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lammps/src/MOLECULE/bond_table.cpp
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bond_table.cpp
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "bond_table.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NONE,LINEAR,SPLINE};
#define MAXLINE 1024
#define BIGNUM 1.0e300
/* ---------------------------------------------------------------------- */
BondTable::BondTable(LAMMPS *lmp) : Bond(lmp)
{
writedata = 0;
ntables = 0;
tables = NULL;
}
/* ---------------------------------------------------------------------- */
BondTable::~BondTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->destroy(setflag);
memory->destroy(r0);
memory->destroy(tabindex);
}
}
/* ---------------------------------------------------------------------- */
void BondTable::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r;
double u,mdu;
ebond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
// force & energy
uf_lookup(type,r,u,mdu);
fbond = mdu/r;
ebond = u;
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondTable::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(tabindex,n+1,"bond:tabindex");
memory->create(r0,n+1,"bond:r0");
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void BondTable::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal bond_style command");
tabstyle = NONE;
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 bond style table");
tablength = force->inumeric(FLERR,arg[1]);
if (tablength < 2) error->all(FLERR,"Illegal number of bond 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 = NULL;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void BondTable::coeff(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal bond_coeff command");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
int me;
MPI_Comm_rank(world,&me);
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"bond: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 bond table length");
tb->lo = tb->rfile[0];
tb->hi = tb->rfile[tb->ninput-1];
if (tb->lo >= tb->hi) error->all(FLERR,"Bond table values are not increasing");
// spline read-in and compute r,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;
r0[i] = tb->r0;
setflag[i] = 1;
count++;
}
ntables++;
if (count == 0) error->all(FLERR,"Illegal bond_coeff command");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
should not be used, since don't know minimum of tabulated function
------------------------------------------------------------------------- */
double BondTable::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondTable::write_restart(FILE *fp)
{
fwrite(&tabstyle,sizeof(int),1,fp);
fwrite(&tablength,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondTable::read_restart(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);
allocate();
}
/* ---------------------------------------------------------------------- */
double BondTable::single(int type, double rsq, int i, int j,
double &fforce)
{
double r = sqrt(rsq);
double u;
double mdu;
uf_lookup(type,r,u,mdu);
fforce = mdu/r;
return u;
}
/* ---------------------------------------------------------------------- */
void BondTable::null_table(Table *tb)
{
tb->rfile = tb->efile = tb->ffile = NULL;
tb->e2file = tb->f2file = NULL;
tb->r = tb->e = tb->de = NULL;
tb->f = tb->df = tb->e2 = tb->f2 = NULL;
}
/* ---------------------------------------------------------------------- */
void BondTable::free_table(Table *tb)
{
memory->destroy(tb->rfile);
memory->destroy(tb->efile);
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
memory->destroy(tb->r);
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 BondTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
double emin = BIGNUM;
// open file
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(FLERR,str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section
param_extract(tb,line);
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
}
// read args on 2nd line of section
// allocate table arrays for file values
fgets(line,MAXLINE,fp);
param_extract(tb,line);
memory->create(tb->rfile,tb->ninput,"bond:rfile");
memory->create(tb->efile,tb->ninput,"bond:efile");
memory->create(tb->ffile,tb->ninput,"bond:ffile");
// read r,e,f table values from file
int itmp;
int cerror = 0;
int r0idx = -1;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
if (NULL == fgets(line,MAXLINE,fp))
error->one(FLERR,"Premature end of file in bond table");
if (4 != sscanf(line,"%d %lg %lg %lg",
&itmp,&tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
if (tb->efile[i] < emin) {
emin = tb->efile[i];
r0idx = i;
}
}
fclose(fp);
// infer r0 from minimum of potential, if not given explicitly
if ((tb->r0 == 0.0) && (r0idx >= 0)) tb->r0 = tb->rfile[r0idx];
// warn if force != dE/dr at any point that is not an inflection point
// check via secant approximation to dE/dr
// skip two end points since do not have surrounding secants
// inflection point is where curvature changes sign
double r,e,f,rprev,rnext,eprev,enext,fleft,fright;
int ferror = 0;
for (int i = 1; i < tb->ninput-1; i++) {
r = tb->rfile[i];
rprev = tb->rfile[i-1];
rnext = tb->rfile[i+1];
e = tb->efile[i];
eprev = tb->efile[i-1];
enext = tb->efile[i+1];
f = tb->ffile[i];
fleft = - (e-eprev) / (r-rprev);
fright = - (enext-e) / (rnext-r);
if (f < fleft && f < fright) ferror++;
if (f > fleft && f > fright) ferror++;
