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< title > fix pimd command — LAMMPS documentation< / title >
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< li > fix pimd command< / li >
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< span id = "index-0" > < / span > < h1 > fix pimd command< a class = "headerlink" href = "#fix-pimd-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID pimd keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > pimd = style name of this fix command< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > method< / em > or < em > fmass< / em > or < em > sp< / em > or < em > temp< / em > or < em > nhc< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > method< / em > value = < em > pimd< / em > or < em > nmpimd< / em > or < em > cmd< / em >
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< em > fmass< / em > value = scaling factor on mass
< em > sp< / em > value = scaling factor on Planck constant
< em > temp< / em > value = temperature (temperarate units)
< em > nhc< / em > value = Nc = number of chains in Nose-Hoover thermostat
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This command performs quantum molecular dynamics simulations based on
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the Feynman path integral to include effects of tunneling and
zero-point motion. In this formalism, the isomorphism of a quantum
partition function for the original system to a classical partition
function for a ring-polymer system is exploited, to efficiently sample
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configurations from the canonical ensemble < a class = "reference internal" href = "#feynman" > < span > (Feynman)< / span > < / a > .
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The classical partition function and its components are given
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by the following equations:< / p >
< img alt = "_images/fix_pimd.jpg" class = "align-center" src = "_images/fix_pimd.jpg" / >
< p > The interested user is referred to any of the numerous references on
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this methodology, but briefly, each quantum particle in a path
integral simulation is represented by a ring-polymer of P quasi-beads,
labeled from 1 to P. During the simulation, each quasi-bead interacts
with beads on the other ring-polymers with the same imaginary time
index (the second term in the effective potential above). The
quasi-beads also interact with the two neighboring quasi-beads through
the spring potential in imaginary-time space (first term in effective
potential). To sample the canonical ensemble, a Nose-Hoover massive
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chain thermostat is applied < a class = "reference internal" href = "run_style.html#tuckerman" > < span > (Tuckerman)< / span > < / a > . With the
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massive chain algorithm, a chain of NH thermostats is coupled to each
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degree of freedom for each quasi-bead. The keyword < em > temp< / em > sets the
target temperature for the system and the keyword < em > nhc< / em > sets the
number < em > Nc< / em > of thermostats in each chain. For example, for a
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simulation of N particles with P beads in each ring-polymer, the total
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number of NH thermostats would be 3 x N x P x Nc.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > This fix implements a complete velocity-verlet integrator
combined with NH massive chain thermostat, so no other time
integration fix should be used.< / p >
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< / div >
< p > The < em > method< / em > keyword determines what style of PIMD is performed. A
value of < em > pimd< / em > is standard PIMD. A value of < em > nmpimd< / em > is for
normal-mode PIMD. A value of < em > cmd< / em > is for centroid molecular dynamics
(CMD). The difference between the styles is as follows.< / p >
< p > In standard PIMD, the value used for a bead’ s fictitious mass is
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arbitrary. A common choice is to use Mi = m/P, which results in the
mass of the entire ring-polymer being equal to the real quantum
particle. But it can be difficult to efficiently integrate the
equations of motion for the stiff harmonic interactions in the ring
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polymers.< / p >
< p > A useful way to resolve this issue is to integrate the equations of
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motion in a normal mode representation, using Normal Mode
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Path-Integral Molecular Dynamics (NMPIMD) < a class = "reference internal" href = "#cao1" > < span > (Cao1)< / span > < / a > . In NMPIMD,
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the NH chains are attached to each normal mode of the ring-polymer and
the fictitious mass of each mode is chosen as Mk = the eigenvalue of
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the Kth normal mode for k > 0. The k = 0 mode, referred to as the
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zero-frequency mode or centroid, corresponds to overall translation of
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the ring-polymer and is assigned the mass of the real particle.< / p >
< p > Motion of the centroid can be effectively uncoupled from the other
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normal modes by scaling the fictitious masses to achieve a partial
adiabatic separation. This is called a Centroid Molecular Dynamics
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(CMD) approximation < a class = "reference internal" href = "#cao2" > < span > (Cao2)< / span > < / a > . The time-evolution (and resulting
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dynamics) of the quantum particles can be used to obtain centroid time
correlation functions, which can be further used to obtain the true
quantum correlation function for the original system. The CMD method
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also uses normal modes to evolve the system, except only the k > 0
modes are thermostatted, not the centroid degrees of freedom.< / p >
< p > The keyword < em > fmass< / em > sets a further scaling factor for the fictitious
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masses of beads, which can be used for the Partial Adiabatic CMD
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< a class = "reference internal" href = "#hone" > < span > (Hone)< / span > < / a > , or to be set as P, which results in the fictitious
masses to be equal to the real particle masses.< / p >
< p > The keyword < em > sp< / em > is a scaling factor on Planck’ s constant, which can
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be useful for debugging or other purposes. The default value of 1.0
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is appropriate for most situations.< / p >
< p > The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
as described in < a class = "reference internal" href = "#calhoun" > < span > (Calhoun)< / span > < / a > . In LAMMPS this is done by using
< a class = "reference internal" href = "Section_howto.html#howto-5" > < span > multi-replica feature< / span > < / a > in LAMMPS, where
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each quasi-particle system is stored and simulated on a separate
partition of processors. The following diagram illustrates this
approach. The original system with 2 ring polymers is shown in red.
Since each ring has 4 quasi-beads (imaginary time slices), there are 4
replicas of the system, each running on one of the 4 partitions of
processors. Each replica (shown in green) owns one quasi-bead in each
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ring.< / p >
< img alt = "_images/pimd.jpg" class = "align-center" src = "_images/pimd.jpg" / >
< p > To run a PIMD simulation with M quasi-beads in each ring polymer using
N MPI tasks for each partition’ s domain-decomposition, you would use P
= MxN processors (cores) and run the simulation as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > mpirun -np P lmp_mpi -partition MxN -in script
< / pre > < / div >
< / div >
< p > Note that in the LAMMPS input script for a multi-partition simulation,
it is often very useful to define a < a class = "reference internal" href = "variable.html" > < em > uloop-style variable< / em > < / a > such as< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > variable ibead uloop M pad
< / pre > < / div >
< / div >
< p > where M is the number of quasi-beads (partitions) used in the
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calculation. The uloop variable can then be used to manage I/O
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related tasks for each of the partitions, e.g.< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > dump dcd all dcd 10 system_${ibead}.dcd
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restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
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read_restart system_${ibead}.restart2
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > A PIMD simulation can be initialized with a single data file read via
the < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command. However, this means all
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quasi-beads in a ring polymer will have identical positions and
velocities, resulting in identical trajectories for all quasi-beads.
To avoid this, users can simply initialize velocities with different
random number seeds assigned to each partition, as defined by the
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uloop variable, e.g.< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > velocity all create 300.0 1234${ibead} rot yes dist gaussian
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
and nhc = 2.< / p >
< hr class = "docutils" / >
< p id = "feynman" > < strong > (Feynman)< / strong > R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
Path Integrals, McGraw-Hill, New York (1965).< / p >
< p id = "tuckerman" > < strong > (Tuckerman)< / strong > M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).< / p >
< p id = "cao1" > < strong > (Cao1)< / strong > J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).< / p >
< p id = "cao2" > < strong > (Cao2)< / strong > J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).< / p >
< p id = "hone" > < strong > (Hone)< / strong > T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
154103 (2006).< / p >
< p id = "calhoun" > < strong > (Calhoun)< / strong > A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
415 (1996).< / p >
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