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Corrected minor rst syntax errors

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This commit is contained in:
Ofir Blumer
2025-02-10 17:36:00 +02:00
parent 54790d6095
commit 2c1cd2ed04
2 changed files with 10 additions and 9 deletions
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8
doc/src/fix_pimd.rst
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@ -1,5 +1,5 @@
.. index:: fix pimd/langevin
.. index:: fix pimd/nvt
.. index:: fix pimd/nvt
fix pimd/langevin command
=========================
@ -20,7 +20,7 @@ Syntax
* keywords for style *pimd/nvt*
.. parsed-literal::
*keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
*keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
*method* value = *pimd* or *nmpimd* or *cmd*
*fmass* value = scaling factor on mass
*sp* value = scaling factor on Planck constant
@ -30,7 +30,7 @@ Syntax
* keywords for style *pimd/langevin*
.. parsed-literal::
*keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
*keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
*method* value = *nmpimd* (default) or *pimd*
*integrator* value = *obabo* or *baoab*
*ensemble* value = *nvt* or *nve* or *nph* or *npt*
@ -250,7 +250,7 @@ system, each running on one of the 4 partitions of processors. Each
replica (shown in green) owns one quasi-bead in each ring.
.. image:: JPG/pimd.jpg
:align: center
:align: center
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

11
doc/src/fix_pimdb.rst
View File

@ -1,5 +1,5 @@
.. index:: fix pimdb/langevin
.. index:: fix pimdb/nvt
.. index:: fix pimdb/nvt
fix pimdb/langevin command
==========================
@ -20,7 +20,7 @@ Syntax
* keywords for style *pimdb/nvt*
.. parsed-literal::
*keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
*keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
*method* value = *pimd* or *nmpimd*
*fmass* value = scaling factor on mass
*sp* value = scaling factor on Planck constant
@ -30,7 +30,7 @@ Syntax
* keywords for style *pimdb/langevin*
.. parsed-literal::
*keywords* = *integrator* or *ensemble* or *fmass* or *temp* or *thermostat* or *tau* or *fixcom* or *lj* or *esych*
*keywords* = *integrator* or *ensemble* or *fmass* or *temp* or *thermostat* or *tau* or *fixcom* or *lj* or *esych*
*integrator* value = *obabo* or *baoab*
*ensemble* value = *nvt* or *nve*
*fmass* value = scaling factor on mass
@ -70,8 +70,7 @@ The major differences from fix *pimd* in terms of capabilities are:
* Fix *pimdb/nvt* the only supports the "pimd" and "nmpimd" methods. Fix *pimdb/langevin* only supports the "pimd" method, which is the default in this fix. These restrictions are related to the use of normal modes, which change in bosons. For similar reasons, *fmmode* of *pimd/langevin* should not be used, and would raise an error if set to a value other than *physical*.
* Fix *pimdb/langevin* currently does not support *ensemble* other than *nve*, *nvt*. The barostat related keywords *iso*, *aniso*, *barostat*, *taup* are not supported.
* Fix *pimdb/langevin* also has a keyword not available in fix *pimd/langevin*: *esynch*, with default *yes*. If set to *no*, some time consuming synchronization of spring energies and
the primitive kinetic energy estimator between processors is avoided.
* Fix *pimdb/langevin* also has a keyword not available in fix *pimd/langevin*: *esynch*, with default *yes*. If set to *no*, some time consuming synchronization of spring energies and the primitive kinetic energy estimator between processors is avoided.
The isomorphism between the partition function of :math:`N` bosonic quantum particles and that of a system of classical ring polymers
at inverse temperature :math:`\beta`
@ -144,6 +143,7 @@ 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.
The contribution of the :math:`P-1` interior springs is printed to the other :math:`P-1` log files.
The contribution of the constant :math:`\frac{PdN}{2 \beta}` (with :math:`d` being the dimentionality) is equally divided over log files.
Restrictions
""""""""""""
@ -161,6 +161,7 @@ The keyword defaults for fix *pimdb/nvt* are method = pimd, fmass = 1.0, sp
The keyord defaults for fix *pimdb/langevin* are integrator = obabo, method = pimd, ensemble = nvt, fmass = 1.0,
temp = 298.15, thermostat = PILE_L, tau = 1.0, fixcom = yes, esynch = yes, and lj = 1 for all its arguments.
----------
.. _book-Tuckerman: