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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3038 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-08-10 20:16:34 +00:00
parent 1dbef4b5f8
commit 427b65ae40
6 changed files with 1410 additions and 0 deletions
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8
src/MOLECULE/Install.csh
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@ -14,6 +14,7 @@ if ($1 == 1) then
cp angle_cosine_squared.cpp ..
cp angle_harmonic.cpp ..
cp angle_hybrid.cpp ..
cp angle_table.cpp ..
cp atom_vec_angle.cpp ..
cp atom_vec_bond.cpp ..
cp atom_vec_full.cpp ..
@ -26,6 +27,7 @@ if ($1 == 1) then
cp bond_morse.cpp ..
cp bond_nonlinear.cpp ..
cp bond_quartic.cpp ..
cp bond_table.cpp ..
cp dihedral.cpp ..
cp dihedral_charmm.cpp ..
cp dihedral_harmonic.cpp ..
@ -51,6 +53,7 @@ if ($1 == 1) then
cp angle_cosine_squared.h ..
cp angle_harmonic.h ..
cp angle_hybrid.h ..
cp angle_table.h ..
cp atom_vec_angle.h ..
cp atom_vec_bond.h ..
cp atom_vec_full.h ..
@ -63,6 +66,7 @@ if ($1 == 1) then
# cp bond_hybrid.h ..
cp bond_nonlinear.h ..
cp bond_quartic.h ..
cp bond_table.h ..
# cp dihedral.h ..
cp dihedral_charmm.h ..
cp dihedral_harmonic.h ..
@ -93,6 +97,7 @@ else if ($1 == 0) then
rm ../angle_cosine_squared.cpp
rm ../angle_harmonic.cpp
rm ../angle_hybrid.cpp
rm ../angle_table.cpp
rm ../atom_vec_angle.cpp
rm ../atom_vec_bond.cpp
rm ../atom_vec_full.cpp
@ -105,6 +110,7 @@ else if ($1 == 0) then
rm ../bond_morse.cpp
rm ../bond_nonlinear.cpp
rm ../bond_quartic.cpp
rm ../bond_table.cpp
rm ../dihedral.cpp
rm ../dihedral_charmm.cpp
rm ../dihedral_harmonic.cpp
@ -130,6 +136,7 @@ else if ($1 == 0) then
rm ../angle_cosine_squared.h
rm ../angle_harmonic.h
rm ../angle_hybrid.h
rm ../angle_table.h
rm ../atom_vec_angle.h
rm ../atom_vec_bond.h
rm ../atom_vec_full.h
@ -142,6 +149,7 @@ else if ($1 == 0) then
rm ../bond_morse.h
rm ../bond_nonlinear.h
rm ../bond_quartic.h
rm ../bond_table.h
# rm ../dihedral.h
rm ../dihedral_charmm.h
rm ../dihedral_harmonic.h

672
src/MOLECULE/angle_table.cpp Normal file
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@ -0,0 +1,672 @@
/* ----------------------------------------------------------------------
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 "angle_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;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{LINEAR,SPLINE};
#define MAXLINE 1024
#define SMALL 0.001
#define TINY 1.E-10
/* ---------------------------------------------------------------------- */
AngleTable::AngleTable(LAMMPS *lmp) : Angle(lmp)
{
ntables = 0;
tables = NULL;
}
/* ---------------------------------------------------------------------- */
AngleTable::~AngleTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->sfree(setflag);
memory->sfree(theta0);
memory->sfree(tabindex);
}
}
/* ---------------------------------------------------------------------- */
void AngleTable::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type,factor;
double eangle,f1[3],f3[3];
double delx1,dely1,delz1,delx2,dely2,delz2;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;
double theta,u,mdu; //mdu: minus du, -du/dx=f
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
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];
domain->minimum_image(delx1,dely1,delz1);
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];
domain->minimum_image(delx2,dely2,delz2);
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;
int n = atom->nangletypes;
theta0 = (double *) memory->smalloc((n+1)*sizeof(double),"angle:theta0");
tabindex = (int *) memory->smalloc((n+1)*sizeof(int),"angle:tabindex");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void AngleTable::settings(int narg, char **arg)
{
if (narg != 2) error->all("Illegal angle_style command");
if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
else error->all("Unknown table style in angle style table");
n = atoi(arg[1]);
nm1 = n - 1;
// 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->sfree(setflag);
memory->sfree(tabindex);
}
allocated = 0;
ntables = 0;
tables = NULL;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void AngleTable::coeff(int which, int narg, char **arg)
{
if (which > 0) return;
if (narg != 3) error->all("Illegal angle_coeff command");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
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("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("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] *= PI/180.0;
tb->ffile[i] *= 180.0/PI;
}
// 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("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)
{
fwrite(&tabstyle,sizeof(int),1,fp);
fwrite(&n,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void AngleTable::read_restart(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&n,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world);
MPI_Bcast(&n,1,MPI_INT,0,world);
nm1 = n - 1;
allocate();
}
/* ---------------------------------------------------------------------- */
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;
u_lookup(type,theta,u);
return u;
}
/* ---------------------------------------------------------------------- */
void AngleTable::null_table(Table *tb)
{
tb->afile = tb->efile = tb->ffile = NULL;
tb->e2file = tb->f2file = NULL;
tb->ang = tb->e = tb->de = NULL;
tb->f = tb->df = tb->e2 = tb->f2 = NULL;
}
/* ---------------------------------------------------------------------- */
void AngleTable::free_table(Table *tb)
{
memory->sfree(tb->afile);
memory->sfree(tb->efile);
memory->sfree(tb->ffile);
memory->sfree(tb->e2file);
memory->sfree(tb->f2file);
memory->sfree(tb->ang);
memory->sfree(tb->e);
memory->sfree(tb->de);
memory->sfree(tb->f);
memory->sfree(tb->df);
memory->sfree(tb->e2);
memory->sfree(tb->f2);
}
/* ----------------------------------------------------------------------
read table file, only called by proc 0
------------------------------------------------------------------------- */
void AngleTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
// open file
FILE *fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one("Did not find keyword in table file");
if (strspn(line," \t\n") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
if (strstr(line,keyword) == line) 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);
tb->afile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:afile");
tb->efile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:efile");
tb->ffile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:ffile");
// read a,e,f table values from file
int itmp;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %lg %lg",
&itmp,&tb->afile[i],&tb->efile[i],&tb->ffile[i]);
}
fclose(fp);
}
/* ----------------------------------------------------------------------
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)
{
tb->e2file = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:e2file");
tb->f2file = (double *)
memory->smalloc(tb->ninput*sizeof(double),"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
tb->delta = PI/ nm1;
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
tb->ang = (double *) memory->smalloc(n*sizeof(double),"angle:ang");
tb->e = (double *) memory->smalloc(n*sizeof(double),"angle:e");
tb->de = (double *) memory->smalloc(nm1*sizeof(double),"angle:de");
tb->f = (double *) memory->smalloc(n*sizeof(double),"angle:f");
tb->df = (double *) memory->smalloc(nm1*sizeof(double),"angle:df");
tb->e2 = (double *) memory->smalloc(n*sizeof(double),"angle:e2");
tb->f2 = (double *) memory->smalloc(n*sizeof(double),"angle:f2");
double a;
for (int i = 0; i < n; 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 < nm1; 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[nm1];
spline(tb->ang,tb->e,n,ep0,epn,tb->e2);
spline(tb->ang,tb->f,n,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 = 180.0;
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);
tb->fplo *= (180.0/PI)*(180.0/PI);
tb->fphi *= (180.0/PI)*(180.0/PI);
} else if (strcmp(word,"EQ") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->theta0 = atof(word);
} else {
error->one("Invalid keyword in angle table parameters");
}
word = strtok(NULL," \t\n\r\f");
}
if (tb->ninput == 0) error->one("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) {
tb->afile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:afile");
tb->efile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:efile");
tb->ffile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"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;
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 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)
{
int itable;
double fraction,value,a,b;
Table *tb = &tables[tabindex[type]];
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * tb->invdelta);
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) {
itable = static_cast<int> ( x * tb->invdelta);
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)
{
int itable;
double fraction,value,a,b;
Table *tb = &tables[tabindex[type]];
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * tb->invdelta);
fraction = (x - tb->ang[itable]) * tb->invdelta;
u = tb->e[itable] + fraction*tb->de[itable];
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ( x * tb->invdelta);
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;
}
}

69
src/MOLECULE/angle_table.h Normal file
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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.
