Nanosurf Lab
https://nanosurf.fzu.cz/wiki/
2024-03-19T06:35:37+0100Nanosurf Lab
https://nanosurf.fzu.cz/wiki/
https://nanosurf.fzu.cz/wiki/lib/tpl/dokuwiki/images/favicon.icotext/html2022-01-13T14:04:27+0100krejcio (krejcio@undisclosed.example.com)probe_particle_model - [Inputs] - adjusting to the latest version of params.ini
https://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_model&rev=1642079067&do=diff
Introduction
Probe particle model code is supposed to simulate AFM ( and to some extent STM and inelastic-STM) images obtained with tip modified by an atom or small molecule (such as Xe, CO, CH4, H2). In all cases the actual particle (atom or molecule) is replaced by a spherical model particle and classical potential (Lenard-Jones) is used for description of Pauli repulsion and Van der Waals attraction.text/html2021-11-16T20:59:56+0100krejcio (krejcio@undisclosed.example.com)probe_particle_stm
https://nanosurf.fzu.cz/wiki/doku.php?id=probe_particle_stm&rev=1637092796&do=diff
!!! Outdated !!!
The repository changed to <https://github.com/Probe-Particle/PPSTM> and all the documentation is copied and updated in its new Wiki <https://github.com/Probe-Particle/PPSTM/wiki>.
What is here is the left-over of the original documentation.
Introduction
A Python/C based package, available at <https://github.com/ondrejkrejci/PPSTM>, which primary purpose is to simulate STM or dI/dV signal obtained with tilting tip apex (like CO, or Xe tip). It can work separately for atext/html2021-09-30T13:06:56+0100krejcio (krejcio@undisclosed.example.com)creating_inputs - Updated FHI-aims output; no need for parallel recompilation any more
https://nanosurf.fzu.cz/wiki/doku.php?id=creating_inputs&rev=1633000016&do=diff
Note: If you work with the flexible-tip=PP-AFM adjust the geometry into the necessary box for the force-field calculations. Don't forget to put the top-most atoms above 0.0, but lower part of the box in the z direction.
At the moment the PP-STM code can read inputs from following DFT codes:text/html2020-05-25T17:06:05+0100dani (dani@undisclosed.example.com)fireball_20.05_ambertools_20
https://nanosurf.fzu.cz/wiki/doku.php?id=fireball_20.05_ambertools_20&rev=1590419165&do=diff
Fireball 20.05 & AmberTools 20
git clone https://github.com/fireball-QMD/progs
cd progs
export FIREBALLHOME=$(pwd)
make libfireball
cd ~
tar -xvf AmberTools20.tar.gz
cd amber20_src
export AMBERHOME=$(pwd)
export MKL_HOME=$MKLROOT
./configure -fireball -noX11 intel
make installtext/html2020-05-25T16:46:22+0100dani (dani@undisclosed.example.com)fireball - [Tutorials]
https://nanosurf.fzu.cz/wiki/doku.php?id=fireball&rev=1590417982&do=diff
Introduction
A project FireballTG is a branch version of a simulation package Fireball. FireballTG provides several differences with respect to the original Fireball code. It can be obtained from <https://github.com/fireball-QMD/progs/>.
New Features
----------
- New input file format FireballTG File Formats
- New internal loop structure decoupling individual taskstext/html2019-11-19T12:34:21+0100dani (dani@undisclosed.example.com)fireball_19.11_ambertools_18
https://nanosurf.fzu.cz/wiki/doku.php?id=fireball_19.11_ambertools_18&rev=1574163261&do=diff
Fireball 19.11 & Amber19
git clone https://github.com/fireball-QMD/progs
cd progs
export FIREBALLHOME=$(pwd)
make libfireball
cd ~
tar -xvf AmberTools19.tar.bz2
cd amber18
export AMBERHOME=$(pwd)
export MKL_HOME=$MKLROOT
cd $AMBERHOME/AmberTools/src/sander
./makedepend > depend
cd $AMBERHOME
./configure -fireball -noX11 intel
make installtext/html2018-10-24T13:35:26+0100krejcio (krejcio@undisclosed.example.com)fepc_au - created
https://nanosurf.fzu.cz/wiki/doku.php?id=fepc_au&rev=1540380926&do=diff
FePc/Au(111)
Created with FHI-AIMS hybrid functional B3LYP XC-functional on 1 Au layer. This test is an example, how the PP-IETS simulations can be done.
