probeType:		atom type of ProbeParticle (to choose L-J potential ),e.g. 8 for CO, 24 for Xe
charge:		effective charge of probe particle [e]
stiffness:		[N/m] harmonic spring potential (x,y,R) components, x,y is bending stiffnes, R particle-tip bond-length stiffnes
r0Probe:		[Å] equilibirum position of probe particle (x,y,R) components, R is bond length, x,y introduce tip asymmetry
PBC:		Periodic boundary conditions [True/False]
gridA:		a-vector of unit cell; recommended format (x,y,0)
gridB:		b-vector of unit cell; recommended format (x,y,0)
gridC:		c-vector of unit cell; recommended format (0,0,z)
scanMin:		start of scanning (x,y,z)
scanMax:		end of scanning (x,y,z)
Amplitude:		[Å] oscillation amplitude for conversion Fz->df
XYZ file:		Load your structure here; otherwise default is used.
XYZ,Q edit:	Columns: proton number, x, y, z, atom charge (0 by default) 76 1 7.045632 6.005611 -0.052888 1 9.897932 2.612197 -0.056977 1 8.275515 4.509515 -0.057868 1 12.336536 10.425943 -0.061919 1 10.715509 12.324061 -0.065323 1 16.494125 2.632622 -0.072583 1 14.956839 0.698789 -0.079367 1 5.466643 7.962519 -0.085229 1 4.119252 12.299946 -0.091880 1 5.654981 1.629818 -0.096675 1 13.565894 8.930339 -0.102428 1 17.696895 4.129069 -0.111232 1 2.913854 10.798495 -0.117723 1 0.297545 6.017947 -0.119833 1 1.347291 8.911106 -0.125463 1 15.144149 6.972857 -0.130108 6 2.621637 3.387846 0.041608 6 17.988938 11.543115 0.040699 6 1.716193 2.269460 0.018212 6 18.895540 0.054478 0.017882 6 16.575842 11.798241 0.012332 6 2.109497 4.737339 0.009629 6 4.035186 3.134891 0.006199 6 18.499818 10.193198 0.002451 6 18.354513 1.408393 0.001604 6 0.292178 2.529691 -0.003373 6 2.257490 0.915606 -0.004814 6 1.355669 12.400083 -0.009079 6 15.663396 10.693414 -0.030448 6 4.946252 4.241253 -0.033541 6 8.460732 9.700865 -0.038889 6 11.676270 3.889107 -0.041915 6 9.391583 8.577526 -0.043681 6 12.150422 5.235737 -0.043939 6 8.879127 7.226840 -0.046517 6 9.803926 6.100857 -0.048195 6 11.219314 6.358704 -0.054127 6 8.935444 11.048405 -0.054497 6 10.806848 8.835347 -0.054677 6 12.627060 2.771968 -0.054972 6 3.027209 5.844935 -0.057576 6 17.580497 9.086605 -0.060951 6 16.927085 1.607633 -0.064027 6 11.731369 7.709659 -0.067418 6 16.055993 0.529668 -0.070768 6 14.500408 4.381420 -0.071641 6 10.264656 3.653143 -0.075683 6 3.685384 0.718704 -0.078631 6 7.056585 9.446452 -0.078930 6 7.456229 7.025883 -0.080345 6 10.348133 11.283277 -0.082597 6 4.555722 1.797893 -0.084698 6 7.986512 12.165758 -0.085296 6 9.355116 4.729159 -0.085830 6 6.111761 10.553022 -0.091448 6 11.256788 10.206991 -0.091880 6 13.555308 5.488978 -0.093712 6 6.563246 8.112073 -0.094303 6 18.781431 3.900094 -0.097607 6 0.697360 4.975730 -0.102561 6 1.829415 11.028494 -0.104764 6 0.948266 9.953749 -0.109176 6 13.153857 7.910469 -0.126679 6 14.047418 6.822746 -0.134791 8 4.404325 5.541330 0.045574 8 16.203088 9.393259 0.045412 8 14.000085 3.084870 0.031321 8 6.611246 11.853332 -0.040567 8 15.736976 4.488921 -0.162471 8 12.372578 1.563458 -0.174728 8 14.425290 10.795586 -0.178975 8 6.184656 4.142140 -0.179801 8 4.874577 10.445600 -0.179936 8 8.241621 0.769431 -0.198561 8 17.864094 7.883718 -0.271502 8 2.739904 7.046718 -0.271630
