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Merge pull request #173 from Varun-nair1997/main
example 7 bug fix and tests/test_ex07 inclusion
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‎examples/example_07/analysis.ipynb‎

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"cells": [
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{
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"cell_type": "markdown",
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"id": "organized-shakespeare",
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"id": "bf354e59",
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"metadata": {},
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"source": [
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"# Example 07: Upsampling calculations"
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]
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},
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{
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"cell_type": "markdown",
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"id": "9dd01e04-93a1-4219-923f-08904414f558",
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"id": "f397582d",
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"metadata": {},
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"source": [
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"In this example, upsampling calculations which can be used to switch a system between two different interatomic potentials is illustrated. \n",
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "satisfactory-kinase",
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"id": "7d67fceb",
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from calphy.input import read_report"
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"from calphy.postprocessing import read_report"
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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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"id": "conditional-colombia",
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"id": "84a4c423",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "established-vienna",
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"id": "72532dbd",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"-3.4389380251304913"
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"-3.440051166622059"
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]
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},
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"execution_count": 3,
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},
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{
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"cell_type": "markdown",
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"id": "5485eee8-5448-43b7-8376-22164d54a294",
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"id": "134dc9f1",
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"metadata": {},
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"source": [
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"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."
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "alive-farming",
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"id": "c21e8e87",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "gorgeous-sunglasses",
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"id": "4845b921",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"-0.25451608590151586"
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"-0.2544850177491684"
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]
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},
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"execution_count": 5,
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},
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{
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"cell_type": "markdown",
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"id": "0d933ab0-bb82-4dcd-b307-03fd8e062c74",
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"id": "252cb4a4",
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"metadata": {},
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"source": [
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"The free energy of the EAM potential, $F_\\mathrm{EAM} = F_\\mathrm{FS} + F_\\mathrm{upsampling}$"
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "ec362ea8-cc19-4ff9-9462-d2335fdece19",
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"id": "8241e478",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"-3.693454111032007"
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"-3.694536184371227"
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},
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"execution_count": 6,
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},
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{
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"cell_type": "markdown",
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"id": "51730d0f-d51c-495d-8c0d-8600f8034410",
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"id": "b728a4bd",
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"metadata": {},
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"source": [
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"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`. "
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "opened-gates",
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"id": "e73096cb",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "differential-robert",
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"id": "6a0ee06c",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"-3.6923377327832667"
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"-3.694201038169466"
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},
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"execution_count": 8,
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},
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{
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"cell_type": "markdown",
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"id": "d79e509b-f0ac-4900-b5e3-18a343e7030d",
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"id": "b89d91c1",
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"metadata": {},
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"source": [
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"We can see that the directly calculation is in meV agreement with the upsampling calculations."
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "pyiron",
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"language": "python",
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"name": "python3"
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"name": "pyiron"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.5"
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"version": "3.11.7"
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}
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},
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"nbformat": 4,

‎tests/test_ex07.py‎

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def test_ex07():
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import calphy
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from calphy.postprocessing import read_report
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# def test_example07_first_cell_runs():
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# notebook_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../examples/example_07/analysis.ipynb'))
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# with open(notebook_path, "r", encoding="utf-8") as f:
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# nb = nbformat.read(f, as_version=4)
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# # Filter just the first code cell
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# first_code_cell = next((cell for cell in nb.cells if cell.cell_type == "code"), None)
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# if not first_code_cell:
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# pytest.fail("No code cell found in example07.ipynb")
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# # Create a minimal notebook with only the first cell
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# nb_single = nbformat.v4.new_notebook()
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# nb_single.cells = [first_code_cell]
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# try:
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# client = NotebookClient(nb_single, timeout=60, kernel_name="pyiron")
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# client.execute()
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# except Exception as e:
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# pytest.fail(f"First code cell in example07.analysis.ipynb failed: {e}")

‎tests/tests_NB.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {
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"collapsed": true
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},
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"outputs": [
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{
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"ename": "ImportError",
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"evalue": "cannot import name 'SocketInterface' from 'pympipool' (/Users/varunnair/opt/anaconda3/lib/python3.7/site-packages/pympipool/__init__.py)",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
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"\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",
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"\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",
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"\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",
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"\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",
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"\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",
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"\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",
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"\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",
24+
"\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",
25+
"\u001b[0;31mImportError\u001b[0m: cannot import name 'SocketInterface' from 'pympipool' (/Users/varunnair/opt/anaconda3/lib/python3.7/site-packages/pympipool/__init__.py)"
26+
]
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}
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],
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"source": [
30+
"import test_helpers as th"
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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": 1,
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"metadata": {},
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"outputs": [
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{
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"ename": "ModuleNotFoundError",
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"evalue": "No module named 'pyscal'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
45+
"\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",
46+
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pyscal'"
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]
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}
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],
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"source": [
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"th.test_nones()\n",
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"th.test_replace_nones()\n",
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"th.test_validate_spring_constants()"
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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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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
85+
}

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