Nanosurf Lab

probe_particle_model - [Inputs] - adjusting to the latest version of params.ini

krejcio (krejcio@undisclosed.example.com) — 2022-01-13T14:04:27+0200

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.

probe_particle_stm

krejcio (krejcio@undisclosed.example.com) — 2021-11-16T20:59:56+0200

!!! Outdated !!! The repository changed to and all the documentation is copied and updated in its new Wiki . What is here is the left-over of the original documentation. Introduction A Python/C based package, available at , 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 a

creating_inputs - Updated FHI-aims output; no need for parallel recompilation any more

krejcio (krejcio@undisclosed.example.com) — 2021-09-30T13:06:56+0200

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:

fireball_20.05_ambertools_20

dani (dani@undisclosed.example.com) — 2020-05-25T17:06:05+0200

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 install

fireball - [Tutorials]

dani (dani@undisclosed.example.com) — 2020-05-25T16:46:22+0200

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 . New Features ---------- - New input file format FireballTG File Formats - New internal loop structure decoupling individual tasks

fireball_19.11_ambertools_18

dani (dani@undisclosed.example.com) — 2019-11-19T12:34:21+0200

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 install

fepc_au - created

krejcio (krejcio@undisclosed.example.com) — 2018-10-24T13:35:26+0200

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 !!!

all_0.0_fermi_none_006.png - created

krejcio (krejcio@undisclosed.example.com) — 2018-10-24T13:33:39+0200

fireball_18.02_ambertools_17

jesus (jesus@undisclosed.example.com) — 2018-03-22T19:21:42+0200

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_amber

benzen_structure_optimization

jesus (jesus@undisclosed.example.com) — 2018-03-08T15:44:08+0200

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 of

didv-cupc_spin-polerized_height_001a.png

krejcio (krejcio@undisclosed.example.com) — 2017-02-28T14:31:59+0200

stm_flat_7x7.png

krejcio (krejcio@undisclosed.example.com) — 2017-02-20T16:50:52+0200

stm_7x7.png

krejcio (krejcio@undisclosed.example.com) — 2017-02-20T16:50:13+0200

didv-7x7.png

krejcio (krejcio@undisclosed.example.com) — 2017-02-20T16:49:42+0200

ptcda_df.png

krejcio (krejcio@undisclosed.example.com) — 2017-01-02T16:16:28+0200

4n-coronene_lumo.png

krejcio (krejcio@undisclosed.example.com) — 2016-12-05T15:25:10+0200

4n-corornene_homo.png

krejcio (krejcio@undisclosed.example.com) — 2016-12-05T15:24:28+0200

4n-coronene.png

krejcio (krejcio@undisclosed.example.com) — 2016-12-05T15:23:44+0200

homo_energy_close.png

krejcio (krejcio@undisclosed.example.com) — 2016-12-05T15:19:42+0200

homo_energy_far.png

krejcio (krejcio@undisclosed.example.com) — 2016-12-05T15:18:13+0200