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lammps/src/CLASS2/dihedral_class2.cpp
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dihedral_class2.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "dihedral_class2.h"
#include "atom.h"
#include "neighbor.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.0000001
/* ---------------------------------------------------------------------- */
DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
DihedralClass2::~DihedralClass2()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(setflag_d);
memory->sfree(setflag_mbt);
memory->sfree(setflag_ebt);
memory->sfree(setflag_at);
memory->sfree(setflag_aat);
memory->sfree(setflag_bb13t);
memory->sfree(k1);
memory->sfree(k2);
memory->sfree(k3);
memory->sfree(phi1);
memory->sfree(phi2);
memory->sfree(phi3);
memory->sfree(mbt_f1);
memory->sfree(mbt_f2);
memory->sfree(mbt_f3);
memory->sfree(mbt_r0);
memory->sfree(ebt_f1_1);
memory->sfree(ebt_f2_1);
memory->sfree(ebt_f3_1);
memory->sfree(ebt_r0_1);
memory->sfree(ebt_f1_2);
memory->sfree(ebt_f2_2);
memory->sfree(ebt_f3_2);
memory->sfree(ebt_r0_2);
memory->sfree(at_f1_1);
memory->sfree(at_f2_1);
memory->sfree(at_f3_1);
memory->sfree(at_theta0_1);
memory->sfree(at_f1_2);
memory->sfree(at_f2_2);
memory->sfree(at_f3_2);
memory->sfree(at_theta0_2);
memory->sfree(aat_k);
memory->sfree(aat_theta0_1);
memory->sfree(aat_theta0_2);
memory->sfree(bb13t_k);
memory->sfree(bb13t_r10);
memory->sfree(bb13t_r30);
}
}
/* ---------------------------------------------------------------------- */
void DihedralClass2::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,j,k,n,type,factor;
double rfactor;
double delx1,dely1,delz1,dely2,delz2,delx2m,dely2m,delz2m;
double delx2,dely3,delz3,r1mag2,r1,r2mag2,r2,r3mag2,r3;
double sb1,rb1,sb2,rb2,sb3,rb3,c0,r12c1;
double r12c2,costh12,costh13,costh23,sc1,sc2,s1,s2,c;
double cosphi,phi,sinphi,a11,a22,a33,a12,a13,a23,sx1,sx2;
double sx12,sy1,sy2,sy12,sz1,sz2,sz12,dphi1,dphi2,dphi3;
double de_dihedral,t1,t2,t3,t4,cos2phi,cos3phi,bt1,bt2;
double bt3,sumbte,db,sumbtf,at1,at2,at3,da,da1,da2,r1_0;
double r3_0,dr1,dr2,tk1,tk2,vx1,vx2,vx3,vy1,vy2,vy3,vz1;
double vz2,vz3,delx3,s12,sin2;
double dcosphidr[4][3],dphidr[4][3],dbonddr[3][4][3],dthetadr[2][4][3];
double fabcd[4][3];
energy = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
if (newton_bond) factor = 4;
else {
factor = 0;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
if (i3 < nlocal) factor++;
if (i4 < nlocal) factor++;
}
rfactor = 0.25 * factor;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(&delx1,&dely1,&delz1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(&delx2,&dely2,&delz2);
delx2m = -delx2;
dely2m = -dely2;
delz2m = -delz2;
domain->minimum_image(&delx2m,&dely2m,&delz2m);
// 3rd bond
delx3 = x[i4][0] - x[i3][0];
dely3 = x[i4][1] - x[i3][1];
delz3 = x[i4][2] - x[i3][2];
domain->minimum_image(&delx3,&dely3,&delz3);
// distances
r1mag2 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(r1mag2);
r2mag2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(r2mag2);
r3mag2 = delx3*delx3 + dely3*dely3 + delz3*delz3;
r3 = sqrt(r3mag2);
sb1 = 1.0/r1mag2;
rb1 = 1.0/r1;
sb2 = 1.0/r2mag2;
rb2 = 1.0/r2;
sb3 = 1.0/r3mag2;
rb3 = 1.0/r3;
c0 = (delx1*delx3 + dely1*dely3 + delz1*delz3) * rb1*rb3;
// angles
r12c1 = rb1*rb2;
r12c2 = rb2*rb3;
costh12 = (delx1*delx2 + dely1*dely2 + delz1*delz2) * r12c1;
costh13 = c0;
costh23 = (delx2m*delx3 + dely2m*dely3 + delz2m*delz3) * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - costh12*costh12,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - costh23*costh23,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + costh12*costh23) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
