PCM

Name PCMCalcMethod
Section Hamiltonian::PCM
Type integer
Default pcm_direct

Defines the method to be used to obtain the PCM potential.

Options:

• pcm_direct:
  Direct sum of the potential generated by the polarization charges regularized with a Gaussian smearing [A. Delgado, et al., J Chem Phys 143, 144111 (2015)].
  
• pcm_poisson:
  Solving the Poisson equation for the polarization charge density.
  

Name PCMCalculation
Section Hamiltonian::PCM
Type logical
Default no

If true, the calculation is performed accounting for solvation effects by using the Integral Equation Formalism Polarizable Continuum Model IEF-PCM formulated in real-space and real-time (J. Chem. Phys. 143, 144111 (2015), Chem. Rev. 105, 2999 (2005), J. Chem. Phys. 139, 024105 (2013)). At the moment, this option is available only for TheoryLevel = DFT. PCM is tested for CalculationMode = gs, while still experimental for other values (in particular, CalculationMode = td).

Name PCMCavity
Section Hamiltonian::PCM
Type string

Name of the file containing the geometry of the cavity hosting the solute molecule. The data must be in atomic units and the file must contain the following information sequentially: T < Number of tesserae s_x(1:T) < coordinates x of the tesserae s_y(1:T) < coordinates y of the tesserae s_z(1:T) < coordinates z of the tesserae A(1:T) < areas of the tesserae R_sph(1:T) < Radii of the spheres to which the tesserae belong normal(1:T,1:3) < Outgoing unitary vectors at the tesserae surfaces

Name PCMChargeSmearNN
Section Hamiltonian::PCM
Type integer
Default 2 * max_area * PCMSmearingFactor

Defines the number of nearest neighbor mesh-points to be taken around each cavity tessera in order to smear the charge when PCMCalcMethod = pcm_poisson. Setting PCMChargeSmearNN = 1 means first nearest neighbors, PCMChargeSmearNN = 2 second nearest neighbors, and so on. The default value is such that the neighbor mesh contains points in a radius equal to the width used for the gaussian smearing.

Name PCMDebyeRelaxTime
Section Hamiltonian::PCM
Type float
Default 0.0

Relaxation time of the solvent within Debye model ($\tau$). Recall Debye dieletric function: $\varepsilon(\omega)=\varepsilon_d+\frac{\varepsilon_0-\varepsilon_d}{1-i\omega\tau}$

Name PCMDrudeLDamping
Section Hamiltonian::PCM
Type float
Default 0.0

Damping factor of the solvent charges oscillations within Drude-Lorentz model ($\gamma$). Recall Drude-Lorentz dielectric function: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$

Name PCMDrudeLOmega
Section Hamiltonian::PCM
Type float
Default $\backslash sqrt\{1/(\backslash varepsilon\_0-1)\}$

Resonance frequency of the solvent within Drude-Lorentz model ($\omega_0$). Recall Drude-Lorentz dielectric function: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$ Default values of $\omega_0$ guarantee to recover static dielectric constant.

Name PCMDynamicEpsilon
Section Hamiltonian::PCM
Type float
Default PCMStaticEpsilon

High-frequency dielectric constant of the solvent ($\varepsilon_d$). $\varepsilon_d=\varepsilon_0$ indicate equilibrium with solvent.

Name PCMEoMInitialCharges
Section Hamiltonian::PCM
Type integer
Default 0

If =0 the propagation of the solvent polarization charges starts from internally generated initial charges in equilibrium with the initial potential. For Debye EOM-PCM, if >0 the propagation of the solvent polarization charges starts from initial charges from input file. if =1, initial pol. charges due to solute electrons are read from input file. else if =2, initial pol. charges due to external potential are read from input file. else if =3, initial pol. charges due to solute electrons and external potential are read from input file. Files should be located in pcm directory and are called ASC_e.dat and ASC_ext.dat, respectively. The latter files are generated after any PCM run and contain the last values of the polarization charges.

Name PCMEpsilonModel
Section Hamiltonian::PCM
Type integer
Default pcm_debye

Define the dielectric function model.

Options:

• pcm_debye:
  Debye model: $\varepsilon(\omega)=\varepsilon_d+\frac{\varepsilon_0-\varepsilon_d}{1-i\omega\tau}$
  
• pcm_drude:
  Drude-Lorentz model: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$
  

Name PCMGamessBenchmark
Section Hamiltonian::PCM
Type logical
Default .false.

If PCMGamessBenchmark is set to "yes", the pcm_matrix is also written in a Gamess format. for benchamarking purposes.

Name PCMKick
Section Hamiltonian::PCM
Type logical
Default no

This variable controls the effect the kick has on the polarization of the solvent. If .true. ONLY the FAST degrees-of-freedom of the solvent follow the kick. The potential due to polarization charges behaves as another kick, i.e., it is a delta-perturbation. If .false. ALL degrees-of-freedom of the solvent follow the kick. The potential due to polarization charges evolves following an equation of motion. When Debye dielectric model is used, just a part of the potential behaves as another kick.