Potentials:	Columns: equlibrium distance R_ii0[Å], binding energy E_ii0[eV], comment (Z, element, ref. of L-J parameters) Note: Number of row = proton number of the element!! 1.4870 0.0006808054 1 H abalone AMBER 2003 OPLS 1.4815 0.0009453220 2 He abalone AMBER 2003 OPLS 2.0000 0.0100000000 3 Li abalone AMBER 2003 OPLS 2.0000 0.0100000000 4 Be 2.0800 0.0037292520 5 B abalone AMBER 2003 OPLS 1.9080 0.0037292524 6 C abalone AMBER 2003 OPLS 1.7800 0.0073719000 7 N abalone AMBER 2003 OPLS 1.6612 0.0091063140 8 O abalone AMBER 2003 OPLS 1.7500 0.0026451670 9 F abalone AMBER 2003 OPLS 1.5435 0.0036425260 10 Ne abalone AMBER 2003 OPLS 2.0000 0.0100000000 11 Na abalone AMBER 2003 OPLS 2.0000 0.0100000000 12 Mg abalone AMBER 2003 OPLS 2.0000 0.0100000000 13 Al 1.9000 0.0254899514 14 Si Gromos Si J. Chem. 2.1000 0.0086726800 15 P abalone AMBER 2003 OPLS 2.0000 0.0108408500 16 S abalone AMBER 2003 OPLS 1.9480 0.0114913010 17 Cl abalone AMBER 2003 OPLS 1.8805 0.0123412240 18 Ar abalone AMBER 2003 OPLS 2.0000 0.0100000000 19 K abalone AMBER 2003 OPLS 2.0000 0.0100000000 20 Ca abalone AMBER 2003 OPLS 2.0000 0.0100000000 21 Sc 2.0000 0.0100000000 22 Ti 2.0000 0.0100000000 23 V 2.0000 0.0100000000 24 Cr 2.0000 0.0100000000 25 Mn 2.0000 0.0100000000 26 Fe 2.0000 0.0100000000 27 Co 2.0000 0.0100000000 28 Ni 2.0000 0.0100000000 29 Cu 2.0000 0.0100000000 30 Zn 2.0000 0.0100000000 31 Ga 2.0000 0.0100000000 32 Ge 2.0000 0.0100000000 33 As 2.0000 0.0100000000 34 Se 2.2200 0.0138762880 35 Br 2.0000 0.0100000000 36 Kr 2.0000 0.0100000000 37 Rb 2.0000 0.0100000000 38 Sr 2.0000 0.0100000000 39 Y 2.0000 0.0100000000 40 Zr 2.0000 0.0100000000 41 Nb 2.0000 0.0100000000 42 Mo 2.0000 0.0100000000 43 Tc 2.0000 0.0100000000 44 Ru 2.0000 0.0100000000 45 Rh 2.0000 0.0100000000 46 Pd 2.0000 0.0100000000 47 Ag 2.0000 0.0100000000 48 Cd 2.0000 0.0100000000 49 In 2.0000 0.0100000000 50 Sn 2.0000 0.0100000000 51 Sb 2.0000 0.0100000000 52 Te 2.3500 0.0173453600 53 I 2.1815 0.0243442128 54 Xe 2.0000 0.0100000000 55 Cs 2.0000 0.0100000000 56 Ba 2.0000 0.0100000000 57 La 2.0000 0.0100000000 58 Ce 2.0000 0.0100000000 59 Pr 2.0000 0.0100000000 60 Nd 2.0000 0.0100000000 61 Pm 2.0000 0.0100000000 62 Sm 2.0000 0.0100000000 63 Eu 2.0000 0.0100000000 64 Gd 2.0000 0.0100000000 65 Tb 2.0000 0.0100000000 66 Dy 2.0000 0.0100000000 67 Ho 2.0000 0.0100000000 68 Er 2.0000 0.0100000000 69 Tm 2.0000 0.0100000000 70 Yb 2.0000 0.0100000000 71 Lu 2.0000 0.0100000000 72 Hf 2.0000 0.0100000000 73 Ta 2.0000 0.0100000000 74 W 2.0000 0.0100000000 75 Re 2.0000 0.0100000000 76 Os 2.0000 0.0100000000 77 Ir 2.0000 0.0100000000 78 Pt 2.0000 0.0100000000 79 Au 2.0000 0.0100000000 80 Hg 2.0000 0.0100000000 81 Tl 2.0000 0.0100000000 82 Pb 2.0000 0.0100000000 83 Bi 2.0000 0.0100000000 84 Po 2.0000 0.0100000000 85 At 2.0000 0.0100000000 86 Rn 2.0000 0.0100000000 87 Fr 2.0000 0.0100000000 88 Ra 2.0000 0.0100000000 89 Ac 2.0000 0.0100000000 90 Th 2.0000 0.0100000000 91 Pa 2.0000 0.0100000000 92 U 2.0000 0.0100000000 93 Np 2.0000 0.0100000000 94 Pu 2.0000 0.0100000000 95 Am 2.0000 0.0100000000 96 Cm 2.0000 0.0100000000 97 Bk 2.0000 0.0100000000 98 Cf 2.0000 0.0100000000 99 Es 2.0000 0.0100000000 100 Fm 2.0000 0.0100000000 101 Md 2.0000 0.0100000000 102 No 2.0000 0.0100000000 103 Lr 2.0000 0.0100000000 104 Rf 2.0000 0.0100000000 105 Db 2.0000 0.0100000000 106 Sg 2.0000 0.0100000000 107 Bh 2.0000 0.0100000000 108 Hs 2.0000 0.0100000000 109 Mt 2.0000 0.0100000000 110 Ds 2.0000 0.0100000000 111 Rg 2.0000 0.0100000000 112 Cn 2.0000 0.0100000000 113 Uut 2.0000 0.0100000000 114 Fl 2.0000 0.0100000000 115 Uup 2.0000 0.0100000000 116 Lv 2.0000 0.0100000000 117 Uus 2.0000 0.0100000000 118 Uuo
Code:		save parameters & launch

