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@12774 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-11-24 17:22:05 +00:00
parent 162e8050ad
commit 53c71398d1
6 changed files with 493 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
doc/Section_commands.html
View File

@ -420,11 +420,11 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A>
<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A>
</TD></TR></TABLE></DIV>
<HR>

1
doc/Section_intro.html
View File

@ -256,6 +256,7 @@ molecular dynamics options:
<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
<LI><A HREF = "fix_qmmm.html">QM/MM coupling</A>
<LI><A HREF = "fix_ipi.html">path-integral molecular dynamics (PIMD)</A>
<LI><A HREF = "fix_gcmc.html">grand canonical Monte Carlo</A> insertions/deletions
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>

156
doc/fix_gle.html Normal file
View File

@ -0,0 +1,156 @@
<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 gle command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID id-group gle Ns Tstart Tstop seed Amatrix <B>noneq Cmatrix</B> <B>every stride</B>
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gle = style name of this fix command
<LI>Ns = number of additional fictitious momenta
<LI>Tstart, Tstop = temperature ramp during the run
<LI>Amatrix = file to read the drift matrix A from
<LI>seed = random number seed to use for generating noise (positive integer)
<LI>zero or more keyword/value pairs may be appended
keyword = <I>noneq</I> and/or <I>every</I>
<I>noneq</I> Cmatrix = file to read the non-equilibrium covariance matrix from
<I>every</I> stride = apply the GLE once every time steps. Reduces the accuracy
of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
sampling. It might change sampling properties when used together with <I>noneq</I>.
</UL>
<P><B>Examples:</B>
</P>
<P>fix 3 boundary gle 6 300 300 31415 smart.A
fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C
</P>
<P><B>Description:</B>
</P>
<P>Apply a Generalized Langevin Equation (GLE) thermostat as described
in <A HREF = "#Ceriotti">(Ceriotti)</A>. The formalism allows one to obtain a number
of different effects ranging from efficient sampling of all
vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
<A HREF = "fix_langevin.html">fix langevin</A>, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
does not need to be used together with <A HREF = "fix_nve.html">fix nve</A>.
</P>
<P>Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion
become
</P>
<P>dq/dt=p/m
d(p,s)/dt=(F,0) - A(p,s) + B dW/dt
</P>
<P>where F is the physical force, A is the drift matrix (that generalizes
the friction in Langevin dynamics), B is the diffusion term and dW/dt
un-correlated Gaussian random forces. The A matrix couples the physical
(q,p) dynamics with that of the additional degrees of freedom,
and makes it possible to obtain effectively a history-dependent
noise and friction kernel.
</P>
<P>The drift matrix should be given as an external file <I>Afile</I>,
as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
optimal for a given application and the system of choice can be
obtained from <A HREF = "#GLE4MD">(GLE4MD)</A>.
</P>
<P>Equilibrium sampling a temperature T is obtained by specifiying the
target value as the <I>Tstart</I> and <I>Tstop</I> arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
can be used for instance to model inexpensively zero-point energy
effects <A HREF = "#Ceriotti2">(Ceriotti2)</A>. This is achieved specifying the
<I>noneq</I> keyword followed by the name of the file that contains the
static covariance matrix for the non-equilibrium dynamics.
</P>
<P>Since integrating GLE dynamics can be costly when used together with
simple potentials, one can use the <I>every</I> optional keyword to
apply the Langevin terms only once every several MD steps, in a
multiple time-step fashion. This should be used with care when doing
non-equilibrium sampling, but should have no effect on equilibrium
averages when using canonical sampling.
</P>
<P>The random number <I>seed</I> must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>The instantaneous values of the extended variables are written to
<A HREF = "restart.html">binary restart files</A>. Because the state of the random
number generator is not saved in restart files, this means you cannot
do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
subtle artefacts in the sampling.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>The GLE thermostat in its current implementation should not be used
with rigid bodies, SHAKE or RATTLE. It is expected that all the
thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.
</P>
<P>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "pair_dpd.html">pair_style
dpd/tstat</A>, <A HREF = "fix_gld.html">fix_gld</A>
</P>
<HR>
<A NAME = "Ceriotti"></A>
<P><B>(Ceriotti)</B> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
1170-80 (2010)
</P>
<A NAME = "GLE4MD"></A>
<P><B>(GLE4MD)</B> <A HREF = "http://epfl-cosmo.github.io/gle4md/">http://epfl-cosmo.github.io/gle4md/</A>
</P>
<A NAME = "Ceriotti2"></A>
<P><B>(Ceriotti2)</B> Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
030603 (2009)
</P>
</HTML>

