forked from lijiext/lammps
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sjplimp
parent
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commit
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@ -1,319 +1,319 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(polymorphic,PairPolymorphic)
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#else
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#ifndef LMP_PAIR_POLYMORPHIC_H
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#define LMP_PAIR_POLYMORPHIC_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairPolymorphic : public Pair {
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public:
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PairPolymorphic(class LAMMPS *);
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virtual ~PairPolymorphic();
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void init_style();
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double init_one(int, int);
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protected:
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class tabularFunction {
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public:
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tabularFunction() {
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size = 0;
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xmin = 0.0;
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xmax = 0.0;
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xmaxsq = xmax*xmax;
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vmax = 0.0;
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xs = NULL;
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ys = NULL;
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ys1 = NULL;
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ys2 = NULL;
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ys3 = NULL;
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ys4 = NULL;
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ys5 = NULL;
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ys6 = NULL;
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}
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tabularFunction(int n) {
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size = n;
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xmin = 0.0;
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xmax = 0.0;
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xmaxsq = xmax*xmax;
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xs = new double[n];
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ys = new double[n];
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ys1 = new double[n];
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ys2 = new double[n];
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ys3 = new double[n];
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ys4 = new double[n];
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ys5 = new double[n];
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ys6 = new double[n];
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}
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tabularFunction(int n, double x1, double x2) {
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size = n;
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xmin = x1;
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xmax = x2;
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xmaxsq = xmax*xmax;
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xs = new double[n];
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ys = new double[n];
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ys1 = new double[n];
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ys2 = new double[n];
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ys3 = new double[n];
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ys4 = new double[n];
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ys5 = new double[n];
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ys6 = new double[n];
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}
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virtual ~tabularFunction() {
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if (xs) delete [] xs;
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if (ys) delete [] ys;
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if (ys1) delete [] ys1;
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if (ys2) delete [] ys2;
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if (ys3) delete [] ys3;
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if (ys4) delete [] ys4;
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if (ys5) delete [] ys5;
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if (ys6) delete [] ys6;
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}
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void set_xrange(double x1, double x2) {
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xmin = x1;
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xmax = x2;
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xmaxsq = xmax*xmax;
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}
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void set_values(int n, double x1, double x2, double * values, double epsilon)
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{
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int i0;
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i0 = n-1;
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// shrink (remove near zero points) reduces cutoff radius, and therefore computational cost
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// do not shrink when x2 < 1.1 (angular function) or x2 > 20.0 (non-radial function)
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if (x2 >= 1.1 && x2 <= 20.0) {
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for (int i = n-1; i >= 0; i--) {
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if (fabs(values[i]) > epsilon) {
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i0 = i;
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break;
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}
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}
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}
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// do not shrink when when list is abnormally small
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if (i0 < 10/n) {
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i0 = n-1;
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} else if (i0 < n-1) {
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values[i0] = 0.0;
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i0 = i0 + 1;
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values[i0] = 0.0;
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}
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xmin = x1;
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xmax = x1 + (x2-x1)/(n -1)*i0;
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xmaxsq = xmax*xmax;
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n = i0+1;
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resize(n);
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memcpy(ys,values,n*sizeof(double));
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initialize();
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}
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void value(double x, double &y, int ny, double &y1, int ny1)
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{
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double ps = (x - xmin) * rdx;
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int ks = ps + 0.5;
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if (ks > size-1) ks = size-1;
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if (ks < 0 ) ks = 0;
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ps = ps - ks;
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if (ny) y = ((ys3[ks]*ps + ys2[ks])*ps + ys1[ks])*ps + ys[ks];
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if (ny1) y1 = (ys6[ks]*ps + ys5[ks])*ps + ys4[ks];
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}
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void print_value()
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{
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printf("%d %f %f %f \n",size,xmin,xmax,rdx);
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printf(" \n");
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for (int i = 0; i < size; i++) {
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printf("%f %f \n",xs[i],ys[i]);
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}
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}
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double get_xmin() {
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return xmin;
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}
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double get_xmax() {
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return xmax;
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}
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double get_xmaxsq() {
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return xmaxsq;
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}
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double get_rdx() {
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return rdx;
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}
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double get_vmax() {
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return vmax;
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}
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protected:
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void resize(int n) {