fprintf(screen,"Dihedral problem: %d %d %d %d %d %d\n",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
cosphi = c;
phi = acos(c);
sinphi = sqrt(1.0 - c*c);
sinphi = MAX(sinphi,SMALL);
a11 = -c*sb1*s1;
a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
a33 = -c*sb3*s2;
a12 = r12c1 * (costh12*c*s1 + costh23*s12);
a13 = rb1*rb3*s12;
a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
sx1 = a11*delx1 + a12*delx2 + a13*delx3;
sx2 = a12*delx1 + a22*delx2 + a23*delx3;
sx12 = a13*delx1 + a23*delx2 + a33*delx3;
sy1 = a11*dely1 + a12*dely2 + a13*dely3;
sy2 = a12*dely1 + a22*dely2 + a23*dely3;
sy12 = a13*dely1 + a23*dely2 + a33*dely3;
sz1 = a11*delz1 + a12*delz2 + a13*delz3;
sz2 = a12*delz1 + a22*delz2 + a23*delz3;
sz12 = a13*delz1 + a23*delz2 + a33*delz3;
// set up d(cos(phi))/d(r) and dphi/dr arrays
dcosphidr[0][0] = -sx1;
dcosphidr[0][1] = -sy1;
dcosphidr[0][2] = -sz1;
dcosphidr[1][0] = sx2 + sx1;
dcosphidr[1][1] = sy2 + sy1;
dcosphidr[1][2] = sz2 + sz1;
dcosphidr[2][0] = sx12 - sx2;
dcosphidr[2][1] = sy12 - sy2;
dcosphidr[2][2] = sz12 - sz2;
dcosphidr[3][0] = -sx12;
dcosphidr[3][1] = -sy12;
dcosphidr[3][2] = -sz12;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
dphi1 = phi - phi1[type];
dphi2 = 2.0*phi - phi2[type];
dphi3 = 3.0*phi - phi3[type];
if (eflag) energy += rfactor * (k1[type]*(1.0 - cos(dphi1)) +
k2[type]*(1.0 - cos(dphi2)) +
k3[type]*(1.0 - cos(dphi3)));
de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
3.0*k3[type]*sin(dphi3);
// torsion forces on all 4 atoms
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
// bond1
dbonddr[0][0][0] = delx1 / r1;
dbonddr[0][0][1] = dely1 / r1;
dbonddr[0][0][2] = delz1 / r1;
dbonddr[0][1][0] = -delx1 / r1;
dbonddr[0][1][1] = -dely1 / r1;
dbonddr[0][1][2] = -delz1 / r1;
// bond2
dbonddr[1][1][0] = delx2 / r2;
dbonddr[1][1][1] = dely2 / r2;
dbonddr[1][1][2] = delz2 / r2;
dbonddr[1][2][0] = -delx2 / r2;
dbonddr[1][2][1] = -dely2 / r2;
dbonddr[1][2][2] = -delz2 / r2;
// bond3
dbonddr[2][2][0] = delx3 / r3;
dbonddr[2][2][1] = dely3 / r3;
dbonddr[2][2][2] = delz3 / r3;
dbonddr[2][3][0] = -delx3 / r3;
dbonddr[2][3][1] = -dely3 / r3;
dbonddr[2][3][2] = -delz3 / r3;
// set up d(theta)/d(r) array
// dthetadr(i,j,k) = angle i, atom j, coordinate k
for (i = 0; i < 2; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
t1 = costh12 / r1mag2;
t2 = costh23 / r2mag2;
t3 = costh12 / r2mag2;
t4 = costh23 / r3mag2;
// angle12
dthetadr[0][0][0] = sc1 * ((t1 * delx1) - (delx2 * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * dely1) - (dely2 * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * delz1) - (delz2 * r12c1));
dthetadr[0][1][0] = sc1 * ((-t1 * delx1) + (delx2 * r12c1) +
(-t3 * delx2) + (delx1 * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * dely1) + (dely2 * r12c1) +
(-t3 * dely2) + (dely1 * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * delz1) + (delz2 * r12c1) +
(-t3 * delz2) + (delz1 * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * delx2) - (delx1 * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * dely2) - (dely1 * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * delz2) - (delz1 * r12c1));
// angle23
dthetadr[1][1][0] = sc2 * ((t2 * delx2) + (delx3 * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * dely2) + (dely3 * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * delz2) + (delz3 * r12c2));
dthetadr[1][2][0] = sc2 * ((-t2 * delx2) - (delx3 * r12c2) +
(t4 * delx3) + (delx2 * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * dely2) - (dely3 * r12c2) +
(t4 * dely3) + (dely2 * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * delz2) - (delz3 * r12c2) +
(t4 * delz3) + (delz2 * r12c2));