142
doc/fix_gle.txt Normal file
View File

@ -0,0 +1,142 @@
"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 gle command :h3
[Syntax:]
fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride] :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
gle = style name of this fix command :l
Ns = number of additional fictitious momenta :l
Tstart, Tstop = temperature ramp during the run :l
Amatrix = file to read the drift matrix A from :l
seed = random number seed to use for generating noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {noneq} and/or {every}
{noneq} Cmatrix = file to read the non-equilibrium covariance matrix from
{every} stride = apply the GLE once every time steps. Reduces the accuracy
of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
sampling. It might change sampling properties when used together with {noneq}.
:ule
[Examples:]
fix 3 boundary gle 6 300 300 31415 smart.A
fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C
[Description:]
Apply a Generalized Langevin Equation (GLE) thermostat as described
in "(Ceriotti)"_#Ceriotti. The formalism allows one to obtain a number
of different effects ranging from efficient sampling of all
vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
"fix langevin"_fix_langevin.html, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
does not need to be used together with "fix nve"_fix_nve.html.
Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion
become
dq/dt=p/m
d(p,s)/dt=(F,0) - A(p,s) + B dW/dt
where F is the physical force, A is the drift matrix (that generalizes
the friction in Langevin dynamics), B is the diffusion term and dW/dt
un-correlated Gaussian random forces. The A matrix couples the physical
(q,p) dynamics with that of the additional degrees of freedom,
and makes it possible to obtain effectively a history-dependent
noise and friction kernel.
The drift matrix should be given as an external file {Afile},
as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
optimal for a given application and the system of choice can be
obtained from "(GLE4MD)"_#GLE4MD.
Equilibrium sampling a temperature T is obtained by specifiying the
target value as the {Tstart} and {Tstop} arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
can be used for instance to model inexpensively zero-point energy
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the
{noneq} keyword followed by the name of the file that contains the
static covariance matrix for the non-equilibrium dynamics.
Since integrating GLE dynamics can be costly when used together with
simple potentials, one can use the {every} optional keyword to
apply the Langevin terms only once every several MD steps, in a
multiple time-step fashion. This should be used with care when doing
non-equilibrium sampling, but should have no effect on equilibrium
averages when using canonical sampling.
The random number {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
[Restart, fix_modify, output, run start/stop, minimize info:]
The instantaneous values of the extended variables are written to
"binary restart files"_restart.html. Because the state of the random
number generator is not saved in restart files, this means you cannot
do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
subtle artefacts in the sampling.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
The GLE thermostat in its current implementation should not be used
with rigid bodies, SHAKE or RATTLE. It is expected that all the
thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.
This fix is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
dpd/tstat"_pair_dpd.html, "fix_gld"_fix_gld.html
:line
:link(Ceriotti)
[(Ceriotti)] Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
1170-80 (2010)
:link(GLE4MD)
[(GLE4MD)] "http://epfl-cosmo.github.io/gle4md/"_http://epfl-cosmo.github.io/gle4md/
:link(Ceriotti2)
[(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
030603 (2009)

