ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@491 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2007-04-19 23:25:27 +00:00
parent d082429dd7
commit aba05c2cf9
45 changed files with 958 additions and 155 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
doc/Eqs/pair_gayberne.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 6.7 KiB

14
doc/Eqs/pair_gayberne.tex Normal file
View File

@ -0,0 +1,14 @@
\documentstyle[12pt]{article}
\begin{document}
$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
\end{document}

BIN
doc/Eqs/pair_gayberne2.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 2.7 KiB

9
doc/Eqs/pair_gayberne2.tex Normal file
View File

@ -0,0 +1,9 @@
\documentstyle[12pt]{article}
\begin{document}
$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b =
\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot {
\frac{c}{ a \cdot b } } $$
\end{document}

BIN
doc/Eqs/pair_gayberne_extra.pdf Normal file
View File

Binary file not shown.

167
doc/Eqs/pair_gayberne_extra.tex Normal file
View File

@ -0,0 +1,167 @@
\documentstyle[12pt]{article}
\begin{document}
\begin{center}
\large{Additional documention for the Gay-Berne ellipsoidal potential \\
as implemented in LAMMPS}
\end{center}
\centerline{Mike Brown, Sandia National Labs, April 2007}
\vspace{0.3in}
The Gay-Berne anisotropic LJ interaction between pairs of dissimilar
ellipsoidal particles is given by
$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
where $\mathbf{A}_1$ and $\mathbf{A}_2$ are the transformation matrices
from the simulation box frame to the body frame and $\mathbf{r}_{12}$
is the center to center vectorb etween the particles.
$U_r$ controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles ($h_{12}$) and the user-specified shift parameter gamma:
$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be
given by the ellipsoid radii. The $\eta$ orientation-dependent energy
based on the user-specified exponent $\upsilon$ is given by
$$ \eta_{12} = [ \frac{ 2 s_1 s_2 }{\det ( \mathbf{G}_{12} )}]^{
\upsilon / 2 } , $$
$$ s_i = [a_i b_i + c_i c_i][a_i b_i]^{ 1 / 2 }, $$
and
$$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 = \mathbf{G}_1 +
\mathbf{G}_2. $$
Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by
the relative well depths (dimensionless energy scales
inversely proportional to the well-depths of the respective
orthogonal configurations of the interacting molecules). The
$\chi$ orientation-dependent energy based on the user-specified
exponent $\mu$ is given by
$$ \chi_{12} = [2 \hat{\mathbf{r}}_{12}^T \mathbf{B}_{12}^{-1}
\hat{\mathbf{r}}_{12}]^\mu, $$
$$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
and
$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
\mathbf{B}_2. $$
Here, we use the distance of closest approach approximation given by the
Perram reference, namely
$$ h_{12} = r - \sigma_{12} ( \mathbf{A}_1, \mathbf{A}_2,
\mathbf{r}_{12} ), $$
$$ r = |\mathbf{r}_{12}|, $$
and
$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}_{12}^T
\mathbf{G}_{12}^{-1} \hat{\mathbf{r}}_{12}.]^{ -1/2 } $$
Forces and Torques: Because the analytic forces and torques have not
been published for this potential, we list them here:
$$ \mathbf{f} = - \eta_{12} ( U_r \cdot { \frac{\partial \chi_{12}
}{\partial r} } + \chi_{12} \cdot { \frac{\partial U_r }{\partial r} }
) $$
where the derivative of $U_r$ is given by (see Allen reference)
$$ \frac{\partial U_r }{\partial r} = \frac{ \partial U_{SLJ} }{
\partial r } \hat{\mathbf{r}}_{12} + r^{-2} \frac{ \partial U_{SLJ} }{
\partial \varphi } [ \mathbf{\kappa} - ( \mathbf{\kappa}^T \cdot
\hat{\mathbf{r}}_{12}) \hat{\mathbf{r}}_{12} ], $$
$$ \frac{ \partial U_{SLJ} }{ \partial \varphi } = 24 \epsilon ( 2
\varrho^{13} - \varrho^7 ) \sigma_{12}^3 / 2 \sigma, $$
$$ \frac{ \partial U_{SLJ} }{ \partial r } = 24 \epsilon ( 2
\varrho^{13} - \varrho^7 ) / \sigma, $$
and
$$ \mathbf{\kappa} = \mathbf{G}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
The derivate of the $\chi$ term is given by
$$ \frac{\partial \chi_{12} }{\partial r} = - r^{-2} \cdot 4.0 \cdot [
\mathbf{\iota} - ( \mathbf{\iota}^T \cdot \hat{\mathbf{r}}_{12} )
\hat{\mathbf{r}}_{12} ] \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu
}, $$
and
$$ \mathbf{\iota} = \mathbf{B}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
The torque is given by:
$$ \mathbf{\tau}_i = U_r \eta_{12} \frac{ \partial \chi_{12} }{
\partial \mathbf{q}_i } + \chi_{12} ( U_r \frac{ \partial \eta_{12} }{
\partial \mathbf{q}_i } + \eta_{12} \frac{ \partial U_r }{ \partial
\mathbf{q}_i } ), $$
$$ \frac{ \partial U_r }{ \partial \mathbf{q}_i } = \mathbf{A}_i \cdot
(- \mathbf{\kappa}^T \cdot \mathbf{G}_i \times \mathbf{f}_k ), $$
$$ \mathbf{f}_k = - r^{-2} \frac{ \delta U_{SLJ} }{ \delta \varphi }
\mathbf{\kappa}, $$
and
$$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
\times \mathbf{\iota} ). $$
For the derivative of the $\eta$ term, we were unable to find a matrix
expression due to the determinant. Let $a_{mi}$ be the mth row of the
rotation matrix $A_i$. Then,
$$ \frac{ \partial \eta_{12} }{ \partial \mathbf{q}_i } = \mathbf{A}_i
\cdot \sum_m \mathbf{a}_{mi} \times \frac{ \partial \eta_{12} }{
\partial \mathbf{a}_{mi} } = \mathbf{A}_i \cdot \sum_m \mathbf{a}_{mi}
\times \mathbf{d}_{mi}, $$
where $d_mi$ represents the mth row of a derivative matrix $D_i$,
$$ \mathbf{D}_i = - \frac{1}{2} \cdot ( \frac{2s1s2}{\det (
\mathbf{G}_{12} ) } )^{ \upsilon / 2 } \cdot {\frac{\upsilon}{\det (
\mathbf{G}_{12} ) }} \cdot \mathbf{E}, $$
where the matrix $E$ gives the derivate with respect to the rotation
matrix,
$$ \mathbf{E} = [ e_{my} ] = \frac{ \partial \eta_{12} }{ \partial
\mathbf{A}_i }, $$
and
$$ e_{my} = \det ( \mathbf{G}_{12} ) \cdot \mbox{trace} [
\mathbf{G}_{12}^{-1} \cdot ( \hat{\mathbf{p}}_y \otimes \mathbf{a}_m +
\mathbf{a}_m \otimes \hat{\mathbf{p}}_y ) \cdot s_{mm}^2 ]. $$
Here, $p_v$ is the unit vector for the axes in the lab frame $(p1=[1, 0,
0], p2=[0, 1, 0], and p3=[0, 0, 1])$ and $s_{mm}$ gives the mth radius of
the ellipsoid $i$.
\end{document}