//printf("Values %d: %g %g %g\n",i,r,e,f);
//printf(" secant %d %d %g: %g %g %g\n",i,ferror,r,fleft,fright,f);
}
if (ferror) {
char str[128];
sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n"
" Should only be flagged at inflection points",ferror,tb->ninput);
error->warning(FLERR,str);
}
// warn if data was read incompletely, e.g. columns were missing
if (cerror) {
char str[128];
sprintf(str,"%d of %d lines in table were incomplete or could not be"
" parsed completely",cerror,tb->ninput);
error->warning(FLERR,str);
}
}
/* ----------------------------------------------------------------------
build spline representation of e,f over entire range of read-in table
this function sets these values in e2file,f2file
------------------------------------------------------------------------- */
void BondTable::spline_table(Table *tb)
{
memory->create(tb->e2file,tb->ninput,"bond:e2file");
memory->create(tb->f2file,tb->ninput,"bond:f2file");
double ep0 = - tb->ffile[0];
double epn = - tb->ffile[tb->ninput-1];
spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file);
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->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
}
double fp0 = tb->fplo;
double fpn = tb->fphi;
spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file);
}
/* ----------------------------------------------------------------------
compute r,e,f vectors from splined values
------------------------------------------------------------------------- */
void BondTable::compute_table(Table *tb)
{
// delta = table spacing for N-1 bins
int tlm1 = tablength-1;
tb->delta = (tb->hi - tb->lo)/ tlm1;
tb->invdelta = 1.0/tb->delta;
tb->deltasq6 = tb->delta*tb->delta / 6.0;
// N-1 evenly spaced bins in r from min to max
// r,e,f = value at lower edge of bin
// de,df values = delta values of e,f
// r,e,f are N in length so de,df arrays can compute difference
memory->create(tb->r,tablength,"bond:r");
memory->create(tb->e,tablength,"bond:e");
memory->create(tb->de,tlm1,"bond:de");
memory->create(tb->f,tablength,"bond:f");
memory->create(tb->df,tlm1,"bond:df");
memory->create(tb->e2,tablength,"bond:e2");
memory->create(tb->f2,tablength,"bond:f2");
double a;
for (int i = 0; i < tablength; i++) {
a = tb->lo + i*tb->delta;
tb->r[i] = a;
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a);
tb->f[i] = splint(tb->rfile,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];
}
double ep0 = - tb->f[0];
double epn = - tb->f[tlm1];
spline(tb->r,tb->e,tablength,ep0,epn,tb->e2);
spline(tb->r,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 r0
N is required, other params are optional
------------------------------------------------------------------------- */
void BondTable::param_extract(Table *tb, char *line)
{
tb->ninput = 0;
tb->fpflag = 0;
tb->r0 = 0.0;
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,"FP") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
} else if (strcmp(word,"EQ") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->r0 = atof(word);
} else {
error->one(FLERR,"Invalid keyword in bond table parameters");
}
word = strtok(NULL," \t\n\r\f");
}
if (tb->ninput == 0) error->one(FLERR,"Bond 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,rfile,efile,ffile,fpflag,fplo,fphi,r0
------------------------------------------------------------------------- */
void BondTable::bcast_table(Table *tb)
{
MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
MPI_Bcast(&tb->r0,1,MPI_INT,0,world);
int me;
MPI_Comm_rank(world,&me);
if (me > 0) {
memory->create(tb->rfile,tb->ninput,"angle:rfile");
memory->create(tb->efile,tb->ninput,"angle:efile");
memory->create(tb->ffile,tb->ninput,"angle:ffile");
}
MPI_Bcast(tb->rfile,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->r0,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
void BondTable::spline(double *x, double *y, int n,
double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
double *u = new double[n];
if (yp1 > 0.99e30) 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 > 0.99e30) 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 BondTable::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 distance x
insure x is between bond min/max
------------------------------------------------------------------------- */
void BondTable::uf_lookup(int type, double x, double &u, double &f)
{
int itable;
double fraction,a,b;
Table *tb = &tables[tabindex[type]];
x = MAX(x,tb->lo);
x = MIN(x,tb->hi);
if (tabstyle == LINEAR) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
u = tb->e[itable] + fraction*tb->de[itable];
f = tb->f[itable] + fraction*tb->df[itable];
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
b = (x - tb->r[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 distance x
insure x is between bond min/max
------------------------------------------------------------------------- */
void BondTable::u_lookup(int type, double x, double &u)
{
int itable;
double fraction,a,b;
Table *tb = &tables[tabindex[type]];
x = MAX(x,tb->lo);
x = MIN(x,tb->hi);
if (tabstyle == LINEAR) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
u = tb->e[itable] + fraction*tb->de[itable];
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
fraction = (x - tb->r[itable]) * tb->invdelta;
b = (x - tb->r[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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