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Updated docs
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@lllangWV
lllangWV committed Mar 29, 2024
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2 changes: 1 addition & 1 deletion docs/.buildinfo
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@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 61e2986449091a7be4f25a8af15fb3b5
config: 96a29a2f0251ba919add6b6d29b22740
tags: 645f666f9bcd5a90fca523b33c5a78b7
2 changes: 2 additions & 0 deletions docs/_downloads/064c0d2777aed39cc8bf9734f26c68a0/plot_noncolinear_qe.py
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pyprocar.bandsplot(
code='qe',
mode='plain',
fermi=18.0536,
dirname=data_dir)

###############################################################################
Expand All @@ -55,6 +56,7 @@
pyprocar.bandsplot(
code='qe',
mode='parametric',
fermi=18.0536,
atoms=atoms,
orbitals=orbitals,
spins=spins,
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60 changes: 60 additions & 0 deletions docs/_downloads/0ae4717a2ffa80a361725a23ff73d2e0/plot_spin_polarized_dos.py
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pyprocar.dosplot(
code='vasp',
mode='plain',
fermi=5.590136,
dirname=data_dir)

###############################################################################
Expand All @@ -46,6 +47,7 @@
pyprocar.dosplot(
code='vasp',
mode='plain',
fermi=5.590136,
spins=spins,
dirname=data_dir)

Expand All @@ -64,6 +66,7 @@
pyprocar.dosplot(
code='vasp',
mode='parametric',
fermi=5.590136,
atoms=atoms,
orbitals=orbitals,
spins=spins,
Expand All @@ -84,6 +87,7 @@
pyprocar.dosplot(
code='vasp',
mode='parametric_line',
fermi=5.590136,
atoms=atoms,
orbitals=orbitals,
spins=spins,
Expand All @@ -103,6 +107,7 @@
pyprocar.dosplot(
code='vasp',
mode='stack_species',
fermi=5.590136,
orbitals=orbitals,
spins=spins,
dirname=data_dir)
Expand All @@ -118,6 +123,7 @@
pyprocar.dosplot(
code='vasp',
mode='stack_orbitals',
fermi=5.590136,
atoms=atoms,
spins=spins,
dirname=data_dir)
Expand All @@ -136,6 +142,60 @@
pyprocar.dosplot(
code='vasp',
mode='stack',
fermi=5.590136,
items=items,
spins=spins,
dirname=data_dir)


###############################################################################
# overlay_species mode
# +++++++++++++++++++++++++++++++++++++++
#
#
#
orbitals=[4,5,6,7,8]
spins=[0,1]

pyprocar.dosplot(
code='vasp',
mode='overlay_species',
fermi=5.590136,
orbitals=orbitals,
spins=spins,
dirname=data_dir)

###############################################################################
# overlay_orbtials mode
# +++++++++++++++++++++++++++++++++++++++
#
#
#
atoms=[0]
spins=[0,1]
pyprocar.dosplot(
code='vasp',
mode='overlay_orbitals',
fermi=5.590136,
atoms=atoms,
spins=spins,
dirname=data_dir)



###############################################################################
# overlay mode
# +++++++++++++++++++++++++++++++++++++++
#
#
#