dthetadr[1][3][0] = -sc2 * ((t4 * delx3) + (delx2 * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * dely3) + (dely2 * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * delz3) + (delz2 * r12c2));
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
cos2phi = cos(2.0*phi);
cos3phi = cos(3.0*phi);
bt1 = mbt_f1[type] * cosphi;
bt2 = mbt_f2[type] * cos2phi;
bt3 = mbt_f3[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r2 - mbt_r0[type];
if (eflag) energy += rfactor * db * sumbte;
// force on bond2
bt1 = -mbt_f1[type] * sinphi;
bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
bt1 = ebt_f1_1[type] * cosphi;
bt2 = ebt_f2_1[type] * cos2phi;
bt3 = ebt_f3_1[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r1 - ebt_r0_1[type];
if (eflag) energy += rfactor * db * (bt1+bt2+bt3);
// force on bond1
bt1 = ebt_f1_1[type] * sinphi;
bt2 = 2.0 * ebt_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * ebt_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
bt1 = ebt_f1_2[type] * cosphi;
bt2 = ebt_f2_2[type] * cos2phi;
bt3 = ebt_f3_2[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r3 - ebt_r0_2[type];
if (eflag) energy += rfactor * db * (bt1+bt2+bt3);
// force on bond3
bt1 = -ebt_f1_2[type] * sinphi;
bt2 = -2.0 * ebt_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * ebt_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
at1 = at_f1_1[type] * cosphi;
at2 = at_f2_1[type] * cos2phi;
at3 = at_f3_1[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh12) - at_theta0_1[type];
if (eflag) energy += rfactor * da * (at1+at2+at3);
// force on angle1
bt1 = at_f1_1[type] * sinphi;
bt2 = 2.0 * at_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * at_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
at1 = at_f1_2[type] * cosphi;
at2 = at_f2_2[type] * cos2phi;
at3 = at_f3_2[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh23) - at_theta0_2[type];
if (eflag) energy += rfactor *da * (at1+at2+at3);
// force on angle2
bt1 = -at_f1_2[type] * sinphi;
bt2 = -2.0 * at_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * at_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
da1 = acos(costh12) - aat_theta0_1[type];
da2 = acos(costh23) - aat_theta0_2[type];
// energy
if (eflag) energy += rfactor * aat_k[type]*da1*da2*cosphi;
// force
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
if (fabs(bb13t_k[type]) > SMALL) {
r1_0 = bb13t_r10[type];
r3_0 = bb13t_r30[type];
dr1 = r1 - r1_0;
dr2 = r3 - r3_0;
tk1 = -bb13t_k[type] * dr1 / r3;
tk2 = -bb13t_k[type] * dr2 / r1;
if (eflag) energy += rfactor * bb13t_k[type]*dr1*dr2;
fabcd[0][0] += tk2 * delx1;
fabcd[0][1] += tk2 * dely1;
fabcd[0][2] += tk2 * delz1;
fabcd[1][0] -= tk2 * delx1;
fabcd[1][1] -= tk2 * dely1;
fabcd[1][2] -= tk2 * delz1;
fabcd[2][0] -= tk1 * delx3;
fabcd[2][1] -= tk1 * dely3;
fabcd[2][2] -= tk1 * delz3;
fabcd[3][0] += tk1 * delx3;
fabcd[3][1] += tk1 * dely3;
fabcd[3][2] += tk1 * delz3;
}
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
}
// virial contribution
if (vflag) {
vx1 = fabcd[0][0];
vx2 = fabcd[2][0] + fabcd[3][0];
vx3 = fabcd[3][0];
vy1 = fabcd[0][1];
vy2 = fabcd[2][1] + fabcd[3][1];
vy3 = fabcd[3][1];
vz1 = fabcd[0][2];
vz2 = fabcd[2][2] + fabcd[3][2];
vz3 = fabcd[3][2];
virial[0] += rfactor * (delx1*vx1 + delx2*vx2 + delx3*vx3);
virial[1] += rfactor * (dely1*vy1 + dely2*vy2 + dely3*vy3);
virial[2] += rfactor * (delz1*vz1 + delz2*vz2 + delz3*vz3);
virial[3] += rfactor * (delx1*vy1 + delx2*vy2 + delx3*vy3);
virial[4] += rfactor * (delx1*vz1 + delx2*vz2 + delx3*vz3);
virial[5] += rfactor * (dely1*vz1 + dely2*vz2 + dely3*vz3);
}
}
}
/* ---------------------------------------------------------------------- */
void DihedralClass2::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
k1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k1");
