From 8106d6ed04f97b7048d6bbd65f598f51f74ea7ba Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 2 Jan 2013 16:52:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9187 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/pair_eff.html | 98 +++++++++++++++++++++++++---------------------- doc/pair_eff.txt | 86 ++++++++++++++++++++++------------------- 2 files changed, 100 insertions(+), 84 deletions(-) diff --git a/doc/pair_eff.html b/doc/pair_eff.html index 5e287f066e..c700843030 100644 --- a/doc/pair_eff.html +++ b/doc/pair_eff.html @@ -15,31 +15,31 @@

pair_style eff/cut cutoff limit_eradius pressure_with_evirials ecp type1 element1 type2 element2 ... typeN elementN

-

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 -

+

Examples:

-

pair_style eff/cut 39.7 +

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
 pair_coeff 1 s 0.320852 2.283269 0.814857 
-pair_coeff 3 22.721015 0.728733 1.103199 17.695345 6.693621 : pre
-

+pair_coeff 3 22.721015 0.728733 1.103199 17.695345 6.693621 
+

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). The eFF for Z<6 was -first introduced by (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. +described in (Jaramillo-Botero). The eFF for Z<6 +was first introduced by (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 @@ -164,17 +164,21 @@ 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. +

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: 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 @@ -190,35 +194,39 @@ partitioning changes, the total energy remains similar).

-

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: +

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:

-

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 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 -/examples/USER/eff/fixed-core). An pseudo-core should be described -with a mass that includes the corresponding nuclear mass, plus all the -core electrons (i.e no outer shell electrons), and a radius equivalent -to that of a corresponding minimized full-electron system. The charge -for a pseudo-core atom should be given by the number of outer shell +

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 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 /examples/USER/eff/fixed-core). An pseudo-core should be +described with a mass that includes the corresponding nuclear mass, +plus all the core electrons (i.e no outer shell electrons), and a +radius equivalent to that of a corresponding minimized full-electron +system. The charge for a pseudo-core atom should be given by the +number of outer shell electrons. +

In general, eFF excels at computing the properties of materials in extreme conditions and tracing the system dynamics over multi-picosend timescales; this is particularly relevant where electron excitations diff --git a/doc/pair_eff.txt b/doc/pair_eff.txt index c79afef59f..cda38f03da 100644 --- a/doc/pair_eff.txt +++ b/doc/pair_eff.txt @@ -15,8 +15,8 @@ pair_style eff/cut cutoff limit_eradius pressure_with_evirials ecp type1 element 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 +type1 ... typeN = LAMMPS atom type +element1 ... element2 = element symbol :ul [Examples:] @@ -27,16 +27,16 @@ pair_style eff/cut 40.0 ecp 1 Si 3 C pair_coeff * * 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 +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 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. +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 @@ -161,17 +161,21 @@ 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. +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: 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 @@ -187,34 +191,38 @@ partitioning changes, the total energy remains similar). :line -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: +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: :c,image(Eqs/eff_ECP1.jpg) :c,image(Eqs/eff_ECP2.jpg) -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 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 -/examples/USER/eff/fixed-core). An pseudo-core should be described -with a mass that includes the corresponding nuclear mass, plus all the -core electrons (i.e no outer shell electrons), and a radius equivalent -to that of a corresponding minimized full-electron system. The charge -for a pseudo-core atom should be given by the number of outer shell +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 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 /examples/USER/eff/fixed-core). An pseudo-core should be +described with a mass that includes the corresponding nuclear mass, +plus all the core electrons (i.e no outer shell electrons), and a +radius equivalent to that of a corresponding minimized full-electron +system. The charge for a pseudo-core atom should be given by the +number of outer shell electrons. + In general, eFF excels at computing the properties of materials in extreme conditions and tracing the system dynamics over multi-picosend timescales; this is particularly relevant where electron excitations