diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index d56dd6cfae..a054489f8c 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -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 diff --git a/doc/src/fix_pimdb.rst b/doc/src/fix_pimdb.rst index f1cf4de6ab..e51470c3c5 100644 --- a/doc/src/fix_pimdb.rst +++ b/doc/src/fix_pimdb.rst @@ -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: