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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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224
src/pair_table.cpp
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@ -5,7 +5,7 @@
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
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.
@ -64,7 +64,7 @@ void PairTable::compute(int eflag, int vflag)
double rsq,factor_lj,fraction,value,a,b;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
@ -83,7 +83,7 @@ void PairTable::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -105,66 +105,66 @@ void PairTable::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq)
error->one(FLERR,"Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fpair = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq)
error->one(FLERR,"Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fpair = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fpair = factor_lj * value;
} else {
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
}
fpair = factor_lj * value;
} else {
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (tabstyle == LOOKUP)
evdwl = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP)
evdwl = tb->e[itable] + fraction*tb->de[itable];
else
evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
evdwl *= factor_lj;
}
if (eflag) {
if (tabstyle == LOOKUP)
evdwl = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP)
evdwl = tb->e[itable] + fraction*tb->de[itable];
else
evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@ -173,7 +173,7 @@ void PairTable::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairTable::allocate()
@ -191,7 +191,7 @@ void PairTable::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairTable::settings(int narg, char **arg)
@ -237,10 +237,10 @@ void PairTable::coeff(int narg, char **arg)
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
int me;
MPI_Comm_rank(world,&me);
tables = (Table *)
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
null_table(tb);
@ -276,9 +276,9 @@ void PairTable::coeff(int narg, char **arg)
// for tabstyle SPLINE, always need to build spline tables
tb->match = 0;
if (tabstyle == LINEAR && tb->ninput == tablength &&
if (tabstyle == LINEAR && tb->ninput == tablength &&
tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1;
if (tb->rflag == BMP && tb->match == 0)
error->all(FLERR,"Bitmapped table in file does not match requested table");
@ -319,7 +319,7 @@ double PairTable::init_one(int i, int j)
/* ----------------------------------------------------------------------
read a table section from a tabulated potential file
only called by proc 0
this function sets these values in Table:
this function sets these values in Table:
ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi,ntablebits
------------------------------------------------------------------------- */
@ -386,8 +386,8 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
if (tb->rflag == RLINEAR)
rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1);
else if (tb->rflag == RSQ) {
rtmp = tb->rlo*tb->rlo +
(tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
rtmp = tb->rlo*tb->rlo +
(tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
rtmp = sqrt(rtmp);
} else if (tb->rflag == BMP) {
rsq_lookup.i = i << nshiftbits;
@ -457,7 +457,7 @@ void PairTable::spline_table(Table *tb)
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]);
tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
(tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
}
@ -477,14 +477,14 @@ void PairTable::param_extract(Table *tb, char *line)
tb->ninput = 0;
tb->rflag = NONE;
tb->fpflag = 0;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
} else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 ||
strcmp(word,"BITMAP") == 0) {
strcmp(word,"BITMAP") == 0) {
if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP;
@ -568,14 +568,14 @@ void PairTable::compute_table(Table *tb)
r = sqrt(rsq);
tb->rsq[i] = rsq;
if (tb->match) {
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
} else {
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
}
}
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
@ -605,11 +605,11 @@ void PairTable::compute_table(Table *tb)
r = sqrt(rsq);
tb->rsq[i] = rsq;
if (tb->match) {
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
} else {
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
}
}
@ -634,7 +634,7 @@ void PairTable::compute_table(Table *tb)
double rsq1 = tb->innersq;
double rsq2 = rsq1 + secant_factor*tb->delta;
fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) /
sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
}
