Nanosurf Lab

2d_stm

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

2D STM This scan is tipical STM scan, the output are the xyz files, where the z-value is the tunelling current over the specific xy position. The ICUTT value should be set as the 0 in the “options.inp” file. The XMIN, XMAX and YMIN, YMAX should be set properly. There is necessary to have

4n-coronene

Anonymous (anonymous@undisclosed.example.com) — 2017-02-20T16:37:00+0200

Theoretical molecule Theoretical prediction for Coronene molecule modified with with four nitrogen atoms (here called as 4n-coronene). The files containing information about its geometry, how it was calculated and how the LCAO coefficients were taken are in the folder

absorbtion_spectra_by_fermi_golden_rule

Anonymous (anonymous@undisclosed.example.com) — 2014-07-24T14:30:00+0200

Absorption spectra by Fermi golden Rule There is a possibility to evaluate rough estimation of UV-VIS absorption spectra by Fermi golden rule between Kohn-Sham orbitals. For a given range of photon energy are selected all pairs of occupied and unoccupied ground-state Kohn-Sham orbital with appropriate energy difference. This two orbitals are than projected onto real space grid and

band_structure

Anonymous (anonymous@undisclosed.example.com) — 2014-10-20T12:42:00+0200

The band structure To obtain the band structure of Si bulk of given lattice parameter we have to perform two steps. First, we need to achieve SCF solution. Therefore, we run a standard bulk calculation as described in the previous chapter. Let's calculate the band structure for the lattice parameter

band_structure_of_nanocrystals

Anonymous (anonymous@undisclosed.example.com) — 2014-11-20T15:43:00+0200

Band structure of nanocrystals The 'fuzzy band structure' of an nanocrystal (i.e. cluster without periodic boundary condition) can be obtained by Fourier transform of it's eigenstates. See Hapala et.al,Phys.Rev.B87,195420. In fireball there are two methods to do this projection.

benzen_eigenvalues

Anonymous (anonymous@undisclosed.example.com) — 2017-03-06T14:55:00+0200

Eigenvalue spectra Once we have obtained the ground state atomic configuration, we can perform electronic structure analysis. To obtain the detail information about the eigen-energy spectra of the benzene molecule, we perform one time-step run with the fixed ground state charges (we suppose our optimized structure is stored in

benzen_structure_optimization

Anonymous (anonymous@undisclosed.example.com) — 2018-03-08T15:44:00+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

bfgs_minimization

Anonymous (anonymous@undisclosed.example.com) — 2014-07-08T11:40:00+0200

BFGS it call l-bfgs-b routine till: - the convergence criteria defined in cg.optional are reached (f(i,j)fmax - the maximum number of steps exceeds setting of input files:

border_search_a_minima_hopping

Anonymous (anonymous@undisclosed.example.com) — 2012-02-13T11:36:00+0200

Vyhoda minimahopingu Minimahoping pouziva dlouhe skoky proto je schopnen nalezt nove lokalni minimum mnohem rychleji nez metadynamika nebo border search Problemem minimahopingu Jako kazdy jiny Monte-Carlo techniky je, ze stavovy prostor prochazi nesystematicky bez vyuziti pameti. Tim zbytence sampluje mnohekrat podobne konfigurace.

border_search_implementace_ve_fireballu

Anonymous (anonymous@undisclosed.example.com) — 2012-01-12T10:00:00+0200

Border Search diskretni spusobem sampluje libovolny stavovy prostor. Tento prostoro muze byt tvoren napriklad atomovymi souradnicemi, ale stejne tak jakymikoli jinymi zobecnenymi souradnicemi. Prtotoze je naprosto nerealisticke prozkoumavat cely stavovy prostor poloh vsech atomu, je mnohem smysluplnejsi border search definovat v prostoru parametru z nichz je az geometrie systemu generovana.