k2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k2");
k3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k3");
phi1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi1");
phi2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi2");
phi3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi3");
mbt_f1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f1");
mbt_f2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f2");
mbt_f3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f3");
mbt_r0 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_r0");
ebt_f1_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f1_1");
ebt_f2_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f2_1");
ebt_f3_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f3_1");
ebt_r0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_r0_1");
ebt_f1_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f1_2");
ebt_f2_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f2_2");
ebt_f3_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f3_2");
ebt_r0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_r0_2");
at_f1_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f1_1");
at_f2_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f2_1");
at_f3_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f3_1");
at_theta0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_theta0_1");
at_f1_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f1_2");
at_f2_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f2_2");
at_f3_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f3_2");
at_theta0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_theta0_2");
aat_k = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:aat_k");
aat_theta0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:aat_theta0_1");
aat_theta0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:aat_theta0_2");
bb13t_k = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_k");
bb13t_r10 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_r10");
bb13t_r30 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_r30");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
setflag_d = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_d");
setflag_mbt = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_mbt");
setflag_ebt = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_ebt");
setflag_at = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_at");
setflag_aat = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_aat");
setflag_bb13t = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_bb13t");
for (int i = 1; i <= n; i++)
setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
setflag_at[i] = setflag_aat[i] = setflag_bb13t[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
which = 0 -> Dihedral coeffs
which = 1 -> MiddleBondTorsion coeffs
which = 2 -> EndBondTorsion coeffs
which = 3 -> AngleTorsion coeffs
which = 4 -> AngleAngleTorsion coeffs
which = 5 -> BondBond13Torsion coeffs
------------------------------------------------------------------------- */
void DihedralClass2::coeff(int which, int narg, char **arg)
{
if (which < 0 || which > 5)
error->all("Invalid coeffs for this dihedral style");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
int count = 0;
if (which == 0) {
if (narg != 7) error->all("Incorrect args for dihedral coefficients");
double k1_one = atof(arg[1]);
double phi1_one = atof(arg[2]);
double k2_one = atof(arg[3]);
double phi2_one = atof(arg[4]);
double k3_one = atof(arg[5]);
double phi3_one = atof(arg[6]);
// convert phi's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
k1[i] = k1_one;
phi1[i] = phi1_one/180.0 * PI;
k2[i] = k2_one;
phi2[i] = phi2_one/180.0 * PI;