if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn =
@ -642,9 +642,9 @@ void PairTable::compute_table(Table *tb)
else {
double rsq2 = tb->cut * tb->cut;
double rsq1 = rsq2 - secant_factor*tb->delta;
fpn = (tb->f[tlm1] / sqrt(rsq2) -
splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
sqrt(rsq1)) / (secant_factor*tb->delta);
fpn = (tb->f[tlm1] / sqrt(rsq2) -
splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
sqrt(rsq1)) / (secant_factor*tb->delta);
}
for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]);
@ -663,7 +663,7 @@ void PairTable::compute_table(Table *tb)
// linear lookup tables of length ntable = 2^n
// stored value = value at lower edge of bin
init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits);
int ntable = 1 << tablength;
int ntablem1 = ntable - 1;
@ -674,7 +674,7 @@ void PairTable::compute_table(Table *tb)
memory->create(tb->de,ntable,"pair:de");
memory->create(tb->df,ntable,"pair:df");
memory->create(tb->drsq,ntable,"pair:drsq");
union_int_float_t minrsq_lookup;
minrsq_lookup.i = 0 << tb->nshiftbits;
minrsq_lookup.i |= maskhi;
@ -689,56 +689,56 @@ void PairTable::compute_table(Table *tb)
r = sqrtf(rsq_lookup.f);
tb->rsq[i] = rsq_lookup.f;
if (tb->match) {
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
} else {
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tb->innersq = minrsq_lookup.f;
for (int i = 0; i < ntablem1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
tb->drsq[i] = 1.0/(tb->rsq[i+1] - tb->rsq[i]);
}
}
// get the delta values for the last table entries
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
tb->de[ntablem1] = tb->e[0] - tb->e[ntablem1];
tb->df[ntablem1] = tb->f[0] - tb->f[ntablem1];
tb->drsq[ntablem1] = 1.0/(tb->rsq[0] - tb->rsq[ntablem1]);
// get the correct delta values at itablemax
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
// if so, compute deltas between rsq and cut*cut
// if tb->match, data at cut*cut is unavailable, so we'll take
// deltas at itablemax-1 as a good approximation
double e_tmp,f_tmp;
int itablemin = minrsq_lookup.i & tb->nmask;
itablemin >>= tb->nshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
int itablemaxm1 = itablemax - 1;
if (itablemax == 0) itablemaxm1 = ntablem1;
itablemin >>= tb->nshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
int itablemaxm1 = itablemax - 1;
if (itablemax == 0) itablemaxm1 = ntablem1;
rsq_lookup.i = itablemax << tb->nshiftbits;
rsq_lookup.i |= maskhi;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < tb->cut*tb->cut) {
if (tb->match) {
tb->de[itablemax] = tb->de[itablemaxm1];
tb->df[itablemax] = tb->df[itablemaxm1];
tb->drsq[itablemax] = tb->drsq[itablemaxm1];
} else {
rsq_lookup.f = tb->cut*tb->cut;
rsq_lookup.f = tb->cut*tb->cut;
r = sqrtf(rsq_lookup.f);
e_tmp = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
f_tmp = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
@ -747,7 +747,7 @@ void PairTable::compute_table(Table *tb)
tb->drsq[itablemax] = 1.0/(rsq_lookup.f - tb->rsq[itablemax]);
}
}
}
}
}
/* ----------------------------------------------------------------------
@ -789,7 +789,7 @@ void PairTable::free_table(Table *tb)
------------------------------------------------------------------------- */
void PairTable::spline(double *x, double *y, int n,
double yp1, double ypn, double *y2)
double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
@ -835,7 +835,7 @@ double PairTable::splint(double *xa, double *ya, double *y2a, int n, double x)
h = xa[khi]-xa[klo];
a = (xa[khi]-x) / h;
b = (x-xa[klo]) / h;
y = a*ya[klo] + b*ya[khi] +
y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
}
@ -886,8 +886,8 @@ void PairTable::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairTable::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
double factor_coul, double factor_lj,
double &fforce)
{
int itable;
double fraction,value,a,b,phi;
@ -911,8 +911,8 @@ double PairTable::single(int i, int j, int itype, int jtype, double rsq,
if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fforce = factor_lj * value;
} else {
@ -930,7 +930,7 @@ double PairTable::single(int i, int j, int itype, int jtype, double rsq,
else if (tabstyle == LINEAR || tabstyle == BITMAP)
phi = tb->e[itable] + fraction*tb->de[itable];
else
phi = a * tb->e[itable] + b * tb->e[itable+1] +
phi = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
return factor_lj*phi;
}
@ -951,7 +951,7 @@ void *PairTable::extract(const char *str, int &dim)
for (int m = 1; m < ntables; m++)
if (tables[m].cut != cut_coul)
error->all(FLERR,
"Pair table cutoffs must all be equal to use with KSpace");
"Pair table cutoffs must all be equal to use with KSpace");
dim = 0;
return &tables[0].cut;
}