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26
doc/Section_commands.html
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@ -384,16 +384,16 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</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_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/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/gpu</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_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</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_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</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_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
@ -426,8 +426,8 @@ angle potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are angle styles contributed by users, which can be used if
@ -460,7 +460,7 @@ description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
</TD></TR></TABLE></DIV>
<HR>

6
doc/Section_commands.txt
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@ -579,6 +579,8 @@ potentials. Click on the style itself for a full description:
"gran/hertz/history"_pair_gran.html,
"gran/hooke"_pair_gran.html,
"gran/hooke/history"_pair_gran.html,
"hbond/dreiding/lj"_pair_hbond_dreiding.html,
"hbond/dreiding/morse"_pair_hbond_dreiding.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
@ -657,6 +659,7 @@ angle potentials. Click on the style itself for a full description:
"class2"_angle_class2.html,
"cosine"_angle_cosine.html,
"cosine/delta"_angle_cosine_delta.html,
"cosine/periodic"_angle_cosine_periodic.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html,
"table"_angle_table.html :tb(c=4,ea=c,w=100)
@ -695,7 +698,8 @@ description:
"hybrid"_improper_hybrid.html,
"class2"_improper_class2.html,
"cvff"_improper_cvff.html,
"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100)
"harmonic"_improper_harmonic.html,
"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
:line

160
doc/Section_howto.html
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@ -16,7 +16,7 @@ certain kinds of LAMMPS simulations.
</P>
4.1 <A HREF = "#4_1">Restarting a simulation</A><BR>
4.2 <A HREF = "#4_2">2d simulations</A><BR>
4.3 <A HREF = "#4_3">CHARMM and AMBER force fields</A><BR>
4.3 <A HREF = "#4_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
4.4 <A HREF = "#4_4">Running multiple simulations from one input script</A><BR>
4.5 <A HREF = "#4_5">Multi-replica simulations</A><BR>
4.6 <A HREF = "#4_6">Granular models</A><BR>
@ -31,8 +31,7 @@ certain kinds of LAMMPS simulations.
4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
4.17 <A HREF = "#4_17">Walls</A><BR>
4.18 <A HREF = "#4_18">Elastic constants</A><BR>
4.19 <A HREF = "#4_19">Computing free energies from thermodyanmic integration</A> <BR>
4.18 <A HREF = "#4_18">Elastic constants</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -167,19 +166,18 @@ the same as in 3d.
</P>
<HR>
<A NAME = "4_3"></A><H4>4.3 CHARMM and AMBER force fields
<A NAME = "4_3"></A><H4>4.3 CHARMM, AMBER, and DREIDING force fields
</H4>
<P>There are many different ways to compute forces in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
and <A HREF = "http://amber.scripps.edu">AMBER</A> molecular dynamics codes, only some of which are
available as options in LAMMPS. A force field has 2 parts: the
formulas that define it and the coefficients used for a particular
system. Here we only discuss formulas implemented in LAMMPS. Setting
<P>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
<A HREF = "read_data.html">read_data</A> command or in the input script with
commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A> for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
@ -193,16 +191,56 @@ field.
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
</P>
<UL><LI><A HREF = "bond_style.html">bond_style</A> harmonic
<LI><A HREF = "angle_style.html">angle_style</A> charmm
<LI><A HREF = "dihedral_style.html">dihedral_style</A> charmm
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm/implicit
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long
<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
<LI><A HREF = "angle_charmm.html">angle_style</A> charmm
<LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm/implicit
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/long
</UL>
<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
<LI><A HREF = "special_bonds.html">special_bonds</A> amber
</UL>
<P>DREIDING is a generic force field developed by the <A HREF = "http://www.wag.caltech.edu">Goddard
group</A> at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
<A HREF = "pair_hbond_dreiding.html">explicit hydrogen bond term</A> to describe
interactions involving a hydrogen atom (H___A) on very electronegative
atoms (N, O, F).
</P>
<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
</P>
<P>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
documentation for the formula it computes.
