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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@368 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-03-08 00:50:47 +00:00
parent 4891e4561c
commit 75181aa0e6
5 changed files with 120 additions and 77 deletions
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28
src/KSPACE/ewald.cpp
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@ -30,6 +30,8 @@
using namespace LAMMPS_NS;
#define SMALL 0.00001
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -78,8 +80,12 @@ void Ewald::init()
// error check
if (domain->triclinic) error->all("Cannot use Ewald with triclinic box");
if (force->dimension == 2) error->all("Cannot use Ewald with 2d simulation");
if (atom->q == NULL)
error->all("Must use charged atom style with kspace style");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all("Cannot use nonperiodic boundaries with Ewald");
if (slabflag == 1) {
@ -99,20 +105,28 @@ void Ewald::init()
double cutoff;
pair->extract_long(&cutoff);
// compute qsum & qsqsum
// compute qsum & qsqsum and warn if not charge-neutral
qsum = qsqsum = 0.0;
for (int i = 0; i < atom->nlocal; i++) {
qsum += atom->q[i];
qsqsum += atom->q[i]*atom->q[i];
}
double tmp;
qsum = 0.0;
for (int i = 0; i < atom->nlocal; i++) qsum += atom->q[i];
MPI_Allreduce(&qsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum = tmp;
qsqsum = 0.0;
for (int i = 0; i < atom->nlocal; i++) qsqsum += atom->q[i]*atom->q[i];
MPI_Allreduce(&qsqsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum = tmp;
if (qsqsum == 0.0)
error->all("Cannot use kspace solver on system with no charge");
if (fabs(qsum) > SMALL && comm->me == 0) {
char str[128];
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
error->warning(str);
}
// setup K-space resolution
g_ewald = (1.35 - 0.15*log(precision))/cutoff;

16
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
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@ -250,17 +250,17 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
delx1 = x[i][0] - x2[0];
dely1 = x[i][1] - x2[1];
delz1 = x[i][2] - x2[2];
domain->minimum_image(&delx1,&dely1,&delz1);
domain->minimum_image(delx1,dely1,delz1);
delx2 = x[iH1][0] - x2[0];
dely2 = x[iH1][1] - x2[1];
delz2 = x[iH1][2] - x2[2];
domain->minimum_image(&delx2,&dely2,&delz2);
domain->minimum_image(delx2,dely2,delz2);
delx3 = x[iH2][0] - x2[0];
dely3 = x[iH2][1] - x2[1];
delz3 = x[iH2][2] - x2[2];
domain->minimum_image(&delx3,&dely3,&delz3);
domain->minimum_image(delx3,dely3,delz3);
tvirial[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]);
tvirial[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]);
@ -329,17 +329,17 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
delx1 = x[j][0] - x1[0];
dely1 = x[j][1] - x1[1];
delz1 = x[j][2] - x1[2];
domain->minimum_image(&delx1,&dely1,&delz1);
domain->minimum_image(delx1,dely1,delz1);
delx2 = x[jH1][0] - x1[0];
dely2 = x[jH1][1] - x1[1];
delz2 = x[jH1][2] - x1[2];
domain->minimum_image(&delx2,&dely2,&delz2);
domain->minimum_image(delx2,dely2,delz2);
delx3 = x[jH2][0] - x1[0];
dely3 = x[jH2][1] - x1[1];
delz3 = x[jH2][2] - x1[2];
domain->minimum_image(&delx3,&dely3,&delz3);
domain->minimum_image(delx3,dely3,delz3);
tvirial[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]);
tvirial[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]);
@ -518,12 +518,12 @@ void PairLJCutCoulLongTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
domain->minimum_image(&delx1,&dely1,&delz1);
domain->minimum_image(delx1,dely1,delz1);
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
domain->minimum_image(&delx2,&dely2,&delz2);
domain->minimum_image(delx2,dely2,delz2);
xM[0] = x[i][0] + alpha * (delx1 + delx2);
xM[1] = x[i][1] + alpha * (dely1 + dely2);

