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lammps/src/USER-UEF/compute_pressure_uef.cpp
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compute_pressure_uef.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
Contributing author: David Nicholson (MIT)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include "compute_pressure_uef.h"
#include "fix_nh_uef.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
* Default values for the ext flags
* ----------------------------------------------------------------------*/
ComputePressureUef::ComputePressureUef(LAMMPS *lmp, int narg, char **arg) :
ComputePressure(lmp, narg, arg)
{
ext_flags[0] = true;
ext_flags[1] = true;
ext_flags[2] = true;
in_fix=false;
}
/* ----------------------------------------------------------------------
* Check for the uef fix
* ----------------------------------------------------------------------*/
void ComputePressureUef::init()
{
ComputePressure::init();
// check to make sure the other uef fix is on
// borrowed from Pieter's nvt/sllod code
int i=0;
for (i=0; i<modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"nvt/uef")==0)
break;
if (strcmp(modify->fix[i]->style,"npt/uef")==0)
break;
}
if (i==modify->nfix)
error->all(FLERR,"Can't use compute pressure/uef without defining a fix nvt/npt/uef");
ifix_uef=i;
((FixNHUef*) modify->fix[ifix_uef])->get_ext_flags(ext_flags);
if (strcmp(temperature->style,"temp/uef") != 0)
error->warning(FLERR,"The temperature used in compute pressure/ued is not of style temp/uef");
}
/* ----------------------------------------------------------------------
* Compute pressure in the directions i corresponding to ext_flag[i]=true
* ----------------------------------------------------------------------*/
double ComputePressureUef::compute_scalar()
{
temperature->compute_scalar();
// if all pressures are external the scalar is found as normal
if (ext_flags[0] && ext_flags[1] && ext_flags[2])
return ComputePressure::compute_scalar();
// otherwise compute the full tensor and average desired components
compute_vector();
addstep(update->ntimestep+1);
int k =0;
scalar = 0;
if (ext_flags[0]) {
scalar += vector[0];
k++;
}
if (ext_flags[1]) {
scalar += vector[1];
k++;
}
if (ext_flags[2]) {
scalar += vector[2];
k++;
}
scalar /= k;
return scalar;
}
/* ----------------------------------------------------------------------
Compute the pressure tensor in the rotated coordinate system
------------------------------------------------------------------------- */
void ComputePressureUef::compute_vector()
{
invoked_vector = update->ntimestep;
if (update->vflag_global != invoked_vector)
error->all(FLERR,"Virial was not tallied on needed timestep");
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
"tensor components with kspace_style msm");
// invoke temperature if it hasn't been already
double *ke_tensor;
if (keflag) {
if (temperature->invoked_vector != update->ntimestep)
temperature->compute_vector();
ke_tensor = temperature->vector;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(6,3);
if (in_fix)
virial_rot(virial,rot);
else
{
double r[3][3];
( (FixNHUef*) modify->fix[ifix_uef])->get_rot(r);
virial_rot(virial,r);
}
if (keflag) {
for (int i = 0; i < 6; i++)
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
} else
for (int i = 0; i < 6; i++)
vector[i] = virial[i] * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(4,2);
if (keflag) {
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
} else {
vector[0] = virial[0] * inv_volume * nktv2p;
vector[1] = virial[1] * inv_volume * nktv2p;
vector[3] = virial[3] * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
* get the current rotation matrix and store it
------------------------------------------------------------------------- */
void ComputePressureUef::update_rot()
{
( (FixNHUef*) modify->fix[ifix_uef])->get_rot(rot);
}
/* ----------------------------------------------------------------------
Transform the pressure tensor to the rotated coordinate system
[P]rot = Q.[P].Q^t
------------------------------------------------------------------------- */
void ComputePressureUef::virial_rot(double *x, const double r[3][3])
{
double t[3][3];
// [00 10 20 ] [ 0 3 4 ] [00 01 02 ]
// [01 11 21 ] [ 3 1 5 ] [10 11 12 ]
// [02 12 22 ] [ 4 5 2 ] [20 21 22 ]
for (int k = 0; k<3; ++k)
{
t[0][k] = x[0]*r[0][k] + x[3]*r[1][k] + x[4]*r[2][k];
t[1][k] = x[3]*r[0][k] + x[1]*r[1][k] + x[5]*r[2][k];
t[2][k] = x[4]*r[0][k] + x[5]*r[1][k] + x[2]*r[2][k];
}
x[0] = r[0][0]*t[0][0] + r[1][0]*t[1][0] + r[2][0]*t[2][0];
x[3] = r[0][0]*t[0][1] + r[1][0]*t[1][1] + r[2][0]*t[2][1];
x[4] = r[0][0]*t[0][2] + r[1][0]*t[1][2] + r[2][0]*t[2][2];
x[1] = r[0][1]*t[0][1] + r[1][1]*t[1][1] + r[2][1]*t[2][1];
x[5] = r[0][1]*t[0][2] + r[1][1]*t[1][2] + r[2][1]*t[2][2];
x[2] = r[0][2]*t[0][2] + r[1][2]*t[1][2] + r[2][2]*t[2][2];
}
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