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98
doc/pair_eff.html
View File

@ -13,25 +13,33 @@
</H3>
<P><B>Syntax:</B>
</P>
<P>pair_style eff/cut cutoff eradius_limit_flag pressure_flag
<P>pair_style eff/cut cutoff limit_eradius pressure_with_evirials ecp type1 element1 type2 element2 ... typeN elementN
</P>
<P>cutoff = global cutoff for Coulombic interactions
limit_eradius = limit electron size (optional)
pressure_with_evirials = include electron virials in system pressure (optional)
type1 ... typeN = lammps atom type
element1 ... element2 = element symbol : ul
</P>
<UL><LI>cutoff = global cutoff for Coulombic interactions
<LI>eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
<LI>pressure_flag = 0 or 1 to define the type of pressure calculation (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
<P>pair_style eff/cut 39.7
pair_style eff/cut 40.0 limit_eradius
pair_style eff/cut 40.0 limit_eradius pressure_with_evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff * *
pair_coeff 2 2 20.0
</PRE>
pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 22.721015 0.728733 1.103199 17.695345 6.693621 : pre
</P>
<P><B>Description:</B>
</P>
<P>This pair style contains a LAMMPS implementation of the electron Force
Field (eFF) potential currently under development at Caltech, as
described in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>. The eFF was
first introduced by <A HREF = "#Su">(Su)</A> in 2007.
described in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>. The eFF for Z<6 was
first introduced by <A HREF = "#Su">(Su)</A> in 2007. It has been extended to higher Zs
by using effective core potentials (ECPs) that now cover up to 2nd and 3rd
row p-block elements of the periodic table.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
@ -138,25 +146,36 @@ individual I,J type pair via the <A HREF = "pair_coeff.html">pair_coeff</A> comm
All type pairs use the same global cutoff specified in the pair_style
command.
</P>
<P>The <I>eradius_limit_flag</I> and <I>pressure_flag</I> settings are optional.
Neither or both must be specified. If not specified they are
both set to 0 by default.
<P>The <I>limit_eradius</I> and <I>pressure_with_evirials</I> settings are optional.
Neither or both must be specified. If not specified they are unset.
</P>
<P>The <I>eradius_limit_flag</I> is used to restrain electrons from becoming
unbounded in size at very high temperatures were the Gaussian wave
<P>The <I>limit_eradius</I> is used to restrain electron size from becoming
excessively diffuse at very high temperatures were the Gaussian wave
packet representation breaks down, and from expanding as free
particles to infinite size. A setting of 0 means do not impose this
restraint. A setting of 1 imposes the restraint. The restraining
harmonic potential takes the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2.
particles to infinite size. If unset, electron radius is free to
increase without bounds. If set, a restraining
harmonic potential of the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2, is applied on the electron radius.
</P>
<P>The <I>pressure_flag</I> is used to control between two types of pressure
computation: if set to 0, the computed pressure does not include the
<P>The <I>pressure_with_evirials</I> is used to control between two types of pressure
computation: if unset, the computed pressure does not include the
electronic radial virials contributions to the total pressure (scalar
or tensor). If set to 1, the computed pressure will include the
or tensor). If set, the computed pressure will include the
electronic radial virial contributions to the total pressure (scalar
and tensor).
</P>
<P>The <I>ecp</I> is used to associate an ECP representation for a particular atom type.
The ECP captures the orbital overlap between a core pseudo particle and valence electrons
within the Pauli repulsion. A list of type:element-symbol pairs may be provided for all
ECP representations, after the "ecp" keyword.
</P>
<P>IMPORTANT NOTE: Default ECP parameters are provided for C, N, O, Al, and Si.
Users can modify these using the <I>pair_coeff</I> command as exemplified above.
For this, the User must distinguish between two different functional forms supported,
one that captures the orbital overlap assuming the s-type core interacts with an s-like valence electron (s-s)
and another that assumes the interaction is s-p. For systems that exhibit significant p-character (e.g. C, N, O)
the s-p form is recommended. The "s" ECP form requires 3 parameters and the "p" 5 parameters.
</P>
<P>IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining this pair_style, one (default) that considers
electrons do not contribute radial virial components (i.e. electrons
@ -171,26 +190,25 @@ partitioning changes, the total energy remains similar).