brainsorm

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Discrete MetaDynamics

bulk_optimization

Anonymous (anonymous@undisclosed.example.com) — 2014-02-09T11:23:00+0200

Lattice parameter In this section, we explain how to optimize the lattice parameter of Si bulk diamond structure. The diamond structure is characterized by two distinct atom per unit cell with relative coordinates (0 ,0 ,0) and (1/4, 1/4, 1/4). The lattice vector is defined in the relative coordinates

calculate_densty_of_states_dos

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

This page describes how to calculate the density of states (DOS) using Fireball. First, we need to obtain SCF-solution for particular geometry. Once we have it, we need to switch on these options: ifixcharge = 1 iwrtdos = 1 Simulation parameters are defined in two additional files:

calculate_e-ph_coupling

Anonymous (anonymous@undisclosed.example.com) — 2014-09-12T15:58:00+0200

Calcualtion of e-ph coupling Here we describe how to calculate the vibrational modes of molecules using dynamical matrix. Note, the calculation of the e-ph coupling is meant only for non periodic systems or with only Gamma k-point. iephc = 1 The calculation e-ph coupling is toggled by the keywords

calculate_u-function

Anonymous (anonymous@undisclosed.example.com) — 2012-11-07T16:57:00+0200

U - function This page shows how to calculate U - function. There is an simple example of calculation U -function for simple CH5N molecule below. Here are input files. ---- CH5N.bas 7 7 1.763266 0.773353 -0.259722 6 0.474220 0.075638 -0.015967 1 2.595372 0.133817 -0.297809 1 2.017882 1.470682 0.480907 1 0.229708 -0.640655 -0.836563 1 -0.382559 0.790390 0.018898 1 0.4017…

choice_of_the_k-point_mesh

Anonymous (anonymous@undisclosed.example.com) — 2014-02-09T13:16:00+0200

In this section, we explain how to choice of the k-point mesh of Si bulk diamond structure. The diamond structure is characterized by two distinct atom per unit cell with relative coordinates (0 ,0 ,0) and (1/4, 1/4, 1/4). The lattice vector is defined in the relative coordinates alat*(1/4, 1/4, 1/4). Detail description of the diamond structure can be found elsewhere. There is an elegant way to rescale atomic coordinates, lattice vector and k-points by only one parameter rescal defined in the se…

classical_md

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

--- Zdenka Chromcova 2010/03/18 11:23 Using: Switching the classic MD on/off The using of classic potential could be switched on/off in file fireball.in : * the implicit settings is off: iclassMD is not defined in fireball.in or iclassicMD = 0 * classic MD on: iclassicMD = 1

cloudview

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

DOWNLOAD * LINUX: Behaviour on some linux instalations is strange. Compilation from source *.pde is recommanded (see part “Compilation”) * MacOS: * Windows: Function * Monte-Carlo render of volumetric data (3D function) * Now

conductance_calculation_using_green_s_function_method

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

This page describes how to calculate transport properties using Fireball. First, we need to obtain SCF-solution for particular geometry. Once we have it, we need to switch on these options: ifixcharge = 1 itrans = 1 Simulation parameters are defined in two additional files:

constrain_dft

Anonymous (anonymous@undisclosed.example.com) — 2012-11-15T15:56:00+0200

Constrain DFT Constrained DFT allows to perform self consistent single electron excitation from arbitrary occupied orbital to unoccupied orbital (see example 1). There is also possibility to use quenching or geometry optimization of system in an excited state (see example 2).

creating_inputs

Anonymous (anonymous@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:

cu_111_surface_and_k-points_sampling

Anonymous (anonymous@undisclosed.example.com) — 2015-05-29T08:11:00+0200

Since we know, that the lattice parameter is 3.66 Angstrom, here is the structure for testing the sufficiency of the k-points sampling of the IBZ. The geometry is in Cu_111.bas file: 5 29 0.00000 1.49419 10.00000 29 0.00000 0.00000 12.11310 29 1.29401 0.74709 14.22620 29 0.00000 1.49419 16.33931 29 0.00000 0.00000 18.45241

