*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***
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INPUT FILE DESCRIPTION
Program: pw.x / Environ / Quantum Espresso
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Input data format: { } = optional, [ ] = it depends, | = or
All quantities whose dimensions are not explicitly specified are in
RYDBERG ATOMIC UNITS
BEWARE: TABS, DOS CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE
Comment lines in namelists can be introduced by a "!", exactly as in fortran
code. Comments lines in ``cards'' can be introduced by either a "!" or a "#"
character in the first position of a line.
With the notable exception of periodic boundary correction schemes, environment
effects are controlled by the following keywords specified in a separate
environ.in input file.
PBC correction schemes are defined via the assume_isolated keyword in the
standard pw input file. In addition to the standard values, assume_isolated can
be set to the following Environ-related options:
assume_isolated .EQ. 'slabx|slaby|slabz' : slab boundary conditions, quadratic
correction to the electrostatic potential, to remove pbc
artifacts due to charged or dipolar slabs
assume_isolated .EQ. 'pcc' : point-countercharge correction, quadratic
correction to the electrostatic potential for isolated systems,
similar results to Makov-Payne
Structure of the environ.in input file:
===============================================================================
&Environ
...
/
========================================================================
NAMELIST: &Environ
THIS NAMELIST IS ALWAYS NEEDED !
+--------------------------------------------------------------------
Variable: environ_type
Type: CHARACTER
Default: 'input'
Description: Set up all of the environment flags according to predefined types:
'input':
Do not use predefined types, read the flags of the different contribution from input
or use the defauls values (which correspond to no contributions).
'vacuum':
All environment contributions (except PBC corrections) are turned off
'water':
Set up the optimized SCCS model for water solvation, including
continuum dielectric effects ( env_static_permittivity = 78.3 ) and
non-electrostatic contributions modelled via pressure ( env_pressure = -0.35 GPa )
and surface tension ( env_surface_tension = 50 dyn/cm ) effects. Cavity parameters
are also set to the optimal values ( rhomax = 0.005; rhomin = 0.0001) derived in
O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136 064102 (2012)
'water-cation':
Set up the SCCS model tuned for water solvation of cations, according to
optimal set of parameters ( env_static_permittivity = 78.3; env_pressure = 0.125 GPa;
env_static_permittivity = 5.0 dyn/cm; rhomax = 0.0035; rhomin = 0.0002 ) derived in
C. Dupont, O. Andreussi and N. Marzari, J. Chem. Phys. 139, 214110 (2013)
'water-anion':
Set up the SCCS model tuned for water solvation of anions, according to
optimal set of parameters ( env_static_permittivity = 78.3; env_pressure = 0.0 GPa;
env_static_permittivity = 0.45 dyn/cm; rhomax = 0.0155; rhomin = 0.0024 ) derived in
C. Dupont, O. Andreussi and N. Marzari, J. Chem. Phys. 139, 214110 (2013)
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: verbose
Type: INTEGER
Default: 0
Description: Control the amount of output written to specific output files, mostly useful for debugging purposes
verbose .EQ. 0 minimal information written to standard output
verbose .EQ. 1 additional information written to environ.debug file
verbose .EQ. 2 dumping of main physical quantities on the real-space grid in the form of
*.cube files
verbose .GE. 3 dumping of several intermediate physical quantites on the real-space grid
as this is done at every SCF step it will slow down the calculation significantly
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: environ_thr
Type: REAL
Default: 1.d-1
Description: Only include/update environment contributions when SCF accuracy is below this threshold.
Since the environment region is defined in terms of the electronic density, the test is done
in order to avoid computing unphysical environment contributions, usually to skip the
environ calculation during the first couple of SCF step.
IMPORTANT: as the SCF accuracy is an extensive property (increases with the number of electrons in
the system), the optimal environ_thr will also vary with system size.
Status: IMPORTANT. The default value is only valid for small systems, while is too conservative for larger systems
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: stype
Type: INTEGER
Default: 1
Description: The shape of the environment region is defined according to a specific switching function of the electronic
density:
stype .EQ. 0 : Original switching function from Fattebert and Gygi.
Requires two parameters: rhomax and tbeta
stype .EQ. 1 : Optimally smooth switching function from the SCCS method of Andreussi et al.
Requires two parameters: rhomax and rhomin
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: rhomax
Type: REAL
Default: 0.005
Description: First parameter of the sw function, roughly corresponding to the density threshold of the solvation model
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: rhomin
Type: REAL
Default: 0.0001
Description: Second parameter of the sw function when stype=1
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: tbeta
Type: REAL
Default: 4.8
Description: Second parameter of the sw function when stype=0
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: env_static_permittivity
Type: REAL
Default: 1.D0
Description: Static dielectric permittivity of the elctrostatic part of the solvation model.
