Partial charge densities and STM simulations - Revision history

Singraber at 08:04, 24 October 2025

2025-10-24T08:04:59Z

← Older revision		Revision as of 08:04, 24 October 2025
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	==Output files==		==Output files==
	The partial valence charge density is written in the {{FILE\|PARCHG}} file. If you want to separate the output by '''k''' points or bands, setting {{TAG\|LSEPB}} and/or {{TAG\|LSEPK}} allows you to write it to multiple PARCHG.. files.		The partial valence charge density is written in the {{FILE\|PARCHG}} file. If you want to separate the output by '''k''' points or bands, setting {{TAG\|LSEPB}} and/or {{TAG\|LSEPK}} allows you to write it to multiple PARCHG.. files.
	If the code is compiled with [[Makefile.include#HDF5_support_(strongly_recommended)\|HDF5 support]], {{~~TAGO~~\|LPARDH5\|.TRUE.}} redirects all output to the {{FILE\|vaspout.h5}} file. In that case {{py4vasp}} can be used to analyze the output and plot [[#Step-by-step instructions for simulating an STM picture\|simulated STM pictures]].		If the code is compiled with [[Makefile.include#HDF5_support_(strongly_recommended)\|HDF5 support]], {{TAG\|LPARDH5\|.TRUE.}} redirects all output to the {{FILE\|vaspout.h5}} file. In that case {{py4vasp}} can be used to analyze the output and plot [[#Step-by-step instructions for simulating an STM picture\|simulated STM pictures]].
	{{NB\|mind\|For spin-polarized calculations, the {{FILE\|PARCHG}} and its variants hold the total density and the magnetization density. For instance, if the 4th band is selected ({{TAG\|IBAND}} {{=}} 4) the first data set in the {{FILE\|PARCHG}} file corresponds to the summed density of the 4th spin up and 4th spin down orbital, whereas the second data set holds the difference between the 4th spin-up and 4th spin-down orbital (magnetization density). Hence, to obtain the charge density corresponding to a specific orbital of a specific spin channel some post-processing of the {{TAG\|PARCHG}} file might be required (building differences or sums). A simple workaround is to use {{TAG\|EINT}} and specify sufficient digits to select only one orbital from either the spin-up or spin-down channel.}}		{{NB\|mind\|For spin-polarized calculations, the {{FILE\|PARCHG}} and its variants hold the total density and the magnetization density. For instance, if the 4th band is selected ({{TAG\|IBAND}} {{=}} 4) the first data set in the {{FILE\|PARCHG}} file corresponds to the summed density of the 4th spin up and 4th spin down orbital, whereas the second data set holds the difference between the 4th spin-up and 4th spin-down orbital (magnetization density). Hence, to obtain the charge density corresponding to a specific orbital of a specific spin channel some post-processing of the {{TAG\|PARCHG}} file might be required (building differences or sums). A simple workaround is to use {{TAG\|EINT}} and specify sufficient digits to select only one orbital from either the spin-up or spin-down channel.}}

Wolloch: /* Step-by-step instructions for simulating an STM picture */

2025-10-15T14:09:57Z

Step-by-step instructions for simulating an STM picture

← Older revision		Revision as of 14:09, 15 October 2025
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	from py4vasp import Calculation		from py4vasp import Calculation
	calc = Calculation.from_file('/path/to/your/vaspout.h5')		calc = Calculation.from_file('/path/to/your/vaspout.h5')
	calc.~~partial_charge~~.to_stm(selection='constant_height(total)', tip_height=4, supercell=[7,7])		calc.partial_density.to_stm(selection='constant_height(total)', tip_height=4, supercell=[7,7])
	This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM plot. More convenient methods are provided in {{py4vasp}} to work with the partial charge data.		This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM plot. More convenient methods are provided in {{py4vasp}} to work with the partial charge data.

