531 lines
15 KiB
C++
531 lines
15 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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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#include "angle_amoeba.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "comm.h"
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#include "force.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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AngleAmoeba::AngleAmoeba(LAMMPS *lmp) : Angle(lmp)
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{
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pflag = nullptr;
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theta0 = nullptr;
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k2 = nullptr;
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k3 = nullptr;
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k4 = nullptr;
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k5 = nullptr;
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k6 = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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AngleAmoeba::~AngleAmoeba()
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{
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if (copymode) return;
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(pflag);
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memory->destroy(theta0);
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memory->destroy(k2);
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memory->destroy(k3);
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memory->destroy(k4);
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memory->destroy(k5);
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memory->destroy(k6);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleAmoeba::compute(int eflag, int vflag)
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{
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int i1,i2,i3,n,type,tflag;
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double delx1,dely1,delz1,delx2,dely2,delz2;
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double eangle,f1[3],f3[3];
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double dtheta,dtheta2,dtheta3,dtheta4,dtheta5,dtheta6,de_angle;
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double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
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double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
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eangle = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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int **anglelist = neighbor->anglelist;
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int **nspecial = atom->nspecial;
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int nanglelist = neighbor->nanglelist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nanglelist; n++) {
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i1 = anglelist[n][0];
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i2 = anglelist[n][1];
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i3 = anglelist[n][2];
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type = anglelist[n][3];
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// tflag = 0 for "angle", 1 for "anglep" in Tinker PRM file
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// atom 2 must have 3 bond partners to invoke anglep() variant
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tflag = pflag[type];
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if (tflag && nspecial[i2][0] == 3) {
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anglep(i1,i2,i3,type,eflag);
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continue;
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}
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// 1st bond
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delx1 = x[i1][0] - x[i2][0];
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dely1 = x[i1][1] - x[i2][1];
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delz1 = x[i1][2] - x[i2][2];
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rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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r1 = sqrt(rsq1);
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// 2nd bond
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delx2 = x[i3][0] - x[i2][0];
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dely2 = x[i3][1] - x[i2][1];
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delz2 = x[i3][2] - x[i2][2];
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rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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r2 = sqrt(rsq2);
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// angle (cos and sin)
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c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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s = sqrt(1.0 - c*c);
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if (s < SMALL) s = SMALL;
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s = 1.0/s;
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// force & energy for angle term
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dtheta = acos(c) - theta0[type];
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dtheta2 = dtheta*dtheta;
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dtheta3 = dtheta2*dtheta;
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dtheta4 = dtheta3*dtheta;
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dtheta5 = dtheta4*dtheta;
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dtheta6 = dtheta5*dtheta;
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de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
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4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 + 6.0*k6[type]*dtheta5;
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a = -de_angle*s;
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a11 = a*c / rsq1;
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a12 = -a / (r1*r2);
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a22 = a*c / rsq2;
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f1[0] = a11*delx1 + a12*delx2;
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f1[1] = a11*dely1 + a12*dely2;
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f1[2] = a11*delz1 + a12*delz2;
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f3[0] = a22*delx2 + a12*delx1;
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f3[1] = a22*dely2 + a12*dely1;
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f3[2] = a22*delz2 + a12*delz1;
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if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
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k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
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// apply force to each of 3 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= f1[0] + f3[0];
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f[i2][1] -= f1[1] + f3[1];
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f[i2][2] -= f1[2] + f3[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
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delx1,dely1,delz1,delx2,dely2,delz2);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleAmoeba::anglep(int i1, int i2, int i3, int type, int eflag)
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{
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int i4;
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tagint i1tag,i3tag,i4tag;
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double xia,yia,zia,xib,yib,zib,xic,yic,zic,xid,yid,zid;
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double xad,yad,zad,xbd,ybd,zbd,xcd,ycd,zcd;
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double xt,yt,zt,rt2;
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double xip,yip,zip,xap,yap,zap,xcp,ycp,zcp;
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double rap2,rcp2;
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double dtheta,dtheta2,dtheta3,dtheta4,dtheta5,dtheta6;
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double xm,ym,zm,rm,dot;
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double cosine,angle;
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double eangle,deddt;
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double dedxip,dedyip,dedzip,dpdxia,dpdyia,dpdzia,dpdxic,dpdyic,dpdzic;
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double delta,delta2,ptrt2,term,terma,termc;
