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7
doc/Section_commands.html
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@ -339,7 +339,8 @@ of each style or click on the style itself for a full description:
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_smd.html">smd</A>
<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale</A>
</TD></TR></TABLE></DIV>
<HR>
@ -363,7 +364,7 @@ each style or click on the style itself for a full description:
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A>
</TD></TR></TABLE></DIV>
<HR>
@ -397,7 +398,7 @@ potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A>
</TD></TR></TABLE></DIV>
<HR>

17
doc/Section_commands.txt
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@ -464,7 +464,14 @@ These are fix styles contributed by users, which can be used if
"atc"_fix_atc.html,
"imd"_fix_imd.html,
"smd"_fix_smd.html :tb(c=4,ea=c)
"langevin/eff"_fix_langevin_eff.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"smd"_fix_smd.html,
"temp/rescale"_fix_temp_rescale_eff.html :tb(c=6,ea=c)
:line
@ -519,7 +526,12 @@ each style or click on the style itself for a full description:
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"ackland/atom"_compute_ackland_atom.html :tb(c=6,ea=c)
"ackland/atom"_compute_ackland_atom.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html :tb(c=6,ea=c)
:line
@ -600,6 +612,7 @@ These are pair styles contributed by users, which can be used if
"cg/cmm/coul/cut"_pair_cmm.html,
"cg/cmm/coul/long"_pair_cmm.html,
"eam/cd"_pair_eam.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html :tb(c=4,ea=c)
:line

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@ -45,8 +45,8 @@ above.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>damage/atom</I> style is part of the "peri" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
<P>This compute is part of the "peri" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

4
doc/compute_damage_atom.txt
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@ -42,8 +42,8 @@ above.
[Restrictions:]
The {damage/atom} style is part of the "peri" package. It is only
enabled if LAMMPS was built with that package. See the "Making
This compute is part of the "peri" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

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@ -0,0 +1,82 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute ke/atom/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/atom/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/atom/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/atom/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom translational
(nuclei and electrons) and radial kinetic energy (electron only) in a
group. The particles are assumed to be nuclei and electrons modeled
with the <A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
<I>ke</I> keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.
</P>
<P>IMPORTANT NOTE: The temperature in eFF should be monitored via the
<A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be printed
with thermodynamic output by using the
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,77 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ke/atom/eff command :h3
[Syntax:]
compute ID group-ID ke/atom/eff :pre
ID, group-ID are documented in "compute"_compute.html command
ke/atom/eff = style name of this compute command :ul
[Examples:]
compute 1 all ke/atom/eff :pre
[Description:]
Define a computation that calculates the per-atom translational
(nuclei and electrons) and radial kinetic energy (electron only) in a
group. The particles are assumed to be nuclei and electrons modeled
with the "electronic force field"_pair_eff.html.
The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the {ke} or {etotal}
keyword used in thermodynamic output, as specified by the
"thermo_style"_thermo_style.html command. For this compute, kinetic
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
{ke} keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.
IMPORTANT NOTE: The temperature in eFF should be monitored via the
"compute temp/eff"_compute_temp_eff.html command, which can be printed
with thermodynamic output by using the
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"dump custom"_dump.html
[Default:] none

