git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10130 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
893
src/kspace.cpp
893
src/kspace.cpp
@ -1,446 +1,447 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "kspace.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "memory.h"
|
||||
#include "atom_masks.h"
|
||||
#include "error.h"
|
||||
#include "suffix.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
|
||||
{
|
||||
energy = 0.0;
|
||||
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
|
||||
|
||||
triclinic_support = 1;
|
||||
ewaldflag = pppmflag = msmflag = dispersionflag = tip4pflag = dipoleflag = 0;
|
||||
compute_flag = 1;
|
||||
group_group_enable = 0;
|
||||
|
||||
order = 5;
|
||||
gridflag = 0;
|
||||
gewaldflag = 0;
|
||||
minorder = 2;
|
||||
overlap_allowed = 1;
|
||||
fftbench = 1;
|
||||
|
||||
order_6 = 5;
|
||||
gridflag_6 = 0;
|
||||
gewaldflag_6 = 0;
|
||||
|
||||
slabflag = 0;
|
||||
differentiation_flag = 0;
|
||||
slab_volfactor = 1;
|
||||
suffix_flag = Suffix::NONE;
|
||||
adjust_cutoff_flag = 1;
|
||||
|
||||
accuracy_absolute = -1.0;
|
||||
two_charge_force = force->qqr2e *
|
||||
(force->qelectron * force->qelectron) /
|
||||
(force->angstrom * force->angstrom);
|
||||
|
||||
maxeatom = maxvatom = 0;
|
||||
eatom = NULL;
|
||||
vatom = NULL;
|
||||
|
||||
datamask = ALL_MASK;
|
||||
datamask_ext = ALL_MASK;
|
||||
|
||||
memory->create(gcons,7,7,"kspace:gcons");
|
||||
gcons[2][0] = 15.0 / 8.0;
|
||||
gcons[2][1] = -5.0 / 4.0;
|
||||
gcons[2][2] = 3.0 / 8.0;
|
||||
gcons[3][0] = 35.0 / 16.0;
|
||||
gcons[3][1] = -35.0 / 16.0;
|
||||
gcons[3][2] = 21.0 / 16.0;
|
||||
gcons[3][3] = -5.0 / 16.0;
|
||||
gcons[4][0] = 315.0 / 128.0;
|
||||
gcons[4][1] = -105.0 / 32.0;
|
||||
gcons[4][2] = 189.0 / 64.0;
|
||||
gcons[4][3] = -45.0 / 32.0;
|
||||
gcons[4][4] = 35.0 / 128.0;
|
||||
gcons[5][0] = 693.0 / 256.0;
|
||||
gcons[5][1] = -1155.0 / 256.0;
|
||||
gcons[5][2] = 693.0 / 128.0;
|
||||
gcons[5][3] = -495.0 / 128.0;
|
||||
gcons[5][4] = 385.0 / 256.0;
|
||||
gcons[5][5] = -63.0 / 256.0;
|
||||
gcons[6][0] = 3003.0 / 1024.0;
|
||||
gcons[6][1] = -3003.0 / 512.0;
|
||||
gcons[6][2] = 9009.0 / 1024.0;
|
||||
gcons[6][3] = -2145.0 / 256.0;
|
||||
gcons[6][4] = 5005.0 / 1024.0;
|
||||
gcons[6][5] = -819.0 / 512.0;
|
||||
gcons[6][6] = 231.0 / 1024.0;
|
||||
|
||||
memory->create(dgcons,7,6,"kspace:dgcons");
|
||||
dgcons[2][0] = -5.0 / 2.0;
|
||||
dgcons[2][1] = 3.0 / 2.0;
|
||||
dgcons[3][0] = -35.0 / 8.0;
|
||||
dgcons[3][1] = 21.0 / 4.0;
|
||||
dgcons[3][2] = -15.0 / 8.0;
|
||||
dgcons[4][0] = -105.0 / 16.0;
|
||||
dgcons[4][1] = 189.0 / 16.0;
|
||||
dgcons[4][2] = -135.0 / 16.0;
|
||||
dgcons[4][3] = 35.0 / 16.0;
|
||||
dgcons[5][0] = -1155.0 / 128.0;
|
||||
dgcons[5][1] = 693.0 / 32.0;
|
||||
dgcons[5][2] = -1485.0 / 64.0;
|
||||
dgcons[5][3] = 385.0 / 32.0;
|
||||
dgcons[5][4] = -315.0 / 128.0;
|
||||
dgcons[6][0] = -3003.0 / 256.0;
|
||||
dgcons[6][1] = 9009.0 / 256.0;
|
||||
dgcons[6][2] = -6435.0 / 128.0;
|
||||
dgcons[6][3] = 5005.0 / 128.0;
|
||||
dgcons[6][4] = -4095.0 / 256.0;
|
||||
dgcons[6][5] = 693.0 / 256.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
KSpace::~KSpace()
|
||||
{
|
||||
memory->destroy(eatom);
|
||||
memory->destroy(vatom);
|
||||
memory->destroy(gcons);
|
||||
memory->destroy(dgcons);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::triclinic_check()
|
||||
{
|
||||
if (domain->triclinic && triclinic_support != 1)
|
||||
error->all(FLERR,"KSpace style does not yet support triclinic geometries");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::compute_dummy(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = evflag_atom = eflag_global = vflag_global =
|
||||
eflag_atom = vflag_atom = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check that pair style is compatible with long-range solver
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::pair_check()
|
||||
{
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"KSpace solver requires a pair style");
|
||||
if (ewaldflag && force->pair->ewaldflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (pppmflag && force->pair->pppmflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (msmflag && force->pair->msmflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (dispersionflag && force->pair->dispersionflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (tip4pflag && force->pair->tip4pflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (dipoleflag && force->pair->dipoleflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup for energy, virial computation
|
||||
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::ev_setup(int eflag, int vflag)
|
||||
{
|
||||
int i,n;
|
||||
|
||||
evflag = 1;
|
||||
|
||||
eflag_either = eflag;
|
||||
eflag_global = eflag % 2;
|
||||
eflag_atom = eflag / 2;
|
||||
|
||||
vflag_either = vflag;
|
||||
vflag_global = vflag % 4;
|
||||
vflag_atom = vflag / 4;
|
||||
|
||||
if (eflag_atom || vflag_atom) evflag_atom = 1;
|
||||
else evflag_atom = 0;
|
||||
|
||||
// reallocate per-atom arrays if necessary
|
||||
|
||||
if (eflag_atom && atom->nmax > maxeatom) {
|
||||
maxeatom = atom->nmax;
|
||||
memory->destroy(eatom);
|
||||
memory->create(eatom,maxeatom,"kspace:eatom");
|
||||
}
|
||||
if (vflag_atom && atom->nmax > maxvatom) {
|
||||
maxvatom = atom->nmax;
|
||||
memory->destroy(vatom);
|
||||
memory->create(vatom,maxvatom,6,"kspace:vatom");
|
||||
}
|
||||
|
||||
// zero accumulators
|
||||
|
||||
if (eflag_global) energy = 0.0;
|
||||
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
|
||||
if (eflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (tip4pflag) n += atom->nghost;
|
||||
for (i = 0; i < n; i++) eatom[i] = 0.0;
|
||||
}
|
||||
if (vflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (tip4pflag) n += atom->nghost;
|
||||
for (i = 0; i < n; i++) {
|
||||
vatom[i][0] = 0.0;
|
||||
vatom[i][1] = 0.0;
|
||||
vatom[i][2] = 0.0;
|
||||
vatom[i][3] = 0.0;
|
||||
vatom[i][4] = 0.0;
|
||||
vatom[i][5] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
estimate the accuracy of the short-range coulomb tables
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double KSpace::estimate_table_accuracy(double q2_over_sqrt, double spr)
|
||||
{
|
||||
double table_accuracy = 0.0;
|
||||
int nctb = force->pair->ncoultablebits;
|
||||
if (nctb) {
|
||||
double empirical_precision[17];
|
||||
empirical_precision[6] = 6.99E-03;
|
||||
empirical_precision[7] = 1.78E-03;
|
||||
empirical_precision[8] = 4.72E-04;
|
||||
empirical_precision[9] = 1.17E-04;
|
||||
empirical_precision[10] = 2.95E-05;
|
||||
empirical_precision[11] = 7.41E-06;
|
||||
empirical_precision[12] = 1.76E-06;
|
||||
empirical_precision[13] = 9.28E-07;
|
||||
empirical_precision[14] = 7.46E-07;
|
||||
empirical_precision[15] = 7.32E-07;
|
||||
empirical_precision[16] = 7.30E-07;
|
||||
if (nctb <= 6) table_accuracy = empirical_precision[6];
|
||||
else if (nctb <= 16) table_accuracy = empirical_precision[nctb];
|
||||
else table_accuracy = empirical_precision[16];
|
||||
table_accuracy *= q2_over_sqrt;
|
||||
if ((table_accuracy > spr) && (comm->me == 0))
|
||||
error->warning(FLERR,"For better accuracy use 'pair_modify table 0'");
|
||||
}
|
||||
|
||||
return table_accuracy;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert box coords vector to transposed triclinic lamda (0-1) coords
|
||||
vector, lamda = [(H^-1)^T] * v, does not preserve vector magnitude
|
||||
v and lamda can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::x2lamdaT(double *v, double *lamda)
|
||||
{
|
||||
double *h_inv = domain->h_inv;
|
||||
double lamda_tmp[3];
|
||||
|
||||
lamda_tmp[0] = h_inv[0]*v[0];
|
||||
