forked from lijiext/lammps
adapt formatting and naming conventions to fully match LAMMPS style. allow rigid and accelerated integrators.
This commit is contained in:
Axel Kohlmeyer
parent
4d2ed30b35
commit
eba4be18c2
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@ -12,14 +12,9 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing Authors: Amulya K. Pervaje and Cody K. Addington
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Contributing Authors: Amulya K. Pervaje and Cody K. Addington,
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(North Carolina State University)
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Contact Email: amulyapervaje@gmail.com
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temper/npt is a modification of temper that is applicable to the NPT ensemble
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uses the npt acceptance criteria for parallel tempering (replica exchange) as given in
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Mori, Y .; Okamoto, Y . Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble. J. Phys. Soc. Japan 2010, 79, 74003.
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temper/npt N M temp fix-ID seed1 seed2 pressure index(optional)
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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
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------------------------------------------------------------------------- */
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#include <math.h>
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@ -49,11 +44,11 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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TemperNpt::TemperNpt(LAMMPS *lmp) : Pointers(lmp) {}
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TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {}
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/* ---------------------------------------------------------------------- */
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TemperNpt::~TemperNpt()
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TemperNPT::~TemperNPT()
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{
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MPI_Comm_free(&roots);
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if (ranswap) delete ranswap;
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@ -68,14 +63,14 @@ TemperNpt::~TemperNpt()
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perform tempering with inter-world swaps
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------------------------------------------------------------------------- */
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void TemperNpt::command(int narg, char **arg)
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void TemperNPT::command(int narg, char **arg)
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{
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if (universe->nworlds == 1)
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error->all(FLERR,"Must have more than one processor partition to temper");
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if (domain->box_exist == 0)
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error->all(FLERR,"temper/npt command before simulation box is defined");
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if (narg != 7 && narg != 8)
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error->universe_all(FLERR,"Illegal temper command");
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error->universe_all(FLERR,"Illegal temper/npt command");
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int nsteps = force->inumeric(FLERR,arg[0]);
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nevery = force->inumeric(FLERR,arg[1]);
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@ -96,15 +91,19 @@ void TemperNpt::command(int narg, char **arg)
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// swap frequency must evenly divide total # of timesteps
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if (nevery <= 0)
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error->universe_all(FLERR,"Invalid frequency in temper command");
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error->universe_all(FLERR,"Invalid frequency in temper/npt command");
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nswaps = nsteps/nevery;
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if (nswaps*nevery != nsteps)
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error->universe_all(FLERR,"Non integer # of swaps in temper command");
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error->universe_all(FLERR,"Non integer # of swaps in temper/npt command");
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// fix style must be appropriate for temperature control, i.e. it needs
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// to provide a working Fix::reset_target() and must not change the volume.
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// fix style must be appropriate for temperature and pressure control,
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// i.e. it needs to provide a working Fix::reset_target() and must also
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// change the volume. This currently only applies to fix npt and
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// fix rigid/npt variants
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if ((strcmp(modify->fix[whichfix]->style,"npt") != 0)) error->universe_all(FLERR,"Tempering temperature fix is not supported");
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if ((strncmp(modify->fix[whichfix]->style,"npt",3) == 0)
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|| (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) == 0))
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error->universe_all(FLERR,"Tempering temperature fix is not supported");
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// setup for long tempering run
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@ -345,7 +344,7 @@ void TemperNpt::command(int narg, char **arg)
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scale kinetic energy via velocities a la Sugita
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------------------------------------------------------------------------- */
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void TemperNpt::scale_velocities(int t_partner, int t_me)
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void TemperNPT::scale_velocities(int t_partner, int t_me)
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{
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double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
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@ -363,7 +362,7 @@ void TemperNpt::scale_velocities(int t_partner, int t_me)
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proc 0 prints current tempering status
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------------------------------------------------------------------------- */
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void TemperNpt::print_status()
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void TemperNPT::print_status()
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{
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if (universe->uscreen) {
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fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep);
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@ -10,20 +10,11 @@
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See the README file in the top-level LAMMPS directory.
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Contributing Authors: Amulya K. Pervaje and Cody K. Addington
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Contact Email: amulyapervaje@gmail.com
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temper/npt is a modification of temper that is applicable to the NPT ensemble
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uses the npt acceptance criteria for parallel tempering (replica exchange) as given in
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Mori, Y .; Okamoto, Y . Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble. J. Phys. Soc. Japan 2010, 79, 74003.
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temper/npt N M temp fix-ID seed1 seed2 pressure index(optional)
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refer to documentation for temper, only difference with temper/npt is that the pressure is
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specified as the 7th argument, the 8th argument is the same optional index argument used in temper
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------------------------------------------------------------------------- */
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#ifdef COMMAND_CLASS
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CommandStyle(temper/npt,TemperNpt)
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CommandStyle(temper/npt,TemperNPT)
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#else
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@ -34,10 +25,10 @@ CommandStyle(temper/npt,TemperNpt)
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namespace LAMMPS_NS {
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class TemperNpt : protected Pointers {
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class TemperNPT : protected Pointers {
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public:
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TemperNpt(class LAMMPS *);
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~TemperNpt();
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TemperNPT(class LAMMPS *);
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~TemperNPT();
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void command(int, char **);
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private:
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@ -76,10 +67,10 @@ E: Must have more than one processor partition to temper
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Cannot use the temper command with only one processor partition. Use
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the -partition command-line option.
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E: TemperNpt command before simulation box is defined
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E: temper/npt command before simulation box is defined
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The temper command cannot be used before a read_data, read_restart, or
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create_box command.
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The temper/npt command cannot be used before a read_data, read_restart,
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or create_box command.
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E: Illegal ... command
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@ -89,21 +80,21 @@ command-line option when running LAMMPS to see the offending line.
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E: Tempering fix ID is not defined
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The fix ID specified by the temper command does not exist.
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The fix ID specified by the temper/npt command does not exist.
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E: Invalid frequency in temper command
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E: Invalid frequency in temper/npt command
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Nevery must be > 0.
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E: Non integer # of swaps in temper command
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E: Non integer # of swaps in temper/npt command
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Swap frequency in temper command must evenly divide the total # of
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timesteps.
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Swap frequency in temper/npt command must evenly divide the total
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# of timesteps.
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E: Tempering temperature fix is not valid
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The fix specified by the temper command is not one that controls
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temperature (nvt or langevin).
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temperature and pressure (npt).
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E: Too many timesteps
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