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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/langevin
.. index:: fix pimd/nvt .. index:: fix pimd/nvt
fix pimd/langevin command fix pimd/langevin command
========================= =========================
@ -20,7 +20,7 @@ Syntax
* keywords for style *pimd/nvt* * keywords for style *pimd/nvt*
.. parsed-literal:: .. 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* *method* value = *pimd* or *nmpimd* or *cmd*
*fmass* value = scaling factor on mass *fmass* value = scaling factor on mass
*sp* value = scaling factor on Planck constant *sp* value = scaling factor on Planck constant
@ -30,7 +30,7 @@ Syntax
* keywords for style *pimd/langevin* * keywords for style *pimd/langevin*
.. parsed-literal:: .. 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* *method* value = *nmpimd* (default) or *pimd*
*integrator* value = *obabo* or *baoab* *integrator* value = *obabo* or *baoab*
*ensemble* value = *nvt* or *nve* or *nph* or *npt* *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. replica (shown in green) owns one quasi-bead in each ring.
.. image:: JPG/pimd.jpg .. image:: JPG/pimd.jpg
:align: center :align: center
To run a PIMD simulation with M quasi-beads in each ring polymer using 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 N MPI tasks for each partition's domain-decomposition, you would use P

11
doc/src/fix_pimdb.rst
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@ -1,5 +1,5 @@
.. index:: fix pimdb/langevin .. index:: fix pimdb/langevin
.. index:: fix pimdb/nvt .. index:: fix pimdb/nvt
fix pimdb/langevin command fix pimdb/langevin command
========================== ==========================
@ -20,7 +20,7 @@ Syntax
* keywords for style *pimdb/nvt* * keywords for style *pimdb/nvt*
.. parsed-literal:: .. 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* *method* value = *pimd* or *nmpimd*
*fmass* value = scaling factor on mass *fmass* value = scaling factor on mass
*sp* value = scaling factor on Planck constant *sp* value = scaling factor on Planck constant
@ -30,7 +30,7 @@ Syntax
* keywords for style *pimdb/langevin* * keywords for style *pimdb/langevin*
.. parsed-literal:: .. 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* *integrator* value = *obabo* or *baoab*
*ensemble* value = *nvt* or *nve* *ensemble* value = *nvt* or *nve*
*fmass* value = scaling factor on mass *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/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* 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 * 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 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 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` 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. 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 :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. The contribution of the constant :math:`\frac{PdN}{2 \beta}` (with :math:`d` being the dimentionality) is equally divided over log files.
Restrictions 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, 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. temp = 298.15, thermostat = PILE_L, tau = 1.0, fixcom = yes, esynch = yes, and lj = 1 for all its arguments.
---------- ----------
.. _book-Tuckerman: .. _book-Tuckerman: