Fragmentation

The description of the bulk and surface fragments for Si(111) and Si(100)
are contained in the file Silicon111fragments.txt




PES for SiH5 and Si2H7

There are two surfaces for SiH5. They are contained in the subdirectories SiH5-PES1
and SiH5-PES2. The nomemclature is that of the article by Frankcombe and Collins

There is one surface for Si2H7.

Description of the files supplied.

The fortran programs and  makefile are contained in this directory. The data files for 
each PES are contained in the subdirectories.

The data file, POT, contains the information required to evaluate second order Taylor 
expansions of the energy at the "data point" geometries.

The files IN_ATOMPERMS, IN_SYSTEM, IN_ZMA contain information (for example the order of the atoms) needed to evaluate the PES for a supplied set of Cartesian coordinates (in Bohr) of the atoms. Some parameters needed to evaluate the weight functions required for the PES interpolation [see, M. A. Collins, Theoretical Chemistry Accounts 2002, 108, 313] have been included in the fortran code.

The file example.f contains a sample main program that reads in a Cartesian geometry for 
either SiH5 or Si2H7 and outputs the energy and Cartesian energy gradients. For verification, the program also evaluates the gradient by finite difference of the energy. Some comments in example.f tell you how to supply the input Cartesian geometry.

To evaluate the PES as you require, you will need to modify/replace example.f Note that there is significant cpu time required to read the POT file and other preliminary computations. Efficiency requires that many different Cartesian geometries are input, rather than executing the program  separately for a succession of geometries.

A makefile is included, which must most likely be modified to accommodate your fortran compiler.

The remaining ".f" files and the traj.inc file contain the subroutines need to evaluate the PES and energy gradient.

A sample input Cartesian geometry is contained in the file INPUTGEOMETRY in SiH5-PES1

Executing
example < INPUTGEOMETRY

should produce the output:
 Energy:
  -290.364154508541     
 Interpolated force:
  7.2408299E-04  1.0211117E-03  1.0211117E-03
 -1.4388030E-03 -1.2786601E-03 -1.2786601E-03
 -4.7721107E-05  1.0618420E-04  1.0618420E-04
  8.1286300E-05  5.2925203E-05 -1.2134355E-04
  8.1286300E-05 -1.2134355E-04  5.2925203E-05
  5.9986854E-04  2.1978265E-04  2.1978265E-04
 Stepped force:
  7.2405726E-04  1.0211153E-03  1.0211124E-03
 -1.4388036E-03 -1.2786444E-03 -1.2786416E-03
 -4.7734262E-05  1.0620056E-04  1.0620624E-04
  8.1294616E-05  5.2941119E-05 -1.2131807E-04
  8.1283251E-05 -1.2132091E-04  5.2941119E-05
  5.9987145E-04  2.1977372E-04  2.1978225E-04