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double f1[3],f2[3],f3[3],f4[3];
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double **x = atom->x;
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double **f = atom->f;
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tagint **special = atom->special;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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// i4 = index of third atom that i2 is bonded to
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i1tag = atom->tag[i1];
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i3tag = atom->tag[i3];
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for (int ibond = 0; ibond < 3; ibond++) {
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i4tag = special[i2][ibond];
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if (i4tag != i1tag && i4tag != i3tag) break;
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}
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i4 = atom->map(i4tag);
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i4 = domain->closest_image(i2,i4);
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// anglep out-of-plane calculation from Tinker
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xia = x[i1][0];
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yia = x[i1][1];
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zia = x[i1][2];
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xib = x[i2][0];
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yib = x[i2][1];
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zib = x[i2][2];
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xic = x[i3][0];
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yic = x[i3][1];
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zic = x[i3][2];
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xid = x[i4][0];
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yid = x[i4][1];
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zid = x[i4][2];
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xad = xia - xid;
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yad = yia - yid;
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zad = zia - zid;
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xbd = xib - xid;
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ybd = yib - yid;
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zbd = zib - zid;
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xcd = xic - xid;
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ycd = yic - yid;
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zcd = zic - zid;
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xt = yad*zcd - zad*ycd;
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yt = zad*xcd - xad*zcd;
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zt = xad*ycd - yad*xcd;
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rt2 = xt*xt + yt*yt + zt*zt;
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delta = -(xt*xbd + yt*ybd + zt*zbd) / rt2;
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xip = xib + xt*delta;
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yip = yib + yt*delta;
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zip = zib + zt*delta;
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xap = xia - xip;
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yap = yia - yip;
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zap = zia - zip;
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xcp = xic - xip;
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ycp = yic - yip;
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zcp = zic - zip;
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rap2 = xap*xap + yap*yap + zap*zap;
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rcp2 = xcp*xcp + ycp*ycp + zcp*zcp;
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// NOTE: can these be 0.0 ? what to do?
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if (rap2 == 0.0 || rcp2 == 0.0) return;
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xm = ycp*zap - zcp*yap;
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ym = zcp*xap - xcp*zap;
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zm = xcp*yap - ycp*xap;
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rm = sqrt(xm*xm + ym*ym + zm*zm);
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rm = MAX(rm,0.0001);
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dot = xap*xcp + yap*ycp + zap*zcp;
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cosine = dot / sqrt(rap2*rcp2);
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cosine = MIN(1.0,MAX(-1.0,cosine));
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// force & energy for angle term
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dtheta = acos(cosine) - theta0[type];
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dtheta2 = dtheta*dtheta;
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dtheta3 = dtheta2*dtheta;
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dtheta4 = dtheta3*dtheta;
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dtheta5 = dtheta4*dtheta;
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dtheta6 = dtheta5*dtheta;
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deddt = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
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4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 + 6.0*k6[type]*dtheta5;
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if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
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k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
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// chain rule terms for first derivative components
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terma = -deddt / (rap2*rm);
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termc = deddt / (rcp2*rm);
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f1[0] = terma * (yap*zm-zap*ym);
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f1[1] = terma * (zap*xm-xap*zm);
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f1[2] = terma * (xap*ym-yap*xm);
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f3[0] = termc * (ycp*zm-zcp*ym);
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f3[1] = termc * (zcp*xm-xcp*zm);
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f3[2] = termc * (xcp*ym-ycp*xm);
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dedxip = -f1[0] - f3[0];
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dedyip = -f1[1] - f3[1];
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dedzip = -f1[2] - f3[2];
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// chain rule components for the projection of the central atom
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delta2 = 2.0 * delta;
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ptrt2 = (dedxip*xt + dedyip*yt + dedzip*zt) / rt2;
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term = (zcd*ybd-ycd*zbd) + delta2*(yt*zcd-zt*ycd);
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dpdxia = delta*(ycd*dedzip-zcd*dedyip) + term*ptrt2;
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term = (xcd*zbd-zcd*xbd) + delta2*(zt*xcd-xt*zcd);
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dpdyia = delta*(zcd*dedxip-xcd*dedzip) + term*ptrt2;
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term = (ycd*xbd-xcd*ybd) + delta2*(xt*ycd-yt*xcd);
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dpdzia = delta*(xcd*dedyip-ycd*dedxip) + term*ptrt2;
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term = (yad*zbd-zad*ybd) + delta2*(zt*yad-yt*zad);
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dpdxic = delta*(zad*dedyip-yad*dedzip) + term*ptrt2;
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term = (zad*xbd-xad*zbd) + delta2*(xt*zad-zt*xad);
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dpdyic = delta*(xad*dedzip-zad*dedxip) + term*ptrt2;
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term = (xad*ybd-yad*xbd) + delta2*(yt*xad-xt*yad);
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dpdzic = delta*(yad*dedxip-xad*dedyip) + term*ptrt2;
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// compute derivative components for this interaction
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f1[0] += dpdxia;
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f1[1] += dpdyia;
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f1[2] += dpdzia;
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f2[0] = dedxip;
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f2[1] = dedyip;
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f2[2] = dedzip;
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f3[0] += dpdxic;
