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adapt formatting and naming conventions to fully match LAMMPS style. allow rigid and accelerated integrators.

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This commit is contained in:
Axel Kohlmeyer
2017-08-31 14:48:30 -04:00
parent 4d2ed30b35
commit eba4be18c2
2 changed files with 30 additions and 40 deletions
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35
src/USER-MISC/temper_npt.cpp
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@ -12,14 +12,9 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing Authors: Amulya K. Pervaje and Cody K. Addington
Contributing Authors: Amulya K. Pervaje and Cody K. Addington,
(North Carolina State University)
Contact Email: amulyapervaje@gmail.com
temper/npt is a modification of temper that is applicable to the NPT ensemble
uses the npt acceptance criteria for parallel tempering (replica exchange) as given in
Mori, Y .; Okamoto, Y . Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble. J. Phys. Soc. Japan 2010, 79, 74003.
temper/npt N M temp fix-ID seed1 seed2 pressure index(optional)
refer to documentation for temper, only difference with temper/npt is that the pressure is specified as the 7th argument, the 8th argument is the same optional index argument used in temper
------------------------------------------------------------------------- */
#include <math.h>
@ -49,11 +44,11 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
TemperNpt::TemperNpt(LAMMPS *lmp) : Pointers(lmp) {}
TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
TemperNpt::~TemperNpt()
TemperNPT::~TemperNPT()
{
MPI_Comm_free(&roots);
if (ranswap) delete ranswap;
@ -68,14 +63,14 @@ TemperNpt::~TemperNpt()
perform tempering with inter-world swaps
------------------------------------------------------------------------- */
void TemperNpt::command(int narg, char **arg)
void TemperNPT::command(int narg, char **arg)
{
if (universe->nworlds == 1)
error->all(FLERR,"Must have more than one processor partition to temper");
if (domain->box_exist == 0)
error->all(FLERR,"temper/npt command before simulation box is defined");
if (narg != 7 && narg != 8)
error->universe_all(FLERR,"Illegal temper command");
error->universe_all(FLERR,"Illegal temper/npt command");
int nsteps = force->inumeric(FLERR,arg[0]);
nevery = force->inumeric(FLERR,arg[1]);
@ -96,15 +91,19 @@ void TemperNpt::command(int narg, char **arg)
// swap frequency must evenly divide total # of timesteps
if (nevery <= 0)
error->universe_all(FLERR,"Invalid frequency in temper command");
error->universe_all(FLERR,"Invalid frequency in temper/npt command");
nswaps = nsteps/nevery;
if (nswaps*nevery != nsteps)
error->universe_all(FLERR,"Non integer # of swaps in temper command");
error->universe_all(FLERR,"Non integer # of swaps in temper/npt command");
// fix style must be appropriate for temperature control, i.e. it needs
// to provide a working Fix::reset_target() and must not change the volume.
// fix style must be appropriate for temperature and pressure control,
// i.e. it needs to provide a working Fix::reset_target() and must also
// change the volume. This currently only applies to fix npt and
// fix rigid/npt variants
if ((strcmp(modify->fix[whichfix]->style,"npt") != 0)) error->universe_all(FLERR,"Tempering temperature fix is not supported");
if ((strncmp(modify->fix[whichfix]->style,"npt",3) == 0)
|| (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) == 0))
error->universe_all(FLERR,"Tempering temperature fix is not supported");
// setup for long tempering run
@ -345,7 +344,7 @@ void TemperNpt::command(int narg, char **arg)
scale kinetic energy via velocities a la Sugita
------------------------------------------------------------------------- */
void TemperNpt::scale_velocities(int t_partner, int t_me)
void TemperNPT::scale_velocities(int t_partner, int t_me)
{
double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
@ -363,7 +362,7 @@ void TemperNpt::scale_velocities(int t_partner, int t_me)
proc 0 prints current tempering status
------------------------------------------------------------------------- */
void TemperNpt::print_status()
void TemperNPT::print_status()
{
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep);