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yotamfe
2025-02-11 13:56:53 +02:00
parent 2c1cd2ed04
commit 17797e4f74
2 changed files with 7 additions and 5 deletions
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10
doc/src/fix_pimdb.rst
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@ -102,8 +102,8 @@ This potential does not include all :math:`N!` permutations, but samples the sam
the potential is the one developed by Feldman and Hirshberg, which scales like :math:`N^2+PN` :ref:`(Feldman) <Feldman>`.
The forces are calculated as weighted averages over the representative permutations,
through an algorithm that scales the same as the one for the potential calculation, :math:`N^2+PN` :ref:`(Feldman) <Feldman>`.
The algorithm employs the minimum image convention to approximate the bosonic periodic boundary conditions.
An elaborate discussion of the validity of the approximation is available in :ref:`(Higer) <HigerFeldman>`.
The minimum-image convention is employed on the springs to account for periodic boundary conditions;
an elaborate discussion of the validity of the approximation is available in :ref:`(Higer) <HigerFeldman>`.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -130,14 +130,14 @@ can be accessed by various :doc:`output commands <Howto_output>`. The quantities
#. kinetic energy of the beads,
#. spring elastic energy of the beads,
#. potential energy of the bead,
#. total energy of all beads (conserved if *ensemble* is *nve*)
#. total energy of all beads (conserved if *ensemble* is *nve*) if *esynch* is *yes*
#. primitive kinetic energy estimator :ref:`(Hirshberg1) <Hirshberg>`
#. virial energy estimator :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`).
The first three are different for different log files, and the others are the same for different log files,
except for the primitive kinetic energy estimator when setting *esynch* to *no*. Then, the primitive kinetic energy estimator is obtained by summing over all log files.
Also note that when *esynch* is set to *no*, the fourth output gives the total energy of all beads excluding the spring elastic energy,
which can be obtained from the second output by summing over all log files.
Also note that when *esynch* is set to *no*, the fourth output gives the total energy of all beads excluding the spring elastic energy; the total classical energy
can then be obtained by adding the sum of second output over all log files.
All vector values calculated by fix *pimdb/langevin* are "extensive".
For both *pimdb/nvt* and *pimdb/langevin*, the contribution of the exterior spring to the primitive estimator is printed to the first log file.

2
src/REPLICA/fix_pimdb_langevin.cpp
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@ -60,6 +60,7 @@ FixPIMDBLangevin::FixPIMDBLangevin(LAMMPS *lmp, int narg, char **arg) :
error->universe_all(FLERR, "Barostat parameters are not available for pimdb.");
}
else if ((strcmp(arg[i], "esynch") == 0) && (strcmp(arg[i + 1], "no") == 0)) {
// CR: validate that the argument of esynch is either "no" or "yes"
synch_energies = false;
}
}
@ -123,6 +124,7 @@ void FixPIMDBLangevin::spring_force() {
/* ---------------------------------------------------------------------- */
void FixPIMDBLangevin::compute_spring_energy() {
// CR: perform this line only if synch_energies
se_bead = bosonic_exchange.get_bead_spring_energy();
if (synch_energies) {
MPI_Allreduce(&se_bead, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);