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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4326 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-06-18 21:54:42 +00:00
parent c71f0cf9f8
commit b3de0db9db
7 changed files with 109 additions and 127 deletions
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85
src/pair_table.cpp
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@ -76,6 +76,7 @@ void PairTable::compute(int eflag, int vflag)
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@ -127,19 +128,19 @@ void PairTable::compute(int eflag, int vflag)
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= nm1)
if (itable >= tlm1)
error->one("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 >= nm1)
if (itable >= tlm1)
error->one("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 >= nm1)
if (itable >= tlm1)
error->one("Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
@ -220,8 +221,8 @@ void PairTable::settings(int narg, char **arg)
else if (strcmp(arg[0],"bitmap") == 0) tabstyle = BITMAP;
else error->all("Unknown table style in pair_style command");
n = force->inumeric(arg[1]);
nm1 = n - 1;
tablength = force->inumeric(arg[1]);
if (tablength < 2) error->all("Illegal number of pair table entries");
// delete old tables, since cannot just change settings
@ -286,15 +287,13 @@ void PairTable::coeff(int narg, char **arg)
// match = 1 if don't need to spline read-in tables
// this is only the case if r values needed by final tables
// exactly match r values read from file
// for tabstyle SPLINE, always need to build spline tables
tb->match = 0;
if (tabstyle == LINEAR && tb->ninput == n &&
if (tabstyle == LINEAR && tb->ninput == tablength &&
tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
if (tabstyle == SPLINE && tb->ninput == n &&
tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
if (tabstyle == BITMAP && tb->ninput == 1 << n &&
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("Bitmapped table in file does not match requested table");
@ -537,6 +536,8 @@ void PairTable::param_extract(Table *tb, char *line)
void PairTable::compute_table(Table *tb)
{
int tlm1 = tablength-1;
// inner = inner table bound
// cut = outer table bound
// delta = table spacing in rsq for N-1 bins
@ -545,7 +546,7 @@ void PairTable::compute_table(Table *tb)
if (tb->rflag) inner = tb->rlo;
else inner = tb->rfile[0];
tb->innersq = inner*inner;
tb->delta = (tb->cut*tb->cut - tb->innersq) / nm1;
tb->delta = (tb->cut*tb->cut - tb->innersq) / tlm1;
tb->invdelta = 1.0/tb->delta;
// direct lookup tables
@ -556,11 +557,11 @@ void PairTable::compute_table(Table *tb)
// e,f are never a match to read-in values, always computed via spline interp
if (tabstyle == LOOKUP) {
tb->e = (double *) memory->smalloc(nm1*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(nm1*sizeof(double),"pair:f");
tb->e = (double *) memory->smalloc(tlm1*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(tlm1*sizeof(double),"pair:f");
double r,rsq;
for (int i = 0; i < nm1; i++) {
for (int i = 0; i < tlm1; i++) {
rsq = tb->innersq + (i+0.5)*tb->delta;
r = sqrt(rsq);
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
@ -577,14 +578,14 @@ void PairTable::compute_table(Table *tb)
// e,f can match read-in values, else compute via spline interp
if (tabstyle == LINEAR) {
tb->rsq = (double *) memory->smalloc(n*sizeof(double),"pair:rsq");
tb->e = (double *) memory->smalloc(n*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(n*sizeof(double),"pair:f");
tb->de = (double *) memory->smalloc(nm1*sizeof(double),"pair:de");
tb->df = (double *) memory->smalloc(nm1*sizeof(double),"pair:df");
tb->rsq = (double *) memory->smalloc(tablength*sizeof(double),"pair:rsq");
tb->e = (double *) memory->smalloc(tablength*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(tablength*sizeof(double),"pair:f");
tb->de = (double *) memory->smalloc(tlm1*sizeof(double),"pair:de");
tb->df = (double *) memory->smalloc(tlm1*sizeof(double),"pair:df");
double r,rsq;
