git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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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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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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@ -114,7 +114,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
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// require atom map to lookup atom IDs
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if (atom->map_style == 0)
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if (atom->map_style == 0)
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error->all(FLERR,"Fix restrain requires an atom map, see atom_modify");
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}
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@ -227,9 +227,9 @@ void FixRestrain::restrain_bond(int m)
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if (i1 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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ids[m][0],ids[m][1],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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ids[m][0],ids[m][1],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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} else {
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@ -237,38 +237,38 @@ void FixRestrain::restrain_bond(int m)
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if (i1 == -1 || i2 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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ids[m][0],ids[m][1],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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ids[m][0],ids[m][1],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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}
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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domain->minimum_image(delx,dely,delz);
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rsq = delx*delx + dely*dely + delz*delz;
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r = sqrt(rsq);
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dr = r - target[m];
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rk = k * dr;
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// force & energy
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if (r > 0.0) fbond = -2.0*rk/r;
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else fbond = 0.0;
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energy = rk*dr;
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// apply force to each of 2 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx*fbond;
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f[i1][1] += dely*fbond;
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f[i1][2] += delz*fbond;
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= delx*fbond;
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f[i2][1] -= dely*fbond;
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@ -303,97 +303,97 @@ void FixRestrain::restrain_angle(int m)
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// newton_bond on: only processor owning i2 computes restraint
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// newton_bond off: only processors owning any of i1-i3 computes restraint
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if (newton_bond) {
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if (i2 == -1 || i2 >= nlocal) return;
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if (i1 == -1 || i3 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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} else {
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if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
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(i3 == -1 || i3 >= nlocal)) return;
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(i3 == -1 || i3 >= nlocal)) return;
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if (i1 == -1 || i2 == -1 || i3 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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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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domain->minimum_image(delx1,dely1,delz1);
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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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domain->minimum_image(delx2,dely2,delz2);
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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
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dtheta = acos(c) - target[m];
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tk = k * dtheta;
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energy = tk*dtheta;
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a = -2.0 * tk * 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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// 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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@ -413,7 +413,7 @@ void FixRestrain::restrain_dihedral(int m)
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double f1[3],f2[3],f3[3],f4[3];
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double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
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double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
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double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
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double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
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double c,s,p,sx2,sy2,sz2;
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double **x = atom->x;
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@ -438,22 +438,22 @@ void FixRestrain::restrain_dihedral(int m)
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if (i1 == -1 || i3 == -1 || i4 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],ids[m][3],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],ids[m][3],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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} else {
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if ((i1 == -1 || i1 >= nlocal) && (i2 == -1 || i2 >= nlocal) &&
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(i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return;
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(i3 == -1 || i3 >= nlocal) && (i4 == -1 || i3 >= nlocal)) return;
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if (i1 == -1 || i2 == -1 || i3 == -1 || i4 == -1) {
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char str[128];
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sprintf(str,
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],ids[m][3],
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comm->me,update->ntimestep);
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"Restrain atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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ids[m][0],ids[m][1],ids[m][2],ids[m][3],
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comm->me,update->ntimestep);
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error->one(FLERR,str);
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}
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}
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@ -464,96 +464,96 @@ void FixRestrain::restrain_dihedral(int m)
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vb1y = x[i1][1] - x[i2][1];
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vb1z = x[i1][2] - x[i2][2];
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domain->minimum_image(vb1x,vb1y,vb1z);
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// 2nd bond