Huebsch: /* Step-by-step instructions for simulating an STM picture */

2025-10-01T08:41:27Z

Step-by-step instructions for simulating an STM picture

Csheldon at 08:53, 6 August 2025

2025-08-06T08:53:39Z

← Older revision		Revision as of 08:53, 6 August 2025
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	==Example==		==Example==
	The images below show an experimental (on the left) and a simulated (on the right) scanning tunneling image of Graphene. The experimental image was measured at room temperature in air at the Department for Earth and Environmental Sciences, LMU, and Center for NanoScience (CeNS), Munich. The simulated image was created with {{py4vasp}} at very similar settings as described in the [[#Step-by-step instructions for simulating an STM picture\|section]] above. ~~<!--This is shown in [https://www.vasp.at/tutorials/latest/surface/part3/ \| part 3 of the surface tutorials ]. -->~~		The images below show an experimental (on the left) and a simulated (on the right) scanning tunneling image of Graphene. The experimental image was measured at room temperature in air at the Department for Earth and Environmental Sciences, LMU, and Center for NanoScience (CeNS), Munich. The simulated image was created with {{py4vasp}} at very similar settings as described in the [[#Step-by-step instructions for simulating an STM picture\|section]] above.

	[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]		[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]

	~~==Tutorials==~~		There are tutorials to calcualte the constant height STM and constant current STM in [https://www.vasp.at/tutorials/latest/surface/part3/ part 3 of the surface tutorials] on our website.
	There are ~~exercises available~~ in ~~the tutorial section of our website for [~~[https://www.vasp.at/tutorials/latest/surface/part3/ ~~constant height and constant current STM]~~].

	== Related tags and articles ==		== Related tags and articles ==
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	{{FILE\|WAVECAR}}		{{FILE\|WAVECAR}}

	~~<!--~~[[Category:Charge density]][[Category:Howto]][[Category:Electronic ground-state properties]]		[[Category:Charge density]][[Category:Howto]][[Category:Electronic ground-state properties]]

Csheldon at 08:23, 6 August 2025

2025-08-06T08:23:11Z

← Older revision		Revision as of 08:23, 6 August 2025
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	[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]		[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]

			==Tutorials==
			There are exercises available in the tutorial section of our website for [[https://www.vasp.at/tutorials/latest/surface/part3/ constant height and constant current STM]].

	== Related tags and articles ==		== Related tags and articles ==

Csheldon at 12:42, 28 May 2025

2025-05-28T12:42:40Z

← Older revision		Revision as of 12:42, 28 May 2025
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	<!--{{TAG\|LPARDH5}} selects if the partial charges are written to {{FILE\|vaspout.h5}} or the {{FILE\|PARCHG}} file.-->		<!--{{TAG\|LPARDH5}} selects if the partial charges are written to {{FILE\|vaspout.h5}} or the {{FILE\|PARCHG}} file.-->
	{{NB\|mind\|All charge densities, including the band-decomposed charge densities, are symmetrized using both the space and point group symmetries. However, when calculating partial charge from selected '''k''' points, this can lead to wrong results due to wrong '''k''' point weights. In that case, the symmetry must be turned off during the initial ground state calculation from which the WAVECAR is generated, as well as during the subsequent band-decomposed charge density calculation.}}		{{NB\|mind\|All charge densities, including the band-decomposed charge densities, are symmetrized using both the space and point group symmetries. However, when calculating partial charge from selected '''k''' points, this can lead to wrong results due to wrong '''k''' point weights. In that case, the symmetry must be turned off during the initial ground state calculation from which the WAVECAR is generated, as well as during the subsequent band-decomposed charge density calculation.}}
	{{NB\|warning\|Band-~~decopmposed~~ partial charge density postprocessing is not supported for noncollinear magnetic calculations ({{TAG\|LNONCOLLINEAR}} {{=}} .TRUE.).}}		{{NB\|warning\|Band-decomposed partial charge density postprocessing is not supported for noncollinear magnetic calculations ({{TAG\|LNONCOLLINEAR}} {{=}} .TRUE.).}}

	==Input tags for selecting and writing the partial charges==		==Input tags for selecting and writing the partial charges==