cu_bulk_parameter_optimization

Anonymous (anonymous@undisclosed.example.com) — 2015-05-28T17:15:00+0200

Lattice parameter In this section, we explain how to optimize the lattice parameter of Ci bulk fcc structure. The fcc structure is characterized by single distinct atom per unit cell with relative coordinates (0 ,0 ,0) . The lattice vector is defined in the relative coordinates

cu_bulk_structure_optimization

Anonymous (anonymous@undisclosed.example.com) — 2015-05-29T00:28:00+0200

Copper has a fcc crystal structure. The unit cell is containing only one atom, thus the Cu_bulk.bas file contains only one atom: 1 29 0.00000 0.00000 0.00000 The unit cell prepared, so [1,1,0] crystallography axis is equal to x axis is written in the Cu_bulk.lvs:

cupc

Anonymous (anonymous@undisclosed.example.com) — 2017-02-28T14:32:00+0200

CuPc model Calculated with FHI-AIMS, PBE+U functional. Cu 3d orbitals had: U = 7eV. control.in and geometry.in files for the FHI-AIMS run are in the directory. Parameters for dI/dV simulations Simulations were proceed s,p and d valence electrons on the sample and

derivative_free_optimization

Anonymous (anonymous@undisclosed.example.com) — 2012-05-24T09:59:00+0200

Derivative Free Optimization * (optimization) * * (Ameba) Pattern search je relativne rychly protoze sampluje pouze vyznacne smery. Minimalne sampluje 1 smer, maximalne 2N. Pamatuje si predchozi smer takze se pohybuje effektivne. problem nastava v okamziku kdy se objevi uzke udoli sikme na hlavni osy. V tom pripade Pattern_search sice konv…

dft_inputs

Anonymous (anonymous@undisclosed.example.com) — 2017-01-26T14:58:00+0200

Hartree potential that may serve as an input for the PPM can be produced by various DFT codes. A slab calculations are necessary for a creation of the Hartree potential. The calculated system should be in the lower part of the unit cell, but z coordinates of the top-most layer has to be above zero! At least 10 Ǎ of vacuum above a slab geometry has to be used. 15-20 Ă of Vacuum are recommended. Here we show examples how to produce a hartree potential, for couple of DFT codes:

discrete_metadynamics

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Problem metadynamiky Metadynamika sampluje nekolikanasobne body ktere uz ma jednou nasamplovane. To ji cini neefektivni v techto ohledech: * V kazdem kroku se sumuje prez mnoho gaussianu (vsechny zatim ulozene) * Energie systemu se vyhodnocuje (tzn. napr. ab-initio vypocet) se provadi opakovane i v oblastech potencialovych jam kde uz byla energie dobre nasamplovana

dump_tb-hamiltonian_for_stm_simulation

Anonymous (anonymous@undisclosed.example.com) — 2012-05-01T21:36:00+0200

Let's assume we already obtained fully relaxed atomic and electronic structure of a desired system. To write down Hamiltonian into a file, we will run only one SCF cycle with fixed charges. In addition we need to switch on a flag iwrtatom in section

fepc_au

Anonymous (anonymous@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 !!!

fire_bfgs_minimization

Anonymous (anonymous@undisclosed.example.com) — 2011-08-12T11:47:00+0200

BFGS it call l-bfgs-b routine till: - the convergence criteria defined in cg.optional are reached (f(i,j)fmax - the maximum number of steps exceeds setting of input files:

fire_minimization

Anonymous (anonymous@undisclosed.example.com) — 2014-07-08T14:20:00+0200

FIRE minimization FIRE ( iquench = -6 ) is molecular dynamics based minimization technique, which use only gradient of the energy potential ( force ), but it often provides performance comparable or even superior to quasi-second-order Quasi-Newton algorithms such as BFGS. It differs from quenched molecular dynamics in the way how velocity is updated (see. pseudocode or references for more details). An other difference from standard quenched-MD (iquench=-1) is that mass of all atoms is set to 4.…