lamda_tmp[1] = h_inv[5]*v[0] + h_inv[1]*v[1];
|
||||
lamda_tmp[2] = h_inv[4]*v[0] + h_inv[3]*v[1] + h_inv[2]*v[2];
|
||||
|
||||
lamda[0] = lamda_tmp[0];
|
||||
lamda[1] = lamda_tmp[1];
|
||||
lamda[2] = lamda_tmp[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert lamda (0-1) coords vector to transposed box coords vector
|
||||
lamda = (H^T) * v, does not preserve vector magnitude
|
||||
v and lamda can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::lamda2xT(double *lamda, double *v)
|
||||
{
|
||||
double *h = domain->h;
|
||||
double v_tmp[3];
|
||||
|
||||
v_tmp[0] = h[0]*lamda[0];
|
||||
v_tmp[1] = h[5]*lamda[0] + h[1]*lamda[1];
|
||||
v_tmp[2] = h[4]*lamda[0] + h[3]*lamda[1] + h[2]*lamda[2];
|
||||
|
||||
v[0] = v_tmp[0];
|
||||
v[1] = v_tmp[1];
|
||||
v[2] = v_tmp[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert triclinic lamda (0-1) coords vector to box coords vector
|
||||
v = H * lamda, does not preserve vector magnitude
|
||||
lamda and v can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::lamda2xvector(double *lamda, double *v)
|
||||
{
|
||||
double *h = domain->h;
|
||||
|
||||
v[0] = h[0]*lamda[0] + h[5]*lamda[1] + h[4]*lamda[2];
|
||||
v[1] = h[1]*lamda[1] + h[3]*lamda[2];
|
||||
v[2] = h[2]*lamda[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert a sphere in box coords to an ellipsoid in lamda (0-1)
|
||||
coords and return the tight (axis-aligned) bounding box, does not
|
||||
preserve vector magnitude
|
||||
see http://www.loria.fr/~shornus/ellipsoid-bbox.html and
|
||||
http://yiningkarlli.blogspot.com/2013/02/bounding-boxes-for-ellipsoidsfigure.html
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::kspacebbox(double r, double *b)
|
||||
{
|
||||
double *h = domain->h;
|
||||
double lx,ly,lz,xy,xz,yz;
|
||||
lx = h[0];
|
||||
ly = h[1];
|
||||
lz = h[2];
|
||||
yz = h[3];
|
||||
xz = h[4];
|
||||
xy = h[5];
|
||||
|
||||
b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy +
|
||||
xy*xy*yz*yz)/(lx*ly*lz);
|
||||
b[1] = r*sqrt(lz*lz + yz*yz)/(ly*lz);
|
||||
b[2] = r/lz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
modify parameters of the KSpace style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::modify_params(int narg, char **arg)
|
||||
{
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"mesh") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
nx_pppm = nx_msm_max = atoi(arg[iarg+1]);
|
||||
ny_pppm = ny_msm_max = atoi(arg[iarg+2]);
|
||||
nz_pppm = nz_msm_max = atoi(arg[iarg+3]);
|
||||
if (nx_pppm == 0 && ny_pppm == 0 && nz_pppm == 0) gridflag = 0;
|
||||
else gridflag = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"mesh/disp") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
nx_pppm_6 = atoi(arg[iarg+1]);
|
||||
ny_pppm_6 = atoi(arg[iarg+2]);
|
||||
nz_pppm_6 = atoi(arg[iarg+3]);
|
||||
if (nx_pppm_6 == 0 || ny_pppm_6 == 0 || nz_pppm_6 == 0) gridflag_6 = 0;
|
||||
else gridflag_6 = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"order") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
order = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"order/disp") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
order_6 = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"minorder") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
minorder = atoi(arg[iarg+1]);
|
||||
if (minorder < 2) error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"overlap") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) overlap_allowed = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) overlap_allowed = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"force") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
accuracy_absolute = atof(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"gewald") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
g_ewald = atof(arg[iarg+1]);
|
||||
