Complex Tip alias Double Probe Particle

Main:

Branch with code specialized mainly on simulations of images obtained with CO-tip: Two probe particles (PPs) can move. Both of them interact with substrate via L-J potential and on both of them could be charged ("s" or other multipoles, but the same for both. Mistake here, there is angle spring!).

Spring Constants:

The spring constants in params.ini Cklat and Oklat are in fact angle spring constants.

Electrostatics:

The electrostatics of the metal tip-base can be represented via two metal (Cu) atoms with the same multipole as PPs, like it is illustrated in the figure above, by setting tip None in the params.ini. E.g. is PTCDA_Hartree example, where the same model as in JACS 140 (10), pp 3532–3536 (2018). Multipole of PPs (and two Cu atoms) can be changed via Omultipole in params.ini (default 's'). Optionally, any possible multipole (eg. dipole) at the position of the metal tip-base last atoms can be set by tip tip pz in the params.ini. Example, simulating the same double electrostatics as in ACS Nano 12, 5274−5283 (2018) used for the best NaCl/Cu results can be found in PTCDA_Hartree_dz2 example.

params.ini example (as from JACS 140 (10), pp 3532–3536 (2018)):

PBC              True  
nPBC             1         1         1   
moleculeShift    0.0       0.0     0.0   
useLJ            True 
Catom            6                        # Z of the upper PP (C)
Oatom            8                        # Z of the lower PP (O)
rC0              0.0 0.0  1.85            # Total Metal atom-C length 1.85  
rO0              0.0 0.0  1.15            # Total C-O length  1.15  
Cklat            0.111                    # the bending spring constant of the harmonic spring potential of tip-C bond  Now it is a bending spring constant. The units should be ev/rad^2, if I am not mistaking
Oklat            0.109                    # the bending spring constant of the harmonic spring potential of C-O bond # C 0.111 & O 0.109 are giving really close results as stiffness 0.24 in Master
Ckrad            20.00                    # C radial stiffness (keep 20.0)
Okrad            20.00                    # O radial stiffness (keep 20.0)
ChargeCuUp       -0.0669933               # charge of upper Cu atom
ChargeCuDown     -0.0627402               # charge of lower Cu atom
CuUpshift        2.2422001068             # Cu-Cu z distance (important only for electrostatics and if tip = None)
Ccharge           0.212718                # charge of upper PP (C)
Ocharge          -0.11767                 # charge of upper PP (O)
Omultipole       's'                      # Multipole of PPs (and Cu atoms iff tip = None)
sigma            0.71                     # Sigma of PPs charge
tip              None                     # Multipole of metal tip-base (If None then, Cu atoms charge is checked)
tipZdisp         0.0                      # z-shift for the metal tip-base multipole
tipsigma         0.71                     # Sigma of metal tip-base 
tipcharge        0.00                     # effective charge (or dipole) of the metallic base of the tip (applied if   tip != None)
scanMin          0.0    0.0    15.5       # start of scanning (x,y,z) 
scanMax          20.0   20.0    19.0      # end of scanning (x,y,z)
Amplitude 1.0                             # [Å] oscilation amplitude for conversion Fz->df

References:

First usage and description:

Marco Di Giovannantonio, José I. Urgel, Uliana Beser, Aliaksandr V. Yakutovich, Jan Wilhelm, Carlo A. Pignedoli, Pascal Ruffieux, Akimitsu Narita, Klaus Müllen, and Roman Fasel, On-Surface Synthesis of Indenofluorene Polymers by Oxidative Five-Membered Ring Formation, J. Am. Chem. Soc. 140 (10), pp 3532–3536 (2018)

The code is briefly described in Supplementary Information (S4, 2nd paragraph).

Charges for 2Cu-C-O tip obtained via:

Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, and Peter A. Kollman, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem., 97 (40), pp 10269–10280 (1993)