</P>
<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
<LI><A HREF = "bond_morse.html">bond_style</A> morse
</UL>
<UL><LI><A HREF = "angle_harmonic.html">angle_style</A> harmonic
<LI><A HREF = "angle_cosine.html">angle_style</A> cosine
<LI><A HREF = "angle_cosine_periodic.html">angle_style</A> cosine/periodic
</UL>
<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
<LI><A HREF = "improper_umbrella.html">improper_style</A> umbrella
</UL>
<UL><LI><A HREF = "pair_buck.html">pair_style</A> buck
<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/cut
<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/long
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/cut
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/long
</UL>
<UL><LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/lj
<LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/morse
</UL>
<UL><LI><A HREF = "special_bonds.html">special_bonds</A> dreiding
</UL>
<HR>
<A NAME = "4_4"></A><H4>4.4 Running multiple simulations from one input script
@ -1610,72 +1648,6 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
</P>
<HR>
<A NAME = "4_19"></A><H4>4.19 Computing free energies from thermodynamic integration
</H4>
<P>Thermodynamic integration is a widely used method to compute free
energies from atomistic simulations. LAMMPS can be used to run
thermodynamic integration calculations using the methods discussed in
this section and the <A HREF = "fix_adapt.html">fix adapt</A> command. Currently,
it is capable of the transformations essential for computing melting
points using the pseudo-supercritical path method developed by <A HREF = "#Eike_Maginn">Eike
and Maginn</A>.
</P>
<P>See the examples/TI directory for more information and sample files
that compute a melting point using the techniques described in this
section. That directory has its own README file. See also the paper
by <A HREF = "#Jayaraman">Jayaraman</A> for an example of using this implementation
of thermodynamic integration in LAMMPS to compute melting points of
alkali nitrate salts, using the steps outlined here.
</P>
<P>In this method, three intermediate "pseudo-supercritical" states are
accessed in the transformation between the liquid and solid
phases. These pseudo-states are a weak liquid, a dense weak liquid,
and an ordered weak phase. The transformation between the liquid and
solid states can also be driven uisng the <A HREF = "fix_adapt.html">fix adapt</A>
command.
</P>
<P>For the transformation from the liquid to the weak phase, the
intermolecular interactions need to be weakened. Appropriate scale
factors, computed by variables you define, and applied to pair styles
by <A HREF = "fix_adapt.html">fix adapt</A>, can be used to do this, as in the
example scripts. The <A HREF = "compute_ti.html">compute ti</A> command can
accumulate the value of dU/d<I>lambda</I>. See <A HREF = "#Jayaraman_Maginn">Jayaraman and
Maginn</A> for more information about calculating a
free energy from dU/d<I>lambda</I>.
</P>
<P>IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
are listed on the <A HREF = "fix_adapt">fix adapt</A> doc page. interaction scaling
is desired. If a pair style is not on that list, it is generally
quite easy to add an extract() method to the pair style, to enable fix
adapt to rescale it.
</P>
<P>Step 2 is the transformation of the simulation box density from the
liquid phase to that of the equilibrated crystal. The parameters for
box1 and box2 should be obtained from equilibrated NPT simulations of
the liquid and crystal phases and used in a <A HREF = "fix_deform.html">fix
deform</A> command to change the box size and/or shape.
It also advisable to use <A HREF = "fix_adapt.html">fix adapt</A> on the pair styles
to prevent overlaps which may occur during the box transformation.
</P>
<P>In step 3, the dense, weak system is transformed to an ordered state,
which has the same ordering as in the equilibrated crystal. Ordering
is achieved by introducing an attractive potential between atoms and
lattice sites. These lattice sites can be calculated as the mean
positions of the atoms in an equilibrium simulation of the
crystal. The <A HREF = "pair_gauss.html">pair/gauss</A> command can be used to
introduce an attractive Gaussian potential between the atoms and their
corresponding lattice sites. The prefactor of the Gaussian pair
potential can be scaled by <A HREF = "fix_adapt.html">fix adapt</A> to turn on the
attractions. Again, the quantity dU/d<I>lambda</I> can be tracked via the
<A HREF = "compute_ti.html">compute ti</A> command.
</P>
<P>Step 4 is the transformation of the ordered state to the final
crystal. In this step, the intermolecular interactions are scaled
back to full strength, while the Gaussian tethers are removed, all via
<A HREF = "fix_adapt.html">fix adapt</A>.
