fleshing out bitorsion fix
This commit is contained in:
Steve Plimpton
@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
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fix pit pitorsions PiTorsions &
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fix bit bitorsions BiTorsions
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pair_style amoeba exclude bitorsion
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pair_style amoeba
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pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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@ -37,6 +37,27 @@ using namespace MathConst;
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#define LB_FACTOR 1.5
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#define MAXLINE 1024
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// spline weighting factors
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static constexpr double WT[16][16] = {
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{ 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
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{-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0, 0.0, 0.0, 0.0, 0.0},
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{ 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0,-3.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0,-2.0, 0.0, 0.0,-1.0},
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{ 0.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0,-2.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0},
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{-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,-3.0, 3.0, 0.0, 0.0,-2.0,-1.0, 0.0, 0.0},
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{ 9.0,-9.0, 9.0,-9.0, 6.0, 3.0,-3.0,-6.0, 6.0,-6.0,-3.0, 3.0, 4.0, 2.0, 1.0, 2.0},
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{-6.0, 6.0,-6.0, 6.0,-4.0,-2.0, 2.0, 4.0,-3.0, 3.0, 3.0,-3.0,-2.0,-1.0,-1.0,-2.0},
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{ 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
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{ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.0,-2.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0},
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{-6.0, 6.0,-6.0, 6.0,-3.0,-3.0, 3.0, 3.0,-4.0, 4.0, 2.0,-2.0,-2.0,-2.0,-1.0,-1.0},
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{ 4.0,-4.0, 4.0,-4.0, 2.0, 2.0,-2.0,-2.0, 2.0,-2.0,-2.0, 2.0, 1.0, 1.0, 1.0, 1.0}
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};
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/* ---------------------------------------------------------------------- */
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FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) :
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@ -499,10 +520,12 @@ void FixAmoebaBiTorsion::post_force(int vflag)
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bcuint1(ftt,ft1,ft2,ft12,x1l,x1u,y1l,y1u,value1,value2,
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e,dedang1,dedang2);
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double ttorunit = 1.0;
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e *= ttorunit;
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dedang1 = sign * ttorunit * radian2degree * dedang1;
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dedang2 = sign * ttorunit * radian2degree * dedang2;
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printf("BiTorsion %d %d %d %d %d: angle12 %g %g: eng %g\n",
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atom->tag[ia],atom->tag[ib],atom->tag[ic],atom->tag[id],atom->tag[ie],
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angle1,angle2,e);
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dedang1 = sign * radian2degree * dedang1;
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dedang2 = sign * radian2degree * dedang2;
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// fraction of energy for each atom
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@ -870,7 +893,7 @@ void FixAmoebaBiTorsion::create_splines()
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else
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nspline(ny-1,tmp1,tmp2,bs,cs,tmp3,tmp4,tmp5,tmp6,tmp7);
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for (int j = 0; i < ny; j++)
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for (int j = 0; j < ny; j++)
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tby[itype][j*nx+i] = bs[j];
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}
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@ -888,7 +911,7 @@ void FixAmoebaBiTorsion::create_splines()
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else
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nspline(ny-1,tmp1,tmp2,bs,cs,tmp3,tmp4,tmp5,tmp6,tmp7);
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for (int j = 0; i < ny; j++)
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for (int j = 0; j < ny; j++)
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tbxy[itype][j*nx+i] = bs[j];
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}
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}
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@ -908,18 +931,8 @@ void FixAmoebaBiTorsion::create_splines()
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}
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/* ----------------------------------------------------------------------
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::cspline(int n, double *xn, double *fn,
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double *b, double *c, double *d,
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double *h, double *du, double *dm,
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double *rc, double *rs)
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{
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}
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/* ----------------------------------------------------------------------
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Tinker method
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nspline() computes coefficients for an nonperiodic cubic spline
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Tinker method nspline()
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computes coefficients for an nonperiodic cubic spline
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with natural boundary conditions where the first and last second
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derivatives are already known
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all vectors are of length n+1 and are indexed from 0 to n inclusive
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@ -990,6 +1003,220 @@ void FixAmoebaBiTorsion::nspline(int n, double *x0, double *y0,
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s2[i] = 6.0*(y0[i+1]-y0[i])/(h[i]*h[i]) - 4.0*s1[i]/h[i] - 2.0*s1[i+1]/h[i];
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}
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/* ----------------------------------------------------------------------
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Tinker method cspline()
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computes coefficients for an periodic interpolating cubic spline
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all vectors are of length n+1 and are indexed from 0 to n inclusive
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n,xn,fn are inputs
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rest of args are outputs
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::cspline(int n, double *xn, double *fn,
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double *b, double *c, double *d,
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double *h, double *du, double *dm,
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double *rc, double *rs)
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{
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int i;
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double temp1,temp2;
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double average = 0.5 * (fn[0] + fn[n]);
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fn[0] = average;
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fn[n] = average;
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// get auxiliary variables and matrix elements on first call
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for (i = 0; i < n; i++)
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h[i] = xn[i+1] - xn[i];
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h[n] = h[0];
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for (i = 1; i < n; i++)
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du[i] = h[i];
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du[n] = h[0];
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for (i = 1; i <= n; i++)
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dm[i] = 2.0 * (h[i-1]+h[i]);
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// compute the right hand side