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@ -0,0 +1,83 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute ke/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
<A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
s^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the <I>ke</I> keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the <A HREF = "compute_temp_eff.html">compute
temp_eff</A> command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.
</P>
<P>IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the <A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be
printed with thermodynamic output by using the
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>See <A HREF = "compute_temp_eff.html">compute temp/eff</A>.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ke/eff command :h3
[Syntax:]
compute ID group-ID ke/eff :pre
ID, group-ID are documented in "compute"_compute.html command
ke/eff = style name of this compute command :ul
[Examples:]
compute 1 all ke/eff :pre
[Description:]
Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
"electronic force field"_pair_eff.html.
The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
s^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the {ke} or {etotal}
keyword used in thermodynamic output, as specified by the
"thermo_style"_thermo_style.html command. For this compute, kinetic
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the {ke} keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the "compute
temp_eff"_compute_temp_eff.html command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.
IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the "compute temp/eff"_compute_temp_eff.html command, which can be
printed with thermodynamic output by using the
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
See "compute temp/eff"_compute_temp_eff.html.
[Output info:]
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:] none
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/deform/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/deform/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/deform/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute myTemp all temp/deform/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons using the electron force field, after subtracting
out a streaming velocity induced by the simulation box changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the <A HREF = "fix_deform_eff.html">fix
deform/eff</A> command. A compute of this style is
created by the <A HREF = "fix_nvt_sllod_eff.html">fix nvt/sllod/eff</A> command to
compute the thermal temperature of atoms for thermostatting purposes.
A compute of this style can also be used by any command that computes
a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_nh.html">fix
npt/eff</A>, etc.
</P>
<P>The calculation performed by this compute is exactly like that
described by the <A HREF = "compute_temp_deform.html">compute temp/deform</A>
command, except that the formula for the temperature includes the
radial electron velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
temp/eff</A> command. Note that only the
translational degrees of freedom for each nuclei or electron are
affected by the streaming velocity adjustment. The radial velocity
component of the electrons is not affected.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform_eff.html">fix
deform/eff</A>, <A HREF = "fix_nvt_sllod_eff.html">fix
nvt/sllod/eff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,72 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/deform/eff command :h3
[Syntax:]
compute ID group-ID temp/deform/eff :pre
ID, group-ID are documented in "compute"_compute.html command
temp/deform/eff = style name of this compute command :ul
[Examples:]
compute myTemp all temp/deform/eff :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons using the electron force field, after subtracting
out a streaming velocity induced by the simulation box changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the "fix
deform/eff"_fix_deform_eff.html command. A compute of this style is
created by the "fix nvt/sllod/eff"_fix_nvt_sllod_eff.html command to
compute the thermal temperature of atoms for thermostatting purposes.
A compute of this style can also be used by any command that computes
a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
npt/eff"_fix_nh.html, etc.
The calculation performed by this compute is exactly like that
described by the "compute temp/deform"_compute_temp_deform.html
command, except that the formula for the temperature includes the
radial electron velocity contributions, as discussed by the "compute
temp/eff"_compute_temp_eff.html command. Note that only the
translational degrees of freedom for each nuclei or electron are
affected by the streaming velocity adjustment. The radial velocity
component of the electrons is not affected.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"compute temp/ramp"_compute_temp_ramp.html, "fix
deform/eff"_fix_deform_eff.html, "fix
nvt/sllod/eff"_fix_nvt_sllod_eff.html
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp/eff
compute myTemp mobile temp/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons using the electron force field. A compute of
this style can be used by commands that compute a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_npt_eff.html">fix
npt/eff</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
includes the radial electron velocity contributions), dim = 2 or 3 =
dimensionality of the simulation, N = number of atoms (only total
number of nuclei in the eFF (see the <A HREF = "pair_style.html">pair_eff</A>
command) in the group, k = Boltzmann constant, and T = temperature.
This expression is summed over all nuclear and electronic degrees of
freedom, essentially by setting the kinetic contribution to the heat
capacity to 3/2k (where only nuclei contribute). This subtlety is
valid for temperatures well below the Fermi temperature, which for
densities two to five times the density of liquid H2 ranges from
86,000 to 170,000 K.
</P>
<P>IMPORTANT NOTE: For eFF models, in order to override the default
temperature reported by LAMMPS in the thermodynamic quantities
reported via the <A HREF = "thermo.html">thermo</A> command, the user should apply a
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
again, the radial electronic velocities are also considered.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/eff command :h3
[Syntax:]
compute ID group-ID temp/eff :pre
ID, group-ID are documented in "compute"_compute.html command
temp/eff = style name of this compute command :ul
[Examples:]
compute 1 all temp/eff
compute myTemp mobile temp/eff :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons using the electron force field. A compute of
this style can be used by commands that compute a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
npt/eff"_fix_npt_eff.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
includes the radial electron velocity contributions), dim = 2 or 3 =
dimensionality of the simulation, N = number of atoms (only total
number of nuclei in the eFF (see the "pair_eff"_pair_style.html
command) in the group, k = Boltzmann constant, and T = temperature.
This expression is summed over all nuclear and electronic degrees of
freedom, essentially by setting the kinetic contribution to the heat
capacity to 3/2k (where only nuclei contribute). This subtlety is
valid for temperatures well below the Fermi temperature, which for
densities two to five times the density of liquid H2 ranges from
86,000 to 170,000 K.
IMPORTANT NOTE: For eFF models, in order to override the default
temperature reported by LAMMPS in the thermodynamic quantities
reported via the "thermo"_thermo.html command, the user should apply a
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
again, the radial electronic velocities are also considered.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
[Restrictions:]
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"compute temp/partial"_compute_temp_partial.html, "compute
temp/region"_compute_temp_region.html, "compute
pressure"_compute_pressure.html
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/region/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/region/eff region-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/region/eff = style name of this compute command
<LI>region-ID = ID of region to use for choosing atoms
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute mine flow temp/region/eff boundary
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons wihtin a geometric region using the electron
force field. A compute of this style can be used by commands that
compute a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>.
</P>
<P>The operation of this compute is exactly like that described by the
<A HREF = "compute_temp_region.html">compute temp/region</A> command, where the
formula for the temperature itself includes the radial electron
velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
temp/eff</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_region.html">compute temp/region</A>, <A HREF = "compute_temp_eff.html">compute
temp/eff</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/region/eff command :h3
[Syntax:]
compute ID group-ID temp/region/eff region-ID :pre
ID, group-ID are documented in "compute"_compute.html command
temp/region/eff = style name of this compute command
region-ID = ID of region to use for choosing atoms :ul
[Examples:]
compute mine flow temp/region/eff boundary :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons wihtin a geometric region using the electron
force field. A compute of this style can be used by commands that
compute a temperature, e.g. "thermo_modify"_thermo_modify.html.
The operation of this compute is exactly like that described by the
"compute temp/region"_compute_temp_region.html command, where the
formula for the temperature itself includes the radial electron
velocity contributions, as discussed by the "compute
temp/eff"_compute_temp_eff.html command.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"compute temp/region"_compute_temp_region.html, "compute
temp/eff"_compute_temp_eff.html, "compute
pressure"_compute_pressure.html
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix langevin/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>langevin/eff = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>damp = damping parameter (time units)
<LI>seed = random number seed to use for white noise (positive integer)
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>scale</I> or <I>tally</I>
<I>scale</I> values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
<I>tally</I> values = <I>no</I> or <I>yes</I>
<I>no</I> = do not tally the energy added/subtracted to atoms
<I>yes</I> = do tally the energy added/subtracted to atoms
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
</PRE>
<P><B>Description:</B>
</P>
<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
to a group of atoms which models an interaction with a background
implicit solvent. Used with <A HREF = "fix_nve_eff.html">fix nve/eff</A>, this command
performs Brownian dynamics (BD), since the total force on each atom
will have the form:
</P>
<PRE>F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
</PRE>
<P>Fc is the conservative force computed via the usual inter-particle
interactions (<A HREF = "pair_style.html">pair_style</A>).
</P>
<P>The Ff and Fr terms are added by this fix on a per-particle basis.
</P>
<P>Ff is a frictional drag or viscous damping term proportional to the
particle's velocity (including the electronic radial degrees of freedom). The proportionality constant for each atom is computed as m/damp, where m is the mass of the particle and damp is the damping factor specified by the user.
</P>
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
<A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used (instead of
a Gaussian random number) for speed.
</P>
<P>Note that the thermostat effect of this fix is applied to the
translational and electronic radial degrees of freedom for the particles in a system. The translational degrees of freedom can also have a bias
velocity removed from them before thermostatting takes place; see the
description below.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the velocities (including electronic radial velocities) and positions of atoms (nuclei and electrons) using the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt/eff</A> command.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. This is not done by default, but only if the
<A HREF = "fix_modify.html">fix_modify</A> command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual <A HREF = "compute.html">compute commands</A> to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
</P>
<P>The <I>damp</I> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 0.1
means to relax the temperature in a timespan of 100 timesteps (for the default 0.001 timesteps and fmsec unit used in eFF - see the <A HREF = "units.html">units</A> command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent. I.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the <A HREF = "fix_viscous.html">fix
viscous</A> command for more details.
</P>
<P>The random # <I>seed</I> must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
</P>
<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increases the relaxation time which is
equivalent to the solvent's viscosity acting on particles with 1/2 the
diameter. This is the opposite effect of scale factors used by the
<A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in fix
<I>langevin</I> is inversely related to the gamma factor in fix <I>viscous</I>.
Also note that the damping factor in fix <I>langevin</I> includes the
particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.
</P>
<P>The keyword <I>tally</I> enables the calculation of the cummulative energy
added/subtracted to the atoms as they are thermostatted. Effectively
it is the energy exchanged between the infinite thermal reservoir and
the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. Note that use of this option requires
setting the <I>tally</I> keyword to <I>yes</I>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the <I>tally</I> keyword to <I>yes</I>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt/eff</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are scale = 1.0 for all types and tally = no.
</P>
<HR>
<A NAME = "Dunweg"></A>
<P><B>(Dunweg)</B> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
</P>
<A NAME = "Schneider"></A>
<P><B>(Schneider)</B> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix langevin/eff command :h3
[Syntax:]
fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
langevin/eff = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random number seed to use for white noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {scale} or {tally}
{scale} values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
{tally} values = {no} or {yes}
{no} = do not tally the energy added/subtracted to atoms
{yes} = do tally the energy added/subtracted to atoms :pre
:ule
[Examples:]
fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre
[Description:]
Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
to a group of atoms which models an interaction with a background
implicit solvent. Used with "fix nve/eff"_fix_nve_eff.html, this command
performs Brownian dynamics (BD), since the total force on each atom
will have the form:
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html).
The Ff and Fr terms are added by this fix on a per-particle basis.
Ff is a frictional drag or viscous damping term proportional to the
particle's velocity (including the electronic radial degrees of
freedom). The proportionality constant for each atom is computed as
m/damp, where m is the mass of the particle and damp is the damping
factor specified by the user.
Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
a Gaussian random number) for speed.
Note that the thermostat effect of this fix is applied to the
translational and electronic radial degrees of freedom for the
particles in a system. The translational degrees of freedom can also
have a bias velocity removed from them before thermostatting takes
place; see the description below.
IMPORTANT NOTE: Unlike the "fix nvt/eff"_fix_nh_eff.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like "fix nve/eff"_fix_nve_eff.html to actually update the velocities
(including electronic radial velocities) and positions of atoms
(nuclei and electrons) using the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by "fix nvt/eff"_fix_nh.html command.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. This is not done by default, but only if the
"fix_modify"_fix_modify.html command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual "compute commands"_compute.html to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
The {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 0.1 means
to relax the temperature in a timespan of 100 timesteps (for the
default 0.001 timesteps and fmsec unit used in eFF - see the
"units"_units.html command). The damp factor can be thought of as
inversely related to the viscosity of the solvent. I.e. a small
relaxation time implies a hi-viscosity solvent and vice versa. See
the discussion about gamma and viscosity in the documentation for the
"fix viscous"_fix_viscous.html command for more details.
The random # {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
The keyword {scale} allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increases the relaxation time which is
equivalent to the solvent's viscosity acting on particles with 1/2 the
diameter. This is the opposite effect of scale factors used by the
"fix viscous"_fix_viscous.html command, since the damp factor in fix
{langevin} is inversely related to the gamma factor in fix {viscous}.
Also note that the damping factor in fix {langevin} includes the
particle mass in Ff, unlike fix {viscous}. Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.
The keyword {tally} enables the calculation of the cummulative energy
added/subtracted to the atoms as they are thermostatted. Effectively
it is the energy exchanged between the infinite thermal reservoir and
the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#4_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"fix langevin"_fix_langevin.html
[Default:]
The option defaults are scale = 1.0 for all types and tally = no.
:line
:link(Dunweg)
[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
:link(Schneider)
[(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978).

