Commit 944289b0 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

final version of pair vashishta/table

parent 956af8ce

doc/html/pair_vashishta.html

+16 −19
Original line number Diff line number Diff line
@@ -145,12 +145,8 @@ pair_style style args 
<li>args = list of arguments for a particular style</li>

</ul>

<pre class="literal-block">

<em>vashishta</em> args = none

<em>vashishta/omp</em> args = none

<em>vashishta/table</em> args = Ntable cutinner

  Ntable = # of tabulation points

  cutinner = tablulate from cutinner to cutoff

<em>vashishta/table/omp</em> args = Ntable cutinner

<em>vashishta</em> or <em>vashishta/omp</em> args = none

<em>vashishta/table</em> or <em>vashishta/table/omp</em> args = Ntable cutinner

  Ntable = # of tabulation points

  cutinner = tablulate from cutinner to cutoff

</pre>
@@ -169,13 +165,13 @@ pair_coeff * * SiC.vashishta Si C 
<div class="section" id="description">

<h2>Description</h2>

<p>The <em>vashishta</em> and <em>vashishta/table</em> styles compute the combined

2-body and 3-body family of potentials developed in the group of

Vashishta and co-workers. By combining repulsive, screened Coulombic,

screened charge-dipole, and dispersion interactions with a bond-angle

energy based on the Stillinger-Weber potential, this potential has

been used to describe a variety of inorganic compounds, including SiO2

<a class="reference internal" href="#vashishta1990"><span class="std std-ref">Vashishta1990</span></a>, SiC <a class="reference internal" href="#vashishta2007"><span class="std std-ref">Vashishta2007</span></a>,

and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.</p>

2-body and 3-body family of potentials developed in the group of Priya

Vashishta and collaborators.  By combining repulsive, screened

Coulombic, screened charge-dipole, and dispersion interactions with a

bond-angle energy based on the Stillinger-Weber potential, this

potential has been used to describe a variety of inorganic compounds,

including SiO2 <a class="reference internal" href="#vashishta1990"><span class="std std-ref">Vashishta1990</span></a>, SiC

<a class="reference internal" href="#vashishta2007"><span class="std std-ref">Vashishta2007</span></a>, and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.</p>

<p>The potential for the energy U of a system of atoms is</p>

<img alt="_images/pair_vashishta.jpg" class="align-center" src="_images/pair_vashishta.jpg" />

<p>where we follow the notation used in <a class="reference internal" href="#branicio2009"><span class="std std-ref">Branicio2009</span></a>.
@@ -323,16 +319,17 @@ script that reads a restart file.</p> 
<hr class="docutils" />

<div class="section" id="restrictions">

<h2>Restrictions</h2>

<p>This pair style is part of the MANYBODY package.  It is only enabled

if LAMMPS was built with that package (which it is by default).  See

the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>

<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be &#8220;on&#8221;

<p>These pair style are part of the MANYBODY package.  They is only

enabled if LAMMPS was built with that package (which it is by

default).  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section

for more info.</p>

<p>These pair styles requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be &#8220;on&#8221;

for pair interactions.</p>

<p>The Vashishta potential files provided with LAMMPS (see the potentials

directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.  You can

use the Vashishta potential with any LAMMPS units, but you would need

to create your own Vashishta potential file with coefficients listed

in the appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>

to create your own potential file with coefficients listed in the

appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>

</div>

<div class="section" id="related-commands">

<h2>Related commands</h2>

doc/src/pair_vashishta.txt

+16 −20
Original line number Diff line number Diff line
@@ -17,12 +17,8 @@ pair_style style args :pre 


style = {vashishta} or {vashishta/table} or {vashishta/omp} or {vashishta/table/omp}

args = list of arguments for a particular style :ul

  {vashishta} args = none

  {vashishta/omp} args = none

  {vashishta/table} args = Ntable cutinner

    Ntable = # of tabulation points

    cutinner = tablulate from cutinner to cutoff

  {vashishta/table/omp} args = Ntable cutinner

  {vashishta} or {vashishta/omp} args = none

  {vashishta/table} or {vashishta/table/omp} args = Ntable cutinner

    Ntable = # of tabulation points

    cutinner = tablulate from cutinner to cutoff :pre
@@ -37,13 +33,13 @@ pair_coeff * * SiC.vashishta Si C :pre 
[Description:]



The {vashishta} and {vashishta/table} styles compute the combined

2-body and 3-body family of potentials developed in the group of

Vashishta and co-workers. By combining repulsive, screened Coulombic,

screened charge-dipole, and dispersion interactions with a bond-angle

energy based on the Stillinger-Weber potential, this potential has

been used to describe a variety of inorganic compounds, including SiO2

"Vashishta1990"_#Vashishta1990, SiC "Vashishta2007"_#Vashishta2007,

and InP "Branicio2009"_#Branicio2009.

2-body and 3-body family of potentials developed in the group of Priya

Vashishta and collaborators.  By combining repulsive, screened

Coulombic, screened charge-dipole, and dispersion interactions with a

bond-angle energy based on the Stillinger-Weber potential, this

potential has been used to describe a variety of inorganic compounds,

including SiO2 "Vashishta1990"_#Vashishta1990, SiC

"Vashishta2007"_#Vashishta2007, and InP "Branicio2009"_#Branicio2009.



