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rLAMMPS lammps
pair_polymorphic.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(polymorphic,PairPolymorphic)
#else
#ifndef LMP_PAIR_POLYMORPHIC_H
#define LMP_PAIR_POLYMORPHIC_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPolymorphic : public Pair {
public:
PairPolymorphic(class LAMMPS *);
virtual ~PairPolymorphic();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
protected:
class tabularFunction {
public:
tabularFunction() {
size = 0;
xmin = 0.0;
xmax = 0.0;
xmaxsq = xmax*xmax;
vmax = 0.0;
xs = NULL;
ys = NULL;
ys1 = NULL;
ys2 = NULL;
ys3 = NULL;
ys4 = NULL;
ys5 = NULL;
ys6 = NULL;
}
tabularFunction(int n) {
size = n;
xmin = 0.0;
xmax = 0.0;
xmaxsq = xmax*xmax;
xs = new double[n];
ys = new double[n];
ys1 = new double[n];
ys2 = new double[n];
ys3 = new double[n];
ys4 = new double[n];
ys5 = new double[n];
ys6 = new double[n];
}
tabularFunction(int n, double x1, double x2) {
size = n;
xmin = x1;
xmax = x2;
xmaxsq = xmax*xmax;
xs = new double[n];
ys = new double[n];
ys1 = new double[n];
ys2 = new double[n];
ys3 = new double[n];
ys4 = new double[n];
ys5 = new double[n];
ys6 = new double[n];
}
virtual ~tabularFunction() {
if (xs) delete [] xs;
if (ys) delete [] ys;
if (ys1) delete [] ys1;
if (ys2) delete [] ys2;
if (ys3) delete [] ys3;
if (ys4) delete [] ys4;
if (ys5) delete [] ys5;
if (ys6) delete [] ys6;
}
void set_xrange(double x1, double x2) {
xmin = x1;
xmax = x2;
xmaxsq = xmax*xmax;
}
void set_values(int n, double x1, double x2, double * values, double epsilon)
{
int i0;
i0 = n-1;
// shrink (remove near zero points) reduces cutoff radius, and therefore computational cost
// do not shrink when x2 < 1.1 (angular function) or x2 > 20.0 (non-radial function)
if (x2 >= 1.1 && x2 <= 20.0) {
for (int i = n-1; i >= 0; i--) {
if (fabs(values[i]) > epsilon) {
i0 = i;
break;
}
}
}
// do not shrink when when list is abnormally small
if (i0 < 10/n) {
i0 = n-1;
} else if (i0 < n-1) {
values[i0] = 0.0;
i0 = i0 + 1;
values[i0] = 0.0;
}
xmin = x1;
xmax = x1 + (x2-x1)/(n -1)*i0;
xmaxsq = xmax*xmax;
n = i0+1;
resize(n);
memcpy(ys,values,n*sizeof(double));
initialize();
}
void value(double x, double &y, int ny, double &y1, int ny1)
{
double ps = (x - xmin) * rdx;
int ks = ps + 0.5;
if (ks > size-1) ks = size-1;
if (ks < 0 ) ks = 0;
ps = ps - ks;
if (ny) y = ((ys3[ks]*ps + ys2[ks])*ps + ys1[ks])*ps + ys[ks];
if (ny1) y1 = (ys6[ks]*ps + ys5[ks])*ps + ys4[ks];
}
void print_value()
{
printf("%d %f %f %f \n",size,xmin,xmax,rdx);
printf(" \n");
for (int i = 0; i < size; i++) {
printf("%f %f \n",xs[i],ys[i]);
}
}
double get_xmin() {
return xmin;
}
double get_xmax() {
return xmax;
}
double get_xmaxsq() {
return xmaxsq;
}
double get_rdx() {
return rdx;
}
double get_vmax() {
return vmax;
}
protected:
void resize(int n) {
if (n != size) {
size = n;
if (xs) delete [] xs;
xs = new double[n];
if (ys) delete [] ys;
ys = new double[n];
if (ys1) delete [] ys1;
ys1 = new double[n];
if (ys2) delete [] ys2;
ys2 = new double[n];
if (ys3) delete [] ys3;
ys3 = new double[n];
if (ys4) delete [] ys4;
ys4 = new double[n];
if (ys5) delete [] ys5;
ys5 = new double[n];
if (ys6) delete [] ys6;
ys6 = new double[n];
}
}
void initialize() {
int n = size;
rdx = (xmax-xmin)/(n-1.0);
vmax = 0.0;
for (int i = 0; i < n; i++) {
if (fabs(ys[i]) > vmax) vmax = fabs(ys[i]);
}
for (int i = 0; i < n; i++) {
xs[i] = xmin+i*rdx;
}
rdx = 1.0 / rdx;