if (g_ewald == 0.0) gewaldflag = 0;
|
||||
else gewaldflag = 1;
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"gewald/disp") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
g_ewald_6 = atof(arg[iarg+1]);
|
||||
if (g_ewald_6 == 0.0) gewaldflag_6 = 0;
|
||||
else gewaldflag_6 = 1;
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"slab") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"nozforce") == 0) {
|
||||
slabflag = 2;
|
||||
} else {
|
||||
slabflag = 1;
|
||||
slab_volfactor = atof(arg[iarg+1]);
|
||||
if (slab_volfactor <= 1.0)
|
||||
error->all(FLERR,"Bad kspace_modify slab parameter");
|
||||
if (slab_volfactor < 2.0 && comm->me == 0)
|
||||
error->warning(FLERR,"Kspace_modify slab param < 2.0 may "
|
||||
"cause unphysical behavior");
|
||||
}
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"compute") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) compute_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) compute_flag = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"fftbench") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) fftbench = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) fftbench = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"diff") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"ad") == 0) differentiation_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"ik") == 0) differentiation_flag = 0;
|
||||
else error->all(FLERR, "Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"cutoff/adjust") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) adjust_cutoff_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) adjust_cutoff_flag = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal kspace_modify command");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *KSpace::extract(const char *str)
|
||||
{
|
||||
if (strcmp(str,"scale") == 0) return (void *) &scale;
|
||||
return NULL;
|
||||
}
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "kspace.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "memory.h"
|
||||
#include "atom_masks.h"
|
||||
#include "error.h"
|
||||
#include "suffix.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
|
||||
{
|
||||
energy = 0.0;
|
||||
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
|
||||
|
||||
triclinic_support = 1;
|
||||
ewaldflag = pppmflag = msmflag = dispersionflag = tip4pflag = dipoleflag = 0;
|
||||
compute_flag = 1;
|
||||
group_group_enable = 0;
|
||||
stagger_flag = 0;
|
||||
|
||||
order = 5;
|
||||
gridflag = 0;
|
||||
gewaldflag = 0;
|
||||
minorder = 2;
|
||||
overlap_allowed = 1;
|
||||
fftbench = 1;
|
||||
|
||||
order_6 = 5;
|
||||
gridflag_6 = 0;
|
||||
gewaldflag_6 = 0;
|
||||
|
||||
slabflag = 0;
|
||||
differentiation_flag = 0;
|
||||
slab_volfactor = 1;
|
||||
suffix_flag = Suffix::NONE;
|
||||
adjust_cutoff_flag = 1;
|
||||
|
||||
accuracy_absolute = -1.0;
|
||||
two_charge_force = force->qqr2e *
|
||||
(force->qelectron * force->qelectron) /
|
||||
(force->angstrom * force->angstrom);
|
||||
|
||||
maxeatom = maxvatom = 0;
|
||||
eatom = NULL;
|
||||
vatom = NULL;
|
||||
|
||||
datamask = ALL_MASK;
|
||||
datamask_ext = ALL_MASK;
|
||||
|
||||
memory->create(gcons,7,7,"kspace:gcons");
|
||||
gcons[2][0] = 15.0 / 8.0;
|
||||
gcons[2][1] = -5.0 / 4.0;
|
||||
gcons[2][2] = 3.0 / 8.0;
|
||||
gcons[3][0] = 35.0 / 16.0;
|
||||
gcons[3][1] = -35.0 / 16.0;
|
||||
gcons[3][2] = 21.0 / 16.0;
|
||||
gcons[3][3] = -5.0 / 16.0;
|
||||
gcons[4][0] = 315.0 / 128.0;
|
||||
gcons[4][1] = -105.0 / 32.0;
|
||||
gcons[4][2] = 189.0 / 64.0;
|
||||
gcons[4][3] = -45.0 / 32.0;
|
||||
gcons[4][4] = 35.0 / 128.0;
|
||||
gcons[5][0] = 693.0 / 256.0;
|
||||
gcons[5][1] = -1155.0 / 256.0;
|
||||
gcons[5][2] = 693.0 / 128.0;
|
||||
gcons[5][3] = -495.0 / 128.0;
|
||||
gcons[5][4] = 385.0 / 256.0;
|
||||
gcons[5][5] = -63.0 / 256.0;
|
||||
gcons[6][0] = 3003.0 / 1024.0;