98
doc/fix_ipi.html Normal file
View File

@ -0,0 +1,98 @@
<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 ipi command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ipi address port [unix]
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ipi = style name of this fix command
<LI>address = internet address (FQDN or IP), or UNIX socket name
<LI>port = port number (ignored for UNIX sockets)
<LI>optional keyword = <I>unix</I>, if present uses a unix socket
</UL>
<P><B>Examples:</B>
</P>
<P>fix 1 all ipi my.server.com 12345
fix 1 all ipi mysocket 666 unix
</P>
<P><B>Description:</B>
</P>
<P>This fix enables LAMMPS to be run as a client for the i-PI Python
wrapper <A HREF = "#IPI">(IPI)</A> for performing a path integral molecular dynamics
(PIMD) simulation. The philosophy behind i-PI is described in the
following publication <A HREF = "#IPICPC">(IPI-CPC)</A>.
</P>
<P>A version of the i-PI package, containing only files needed for use
with LAMMPS, is provided in the tools/i-pi directory. See the
tools/i-pi/manual.pdf for an introduction to i-PI. The
examples/USER/i-pi directory contains example scripts for using i-PI
with LAMMPS.
</P>
<P>In brief, the path integral molecular dynamics is performed by the
Python wrapper, while the client (LAMMPS in this case) simply computes
forces and energy for each configuration. The communication between
the two components takes place using sockets, and is reduced to the
bare minimum. All the parameters of the dynamics are specified in the
input of i-PI, and all the parameters of the force field must be
specified as LAMMPS inputs, preceding the <I>fix ipi</I> command.
</P>
<P>The server address must be specified by the <I>address</I> argument, and
can be either the IP address, the fully-qualified name of the server,
or the name of a UNIX socket for local, faster communication. In the
case of internet sockets, the <I>port</I> argument specifies the port
number on which i-PI is listening, while the <I>unix</I> optional switch
specifies that the socket is a UNIX socket.
</P>
<P>Note that there is no check of data integrity, or that the atomic
configurations make sense. It is assumed that the species in the i-PI
input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>There is no restart information associated with this fix, since all
the dynamical parameters are dealt with by i-PI.
</P>
<P><B>Restrictions:</B>
</P>
<P>Using this fix on anything other than all atoms requires particular
care, since i-PI will know nothing on atoms that are not those whose
coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.
</P>
<P>This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info. Because of
the use of UNIX domain sockets, this fix will only work in a UNIX
environment.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>
</P>
<HR>
<A NAME = "IPICPC"></A>
<P><B>(IPI-CPC)</B> Ceriotti, More and Manolopoulos,
Comp. Phys. Comm., 185, 1019–1026 (2014)
</P>
<A NAME = "IPI"></A>
<P><B>(IPI)</B>
<A HREF = "http://epfl-cosmo.github.io/gle4md/index.html?page=ipi">http://epfl-cosmo.github.io/gle4md/index.html?page=ipi</A>
</P>
</HTML>

91
doc/fix_ipi.txt Normal file
View File

@ -0,0 +1,91 @@
"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 ipi command :h3
[Syntax:]
fix ID group-ID ipi address port \[unix\] :pre
ID, group-ID are documented in "fix"_fix.html command
ipi = style name of this fix command
address = internet address (FQDN or IP), or UNIX socket name
port = port number (ignored for UNIX sockets)
optional keyword = {unix}, if present uses a unix socket :ul
[Examples:]
fix 1 all ipi my.server.com 12345
fix 1 all ipi mysocket 666 unix
[Description:]
This fix enables LAMMPS to be run as a client for the i-PI Python
wrapper "(IPI)"_#IPI for performing a path integral molecular dynamics
(PIMD) simulation. The philosophy behind i-PI is described in the
following publication "(IPI-CPC)"_#IPICPC.
A version of the i-PI package, containing only files needed for use
with LAMMPS, is provided in the tools/i-pi directory. See the
tools/i-pi/manual.pdf for an introduction to i-PI. The
examples/USER/i-pi directory contains example scripts for using i-PI
with LAMMPS.
In brief, the path integral molecular dynamics is performed by the
Python wrapper, while the client (LAMMPS in this case) simply computes
forces and energy for each configuration. The communication between
the two components takes place using sockets, and is reduced to the
bare minimum. All the parameters of the dynamics are specified in the
input of i-PI, and all the parameters of the force field must be
specified as LAMMPS inputs, preceding the {fix ipi} command.
The server address must be specified by the {address} argument, and
can be either the IP address, the fully-qualified name of the server,
or the name of a UNIX socket for local, faster communication. In the
case of internet sockets, the {port} argument specifies the port
number on which i-PI is listening, while the {unix} optional switch
specifies that the socket is a UNIX socket.
Note that there is no check of data integrity, or that the atomic
configurations make sense. It is assumed that the species in the i-PI
input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.
[Restart, fix_modify, output, run start/stop, minimize info:]
There is no restart information associated with this fix, since all
the dynamical parameters are dealt with by i-PI.
[Restrictions:]
Using this fix on anything other than all atoms requires particular
care, since i-PI will know nothing on atoms that are not those whose
coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. Because of
the use of UNIX domain sockets, this fix will only work in a UNIX
environment.
[Related commands:]
"fix nve"_fix_nve.html
:line
:link(IPICPC)
[(IPI-CPC)] Ceriotti, More and Manolopoulos,
Comp. Phys. Comm., 185, 1019–1026 (2014)
:link(IPI)
[(IPI)]
"http://epfl-cosmo.github.io/gle4md/index.html?page=ipi"_http://epfl-cosmo.github.io/gle4md/index.html?page=ipi