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@ -0,0 +1,485 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt/eff command
</H3>
<H3>fix npt/eff command
</H3>
<H3>fix nph/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style_name keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>
<P>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. In addition to acting on the nuclear positions and velocities, they generate radius and radial velocities sampled for the electron wave packets in eFF. This is
achieved by adding some dynamic variables which are coupled to the
particle velocities (thermostatting) and simulation domain dimensions
(barostatting). In addition to basic thermostatting and barostatting,
these fixes can also create a chain of thermostats coupled to the
particle thermostat, and another chain of thermostats coupled to the
barostat variables. The barostat can be coupled to the overall box
volume, or to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I>
tilt dimensions. The external pressure of the barostat can be
specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
The user must be cautious when using very high anisotropic pressures, since the spherical Gaussians that represent the electrons in eFF will not deform anisotropically. When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
</P>
<P>The equations of motion used are those of Shinoda et al. in
<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
energy proposed by Parrinello and Rahman in
<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and
rRESPA integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
</P>
<HR>
<P>The thermostat for fix styles <I>nvt</I> and <I>npt</I> is specified using the
<I>temp</I> keyword. Other thermostat-related keywords are <I>tchain</I>,
<I>tloop</I> and <I>drag</I>, which are discussed below.
</P>
<P>The thermostat is applied to the translational degrees of freedom
for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a
ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, using the default eFF (electron) units, a value of 1.0 means to relax
the temperature in a timespan of (roughly) 100 time steps. This is because the default time unit in eFF is fmsec, while the default timestep is set to 0.001 fmsec (see the <A HREF = "units.html">units</A> command). The atoms in the fix group are the only ones whose velocities (including the radial electronic velocities) and positions are updated
by the velocity/position update portion of the integration.
</P>
<HR>
<P>The barostat for fix styles <I>npt/eff</I> and <I>nph/eff</I> is specified using one or
more of the <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>,
and <I>couple</I> keywords. These keywords give you the ability to specify
all 6 components of an external stress tensor, and to couple various
of these components together so that the dimensions they represent are
varied together during a constant-pressure simulation. Again, results with stress tensors containing large anisotropic character should be read with caution in the current eFF formulation.
</P>
<P>Other barostat-related keywords are <I>pchain</I>, <I>mtk</I>, <I>ploop</I>,
<I>nreset</I>, <I>drag</I>, and <I>dilate</I>, which are discussed below.
</P>
<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
</P>
<P>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the <I>y</I> keyword is used, the y-box length will change. If
the <I>xy</I> keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the <A HREF = "fix_deform_eff.html">fix
deform/eff</A> command.
</P>
<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.
</P>
<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
<I>Tdamp</I> parameter, determining the time scale on which pressure is
relaxed. For example, a value of 1.0 means to relax the pressure
in a timespan of (roughly) 1000 timesteps for the eFF default time unit (fmsec - see
the <A HREF = "units.html">units</A> command), considering the default timestep is 0.001.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new
positions, unless the keyword <I>dilate</I> is specified with a value of
<I>partial</I>, in which case only the atoms in the fix group are
re-scaled. The latter can be useful for leaving the coordinates of
atoms in a solid substrate unchanged and controlling the pressure of a
surrounding fluid.
</P>
<P>IMPORTANT NOTE: there are two different pressures that can be reported for eFF when defining the pair_style (see <A HREF = "pair_eff_cut.html">pair eff/cut</A> to understand these settings), one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial electronic contributions to the virials are only tallied if the flexible pressure option is set, and this will affect both global and per-atom quantities. In principle, the true pressure of a system is somewhere in between the rigid and the flexible eFF pressures, but, for most cases, the difference between these two pressures will not be significant over long-term averaged runs (i.e. even though the energy partitioning changes, the total energy remains similar).
</P>
<HR>
<P>The <I>couple</I> keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, <I>xz</I>
means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
dimension is simply ignored.
</P>
<HR>
<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
</P>
<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz
</PRE>
<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none
</PRE>
<P>The keyword <I>tri</I> means <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, and <I>yz</I> dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
specifying these 7 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy 0.0 0.0 Pdamp
yz 0.0 0.0 Pdamp
xz 0.0 0.0 Pdamp
couple none
</PRE>
<HR>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <I>drag</I> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.
</P>
<P>An alternative way to control initial oscillations is to use chain
thermostats. The keyword <I>tchain</I> determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword <I>pchain</I> specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.
</P>
<P>The <I>mtk</I> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<A HREF = "#Martyna">(Martyna)</A>. Specifying <I>no</I> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <I>yes</I> is more correct, but in many cases the difference is
negligible.
</P>
<P>The keyword <I>tloop</I> can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <I>tloop</I> substeps, each of
length <I>dt</I>/<I>tloop</I>. This corresponds to using a first-order
Suzuki-Yoshida scheme <A HREF = "#Tuckerman2006">(Tuckerman2006)</A>. The keyword
<I>ploop</I> does the same thing for the barostat thermostat.
</P>
<P>The keyword <I>nreset</I> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of <I>nstep</I>
means that every <I>nstep</I> timesteps, the reference dimensions are set
to those of the current simulation domain.
</P>
<HR>
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
imposes reasonable limits on how large the tilt values can be, and
exits with an error if these are exceeded. This error typically
indicates that there is something badly wrong with how the simulation
was constructed. The three most common sources of this error are
using keyword <I>tri</I> on a liquid system, specifying an external shear
stress tensor that exceeds the yield stress of the solid, and
specifying values of <I>Pstart</I> that are too far from the current stress
value. In other words, triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs
thermostatting but NO time integration, these fixes perform
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as <A HREF = "fix_nve_eff.html">fix nve/eff</A> on
atoms to which this fix is applied. Likewise, the <I>temp</I> options for
fix nvt/eff and fix npt/eff should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix
langevin/eff</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
commands.
</P>
<P>IMPORTANT NOTE: currently, there is no available option for the user to set or create temperature distributions that include the radial electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A> command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
</P>
<HR>
<P>These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/eff
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<PRE>compute fix-ID_temp all temp/eff
compute fix-ID_press all pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_eff.html">compute temp/eff</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt/eff, the group for the new computes
is the same as the fix group. For fix nph/eff and fix npt/eff, the group for
the new computes is "all" since pressure is computed for the entire
system.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, fix nvt/eff and fix npt/eff can
be used with <A HREF = "compute.html">compute commands</A> that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>These fixes writes the state of all the thermostat and barostat
variables to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by these fixes. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<P>IMPORTANT NOTE:
</P>
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
compute as an argument when it is specified. The <I>temp</I> keyword will
override this (for the pressure compute being used by fix npt/eff), but
only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
compute specified by the <I>press</I> keyword will be unaffected by the
<I>temp</I> setting.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar values calculated by
this fix are "extensive"; the vector values are "intensive".
</P>
<P>The scalar is the cumulative energy change due to the fix.
</P>
<P>The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords <I>tchain</I> and <I>pchain</I>,
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then <I>tchain</I> is 0. If no
barostatting is done, then <I>pchain</I> is 0. In the following list,
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if <I>couple xyz</I> is used or <I>couple xy</I> for a 2d
simulation, otherwise its value is 3.
</P>
<P>The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:
</P>
<UL><LI>eta[tchain] = particle thermostat displacements
<LI>eta_dot[tchain] = particle thermostat velocities
<LI>omega[ndof] = barostat displacements
<LI>omega_dot[ndof] = barostat velocities
<LI>etap[pchain] = barostat thermostat displacements
<LI>etap_dot[pchain] = barostat thermostat velocities
<LI>PE_eta[tchain] = potential energy of each particle thermostat displacement
<LI>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity
<LI>PE_omega[ndof] = potential energy of each barostat displacement
<LI>KE_omega_dot[ndof] = kinetic energy of each barostat velocity
<LI>PE_etap[pchain] = potential energy of each barostat thermostat displacement
<LI>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity
<LI>PE_strain[1] = scalar strain energy
</UL>
<P>These fixes can ramp their external temperature and pressure over
multiple runs, using the <I>start</I> and <I>stop</I> keywords of the
<A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for details of
how to do this.
</P>
<P>These fixes are not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P>These fixes can be used with either the <I>verlet</I> or <I>respa</I>
<A HREF = "run_style.html">integrators</A>. When using one of the barostat fixes
with <I>respa</I>, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
</P>
<CENTER><IMG SRC = "Eqs/fix_nh1.jpg">
</CENTER>
<P>This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
</P>
<P>IMPORTANT NOTE: using the <I>respa</I> integrator may be useful for the simulations that sample the electronic motions at a faster pace than the nuclear motions.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword (<I>y</I> dimension in <I>xy</I>) is periodic. The
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
<A HREF = "read_restart.html">read_restart</A> commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
</P>
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.
</P>
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with only electrons is not defined in the current temperature calculations, a practical example would be a uniform electron gas or a very hot plasma, where electrons remain delocalized from the nuclei. This is because, even though electron virials are included in the temperature calculation, these are averaged over the nuclear degrees of freedom only. In such cases a corrective term must be added to the pressure to get the correct kinetic contribution.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
</P>
<HR>
<A NAME = "Martyna"></A>
<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
</P>
<A NAME = "Parrinello"></A>
<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
</P>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
</P>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt/eff command :h3
fix npt/eff command :h3
fix nph/eff command :h3
[Syntax:]
fix ID group-ID style_name keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt/eff} or {npt/eff} or {nph/eff} :l
one or more keyword value pairs may be appended
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tchain} value = length of thermostat chain (1 = single thermostat)
{pchain} values = length of thermostat chain on barostat (0 = no thermostat)
{mtk} value = {yes} or {no} = add in MTK adjustment term or not
{tloop} value = number of sub-cycles to perform on thermostat
{ploop} value = number of sub-cycles to perform on barostat thermostat
{nreset} value = reset reference cell every this many timesteps
