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Final changes to fix_box_relax and fix_nh 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3960 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2010-04-07 18:33:34 +00:00
parent 9921249796
commit 28bbe502e5
4 changed files with 44 additions and 44 deletions
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8
doc/fix_box_relax.html
View File

@ -32,7 +32,7 @@ keyword = <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all box/relax ixo 0.0 vmax 0.001
<PRE>fix 1 all box/relax iso 0.0 vmax 0.001
fix 2 water box/relax aniso 0.0 dilate partial
fix 2 ice box/relax tri 0.0 couple xy nreset 100
</PRE>
@ -151,7 +151,7 @@ change by more than 1/10 of a percent.
</P>
<HR>
<P>With this fix, the potential energy used by the minimzer is augmented
<P>With this fix, the potential energy used by the minimizer is augmented
by an additional energy provided by the fix. The overall objective
function then is:
</P>
@ -167,7 +167,7 @@ global system stress tensor <B>P</B> will satisfy the relation:
</P>
<CENTER><IMG SRC = "Eqs/fix_box_relax2.jpg">
</CENTER>
<P>where <B>I</B> is the identity matric, <B>h</B>_0 is the box dimension tensor of
<P>where <B>I</B> is the identity matrix, <B>h</B>_0 is the box dimension tensor of
the reference cell, and <B>h</B>_0<I>d</I> is the diagonal part of
<B>h</B>_0. <B>S</B>_<I>t</I> is a symmetric stress tensor that is chosen by LAMMPS
so that the upper-triangular components of <B>P</B> equal the stress tensor
@ -205,7 +205,7 @@ be done by outputting the pressure from the fix this command creates
<P>IMPORTANT NOTE: Because pressure is often a very sensitive function of
volume, it can be difficult for the minimizer to equilibrate the
system the desired pressure with high precision, particularly for
solids. Some techiniques that seem to help are (a) use the
solids. Some techniques that seem to help are (a) use the
"min_modify line quadratic" option when minimizing with box
relaxations, and (b) minimize several times in succession if need be,
to drive the pressure closer to the target pressure. Also note that

8
doc/fix_box_relax.txt
View File

@ -26,7 +26,7 @@ keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz}
[Examples:]
fix 1 all box/relax ixo 0.0 vmax 0.001
fix 1 all box/relax iso 0.0 vmax 0.001
fix 2 water box/relax aniso 0.0 dilate partial
fix 2 ice box/relax tri 0.0 couple xy nreset 100 :pre
@ -145,7 +145,7 @@ change by more than 1/10 of a percent.
:line
With this fix, the potential energy used by the minimzer is augmented
With this fix, the potential energy used by the minimizer is augmented
by an additional energy provided by the fix. The overall objective
function then is:
@ -161,7 +161,7 @@ global system stress tensor [P] will satisfy the relation:
:c,image(Eqs/fix_box_relax2.jpg)
where [I] is the identity matric, [h]_0 is the box dimension tensor of
where [I] is the identity matrix, [h]_0 is the box dimension tensor of
the reference cell, and [h]_0{d} is the diagonal part of
[h]_0. [S]_{t} is a symmetric stress tensor that is chosen by LAMMPS
so that the upper-triangular components of [P] equal the stress tensor
@ -199,7 +199,7 @@ be done by outputting the pressure from the fix this command creates
IMPORTANT NOTE: Because pressure is often a very sensitive function of
volume, it can be difficult for the minimizer to equilibrate the
system the desired pressure with high precision, particularly for
solids. Some techiniques that seem to help are (a) use the
solids. Some techniques that seem to help are (a) use the
"min_modify line quadratic" option when minimizing with box
relaxations, and (b) minimize several times in succession if need be,
to drive the pressure closer to the target pressure. Also note that

36
doc/fix_nh.html
View File

@ -219,7 +219,7 @@ 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 norminal NVT, NPT, or NPH ensembles.
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
@ -227,7 +227,7 @@ 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
bvarostat variables.
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
@ -258,7 +258,7 @@ to those of the current simulation domain.
<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 dratically deformed simulation box. LAMMPS
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
@ -368,7 +368,7 @@ 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 cummulative energy change due to the fix.
<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
@ -386,18 +386,18 @@ simulation, otherwise its value is 3.
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<B>tchain</B> = what for each T chain
<LI>eta_dot<B>tchain</B> = what for each T chain
<LI>omega<B>ndof</B> = what for each barostat DOF
<LI>omega_dot<B>ndof</B> = what for each barostat DOF
<LI>etap<B>pchain</B> = what for each P chain
<LI>etap_dot<B>pchain</B> = what for each P chain
<LI>PE_eta<B>tchain</B> = potential energy for each T chain
<LI>KE_eta_dot<B>tchain</B> = what for each T chain
<LI>PE_omega<B>ndof</B> = what for each barostat DOF
<LI>KE_omega_dot<B>ndof</B> = what for each barostat DOF
<LI>PE_etap<B>pchain</B> = what for each P chain
<LI>KE_etap_dot<B>pchain</B> = what for each P chain
<UL><LI>eta<B>tchain</B> = particle thermostat displacements
<LI>eta_dot<B>tchain</B> = particle thermostat velocities
<LI>omega<B>ndof</B> = barostat displacements
<LI>omega_dot<B>ndof</B> = barostat velocities
<LI>etap<B>pchain</B> = barostat thermostat displacements
<LI>etap_dot<B>pchain</B> = barostat thermostat velocities
<LI>PE_eta<B>tchain</B> = potential energy of each particle thermostat displacement
<LI>KE_eta_dot<B>tchain</B> = kinetic energy of each particle thermostat velocity
<LI>PE_omega<B>ndof</B> = potential energy of each barostat displacement
<LI>KE_omega_dot<B>ndof</B> = kinetic energy of each barostat velocity
<LI>PE_etap<B>pchain</B> = potential energy of each barostat thermostat displacement
<LI>KE_etap_dot<B>pchain</B> = kinetic energy of each barostat thermostat velocity
<LI>PE_strain<B>1</B> = scalar strain energy
</UL>
<P>These fixes can ramp their external temperature and pressure over
@ -429,8 +429,8 @@ is not allowed in the Nose/Hoover formulation.
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are tchain = 3, pchain = 0, mtk = yes, tloop =
ploopt = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
<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>

36
doc/fix_nh.txt
View File

@ -211,7 +211,7 @@ 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 norminal NVT, NPT, or NPH ensembles.
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
@ -219,7 +219,7 @@ 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
bvarostat variables.
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
@ -250,7 +250,7 @@ to those of the current simulation domain.
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 dratically deformed simulation box. LAMMPS
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
@ -360,7 +360,7 @@ 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 cummulative energy change due to the fix.
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
@ -378,18 +378,18 @@ 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] = what for each T chain
eta_dot[tchain] = what for each T chain
omega[ndof] = what for each barostat DOF
omega_dot[ndof] = what for each barostat DOF
etap[pchain] = what for each P chain
etap_dot[pchain] = what for each P chain
PE_eta[tchain] = potential energy for each T chain
KE_eta_dot[tchain] = what for each T chain
PE_omega[ndof] = what for each barostat DOF
KE_omega_dot[ndof] = what for each barostat DOF
PE_etap[pchain] = what for each P chain
KE_etap_dot[pchain] = what for each P chain
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
@ -421,8 +421,8 @@ is not allowed in the Nose/Hoover formulation.
[Default:]
The keyword defaults are tchain = 3, pchain = 0, mtk = yes, tloop =
ploopt = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
:line