ChemShell Tutorial

Search the manual:

The ChemShell matrix Object

The ChemShell matrix object stores a general matrix of rank 2.

Within ChemShell matrix objects serve many purposes, the most important ones for (geometry) optimisation is the storage and manipulation of function values, gradients and Hessians.

A matrix object is generated by the command create_matrix. As an example, consider a 4x4 matrix:

% create_matrix matrix=a datatype=real dimensions= {4 4} name=A  {
1. 3. 5. -6.3
12.8 2.9 -0.3 2.0
-1.2 4.5 6. 9.
-2.5 3.2 8.6 0.3
}
% print_matrix matrix=a
listing of matrix A 
                1           2           3           4   
1     :       1.0000      3.0000      5.0000     -6.3000
2     :      12.8000      2.9000     -0.3000      2.0000
3     :      -1.2000      4.5000      6.0000      9.0000
4     :      -2.5000      3.2000      8.6000      0.3000
%

Note that from Tcl, the matrix is referred to by the name given by the matrix= argument. The name= argument serves to give the matrix a title, which shows up in e.g. the output of the print_matrix command.

A complete set of matrix algebra operations is available.

Here we give a few as examples.

% diagonalise_matrix matrix=a evals=evals_a evecs=evecs_a
% print_matrix matrix=evals_a
listing of matrix A eigenvalues 
                1   
1     :     -12.2850
2     :      -5.8306
3     :      11.7436
4     :      16.5720
% print_matrix matrix=evecs_a
listing of matrix A eigenvectors 
                1           2           3           4   
1     :       0.6974     -0.0631     -0.5474      0.4582
2     :      -0.6674      0.1269     -0.3072      0.6664
3     :       0.0959     -0.6172      0.6057      0.4929
4     :       0.2428      0.7739      0.4889      0.3211
% get_matrix_element matrix=evecs_a indices= {0 0} format=%f
0.697422
% set_matrix_element matrix=evecs_a indices= {0 0} value=0.3
% print_matrix matrix=evecs_a
listing of matrix A eigenvectors 
                1           2           3           4   
1     :       0.3000     -0.0631     -0.5474      0.4582
2     :      -0.6674      0.1269     -0.3072      0.6664
3     :       0.0959     -0.6172      0.6057      0.4929
4     :       0.2428      0.7739      0.4889      0.3211
% 

Further examples can be found in chemsh/examples/matrix