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lammps/src/MOLECULE/angle_table.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
#include "angle_table.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "table_file_reader.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using MathConst::DEG2RAD;
using MathConst::MY_PI;
using MathConst::RAD2DEG;
enum { LINEAR, SPLINE };
#define SMALL 0.001
#define TINY 1.E-10
/* ---------------------------------------------------------------------- */
AngleTable::AngleTable(LAMMPS *_lmp) : Angle(_lmp)
{
writedata = 0;
ntables = 0;
tables = nullptr;
}
/* ---------------------------------------------------------------------- */
AngleTable::~AngleTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->destroy(setflag);
memory->destroy(theta0);
memory->destroy(tabindex);
}
}
/* ---------------------------------------------------------------------- */
void AngleTable::compute(int eflag, int vflag)
{
int i1, i2, i3, n, type;
double eangle, f1[3], f3[3];
double delx1, dely1, delz1, delx2, dely2, delz2;
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
double theta, u, mdu; //mdu: minus du, -du/dx=f
eangle = 0.0;
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
c /= r1 * r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c * c);
if (s < SMALL) s = SMALL;
s = 1.0 / s;
// tabulated force & energy
theta = acos(c);
uf_lookup(type, theta, u, mdu);
if (eflag) eangle = u;
a = mdu * s;
a11 = a * c / rsq1;
a12 = -a / (r1 * r2);
a22 = a * c / rsq2;
f1[0] = a11 * delx1 + a12 * delx2;
f1[1] = a11 * dely1 + a12 * dely2;
f1[2] = a11 * delz1 + a12 * delz2;
f3[0] = a22 * delx2 + a12 * delx1;
f3[1] = a22 * dely2 + a12 * dely1;
f3[2] = a22 * delz2 + a12 * delz1;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag)
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
delz2);
}
}
/* ---------------------------------------------------------------------- */
void AngleTable::allocate()
{
allocated = 1;
const int np1 = atom->nangletypes + 1;
memory->create(theta0, np1, "angle:theta0");
memory->create(tabindex, np1, "angle:tabindex");
memory->create(setflag, np1, "angle:setflag");
for (int i = 1; i < np1; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void AngleTable::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR, "Illegal angle_style command");
if (strcmp(arg[0], "linear") == 0)
tabstyle = LINEAR;
else if (strcmp(arg[0], "spline") == 0)
tabstyle = SPLINE;
else
error->all(FLERR, "Unknown table style in angle style table");
tablength = utils::inumeric(FLERR, arg[1], false, lmp);
if (tablength < 2) error->all(FLERR, "Illegal number of angle table entries");
// delete old tables, since cannot just change settings
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->destroy(setflag);
memory->destroy(tabindex);
}
allocated = 0;
ntables = 0;
tables = nullptr;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void AngleTable::coeff(int narg, char **arg)
{
if (narg != 3) error->all(FLERR, "Illegal angle_coeff command");
if (!allocated) allocate();
int ilo, ihi;
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
int me;
MPI_Comm_rank(world, &me);
tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "angle:tables");
Table *tb = &tables[ntables];
null_table(tb);
if (me == 0) read_table(tb, arg[1], arg[2]);
bcast_table(tb);
// error check on table parameters
if (tb->ninput <= 1) error->one(FLERR, "Invalid angle table length");
double alo, ahi;
alo = tb->afile[0];
ahi = tb->afile[tb->ninput - 1];
if (fabs(alo - 0.0) > TINY || fabs(ahi - 180.0) > TINY)
error->all(FLERR, "Angle table must range from 0 to 180 degrees");
// convert theta from degrees to radians
for (int i = 0; i < tb->ninput; i++) {
tb->afile[i] *= DEG2RAD;
tb->ffile[i] *= RAD2DEG;
}
// spline read-in and compute a,e,f vectors within table
spline_table(tb);
compute_table(tb);
// store ptr to table in tabindex
int count = 0;
for (int i = ilo; i <= ihi; i++) {
tabindex[i] = ntables;
setflag[i] = 1;
theta0[i] = tb->theta0;
count++;
}
ntables++;
if (count == 0) error->all(FLERR, "Illegal angle_coeff command");
}
/* ----------------------------------------------------------------------
return an equilbrium angle length
should not be used, since don't know minimum of tabulated function
------------------------------------------------------------------------- */
double AngleTable::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void AngleTable::write_restart(FILE *fp)
{
write_restart_settings(fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void AngleTable::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void AngleTable::write_restart_settings(FILE *fp)
{
fwrite(&tabstyle, sizeof(int), 1, fp);
fwrite(&tablength, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void AngleTable::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR, &tabstyle, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &tablength, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&tabstyle, 1, MPI_INT, 0, world);