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
[Description:]
These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. In addition to acting on the nuclear positions and velocities, they generate radius and radial velocities sampled for the electron wave packets in eFF. This is
achieved by adding some dynamic variables which are coupled to the
particle velocities (thermostatting) and simulation domain dimensions
(barostatting). In addition to basic thermostatting and barostatting,
these fixes can also create a chain of thermostats coupled to the
particle thermostat, and another chain of thermostats coupled to the
barostat variables. The barostat can be coupled to the overall box
volume, or to individual dimensions, including the {xy}, {xz} and {yz}
tilt dimensions. The external pressure of the barostat can be
specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
The user must be cautious when using very high anisotropic pressures, since the spherical Gaussians that represent the electrons in eFF will not deform anisotropically. When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
The equations of motion used are those of Shinoda et al. in
"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of
Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
energy proposed by Parrinello and Rahman in
"(Parrinello)"_#Parrinello. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and
rRESPA integrators derived by Tuckerman et al. in "(Tuckerman)"_#Tuckerman.
:line
The thermostat for fix styles {nvt} and {npt} is specified using the
{temp} keyword. Other thermostat-related keywords are {tchain},
{tloop} and {drag}, which are discussed below.
The thermostat is applied to the translational degrees of freedom
for both nuclei and electrons, and for the radial electronic degrees of freedom. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a
ramped value during the run from {Tstart} to {Tstop}. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, using the default eFF (electron) units, a value of 1.0 means to relax
the temperature in a timespan of (roughly) 100 time steps. This is because the default time unit in eFF is fmsec, while the default timestep is set to 0.001 fmsec (see the "units"_units.html command). The atoms in the fix group are the only ones whose velocities (including the radial electronic velocities) and positions are updated
by the velocity/position update portion of the integration.
:line
The barostat for fix styles {npt/eff} and {nph/eff} is specified using one or
more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, {xz}, {yz},
and {couple} keywords. These keywords give you the ability to specify
all 6 components of an external stress tensor, and to couple various
of these components together so that the dimensions they represent are
varied together during a constant-pressure simulation. Again, results with stress tensors containing large anisotropic character should be read with caution in the current eFF formulation.
Other barostat-related keywords are {pchain}, {mtk}, {ploop},
{nreset}, {drag}, and {dilate}, which are discussed below.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read
data"_read_data.html, and "read_restart"_read_restart.html commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
The target pressures for each of the 6 components of the stress tensor
can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz}
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from {Pstart} to {Pstop}.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the {y} keyword is used, the y-box length will change. If
the {xy} keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the "fix
deform/eff"_fix_deform_eff.html command.
Note that in order to use the {xy}, {xz}, or {yz} keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.
For all barostat keywords, the {Pdamp} parameter operates like the
{Tdamp} parameter, determining the time scale on which pressure is
relaxed. For example, a value of 1.0 means to relax the pressure
in a timespan of (roughly) 1000 timesteps for the eFF default time unit (fmsec - see
the "units"_units.html command), considering the default timestep is 0.001.
Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new
positions, unless the keyword {dilate} is specified with a value of
{partial}, in which case only the atoms in the fix group are
re-scaled. The latter can be useful for leaving the coordinates of
atoms in a solid substrate unchanged and controlling the pressure of a
surrounding fluid.
IMPORTANT NOTE: there are two different pressures that can be reported for eFF when defining the pair_style (see "pair eff/cut"_pair_eff_cut.html to understand these settings), one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial electronic contributions to the virials are only tallied if the flexible pressure option is set, and this will affect both global and per-atom quantities. In principle, the true pressure of a system is somewhere in between the rigid and the flexible eFF pressures, but, for most cases, the difference between these two pressures will not be significant over long-term averaged runs (i.e. even though the energy partitioning changes, the total energy remains similar).
:line
The {couple} keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, {xz}
means the {Pxx} and {Pzz} components of the stress tensor are coupled.
{Xyz} means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must
be identical. {Couple xyz} can be used for a 2d simulation; the {z}
dimension is simply ignored.
:line
The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
The keyword {iso} means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz :pre
The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled
independently using the {Pxx}, {Pyy}, and {Pzz} components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none :pre
The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
specifying these 7 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy 0.0 0.0 Pdamp
yz 0.0 0.0 Pdamp
xz 0.0 0.0 Pdamp
couple none :pre
:line
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional {drag} keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.
An alternative way to control initial oscillations is to use chain
thermostats. The keyword {tchain} determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword {pchain} specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.
The {mtk} keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
"(Martyna)"_#Martyna. Specifying {no} reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using {yes} is more correct, but in many cases the difference is
negligible.
The keyword {tloop} can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into {tloop} substeps, each of
length {dt}/{tloop}. This corresponds to using a first-order
Suzuki-Yoshida scheme "(Tuckerman2006)"_#Tuckerman2006. The keyword
{ploop} does the same thing for the barostat thermostat.
The keyword {nreset} controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of {nstep}
means that every {nstep} timesteps, the reference dimensions are set
to those of the current simulation domain.
:line
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
{xz}, {yz} can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
imposes reasonable limits on how large the tilt values can be, and
exits with an error if these are exceeded. This error typically
indicates that there is something badly wrong with how the simulation
was constructed. The three most common sources of this error are
using keyword {tri} on a liquid system, specifying an external shear
stress tensor that exceeds the yield stress of the solid, and
specifying values of {Pstart} that are too far from the current stress
value. In other words, triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults.
IMPORTANT NOTE: Unlike the "fix
temp/berendsen"_fix_temp_berendsen.html command which performs
thermostatting but NO time integration, these fixes perform
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as "fix nve/eff"_fix_nve_eff.html on
atoms to which this fix is applied. Likewise, the {temp} options for
fix nvt/eff and fix npt/eff should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by "fix
langevin/eff"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
commands.
IMPORTANT NOTE: currently, there is no available option for the user to set or create temperature distributions that include the radial electronic degrees of freedom with the "velocity"_velocity.html command, so the the user must allow for these to equilibrate (i.e. evolve thermal partitioning) through integration.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
compute fix-ID_temp group-ID temp/eff
compute fix-ID_press group-ID pressure fix-ID_temp :pre
compute fix-ID_temp all temp/eff
compute fix-ID_press all pressure fix-ID_temp :pre
See the "compute temp/eff"_compute_temp_eff.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt/eff, the group for the new computes
is the same as the fix group. For fix nph/eff and fix npt/eff, the group for
the new computes is "all" since pressure is computed for the entire
system.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, fix nvt/eff and fix npt/eff can
be used with "compute commands"_compute.html that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the "fix_modify"_fix_modify.html command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
These fixes writes the state of all the thermostat and barostat
variables to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by these fixes. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
IMPORTANT NOTE:
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
"pressure compute"_compute_pressure.html defines its own temperature
compute as an argument when it is specified. The {temp} keyword will
override this (for the pressure compute being used by fix npt/eff), but
only if the {temp} keyword comes after the {press} keyword. If the
{temp} keyword comes before the {press} keyword, then the new pressure
compute specified by the {press} keyword will be unaffected by the
{temp} setting.
The "fix_modify"_fix_modify.html {energy} option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar values calculated by
this fix are "extensive"; the vector values are "intensive".
The scalar is the cumulative energy change due to the fix.
The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords {tchain} and {pchain},
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then {tchain} is 0. If no
barostatting is done, then {pchain} is 0. In the following list,
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if {couple xyz} is used or {couple xy} for a 2d
simulation, otherwise its value is 3.
The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:
eta\[tchain\] = particle thermostat displacements
eta_dot\[tchain\] = particle thermostat velocities
omega\[ndof\] = barostat displacements
omega_dot\[ndof\] = barostat velocities
etap\[pchain\] = barostat thermostat displacements
etap_dot\[pchain\] = barostat thermostat velocities
PE_eta\[tchain\] = potential energy of each particle thermostat displacement
KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity
PE_omega\[ndof\] = potential energy of each barostat displacement
KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity
PE_etap\[pchain\] = potential energy of each barostat thermostat displacement
KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity
PE_strain\[1\] = scalar strain energy :ul
These fixes can ramp their external temperature and pressure over
multiple runs, using the {start} and {stop} keywords of the
"run"_run.html command. See the "run"_run.html command for details of
how to do this.
These fixes are not invoked during "energy
minimization"_minimize.html.
These fixes can be used with either the {verlet} or {respa}
"integrators"_run_style.html. When using one of the barostat fixes
with {respa}, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
:c,image(Eqs/fix_nh1.jpg)
This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
IMPORTANT NOTE: using the {respa} integrator may be useful for the simulations that sample the electronic motions at a faster pace than the nuclear motions.
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Non-periodic dimensions cannot be barostatted. {Z}, {xz}, and {yz},
cannot be barostatted 2D simulations. {Xy}, {xz}, and {yz} can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword ({y} dimension in {xy}) is periodic. The
"create_box"_create_box.html, "read data"_read_data.html, and
"read_restart"_read_restart.html commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
For the {temp} keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.
IMPORTANT NOTE: The temperature for systems (regions or groups) with only electrons is not defined in the current temperature calculations, a practical example would be a uniform electron gas or a very hot plasma, where electrons remain delocalized from the nuclei. This is because, even though electron virials are included in the temperature calculation, these are averaged over the nuclear degrees of freedom only. In such cases a corrective term must be added to the pressure to get the correct kinetic contribution.
[Related commands:]
"fix nve/eff"_fix_nve_eff.html, "fix_modify"_fix_modify.html, "run_style"_run_style.html
[Default:]
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
:line
:link(Martyna)
[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
:link(Parrinello)
[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
:link(Tuckerman)
[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

