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debug for improper amoeba

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This commit is contained in:
Steve Plimpton
2022-04-13 17:05:44 -06:00
parent 578a9ab161
commit 2c7badfa43
3 changed files with 14 additions and 8 deletions
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2
examples/amoeba/in.ubiquitin
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@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba include angle
pair_style amoeba include improper
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes

12
src/AMOEBA/angle_amoeba.cpp
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@ -116,17 +116,17 @@ void AngleAmoeba::compute(int eflag, int vflag)
if (enable_angle) {
tflag = pflag[type];
//if (tflag && nspecial[i2][0] == 3)
// tinker_anglep(i1,i2,i3,type,eflag);
//else
// tinker_angle(i1,i2,i3,type,eflag);
if (tflag && nspecial[i2][0] == 3)
tinker_anglep(i1,i2,i3,type,eflag);
else
tinker_angle(i1,i2,i3,type,eflag);
// bondangle = bond-stretch cross term in Tinker
if (ba_k1[type] != 0.0)
tinker_bondangle(i1,i2,i3,type,eflag);
}
// Urey-Bradley H-H bond term within water molecules
if (enable_urey) {

8
src/AMOEBA/improper_amoeba.cpp
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@ -197,7 +197,13 @@ void ImproperAmoeba::compute(int eflag, int vflag)
fd[2] = dedcos * (dccdzid+deedzid);
fb[0] = -fa[0] - fc[0] - fd[0];
fb[1] = -fa[1] - fc[1] - fd[1];
fb[2] = -fa[1] - fc[2] - fd[2];
fb[2] = -fa[2] - fc[2] - fd[2];
printf("IMP DBAC %d %d %d %d: angle %g eng %g dedcos %g "
"fD %g %g %g fA %g %g %g fC %g %g %g\n",
atom->tag[id],atom->tag[ib],atom->tag[ia],atom->tag[ic],
angle,e,dedcos,fd[0],fd[1],fd[2],fa[0],fa[1],fa[2],
fc[0],fc[1],fc[2]);
// apply force to each of 4 atoms