120
src/KSPACE/pppm.cpp
View File

@ -36,15 +36,15 @@
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAXORDER 7
#define OFFSET 4096
#define SMALL 0.00001
#define LARGE 10000.0
#define EPS_HOC 1.0e-7
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
@ -105,8 +105,13 @@ void PPPM::init()
// error check
if (domain->triclinic)
error->all("Cannot (yet) use PPPM with triclinic box");
if (force->dimension == 2) error->all("Cannot use PPPM with 2d simulation");
if (atom->q == NULL)
error->all("Must use charged atom style with kspace style");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all("Cannot use nonperiodic boundaries with PPPM");
if (slabflag == 1) {
@ -169,6 +174,8 @@ void PPPM::init()
MPI_Allreduce(&qsqsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum = tmp;
if (qsqsum == 0.0)
error->all("Cannot use kspace solver on system with no charge");
if (fabs(qsum) > SMALL && me == 0) {
char str[128];
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
@ -214,36 +221,60 @@ void PPPM::init()
// effectively nlo_in,nhi_in + ghost cells
// nlo,nhi = global coords of grid pt to "lower left" of smallest/largest
// position a particle in my box can be at
// particle position bound = subbox + skin/2.0 + qdist
// dist[3] = particle position bound = subbox + skin/2.0 + qdist
// qdist = offset due to TIP4P fictitious charge
// convert to triclinic if necessary
// nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping
// for slab PPPM, assign z grid as if it were not extended
int nlo,nhi;
double cuthalf = 0.5 * neighbor->skin + qdist;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
triclinic = domain->triclinic;
double *prd,*sublo,*subhi;
if (triclinic == 0) {
prd = domain->prd;
boxlo = domain->boxlo;
sublo = domain->sublo;
subhi = domain->subhi;
} else {
prd = domain->prd_lamda;
boxlo = domain->boxlo_lamda;
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
nlo = static_cast<int> ((domain->subxlo-cuthalf-domain->boxxlo) *
double dist[3];
double cuthalf = 0.5 * neighbor->skin + qdist;
if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf;
else {
dist[0] = cuthalf/domain->prd[0];
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
int nlo,nhi;
nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nhi = static_cast<int> ((domain->subxhi+cuthalf-domain->boxxlo) *
nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nxlo_out = nlo + nlower;
nxhi_out = nhi + nupper;
nlo = static_cast<int> ((domain->subylo-cuthalf-domain->boxylo) *
nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nhi = static_cast<int> ((domain->subyhi+cuthalf-domain->boxylo) *
nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nylo_out = nlo + nlower;
nyhi_out = nhi + nupper;
nlo = static_cast<int> ((domain->subzlo-cuthalf-domain->boxzlo) *
nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nhi = static_cast<int> ((domain->subzhi+cuthalf-domain->boxzlo) *
nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nzlo_out = nlo + nlower;
nzhi_out = nhi + nupper;
@ -426,18 +457,19 @@ void PPPM::init()
void PPPM::setup()
{
int i,j,k,l,m,n;
double *prd;
// volume-dependent factors
// adjust z dimension for 2d slab PPPM
// z dimension for 3d PPPM is zprd since slab_volfactor = 1.0
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
// adjustment of z dimension for 2d slab PPPM
// 3d PPPM just uses zprd since slab_volfactor = 1.0
if (triclinic == 0) prd = domain->prd;
else prd = domain->prd_lamda;
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
delxinv = nx_pppm/xprd;
@ -579,6 +611,14 @@ void PPPM::compute(int eflag, int vflag)
{
int i;
// convert atoms from box to lamda coords
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
domain->x2lamda(atom->nlocal);
}
// extend size of nlocal-dependent arrays if necessary
if (atom->nlocal > nmax) {
@ -641,6 +681,10 @@ void PPPM::compute(int eflag, int vflag)
// 2d slab correction
if (slabflag) slabcorr(eflag);
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
@ -781,7 +825,8 @@ void PPPM::set_grid()
double q2 = qsqsum / force->dielectric;
double natoms = atom->natoms;
// adjustment of z dimension for 2d slab PPPM
// use xprd,yprd,zprd even if triclinic so grid size is the same
// adjust z dimension for 2d slab PPPM
// 3d PPPM just uses zprd since slab_volfactor = 1.0
double xprd = domain->xprd;
@ -1387,9 +1432,6 @@ void PPPM::particle_map()
double **x = atom->x;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
@ -1398,9 +1440,9 @@ void PPPM::particle_map()
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx = static_cast<int> ((x[i][0]-boxxlo)*delxinv+shift) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxylo)*delyinv+shift) - OFFSET;
nz = static_cast<int> ((x[i][2]-boxzlo)*delzinv+shift) - OFFSET;
nx = static_cast<int> ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET;
nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET;
part2grid[i][0] = nx;
part2grid[i][1] = ny;
@ -1443,18 +1485,15 @@ void PPPM::make_rho()
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
for (int i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxxlo)*delxinv;
dy = ny+shiftone - (x[i][1]-boxylo)*delyinv;
dz = nz+shiftone - (x[i][2]-boxzlo)*delzinv;
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
@ -1614,18 +1653,15 @@ void PPPM::fieldforce()
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxxlo)*delxinv;
dy = ny+shiftone - (x[i][1]-boxylo)*delyinv;
dz = nz+shiftone - (x[i][2]-boxzlo)*delzinv;
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);