2
doc/Eqs/pair_lj.tex
View File

@ -8,4 +8,4 @@ $$
\qquad r < r_c
$$
\end{document}
\end{document}

27
doc/Section_commands.html
View File

@ -319,11 +319,11 @@ description:
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
@ -334,7 +334,8 @@ description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A><A HREF = "compute_variable_atom.html">variable/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
</TD></TR></TABLE></DIV>
<HR>
@ -347,13 +348,13 @@ full description:
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_gran.html">gran/history</A></TD><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_gran.html">gran/history</A></TD><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
</TD></TR></TABLE></DIV>
<HR>

6
doc/Section_commands.txt
View File

@ -394,6 +394,7 @@ description:
"nph"_fix_nph.html,
"npt"_fix_npt.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/gran"_fix_nve_gran.html,
"nve/noforce"_fix_nve_noforce.html,
"nvt"_fix_nvt.html,
@ -436,9 +437,11 @@ description:
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/partial"_compute_temp_partial.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html
"temp/region"_compute_temp_region.html,
"variable"_compute_variable.html,
"variable/atom"_compute_variable_atom.html :tb(c=6,ea=c)
:line
@ -459,6 +462,7 @@ full description:
"eam/alloy/opt"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"gayberne"_pair_gayberne.html,
"gran/hertzian"_pair_gran.html,
"gran/history"_pair_gran.html,
"gran/no_history"_pair_gran.html,

56
doc/Section_start.html
View File

@ -272,6 +272,7 @@ can see the list of packages by typing "make package". The current
list of packages is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >asphere </TD><TD > aspherical particles</TD></TR>
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
@ -293,7 +294,7 @@ This will produce a smaller executable which may run a bit faster.
<P>By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
editing of your machine Makefile.
editing of your src/MAKE/Makefile.machine.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@ -316,33 +317,19 @@ overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
</P>
<P>To use the "poems" package you must build LAMMPS with the POEMS
library, which computes the constrained rigid-body motion of
articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI) and a version is included in the LAMMPS distribution
under the "lib" directory. To build LAMMPS with POEMS, you must use a
low-level LAMMPS Makefile that includes the POEMS directory in its
paths. See Makefile.g++_poems as an example. You must also build
POEMS itself as a library before building LAMMPS, so that LAMMPS can
link against it. The POEMS library is built by typing "make" from
within the poems directory with the appropriate Makefile, e.g. "make
-f Makefile.g++". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
</P>
<P>To use the "meam" package you must build LAMMPS with the MEAM library,
which computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia and is included under the "lib" directory. To build
LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
includes the MEAM directory in its paths. See Makefile.linux_meam as
an example. You must also build MEAM itself as a library before
building LAMMPS, so that LAMMPS can link against it. This requires a
F90 compiler. The library is built by typing "make" from within the
meam directory with the appropriate Makefile, e.g. "make -f
Makefile.icc". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
<P>To use the "meam" package you must build LAMMPS with the MEAM library
in lib/meam, which computes the modified embedded atom method
potential, which is a generalization of EAM potentials that can be
used to model a wider variety of materials. This MEAM implementation
was written by Greg Wagner at Sandia. To build LAMMPS with MEAM, you
must use a low-level LAMMPS Makefile that includes the MEAM directory
in its paths. See Makefile.linux_meam as an example. You must also
build MEAM itself as a library before building LAMMPS, so that LAMMPS
can link against it. This requires a F90 compiler. The library is
built by typing "make" from within the meam directory with the
appropriate Makefile, e.g. "make -f Makefile.icc". If one of the
provided Makefiles is not appropriate for your system you can edit or
add one as needed.
</P>
<P>Note that linking a Fortran library to a C++ code can be problematic
(e.g. Fortran routine names can't be found due to non-standard
@ -350,6 +337,19 @@ underscore rules) and typically requires additional C++ or F90
libraries be included in the link. You may need to read documentation
for your compiler about how to do this correctly.
</P>
<P>To use the "poems" package you must build LAMMPS with the POEMS
library in lib/poems, which computes the constrained rigid-body motion
of articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI). To build LAMMPS with POEMS, you must use a low-level
LAMMPS Makefile that includes the POEMS directory in its paths. See
Makefile.g++_poems as an example. You must also build POEMS itself as
a library before building LAMMPS, so that LAMMPS can link against it.
The POEMS library is built by typing "make" from within the poems
directory with the appropriate Makefile, e.g. "make -f Makefile.g++".
If one of the provided Makefiles is not appropriate for your system
you can edit or add one as needed.
</P>
<H4><A NAME = "2_4"></A>2.4 Building LAMMPS as a library
</H4>
<P>LAMMPS can be built as a library, which can then be called from