This keyword (like all the env_* keywords) is also the flag which controls the activation
of the specific contribution: if set equal to one (=vacuum) no dielectric effects from the environment.
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: env_optical_permittivity
Type: REAL
Default: 1.D0
Description: Optical dielectric permittivity of the continuum environment, only needed for TDDFPT calculations.
If set equal to one (=vacuum) no dielectric effects in linear response calculations.
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: eps_mode
Type: CHARACTER
Default: 'electronic'
Description: Choice of the density that controls the shape of the environment region
for the calculation of the dielectric effects (all other effects are
defined on the electronic density alone)
'electronic': dielectric depends self-consist. on electronic density
'ionic': dielectric defined on a fictitious ionic density, generated
as the sum of exponential functions centered on atomic
positions of width specified in input by solvationrad(ityp)
'full': similar to electronic, but an extra density is added to
represent the core electrons and the nuclei. This extra
density is defined as the sum of gaussian functions centered
on atomic positions of width equal to atomicspread(ityp)
'external': dielectric defined on the electronic density plus an
additional fictitious density defined by the neutral
external charges
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: solvationrad(i), i=1,ntyp
Type: REAL
Default: 3.0
Description: Only used if eps_mode .EQ. ionic (see eps_mode)
Each atom type has a corresponding radius, which controls the shape of the dielectric region,
according to the model of
V. M. Sanchez, M. Sued and D. A. Scherlis, J. Chem. Phys. 131, 174108 (2009)
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: atomicspread(i), i=1,ntyp
Type: REAL
Default: 0.5
Description: In the calculation of electrostatic interactions in the continuum
dielectric environment, ionic charge densities are modelled as gaussians of fixed spread,
as specified by atomicspread(ityp) for each atomic type.
Results are identical to using point-like charges (as is usually done in PW), unless the gaussian
spreads are too large. The default value of 0.5 a.u. was derived to be safe enough in most
common atom types. A too small value may require larger density cutoffs (ecutrho).
IMPORTANT: atomicspread is also used, in combination with eps_mode .EQ. 'full' to fix problems
in the definition of the dielectric region due to missing core electrons. In this case, the
fictitious ionic density given by the sum of all atomic gaussians is added to the electronic
density in the calculation of the dielectric function.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: add_jellium
Type: LOGICAL
Default: .FALSE.
Description: Control if jellium polarization is included in the calculation of dielectric environment effects on
charged solutes. The jellium contribution, although it formally needs to be considered, is a PBC
artifact and needs to be removed when applying periodic boundary correction schemes. Thus, in any
reasonable simulation there is no need to explicitly include the jellium contribution.
Status: OBSOLETE
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: mixtype
Type: CHARACTER
Default: 'linear'
Description: Internal mixing schemes for the polarization density:
'linear': linear mixing, usually good enough.
'anderson': Anderson mixing, local implementation, working but not carefully tested.
'diis': Pulay's Direct Inversion in Iterative Subspace (DIIS) method, local implementation,
working but not carefully tested.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: mixrhopol
Type: REAL
Default: 0.5
Description: Linear mixing parameter, usually does not affect results (and it shouldn't) and does not
affect performances, large values work fine in most common applications.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: tolrhopol
Type: REAL
Default: 1.D-10
Description: Accuracy on polarization charge iterations: higher accuracies will require more polarization cycles,
but will ensure smoother SCF convergece. As polarization iterations are usually cheaper than SCF cycles,
it is recommended to increase polarization accuracy whenever the SCF has problems converging.
Values of tolrhopol up to 1.D-13 are plausible for difficult systems. (NOTE that too low density cutoffs
may also play a role in poor SCF convergece).
Status: IMPORTANT
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: ndiis
Type: INTEGER
Default: 1
Description: If using DIIS as mixing scheme for polarization density ( mixtype .EQ. 'diis' ), ndiis controls the
dimension of the iterative subspace. New guess for the density keeps track of the previous ndiis guesses.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: env_surface_tension
Type: REAL
Default: 0.D0
Description: Surface tension (gamma) of the environment in CGS units dyn/cm.
This keyword controls the activation of the surface-dependent contribution to the solute's Hamiltonian (gamma*S):
if set equal to 0.D0 no surface contribution from the environment.
This contribution may be straighforwardly used to compute cavitation free energies, as proposed by Scherlis et al. in
J. Chem. Phys. 124, 074103 (2006). NOTE that the current implementation uses an improved definition of the
quantum-surface O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136 064102 (2012).
This contribution can also be used as a simplified approach to the more general non-electrostatic contributions
to solvation, as in the SCCS approach. In this second case, env_surface_tension needs not to correspond to the
real surface tension of the solvent, but is used as a fitting parameter.