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temp1 = (fn[1]-fn[0]) / h[0];
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for (i = 1; i < n; i++) {
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temp2 = (fn[i+1]-fn[i]) / h[i];
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rs[i] = 3.0 * (temp2-temp1);
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temp1 = temp2;
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}
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rs[n] = 3.0 * ((fn[1]-fn[0])/h[0]-temp1);
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// solve the linear system with factorization
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int iflag;
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cytsy(n,dm,du,rc,rs,c,iflag);
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if (iflag != 1) return;
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// compute remaining spline coefficients
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c[0] = c[n];
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for (i = 0; i < n; i++) {
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b[i] = (fn[i+1]-fn[i])/h[i] - h[i]/3.0*(c[i+1]+2.0*c[i]);
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d[i] = (c[i+1]-c[i]) / (3.0*h[i]);
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}
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b[n] = (fn[1]-fn[n])/h[n] - h[n]/3.0*(c[1]+2.0*c[n]);
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}
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/* ----------------------------------------------------------------------
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Tinker method cytsy()
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solve cyclic tridiagonal system
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all vectors are of length n+1 and are indexed from 0 to n inclusive
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n,dm,du are inputs
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du,cr,rs,x,iflag are outputs
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::cytsy(int n, double *dm, double *du,
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double *cr, double *rs, double *x, int &iflag)
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{
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iflag = -2;
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if (n < 3) return;
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cytsyp(n,dm,du,cr,iflag);
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// update and back substitute as necessary
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if (iflag == 1) cytsys(n,dm,du,cr,rs,x);
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}
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/* ----------------------------------------------------------------------
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Tinker method ctsys()
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tridiagonal Cholesky factorization
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all vectors are of length n+1 and are indexed from 0 to n inclusive
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n,dm,du are inputs
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du,cr,iflag are outputs
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::cytsyp(int n, double *dm, double *du,
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double *cr, int &iflag)
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{
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int i;
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double temp1,temp2;
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// set error bound and test for condition n greater than 2
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double eps = 1.0e-8;
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iflag = -2;
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if (n < 3) return;
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// checking to see if matrix is positive definite
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double row = fabs(dm[1]) + fabs(du[1]) + fabs(du[n]);
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if (row == 0.0) {
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iflag = 0;
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return;
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}
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double d = 1.0 / row;
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if (dm[1] < 0.0) {
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iflag = -1;
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return;
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} else if (fabs(dm[1])*d <= eps) {
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iflag = 0;
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return;
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}
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// factoring a while checking for a positive definite and
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// strong nonsingular matrix a
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temp1 = du[1];
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du[1] = du[1] / dm[1];
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cr[1] = du[n] / dm[1];
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for (i = 2; i < n; i++) {
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row = fabs(dm[i]) + fabs(du[i]) + fabs(temp1);
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if (row == 0.0) {
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iflag = 0;
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return;
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}
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d = 1.0 / row;
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dm[i] = dm[i] - temp1*du[i-1];
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if (dm[i] < 0.0) {
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iflag = -1;
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return;
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} else if (abs(dm[i])*d <= eps) {
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iflag = 0;
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return;
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}
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if (i < n-1) {
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cr[i] = -temp1 * cr[i-1] / dm[i];
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temp1 = du[i];
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du[i] = du[i] / dm[i];
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} else {
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temp2 = du[i];
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du[i] = (du[i] - temp1*cr[i-1]) / dm[i];
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}
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}
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row = fabs(du[n]) + fabs(dm[n]) + fabs(temp2);
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if (row == 0.0) {
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iflag = 0;
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return;
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}
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d = 1.0 / row;
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dm[n] = dm[n] - dm[n-1]*du[n-1]*du[n-1];
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temp1 = 0.0;
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for (i = 1; i < n-1; i++)
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temp1 += dm[i]*cr[i]*cr[i];
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dm[n] = dm[n] - temp1;
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if (dm[n] < 0.0) {
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iflag = -1;
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return;
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} else if (fabs(dm[n])*d <= eps) {
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iflag = 0;
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return;
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}
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iflag = 1;
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}
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/* ----------------------------------------------------------------------
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Tinker method cytsys()
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tridiagonal solution from factors
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all vectors are of length n+1 and are indexed from 0 to n inclusive
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n,dm,du,cr are inputs
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rs,x are outputs
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::cytsys(int n, double *dm, double *du,
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double *cr, double *rs, double *x)
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{
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int i;
