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a few improvements for the tutorials #1132

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a few improvements for the tutorials #1132

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9279131
test commit
QuantumChemist Feb 25, 2025
091cb6b
test commit
QuantumChemist Feb 25, 2025
567f334
small improvements
QuantumChemist Feb 25, 2025
c230fe8
small improvements
QuantumChemist Feb 25, 2025
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6 changes: 3 additions & 3 deletions tutorials/grueneisen_workflow.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,15 @@
"id": "0",
"metadata": {},
"source": [
"# Grueneisen Workflow (VASP)"
"# Grüneisen Workflow (VASP)"
]
},
{
"cell_type": "markdown",
"id": "1",
"metadata": {},
"source": [
"This part is needed for the execution in the notebook.\n"
"This part is mocking the VASP calculation to facilitate the execution in the notebook.\n"
]
},
{
Expand Down Expand Up @@ -45,7 +45,7 @@
"id": "3",
"metadata": {},
"source": [
"Let's load all required Makers."
"Let's load all required Makers to set up the calculation settings for VASP."
]
},
{
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52 changes: 22 additions & 30 deletions tutorials/qha_workflow.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -76,21 +76,13 @@
]
},
{
"cell_type": "raw",
"cell_type": "markdown",
"id": "3",
"metadata": {},
"source": [
"This tutorial will make use of a quasi-harmonic workflow\n",
" that allows to include volume-dependent anharmonicity \n",
" into the calculation of phonon free energies.\n",
" Please check out the paper by Togo to learn about the\n",
"exact implementation as we will rely on Phonopy to perform the quasi-harmonic approximation.\n",
" https://doi.org/10.7566/JPSJ.92.012001.\n",
" At the moment, we perform harmonic free\n",
" energy calculation along a volume curve\n",
" to arrive at free energy-volume curves\n",
" that are the starting point for the q\n",
" uasi-harmonic approximation."
"This tutorial will make use of a quasi-harmonic workflow that allows to include volume-dependent anharmonicity into the calculation of phonon free energies.\n",
"Please check out the paper by Togo to learn about the exact implementation as we will rely on Phonopy to perform the quasi-harmonic approximation: https://doi.org/10.7566/JPSJ.92.012001.\n",
"At the moment, we perform harmonic free energy calculation along a volume curve to arrive at free energy-volume curves that are the starting point for the quasi-harmonic approximation."
]
},
{
Expand Down Expand Up @@ -125,13 +117,9 @@
"metadata": {},
"source": [
"Then one can use the `QhaMaker` to generate a `Flow`.\n",
"First, the structure will be optimized than the\n",
"structures will be optimized at constant volume\n",
"along an energy volume curve. Please make sure the structural optimizations are tight enough. At each of these\n",
"volumes, a phonon run will then be performed.\n",
"The quasi-harmonic approximation is only valid\n",
"if the harmonic phonon curves don't show any\n",
"imaginary modes. However, for testing, you\n",
"First, the structure will be optimized than the structures will be optimized at constant volume along an energy volume curve. \n",
"Please make sure the structural optimizations are tight enough. At each of these volumes, a phonon run will then be performed.\n",
"The quasi-harmonic approximation is only valid if the harmonic phonon curves don't show any imaginary modes. However, for testing, you\n",
"can also switch off this option."
]
},
Expand All @@ -140,11 +128,7 @@
"id": "7",
"metadata": {},
"source": [
"Before we start the quasi-harmonic workflow,\n",
"we adapt the first relaxation, the relaxation\n",
"with different volumes and the static runs for\n",
"the phonon calculation. As we deal with Si,\n",
"we will not add the non-analytical term correction."
"Before we start the quasi-harmonic workflow, we adapt the first relaxation, the relaxation with different volumes and the static runs for the phonon calculation. As we deal with Si, we will not add the non-analytical term correction. For this we load the respective Makers."
]
},
{
Expand Down Expand Up @@ -251,10 +235,18 @@
"phonon_displacement_maker.name = \"dft phonon static\""
]
},
{
"cell_type": "markdown",
"id": "9",
"metadata": {},
"source": [
"Then we can construct a `QhaMaker` flow as follows:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9",
"id": "10",
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -286,7 +278,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "10",
"id": "11",
"metadata": {
"jupyter": {
"is_executing": true
Expand All @@ -306,7 +298,7 @@
},
{
"cell_type": "markdown",
"id": "11",
"id": "12",
"metadata": {},
"source": [
"## Let's retrieve the data and analyze it"
Expand All @@ -315,7 +307,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "12",
"id": "13",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -335,7 +327,7 @@
},
{
"cell_type": "markdown",
"id": "13",
"id": "14",
"metadata": {},
"source": [
"You can then plot some of the output free energy volume curves"
Expand All @@ -344,7 +336,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "14",
"id": "15",
"metadata": {},
"outputs": [],
"source": [
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