54
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@ -0,0 +1,54 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/eff = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE integration to update position and velocity for
atoms in the group each timestep, including the translational and radial electron motions. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt/eff</A>, <A HREF = "fix_nh.html">fix npt/eff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

49
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@ -0,0 +1,49 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nve/eff command :h3
[Syntax:]
fix ID group-ID nve/eff :pre
ID, group-ID are documented in "fix"_fix.html command
nve/eff = style name of this fix command :ul
[Examples:]
fix 1 all nve/eff :pre
[Description:]
Perform constant NVE integration to update position and velocity for
atoms in the group each timestep, including the translational and radial electron motions. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"fix nvt/eff"_fix_nh.html, "fix npt/eff"_fix_nh.html
[Default:] none

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt/sllod/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nvt/sllod/eff keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nvt/sllod/eff = style name of this fix command
<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command can be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover temperature
thermostat. In eFF, this will include the radius and radial velocity of the electrons.
V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
</P>
<P>This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the <A HREF = "fix_deform.html">fix
deform</A> command, so each point in the simulation box
can be thought of as having a "streaming" velocity. The streaming velocity will only affect the translational degrees of freedom in eFF. This position-dependent streaming velocity is subtracted from each atom's
actual velocity to yield a thermal velocity which is used for
temperature computation and thermostatting. The thermal velocity is computed over all degrees of freedom, including the electronic ones. For example, if the box
is being sheared in x, relative to y, then points at the bottom of the
box (low y) have a small x velocity, while points at the top of the
box (hi y) have a large x velocity. These velocities do not
contribute to the thermal "temperature" of the atom, hence the use of this command.
</P>
<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
remapping either atom coordinates or velocities to the changing
simulation box. To use fix nvt/sllod, fix deform should NOT remap
atom positions, because fix nvt/sllod adjusts the atom positions and
velocities to create a velocity profile that matches the changing box
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
periodic boundaries since that is consistent with maintaining the
velocity profile created by fix nvt/sllod. LAMMPS will give an
error if this setting is not consistent.
</P>
<P>The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what is
implemented in LAMMPS in a velocity Verlet formulation.
</P>
<P>Additional parameters affecting the thermostat are specified by
keywords and values documented with the <A HREF = "fix_nh_eff.html">fix nvt/eff</A>
command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
keywords.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/deform/eff", as if this command had
been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/deform/eff
</PRE>
<P>See the <A HREF = "compute_temp_deform_eff.html">compute temp/deform/eff</A> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes the same global scalar and global vector of
quantities as does the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
Setting tchain to larger values can result in poor equilibration.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_langevin_eff.html">fix langevin/eff</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform_eff.html">compute temp/deform/eff</A>
</P>
<P><B>Default:</B> Same as <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, except tchain = 1.
</P>
<HR>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).
</P>
</HTML>

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@ -0,0 +1,146 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt/sllod/eff command :h3
[Syntax:]
fix ID group-ID nvt/sllod/eff keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
nvt/sllod/eff = style name of this fix command
additional thermostat related keyword/value pairs from the "fix nvt/eff"_fix_nh_eff.html command can be appended :ul
[Examples:]
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover temperature
thermostat. In eFF, this will include the radius and radial velocity of the electrons.
V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the "fix
deform"_fix_deform.html command, so each point in the simulation box
can be thought of as having a "streaming" velocity. The streaming velocity will only affect the translational degrees of freedom in eFF. This position-dependent streaming velocity is subtracted from each atom's
actual velocity to yield a thermal velocity which is used for
temperature computation and thermostatting. The thermal velocity is computed over all degrees of freedom, including the electronic ones. For example, if the box
is being sheared in x, relative to y, then points at the bottom of the
box (low y) have a small x velocity, while points at the top of the
box (hi y) have a large x velocity. These velocities do not
contribute to the thermal "temperature" of the atom, hence the use of this command.
IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
remapping either atom coordinates or velocities to the changing
simulation box. To use fix nvt/sllod, fix deform should NOT remap
atom positions, because fix nvt/sllod adjusts the atom positions and
velocities to create a velocity profile that matches the changing box
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
periodic boundaries since that is consistent with maintaining the
velocity profile created by fix nvt/sllod. LAMMPS will give an
error if this setting is not consistent.
The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
implemented in LAMMPS in a velocity Verlet formulation.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt/eff"_fix_nh_eff.html
command. See, for example, discussion of the {temp} and {drag}
keywords.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/deform/eff", as if this command had
been issued:
compute fix-ID_temp group-ID temp/deform/eff :pre
See the "compute temp/deform/eff"_compute_temp_deform_eff.html command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix nvt/eff"_fix_nh_eff.html command.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix works best without Nose-Hoover chain thermostats i.e. using tchain = 1.
Setting tchain to larger values can result in poor equilibration.
[Related commands:]
"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix langevin/eff"_fix_langevin_eff.html,
"fix_modify"_fix_modify.html, "compute temp/deform/eff"_compute_temp_deform_eff.html
[Default:] Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1.
:line
:link(Tuckerman)
[(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).

40
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View File

@ -9,14 +9,14 @@
<HR>
<H3>fix temp/rescale command
<H3>fix temp/rescale/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction
<PRE>fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale = style name of this fix command
<LI>temp/rescale/eff = style name of this fix command
<LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
@ -24,21 +24,15 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
<PRE>fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
</P>
<P>The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
<P>The rescaling is applied to the translational degrees of freedom
for all particles, and the electronic radial degrees of freedom. The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
</P>
<P>Rescaling is performed every N timesteps. The target temperature is a
ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
@ -51,15 +45,14 @@ difference between the actual and desired temperature. E.g. if
<I>fraction</I> = 1.0, the temperature is reset to exactly the desired
value.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt/eff</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
fix, like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the positions of atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt/eff</A> or <A HREF = "fix_langevin_eff.html">fix
langevin/eff</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
@ -69,10 +62,9 @@ thermostatting.
creates its own compute of style "temp", as if one of this command had
been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
<PRE>compute fix-ID_temp group-ID temp/eff
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> for details. Note that the
ID of the new compute is the fix-ID + underscore + "temp", and the
<P>See the <A HREF = "compute_temp_eff.html">compute temp/eff</A> for details. Note that the ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
@ -127,11 +119,15 @@ calculated by this fix is "extensive".
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_nh.html">fix nvt</A>,
<P><A HREF = "fix_langevin.html">fix langevin/eff</A>, <A HREF = "fix_nh.html">fix nvt/eff</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none