2
src/KSPACE/pppm.h
View File

@ -66,6 +66,8 @@ class PPPM : public KSpace {
int **part2grid; // storage for particle -> grid mapping
int nmax;
int triclinic; // domain settings, orthog or triclinic
double *boxlo;
// TIP4P settings
int typeH,typeO; // atom types of TIP4P water H and O atoms
double qdist; // distance from O site to negative charge

31
src/KSPACE/pppm_tip4p.cpp
View File

@ -45,9 +45,6 @@ void PPPMTIP4P::particle_map()
int *type = atom->type;
double **x = atom->x;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
@ -60,9 +57,9 @@ void PPPMTIP4P::particle_map()
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx = static_cast<int> ((xi[0]-boxxlo)*delxinv+shift) - OFFSET;
ny = static_cast<int> ((xi[1]-boxylo)*delyinv+shift) - OFFSET;
nz = static_cast<int> ((xi[2]-boxzlo)*delzinv+shift) - OFFSET;
nx = static_cast<int> ((xi[0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((xi[1]-boxlo[1])*delyinv+shift) - OFFSET;
nz = static_cast<int> ((xi[2]-boxlo[2])*delzinv+shift) - OFFSET;
part2grid[i][0] = nx;
part2grid[i][1] = ny;
@ -107,9 +104,6 @@ void PPPMTIP4P::make_rho()
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
@ -120,9 +114,9 @@ void PPPMTIP4P::make_rho()
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxxlo)*delxinv;
dy = ny+shiftone - (xi[1]-boxylo)*delyinv;
dz = nz+shiftone - (xi[2]-boxzlo)*delzinv;
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
@ -167,9 +161,6 @@ void PPPMTIP4P::fieldforce()
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double boxylo = domain->boxylo;
double boxzlo = domain->boxzlo;
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
@ -180,9 +171,9 @@ void PPPMTIP4P::fieldforce()
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxxlo)*delxinv;
dy = ny+shiftone - (xi[1]-boxylo)*delyinv;
dz = nz+shiftone - (xi[2]-boxzlo)*delzinv;
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
@ -251,12 +242,12 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
domain->minimum_image(&delx1,&dely1,&delz1);
domain->minimum_image(delx1,dely1,delz1);
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
domain->minimum_image(&delx2,&dely2,&delz2);
domain->minimum_image(delx2,dely2,delz2);
xM[0] = x[i][0] + alpha * (delx1 + delx2);
xM[1] = x[i][1] + alpha * (dely1 + dely2);