MPI_Bcast(&tablength, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
double AngleTable::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1, dely1, delz1);
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2, dely2, delz2);
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
c /= r1 * r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double theta = acos(c);
double u = 0.0;
u_lookup(type, theta, u);
return u;
}
/* ---------------------------------------------------------------------- */
void AngleTable::null_table(Table *tb)
{
tb->afile = tb->efile = tb->ffile = nullptr;
tb->e2file = tb->f2file = nullptr;
tb->ang = tb->e = tb->de = nullptr;
tb->f = tb->df = tb->e2 = tb->f2 = nullptr;
}
/* ---------------------------------------------------------------------- */
void AngleTable::free_table(Table *tb)
{
memory->destroy(tb->afile);
memory->destroy(tb->efile);
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
memory->destroy(tb->ang);
memory->destroy(tb->e);
memory->destroy(tb->de);
memory->destroy(tb->f);
memory->destroy(tb->df);
memory->destroy(tb->e2);
memory->destroy(tb->f2);
}
/* ----------------------------------------------------------------------
read table file, only called by proc 0
------------------------------------------------------------------------- */
void AngleTable::read_table(Table *tb, char *file, char *keyword)
{
TableFileReader reader(lmp, file, "angle");
char *line = reader.find_section_start(keyword);
if (!line) { error->one(FLERR, "Did not find keyword in table file"); }
// read args on 2nd line of section
// allocate table arrays for file values
line = reader.next_line();
param_extract(tb, line);
memory->create(tb->afile, tb->ninput, "angle:afile");
memory->create(tb->efile, tb->ninput, "angle:efile");
memory->create(tb->ffile, tb->ninput, "angle:ffile");
// read a,e,f table values from file
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
line = reader.next_line();
try {
ValueTokenizer values(line);
values.next_int();
tb->afile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException &e) {
error->one(FLERR, "Error parsing angle table '{}' line {} of {}. {}\nLine was: {}", keyword,
i + 1, tb->ninput, e.what(), line);
}
}
}
/* ----------------------------------------------------------------------
build spline representation of e,f over entire range of read-in table
this function sets these values in e2file,f2file
------------------------------------------------------------------------- */
void AngleTable::spline_table(Table *tb)
{
memory->create(tb->e2file, tb->ninput, "angle:e2file");
memory->create(tb->f2file, tb->ninput, "angle:f2file");
double ep0 = -tb->ffile[0];
double epn = -tb->ffile[tb->ninput - 1];
spline(tb->afile, tb->efile, tb->ninput, ep0, epn, tb->e2file);
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]);
tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) /
(tb->afile[tb->ninput - 1] - tb->afile[tb->ninput - 2]);
}
double fp0 = tb->fplo;
double fpn = tb->fphi;
spline(tb->afile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file);
}
/* ----------------------------------------------------------------------
compute a,e,f vectors from splined values
------------------------------------------------------------------------- */
void AngleTable::compute_table(Table *tb)
{
// delta = table spacing in angle for N-1 bins
int tlm1 = tablength - 1;
tb->delta = MY_PI / tlm1;
tb->invdelta = 1.0 / tb->delta;
tb->deltasq6 = tb->delta * tb->delta / 6.0;
// N-1 evenly spaced bins in angle from 0 to PI
// ang,e,f = value at lower edge of bin
// de,df values = delta values of e,f
// ang,e,f are N in length so de,df arrays can compute difference
memory->create(tb->ang, tablength, "angle:ang");
memory->create(tb->e, tablength, "angle:e");
memory->create(tb->de, tablength, "angle:de");
memory->create(tb->f, tablength, "angle:f");
memory->create(tb->df, tablength, "angle:df");
memory->create(tb->e2, tablength, "angle:e2");
memory->create(tb->f2, tablength, "angle:f2");
double a;
for (int i = 0; i < tablength; i++) {
a = i * tb->delta;
tb->ang[i] = a;
tb->e[i] = splint(tb->afile, tb->efile, tb->e2file, tb->ninput, a);
tb->f[i] = splint(tb->afile, tb->ffile, tb->f2file, tb->ninput, a);
}
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];
}
// get final elements from linear extrapolation
tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2];
tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2];
double ep0 = -tb->f[0];
double epn = -tb->f[tlm1];
spline(tb->ang, tb->e, tablength, ep0, epn, tb->e2);
spline(tb->ang, tb->f, tablength, tb->fplo, tb->fphi, tb->f2);
}
/* ----------------------------------------------------------------------
extract attributes from parameter line in table section
format of line: N value FP fplo fphi EQ theta0
N is required, other params are optional