40
doc/fix_temp_rescale.txt
View File

@ -6,14 +6,14 @@
:line
fix temp/rescale command :h3
fix temp/rescale/eff command :h3
[Syntax:]
fix ID group-ID temp/rescale N Tstart Tstop window fraction :pre
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction :pre
ID, group-ID are documented in "fix"_fix.html command
temp/rescale = style name of this fix command
temp/rescale/eff = style name of this fix command
N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
@ -21,21 +21,15 @@ fraction = rescale to target temperature by this fraction :ul
[Examples:]
fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 :pre
[Description:]
Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
The rescaling is applied to the translational degrees of freedom
for all particles, and the electronic radial degrees of freedom. The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
Rescaling is performed every N timesteps. The target temperature is a
ramped value between the {Tstart} and {Tstop} temperatures at the
@ -48,15 +42,14 @@ difference between the actual and desired temperature. E.g. if
{fraction} = 1.0, the temperature is reset to exactly the desired
value.
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
IMPORTANT NOTE: Unlike the "fix nvt/eff"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like "fix nve"_fix_nve.html to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
fix, like "fix nve/eff"_fix_nve_eff.html to actually update the positions of atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
by another fix - e.g. by "fix nvt/eff"_fix_nh.html or "fix
langevin/eff"_fix_langevin_eff.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
@ -66,10 +59,9 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
compute fix-ID_temp group-ID temp :pre
compute fix-ID_temp group-ID temp/eff :pre
See the "compute temp"_compute_temp.html for details. Note that the
ID of the new compute is the fix-ID + underscore + "temp", and the
See the "compute temp/eff"_compute_temp_eff.html for details. Note that the ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see
@ -124,11 +116,15 @@ This fix can ramp its target temperature over multiple runs, using the
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"fix langevin"_fix_langevin.html, "fix nvt"_fix_nh.html,
"fix langevin/eff"_fix_langevin.html, "fix nvt/eff"_fix_nh.html,
"fix_modify"_fix_modify.html
[Default:] none

274
doc/pair_eff.html Normal file
View File

@ -0,0 +1,274 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style eff/cut command
</H3>
<P><B>Syntax:</B>
</P>
<P>pair_style eff/cut cutoff eradius_limit_flag pressure_flag
</P>
<P>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)
</P>
<P><B>Examples:</B>
</P>
<PRE>pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
pair_coeff * *
pair_coeff 2 2 20.0
</PRE>
<P><B>Description:</B>
</P>
<P>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.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. Yet, eFF relies on a simplification of the electronic
wavefunction in which electrons are described as floating Gaussian
wave packets whose position and size respond to the various dynamic
forces between interacting classical nuclear particles and spherical
Gaussian electron wavepackets. The wavefunction is taken to be a
Hartree product of the wave packets. To compensate for the lack of
explicit antisymmetry in the resulting wavefunction, a spin-dependent
Pauli potential is included in the Hamiltonian. Substituting this
wavefunction into the time-dependent Schrodinger equation produces
equations of motion that correspond - to second order - to classical
Hamiltonian relations between electron position and size, and their
conjugate momenta. The N-electron wavefunction is described as a
product of one-electron Gaussian functions, whose size is a dynamical
variable and whose position is not constrained to a nuclear
center. This form allows for straightforward propagation of the
wavefunction, with time, using a simple formulation from which the
equations of motion are then integrated with conventional MD
algorithms. In addition to this spin-dependent Pauli repulsion
potential term between Gaussians, eFF includes the electron kinetic
energy from the Gaussians. These two terms are based on
first-principles quantum mechanics. On the other hand, nuclei are
described as point charges, which interact with other nuclei and
electrons through standard electrostatic potential forms.
</P>
<P>The full Hamiltonian (shown below), contains then a standard
description for electrostatic interactions between a set of
delocalized point and Gaussian charges which include, nuclei-nuclei
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
mixed QM-classical mechanics method rather than a conventional force
field method (in which electron motions are averaged out into ground
state nuclear motions, i.e a single electronic state, and particle
interactions are described via empirically parameterized interatomic
potential functions). This makes eFF uniquely suited to simulate
materials over a wide range of temperatures and pressures where
electronically excited and ionized states of matter can occur and
coexist. Furthermore, the interactions between particles -nuclei and
electrons- reduce to the sum of a set of effective pairwise potentials
in the eFF formulation. The <I>eff/cut</I> style computes the pairwise
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
potentials between electrons (E_KE) for a total energy expression
given as,
</P>
<CENTER><IMG SRC = "Eqs/eff_energy_expression.jpg">
</CENTER>
<P>The individual terms are defined as follows:
</P>
<CENTER><IMG SRC = "Eqs/eff_KE.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_NN.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_Ne.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_ee.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_Pauli.jpg">
</CENTER>
<P>where, s_i correspond to the electron sizes, the sigmas i's to the
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
to the distances between the nuclei or the nuclei and electrons, and
r_ij to the distances between electrons. For additional details see
<A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
</P>
<P>The overall electrostatics energy is given in Hartree units of energy
by default and can be modified by an energy-conversion constant,
according to the units chosen (see <A HREF = "units.html">electron_units</A>). The
cutoff Rc, given in Bohrs (by default), truncates the interaction
distance. The recommended cutoff for this pair style should follow
the minimum image criterion, i.e. half of the minimum unit cell
length.
</P>
<P>Style <I>eff/long</I> (not yet available) computes the same interactions as
style <I>eff/cut</I> except that an additional damping factor is applied so
it can be used in conjunction with the
<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>These potentials are designed to be used with <A HREF = "atom_electron.html">atom_style
electron</A> definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cutoff (distance units)
</UL>
<P>For <I>eff/cut</I>, the cutoff coefficient is optional. If it is not used
(as in some of the examples above), the default global value specified
in the pair_style command is used.
</P>
<P>For <I>eff/long</I> (not yet available) no cutoff will be specified for an
individual I,J type pair via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
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>
<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
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.
</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
electronic radial virials contributions to the total pressure (scalar
or tensor). If set to 1, the computed pressure will include the
electronic radial virial contributions to the total pressure (scalar
and tensor).
</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
treated as incompressible 'rigid' spheres) and one that does. The
radial electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
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>
<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 for atoms with a large number of core
electrons using core approximating pseudo-potentials.
</P>
<P>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
can change significantly the nature of bonding in the system. It can
capture with surprising accuracy the behavior of such systems because
it describes consistently and in an unbiased manner many different
kinds of bonds, including covalent, ionic, multicenter, ionic, and
plasma, and how they interconvert and/or change when they become
excited. eFF also excels in computing the relative thermochemistry of
isodemic reactions and conformational changes, where the bonds of the
reactants are of the same type as the bonds of the products. eFF
assumes that kinetic energy differences dominate the overall exchange
energy, which is true when the electrons present are nearly spherical
and nodeless and valid for covalent compounds such as dense hydrogen,
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
metals (e.g. beryllium) and semimetals such as boron; and various
compounds containing ionic and/or multicenter bonds, such as boron
dihydride.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the cutoff distance for the
<I>eff/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
See the "pair_modify" command for details.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant for
these pair styles.
</P>
<P>The <I>eff/long</I> (not yet available) style supports the
<A HREF = "pair_modify.html">pair_modify</A> table option for tabulation of the
short-range portion of the long-range Coulombic interaction.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>These pair styles will only be enabled if LAMMPS is built with the
"user-eff" package. It will only be enabled if LAMMPS was built with
that package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section
for more info.
</P>
<P>These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
<A HREF = "atom_style.html">atom_style</A>. The <I>electron</I> atom style does all of
this.
</P>
<P>Thes pair styles require you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost
atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B>
</P>
<P>If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
</P>
<HR>
<A NAME = "Su"></A>
<P><B>(Su)</B> Su and Goddard, Excited Electron Dynamics Modeling of Warm
Dense Matter, Phys Rev Lett, 99:185003 (2007).
</P>
<A NAME = "Jaramillo-Botero"></A>
<P><B>(Jaramillo-Botero_2010)</B> Jaramillo-Botero, Su, Qi, Goddard,
Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for
Describing Material Properties and Phenomena in Extreme Environments,
to appear in J Comp Chem (2010).
</P>
</HTML>