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if (n != size) {
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size = n;
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if (xs) delete [] xs;
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xs = new double[n];
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if (ys) delete [] ys;
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ys = new double[n];
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if (ys1) delete [] ys1;
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ys1 = new double[n];
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if (ys2) delete [] ys2;
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ys2 = new double[n];
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if (ys3) delete [] ys3;
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ys3 = new double[n];
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if (ys4) delete [] ys4;
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ys4 = new double[n];
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if (ys5) delete [] ys5;
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ys5 = new double[n];
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if (ys6) delete [] ys6;
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ys6 = new double[n];
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}
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}
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void initialize() {
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int n = size;
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rdx = (xmax-xmin)/(n-1.0);
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vmax = 0.0;
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for (int i = 0; i < n; i++) {
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if (fabs(ys[i]) > vmax) vmax = fabs(ys[i]);
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}
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for (int i = 0; i < n; i++) {
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xs[i] = xmin+i*rdx;
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}
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rdx = 1.0 / rdx;
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ys1[0] = ys[1] - ys[0];
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ys1[1] = 0.5 * (ys[2] - ys[0]);
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ys1[n-2] = 0.5 * (ys[n-1] - ys[n-3]);
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ys1[n-1] = ys[n-1] - ys[n-2];
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for (int i = 2; i < n-2; i++) {
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ys1[i]=((ys[i-2]-ys[i+2])+ 8.0*(ys[i+1]-ys[i-1]))/12.0;
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}
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for (int i = 0; i < n-1; i++) {
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ys2[i]=3.0*(ys[i+1]-ys[i])-2.0*ys1[i]-ys1[i+1];
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ys3[i]=ys1[i]+ys1[i+1]-2.0*(ys[i+1]-ys[i]);
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}
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ys2[n-1]=0.0;
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ys3[n-1]=0.0;
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for (int i = 0; i < n; i++) {
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ys4[i]=ys1[i]*rdx;
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ys5[i]=2.0*ys2[i]*rdx;
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ys6[i]=3.0*ys3[i]*rdx;
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}
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}
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int size;
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double xmin,xmax,xmaxsq,rdx,vmax;
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double * ys, * ys1, * ys2, * ys3, * ys4, * ys5, * ys6;
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double * xs;
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};
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struct PairParameters {
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double cut;
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double cutsq;
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bool xi; // "indicator"
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class tabularFunction * U;
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class tabularFunction * V;
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class tabularFunction * W;
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class tabularFunction * P;
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class tabularFunction * F;
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PairParameters() {
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cut = 0.0;
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cutsq = 0.0;
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xi = true;
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U = NULL;
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V = NULL;
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W = NULL;
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P = NULL;
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F = NULL;
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};
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};
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struct TripletParameters {
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class tabularFunction * G;
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TripletParameters() {
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G = NULL;
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};
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};
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double epsilon;
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bool eta; // global indicator
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int nx,nr,ng; // table sizes
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double maxX;
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// parameter sets
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PairParameters * pairParameters; // for I-J interaction
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TripletParameters * tripletParameters; // for I-J-K interaction
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int neighsize,numneighV,numneighW,numneighW1;
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int *firstneighV,*firstneighW,*firstneighW1;
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double *delxV,*delyV,*delzV,*drV;
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double *delxW,*delyW,*delzW,*drW;
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char **elements; // names of unique elements
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int **elem2param; // map: element pairs to parameters
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int ***elem3param; // map: element triplets to parameters
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int *map; // mapping from atom types to elements
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double cutmax; // max cutoff for all elements
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double cutmaxsq;
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int nelements; // # of unique elements
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int npair,ntriple;
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int *match;
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void allocate();
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void grab(FILE *, int, double *);
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virtual void read_file(char *);
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void setup();
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void write_tables(int);
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void attractive(PairParameters *, TripletParameters *, double, double,
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double, double *, double *, double *, double *, double *);
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void ters_zetaterm_d(double, double *, double, double *, double, double *,
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double *, double *, PairParameters *, TripletParameters *);
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void costheta_d(double *, double, double *, double,
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double *, double *, double *);
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// inlined functions for efficiency
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inline double vec3_dot(const double x[3], const double y[3]) const {
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return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
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}
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inline void vec3_add(const double x[3], const double y[3],
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double * const z) const {
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z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
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}
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inline void vec3_scale(const double k, const double x[3],
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double y[3]) const {
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y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
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}
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inline void vec3_scaleadd(const double k, const double x[3],
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const double y[3], double * const z) const {
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z[0] = k*x[0]+y[0];