------------------------------------------------------------------------- */
#ifndef ANGLE_TABLE_H
#define ANGLE_TABLE_H
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleTable : public Angle {
public:
AngleTable(class LAMMPS *);
~AngleTable();
void compute(int, int);
void settings(int, char **);
void coeff(int, int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
double single(int, int, int, int);
private:
int tabstyle,n,nm1;
double *theta0;
struct Table {
int ninput,fpflag;
double fplo,fphi,theta0;
double *afile,*efile,*ffile;
double *e2file,*f2file;
double delta,invdelta,deltasq6;
double *ang,*e,*de,*f,*df,*e2,*f2;
};
int ntables;
Table *tables;
int *tabindex;
void allocate();
void null_table(Table *);
void free_table(Table *);
void read_table(Table *, char *, char *);
void bcast_table(Table *);
void spline_table(Table *);
void compute_table(Table *);
void param_extract(Table *, char *);
void spline(double *, double *, int, double, double, double *);
double splint(double *, double *, double *, int, double);
void uf_lookup(int, double, double &, double &);
void u_lookup(int, double, double &);
};
}
#endif

588
src/MOLECULE/bond_table.cpp Normal file
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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{LINEAR,SPLINE};
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
BondTable::BondTable(LAMMPS *lmp) : Bond(lmp)
{
ntables = 0;
tables = NULL;
}
/* ---------------------------------------------------------------------- */
BondTable::~BondTable()
{
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->sfree(setflag);
memory->sfree(r0);
memory->sfree(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];
domain->minimum_image(delx,dely,delz);
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;
tabindex = (int *) memory->smalloc((n+1)*sizeof(int),"bond:tabindex");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"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("Illegal bond_style command");
if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
else error->all("Unknown table style in bond style table");
n = atoi(arg[1]);
nm1 = n - 1;
// 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->sfree(setflag);
memory->sfree(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("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("Invalid bond table length");
// 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("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(&n,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(&n,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world);
MPI_Bcast(&n,1,MPI_INT,0,world);
nm1 = n - 1;
allocate();
}
/* ---------------------------------------------------------------------- */
double BondTable::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double u;
u_lookup(type,r,u);
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->sfree(tb->rfile);
memory->sfree(tb->efile);
memory->sfree(tb->ffile);
memory->sfree(tb->e2file);
memory->sfree(tb->f2file);
memory->sfree(tb->r);
memory->sfree(tb->e);
memory->sfree(tb->de);
memory->sfree(tb->f);
memory->sfree(tb->df);
memory->sfree(tb->e2);
memory->sfree(tb->f2);
}
/* ----------------------------------------------------------------------
read table file, only called by proc 0
------------------------------------------------------------------------- */
void BondTable::read_table(Table *tb, char *file, char *keyword)
{
char line[MAXLINE];
// open file
FILE *fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one("Did not find keyword in table file");
if (strspn(line," \t\n") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
if (strstr(line,keyword) == line) 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);
tb->rfile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"bond:rfile");
tb->efile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"bond:efile");
tb->ffile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"bond:ffile");
// read r,e,f table values from file
int itmp;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %lg %lg",
&itmp,&tb->rfile[i],&tb->efile[i],&tb->ffile[i]);
}
fclose(fp);
}
/* ----------------------------------------------------------------------