ys1[0] = ys[1] - ys[0];
ys1[1] = 0.5 * (ys[2] - ys[0]);
ys1[n-2] = 0.5 * (ys[n-1] - ys[n-3]);
ys1[n-1] = ys[n-1] - ys[n-2];
for (int i = 2; i < n-2; i++) {
ys1[i]=((ys[i-2]-ys[i+2])+ 8.0*(ys[i+1]-ys[i-1]))/12.0;
}
for (int i = 0; i < n-1; i++) {
ys2[i]=3.0*(ys[i+1]-ys[i])-2.0*ys1[i]-ys1[i+1];
ys3[i]=ys1[i]+ys1[i+1]-2.0*(ys[i+1]-ys[i]);
}
ys2[n-1]=0.0;
ys3[n-1]=0.0;
for (int i = 0; i < n; i++) {
ys4[i]=ys1[i]*rdx;
ys5[i]=2.0*ys2[i]*rdx;
ys6[i]=3.0*ys3[i]*rdx;
}
}
int size;
double xmin,xmax,xmaxsq,rdx,vmax;
double * ys, * ys1, * ys2, * ys3, * ys4, * ys5, * ys6;
double * xs;
};
struct PairParameters {
double cut;
double cutsq;
bool xi; // "indicator"
class tabularFunction * U;
class tabularFunction * V;
class tabularFunction * W;
class tabularFunction * P;
class tabularFunction * F;
PairParameters() {
cut = 0.0;
cutsq = 0.0;
xi = true;
U = NULL;
V = NULL;
W = NULL;
P = NULL;
F = NULL;
};
};
struct TripletParameters {
class tabularFunction * G;
TripletParameters() {
G = NULL;
};
};
double epsilon;
bool eta; // global indicator
int nx,nr,ng; // table sizes
double maxX;
// parameter sets
PairParameters * pairParameters; // for I-J interaction
TripletParameters * tripletParameters; // for I-J-K interaction
int neighsize,numneighV,numneighW,numneighW1;
int *firstneighV,*firstneighW,*firstneighW1;
double *delxV,*delyV,*delzV,*drV;
double *delxW,*delyW,*delzW,*drW;
char **elements; // names of unique elements
int **elem2param; // map: element pairs to parameters
int ***elem3param; // map: element triplets to parameters
int *map; // mapping from atom types to elements
double cutmax; // max cutoff for all elements
double cutmaxsq;
int nelements; // # of unique elements
int npair,ntriple;
int *match;
void allocate();
void grab(FILE *, int, double *);
virtual void read_file(char *);
void setup_params();
void write_tables(int);
void attractive(PairParameters *, TripletParameters *, double, double,
double, double *, double *, double *, double *, double *);
void ters_zetaterm_d(double, double *, double, double *, double, double *,
double *, double *, PairParameters *, TripletParameters *);
void costheta_d(double *, double, double *, double,
double *, double *, double *);
// inlined functions for efficiency
inline double vec3_dot(const double x[3], const double y[3]) const {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
inline void vec3_add(const double x[3], const double y[3],
double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(const double k, const double x[3],
double y[3]) const {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
inline void vec3_scaleadd(const double k, const double x[3],
const double y[3], double * const z) const {
z[0] = k*x[0]+y[0];
z[1] = k*x[1]+y[1];
z[2] = k*x[2]+y[2];
}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style polymorphic requires atom IDs
This is a requirement to use the polymorphic potential.
E: Pair style polymorphic requires newton pair on
See the newton command. This is a restriction to use the polymorphic
potential.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Cannot open polymorphic potential file %s
The specified polymorphic potential file cannot be opened. Check that
the path and name are correct.
E: Incorrect number of elements in potential file
Self-explanatory.
E: Element not defined in potential file
The specified element is not in the potential file.
*/
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