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z[1] = k*x[1]+y[1];
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z[2] = k*x[2]+y[2];
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}
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};
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}
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#endif
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#endif
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(polymorphic,PairPolymorphic)
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#else
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#ifndef LMP_PAIR_POLYMORPHIC_H
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#define LMP_PAIR_POLYMORPHIC_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairPolymorphic : public Pair {
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public:
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PairPolymorphic(class LAMMPS *);
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virtual ~PairPolymorphic();
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void init_style();
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double init_one(int, int);
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protected:
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class tabularFunction {
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public:
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tabularFunction() {
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size = 0;
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xmin = 0.0;
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xmax = 0.0;
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xmaxsq = xmax*xmax;
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vmax = 0.0;
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xs = NULL;
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ys = NULL;
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ys1 = NULL;
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ys2 = NULL;
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ys3 = NULL;
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ys4 = NULL;
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ys5 = NULL;
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ys6 = NULL;
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}
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tabularFunction(int n) {
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size = n;
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xmin = 0.0;
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xmax = 0.0;
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xmaxsq = xmax*xmax;
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xs = new double[n];
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ys = new double[n];
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ys1 = new double[n];
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ys2 = new double[n];
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ys3 = new double[n];
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ys4 = new double[n];
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ys5 = new double[n];
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ys6 = new double[n];
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}
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tabularFunction(int n, double x1, double x2) {
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size = n;
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xmin = x1;
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xmax = x2;
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xmaxsq = xmax*xmax;
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xs = new double[n];
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ys = new double[n];
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ys1 = new double[n];
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ys2 = new double[n];
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ys3 = new double[n];
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ys4 = new double[n];
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ys5 = new double[n];
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ys6 = new double[n];
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}
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virtual ~tabularFunction() {
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if (xs) delete [] xs;
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if (ys) delete [] ys;
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if (ys1) delete [] ys1;
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if (ys2) delete [] ys2;
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if (ys3) delete [] ys3;
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if (ys4) delete [] ys4;
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if (ys5) delete [] ys5;
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if (ys6) delete [] ys6;
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}
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void set_xrange(double x1, double x2) {
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xmin = x1;
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xmax = x2;
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xmaxsq = xmax*xmax;
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}
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void set_values(int n, double x1, double x2, double * values, double epsilon)
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{
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int i0;
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i0 = n-1;
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// shrink (remove near zero points) reduces cutoff radius, and therefore computational cost
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// do not shrink when x2 < 1.1 (angular function) or x2 > 20.0 (non-radial function)
|
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if (x2 >= 1.1 && x2 <= 20.0) {
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for (int i = n-1; i >= 0; i--) {
|
||||
if (fabs(values[i]) > epsilon) {
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i0 = i;
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break;
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}
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||||
}
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}
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// do not shrink when when list is abnormally small
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if (i0 < 10/n) {
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i0 = n-1;
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} else if (i0 < n-1) {
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values[i0] = 0.0;
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i0 = i0 + 1;
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values[i0] = 0.0;
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}
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xmin = x1;
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xmax = x1 + (x2-x1)/(n -1)*i0;
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xmaxsq = xmax*xmax;
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n = i0+1;
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resize(n);
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memcpy(ys,values,n*sizeof(double));
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initialize();
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}
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void value(double x, double &y, int ny, double &y1, int ny1)
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{
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double ps = (x - xmin) * rdx;
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int ks = ps + 0.5;
|
||||
if (ks > size-1) ks = size-1;
|
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if (ks < 0 ) ks = 0;
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ps = ps - ks;
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if (ny) y = ((ys3[ks]*ps + ys2[ks])*ps + ys1[ks])*ps + ys[ks];
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||||
if (ny1) y1 = (ys6[ks]*ps + ys5[ks])*ps + ys4[ks];
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}
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void print_value()
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{
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printf("%d %f %f %f \n",size,xmin,xmax,rdx);
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printf(" \n");
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||||
for (int i = 0; i < size; i++) {
|
||||
printf("%f %f \n",xs[i],ys[i]);
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}
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||||
}
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double get_xmin() {
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return xmin;
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}
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double get_xmax() {
|
||||
return xmax;
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||||
}
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double get_xmaxsq() {
|
||||
return xmaxsq;
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||||
}
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||||
double get_rdx() {
|
||||
return rdx;
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||||
}
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||||
double get_vmax() {
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||||
return vmax;
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}
|
||||
|
||||
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();
|
||||
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
|
||||
|
|
|
|||
Loading…
Reference in New Issue