</P>
<HR>
<P>IMPORTANT NOTE: The currently implemented eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6.
Users interested in applying eFF should restrict to systems where
electrons are s-like, or contain p character only insofar as a single
lobe of electron density is shifted away from the nuclear center. See
further details about some of the virtues and current limitations of
the method in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
<P>IMPORTANT NOTE: This implemention of eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6 in "all electron" representations.
For systems with increasingly non-spherical electrons, Users should use the ECP representations.
ECPs are now supported and validated for most of the 2nd and 3rd row elements of the p-block.
Predefined parameters are provided for C, N, O, Al, and Si. The ECP captures the orbital overlap
between the core and valence electrons (i.e. Pauli repulsion) with one of the functional forms:
</P>
<P>Work is underway to extend the eFF to higher Z elements with
increasingly non-spherical electrons (p-block and d-block), to provide
explicit terms for electron correlation/exchange, and to improve its
computational efficiency via atom models with fixed 2 s core electrons
and atom models represented as pseudo-cores plus valence electrons.
<CENTER><IMG SRC = "Eqs/eff_ECP1.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_ECP2.jpg">
</CENTER>
<P>Where the 1st form correspond to core interactions with s-type valence electrons
and the 2nd to core interactions with p-type valence electrons.
</P>
<P>The current version adds support for models with fixed-core and
effective pseudo-core (i.e. effective core pseudopotentials, ECP)
<P>The current version adds full support for models with fixed-core and ECP
definitions. to enable larger timesteps (i.e. by avoiding the high
frequency vibrational modes -translational and radial- of the 2 s
electrons), and in the ECP case to reduce the p-character effects in
higher Z elements (e.g. Silicon). A fixed-core should be defined with
electrons), and in the ECP case to reduce the increased orbital complexity in higher Z elements (up to Z<18).
A fixed-core should be defined with
a mass that includes the corresponding nuclear mass plus the 2 s
electrons in atomic mass units (2x5.4857990943e-4), and a radius
equivalent to that of minimized 1s electrons (see examples under
@ -271,7 +289,7 @@ atoms.
</P>
<P><B>Default:</B>
</P>
<P>If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
<P>If not specified, limit_eradius = 0 and pressure_with_evirials = 0.
</P>
<HR>

89
doc/pair_eff.txt
View File

@ -10,25 +10,33 @@ pair_style eff/cut command :h3
[Syntax:]
pair_style eff/cut cutoff eradius_limit_flag pressure_flag
pair_style eff/cut cutoff limit_eradius pressure_with_evirials ecp type1 element1 type2 element2 ... typeN elementN
cutoff = global cutoff for Coulombic interactions
eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
pressure_flag = 0 or 1 to define the type of pressure calculation (optional) :ul
limit_eradius = limit electron size (optional)
pressure_with_evirials = include electron virials in system pressure (optional)
type1 ... typeN = lammps atom type
element1 ... element2 = element symbol : ul
[Examples:]
pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
pair_style eff/cut 40.0 limit_eradius
pair_style eff/cut 40.0 limit_eradius pressure_with_evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff * *
pair_coeff 2 2 20.0 :pre
pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 22.721015 0.728733 1.103199 17.695345 6.693621 : pre
[Description:]
This pair style contains a LAMMPS implementation of the electron Force
Field (eFF) potential currently under development at Caltech, as
described in "(Jaramillo-Botero)"_#Jaramillo-Botero. The eFF was
first introduced by "(Su)"_#Su in 2007.
described in "(Jaramillo-Botero)"_#Jaramillo-Botero. The eFF for Z<6 was
first introduced by "(Su)"_#Su in 2007. It has been extended to higher Zs
by using effective core potentials (ECPs) that now cover up to 2nd and 3rd
row p-block elements of the periodic table.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
@ -135,25 +143,36 @@ individual I,J type pair via the "pair_coeff"_pair_coeff.html command.
All type pairs use the same global cutoff specified in the pair_style
command.
The {eradius_limit_flag} and {pressure_flag} settings are optional.
Neither or both must be specified. If not specified they are
both set to 0 by default.
The {limit_eradius} and {pressure_with_evirials} settings are optional.