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vb2x = x[i3][0] - x[i2][0];
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vb2y = x[i3][1] - x[i2][1];
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vb2z = x[i3][2] - x[i2][2];
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domain->minimum_image(vb2x,vb2y,vb2z);
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vb2xm = -vb2x;
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vb2ym = -vb2y;
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vb2zm = -vb2z;
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domain->minimum_image(vb2xm,vb2ym,vb2zm);
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// 3rd bond
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vb3x = x[i4][0] - x[i3][0];
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vb3y = x[i4][1] - x[i3][1];
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vb3z = x[i4][2] - x[i3][2];
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domain->minimum_image(vb3x,vb3y,vb3z);
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ax = vb1y*vb2zm - vb1z*vb2ym;
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ay = vb1z*vb2xm - vb1x*vb2zm;
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az = vb1x*vb2ym - vb1y*vb2xm;
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bx = vb3y*vb2zm - vb3z*vb2ym;
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by = vb3z*vb2xm - vb3x*vb2zm;
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bz = vb3x*vb2ym - vb3y*vb2xm;
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rasq = ax*ax + ay*ay + az*az;
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rbsq = bx*bx + by*by + bz*bz;
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rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
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rg = sqrt(rgsq);
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rginv = ra2inv = rb2inv = 0.0;
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if (rg > 0) rginv = 1.0/rg;
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if (rasq > 0) ra2inv = 1.0/rasq;
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if (rbsq > 0) rb2inv = 1.0/rbsq;
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rabinv = sqrt(ra2inv*rb2inv);
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c = (ax*bx + ay*by + az*bz)*rabinv;
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s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
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// error check
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if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
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int me;
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MPI_Comm_rank(world,&me);
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if (screen) {
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char str[128];
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sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " %d %d %d %d",
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me,update->ntimestep,
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atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
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me,update->ntimestep,
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atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
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error->warning(FLERR,str);
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fprintf(screen," 1st atom: %d %g %g %g\n",
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me,x[i1][0],x[i1][1],x[i1][2]);
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me,x[i1][0],x[i1][1],x[i1][2]);
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fprintf(screen," 2nd atom: %d %g %g %g\n",
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me,x[i2][0],x[i2][1],x[i2][2]);
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me,x[i2][0],x[i2][1],x[i2][2]);
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fprintf(screen," 3rd atom: %d %g %g %g\n",
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me,x[i3][0],x[i3][1],x[i3][2]);
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me,x[i3][0],x[i3][1],x[i3][2]);
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fprintf(screen," 4th atom: %d %g %g %g\n",
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me,x[i4][0],x[i4][1],x[i4][2]);
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me,x[i4][0],x[i4][1],x[i4][2]);
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}
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}
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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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mult = 1; // multiplicity
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p = 1.0;
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df1 = 0.0;
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for (i = 0; i < mult; i++) {
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ddf1 = p*c - df1*s;
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df1 = p*s + df1*c;
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p = ddf1;
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}
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p = p*cos_target[m] + df1*sin_target[m];
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df1 = df1*cos_target[m] - ddf1*sin_target[m];
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df1 *= -mult;
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p += 1.0;
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energy = k * p;
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energy = k * p;
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fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
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hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
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fga = fg*ra2inv*rginv;
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hgb = hg*rb2inv*rginv;
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gaa = -ra2inv*rg;
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gbb = rb2inv*rg;
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dtfx = gaa*ax;
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dtfy = gaa*ay;
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dtfz = gaa*az;
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@ -563,49 +563,49 @@ void FixRestrain::restrain_dihedral(int m)
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dthx = gbb*bx;
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dthy = gbb*by;
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dthz = gbb*bz;
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df = -k * df1;
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sx2 = df*dtgx;
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sy2 = df*dtgy;
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sz2 = df*dtgz;
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f1[0] = df*dtfx;
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f1[1] = df*dtfy;
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f1[2] = df*dtfz;
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f2[0] = sx2 - f1[0];
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f2[1] = sy2 - f1[1];
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f2[2] = sz2 - f1[2];
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f4[0] = df*dthx;
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f4[1] = df*dthy;
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f4[2] = df*dthz;
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f3[0] = -sx2 - f4[0];
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f3[1] = -sy2 - f4[1];
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f3[2] = -sz2 - f4[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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Reference in New Issue
Block a user