fireball.in

Anonymous (anonymous@undisclosed.example.com) — 2012-12-03T11:52:00+0200

Write out options iwrtcdcoefs = 0 or 1 # write coefficients of wavefunction C_i,mu iwrtcharges = 0 or 1 iwrtdensity = 0 or 1 # write out density matrix to standard output iwrteigen = 0 or 1 # write out eigenvalues iwrtefermi = 0 or 1 # write out occupation numbers of states iwrtfpieces = 0 or 1 # write out pieces of force iwrthampiece = 0 or 1 # write out pieces of hamiltonian iwrtcomponents = 0 or 1 i…

fireball

Anonymous (anonymous@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_12.11_amber_14_ambertools_15

Anonymous (anonymous@undisclosed.example.com) — 2017-03-04T01:19:00+0200

* Compile amber14 with AmberTools 15 * Download Fireball library and script * Download Fdata for HCNO * Change the config.h file and (make serial) in sander folder. cd amber14 ./configure intel make install cd make_fireball_qmmm/ ./make.sh change : src/AmberTools/config.h cd AmberTools/src/sander/ make serial //------------------------------------------ Example of config.h : #FLIBS= -l…

fireball_18.02_ambertools_17

Anonymous (anonymous@undisclosed.example.com) — 2018-03-22T19:21:00+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

fireball_19.11_ambertools_18

Anonymous (anonymous@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

fireball_20.05_ambertools_20

Anonymous (anonymous@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

fireballtg_file_formats

Anonymous (anonymous@undisclosed.example.com) — 2018-03-08T15:40:00+0200

Here you can find a list of parameters defined in fireball.in file and their default settings Begin of each section is defined by a line containing &NAMELIST and ended by a line containing a string &END. If more than one section with the same name is defined only the first listed instance is considered. List of the active sections:

fortran

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

manual svn Pointers on functions and subroutines in Fortran It works with both ifort 10 and gfortran-4.4 example 1: main.f90 module HelloWorld procedure(), pointer :: ptr contains subroutine Hello1() print *,'Ahoj' end subroutine subroutine Hello2(a) integer, intent(in) :: a print *,'Nazdar',a end subroutine end module program main use HelloWorld implicit none ptr => Hello1 call ptr ptr => Hello2 ca…

generating_potentials

Anonymous (anonymous@undisclosed.example.com) — 2017-01-26T14:55:00+0200

Generating force-fields and running AFM scans in PP-STM do not differ that much from those showed at . The creation of input files for the PP-AFM pre-calcultions is described at . From a GPAW DFT code there is now way, how to get a hartree potential at the moment. But the L-J force field can still be created from an *.xyz file with geometry of the sample's system.

generation_of_tip_e_str.inp_files_for_stm_simulation

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

This page describes how to generate, using Fireball, the tip_e_str.inp with the retarded and advanced green functions and the density of states (DOS) for the STM program . First, we need to obtain SCF-solution for particular geometry. Once we have it, we need to switch on these options:

grid

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

List of files related/modified to the Kohn-Sham: MODULES/ grid.f90 interactions.f90 (M) density.f90 (M) options.f90 (M) outputs.f90 (M) ALLOCATIONS/ allocate_grid.f90 allocate_rho.f90 (M) reallocate_rho.f90 (M) reallocate_neigh.f90 (M) ASSEMBLERS/

how_to_prepare_the_new_tip_and_sample_for_stm_simulations

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

The geometry First of all we need the “*.bas” file of the tip and sample geometry (separately). We can use the Jmol to view the “*.xyz” file. Tip should have tip apex at 0.0 0.0 xy position. We have even to prepare the “Fdata” of given properties of elements of tip and sample we will use. For followings we should run the fireball to relax these structures. If you are using new FIREBALL input format, set up followings at the “fireball.in” file:

i._the_geometry_and_the_files

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

input_parameters

Anonymous (anonymous@undisclosed.example.com) — 2017-05-05T15:38:00+0200

Reading parameters fermi=None # or 0.0 -- the Fermi level is taken from the DFT calculations; e.g. -0.5 -- the Fermi level is shifted by -0.5 eV. orbs = 'sp' # s and p orbitals of the sample -- calculations approx. 4× faster than 'spd', more tip orbitals allowed (