56
doc/Section_start.txt
View File

@ -266,6 +266,7 @@ fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
asphere : aspherical particles
class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
@ -286,7 +287,7 @@ This will produce a smaller executable which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
editing of your machine Makefile.
editing of your src/MAKE/Makefile.machine.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
@ -309,33 +310,19 @@ overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
To use the "poems" package you must build LAMMPS with the POEMS
library, which computes the constrained rigid-body motion of
articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI) and a version is included in the LAMMPS distribution
under the "lib" directory. To build LAMMPS with POEMS, you must use a
low-level LAMMPS Makefile that includes the POEMS directory in its
paths. See Makefile.g++_poems as an example. You must also build
POEMS itself as a library before building LAMMPS, so that LAMMPS can
link against it. The POEMS library is built by typing "make" from
within the poems directory with the appropriate Makefile, e.g. "make
-f Makefile.g++". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
To use the "meam" package you must build LAMMPS with the MEAM library,
which computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia and is included under the "lib" directory. To build
LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
includes the MEAM directory in its paths. See Makefile.linux_meam as
an example. You must also build MEAM itself as a library before
building LAMMPS, so that LAMMPS can link against it. This requires a
F90 compiler. The library is built by typing "make" from within the
meam directory with the appropriate Makefile, e.g. "make -f
Makefile.icc". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
To use the "meam" package you must build LAMMPS with the MEAM library
in lib/meam, which computes the modified embedded atom method
potential, which is a generalization of EAM potentials that can be
used to model a wider variety of materials. This MEAM implementation
was written by Greg Wagner at Sandia. To build LAMMPS with MEAM, you
must use a low-level LAMMPS Makefile that includes the MEAM directory
in its paths. See Makefile.linux_meam as an example. You must also
build MEAM itself as a library before building LAMMPS, so that LAMMPS
can link against it. This requires a F90 compiler. The library is
built by typing "make" from within the meam directory with the
appropriate Makefile, e.g. "make -f Makefile.icc". If one of the
provided Makefiles is not appropriate for your system you can edit or
add one as needed.
Note that linking a Fortran library to a C++ code can be problematic
(e.g. Fortran routine names can't be found due to non-standard
@ -343,6 +330,19 @@ underscore rules) and typically requires additional C++ or F90
libraries be included in the link. You may need to read documentation
for your compiler about how to do this correctly.
To use the "poems" package you must build LAMMPS with the POEMS
library in lib/poems, which computes the constrained rigid-body motion
of articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI). To build LAMMPS with POEMS, you must use a low-level
LAMMPS Makefile that includes the POEMS directory in its paths. See
Makefile.g++_poems as an example. You must also build POEMS itself as
a library before building LAMMPS, so that LAMMPS can link against it.
The POEMS library is built by typing "make" from within the poems
directory with the appropriate Makefile, e.g. "make -f Makefile.g++".
If one of the provided Makefiles is not appropriate for your system
you can edit or add one as needed.
2.4 Building LAMMPS as a library :h4,link(2_4)
LAMMPS can be built as a library, which can then be called from

23
doc/atom_style.html
View File

@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dpd</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -53,18 +53,23 @@ velocities, atom IDs and types.
<LI><I>bond</I> = bonds - e.g. bead-spring polymers
<LI><I>charge</I> = charge
<LI><I>dpd</I> = default values, also communicates velocities
<LI><I>ellipsoid</I> = quaternion for particle orientation, angular velocity/momentum
<LI><I>molecular</I> = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
<LI><I>full</I> = molecular + charge - e.g. biomolecules, charged polymers
<LI><I>granular</I> = granular atoms with rotational properties
</UL>
<P>Typical simulations with a single pair potential will use only one of
these styles. For cases where multiple pair potentials will be used
(see the <A HREF = "pair_style.html">pair_style</A> <I>hybrid</I> command), it may be
necessary to use multiple atom styles. Another example is doing a DPD
simulations with bonds or angles. In these cases the <I>hybrid</I> style
can be used to list multiple atom styles. Atoms will then store and
communicate the union of all quantities implied by the individual
styles.
<P>Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the <I>charge</I> style.
If some atoms have bonds, but others do not, use the <I>bond</I> style.
The only scenario where the <I>hybrid</I> style is needed is if there is no
single style which defines all needed properties of all atoms.
E.g. if you want charged DPD particles, you would need to use
"atom_style hybrid dpd charge". When a hybrid style is used, atoms
store and communicate the union of all quantities implied by the
individual styles.
</P>
<P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
section</A>.

23
doc/atom_style.txt
View File

@ -12,7 +12,7 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dpd} or \
style = {angle} or {atomic} or {bond} or {charge} or {dpd} or {ellipsoid} or \
{full} or {granular} or {molecular} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -50,18 +50,23 @@ velocities, atom IDs and types.
{bond} = bonds - e.g. bead-spring polymers
{charge} = charge
{dpd} = default values, also communicates velocities
{ellipsoid} = quaternion for particle orientation, angular velocity/momentum
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
{full} = molecular + charge - e.g. biomolecules, charged polymers
{granular} = granular atoms with rotational properties :ul
Typical simulations with a single pair potential will use only one of
these styles. For cases where multiple pair potentials will be used
(see the "pair_style"_pair_style.html {hybrid} command), it may be
necessary to use multiple atom styles. Another example is doing a DPD
simulations with bonds or angles. In these cases the {hybrid} style
can be used to list multiple atom styles. Atoms will then store and
communicate the union of all quantities implied by the individual
styles.
Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the {charge} style.
If some atoms have bonds, but others do not, use the {bond} style.
The only scenario where the {hybrid} style is needed is if there is no
single style which defines all needed properties of all atoms.
E.g. if you want charged DPD particles, you would need to use
"atom_style hybrid dpd charge". When a hybrid style is used, atoms
store and communicate the union of all quantities implied by the
individual styles.
LAMMPS can be extended with new atom styles; see "this
section"_Section_modify.html.

1
doc/compute.html
View File

@ -75,6 +75,7 @@ defined in LAMMPS:
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature after subtracting a ramped velocity component
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_variable.html">variable</A> - calculate a scalar value from a variable
<LI><A HREF = "compute_variable_atom.html">variable/atom</A> - calculate a formula for each atom
</UL>
<P><B>Restrictions:</B> none

1
doc/compute.txt
View File

@ -72,6 +72,7 @@ defined in LAMMPS:
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/ramp"_compute_temp_ramp.html - temperature after subtracting a ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"variable"_compute_variable.html - calculate a scalar value from a variable
"variable/atom"_compute_variable_atom.html - calculate a formula for each atom :ul
[Restrictions:] none

47
doc/compute_temp_asphere.html Normal file
View File

@ -0,0 +1,47 @@
<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/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/asphere
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/asphere = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp/asphere
compute myTemp mobile temp/asphere
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
aspherical or ellipsoidal particles. The computation is similar to
<A HREF = "compute_temp.html">compute_temp</A>, however, additional degrees of
freedom (2 or 3) are incorporated for particles where the principal
moments of inertia are unequal. The associated kinetic energy thus
includes a rotational term KE_rotational = 1/2 I w^2, where I is the
moment of inertia and w is the angular velocity.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

42
doc/compute_temp_asphere.txt Executable file
View File

@ -0,0 +1,42 @@
"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/asphere command :h3
[Syntax:]
compute ID group-ID temp/asphere :pre
ID, group-ID are documented in "compute"_compute.html command
temp/asphere = style name of this compute command :ul
[Examples:]
compute 1 all temp/asphere
compute myTemp mobile temp/asphere :pre
[Description:]
Define a computation that calculates the temperature of a group of
aspherical or ellipsoidal particles. The computation is similar to
"compute_temp"_compute_temp.html, however, additional degrees of
freedom (2 or 3) are incorporated for particles where the principal
moments of inertia are unequal. The associated kinetic energy thus
includes a rotational term KE_rotational = 1/2 I w^2, where I is the
moment of inertia and w is the angular velocity.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
[Related commands:]
"compute temp"_compute_temp.html
[Default:] none

2
doc/compute_temp_region.html
View File

@ -36,7 +36,7 @@ temp/rescale</A>, etc.
<P>Note that a <I>region</I>-style temperature can be used to thermostat with
<A HREF = "fix_temp_rescale.html">fix temp/rescale</A> or <A HREF = "fix_langevin.html">fix
langevin</A>, but should probably not be used with
Nose/Hoover style fixes (<A HREF = "fix_nvt.html<A HREF = "fix_npt.html">>fix nvt</A>, fix
Nose/Hoover style fixes (<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_npt.html">fix
npt</A>, or <A HREF = "fix_nph.html">fix nph</A>), if the
degrees-of-freedom included in the computed T varies with time.
</P>

2
doc/compute_temp_region.txt
View File

@ -33,7 +33,7 @@ temp/rescale"_fix_temp_rescale.html, etc.
Note that a {region}-style temperature can be used to thermostat with
"fix temp/rescale"_fix_temp_rescale.html or "fix
langevin"_fix_langevin.html, but should probably not be used with
Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, fix
Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, "fix
npt"_fix_npt.html, or "fix nph"_fix_nph.html), if the
degrees-of-freedom included in the computed T varies with time.