|
||||
gcons[6][1] = -3003.0 / 512.0;
|
||||
gcons[6][2] = 9009.0 / 1024.0;
|
||||
gcons[6][3] = -2145.0 / 256.0;
|
||||
gcons[6][4] = 5005.0 / 1024.0;
|
||||
gcons[6][5] = -819.0 / 512.0;
|
||||
gcons[6][6] = 231.0 / 1024.0;
|
||||
|
||||
memory->create(dgcons,7,6,"kspace:dgcons");
|
||||
dgcons[2][0] = -5.0 / 2.0;
|
||||
dgcons[2][1] = 3.0 / 2.0;
|
||||
dgcons[3][0] = -35.0 / 8.0;
|
||||
dgcons[3][1] = 21.0 / 4.0;
|
||||
dgcons[3][2] = -15.0 / 8.0;
|
||||
dgcons[4][0] = -105.0 / 16.0;
|
||||
dgcons[4][1] = 189.0 / 16.0;
|
||||
dgcons[4][2] = -135.0 / 16.0;
|
||||
dgcons[4][3] = 35.0 / 16.0;
|
||||
dgcons[5][0] = -1155.0 / 128.0;
|
||||
dgcons[5][1] = 693.0 / 32.0;
|
||||
dgcons[5][2] = -1485.0 / 64.0;
|
||||
dgcons[5][3] = 385.0 / 32.0;
|
||||
dgcons[5][4] = -315.0 / 128.0;
|
||||
dgcons[6][0] = -3003.0 / 256.0;
|
||||
dgcons[6][1] = 9009.0 / 256.0;
|
||||
dgcons[6][2] = -6435.0 / 128.0;
|
||||
dgcons[6][3] = 5005.0 / 128.0;
|
||||
dgcons[6][4] = -4095.0 / 256.0;
|
||||
dgcons[6][5] = 693.0 / 256.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
KSpace::~KSpace()
|
||||
{
|
||||
memory->destroy(eatom);
|
||||
memory->destroy(vatom);
|
||||
memory->destroy(gcons);
|
||||
memory->destroy(dgcons);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::triclinic_check()
|
||||
{
|
||||
if (domain->triclinic && triclinic_support != 1)
|
||||
error->all(FLERR,"KSpace style does not yet support triclinic geometries");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::compute_dummy(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = evflag_atom = eflag_global = vflag_global =
|
||||
eflag_atom = vflag_atom = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check that pair style is compatible with long-range solver
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::pair_check()
|
||||
{
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"KSpace solver requires a pair style");
|
||||
if (ewaldflag && force->pair->ewaldflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (pppmflag && force->pair->pppmflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (msmflag && force->pair->msmflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (dispersionflag && force->pair->dispersionflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (tip4pflag && force->pair->tip4pflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
if (dipoleflag && force->pair->dipoleflag == 0)
|
||||
error->all(FLERR,"KSpace style is incompatible with Pair style");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup for energy, virial computation
|
||||
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::ev_setup(int eflag, int vflag)
|
||||
{
|
||||
int i,n;
|
||||
|
||||
evflag = 1;
|
||||
|
||||
eflag_either = eflag;
|
||||
eflag_global = eflag % 2;
|
||||
eflag_atom = eflag / 2;
|
||||
|
||||
vflag_either = vflag;
|
||||
vflag_global = vflag % 4;
|
||||
vflag_atom = vflag / 4;
|
||||
|
||||
if (eflag_atom || vflag_atom) evflag_atom = 1;
|
||||
else evflag_atom = 0;
|
||||
|
||||
// reallocate per-atom arrays if necessary
|
||||
|
||||
if (eflag_atom && atom->nmax > maxeatom) {
|
||||
maxeatom = atom->nmax;
|
||||
memory->destroy(eatom);
|
||||
memory->create(eatom,maxeatom,"kspace:eatom");
|
||||
}
|
||||
if (vflag_atom && atom->nmax > maxvatom) {
|
||||
maxvatom = atom->nmax;
|
||||
memory->destroy(vatom);
|
||||
memory->create(vatom,maxvatom,6,"kspace:vatom");
|
||||
}
|
||||
|
||||
// zero accumulators
|
||||
|
||||
if (eflag_global) energy = 0.0;
|
||||
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
|
||||
if (eflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (tip4pflag) n += atom->nghost;
|
||||
for (i = 0; i < n; i++) eatom[i] = 0.0;
|
||||
}
|
||||
if (vflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (tip4pflag) n += atom->nghost;
|
||||
for (i = 0; i < n; i++) {
|
||||