intro

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

A project FireballTG is a branch version of a simulation package Fireball.FireballTG provides several differences with respect to the original Fireball code. New Features ---------- - New input file format FireballTG File Formats - New internal loop structure decoupling individual tasks

kohn-sham_grid_calculation

Anonymous (anonymous@undisclosed.example.com) — 2016-11-24T15:25:00+0200

to run grid calcualtin it is necessary to put basis functions (.wf*) into ./Fdata/basis then switch on iks=1, and off imcweda = 0, idogs = 0, as shown in following firebal.in example &OPTION basisfile = answer.bas lvsfile = cel.lvs icluster = 0 nstepf = 1 sigmatol = 0.0000000001 max_scf_iterations = 100 dt = 0.5 iqout = 0 ifixcharge = 0 iks = 1 imcweda = 0 idogs = 0 &END &MESH ifixg0 = 1 # this will fix origin of grid g0 = 0.0,0.0,0.0 # in this position &END

kvadraticka_evoluce

Anonymous (anonymous@undisclosed.example.com) — 2011-10-20T23:04:00+0200

Motivace a pozadí problému Klasické evoluční optimalizační metody (jako např. Differenciální evoluce) využívají obvykle lineárních vektorových operací s vybranými nejlepšími jedinci z populace. Tyto operace bývají nejčastěji dvojího druhu

linear_stm

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

The Linear STM The linear scanning gives us the current profile from the A point to the B point at constant height of the tip. To run this kind of scan we need to change some values at the “scan.inp” and “options.inp” files. options.inp

mdet

Anonymous (anonymous@undisclosed.example.com) — 2016-04-13T17:29:00+0200

MDET In the Fireball code, it is possible to perform nonadiabatic molecular dynamics (MDET). The method which is implemented here belongs to the group of semi-classical techniques based on trajerctories. The method use Tully's fewest switching method ref: J.C.Tully, JCP 93, 1061 (1990). MDET simulations is switch on by flag imdet=1 in fireball.in. Ionic integration time step has a value dt = 0.5 fs. Integration time step of the electrons is denoted nddt = 100 and its optimal value is 100 which …

molecular_dynamics

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Molecular dynamics In this section we describe how to simulate molecular dynamics in NVT and NVE ensembles. In the canonical ensemble are N,V,T respectively N,V,E conserved. There are implemented two methods to hold temperature constant in fireball. The first one is velocity rescaling and the second is Nose- Hoover chain thermostat. These options are driven by keyword:

neb_simulation

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Input Here we provide brief description how to run Nudged Elastic Band ([ NEB]) simulations to explore reaction pathways between two known atomic configurations. More details about the method including list of references can be found [ here]. To start, we need an initial and final atomic configuration.

number_of_accessible_atoms_for_electronic_state

Anonymous (anonymous@undisclosed.example.com) — 2014-12-12T11:06:00+0200

Number of accessible atoms for electronic state There is a possibility to calculate number of accessible atoms for each electronic state. See James P. Lewis et.al, Phys.Chem.B 2003,2581-2587 . input files To write out number of accessible atoms for electronic states keyword iwrtpop must be set equal to 1 in

older_documentation

Anonymous (anonymous@undisclosed.example.com) — 2016-12-07T13:27:00+0200

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. Newer version is also able treat electrostatic forces if external electrostatic force field in .xsf format…

organization_structure_of_the_grid

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

General Overview SCF chart flow List of files List of files related/modified to the Kohn-Sham module: (M) stands for a modified file MODULES/ grid.f90 interactions.f90 (M) density.f90 (M) options.f90 (M) outputs.f90 (M) ALLOCATIONS/ allocate_grid.f90 allocate_rho.f90 (M) reallocate_rho.f90 (M) reallocate_neigh.f90 (M)

probe_particle_model

Anonymous (anonymous@undisclosed.example.com) — 2022-01-13T14:15:40+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