</P>
<HR>
<HR>
<A NAME = "Berendsen"></A>
@ -1698,6 +1670,11 @@ J Chem Phys, 120, 9665 (2004).
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
<A NAME = "Jorgensen"></A>
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
@ -1711,19 +1688,4 @@ Phys, 79, 926 (1983).
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
<A NAME = "Eike_Maginn"></A>
<P><B>(Eike and Maginn)</B> Eike and Maginn, J Chem Phys, 124,
164503 (2006).
</P>
<A NAME = "Jayaraman_Maginn"></A>
<P><B>(Jayaraman and Maginn)</B> Jayaraman and Maginn, Journal of Chemical Physics,
127, 214504 (2007).
</P>
<A NAME = "Jayaraman"></A>
<P><B>(Jayaraman)</B> Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
and Engineering Chemistry Research, 49, 559-571 (2010).
</P>
</HTML>

156
doc/Section_howto.txt
View File

@ -13,7 +13,7 @@ certain kinds of LAMMPS simulations.
4.1 "Restarting a simulation"_#4_1
4.2 "2d simulations"_#4_2
4.3 "CHARMM and AMBER force fields"_#4_3
4.3 "CHARMM, AMBER, and DREIDING force fields"_#4_3
4.4 "Running multiple simulations from one input script"_#4_4
4.5 "Multi-replica simulations"_#4_5
4.6 "Granular models"_#4_6
@ -28,8 +28,7 @@ certain kinds of LAMMPS simulations.
4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#4_15
4.16 "Thermostatting, barostatting and computing temperature"_#4_16
4.17 "Walls"_#4_17
4.18 "Elastic constants"_#4_18
4.19 "Computing free energies from thermodyanmic integration"_#4_19 :all(b)
4.18 "Elastic constants"_#4_18 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -164,19 +163,18 @@ the same as in 3d.
:line
4.3 CHARMM and AMBER force fields :link(4_3),h4
4.3 CHARMM, AMBER, and DREIDING force fields :link(4_3),h4
There are many different ways to compute forces in the "CHARMM"_charmm
and "AMBER"_amber molecular dynamics codes, only some of which are
available as options in LAMMPS. A force field has 2 parts: the
formulas that define it and the coefficients used for a particular
system. Here we only discuss formulas implemented in LAMMPS. Setting
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#Cornell for a description of the AMBER force
@ -189,16 +187,56 @@ These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
"bond_style"_bond_style.html harmonic
"angle_style"_angle_style.html charmm
"dihedral_style"_dihedral_style.html charmm
"pair_style"_pair_style.html lj/charmm/coul/charmm
"pair_style"_pair_style.html lj/charmm/coul/charmm/implicit
"pair_style"_pair_style.html lj/charmm/coul/long :ul
"bond_style"_bond_harmonic.html harmonic
"angle_style"_angle_charmm.html charmm
"dihedral_style"_dihedral_charmm.html charmm
"pair_style"_pair_charmm.html lj/charmm/coul/charmm
"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
DREIDING is a generic force field developed by the "Goddard
group"_http://www.wag.caltech.edu at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
interactions involving a hydrogen atom (H___A) on very electronegative
atoms (N, O, F).
See "(Mayo)"_#Mayo for a description of the DREIDING force field
These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"bond_style"_bond_morse.html morse :ul
"angle_style"_angle_harmonic.html harmonic
"angle_style"_angle_cosine.html cosine
"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
"dihedral_style"_dihedral_charmm.html charmm
"improper_style"_improper_umbrella.html umbrella :ul
"pair_style"_pair_buck.html buck
"pair_style"_pair_buck.html buck/coul/cut
"pair_style"_pair_buck.html buck/coul/long
"pair_style"_pair_lj.html lj/cut
"pair_style"_pair_lj.html lj/cut/coul/cut
"pair_style"_pair_lj.html lj/cut/coul/long :ul
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
"special_bonds"_special_bonds.html dreiding :ul
:line
4.4 Running multiple simulations from one input script :link(4_4),h4
@ -1596,72 +1634,6 @@ tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
4.19 Computing free energies from thermodynamic integration :link(4_19),h4
Thermodynamic integration is a widely used method to compute free
energies from atomistic simulations. LAMMPS can be used to run
thermodynamic integration calculations using the methods discussed in
this section and the "fix adapt"_fix_adapt.html command. Currently,
it is capable of the transformations essential for computing melting
points using the pseudo-supercritical path method developed by "Eike
and Maginn"_#Eike_Maginn.