268
doc/pair_eff.txt Normal file
View File

@ -0,0 +1,268 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style eff/cut command :h3
[Syntax:]
pair_style eff/cut cutoff eradius_limit_flag pressure_flag
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)
[Examples:]
pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
pair_coeff * *
pair_coeff 2 2 20.0 :pre
[Description:]
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.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. Yet, eFF relies on a simplification of the electronic
wavefunction in which electrons are described as floating Gaussian
wave packets whose position and size respond to the various dynamic
forces between interacting classical nuclear particles and spherical
Gaussian electron wavepackets. The wavefunction is taken to be a
Hartree product of the wave packets. To compensate for the lack of
explicit antisymmetry in the resulting wavefunction, a spin-dependent
Pauli potential is included in the Hamiltonian. Substituting this
wavefunction into the time-dependent Schrodinger equation produces
equations of motion that correspond - to second order - to classical
Hamiltonian relations between electron position and size, and their
conjugate momenta. The N-electron wavefunction is described as a
product of one-electron Gaussian functions, whose size is a dynamical
variable and whose position is not constrained to a nuclear
center. This form allows for straightforward propagation of the
wavefunction, with time, using a simple formulation from which the
equations of motion are then integrated with conventional MD
algorithms. In addition to this spin-dependent Pauli repulsion
potential term between Gaussians, eFF includes the electron kinetic
energy from the Gaussians. These two terms are based on
first-principles quantum mechanics. On the other hand, nuclei are
described as point charges, which interact with other nuclei and
electrons through standard electrostatic potential forms.
The full Hamiltonian (shown below), contains then a standard
description for electrostatic interactions between a set of
delocalized point and Gaussian charges which include, nuclei-nuclei
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
mixed QM-classical mechanics method rather than a conventional force
field method (in which electron motions are averaged out into ground
state nuclear motions, i.e a single electronic state, and particle
interactions are described via empirically parameterized interatomic
potential functions). This makes eFF uniquely suited to simulate
materials over a wide range of temperatures and pressures where
electronically excited and ionized states of matter can occur and
coexist. Furthermore, the interactions between particles -nuclei and
electrons- reduce to the sum of a set of effective pairwise potentials
in the eFF formulation. The {eff/cut} style computes the pairwise
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
potentials between electrons (E_KE) for a total energy expression
given as,
:c,image(Eqs/eff_energy_expression.jpg)
The individual terms are defined as follows:
:c,image(Eqs/eff_KE.jpg)
:c,image(Eqs/eff_NN.jpg)
:c,image(Eqs/eff_Ne.jpg)
:c,image(Eqs/eff_ee.jpg)
:c,image(Eqs/eff_Pauli.jpg)
where, s_i correspond to the electron sizes, the sigmas i's to the
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
to the distances between the nuclei or the nuclei and electrons, and
r_ij to the distances between electrons. For additional details see
"(Jaramillo-Botero)"_#Jaramillo-Botero.
The overall electrostatics energy is given in Hartree units of energy
by default and can be modified by an energy-conversion constant,
according to the units chosen (see "electron_units"_units.html). The
cutoff Rc, given in Bohrs (by default), truncates the interaction
distance. The recommended cutoff for this pair style should follow
the minimum image criterion, i.e. half of the minimum unit cell
length.
Style {eff/long} (not yet available) computes the same interactions as
style {eff/cut} except that an additional damping factor is applied so
it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
These potentials are designed to be used with "atom_style
electron"_atom_electron.html definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cutoff (distance units) :ul
For {eff/cut}, the cutoff coefficient is optional. If it is not used
(as in some of the examples above), the default global value specified
in the pair_style command is used.
For {eff/long} (not yet available) no cutoff will be specified for an
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 {eradius_limit_flag} is used to restrain electrons from becoming
unbounded in size 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.
The {pressure_flag} is used to control between two types of pressure
computation: if set to 0, 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
electronic radial virial contributions to the total pressure (scalar
and tensor).
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
treated as incompressible 'rigid' spheres) and one that does. The
radial electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
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.
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 for atoms with a large number of core
electrons using core approximating pseudo-potentials.
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
can change significantly the nature of bonding in the system. It can
capture with surprising accuracy the behavior of such systems because
it describes consistently and in an unbiased manner many different
kinds of bonds, including covalent, ionic, multicenter, ionic, and
plasma, and how they interconvert and/or change when they become
excited. eFF also excels in computing the relative thermochemistry of
isodemic reactions and conformational changes, where the bonds of the
reactants are of the same type as the bonds of the products. eFF
assumes that kinetic energy differences dominate the overall exchange
energy, which is true when the electrons present are nearly spherical
and nodeless and valid for covalent compounds such as dense hydrogen,
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
metals (e.g. beryllium) and semimetals such as boron; and various
compounds containing ionic and/or multicenter bonds, such as boron
dihydride.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the cutoff distance for the
{eff/cut} style can be mixed. The default mix value is {geometric}.
See the "pair_modify" command for details.
The "pair_modify"_pair_modify.html shift option is not relevant for
these pair styles.
The {eff/long} (not yet available) style supports the
"pair_modify"_pair_modify.html table option for tabulation of the
short-range portion of the long-range Coulombic interaction.
These pair styles do not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
These pair styles will only be enabled if LAMMPS is built with the
"user-eff" package. It will only be enabled if LAMMPS was built with
that package. See the "Making LAMMPS"_Section_start.html#2_3 section
for more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
"atom_style"_atom_style.html. The {electron} atom style does all of
this.
Thes pair styles require you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost
atoms.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:]
If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
:line
:link(Su)
[(Su)] Su and Goddard, Excited Electron Dynamics Modeling of Warm
Dense Matter, Phys Rev Lett, 99:185003 (2007).
:link(Jaramillo-Botero)
[(Jaramillo-Botero_2010)] Jaramillo-Botero, Su, Qi, Goddard,
Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for
Describing Material Properties and Phenomena in Extreme Environments,
to appear in J Comp Chem (2010).