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)
{
tb->e2file = (double *)
memory->smalloc(tb->ninput*sizeof(double),"bond:e2file");
tb->f2file = (double *)
memory->smalloc(tb->ninput*sizeof(double),"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
tb->delta = (tb->rfile[tb->ninput-1] - tb->rfile[0])/ nm1;
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
tb->r = (double *) memory->smalloc(n*sizeof(double),"bond:r");
tb->e = (double *) memory->smalloc(n*sizeof(double),"bond:e");
tb->de = (double *) memory->smalloc(nm1*sizeof(double),"bond:de");
tb->f = (double *) memory->smalloc(n*sizeof(double),"bond:f");
tb->df = (double *) memory->smalloc(nm1*sizeof(double),"bond:df");
tb->e2 = (double *) memory->smalloc(n*sizeof(double),"bond:e2");
tb->f2 = (double *) memory->smalloc(n*sizeof(double),"bond:f2");
double a;
for (int i = 0; i < n; i++) {
a = 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 < nm1; 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[nm1];
spline(tb->r,tb->e,n,ep0,epn,tb->e2);
spline(tb->r,tb->f,n,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("Invalid keyword in bond table parameters");
}
word = strtok(NULL," \t\n\r\f");
}
if (tb->ninput == 0) error->one("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) {
tb->rfile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:rfile");
tb->efile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"angle:efile");
tb->ffile = (double *)
memory->smalloc(tb->ninput*sizeof(double),"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
------------------------------------------------------------------------- */
void BondTable::uf_lookup(int type, double x, double &u, double &f)
{
int itable;
double fraction,value,a,b;
Table *tb = &tables[tabindex[type]];
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * 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->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
------------------------------------------------------------------------- */
void BondTable::u_lookup(int type, double x, double &u)
{
int itable;
double fraction,value,a,b;
Table *tb = &tables[tabindex[type]];
if (tabstyle == LINEAR) {
itable = static_cast<int> ( x * 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->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;
}
}

69
src/MOLECULE/bond_table.h Normal file
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@ -0,0 +1,69 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef BOND_TABLE_H
#define BOND_TABLE_H
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondTable : public Bond {
public:
BondTable(class LAMMPS *);
~BondTable();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
double single(int, double, int, int);
private:
int tabstyle,n,nm1;
double *r0;
struct Table {
int ninput,fpflag;
double fplo,fphi,r0;
double *rfile,*efile,*ffile;
double *e2file,*f2file;
double delta,invdelta,deltasq6;
double *r,*e,*de,*f,*df,*e2,*f2;
};
int ntables;
Table *tables;
int *tabindex;
void allocate();
void null_table(Table *);
void free_table(Table *);
void read_table(Table *, char *, char *);
void bcast_table(Table *);
void spline_table(Table *);
void compute_table(Table *);
void param_extract(Table *, char *);
void spline(double *, double *, int, double, double, double *);
double splint(double *, double *, double *, int, double);
void uf_lookup(int, double, double &, double &);
void u_lookup(int, double, double &);
};
}
#endif

4
src/MOLECULE/style_molecule.h
View File

@ -18,6 +18,7 @@
#include "angle_cosine_squared.h"
#include "angle_harmonic.h"
#include "angle_hybrid.h"
#include "angle_table.h"
#endif
#ifdef AngleClass
@ -27,6 +28,7 @@ AngleStyle(cosine/delta,AngleCosineDelta)
AngleStyle(cosine/squared,AngleCosineSquared)
AngleStyle(harmonic,AngleHarmonic)
AngleStyle(hybrid,AngleHybrid)
AngleStyle(table,AngleTable)
#endif
#ifdef AtomInclude
@ -51,6 +53,7 @@ AtomStyle(molecular,AtomVecMolecular)
#include "bond_morse.h"
#include "bond_nonlinear.h"
#include "bond_quartic.h"
#include "bond_table.h"
#endif
#ifdef BondClass
@ -61,6 +64,7 @@ BondStyle(hybrid,BondHybrid)
BondStyle(morse,BondMorse)
BondStyle(nonlinear,BondNonlinear)
BondStyle(quartic,BondQuartic)
BondStyle(table,BondTable)
#endif
#ifdef DihedralInclude