for (int i = 0; i < n; i++) {
for (int i = 0; i < tablength; i++) {
rsq = tb->innersq + i*tb->delta;
r = sqrt(rsq);
tb->rsq[i] = rsq;
@ -597,7 +598,7 @@ void PairTable::compute_table(Table *tb)
}
}
for (int i = 0; i < nm1; i++) {
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];
}
@ -612,16 +613,16 @@ void PairTable::compute_table(Table *tb)
// e,f can match read-in values, else compute via spline interp
if (tabstyle == SPLINE) {
tb->rsq = (double *) memory->smalloc(n*sizeof(double),"pair:rsq");
tb->e = (double *) memory->smalloc(n*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(n*sizeof(double),"pair:f");
tb->e2 = (double *) memory->smalloc(n*sizeof(double),"pair:e2");
tb->f2 = (double *) memory->smalloc(n*sizeof(double),"pair:f2");
tb->rsq = (double *) memory->smalloc(tablength*sizeof(double),"pair:rsq");
tb->e = (double *) memory->smalloc(tablength*sizeof(double),"pair:e");
tb->f = (double *) memory->smalloc(tablength*sizeof(double),"pair:f");
tb->e2 = (double *) memory->smalloc(tablength*sizeof(double),"pair:e2");
tb->f2 = (double *) memory->smalloc(tablength*sizeof(double),"pair:f2");
tb->deltasq6 = tb->delta*tb->delta / 6.0;
double r,rsq;
for (int i = 0; i < n; i++) {
for (int i = 0; i < tablength; i++) {
rsq = tb->innersq + i*tb->delta;
r = sqrt(rsq);
tb->rsq[i] = rsq;
@ -637,8 +638,8 @@ void PairTable::compute_table(Table *tb)
// ep0,epn = dE/dr at inner and at cut
double ep0 = - tb->f[0];
double epn = - tb->f[nm1];
spline(tb->rsq,tb->e,n,ep0,epn,tb->e2);
double epn = - tb->f[tlm1];
spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2);
// fp0,fpn = dh/dg at inner and at cut
// h(r) = f(r)/r and g(r) = r^2
@ -657,17 +658,17 @@ void PairTable::compute_table(Table *tb)
}
if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn =
(tb->fphi/tb->cut - tb->f[nm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut);
(tb->fphi/tb->cut - tb->f[tlm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut);
else {
double rsq2 = tb->cut * tb->cut;
double rsq1 = rsq2 - secant_factor*tb->delta;
fpn = (tb->f[nm1] / sqrt(rsq2) -
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 < n; i++) tb->f[i] /= sqrt(tb->rsq[i]);
spline(tb->rsq,tb->f,n,fp0,fpn,tb->f2);
for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]);
spline(tb->rsq,tb->f,tablength,fp0,fpn,tb->f2);
}
// bitmapped linear tables
@ -683,8 +684,8 @@ 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,n,masklo,maskhi,tb->nmask,tb->nshiftbits);
int ntable = 1 << n;
init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits);
int ntable = 1 << tablength;
int ntablem1 = ntable - 1;
tb->rsq = (double *) memory->smalloc(ntable*sizeof(double),"pair:rsq");
@ -885,7 +886,7 @@ void PairTable::read_restart(FILE *fp)
void PairTable::write_restart_settings(FILE *fp)
{
fwrite(&tabstyle,sizeof(int),1,fp);
fwrite(&n,sizeof(int),1,fp);
fwrite(&tablength,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
@ -896,11 +897,10 @@ void PairTable::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&n,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world);
MPI_Bcast(&n,1,MPI_INT,0,world);
nm1 = n - 1;
MPI_Bcast(&tablength,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
@ -911,23 +911,24 @@ double PairTable::single(int i, int j, int itype, int jtype, double rsq,
{
int itable;
double fraction,value,a,b,phi;
int tlm1 = tablength - 1;
Table *tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq) error->one("Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= nm1) error->one("Pair distance > table outer cutoff");
if (itable >= tlm1) error->one("Pair distance > table outer cutoff");
fforce = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= nm1) error->one("Pair distance > table outer cutoff");
if (itable >= tlm1) error->one("Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fforce = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= nm1) error->one("Pair distance > table outer cutoff");
if (itable >= tlm1) error->one("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] +