Description

This is a web interface of the Probe Particle Model for simulation of high-resolution atomic force microscopy images (see references to publications below).

Model geometry

The geometry of the structure supplied in .xyz format is automatically shifted so that the topmost atom of sample is positioned -1.0Å below zero (zero means closest approach of probe particle). Closer approaches would lead to unrealisticaly high repulsive forces.

The geometry alignment also depends on setting of the periodic boundary conditions (PBC) mode. For a PBC = True setting, the sampling grid is defined manually by setting gridA, gridB, gridC vectors. For non-periodic boundary conditions (PBC = False) an orthogonal sampling grid around the molecule is created automatically with margins 3.0Å on each side.

Electrostatic field

In this web version of the code, it is possible to include electrostatic field of sample approximated only by partial atomic charges (i.e. point charges). To do so, just put appropriated partial atomic charge [e+] into the 5th column of your input geometry (the .xyz file). For lines where 5th column is missing, the partial atomic charge Q_i is automatically assumed to be zero.

WARNING: In case of periodic systems (PBC = True), please ensure that the sum of all charges of all atoms in the system is zero. If there is nonzero net charge of the supercell, the electrostatic force decays very slowly. This would lead to artefacts on the borders of the sampling grid, since we consider interaction just to the neares neighbor supercell.

NOTE: For more accurate description of the electrostatics, it is possible to download the full code from the links bellow, which allows to read the electrostatic forcefield on a grid (e.g. from an XCrysDen .xsf file).

Code and more documentation

The full code can be downloaded from github here. There are two implementations available:

a) Python + C++ implementation used on this webpage
or
b) older Fortran90 implementation used in the publications cited below.

For more detailed information including technical details, please, see our github wiki

PyProbe Web interface 0.2 Alpha

Description

Model geometry

Electrostatic field

Code and more documentation

References