Csheldon at 11:59, 28 May 2025

2025-05-28T11:59:49Z

← Older revision		Revision as of 11:59, 28 May 2025
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	==Example==		==Example==
	The images below show an experimental (on the left) and a simulated (on the right) scanning tunneling image of Graphene. The experimental image was measured at room temperature in air at the Department for Earth and Environmental Sciences, LMU, and Center for NanoScience (CeNS), Munich. The simulated image was created with {{py4vasp}} at very similar settings as described in the [[#Step-by-step instructions for simulating an STM picture\|section]] above.		The images below show an experimental (on the left) and a simulated (on the right) scanning tunneling image of Graphene. The experimental image was measured at room temperature in air at the Department for Earth and Environmental Sciences, LMU, and Center for NanoScience (CeNS), Munich. The simulated image was created with {{py4vasp}} at very similar settings as described in the [[#Step-by-step instructions for simulating an STM picture\|section]] above. <!--This is shown in [https://www.vasp.at/tutorials/latest/surface/part3/ \| part 3 of the surface tutorials ]. -->

	[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]		[[File:STM Graphite exp sim.png\|800px\|Fig 1. Experimental (left) and simulated (right) STM image of Graphene.]]

Wolloch: Wolloch moved page Construction:Partial charge densities and STM simulations to Partial charge densities and STM simulations

2024-12-20T10:59:50Z

Wolloch moved page Construction:Partial charge densities and STM simulations to Partial charge densities and STM simulations

← Older revision	Revision as of 10:59, 20 December 2024
(No difference)

Wolloch: /* Step-by-step instructions for simulating an STM picture */

2024-12-20T10:59:37Z

Step-by-step instructions for simulating an STM picture

← Older revision		Revision as of 10:59, 20 December 2024
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	This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM plot. More convenient methods are provided in {{py4vasp}} to work with the partial charge data.		This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM plot. More convenient methods are provided in {{py4vasp}} to work with the partial charge data.

	''' Alternative Step 5''' (optional, if VASP is compiled without HDF5 support): Load the resulting {{FILE\|PARCHG}} file with your favorite visualization program to view constant-height images by looking at slices through the data or constant current images by using isosurfaces.~~-->~~		''' Alternative Step 5''' (optional, if VASP is compiled without HDF5 support): Load the resulting {{FILE\|PARCHG}} file with your favorite visualization program to view constant-height images by looking at slices through the data or constant current images by using isosurfaces.

	==Example==		==Example==

Wolloch: /* Step-by-step instructions for simulating an STM picture */

2024-12-20T10:59:12Z

Step-by-step instructions for simulating an STM picture

← Older revision		Revision as of 10:59, 20 December 2024
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	calc = Calculation.from_file('/path/to/your/vaspout.h5')		calc = Calculation.from_file('/path/to/your/vaspout.h5')
	calc.partial_charge.to_stm(selection='constant_height(total)', tip_height=4, supercell=[7,7])		calc.partial_charge.to_stm(selection='constant_height(total)', tip_height=4, supercell=[7,7])
	This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM ~~plotting, and many more~~ convenient methods are provided in {{py4vasp}} to work with the partial charge data.		This will plot the simulation of an STM image in constant height mode, with the tip 4<span>Å</span> above the surface. A 7 by 7 supercell is plotted. Under the hood, the data is pre-processed with Gaussian smoothening for the STM plot. More convenient methods are provided in {{py4vasp}} to work with the partial charge data.

	''' Alternative Step 5''' (optional, if VASP is compiled without HDF5 support): Load the resulting {{FILE\|PARCHG}} file with your favorite visualization program to view constant-height images by looking at slices through the data or constant current images by using isosurfaces.-->		''' Alternative Step 5''' (optional, if VASP is compiled without HDF5 support): Load the resulting {{FILE\|PARCHG}} file with your favorite visualization program to view constant-height images by looking at slices through the data or constant current images by using isosurfaces.-->

← Older revision		Revision as of 08:41, 1 October 2025
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	In this example, we will produce a partial charge density useful for STM picture simulation. Note that the bias voltage and tip distance from an experiment do not always translate one-to-one to the simulation.		In this example, we will produce a partial charge density useful for STM picture simulation. Note that the bias voltage and tip distance from an experiment do not always translate one-to-one to the simulation.