55
doc/compute_variable.html Normal file
View File

@ -0,0 +1,55 @@
<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 variable command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID variable name
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>variable/atom = style name of this compute command
<LI>name = variable name to invoke to compute a scalar quantity
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all variable myTemp
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates a formula that returns a scalar
quantity. This quantity can be time averaged and output via the <A HREF = "fix_ave_time.html">fix
ave/time</A> command. It could also be output via the
<A HREF = "thermo_style.html">thermo_style custom</A> command, although it makes
more sense to access the variable directly in this case.
</P>
<P>The formula is defined by the <A HREF = "variable.html">variable equal</A> command.
A variable of style <I>equal</I> can access properties of the system, such
as volume or temperature, and also reference individual atom
attributes, such as its coordinates or velocity.
</P>
<P>For example, these 3 commands would time average the system density
(assuming the volume fluctuates) temperature and output the average
value periodically to the file den.profile:
</P>
<PRE>variable den equal div(atoms,vol)
compute density all variable den
fix 1 all ave/time 1 1000 density 0 den.profile
</PRE>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "variable.html">variable</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

50
doc/compute_variable.txt Normal file
View File

@ -0,0 +1,50 @@
"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 variable command :h3
[Syntax:]
compute ID group-ID variable name :pre
ID, group-ID are documented in "compute"_compute.html command
variable/atom = style name of this compute command
name = variable name to invoke to compute a scalar quantity :ul
[Examples:]
compute 1 all variable myTemp :pre
[Description:]
Define a computation that calculates a formula that returns a scalar
quantity. This quantity can be time averaged and output via the "fix
ave/time"_fix_ave_time.html command. It could also be output via the
"thermo_style custom"_thermo_style.html command, although it makes
more sense to access the variable directly in this case.
The formula is defined by the "variable equal"_variable.html command.
A variable of style {equal} can access properties of the system, such
as volume or temperature, and also reference individual atom
attributes, such as its coordinates or velocity.
For example, these 3 commands would time average the system density
(assuming the volume fluctuates) temperature and output the average
value periodically to the file den.profile:
variable den equal div(atoms,vol)
compute density all variable den
fix 1 all ave/time 1 1000 density 0 den.profile :pre
[Restrictions:] none
[Related commands:]
"fix ave/time"_fix_ave_time.html, "variable"_variable.html
[Default:] none

19
doc/dump.html
View File

@ -37,7 +37,8 @@
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID[N]
@ -52,7 +53,8 @@
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
tqx,tqy,tqz = torque on dipolar atoms
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
@ -228,10 +230,15 @@ directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> keywords. The
<A HREF = "dump_modify.html">dump_modify</A> command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
</P>
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I>, <I>tqy</I>, <I>tqx</I>, <I>tqy</I> keywords are specific
to dipolar systems defined with an atom style of <I>dipole</I>. The first
3 give the orientation of the atom's dipole. The latter 3 give the
torque on the dipolar atoms.
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> keywords are specific to dipolar systems
defined with an atom style of <I>dipole</I>. They give the orientation of
the atom's dipole.
</P>
<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I>, <I>tqx</I>, <I>tqy</I>, <I>tqz</I> keywords
are specific to aspherical particles defined with an atom style of
<I>ellipsoid</I>. The first 4 are the components of the quaternion that
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
</P>
<P>The <I>epair</I>, <I>ke</I>, <I>etotal</I>, <I>centro</I>, and <I>sxx</I>, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +

19
doc/dump.txt
View File

@ -28,7 +28,8 @@ args = list of arguments for a particular style :l
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID\[N\]
@ -43,7 +44,8 @@ args = list of arguments for a particular style :l
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
tqx,tqy,tqz = torque on dipolar atoms
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
@ -218,10 +220,15 @@ directly using the {ix}, {iy}, {iz} keywords. The
"dump_modify"_dump_modify.html command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} keywords are specific
to dipolar systems defined with an atom style of {dipole}. The first
3 give the orientation of the atom's dipole. The latter 3 give the
torque on the dipolar atoms.
The {mux}, {muy}, {muz} keywords are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of
the atom's dipole.
The {quatw}, {quati}, {quatj}, {quatk}, {tqx}, {tqy}, {tqz} keywords
are specific to aspherical particles defined with an atom style of
{ellipsoid}. The first 4 are the components of the quaternion that
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +

43
doc/fix_nve_asphere.html Normal file
View File

@ -0,0 +1,43 @@
<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/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/asphere
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/asphere = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/asphere
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position, velocity, and angular
velocity for aspherical or ellipsoidal particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

38
doc/fix_nve_asphere.txt Executable file
View File

@ -0,0 +1,38 @@
"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/asphere command :h3
[Syntax:]
fix ID group-ID nve/asphere :pre
ID, group-ID are documented in "fix"_fix.html command
nve/asphere = style name of this fix command :ul
[Examples:]
fix 1 all nve/asphere :pre
[Description:]
Perform constant NVE updates of position, velocity, and angular
velocity for aspherical or ellipsoidal particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
[Related commands:]
"fix nve"_fix_nve.html
[Default:] none

6
doc/next.html
View File

@ -77,7 +77,7 @@ finished.
<P>Jump and next commands can also be nested to enable multi-level loops.
For example, this script will run 15 simulations in a double loop.
</P>
<P>variable i loop 3
<PRE>variable i loop 3
variable j loop 5
clear
...
@ -87,8 +87,8 @@ run 10000
next j
jump in.script
next i
jump in.script
</P>
jump in.script
</PRE>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

2
doc/next.txt
View File

@ -84,7 +84,7 @@ run 10000
next j
jump in.script
next i
jump in.script
jump in.script :pre
[Restrictions:] none

6
doc/pair_charmm.html
View File

@ -113,6 +113,12 @@ because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
</P>
<P>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all CHARMM potentials is to use the <I>arithmetic</I> formulas documented
by the <A HREF = "pair_modify.html">pair_modify</A> command. The <A HREF = "pair_modify.html">pair_modify
mix</A> setting is thus ignored for CHARMM potentials.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>

6
doc/pair_charmm.txt
View File

@ -106,6 +106,12 @@ because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all CHARMM potentials is to use the {arithmetic} formulas documented
by the "pair_modify"_pair_modify.html command. The "pair_modify
mix"_pair_modify.html setting is thus ignored for CHARMM potentials.
[Restrictions:]
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}

8
doc/pair_class2.html
View File

@ -86,6 +86,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
</P>
<P>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the <I>sixthpower</I> formulas documented
by the <A HREF = "pair_modify.html">pair_modify</A> command. The <A HREF = "pair_modify.html">pair_modify
mix</A> setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
</P>
<P><B>Restrictions:</B>
</P>
<P>These styles are part of the "class2" package. They are only enabled

8
doc/pair_class2.txt
View File

@ -80,6 +80,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the {sixthpower} formulas documented
by the "pair_modify"_pair_modify.html command. The "pair_modify
mix"_pair_modify.html setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
[Restrictions:]
These styles are part of the "class2" package. They are only enabled

1
doc/pair_coeff.html
View File

@ -93,6 +93,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects

1
doc/pair_coeff.txt
View File

@ -90,6 +90,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects

125
doc/pair_gayberne.html Normal file
View File

@ -0,0 +1,125 @@
<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 gayberne command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style gayberne gamma upsilon mu cutoff
</PRE>
<UL><LI>gamma = shift for potential minimum (typically 1)
<LI>upsilon = exponent for eta orientation-dependent energy function
<LI>mu = exponent for chi orientation-dependent energy function
<LI>cutoff = global cutoff for interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>gayberne</I> computes a Gay-Berne anisotropic LJ interaction
<A HREF = "#Beradi">(Beradi)</A> between pairs of ellipsoidal particles via the
formulas
</P>
<CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
</CENTER>
<P>where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma.
</P>
<P>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures <A HREF = "#Everaers">(Everaers)</A>:
</P>
<CENTER><IMG SRC = "Eqs/pair_gayberne2.jpg">
</CENTER>
<P>The variable names utilized as potential parameters are for the most
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>.
Use of this pair style requires the
<A HREF = "fix_nve_asphere.html">fix nve/asphere</A> in order to integrate particle
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
be used since it defines the rotation state of the ellipsoidal
particles.
</P>
<P>More details of the Gay-Berne formulation are given in the references
listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>.
</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:
</P>
<UL><LI>epsilon = well depth (energy units)
<LI>sigma = minimum effective particle radii (distance units)
<LI>a = ellipsoid radius in x dimension (distance units)
<LI>b = ellipsoid radius in y dimension (distance units)
<LI>c = ellipsoid radius in z dimension (distance units)
<LI>epsilon_a = relative well depth for side-to-side interactions
<LI>epsilon_b = relative well depth for face-to-face interactions
<LI>epsilon_c = relative well depth for end-to-end interactions
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
</P>
<P>The epsilon and sigma parameters are mixed for I != J atom pairings
the same as Lennard-Jones parameters; see the <A HREF = "pair_modify.html">pair_modify
mix</A> documentation for details. The other parameters
(except cutoff) are really specific to a single atom type, and not a
pair of atoms. Thus they are applied to atom type I only.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with <A HREF = "atom_style.html">atom_style ellipsoid</A>.
</P>
<P>The use of this potential requires additional fixes as described
above. The "shift yes" option currently cannot be used with this
potential to shift energies to 0 at the cutoff due to the anisotropic
dependence of the interaction. Angular velocities are all set to zero
initially. The Gay-Berne potential does not become isotropic as r
increases <A HREF = "#Everaers">(Everaers)</A>. The distance of closest approach
approximation becomes less accurate as the shape of ellipsoids becomes
more dissimilar (high aspect ratio particles).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Everaers"></A>
<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
</P>
<A NAME = "Berardi"></A>
<P><B>(Berardi)</B> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
</P>
<A NAME = "Perram"></A>
<P><B>(Perram)</B> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
</P>
<A NAME = "Allen"></A>
<P><B>(Allen)</B> Allen and Germano, Mol Phys 104, 3225-3235 (2006).
</P>
</HTML>