Name PCMLocalField
Section Hamiltonian::PCM
Type logical
Default no

This variable is a flag for including local field effects when an external field is applied. The total field interacting with the molecule (also known as cavity field) is not the bare field in the solvent (the so-called Maxwell field), but it also include a contribution due to the polarization of the solvent. The latter is calculated here within the PCM framework. See [G. Gil, et al., J. Chem. Theory Comput., 2019, 15 (4), pp 2306–2319].

Name PCMQtotTol
Section Hamiltonian::PCM
Type float
Default 0.5

If PCMRenormCharges=.true. and $\delta Q = |[\sum_i q_i| - ((\epsilon-1)/\epsilon)*|Q_M]|>PCMQtotTol$ the polarization charges will be normalized as $q_i^\prime=q_i + signfunction(e, n, \delta Q) (q_i/q_{tot})*\delta Q$ with $q_{tot} = \sum_i q_i$. For values of $\delta Q > 0.5$ (printed by the code in the file pcm/pcm_info.out) even, if polarization charges are renormalized, the calculated results might be inaccurate or erroneous.

Name PCMRadiusScaling
Section Hamiltonian::PCM
Type float

Scales the radii of the spheres used to build the solute cavity surface. The default value depends on the choice of PCMVdWRadii: 1.2 for pcm_vdw_optimized and 1.0 for pcm_vdw_species.

Name PCMRenormCharges
Section Hamiltonian::PCM
Type logical
Default .false.

If .true. renormalization of the polarization charges is performed to enforce fulfillment of the Gauss law, $\sum_i q_i^{e/n} = -[(\epsilon-1)/\epsilon] Q_M^{e/n}$ where $q_i^{e/n}$ are the polarization charges induced by the electrons/nuclei of the molecule and $Q_M^{e/n}$ is the nominal electronic/nuclear charge of the system. This can be needed to treat molecules in weakly polar solvents.

Name PCMSmearingFactor
Section Hamiltonian::PCM
Type float
Default 1.0

Parameter used to control the width (area of each tessera) of the Gaussians used to distribute the polarization charges on each tessera (arXiv:1507.05471). If set to zero, the solvent reaction potential in real-space is defined by using point charges.

Name PCMSolute
Section Hamiltonian::PCM
Type logical
Default yes

This variable is a flag for including polarization effects of the solvent due to the solute. (Useful for analysis) When external fields are applied, turning off the solvent-molecule interaction (PCMSolute=no) and activating the solvent polarization due to the applied field (PCMLocalField=yes) allows to include only local field effects.

Name PCMSpheresOnH
Section Hamiltonian::PCM
Type logical
Default no

If true, spheres centered at the Hydrogens atoms are included to build the solute cavity surface.

Name PCMStaticEpsilon
Section Hamiltonian::PCM
Type float
Default 1.0

Static dielectric constant of the solvent ($\varepsilon_0$). 1.0 indicates gas phase.

Name PCMTDLevel
Section Hamiltonian::PCM
Type integer
Default eq

When CalculationMode=td, PCMTDLevel it sets the way the time-depenendent solvent polarization is propagated.

Options:

• eq:
  If PCMTDLevel=eq, the solvent is always in equilibrium with the solute or the external field, i.e., the solvent polarization follows instantaneously the changes in solute density or in the external field. PCMTDLevel=neq and PCMTDLevel=eom are both nonequilibrium runs.
  
• neq:
  If PCMTDLevel=neq, solvent polarization charges are splitted in two terms: one that follows instantaneously the changes in the solute density or in the external field (dynamical polarization charges), and another that lag behind in the evolution w.r.t. the solute density or the external field (inertial polarization charges).
  
• eom:
  If PCMTDLevel=eom, solvent polarization charges evolves following an equation of motion, generalizing 'neq' propagation. The equation of motion used here depends on the value of PCMEpsilonModel.
  

Name PCMTessMinDistance
Section Hamiltonian::PCM
Type float
Default 0.1

Minimum distance between tesserae. Any two tesserae having smaller distance in the starting tesselation will be merged together.

Name PCMTessSubdivider
Section Hamiltonian::PCM
Type integer
Default 1

Allows to subdivide further each tessera refining the discretization of the cavity tesselation. Can take only two values, 1 or 4. 1 corresponds to 60 tesserae per sphere, while 4 corresponds to 240 tesserae per sphere.

Name PCMUpdateIter
Section Hamiltonian::PCM
Type integer
Default 1

Defines how often the PCM potential is updated during time propagation.

Name PCMVdWRadii
Section Hamiltonian::PCM
Type integer
Default pcm_vdw_optimized

This variable selects which van der Waals radius will be used to generate the solvent cavity.

Options:

• pcm_vdw_optimized:
  Use the van der Waals radius optimized by Stefan Grimme in J. Comput. Chem. 27: 1787-1799, 2006, except for C, N and O, reported in J. Chem. Phys. 120, 3893 (2004).
  
• pcm_vdw_species:
  The vdW radii are set from the share/pseudopotentials/elements file. These values are obtained from Alvarez S., Dalton Trans., 2013, 42, 8617-8636. Values can be changed in the Species block.