------------------------------------------------------------------------- */
void AngleTable::param_extract(Table *tb, char *line)
{
tb->ninput = 0;
tb->fpflag = 0;
tb->theta0 = MY_PI;
try {
ValueTokenizer values(line);
while (values.has_next()) {
std::string word = values.next_string();
if (word == "N") {
tb->ninput = values.next_int();
} else if (word == "FP") {
tb->fpflag = 1;
tb->fplo = values.next_double();
tb->fphi = values.next_double();
tb->fplo *= RAD2DEG * RAD2DEG;
tb->fphi *= RAD2DEG * RAD2DEG;
} else if (word == "EQ") {
tb->theta0 = DEG2RAD * values.next_double();
} else {
error->one(FLERR, "Invalid keyword in angle table parameters");
}
}
} catch (TokenizerException &e) {
error->one(FLERR, e.what());
}
if (tb->ninput == 0) error->one(FLERR, "Angle table parameters did not set N");
}
/* ----------------------------------------------------------------------
broadcast read-in table info from proc 0 to other procs
this function communicates these values in Table:
ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0
------------------------------------------------------------------------- */
void AngleTable::bcast_table(Table *tb)
{
MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world);
int me;
MPI_Comm_rank(world, &me);
if (me > 0) {
memory->create(tb->afile, tb->ninput, "angle:afile");
memory->create(tb->efile, tb->ninput, "angle:efile");
memory->create(tb->ffile, tb->ninput, "angle:ffile");
}
MPI_Bcast(tb->afile, tb->ninput, MPI_DOUBLE, 0, world);
MPI_Bcast(tb->efile, tb->ninput, MPI_DOUBLE, 0, world);
MPI_Bcast(tb->ffile, tb->ninput, MPI_DOUBLE, 0, world);
MPI_Bcast(&tb->fpflag, 1, MPI_INT, 0, world);
if (tb->fpflag) {
MPI_Bcast(&tb->fplo, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&tb->fphi, 1, MPI_DOUBLE, 0, world);
}
MPI_Bcast(&tb->theta0, 1, MPI_DOUBLE, 0, world);
}
/* ----------------------------------------------------------------------
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
void AngleTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2)
{
int i, k;
double p, qn, sig, un;
auto u = new double[n];
if (yp1 > 0.99e300)
y2[0] = u[0] = 0.0;
else {
y2[0] = -0.5;
u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1);
}
for (i = 1; i < n - 1; i++) {
sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]);
p = sig * y2[i - 1] + 2.0;
y2[i] = (sig - 1.0) / p;
u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]);
u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p;
}
if (ypn > 0.99e300)
qn = un = 0.0;
else {
qn = 0.5;
un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
}
y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0);
for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k];
delete[] u;
}
/* ---------------------------------------------------------------------- */
double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
{
int klo, khi, k;
double h, b, a, y;
klo = 0;
khi = n - 1;
while (khi - klo > 1) {
k = (khi + klo) >> 1;
if (xa[k] > x)
khi = k;
else
klo = k;
}
h = xa[khi] - xa[klo];
a = (xa[khi] - x) / h;
b = (x - xa[klo]) / h;
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;
}
/* ----------------------------------------------------------------------
calculate potential u and force f at angle x
------------------------------------------------------------------------- */
void AngleTable::uf_lookup(int type, double x, double &u, double &f)
{
if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }
double fraction, a, b;
const Table *tb = &tables[tabindex[type]];
// invdelta is based on tablength-1
int itable = static_cast<int>(x * tb->invdelta);
if (itable < 0) itable = 0;
if (itable >= tablength) itable = tablength - 1;
if (tabstyle == LINEAR) {
fraction = (x - tb->ang[itable]) * tb->invdelta;
u = tb->e[itable] + fraction * tb->de[itable];
f = tb->f[itable] + fraction * tb->df[itable];
} else if (tabstyle == SPLINE) {
fraction = (x - tb->ang[itable]) * tb->invdelta;
b = (x - tb->ang[itable]) * tb->invdelta;
a = 1.0 - b;
u = 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;
f = 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;
}
}
/* ----------------------------------------------------------------------
calculate potential u at angle x
------------------------------------------------------------------------- */
void AngleTable::u_lookup(int type, double x, double &u)
{
if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }
double fraction, a, b;
const Table *tb = &tables[tabindex[type]];
int itable = static_cast<int>(x * tb->invdelta);
if (itable < 0) itable = 0;
if (itable >= tablength) itable = tablength - 1;
if (tabstyle == LINEAR) {
fraction = (x - tb->ang[itable]) * tb->invdelta;
u = tb->e[itable] + fraction * tb->de[itable];
} else if (tabstyle == SPLINE) {
fraction = (x - tb->ang[itable]) * tb->invdelta;
b = (x - tb->ang[itable]) * tb->invdelta;
a = 1.0 - b;
u = 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;
}
}
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