See O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136 064102 (2012)
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: delta
Type: REAL
Default: 0.00001D0
Description: Finite difference numerical parameter used in the calculation of the quantum surface of the solute
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: env_pressure
Type: REAL
Default: 0.D0
Description: External pressure (P) of the environment in GPa.
This keyword controls the activation of the volume-dependet contribution to the solute's Hamiltonian (P*V):
if set equal to 0.D0 no volume contribution from the environment.
This contribution may be straightforwardly used to compute the electronic entalpy, i.e. to model finite systems
under pressure, as proposed by M. Cococcioni et al. in Phys. Rev. Lett. 94, 145501 (2005).
This contribution can also be used as a simplified approach to more complex and general non-electrostatic contributions
to solvation, as in the SCCS approach. In this second case, env_pressure needs not correspond to the real external
pressure of the environment, but is used as a fitting parameter (and can assume negative values).
See O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136 064102 (2012)
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: env_extcharge_n
Type: INTEGER
Default: 0
Description: Number of fixed external charges. This keyword controls how many fixed external densities of charge need to be
included in the simulation box. Shape, position and amount of charge of each external density needs to be specified
with the appropriate extcharge_* keywords.
Status: REQUIRED
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_origin(1:3)
Type: REAL
Default: 0.D0 0.D0 0.D0
Description: Placement of external charge densities is done with respect to this origin of coordinates. If no origin is
specified, assume as origin the center of ionic charge (it may introduce artifacts for geometry optimizations)
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_dim(i), i=1,nextchg
Type: INTEGER
Default: 0
Description: Dimensionality of the i-th external charge density.
dim .EQ. 0 : point-like (actually gaussian shaped) charge density
dim .EQ. 1 : linear (gaussian spreaded) charge density
dim .EQ. 2 : planar (gaussian spreaded) charge density
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_axis(i), i=1,nextchg
Type: INTEGER
Default: 1
Description: Axis of the i-th external charge density.
if dim.EQ.0 : axis has no meaning/use
if dim.EQ.1 : axis identifies the direction of the linear
charge density: axis.EQ.1|2|3 means lines along x|y|z respectively
if dim.EQ.2 : axis identifies the direction ortogonal to the planar
charge density: axis.EQ.1|2|3 means planes ortogonal to x|y|z
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_spread(i), i=1,nextchg
Type: REAL
Default: 0.5D0
Description: Spread of the i-th external charge density, assuming gaussian shapes in 1-2-3 dimensions
are used.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_charge(i), i=1,nextchg
Type: REAL
Default: 0.D0
Description: Total charge of the i-th external charge density in the unit cell. If the external charge is specified
as neutral, it does not affect the electrostatics of the system, but the external density can still
be used to define artificial regions where the dielectric continuum is excluded
(using the eps_mode = 'external' option)
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: extcharge_pos(1:3,iext)
Type: REAL
Default: 0.0 0.0 0.0
Description: Position (i=1,3) of the i-th (iext) external charge density, computed with respect to the origin specified by
extcharge_origin. For dim .EQ. 0|1|2 one needs to specify 3|2|1 coordinates.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: ifdtype
Type: INTEGER
Default: 1
Description: The gradient of the dielectric function is computed in real-space using finite differences.
Different finite differences schemes have been implemented following
P. Holoborodko, Smooth noise robust differentiators, 2008
http://www.holoborodko.com/pavel/numerical-methods/numerical-derivative/smooth-low-noise-differentiators
Each scheme can exploit different numbers of points of the real-space grid (as defined by nfdpoint).
ifdtype .EQ. 1 : Central differences
ifdtype .EQ. 2 : Low-noise Lanczos (m=2)
ifdtype .EQ. 3 : Low-noise Lanczos (m=4)
ifdtype .EQ. 4 : Smooth noise-robust (n=2)
ifdtype .EQ. 5 : Smooth noise-robust (n=4)
Central differences are used by default and have been tested more deeply. The other schemes work fine,
but are not deeply tested in terms of performances.
Status: OPTIONAL
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: nfdpoint
Type: INTEGER
Default: 1
Description: Number of point from the real-space grid, to be used by the different finite-difference schemes to compute gradients.
Number of points = 2 * nfdpoint + 1
e.g. ifdtype.EQ.1 .AND. nfdpoint.EQ.1 correspond to central differences with three points
IMPORTANT: nfdpoint .EQ. 1 seems to be enough for most applications, but more refinied finite-difference schemes are
needed (nfdpoint.EQ.2 is enough) for energy conservation in MD simulations in continuum dielectric.
See test case reported in O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136 064102 (2012)
Status: IMPORTANT
+--------------------------------------------------------------------
===END OF NAMELIST======================================================