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// updating phase
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double temp = rs[1];
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rs[1] = temp / dm[1];
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double sum = cr[1] * temp;
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for (i = 2; i < n; i++) {
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temp = rs[i] - du[i-1]*temp;
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rs[i] = temp / dm[i];
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if (i != n-1) sum += cr[i]*temp;
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}
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temp = rs[n] - du[n-1]*temp;
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temp = temp - sum;
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rs[n] = temp / dm[n];
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// back substitution phase
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x[n] = rs[n];
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x[n-1] = rs[n-1] - du[n-1]*x[n];
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for (i = n-2; i > 0; i--)
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x[i] = rs[i] - du[i]*x[i+1] - cr[i]*x[n];
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}
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/* ----------------------------------------------------------------------
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------------------------------------------------------------------------- */
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@ -999,14 +1226,80 @@ void FixAmoebaBiTorsion::chkttor(int ib, int ic, int id,
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}
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/* ----------------------------------------------------------------------
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perform bicubic spline interpolation
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based on Tinker bcuint1.f
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input = all args except last 3
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output = ansy,ansy1,ansy2
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::bcuint1(double *ftt, double *ft1,
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double *ft2, double *ft12,
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double x1l, double x1u, double y1l, double y1u,
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double value1, double value2,
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double &e, double &dedang1, double &dedang2)
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void FixAmoebaBiTorsion::bcuint1(double *y, double *y1,
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double *y2, double *y12,
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double x1l, double x1u, double x2l, double x2u,
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double x1, double x2,
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double &ansy, double &ansy1, double &ansy2)
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{
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double c[4][4];
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// get coefficients, then perform bicubic interpolation
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bcucof(y,y1,y2,y12,x1u-x1l,x2u-x2l,c);
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double t = (x1-x1l) / (x1u-x1l);
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double u = (x2-x2l) / (x2u-x2l);
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ansy = ansy1 = ansy2 = 0.0;
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for (int i = 4; i >= 1; i--) {
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ansy = t*ansy + ((c[i][3]*u+c[i][2])*u+c[i][1])*u + c[i][0];
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ansy1 = u*ansy1 + (3.0*c[3][i]*t+2.0*c[2][i])*t + c[1][i];
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ansy2 = t*ansy2 + (3.0*c[i][3]*u+2.0*c[i][2])*u + c[i][1];
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}
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ansy1 /= x1u-x1l;
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ansy2 /= x2u-x2l;
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}
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/* ----------------------------------------------------------------------
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compute bicubic spline coeffs
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based on Tinker bcucof.f
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input = all args except c
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output = c
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------------------------------------------------------------------------- */
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void FixAmoebaBiTorsion::bcucof(double *y, double *y1, double *y2, double *y12,
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double d1, double d2, double c[4][4])
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{
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int i,j,k;
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double xx;
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double x[16],cl[16];
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// pack a temporary vector of corner values
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double d1d2 = d1 * d2;
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for (i = 0; i < 4; i++) {
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x[i] = y[i];
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x[i+4] = y1[i] * d1;
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x[i+8] = y2[i] * d2;
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x[i+12] = y12[i] * d1d2;
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}
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// matrix multiply by the stored weight table
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for (i = 0; i < 16; i++) {
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xx = 0.0;
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for (k = 0; k < 16; k++)
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xx += WT[i][k]*x[k];
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cl[i] = xx;
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}
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// unpack the result into the coefficient table
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j = 0;
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for (i = 0; i < 4; i++) {
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for (k = 0; k < 4; k++) {
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c[i][k] = cl[j++];
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}
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}
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}
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// ----------------------------------------------------------------------
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@ -1416,7 +1709,7 @@ double FixAmoebaBiTorsion::memory_usage()
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{
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int nmax = atom->nmax;
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double bytes = (double)nmax * sizeof(int); // num_bitorsion
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bytes += (double)nmax*BITORSIONMAX * sizeof(int); // bitorsion_type
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bytes += (double)nmax*BITORSIONMAX * sizeof(int); // bitorsion_type
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bytes += (double)5*nmax*BITORSIONMAX * sizeof(int); // bitorsion_atom 12345
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bytes += (double)6*max_bitorsion_list * sizeof(int); // bitorsion_list
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return bytes;
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@ -101,15 +101,22 @@ class FixAmoebaBiTorsion : public Fix {
|
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|
||||
void read_grid_data(char *);
|
||||
void create_splines();
|
||||
void cspline(int, double *, double *, double *, double *, double *,
|
||||
double *, double *, double *, double *, double *);
|
||||
void nspline(int, double *, double *, double *, double *,
|
||||
double *, double *, double *, double *, double *);
|
||||
void cspline(int, double *, double *, double *, double *, double *,
|
||||
double *, double *, double *, double *, double *);
|
||||
void cytsy(int, double *, double *, double *, double *, double *, int &);
|
||||
void cytsyp(int, double *, double *, double *, int &);
|
||||
void cytsys(int, double *, double *, double *, double *, double *);
|
||||
|
||||
void chkttor(int, int, int, double &, double &, double &);
|
||||
void bcuint1(double *, double *, double *, double *,
|
||||
double, double, double, double, double, double,
|
||||
double &, double &, double &);
|
||||
void bcucof(double *, double *, double *, double *, double, double,
|
||||
double [][4]);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user