items={'Fe':[4,5,6,7,8]}
spins=[0,1]
pyprocar.dosplot(
code='vasp',
mode='overlay',
fermi=5.590136,
items=items,
spins=spins,
dirname=data_dir)
8 changes: 4 additions & 4 deletions docs/_downloads/0b72843559a0e5323f24e00c93009819/plot_fermi3d_plain.ipynb
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Expand Up @@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plotting fermi3d plain {#ref_plotting_fermi3d_plain}\r\n\r\nSymmetry does not currently work! Make sure for fermi surface\r\ncalculations turn off symmetry\r\n\r\nPlotting fermi3d plain example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='fermi')\r\n```\r\n"
"\n\n# Plotting fermi3d plain\n\nSymmetry does not currently work! Make sure for fermi surface calculations turn off symmetry\n\nPlotting fermi3d plain example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='fermi')\n"
]
},
{
Expand Down Expand Up @@ -33,7 +33,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"importing pyprocar and specifying local data_dir\r\n"
"importing pyprocar and specifying local data_dir\n\n"
]
},
{
Expand All @@ -51,7 +51,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plain mode\r\n"
"## Plain mode\n\n\n\n"
]
},
{
Expand All @@ -69,7 +69,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Parametric mode\r\n"
"## Parametric mode\n\n\n\n"
]
},
{
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36 changes: 18 additions & 18 deletions docs/_downloads/108db922454e1f15c7e1561bfc36c9de/plot_colinear.ipynb
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Expand Up @@ -4,14 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plotting band structure {#ref_plotting_colinear_bands}\r\n\r\nPlotting band structure example.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n"
"\n\n# Plotting band structure\n\nPlotting band structure example.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"importing pyprocar and specifying local data_dir\r\n"
"importing pyprocar and specifying local data_dir\n\n"
]
},
{
Expand All @@ -29,7 +29,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plain mode\r\n"
"## Plain mode\n\n"
]
},
{
Expand All @@ -40,14 +40,14 @@
},
"outputs": [],
"source": [
"pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n dirname=data_dir)"
"pyprocar.bandsplot(\n code='vasp', \n mode='plain',\n fermi=5.599480,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Parametric mode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n"
"## Parametric mode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n"
]
},
{
Expand All @@ -58,14 +58,14 @@
},
"outputs": [],
"source": [
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# parametric_linemode\r\n\r\nFor details on the meaning of the indices of the atomic projection\r\nplease refer to the user guide :ref:\\'atomic_projections\\'\r\n"
"## parametric_linemode\n\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n"
]
},
{
Expand All @@ -76,14 +76,14 @@
},
"outputs": [],
"source": [
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='parametric',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Scatter mode\r\n"
"## Scatter mode\n\n\n\n\n"
]
},
{
Expand All @@ -94,14 +94,14 @@
},
"outputs": [],
"source": [
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
"atoms=[0]\norbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='scatter',\n fermi=5.599480,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# overlay_species mode\r\n"
"## overlay_species mode\n\n\n\n\n"
]
},
{
Expand All @@ -112,14 +112,14 @@
},
"outputs": [],
"source": [
"orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_species',\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
"orbitals=[4,5,6,7,8]\nspins=[0]\n\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_species',\n fermi=5.599480,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# overlay_orbtials mode\r\n"
"## overlay_orbtials mode\n\n\n\n\n"
]
},
{
Expand All @@ -130,14 +130,14 @@
},
"outputs": [],
"source": [
"atoms=[0]\nspins=[0]\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_orbitals',\n atoms=atoms,\n spins=spins,\n dirname=data_dir)"
"atoms=[0]\nspins=[0]\npyprocar.bandsplot(\n code='vasp', \n mode='overlay_orbitals',\n fermi=5.599480,\n atoms=atoms,\n spins=spins,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# overlay mode\r\n"
"## overlay mode\n\n\n\n\n"
]
},
{
Expand All @@ -148,14 +148,14 @@
},
"outputs": [],
"source": [
"items={'Fe':[4,5,6,7,8]}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n items=items,\n dirname=data_dir)"
"items={'Fe':[4,5,6,7,8]}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n fermi=5.599480,\n items=items,\n dirname=data_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# overlay mode by orbital names\r\n"
"### overlay mode by orbital names\n\n\n\n\n"
]
},
{
Expand All @@ -166,7 +166,7 @@
},
"outputs": [],
"source": [
"items={'Fe':['p','d']}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n items=items,\n dirname=data_dir)"
"items={'Fe':['p','d']}\npyprocar.bandsplot(\n code='vasp', \n mode='overlay',\n fermi=5.599480,\n items=items,\n dirname=data_dir)"
]
}
],
Expand Down
8 changes: 4 additions & 4 deletions docs/_downloads/118695b22cb342905260e71e7c4f819c/plot_noncolinear_dos_qe.ipynb