	'''Step 1''': Ensure that the ground state calculation has a well-converged charge density (low rms(c) in the standard output or the {{FILE\|OSZICAR}}).		'''Step 1''': Ensure that the ground-state calculation has a well-converged charge density (low rms(c) in the standard output or the {{FILE\|OSZICAR}}).
	The '''k''' point mesh should be well converged to get good results for STM simulations.		The '''k''' point mesh should be well converged to get good results for STM simulations.

	'''Step 2''': Copy {{FILE\|POSCAR}}, {{FILE\|KPOINTS}}, and {{FILE\|WAVECAR}} to a new directory.		'''Step 2''': Copy {{FILE\|POSCAR}}, {{FILE\|KPOINTS}}, and {{FILE\|WAVECAR}} to a new directory.

	'''Step 3''': Prepare an appropriate {{FILE\|INCAR}} file in the new directory, making sure you specify the same settings for {{TAG\|ENCUT}}, {{TAG\|ISYM}}, and {{TAG\|ISPIN}} as in the ~~groundstate~~ calculation. This could be a possible {{FILE\|INCAR}}:		'''Step 3''': Prepare an appropriate {{FILE\|INCAR}} file in the new directory, making sure you specify the same settings for {{TAG\|ENCUT}}, {{TAG\|ISYM}}, and {{TAG\|ISPIN}} as in the ground-state calculation. This could be a possible {{FILE\|INCAR}}:
	{{TAG\|SYSTEM}} = STM simulation		{{TAG\|SYSTEM}} = STM simulation
	{{TAG\|ENCUT}} = 520		{{TAG\|ENCUT}} = 520
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	{{TAG\|LSEPB}} = .FALSE.		{{TAG\|LSEPB}} = .FALSE.
	{{TAG\|LSEPK}} = .FALSE.		{{TAG\|LSEPK}} = .FALSE.
	{{TAG\|LPARD}} = .TRUE. activates the partial charge mode and assures that the WAVECAR file is read.		{{TAG\|LPARD}} = .TRUE. activates the partial charge mode and assures that the {{FILE\|WAVECAR}} file is read.
	{{TAG\|LPARDH5}} = .TRUE. redirect the output to the {{FILE\|vaspout.h5}} file allowing the use of {{py4vasp}} for plotting the simulated STM picture.		{{TAG\|LPARDH5}} = .TRUE. redirect the output to the {{FILE\|vaspout.h5}} file allowing the use of {{py4vasp}} for plotting the simulated STM picture.
	{{TAG\|ENCUT}} and {{TAG\|ISPIN}} settings are copied over from the ground state calculation. {{TAG\|NBMOD}} = -3 and {{TAG\|EINT}} = -0.2 0.05 ensure that the bands from <math>\epsilon_f-0.2</math> to <math>\epsilon_f+0.05</math> eV are included (corresponding to a negative bias voltage of about 0.2 Volt). The two remaining tags, {{TAG\|LSEPB}} and {{TAG\|LSEPK}} are set to their default values (.FALSE.) and are there for clarity only. We want to sum up the contributions of all bands in the energy range at all '''k''' points without separating any of this information.		{{TAG\|ENCUT}} and {{TAG\|ISPIN}} settings are copied over from the ground-state calculation. {{TAG\|NBMOD}} = -3 and {{TAG\|EINT}} = -0.2 0.05 ensure that the bands from <math>\epsilon_f-0.2</math> to <math>\epsilon_f+0.05</math> eV are included (corresponding to a negative bias voltage of about 0.2 Volt). The two remaining tags, {{TAG\|LSEPB}} and {{TAG\|LSEPK}} are set to their default values (.FALSE.) and are there for clarity only. We want to sum up the contributions of all bands in the energy range at all '''k''' points without separating any of this information.

	'''Step 4''': Run VASP. No electronic (or ionic) minimization is performed, so the calculation is rapid and does not require parallelization.		'''Step 4''': Run VASP. No electronic (or ionic) minimization is performed, so the calculation is rapid and does not require parallelization.