The potential for the energy U of a system of atoms is
@@ -215,18 +211,19 @@ This pair style can only be used via the {pair} keyword of the 


[Restrictions:]



This pair style is part of the MANYBODY package.  It is only enabled

if LAMMPS was built with that package (which it is by default).  See

the "Making LAMMPS"_Section_start.html#start_3 section for more info.

These pair style are part of the MANYBODY package.  They is only

enabled if LAMMPS was built with that package (which it is by

default).  See the "Making LAMMPS"_Section_start.html#start_3 section

for more info.



This pair style requires the "newton"_newton.html setting to be "on"

These pair styles requires the "newton"_newton.html setting to be "on"

for pair interactions.



The Vashishta potential files provided with LAMMPS (see the potentials

directory) are parameterized for metal "units"_units.html.  You can

use the Vashishta potential with any LAMMPS units, but you would need

to create your own Vashishta potential file with coefficients listed

in the appropriate units if your simulation doesn't use "metal" units.

to create your own potential file with coefficients listed in the

appropriate units if your simulation doesn't use "metal" units.



[Related commands:]
@@ -247,4 +244,3 @@ J. P. Rino. J. Appl. Phys. 101, 103515 (2007). 
:link(Branicio2009)

[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed

Matter 21 (2009) 095002

examples/vashishta/in.vashishta.inp

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+75 −0
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# calculate the energy volume curve for InP zincblende



# define volume range and filename



variable	ndelta equal 100

variable	volatom_min equal 20.0

variable	volatom_max equal 29.0

variable	evsvolfile string evsvol.dat



# set up cell 



units		metal

 

boundary	p p p



# setup loop variables for box volume



variable	amin equal ${volatom_min}^(1/3)*2

variable 	delta equal (${volatom_max}-${volatom_min})/${ndelta} 

variable	scale equal (${delta}/v_volatom+1)^(1/3)



# set up 8 atom InP zincblende unit cell



lattice diamond ${amin}



region		box prism &

	 	0 1 &

		0 1 &

		0 1 &

		0 0 0



create_box	2 box



create_atoms	1	box       &

			basis 5 2 &

			basis 6 2 &

			basis 7 2 &

			basis 8 2



mass 		1 114.76

mass 		2 30.98



# choose potential



pair_style	vashishta

pair_coeff 	* * InP.vashishta In P



# setup neighbor style



neighbor 	1.0 nsq

neigh_modify 	once no every 1 delay 0 check yes



# setup output



thermo_style 	custom step temp pe press vol

thermo_modify 	norm no

variable 	volatom equal vol/atoms

variable 	eatom equal pe/atoms

print 		"# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}



# loop over range of volumes



label 		loop

variable 	i loop ${ndelta}



change_box 	all x scale ${scale} y scale ${scale} z scale ${scale} remap



# calculate energy

# no energy minimization needed for zincblende

 

run 		0

print 		"${volatom} ${eatom}" append ${evsvolfile}



next 		i

jump 		SELF loop

examples/vashishta/in.vashishta.sio2

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+28 −0
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# test Vashishta potential for quartz



units		metal

boundary	p p p



atom_style	atomic



read_data	data.quartz



replicate       4 4 4

velocity	all create 2000.0 277387 mom yes

displace_atoms	all move 0.05 0.9 0.4 units box



pair_style 	vashishta

pair_coeff	* *  SiO.1990.vashishta Si O



neighbor	0.3 bin

neigh_modify	delay 10



fix		1 all nve

thermo		10

timestep	0.001



#dump		1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz

#dump_modify	1 element Si O



run		100

examples/vashishta/in.vashishta.table.inp

0 → 100644
+75 −0
Original line number Diff line number Diff line 
# calculate the energy volume curve for InP zincblende



# define volume range and filename



variable	ndelta equal 100

variable	volatom_min equal 20.0

variable	volatom_max equal 29.0

variable	evsvolfile string evsvol.dat



# set up cell 



units		metal

 

boundary	p p p



# setup loop variables for box volume



variable	amin equal ${volatom_min}^(1/3)*2

variable 	delta equal (${volatom_max}-${volatom_min})/${ndelta} 

variable	scale equal (${delta}/v_volatom+1)^(1/3)



# set up 8 atom InP zincblende unit cell



lattice diamond ${amin}



region		box prism &

	 	0 1 &

		0 1 &

		0 1 &

		0 0 0



create_box	2 box



create_atoms	1	box       &

			basis 5 2 &

			basis 6 2 &

			basis 7 2 &

			basis 8 2



mass 		1 114.76

mass 		2 30.98



# choose potential



pair_style 	vashishta/table 100000 0.2

pair_coeff 	* * InP.vashishta In P



# setup neighbor style



neighbor 	1.0 nsq

neigh_modify 	once no every 1 delay 0 check yes



# setup output



thermo_style 	custom step temp pe press vol

thermo_modify 	norm no

variable 	volatom equal vol/atoms

variable 	eatom equal pe/atoms

print 		"# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}



# loop over range of volumes



label 		loop

variable 	i loop ${ndelta}



change_box 	all x scale ${scale} y scale ${scale} z scale ${scale} remap



# calculate energy

# no energy minimization needed for zincblende

 

run 		0

print 		"${volatom} ${eatom}" append ${evsvolfile}



next 		i

jump 		SELF loop

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