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Expand Up @@ -4,14 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plotting non colinear dos in Quantum Espresso {#ref_plotting_noncolinear_dos_qe}\r\n\r\nPlotting non colinear dos in Quantum Espresso.\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='qe', \r\n spin_calc_type='non-colinear',\r\n calc_type='dos')\r\n```\r\n"
"\n\n# Plotting non colinear dos in Quantum Espresso\n\nPlotting non colinear dos in Quantum Espresso.\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='qe', \n spin_calc_type='non-colinear',\n calc_type='dos')\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"importing pyprocar and specifying local data_dir\r\n"
"importing pyprocar and specifying local data_dir\n\n"
]
},
{
Expand All @@ -29,7 +29,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Parametric mode\r\n\r\nQuantum Espresso expresses the projections in the coupled basis,\r\ntherefore orbitals takes different meanings. For details on the meaning\r\nof the indices of the atomic projection please refer to the user guide\r\n:ref:\\'atomic_projections\\'\r\n"
"## Parametric mode\nQuantum Espresso expresses the projections in the coupled basis, \ntherefore orbitals takes different meanings.\nFor details on the meaning of the indices of the atomic projection please refer to the user guide :ref:'atomic_projections'\n\n\n\n\n"
]
},
{
Expand All @@ -40,7 +40,7 @@
},
"outputs": [],
"source": [
"atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
"atoms=[0]\nspins=[0]\norbitals=[8,9,10,11,12,13,14,15,16,17]\n\npyprocar.dosplot(\n code='qe', \n mode='parametric',\n fermi=18.0536,\n atoms=atoms,\n orbitals=orbitals,\n spins=spins,\n dirname=data_dir)"
]
}
],
Expand Down
6 changes: 3 additions & 3 deletions docs/_downloads/1d7bddaa2f20c6f6d31ec8edb52ba8e9/plot_kpath_generation.ipynb
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Expand Up @@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example of kpath_generator {#ref_example_kpath_generator}\r\n\r\nIn order to plot a band structure, one must define a set of $k$-points\r\nfollowing a desired $k$-path in momentum space. PyProcar\\'s $k$-path\r\ngeneration utility enables a the user to automatically generate a\r\nsuitable and sufficient $k$-path given the crystal structure, typically\r\nread from the POSCAR file (VASP).\r\n\r\n``` {caption=\"General Format\"}\r\npyprocar.kpath(infile, outfile, grid-size, with-time-reversal, recipe, threshold, symprec, angle-tolerance,supercell_matrix)\r\n```\r\n\r\nFirst download the example files with the code below. Then replace\r\ndata_dir below.\r\n\r\n``` {caption=\"Downloading example\"}\r\ndata_dir = pyprocar.download_example(save_dir='', \r\n material='Fe',\r\n code='vasp', \r\n spin_calc_type='non-spin-polarized',\r\n calc_type='bands')\r\n```\r\n\r\nThis information is automatically written to a KPOINTS file. The\r\nretrieved $k$-path can be used for other DFT codes with slight\r\nmodifications.\r\n\r\nMore details regarding these parameters can be found in the [SeeK-path\r\nmanual](https://seekpath.readthedocs.io/en/latest/module_guide/index.html).\r\nThe $k$-path generation utility within PyProcar is based on the Python\r\nlibrary **seekpath** developed by Hinuma et al:\r\n\r\n Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Computational Materials Science 128 (2017) 140\u2013184.doi:10.1016/j.commatsci.2016.10.015.\r\n"
"\n\n# Example of kpath_generator \n\nIn order to plot a band structure, one must define a set of $k$-points following a desired $k$-path in momentum space. \nPyProcar's $k$-path generation utility enables a the user to automatically generate \na suitable and sufficient $k$-path given the crystal structure, typically read from the POSCAR file (VASP). \n\n\n.. code-block::\n :caption: General Format\n\n pyprocar.kpath(infile, outfile, grid-size, with-time-reversal, recipe, threshold, symprec, angle-tolerance,supercell_matrix)\n\n\nFirst download the example files with the code below. Then replace data_dir below.\n\n.. code-block::\n :caption: Downloading example\n\n data_dir = pyprocar.download_example(save_dir='', \n material='Fe',\n code='vasp', \n spin_calc_type='non-spin-polarized',\n calc_type='bands')\n\nThis information is automatically written to a KPOINTS file. The retrieved $k$-path can be used for other DFT codes with slight modifications.\n\nMore details regarding these parameters can be found in the [SeeK-path manual](https://seekpath.readthedocs.io/en/latest/module_guide/index.html).\nThe $k$-path generation utility within PyProcar is based on the Python library **seekpath** developed by Hinuma et al::\n\n Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Computational Materials Science 128 (2017) 140\u2013184.doi:10.1016/j.commatsci.2016.10.015.\n"
]
},
{
Expand All @@ -22,7 +22,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Plotting K Path\r\n"
"## Plotting K Path\n\n"
]
},
{
Expand All @@ -40,7 +40,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"importing pyprocar and specifying local data_dir\r\n"
"importing pyprocar and specifying local data_dir\n\n"
]
},
{
Expand Down
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