Neither or both must be specified. If not specified they are unset.
The {eradius_limit_flag} is used to restrain electrons from becoming
unbounded in size at very high temperatures were the Gaussian wave
The {limit_eradius} is used to restrain electron size from becoming
excessively diffuse at very high temperatures were the Gaussian wave
packet representation breaks down, and from expanding as free
particles to infinite size. A setting of 0 means do not impose this
restraint. A setting of 1 imposes the restraint. The restraining
harmonic potential takes the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2.
particles to infinite size. If unset, electron radius is free to
increase without bounds. If set, a restraining
harmonic potential of the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2, is applied on the electron radius.
The {pressure_flag} is used to control between two types of pressure
computation: if set to 0, the computed pressure does not include the
The {pressure_with_evirials} is used to control between two types of pressure
computation: if unset, the computed pressure does not include the
electronic radial virials contributions to the total pressure (scalar
or tensor). If set to 1, the computed pressure will include the
or tensor). If set, the computed pressure will include the
electronic radial virial contributions to the total pressure (scalar
and tensor).
The {ecp} is used to associate an ECP representation for a particular atom type.
The ECP captures the orbital overlap between a core pseudo particle and valence electrons
within the Pauli repulsion. A list of type:element-symbol pairs may be provided for all
ECP representations, after the "ecp" keyword.
IMPORTANT NOTE: Default ECP parameters are provided for C, N, O, Al, and Si.
Users can modify these using the {pair_coeff} command as exemplified above.
For this, the User must distinguish between two different functional forms supported,
one that captures the orbital overlap assuming the s-type core interacts with an s-like valence electron (s-s)
and another that assumes the interaction is s-p. For systems that exhibit significant p-character (e.g. C, N, O)
the s-p form is recommended. The "s" ECP form requires 3 parameters and the "p" 5 parameters.
IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining this pair_style, one (default) that considers
electrons do not contribute radial virial components (i.e. electrons
@ -168,26 +187,24 @@ partitioning changes, the total energy remains similar).
:line
IMPORTANT NOTE: The currently implemented eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6.
Users interested in applying eFF should restrict to systems where
electrons are s-like, or contain p character only insofar as a single
lobe of electron density is shifted away from the nuclear center. See
further details about some of the virtues and current limitations of
the method in "(Jaramillo-Botero)"_#Jaramillo-Botero.
IMPORTANT NOTE: This implemention of eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6 in "all electron" representations.
For systems with increasingly non-spherical electrons, Users should use the ECP representations.
ECPs are now supported and validated for most of the 2nd and 3rd row elements of the p-block.
Predefined parameters are provided for C, N, O, Al, and Si. The ECP captures the orbital overlap
between the core and valence electrons (i.e. Pauli repulsion) with one of the functional forms:
Work is underway to extend the eFF to higher Z elements with
increasingly non-spherical electrons (p-block and d-block), to provide
explicit terms for electron correlation/exchange, and to improve its
computational efficiency via atom models with fixed 2 s core electrons
and atom models represented as pseudo-cores plus valence electrons.
:c,image(Eqs/eff_ECP1.jpg)
:c,image(Eqs/eff_ECP2.jpg)
The current version adds support for models with fixed-core and
effective pseudo-core (i.e. effective core pseudopotentials, ECP)
Where the 1st form correspond to core interactions with s-type valence electrons
and the 2nd to core interactions with p-type valence electrons.
The current version adds full support for models with fixed-core and ECP
definitions. to enable larger timesteps (i.e. by avoiding the high
frequency vibrational modes -translational and radial- of the 2 s
electrons), and in the ECP case to reduce the p-character effects in
higher Z elements (e.g. Silicon). A fixed-core should be defined with
electrons), and in the ECP case to reduce the increased orbital complexity in higher Z elements (up to Z<18).
A fixed-core should be defined with
a mass that includes the corresponding nuclear mass plus the 2 s
electrons in atomic mass units (2x5.4857990943e-4), and a radius
equivalent to that of minimized 1s electrons (see examples under
@ -268,7 +285,7 @@ atoms.
[Default:]
If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
If not specified, limit_eradius = 0 and pressure_with_evirials = 0.
:line