vatom[i][0] = 0.0;
|
||||
vatom[i][1] = 0.0;
|
||||
vatom[i][2] = 0.0;
|
||||
vatom[i][3] = 0.0;
|
||||
vatom[i][4] = 0.0;
|
||||
vatom[i][5] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
estimate the accuracy of the short-range coulomb tables
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double KSpace::estimate_table_accuracy(double q2_over_sqrt, double spr)
|
||||
{
|
||||
double table_accuracy = 0.0;
|
||||
int nctb = force->pair->ncoultablebits;
|
||||
if (nctb) {
|
||||
double empirical_precision[17];
|
||||
empirical_precision[6] = 6.99E-03;
|
||||
empirical_precision[7] = 1.78E-03;
|
||||
empirical_precision[8] = 4.72E-04;
|
||||
empirical_precision[9] = 1.17E-04;
|
||||
empirical_precision[10] = 2.95E-05;
|
||||
empirical_precision[11] = 7.41E-06;
|
||||
empirical_precision[12] = 1.76E-06;
|
||||
empirical_precision[13] = 9.28E-07;
|
||||
empirical_precision[14] = 7.46E-07;
|
||||
empirical_precision[15] = 7.32E-07;
|
||||
empirical_precision[16] = 7.30E-07;
|
||||
if (nctb <= 6) table_accuracy = empirical_precision[6];
|
||||
else if (nctb <= 16) table_accuracy = empirical_precision[nctb];
|
||||
else table_accuracy = empirical_precision[16];
|
||||
table_accuracy *= q2_over_sqrt;
|
||||
if ((table_accuracy > spr) && (comm->me == 0))
|
||||
error->warning(FLERR,"For better accuracy use 'pair_modify table 0'");
|
||||
}
|
||||
|
||||
return table_accuracy;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert box coords vector to transposed triclinic lamda (0-1) coords
|
||||
vector, lamda = [(H^-1)^T] * v, does not preserve vector magnitude
|
||||
v and lamda can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::x2lamdaT(double *v, double *lamda)
|
||||
{
|
||||
double *h_inv = domain->h_inv;
|
||||
double lamda_tmp[3];
|
||||
|
||||
lamda_tmp[0] = h_inv[0]*v[0];
|
||||
lamda_tmp[1] = h_inv[5]*v[0] + h_inv[1]*v[1];
|
||||
lamda_tmp[2] = h_inv[4]*v[0] + h_inv[3]*v[1] + h_inv[2]*v[2];
|
||||
|
||||
lamda[0] = lamda_tmp[0];
|
||||
lamda[1] = lamda_tmp[1];
|
||||
lamda[2] = lamda_tmp[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert lamda (0-1) coords vector to transposed box coords vector
|
||||
lamda = (H^T) * v, does not preserve vector magnitude
|
||||
v and lamda can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::lamda2xT(double *lamda, double *v)
|
||||
{
|
||||
double *h = domain->h;
|
||||
double v_tmp[3];
|
||||
|
||||
v_tmp[0] = h[0]*lamda[0];
|
||||
v_tmp[1] = h[5]*lamda[0] + h[1]*lamda[1];
|
||||
v_tmp[2] = h[4]*lamda[0] + h[3]*lamda[1] + h[2]*lamda[2];
|
||||
|
||||
v[0] = v_tmp[0];
|
||||
v[1] = v_tmp[1];
|
||||
v[2] = v_tmp[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert triclinic lamda (0-1) coords vector to box coords vector
|
||||
v = H * lamda, does not preserve vector magnitude
|
||||
lamda and v can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::lamda2xvector(double *lamda, double *v)
|
||||
{
|
||||
double *h = domain->h;
|
||||
|
||||
v[0] = h[0]*lamda[0] + h[5]*lamda[1] + h[4]*lamda[2];
|
||||
v[1] = h[1]*lamda[1] + h[3]*lamda[2];
|
||||
v[2] = h[2]*lamda[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert a sphere in box coords to an ellipsoid in lamda (0-1)
|
||||
coords and return the tight (axis-aligned) bounding box, does not
|
||||
preserve vector magnitude
|
||||
see http://www.loria.fr/~shornus/ellipsoid-bbox.html and
|
||||
http://yiningkarlli.blogspot.com/2013/02/bounding-boxes-for-ellipsoidsfigure.html
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::kspacebbox(double r, double *b)
|
||||
{
|
||||
double *h = domain->h;
|
||||
double lx,ly,lz,xy,xz,yz;
|
||||
lx = h[0];
|
||||
ly = h[1];
|
||||
lz = h[2];
|
||||
yz = h[3];
|
||||
xz = h[4];
|
||||
xy = h[5];
|
||||
|
||||
b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy +
|
||||
xy*xy*yz*yz)/(lx*ly*lz);
|
||||
b[1] = r*sqrt(lz*lz + yz*yz)/(ly*lz);