k3[i] = k3_one;
phi3[i] = phi3_one/180.0 * PI;
setflag_d[i] = 1;
count++;
}
}
if (which == 1) {
if (narg != 5) error->all("Incorrect args for dihedral coefficients");
double f1_one = atof(arg[1]);
double f2_one = atof(arg[2]);
double f3_one = atof(arg[3]);
double r0_one = atof(arg[4]);
for (int i = ilo; i <= ihi; i++) {
mbt_f1[i] = f1_one;
mbt_f2[i] = f2_one;
mbt_f3[i] = f3_one;
mbt_r0[i] = r0_one;
setflag_mbt[i] = 1;
count++;
}
}
if (which == 2) {
if (narg != 9) error->all("Incorrect args for dihedral coefficients");
double f1_1_one = atof(arg[1]);
double f2_1_one = atof(arg[2]);
double f3_1_one = atof(arg[3]);
double f1_2_one = atof(arg[4]);
double f2_2_one = atof(arg[5]);
double f3_2_one = atof(arg[6]);
double r0_1_one = atof(arg[7]);
double r0_2_one = atof(arg[8]);
for (int i = ilo; i <= ihi; i++) {
ebt_f1_1[i] = f1_1_one;
ebt_f2_1[i] = f2_1_one;
ebt_f3_1[i] = f3_1_one;
ebt_f1_2[i] = f1_2_one;
ebt_f2_2[i] = f2_2_one;
ebt_f3_2[i] = f3_2_one;
ebt_r0_1[i] = r0_1_one;
ebt_r0_2[i] = r0_2_one;
setflag_ebt[i] = 1;
count++;
}
}
if (which == 3) {
if (narg != 9) error->all("Incorrect args for dihedral coefficients");
double f1_1_one = atof(arg[1]);
double f2_1_one = atof(arg[2]);
double f3_1_one = atof(arg[3]);
double f1_2_one = atof(arg[4]);
double f2_2_one = atof(arg[5]);
double f3_2_one = atof(arg[6]);
double theta0_1_one = atof(arg[7]);
double theta0_2_one = atof(arg[8]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
at_f1_1[i] = f1_1_one;
at_f2_1[i] = f2_1_one;
at_f3_1[i] = f3_1_one;
at_f1_2[i] = f1_2_one;
at_f2_2[i] = f2_2_one;
at_f3_2[i] = f3_2_one;
at_theta0_1[i] = theta0_1_one/180.0 * PI;
at_theta0_2[i] = theta0_2_one/180.0 * PI;
setflag_at[i] = 1;
count++;
}
}
if (which == 4) {
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
double k_one = atof(arg[1]);
double theta0_1_one = atof(arg[2]);
double theta0_2_one = atof(arg[3]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
aat_k[i] = k_one;
aat_theta0_1[i] = theta0_1_one/180.0 * PI;
aat_theta0_2[i] = theta0_2_one/180.0 * PI;
setflag_aat[i] = 1;
count++;
}
}
if (which == 5) {
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
double k_one = atof(arg[1]);
double r10_one = atof(arg[2]);
double r30_one = atof(arg[3]);
for (int i = ilo; i <= ihi; i++) {
bb13t_k[i] = k_one;
bb13t_r10[i] = r10_one;
bb13t_r30[i] = r30_one;
setflag_bb13t[i] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
for (int i = ilo; i <= ihi; i++)
if (setflag_d[i] == 1 && setflag_mbt[i] == 1 && setflag_ebt[i] == 1 &&
setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralClass2::write_restart(FILE *fp)
{
fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralClass2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_r0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f1_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f2_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f3_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_r0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f1_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f2_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f3_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_r0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f1_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f2_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f3_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f1_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f2_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f3_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_r10[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_r30[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
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