul 9, 2025
19a30f3
Update test_ex07.py
Varun-nair1997 Jul 9, 2025
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44 changes: 22 additions & 22 deletions examples/example_07/analysis.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,15 +2,15 @@
"cells": [
{
"cell_type": "markdown",
"id": "organized-shakespeare",
"id": "bf354e59",
"metadata": {},
"source": [
"# Example 07: Upsampling calculations"
]
},
{
"cell_type": "markdown",
"id": "9dd01e04-93a1-4219-923f-08904414f558",
"id": "f397582d",
"metadata": {},
"source": [
"In this example, upsampling calculations which can be used to switch a system between two different interatomic potentials is illustrated. \n",
Expand All @@ -33,18 +33,18 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "satisfactory-kinase",
"id": "7d67fceb",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from calphy.input import read_report"
"from calphy.postprocessing import read_report"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "conditional-colombia",
"id": "84a4c423",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -54,13 +54,13 @@
{
"cell_type": "code",
"execution_count": 3,
"id": "established-vienna",
"id": "72532dbd",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-3.4389380251304913"
"-3.440051166622059"
]
},
"execution_count": 3,
Expand All @@ -74,7 +74,7 @@
},
{
"cell_type": "markdown",
"id": "5485eee8-5448-43b7-8376-22164d54a294",
"id": "134dc9f1",
"metadata": {},
"source": [
"Now we can transform FS to EAM potential (see input file above). After running the calculation, we can check the free energy of this alchemical transformation."
Expand All @@ -83,7 +83,7 @@
{
"cell_type": "code",
"execution_count": 4,
"id": "alive-farming",
"id": "c21e8e87",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -93,13 +93,13 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "gorgeous-sunglasses",
"id": "4845b921",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-0.25451608590151586"
"-0.2544850177491684"
]
},
"execution_count": 5,
Expand All @@ -113,7 +113,7 @@
},
{
"cell_type": "markdown",
"id": "0d933ab0-bb82-4dcd-b307-03fd8e062c74",
"id": "252cb4a4",
"metadata": {},
"source": [
"The free energy of the EAM potential, $F_\\mathrm{EAM} = F_\\mathrm{FS} + F_\\mathrm{upsampling}$"
Expand All @@ -122,13 +122,13 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "ec362ea8-cc19-4ff9-9462-d2335fdece19",
"id": "8241e478",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-3.693454111032007"
"-3.694536184371227"
]
},
"execution_count": 6,
Expand All @@ -142,7 +142,7 @@
},
{
"cell_type": "markdown",
"id": "51730d0f-d51c-495d-8c0d-8600f8034410",
"id": "b728a4bd",
"metadata": {},
"source": [
"We can verify this calculation by directly computing the free energy of the EAM potential. The input file is available at `pot2/input-fe.yaml`. "
Expand All @@ -151,7 +151,7 @@
{
"cell_type": "code",
"execution_count": 7,
"id": "opened-gates",
"id": "e73096cb",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -161,13 +161,13 @@
{
"cell_type": "code",
"execution_count": 8,
"id": "differential-robert",
"id": "6a0ee06c",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-3.6923377327832667"
"-3.694201038169466"
]
},
"execution_count": 8,
Expand All @@ -181,7 +181,7 @@
},
{
"cell_type": "markdown",
"id": "d79e509b-f0ac-4900-b5e3-18a343e7030d",
"id": "b89d91c1",
"metadata": {},
"source": [
"We can see that the directly calculation is in meV agreement with the upsampling calculations."
Expand All @@ -190,9 +190,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "pyiron",
"language": "python",
"name": "python3"
"name": "pyiron"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -204,7 +204,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.11.7"
}
},
"nbformat": 4,
Expand Down
25 changes: 25 additions & 0 deletions tests/test_ex07.py
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@@ -0,0 +1,25 @@
def test_ex07():
import calphy
from calphy.postprocessing import read_report

# def test_example07_first_cell_runs():
# notebook_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../examples/example_07/analysis.ipynb'))

# with open(notebook_path, "r", encoding="utf-8") as f:
# nb = nbformat.read(f, as_version=4)

# # Filter just the first code cell
# first_code_cell = next((cell for cell in nb.cells if cell.cell_type == "code"), None)

# if not first_code_cell:
# pytest.fail("No code cell found in example07.ipynb")

# # Create a minimal notebook with only the first cell
# nb_single = nbformat.v4.new_notebook()
# nb_single.cells = [first_code_cell]

# try:
# client = NotebookClient(nb_single, timeout=60, kernel_name="pyiron")
# client.execute()
# except Exception as e:
# pytest.fail(f"First code cell in example07.analysis.ipynb failed: {e}")
85 changes: 85 additions & 0 deletions tests/tests_NB.ipynb
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@@ -0,0 +1,85 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [
{
"ename": "ImportError",
"evalue": "cannot import name 'SocketInterface' from 'pympipool' (/Users/varunnair/opt/anaconda3/lib/python3.7/site-packages/pympipool/__init__.py)",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-2-0422ff8f98f0>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;31m# import test_integrators\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;31m# import test_options\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mtest_solid_methods\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/Desktop/ICAMS_HIWI/calphy/calphy/tests/test_solid_methods.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpytest\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minput\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mread_inputfile\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolid\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mSolid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mliquid\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLiquid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/calphy/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minput\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mCalculation\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mliquid\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLiquid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolid\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mSolid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0malchemy\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mAlchemy\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroutines\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mMeltingTemp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/calphy/liquid.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 27\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mintegrators\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 28\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyscal\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraj_process\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mptp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 29\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlattice\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpl\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 30\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhelpers\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mph\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 31\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcalphy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mphase\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mcph\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/calphy/lattice.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 24\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmendeleev\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0melement\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 25\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 26\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpylammpsmpi\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLammpsLibrary\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 27\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 28\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpyscal\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcore\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/pylammpsmpi/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpylammpsmpi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlammps_wrapper\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLammpsLibrary\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0m_version\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mget_versions\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0m__version__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_versions\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"version\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/pylammpsmpi/lammps_wrapper.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mpylammpsmpi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcommands\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcommand_list\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mthermo_list\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfunc_list\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprop_list\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpylammpsmpi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlammps\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLammpsBase\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 7\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0m__author__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Sarath Menon, Jan Janssen\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/anaconda3/lib/python3.7/site-packages/pylammpsmpi/utils/lammps.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpympipool\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mSocketInterface\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 7\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mImportError\u001b[0m: cannot import name 'SocketInterface' from 'pympipool' (/Users/varunnair/opt/anaconda3/lib/python3.7/site-packages/pympipool/__init__.py)"
]
}
],
"source": [
"import test_helpers as th"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'pyscal'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-1-e8e6f8f7118e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mpyscal\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pyscal'"
]
}
],
"source": [
"th.test_nones()\n",
"th.test_replace_nones()\n",
"th.test_validate_spring_constants()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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