Merge pull request #2137 from jtclemm/ptemp

  .. parsed-literal::

     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*

     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *ptemp* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*

       *temp* values = Tstart Tstop Tdamp

         Tstart,Tstop = external temperature at start/end of run

         Tdamp = temperature damping parameter (time units)

       *nreset* value = reset reference cell every this many timesteps

       *drag* value = Df

         Df = drag factor added to barostat/thermostat (0.0 = no drag)

       *ptemp* value = Ttarget

         Ttarget = target temperature for barostat

       *dilate* value = dilate-group-ID

         dilate-group-ID = only dilate atoms in this group due to barostat volume changes

       *scalexy* value = *yes* or *no* = scale xy with ly

   time units, and that timesteps are NOT the same as time units for most

   :doc:`units <units>` settings.

The relaxation rate of the barostat is set by its inertia :math:`W`:

.. math::

   W = (N + 1) k T_{\rm target} P_{\rm damp}^2

where :math:`N` is the number of atoms, :math:`k` is the Boltzmann constant,

and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.

If a thermostat is defined, :math:`T_{\rm target}` is the target temperature

of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`

is set to the current temperature of the system when the barostat is initialized.

If this temperature is too low the simulation will quit with an error.

Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to

a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature

of exactly zero.

If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be

manually specified using the *Ptemp* parameter. This may be useful if the

barostat is initialized when the current temperature does not reflect the

steady state temperature of the system. This keyword may also be useful in

athermal simulations where the temperature is not well defined.

Regardless of what atoms are in the fix group (the only atoms which

are time integrated), a global pressure or stress tensor is computed

for all atoms.  Similarly, when the size of the simulation box is

atc

AtC

ATC

athermal

athomps

atm

atomeye

#define DELTAFLIP 0.1

#define TILTMAX 1.5

#define EPSILON 1.0e-6

enum{NOBIAS,BIAS};

enum{NONE,XYZ,XY,YZ,XZ};

  flipflag = 1;

  dipole_flag = 0;

  dlm_flag = 0;

  p_temp_flag = 0;

  tcomputeflag = 0;

  pcomputeflag = 0;

      drag = force->numeric(FLERR,arg[iarg+1]);

      if (drag < 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command");

      iarg += 2;

    } else if (strcmp(arg[iarg],"ptemp") == 0) {

      if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");

      p_temp = force->numeric(FLERR,arg[iarg+1]);

      p_temp_flag = 1;

      if (p_temp <= 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command");

      iarg += 2;

    } else if (strcmp(arg[iarg],"dilate") == 0) {

      if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");

      if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;

      (p_flag[5] && p_period[5] <= 0.0))

    error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0");

  // check that ptemp is not defined with a thermostat

  if (tstat_flag && p_temp_flag)

    error->all(FLERR,"Thermostat in fix nvt/npt/nph is incompatible with ptemp command");

  // set pstat_flag and box change and restart_pbc variables

  pre_exchange_flag = 0;

  } else if (pstat_flag) {

    // t0 = reference temperature for masses

    // set equal to either ptemp or the current temperature

    // cannot be done in init() b/c temperature cannot be called there

    // is b/c Modify::init() inits computes after fixes due to dof dependence

    // guesstimate a unit-dependent t0 if actual T = 0.0

    // error if T less than 1e-6

    // if it was read in from a restart file, leave it be

    if (t0 == 0.0) {

      if(p_temp_flag) {

        t0 = p_temp;

      } else {

        t0 = temperature->compute_scalar();

      if (t0 == 0.0) {

        if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;

        else t0 = 300.0;

        if(t0 < EPSILON)

          error->all(FLERR, "Current temperature too close to zero, consider using ptemp setting");

      }

    }

    t_target = t0;

  char *id_dilate;                 // group name to dilate

  class Irregular *irregular;      // for migrating atoms after box flips

  double p_temp;                   // target temperature for barostat

  int p_temp_flag;

  int nlevels_respa;

  double *step_respa;

Self-explanatory.

E: Thermostat in fix nvt/npt/nph is incompatible with ptemp command

Self-explanatory.

E: Cannot use fix npt and fix deform on same component of stress tensor

This would be changing the same box dimension twice.

Self-explanatory.

E: Current temperature too close to zero, consider using ptemp setting

The current temperature is close to zero and may cause numerical instability. The user may want to specify a different target temperature using the ptemp setting.

E: Non-numeric pressure - simulation unstable

UNDOCUMENTED