See the examples/TI directory for more information and sample files
that compute a melting point using the techniques described in this
section. That directory has its own README file. See also the paper
by "Jayaraman"_#Jayaraman for an example of using this implementation
of thermodynamic integration in LAMMPS to compute melting points of
alkali nitrate salts, using the steps outlined here.
In this method, three intermediate "pseudo-supercritical" states are
accessed in the transformation between the liquid and solid
phases. These pseudo-states are a weak liquid, a dense weak liquid,
and an ordered weak phase. The transformation between the liquid and
solid states can also be driven uisng the "fix adapt"_fix_adapt.html
command.
For the transformation from the liquid to the weak phase, the
intermolecular interactions need to be weakened. Appropriate scale
factors, computed by variables you define, and applied to pair styles
by "fix adapt"_fix_adapt.html, can be used to do this, as in the
example scripts. The "compute ti"_compute_ti.html command can
accumulate the value of dU/d{lambda}. See "Jayaraman and
Maginn"_#Jayaraman_Maginn for more information about calculating a
free energy from dU/d{lambda}.
IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
are listed on the "fix adapt"_fix_adapt doc page. interaction scaling
is desired. If a pair style is not on that list, it is generally
quite easy to add an extract() method to the pair style, to enable fix
adapt to rescale it.
Step 2 is the transformation of the simulation box density from the
liquid phase to that of the equilibrated crystal. The parameters for
box1 and box2 should be obtained from equilibrated NPT simulations of
the liquid and crystal phases and used in a "fix
deform"_fix_deform.html command to change the box size and/or shape.
It also advisable to use "fix adapt"_fix_adapt.html on the pair styles
to prevent overlaps which may occur during the box transformation.
In step 3, the dense, weak system is transformed to an ordered state,
which has the same ordering as in the equilibrated crystal. Ordering
is achieved by introducing an attractive potential between atoms and
lattice sites. These lattice sites can be calculated as the mean
positions of the atoms in an equilibrium simulation of the
crystal. The "pair/gauss"_pair_gauss.html command can be used to
introduce an attractive Gaussian potential between the atoms and their
corresponding lattice sites. The prefactor of the Gaussian pair
potential can be scaled by "fix adapt"_fix_adapt.html to turn on the
attractions. Again, the quantity dU/d{lambda} can be tracked via the
"compute ti"_compute_ti.html command.
Step 4 is the transformation of the ordered state to the final
crystal. In this step, the intermolecular interactions are scaled
back to full strength, while the Gaussian tethers are removed, all via
"fix adapt"_fix_adapt.html.
:line
:line
@ -1681,6 +1653,10 @@ J Chem Phys, 120, 9665 (2004).
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
:link(Jorgensen)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
@ -1690,15 +1666,3 @@ Phys, 79, 926 (1983).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
:link(Eike_Maginn)
[(Eike and Maginn)] Eike and Maginn, J Chem Phys, 124,
164503 (2006).
:link(Jayaraman_Maginn)
[(Jayaraman and Maginn)] Jayaraman and Maginn, Journal of Chemical Physics,
127, 214504 (2007).
:link(Jayaraman)
[(Jayaraman)] Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
and Engineering Chemistry Research, 49, 559-571 (2010).

62
doc/compute_pair.html
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@ -13,15 +13,17 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pair pstyle
<PRE>compute ID group-ID pair pstyle evalue
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pair = style name of this compute command
<LI>pstyle = style name of a pair style that calculates additional values
<LI>pstyle = style name of a pair style that calculates additional values
<LI>evalue = <I>epair</I> or <I>evdwl</I> or <I>evoul</I> or blank (optional setting)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair reax
</PRE>
<P><B>Description:</B>
@ -31,32 +33,44 @@ pair style, sums them across processors, and makes them accessible for
output or further processing by other commands. The group specified
for this command is ignored.
</P>
<P>The specified <I>pstyle</I> must be a pair style that produces additional
values. If a <A HREF = "pair_hybrid.html">hybrid pair style</A> is used, then
<I>pstyle</I> should be the name of a sub-style.
<P>The specified <I>pstyle</I> must be a pair style used in your simulation
either by itself or as a sub-style in a <A HREF = "pair_hybrid.html">pair_style hybrid or
hybrid/overlay</A> command.
</P>
<P>All pair styles tally a potential energy, which is accessed by the
<A HREF = "compute_pe.html">compute pe</A> and <A HREF = "compute_pe_atom.html">compute
pe/atom</A> commands. Some pair styles tally one or
more additional values, such as a breakdown of the total pair
potential energy into sub-categories. See the doc page for
<P>The <I>evalue</I> setting is optional; it may be left off the command. All
pair styles tally a potential energy <I>epair</I> which may be broken into
two parts: <I>evdwl</I> and <I>ecoul</I> such that <I>epair</I> = <I>evdwl</I> + <I>evoul</I>.
If the pair style calculates Coulombic interactions, their energy will
be tallied in <I>ecoul</I>. Everything else (whether it is a Lennard-Jones
style van der Waals interaction or not) is tallied in <I>evdwl</I>. If
<I>evalue</I> is specified as <I>epair</I> or left out, then <I>epair</I> is stored
as a global scalar by this compute. This is useful when using
<A HREF = "pair_hybrid.html">pair_style hybrid</A> if you want to know the portion
of the total energy contributed by one sub-style. If <I>evalue</I> is
specfied as <I>evdwl</I> or <I>ecoul</I>, then just that portion of the energy
is stored as a global scalar.
</P>
<P>Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into a dozen or so components is tallied by the
<A HREF = "pair_reax.html">pair_style reax</A> commmand. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
<A HREF = "pair_style.html">individual pair styles</A> for info on these values.
</P>
<P>The compute pair command lets you access this data as a global vector
of values and then use other <A HREF = "Section_howto.html#4_15">output options</A>
that work with <A HREF = "compute.html">compute commands</A> to see or use the
values.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length >= 1, as determined
by the pair style. These values can be used by any command that uses
global 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>This compute calculates a global scalar which is <I>epair</I> or <I>evdwl</I> or
<I>evoul</I>. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. 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 vector values calculated by this compute are "extensive". They
are in whatever units the pair style produces.
<P>The scalar and vector values calculated by this compute are
"extensive".
</P>
<P>The scalar value will be in energy <A HREF = "units.html">units</A>. The vector
values will typically also be in energy <A HREF = "units.html">units</A>, but
see the doc page for the pair style for details.
</P>
<P><B>Restrictions:</B> none
</P>
@ -64,6 +78,8 @@ are in whatever units the pair style produces.
</P>
<P><A HREF = "compute_pe.html">compute pe</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The default for <I>evalue</I> is <I>epair</I>.
</P>
</HTML>

62
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@ -10,15 +10,17 @@ compute pair command :h3
[Syntax:]
compute ID group-ID pair pstyle :pre
compute ID group-ID pair pstyle evalue :pre
ID, group-ID are documented in "compute"_compute.html command
pair = style name of this compute command
pstyle = style name of a pair style that calculates additional values :ul
pstyle = style name of a pair style that calculates additional values
evalue = {epair} or {evdwl} or {evoul} or blank (optional setting) :ul
[Examples:]
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair reax :pre
[Description:]
@ -28,32 +30,44 @@ pair style, sums them across processors, and makes them accessible for
output or further processing by other commands. The group specified
for this command is ignored.
The specified {pstyle} must be a pair style that produces additional
values. If a "hybrid pair style"_pair_hybrid.html is used, then
{pstyle} should be the name of a sub-style.
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html command.
All pair styles tally a potential energy, which is accessed by the
"compute pe"_compute_pe.html and "compute
pe/atom"_compute_pe_atom.html commands. Some pair styles tally one or
more additional values, such as a breakdown of the total pair
potential energy into sub-categories. See the doc page for
The {evalue} setting is optional; it may be left off the command. All
pair styles tally a potential energy {epair} which may be broken into
two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {evoul}.
If the pair style calculates Coulombic interactions, their energy will
be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones
style van der Waals interaction or not) is tallied in {evdwl}. If
{evalue} is specified as {epair} or left out, then {epair} is stored
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
specfied as {evdwl} or {ecoul}, then just that portion of the energy
is stored as a global scalar.
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into a dozen or so components is tallied by the
"pair_style reax"_pair_reax.html commmand. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
"individual pair styles"_pair_style.html for info on these values.
The compute pair command lets you access this data as a global vector
of values and then use other "output options"_Section_howto.html#4_15
that work with "compute commands"_compute.html to see or use the
values.
[Output info:]
This compute calculates a global vector of length >= 1, as determined
by the pair style. These values can be used by any command that uses
global vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
This compute calculates a global scalar which is {epair} or {evdwl} or
{evoul}. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. 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 vector values calculated by this compute are "extensive". They
are in whatever units the pair style produces.
The scalar and vector values calculated by this compute are
"extensive".
The scalar value will be in energy "units"_units.html. The vector
values will typically also be in energy "units"_units.html, but
see the doc page for the pair style for details.
[Restrictions:] none
@ -61,4 +75,6 @@ are in whatever units the pair style produces.
"compute pe"_compute_pe.html
[Default:] none
[Default:]
The default for {evalue} is {epair}.

37
doc/special_bonds.html
View File

@ -17,10 +17,11 @@
</PRE>
<UL><LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>dreiding</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
<PRE> <I>amber</I> values = none
<I>charmm</I> values = none
<I>dreiding</I> values = none
<I>fene</I> values = none
<I>lj/coul</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
@ -80,7 +81,8 @@ details.
<P>The <I>amber</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
is the default for a commonly used version of the AMBER force field,
where the last value is really 5/6.
where the last value is really 5/6. See <A HREF = "#Cornell">(Cornell)</A> for a
description of the AMBER force field.
</P>
<P>The <I>charmm</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
LJ and Coulombic interactions, which is the default for a commonly
@ -89,11 +91,17 @@ used version of the CHARMM force field. Note that in pair styles
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
commands for more information.
commands for more information. See <A HREF = "#MacKerell">(MacKerell)</A> for a
description of the CHARMM force field.
</P>
<P>The <I>dreiding</I> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
LJ and Coulombic interactions, which is the default for the Dreiding
force field, as discussed in <A HREF = "#Mayo">(Mayo)</A>.
</P>
<P>The <I>fene</I> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>.
coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>. See
<A HREF = "#Kremer">(Kremer)</A> for a description of FENE bonds.
</P>
<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
@ -150,4 +158,25 @@ you do not do this, you may get an error when bonds are added.
<P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
angle = no, dihedral = no, and extra = 0.
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
</HTML>

34
doc/special_bonds.txt
View File

@ -13,9 +13,10 @@ special_bonds command :h3
special_bonds keyword values ... :pre
one or more keyword/value pairs may be appended :ulb,l
keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
{amber} values = none
{charmm} values = none
{dreiding} values = none
{fene} values = none
{lj/coul} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
@ -74,7 +75,8 @@ details.
The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
is the default for a commonly used version of the AMBER force field,
where the last value is really 5/6.
where the last value is really 5/6. See "(Cornell)"_#Cornell for a
description of the AMBER force field.
The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
LJ and Coulombic interactions, which is the default for a commonly
@ -83,11 +85,17 @@ used version of the CHARMM force field. Note that in pair styles
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
commands for more information.
commands for more information. See "(MacKerell)"_#MacKerell for a
description of the CHARMM force field.
The {dreiding} keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
LJ and Coulombic interactions, which is the default for the Dreiding
force field, as discussed in "(Mayo)"_#Mayo.
The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with "FENE bonds"_bond_fene.html.
coarse-grained polymer model with "FENE bonds"_bond_fene.html. See
"(Kremer)"_#Kremer for a description of FENE bonds.
The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
be set explicitly. The {lj/coul} keyword sets both the LJ and
@ -143,3 +151,21 @@ you do not do this, you may get an error when bonds are added.
All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
angle = no, dihedral = no, and extra = 0.
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).