116
doc/pair_gayberne.txt Executable file
View File

@ -0,0 +1,116 @@
"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 gayberne command :h3
[Syntax:]
pair_style gayberne gamma upsilon mu cutoff :pre
gamma = shift for potential minimum (typically 1)
upsilon = exponent for eta orientation-dependent energy function
mu = exponent for chi orientation-dependent energy function
cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
Style {gayberne} computes a Gay-Berne anisotropic LJ interaction
"(Beradi)"_#Beradi between pairs of ellipsoidal particles via the
formulas
:c,image(Eqs/pair_gayberne.jpg)
where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma.
For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures "(Everaers)"_#Everaers:
:c,image(Eqs/pair_gayberne2.jpg)
The variable names utilized as potential parameters are for the most
part taken from "(Everaers)"_#Everaers in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given "here"_Eqs/pair_gayberne_extra.pdf.
Use of this pair style requires the
"fix nve/asphere"_fix_nve_asphere.html in order to integrate particle
rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
be used since it defines the rotation state of the ellipsoidal
particles.
More details of the Gay-Berne formulation are given in the references
listed below and in "this document"_Eqs/pair_gayberne_extra.pdf.
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:
epsilon = well depth (energy units)
sigma = minimum effective particle radii (distance units)
a = ellipsoid radius in x dimension (distance units)
b = ellipsoid radius in y dimension (distance units)
c = ellipsoid radius in z dimension (distance units)
epsilon_a = relative well depth for side-to-side interactions
epsilon_b = relative well depth for face-to-face interactions
epsilon_c = relative well depth for end-to-end interactions
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
The epsilon and sigma parameters are mixed for I != J atom pairings
the same as Lennard-Jones parameters; see the "pair_modify
mix"_pair_modify.html documentation for details. The other parameters
(except cutoff) are really specific to a single atom type, and not a
pair of atoms. Thus they are applied to atom type I only.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with "atom_style ellipsoid"_atom_style.html.
The use of this potential requires additional fixes as described
above. The "shift yes" option currently cannot be used with this
potential to shift energies to 0 at the cutoff due to the anisotropic
dependence of the interaction. Angular velocities are all set to zero
initially. The Gay-Berne potential does not become isotropic as r
increases "(Everaers)"_#Everaers. The distance of closest approach
approximation becomes less accurate as the shape of ellipsoids becomes
more dissimilar (high aspect ratio particles).
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html,
"compute temp/asphere"_compute_temp_asphere.html
[Default:] none
:line
:link(Everaers)
[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
:link(Berardi)
[(Berardi)] Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
:link(Perram)
[(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
:link(Allen)
[(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006).

7
doc/pair_lj_expand.html
View File

@ -49,6 +49,13 @@ commands:
<P>The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
</P>
<P>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule is set by the
<A HREF = "pair_modify.html">pair_modify</A> command. Additionally, the delta
coefficient is always mixed by the rule
</P>
<PRE>delta_ij = (delta_i + delta_j) / 2
</PRE>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

7
doc/pair_lj_expand.txt
View File

@ -46,6 +46,13 @@ cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule is set by the
"pair_modify"_pair_modify.html command. Additionally, the delta
coefficient is always mixed by the rule
delta_ij = (delta_i + delta_j) / 2 :pre
[Restrictions:] none
[Related commands:]

26
doc/pair_modify.html
View File

@ -49,13 +49,15 @@ not affected by this setting.
</P>
<P>The <I>mix</I> keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
J, when I != J. (I = J coefficients are set explicitly in the data
file or input script.) The <A HREF = "pair_coeff.html">pair_coeff</A> command can
be used in the input script to specify epilon/sigma for a specific I,J
pairing, which overrides the setting of the <I>mix</I> keyword. In each
case, the LJ cutoff is mixed the same way as sigma.
J, when I != J. Coefficients for I = J are set explicitly in the data
file or input script. The <A HREF = "pair_coeff.html">pair_coeff</A> command can be
used in the input script to specify epilon/sigma for a specific I != J
pairing, which overrides the setting of the <I>mix</I> keyword.
</P>
<P>These are the formulas used by the 3 <I>mix</I> options:
<P>These are the formulas used by the 3 <I>mix</I> options. In each case, the
LJ cutoff is mixed the same way as sigma. Note that some of these
options are not available for certain pair styles. See the doc page
for individual pair styles for those restrictions.
</P>
<P><I>geometric</I>
</P>
@ -71,17 +73,7 @@ sigma_ij = (sigma_i + sigma_j) / 2
</P>
<PRE>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</PRE>
<P>Style <I>soft</I> only uses a pre-factor coefficient, which is always mixed
geometrically, regardless of the <I>mix</I> setting. The <I>charmm</I> styles
are always mixed arithmetically, regardless of the <I>mix</I> setting. The
<I>class2</I> styles are always mixed as a sixthpower, regardless of the
<I>mix</I> setting, except that the cutoff is mixed according to the mix
setting. Style <I>lj/expand</I> always mixes its delta coefficient using
the rule
</P>
<PRE>delta_ij = (delta_i + delta_j) / 2
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</PRE>
<P>The <I>table</I> keyword applies to pair styles with a long-range Coulombic
term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a