Anonymous (anonymous@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

prokop_hapala

Anonymous (anonymous@undisclosed.example.com) — 2012-11-30T13:01:00+0200

FORTRAN HELP Object-Oriented Programming in Fortran 2003 module myModule implicit none type myType integer :: n real, dimension (:, :), allocatable :: Rs contains procedure :: myMethod end type subSystem type (myType) :: myInstance contains subroutine myMethod ( this, myVar) class (subSystem) :: this real :: myVar integer i allocate (this%Rs(3,this%n)) do i = 1, this%n this…

reading_procedures

Anonymous (anonymous@undisclosed.example.com) — 2017-05-05T17:22:00+0200

At this moment there are three procedures that can read input files: Fireball read_FIREBALL_all(name = 'phi_' , geom='answer.bas', fermi=None, orbs = 'sp', pbc=(1,1), imaginary = False, cut_min=-15.0, cut_max=5.0, cut_at=-1, lvs = None, lower_atoms=[], lower_coefs=[])

results

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

TDSE

rgl_potential

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

RGL potential defined in DASSEMBLERS/getforce_classic_RGL.f90 Used form of the interaction and parameters from Riccardo Ferrando: * Philos. Mag. A 59 (1989) 321 * J.Chem.Phys 122 (2005) 194308 Ag-Cu,Ag-Ni,Au-Cu,Ag-Au,Ag-Pd,Pd-Pt,Ag-Ni Input file with parameters Cdata/RGL.dat:

sample_hamiltonian

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Sample Hamiltonian (Atomo_i, struc.inp files) Once we have the “CHARGES” we can produce the “Atomo_i” files by the FIREBALL. “CHARGES” file has to be at the same directory when you are running the FIREBALL. To the “fireball.in” we will write:

scf_for_excited_states

Anonymous (anonymous@undisclosed.example.com) — 2012-11-15T15:20:00+0200

scissor_operator

Anonymous (anonymous@undisclosed.example.com) — 2011-12-06T13:19:00+0200

Scissor operator (by Enrique) Scisor operator computation is composed from 3 steps * Export molecular orbitals coefficients from free standing molecule SCF by setting iwrtcdcoefs = 1 * set koopmans shifts for orbitals of molecule (file koopman_shift)

si_7x7

Anonymous (anonymous@undisclosed.example.com) — 2017-02-20T16:51:00+0200

Si (111) 7×7 model Calculated with FireballTG,McWEDA-LDA functional. The slab has 6Si layers+ 1 hydrogen passivating layer. Only Γ k-point was used Parameters for STM simulations Simulations were proceed s,p and d valence electrons on the sample and

smeagol

Anonymous (anonymous@undisclosed.example.com) — 2012-12-04T15:59:00+0200

Equilibriom Kpoins melo by to fungovat, skousel jsem 1D H chain, H111 bulk, a Si100 bulk, vsude to fungovalo pro vice k-bodu. Chyba vznikala pri jednom k-bodu, protoze se v tom pripade pouzivala na inverovani GF lapack subrutina pro symetricke matice Predelal sem to aby se vzdy pouzivala subrutina pro obecne matice

smeagol_usage

Anonymous (anonymous@undisclosed.example.com) — 2012-11-30T15:21:00+0200

Tutorial H-chain in PDF There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary (no much text explanatiobn included) The input data files for this tutorial could be downloaded here Wiki Tutorial on H-chain Intro

start

Anonymous (anonymous@undisclosed.example.com) — 2016-12-05T14:52:00+0200

Tools Computational code Fireball STM code Probe Particle Model Probe Particle STM Visualization tools * : Volumetric visualization of 3D function (.xsf file) CloudView * : STMview for OpenDX STMview Scripts * fireball *wf* to *state* convertor: wf2state * shift .xyz in periodic lattice by lattice vectors modxyz *

