Run as standalone

The standalone application requires an input file within the specific format outlined below. Run the code as

> ./src/ddx_driver *path-to-input-file*

Example: (using the default input-file)

> ./src/ddx_driver ../tests/Input-example.txt

Description of input parameters in input-file

Line number	type	description
1	String	Filename for Log-file where information about the convergence of the linear solver is saved, the void string '' means that no log-file is saved
2	Integer	Number of OpenMP cores to be used
3	Integer	Specification of the model 1: COSMO, 2: PCM, 3: LPB
4	Integer	Maximal degree \(\ell_{\max}\) of modeling spherical harmonics
5	Integer	Approximate number of Lebedev grid points
6	Float	Dielectric permittivity constant \(\varepsilon_s\) of the bulk solvent
7	Float	Shift \(s\) of the regularized characteristic function \(\chi_\eta\), range=[-1,1]. Recommended value: -1 for ddcosmo and 0 for ddpcm or ddplpb
8	Float	Regularization parameter \(\eta\) of the smoothing function \(\chi_\eta\), range=[0,1]. Recommended value: 0.1
9	Float	Debye Hückel parameter \(\kappa_s\) of the bulk solvent
10	Integer	Whether to compute and store sparse matrices (1) or apply the matrix-vector product on the fly (0), range={0,1} The sparse matrices are the solution matrix of ddCOSMO referred to as \(L\) used in ddCOSMO and ddPCM, and the matrices \(A\) and \(B\) in ddLPB.
11	Float	The relative threshold \(tol\) for the iterative solver
12	Integer	Maximum number of iterations of the iterative solver before stopping
13	Integer	Number of Jacobi/DIIS extrapolation points
14	Integer	Whether to compute (1) or not (0) the forces, range={0,1}
15	Integer	Whether to use (1) or not (0) the FMM, range={0,1}
16	Integer	Max degree of multipole spherical harmonics \(\tilde\ell_{\max}\) for the FMM (recommended value \(\tilde\ell_{\max}=\ell_{\max}\))
17	Integer	Max degree of local spherical harmonics \(p_{\max}\) for the FMM (recommended value \(p_{\max}=6\))
18	Integer	Number of spheres of the atomic structure
19–END	Float[5]	The flollowing lines specify for each atom (should be consistent with entry on line 20) the values c,x,y,z,r where the partial charge (c), x-coordinate (x), y-coordinate (y), z-coordinate (z), radius (r) are listed (see example below). The charges are in atomic units and the coordinates and the radii in Ångstrom.

Remarks:

1. The order of the lines is essential

Example of an input file:

''          ! Name of log-file for convergence history of the solvers 
1           ! Number of OpenMP cores to be used
1           ! Specification of the model: 1 for COSMO, 2 for PCM and 3 for LPB
7           ! Maximal degree of modeling spherical harmonics
302         ! Approximate number of Lebedev grid points
78.3553     ! Dielectric permittivity constant
0.0         ! Shift of the regularized characteristic function
0.1         ! Regularization parameter
0.0         ! Debye Hückel parameter
0           ! Whether to compute and store sparse matrices (1) or not (0)
1d-8        ! The relative threshold for the iterative solver
100         ! Maximum number of iterations
20          ! Number of Jacobi DIIS extrapolation points
1           ! Whether to compute (1) or not (0) forces
1           ! Whether to use (1) or not (0) the FMM
7           ! Max degree of multipole spherical harmonics for the FMM
6           ! Max degree of local spherical harmonics for the FMM
12          ! Number of spheres of the atomic structure
-0.04192   0.00000   2.29035   1.32281   4.00253    ! partial charge[a.u.], x[Å], y[Å], z[Å], radius[Å]
-0.04192   0.00000   2.29035  -1.32281   4.00253
-0.04198   0.00000   0.00000  -2.64562   4.00253
-0.04192   0.00000  -2.29035  -1.32281   4.00253
-0.04192   0.00000  -2.29035   1.32281   4.00253
-0.04198   0.00000   0.00000   2.64562   4.00253
 0.04193   0.00103   4.05914   2.34326   2.99956
 0.04193   0.00103   4.05914  -2.34326   2.99956
 0.04197   0.00000   0.00000  -4.68652   2.99956
 0.04193  -0.00103  -4.05914  -2.34326   2.99956
 0.04193  -0.00103  -4.05914   2.34326   2.99956
 0.04197   0.00000   0.00000   4.68652   2.99956