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angle amoeba with cross-term

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This commit is contained in:
Steve Plimpton
2021-12-16 08:38:23 -07:00
parent c479d78854
commit 7bfc2f2b8f
2 changed files with 106 additions and 95 deletions
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1
examples/amoeba/in.ubiquitin
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@ -2,6 +2,7 @@
units real units real
boundary p p p boundary p p p
atom_modify sort 0 0.0
atom_style amoeba atom_style amoeba

22
src/AMOEBA/angle_amoeba.cpp
View File

@ -111,8 +111,8 @@ void AngleAmoeba::compute(int eflag, int vflag)
if (tflag && nspecial[i2][0] == 3) { if (tflag && nspecial[i2][0] == 3) {
anglep(i1,i2,i3,type,eflag); anglep(i1,i2,i3,type,eflag);
continue;
} } else {
// 1st bond // 1st bond
@ -171,11 +171,19 @@ void AngleAmoeba::compute(int eflag, int vflag)
//if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 + //if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
// k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6; // k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
eangle = 0.0; }
// force & energy for bond-angle term // force & energy for bond-angle term
// bond-stretch cross term in Tinker // bond-stretch cross term in Tinker
if (ba_k1[type] > 0.0) {
//NOTE: depends on r1,r2,c,s,rsq1,rsq2,delxyz1,delxyz2,dtheta
dr1 = r1 - ba_r1[type]; dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type]; dr2 = r2 - ba_r2[type];
@ -215,10 +223,12 @@ void AngleAmoeba::compute(int eflag, int vflag)
f3[1] -= vy21 + b2*dely2 + vy22; f3[1] -= vy21 + b2*dely2 + vy22;
f3[2] -= vz21 + b2*delz2 + vz22; f3[2] -= vz21 + b2*delz2 + vz22;
if (eflag) eangle += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta; //if (eflag) eangle += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
if (eflag) eangle = ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
printf("Stretch-Bend: %ld %d %d: eng %g\n", printf("Stretch-Bend: %ld %d %d: eng %g\n",
atom->tag[i1],atom->tag[i2],atom->tag[i3],eangle); atom->tag[i1],atom->tag[i2],atom->tag[i3],eangle);
}
// apply force to each of 3 atoms // apply force to each of 3 atoms
@ -350,8 +360,8 @@ void AngleAmoeba::anglep(int i1, int i2, int i3, int type, int eflag)
deddt = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 + deddt = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 + 6.0*k6[type]*dtheta5; 4.0*k4[type]*dtheta3 + 5.0*k5[type]*dtheta4 + 6.0*k6[type]*dtheta5;
if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 + //if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 +
k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6; // k4[type]*dtheta4 + k5[type]*dtheta5 + k6[type]*dtheta6;
// chain rule terms for first derivative components // chain rule terms for first derivative components