stm_code

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Introduction Tutorials * Preparation of the tip and sample for STM simulations * The geometry and the files * Sample Hamiltonian * The tip structure * The hoppings * The scanning modes * The files * Linear STM * 2D STM * Examples * 1D scan line Examples

stmview

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

DOWNLOAD * - This fork version enable manual selection of minimum offset and scaling for rubbersheed. See the picture 4. This would enable to set better positioning and roughness of the surface map in case when the default (automatic) positioning is not appropriate. Sometimes (if data in STM map has high values >1, the positioning of surface could be far from geometry)

tdse

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

General Overview Time dependent Kohn-Sham equation SCF chart flow

tersoff_potential

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Tersoff potential defined in DASSEMBLERS/getforce_classic_Tersoff.f90 The implementation uses the shape of tersoff potential published in: * PRB37(1988)6991 * PRB39(1989)5566 (alloys) (with aij=1) The parameters of the potential are defined in file Cdata/Tersoff.dat.

the_files

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Files we will need For succesful simulation of STM, we will need (except the STM code) several files. First of all we'll need the right “Fdata” directory (or the link) at our computation directory. Even this files, we will use: Atomo_i options.inp

the_geometry_and_the_files

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

The geometry First of all we need the *.bas file of the tip and sample geometry (separately). We can use the Jmol to view the *.xyz file. Tip should have tip apex at 0.0 0.0 xy-position. We have even to prepare the Fdata of given properties of elements of tip and sample we will use. For followings we should run the fireball to relax these structures. If you are using new

the_hoppings

Anonymous (anonymous@undisclosed.example.com) — 2014-07-08T13:35:00+0200

The hoppings ( interactions_i_j.dat or tip_sample_i_j.inp files ) In our approximation, we use a dimer formed by one kind of atom from the tip and another kind from the sample. We have to generate a “tip_sample_i_j.inp” (or “interaction_i_j.dat

the_tip_structure

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

The tip_e_str.inp file The “tip_e_str.inp” file contains informations about the density of states of the tip. Than we need to run the FIREBALL code with the following settings of “fireball.in” file: &OPTION part ‐ basisfile =

tutorial

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

'Intro' ---------- Here you can find several tutorials explaining some post-processing utilities. These utilities are available in newest version of Fireball. Keep in mind, that the input files of this version are different from those of older versions (for details see here).

tutorials

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

How to prepare the new tip and sample for STM simulations

uphill_damped_md

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

Několik vylepšení minimalizace pomocí tlumené molekulární dynamiky 1) Fiktivní hmotnosti Všchny částice mají nastavené hmotnosti tak, aby jejich vibrační mody byly podobné, tzn. za předpokladu že na všechny částice působí stejná síla, mělyby by být jejich hmotnosti stejné. V opačném případě se hmotnost určuje podle maximální síly na která kdy na částici působila

vibrational_modes

Anonymous (anonymous@undisclosed.example.com) — 2014-09-12T15:41:00+0200

Vibrational modes In this section we describe how to calculate the vibrational modes of molecules using dynamical matrix. Vibrational modes are obtained from eigenvalues of the dynamical matrix. The elements of the matrix are defined as second derivatives of energy with respect to geometry. The first derivatives with respect to geometry are forces.The second derivatives are obtained from the different of two forces and displacement. At first calculate optimization structure of the molecule and …

wiki_editing_title

Anonymous (anonymous@undisclosed.example.com) — 2011-07-25T23:24:00+0200

wiki editing content

wiki_playground

Anonymous (anonymous@undisclosed.example.com) — 2012-11-30T13:15:00+0200

Level 1 Headline text text text text text text text text text text text text text text text text text text Level 2 Headline text text text text text text text text text text text text text text text text text text Level 3 Headline

wiki_test

Anonymous (anonymous@undisclosed.example.com) — 2011-02-18T13:13:00+0200

\frac{\sum_{n=1}^N x^{\sqrt{n+1}}-x^{x^{2n}}}{(\ln(x)+2x^{4x+1289})^{\frac{1}{2}}}