26
doc/pair_modify.txt
View File

@ -43,13 +43,15 @@ not affected by this setting.
The {mix} keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
J, when I != J. (I = J coefficients are set explicitly in the data
file or input script.) The "pair_coeff"_pair_coeff.html command can
be used in the input script to specify epilon/sigma for a specific I,J
pairing, which overrides the setting of the {mix} keyword. In each
case, the LJ cutoff is mixed the same way as sigma.
J, when I != J. Coefficients for I = J are set explicitly in the data
file or input script. The "pair_coeff"_pair_coeff.html command can be
used in the input script to specify epilon/sigma for a specific I != J
pairing, which overrides the setting of the {mix} keyword.
These are the formulas used by the 3 {mix} options:
These are the formulas used by the 3 {mix} options. In each case, the
LJ cutoff is mixed the same way as sigma. Note that some of these
options are not available for certain pair styles. See the doc page
for individual pair styles for those restrictions.
{geometric}
@ -65,17 +67,7 @@ sigma_ij = (sigma_i + sigma_j) / 2 :pre
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
Style {soft} only uses a pre-factor coefficient, which is always mixed
geometrically, regardless of the {mix} setting. The {charmm} styles
are always mixed arithmetically, regardless of the {mix} setting. The
{class2} styles are always mixed as a sixthpower, regardless of the
{mix} setting, except that the cutoff is mixed according to the mix
setting. Style {lj/expand} always mixes its delta coefficient using
the rule
delta_ij = (delta_i + delta_j) / 2 :pre
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
The {table} keyword applies to pair styles with a long-range Coulombic
term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a

6
doc/pair_soft.html
View File

@ -54,6 +54,12 @@ or switch to a new pair style.
<P>The last coefficient is optional. If not specified, the global soft
cutoff is used.
</P>
<P>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for Astart and Astop is
as follows:
</P>
<PRE>A_ij = sqrt(A_i * A_j)
</PRE>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

6
doc/pair_soft.txt
View File

@ -51,6 +51,12 @@ or switch to a new pair style.
The last coefficient is optional. If not specified, the global soft
cutoff is used.
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for Astart and Astop is
as follows:
A_ij = sqrt(A_i * A_j) :pre
[Restrictions:] none
[Related commands:]

1
doc/pair_style.html
View File

@ -99,6 +99,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects

1
doc/pair_style.txt
View File

@ -96,6 +96,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects

26
doc/read_data.html
View File

@ -253,6 +253,7 @@ line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z
@ -266,7 +267,8 @@ line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
<LI>q = charge on atom
<LI>diameter = diameter of atom
<LI>density = density of atom
<LI>x,y,z = coordinates of atom
<LI>x,y,z = coordinates of atom
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
</UL>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
@ -575,15 +577,25 @@ script.
<LI>line syntax: depends on atom style
</UL>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >all styles except granular</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz phix phiy phiz
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz wx wy wz
</TD></TR></TABLE></DIV>
<P>where the keywords have these meanings:
</P>
<UL><LI>vx,vy,vz = translational velocity of atom
<LI>lx,ly,lz = angular momentum of aspherical atom
<LI>wx,wy,wz = angular velocity of granular atom
</UL>
<P>The velocity lines can appear in any order. This section can only be
used after an <I>Atoms</I> section. The <I>Atoms</I> section must have assigned
a unique atom ID to each atom so that velocities can be assigned in
this way. Vx,vy,vz are in <A HREF = "units.html">units</A> of velocity.
Phix,phiy,phiz are in units of angular velocity (radians/time).
used after an <I>Atoms</I> section. This is because the <I>Atoms</I> section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
</P>
<P>Vx,vy,vz are in <A HREF = "units.html">units</A> of velocity. Lx, ly, lz are in
units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
units of angular velocity (radians/time).
</P>
<P>Translational velocities can also be set by the
<A HREF = "velocity.html">velocity</A> command in the input script.

26
doc/read_data.txt
View File

@ -231,6 +231,7 @@ atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dpd: atom-ID atom-type x y z
ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
molecular: atom-ID molecule-ID atom-type x y z :tb(s=:)
@ -243,7 +244,8 @@ type-ID = type of atom (1-Ntype)
q = charge on atom
diameter = diameter of atom
density = density of atom
x,y,z = coordinates of atom :ul
x,y,z = coordinates of atom
quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
@ -491,14 +493,24 @@ script.
one line per atom
line syntax: depends on atom style :ul
all styles except granular: atom-ID vx vy vz
granular: atom-ID vx vy vz phix phiy phiz :tb(s=:)
all styles except those listed: atom-ID vx vy vz
ellipsoid: atom-ID vx vy vz lx ly lz
granular: atom-ID vx vy vz wx wy wz :tb(s=:)
where the keywords have these meanings:
vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of granular atom :ul
The velocity lines can appear in any order. This section can only be
used after an {Atoms} section. The {Atoms} section must have assigned
a unique atom ID to each atom so that velocities can be assigned in
this way. Vx,vy,vz are in "units"_units.html of velocity.
Phix,phiy,phiz are in units of angular velocity (radians/time).
used after an {Atoms} section. This is because the {Atoms} section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
Vx,vy,vz are in "units"_units.html of velocity. Lx, ly, lz are in
units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
units of angular velocity (radians/time).
Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.