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f3[1] += dpdyic;
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f3[2] += dpdzic;
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f4[0] = -f1[0] - f2[0] - f3[0];
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f4[1] = -f1[1] - f2[1] - f3[1];
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f4[2] = -f1[2] - f2[2] - f3[2];
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// apply force to each of 4 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] += f2[0];
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f[i2][1] += f2[1];
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f[i2][2] += f2[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (newton_bond || i4 < nlocal) {
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f[i4][0] += f4[0];
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f[i4][1] += f4[1];
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f[i4][2] += f4[2];
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}
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if (evflag) ev_tally4(i1,i2,i3,14,nlocal,newton_bond,eangle,f1,f2,f3,f4);
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}
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/* ---------------------------------------------------------------------- */
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void AngleAmoeba::allocate()
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{
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allocated = 1;
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int n = atom->nangletypes;
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memory->create(pflag,n+1,"angle:pflag");
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memory->create(theta0,n+1,"angle:theta0");
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memory->create(k2,n+1,"angle:k2");
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memory->create(k3,n+1,"angle:k3");
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memory->create(k4,n+1,"angle:k4");
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memory->create(k5,n+1,"angle:k5");
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memory->create(k6,n+1,"angle:k6");
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memory->create(setflag,n+1,"angle:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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void AngleAmoeba::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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int ilo,ihi;
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utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
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int count = 0;
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if (narg != 8) error->all(FLERR,"Incorrect args for angle coefficients");
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int pflag_one = utils::inumeric(FLERR,arg[1],false,lmp);
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double theta0_one = utils::numeric(FLERR,arg[2],false,lmp);
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double k2_one = utils::numeric(FLERR,arg[3],false,lmp);
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double k3_one = utils::numeric(FLERR,arg[4],false,lmp);
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double k4_one = utils::numeric(FLERR,arg[5],false,lmp);
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double k5_one = utils::numeric(FLERR,arg[6],false,lmp);
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double k6_one = utils::numeric(FLERR,arg[7],false,lmp);
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// convert theta0 from degrees to radians
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for (int i = ilo; i <= ihi; i++) {
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pflag[i] = pflag_one;
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theta0[i] = theta0_one/180.0 * MY_PI;
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k2[i] = k2_one;
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k3[i] = k3_one;
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k4[i] = k4_one;
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k5[i] = k5_one;
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k6[i] = k6_one;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
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for (int i = ilo; i <= ihi; i++) setflag[i] = 1;
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}
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/* ---------------------------------------------------------------------- */
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double AngleAmoeba::equilibrium_angle(int i)
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{
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return theta0[i];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void AngleAmoeba::write_restart(FILE *fp)
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{
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fwrite(&pflag[1],sizeof(int),atom->nangletypes,fp);
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fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&k2[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&k3[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&k4[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&k5[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&k6[1],sizeof(double),atom->nangletypes,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void AngleAmoeba::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0) {
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utils::sfread(FLERR,&pflag[1],sizeof(int),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&k5[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&k6[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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}
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MPI_Bcast(&pflag[1],atom->nangletypes,MPI_INT,0,world);
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MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&k3[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&k4[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&k5[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&k6[1],atom->nangletypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void AngleAmoeba::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nangletypes; i++)
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fprintf(fp,"%d %d %g %g %g %g %g %g\n",
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i,pflag[i],theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i],k5[i],k6[i]);
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}
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/* ---------------------------------------------------------------------- */
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double AngleAmoeba::single(int type, int i1, int i2, int i3)
|
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{
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double **x = atom->x;
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double delx1 = x[i1][0] - x[i2][0];
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double dely1 = x[i1][1] - x[i2][1];
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double delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1,dely1,delz1);
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double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
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|
|
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double delx2 = x[i3][0] - x[i2][0];
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double dely2 = x[i3][1] - x[i2][1];
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double delz2 = x[i3][2] - x[i2][2];
|
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domain->minimum_image(delx2,dely2,delz2);
|
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double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
|
|
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double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
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c /= r1*r2;
|
|
if (c > 1.0) c = 1.0;
|
|
if (c < -1.0) c = -1.0;
|
|
|
|
double s = sqrt(1.0 - c*c);
|
|
if (s < SMALL) s = SMALL;
|
|
s = 1.0/s;
|
|
|
|
double dtheta = acos(c) - theta0[type];
|
|
double dtheta2 = dtheta*dtheta;
|
|
double dtheta3 = dtheta2*dtheta;
|
|
double dtheta4 = dtheta3*dtheta;
|
|
double dtheta5 = dtheta4*dtheta;
|
|
double dtheta6 = dtheta5*dtheta;
|
|
|
|
double energy = k2[type]*dtheta2 + k3[type]*dtheta3 + k4[type]*dtheta4
|
|
+ k5[type]*dtheta5 + k6[type]*dtheta6;
|
|
|
|
return energy;
|
|
}
|