|
||||
b[2] = r/lz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
modify parameters of the KSpace style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void KSpace::modify_params(int narg, char **arg)
|
||||
{
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"mesh") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
nx_pppm = nx_msm_max = atoi(arg[iarg+1]);
|
||||
ny_pppm = ny_msm_max = atoi(arg[iarg+2]);
|
||||
nz_pppm = nz_msm_max = atoi(arg[iarg+3]);
|
||||
if (nx_pppm == 0 && ny_pppm == 0 && nz_pppm == 0) gridflag = 0;
|
||||
else gridflag = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"mesh/disp") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
nx_pppm_6 = atoi(arg[iarg+1]);
|
||||
ny_pppm_6 = atoi(arg[iarg+2]);
|
||||
nz_pppm_6 = atoi(arg[iarg+3]);
|
||||
if (nx_pppm_6 == 0 || ny_pppm_6 == 0 || nz_pppm_6 == 0) gridflag_6 = 0;
|
||||
else gridflag_6 = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"order") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
order = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"order/disp") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
order_6 = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"minorder") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
minorder = atoi(arg[iarg+1]);
|
||||
if (minorder < 2) error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"overlap") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) overlap_allowed = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) overlap_allowed = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"force") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
accuracy_absolute = atof(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"gewald") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
g_ewald = atof(arg[iarg+1]);
|
||||
if (g_ewald == 0.0) gewaldflag = 0;
|
||||
else gewaldflag = 1;
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"gewald/disp") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
g_ewald_6 = atof(arg[iarg+1]);
|
||||
if (g_ewald_6 == 0.0) gewaldflag_6 = 0;
|
||||
else gewaldflag_6 = 1;
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"slab") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"nozforce") == 0) {
|
||||
slabflag = 2;
|
||||
} else {
|
||||
slabflag = 1;
|
||||
slab_volfactor = atof(arg[iarg+1]);
|
||||
if (slab_volfactor <= 1.0)
|
||||
error->all(FLERR,"Bad kspace_modify slab parameter");
|
||||
if (slab_volfactor < 2.0 && comm->me == 0)
|
||||
error->warning(FLERR,"Kspace_modify slab param < 2.0 may "
|
||||
"cause unphysical behavior");
|
||||
}
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"compute") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) compute_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) compute_flag = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"fftbench") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) fftbench = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) fftbench = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"diff") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"ad") == 0) differentiation_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"ik") == 0) differentiation_flag = 0;
|
||||
else error->all(FLERR, "Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"cutoff/adjust") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) adjust_cutoff_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) adjust_cutoff_flag = 0;
|
||||
else error->all(FLERR,"Illegal kspace_modify command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal kspace_modify command");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *KSpace::extract(const char *str)
|
||||
{
|
||||
if (strcmp(str,"scale") == 0) return (void *) &scale;
|
||||
return NULL;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user