!!! BEWARE: This is not exactly the same results as in PRL 119, 166001 (2017), since there was used electrostatics for the PP-AFM precalculations !!!text/html2018-10-24T13:33:39+0100krejcio (krejcio@undisclosed.example.com)all_0.0_fermi_none_006.png - created
https://nanosurf.fzu.cz/wiki/doku.php?image=all_0.0_fermi_none_006.png&ns=&rev=1540380819&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=430&h=499&t=1540380819&tok=ab386a&media=all_0.0_fermi_none_006.png" alt="all_0.0_fermi_none_006.png" />text/html2018-03-22T19:21:42+0100jesus (jesus@undisclosed.example.com)fireball_18.02_ambertools_17
https://nanosurf.fzu.cz/wiki/doku.php?id=fireball_18.02_ambertools_17&rev=1521742902&do=diff
Fireball & Amber with EXTERN (mpi)
mkdir fireball
cd fireball
export FIREBALLHOME=$(pwd)
git clone https://github.com/fireball-QMD/progs
cd progs
change in Makefile:
* MACHINE = your options
* PARALLEL = MPI
* METHOD = SCALAPACK
make server_ambertext/html2018-03-08T15:44:08+0100jesus (jesus@undisclosed.example.com)benzen_structure_optimization
https://nanosurf.fzu.cz/wiki/doku.php?id=benzen_structure_optimization&rev=1520520248&do=diff
Here we describe how to perform structure optimization of a simple molecule using the new version of the Fireball code.
There are minimal steps required to optimize atomic structure using quenching optimization method:
atomic structure
In this particular case, we are about to optimize atomic structure oftext/html2017-02-28T14:31:59+0100krejcio (krejcio@undisclosed.example.com)didv-cupc_spin-polerized_height_001a.png
https://nanosurf.fzu.cz/wiki/doku.php?image=didv-cupc_spin-polerized_height_001a.png&ns=&rev=1488288719&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=500&h=275&t=1488288660&tok=04020e&media=didv-cupc_spin-polerized_height_001a.png" alt="didv-cupc_spin-polerized_height_001a.png" />text/html2017-02-20T16:50:52+0100krejcio (krejcio@undisclosed.example.com)stm_flat_7x7.png
https://nanosurf.fzu.cz/wiki/doku.php?image=stm_flat_7x7.png&ns=&rev=1487605852&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=499&h=169&t=1487605800&tok=d7a100&media=stm_flat_7x7.png" alt="stm_flat_7x7.png" />text/html2017-02-20T16:50:13+0100krejcio (krejcio@undisclosed.example.com)stm_7x7.png
https://nanosurf.fzu.cz/wiki/doku.php?image=stm_7x7.png&ns=&rev=1487605813&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=499&h=169&t=1487605800&tok=d67c44&media=stm_7x7.png" alt="stm_7x7.png" />text/html2017-02-20T16:49:42+0100krejcio (krejcio@undisclosed.example.com)didv-7x7.png
https://nanosurf.fzu.cz/wiki/doku.php?image=didv-7x7.png&ns=&rev=1487605782&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=499&h=169&t=1487605740&tok=395640&media=didv-7x7.png" alt="didv-7x7.png" />text/html2017-01-02T16:16:28+0100krejcio (krejcio@undisclosed.example.com)ptcda_df.png
https://nanosurf.fzu.cz/wiki/doku.php?image=ptcda_df.png&ns=&rev=1483370188&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=433&h=321&t=1483370160&tok=8c278f&media=ptcda_df.png" alt="ptcda_df.png" />text/html2016-12-05T15:25:10+0100krejcio (krejcio@undisclosed.example.com)4n-coronene_lumo.png
https://nanosurf.fzu.cz/wiki/doku.php?image=4n-coronene_lumo.png&ns=&rev=1480947910&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=499&h=269&t=1480947900&tok=ec4722&media=4n-coronene_lumo.png" alt="4n-coronene_lumo.png" />text/html2016-12-05T15:24:28+0100krejcio (krejcio@undisclosed.example.com)4n-corornene_homo.png
https://nanosurf.fzu.cz/wiki/doku.php?image=4n-corornene_homo.png&ns=&rev=1480947868&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=499&h=269&t=1480947840&tok=24527c&media=4n-corornene_homo.png" alt="4n-corornene_homo.png" />text/html2016-12-05T15:23:44+0100krejcio (krejcio@undisclosed.example.com)4n-coronene.png
https://nanosurf.fzu.cz/wiki/doku.php?image=4n-coronene.png&ns=&rev=1480947824&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=500&h=258&t=1480947780&tok=8d2a9a&media=4n-coronene.png" alt="4n-coronene.png" />text/html2016-12-05T15:19:42+0100krejcio (krejcio@undisclosed.example.com)homo_energy_close.png
https://nanosurf.fzu.cz/wiki/doku.php?image=homo_energy_close.png&ns=&rev=1480947582&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=500&h=263&t=1480947540&tok=fd121d&media=homo_energy_close.png" alt="homo_energy_close.png" />text/html2016-12-05T15:18:13+0100krejcio (krejcio@undisclosed.example.com)homo_energy_far.png
https://nanosurf.fzu.cz/wiki/doku.php?image=homo_energy_far.png&ns=&rev=1480947493&tab_details=history&mediado=diff&do=media
<img src="https://nanosurf.fzu.cz/wiki/lib/exe/fetch.php?w=500&h=263&t=1480947480&tok=e765e3&media=homo_energy_far.png" alt="homo_energy_far.png" />