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bug fixes

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This commit is contained in:
Steve Plimpton
2022-03-15 09:35:42 -06:00
parent 1d86b3e270
commit 7a32832b88
5 changed files with 19 additions and 30 deletions
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2
examples/amoeba/data.ubiquitin
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@ -14,7 +14,7 @@ LAMMPS data file created from Tinker ubiquitin.xyz and amoeba_ubiquitin.prm file
0 41.91 ylo yhi 0 41.91 ylo yhi
0 41.91 zlo zhi 0 41.91 zlo zhi
6 pitorsion types 6 pitorsion types
106 bitorsions 71 bitorsions
106 pitorsions 106 pitorsions
Masses Masses

7
examples/amoeba/in.ubiquitin
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@ -26,9 +26,10 @@ fix extra2 all property/atom i_polaxe
#read_data data.ubiquitin fix amtype NULL "Tinker Types" #read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" & read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pitorsion "pitorsion types" "PiTorsion Coeffs" & fix pitorsion "pitorsion types" "PiTorsion Coeffs" &
fix pitorsion pitorsions PiTorsions fix pitorsion pitorsions PiTorsions &
fix bitorsion bitorsions BiTorsions
pair_style amoeba include bitorsion pair_style amoeba exclude bitorsion
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
@ -38,7 +39,7 @@ special_bonds lj/coul 0.5 0.5 0.5 one/five yes
compute virial all pressure NULL virial compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*] emol etotal #press c_virial[*]
# zero step run # zero step run

34
src/AMOEBA/fix_bitorsion.cpp
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@ -132,11 +132,9 @@ FixBiTorsion::FixBiTorsion(LAMMPS *lmp, int narg, char **arg) :
max_bitorsion_list = 0; max_bitorsion_list = 0;
bitorsion_list = nullptr; bitorsion_list = nullptr;
// BiTorsion grid data // zero thermo energy
ntypes = 0; ebitorsion = 0.0;
nxgrid,nygrid = nullptr;
btgrid = nullptr;
} }
/* --------------------------------------------------------------------- */ /* --------------------------------------------------------------------- */
@ -166,7 +164,7 @@ FixBiTorsion::~FixBiTorsion()
delete [] nxgrid; delete [] nxgrid;
delete [] nygrid; delete [] nygrid;
for (int itype = 0; itype < ntypes; itype++) for (int itype = 1; itype <= ntypes; itype++)
memory->destroy(btgrid[itype]); memory->destroy(btgrid[itype]);
delete [] btgrid; delete [] btgrid;
} }
@ -304,7 +302,7 @@ void FixBiTorsion::pre_neighbor()
bitorsion_list[nbitorsion_list][2] = atom3; bitorsion_list[nbitorsion_list][2] = atom3;
bitorsion_list[nbitorsion_list][3] = atom4; bitorsion_list[nbitorsion_list][3] = atom4;
bitorsion_list[nbitorsion_list][4] = atom5; bitorsion_list[nbitorsion_list][4] = atom5;
bitorsion_list[nbitorsion_list][6] = bitorsion_type[i][m]; bitorsion_list[nbitorsion_list][5] = bitorsion_type[i][m];
nbitorsion_list++; nbitorsion_list++;
} }
} }
@ -399,7 +397,7 @@ void FixBiTorsion::post_force(int vflag)
id = bitorsion_list[n][3]; id = bitorsion_list[n][3];
ie = bitorsion_list[n][4]; ie = bitorsion_list[n][4];
// NOTE: is a btype ever needed, maybe as index into spline tables? // NOTE: is a btype ever used, i.e. as index into spline tables?
btype = bitorsion_list[n][5]; btype = bitorsion_list[n][5];
@ -721,16 +719,16 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file)
MPI_Bcast(&ntypes,1,MPI_INT,0,world); MPI_Bcast(&ntypes,1,MPI_INT,0,world);
if (ntypes == 0) error->all(FLERR,"Fix bitorsion file has no types"); if (ntypes == 0) error->all(FLERR,"Fix bitorsion file has no types");
btgrid = new double***[ntypes]; btgrid = new double***[ntypes+1];
nxgrid = new int[ntypes]; nxgrid = new int[ntypes+1];
nygrid = new int[ntypes]; nygrid = new int[ntypes+1];
// read one array for each BiTorsion type from file // read one array for each BiTorsion type from file
int tmp,nx,ny; int tmp,nx,ny;
double xgrid,ygrid,value; double xgrid,ygrid,value;
for (int itype = 0; itype < ntypes; itype++) { for (int itype = 1; itype <= ntypes; itype++) {
if (me == 0) { if (me == 0) {
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp);
@ -766,20 +764,6 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file)
} }
if (me == 0) fclose(fp); if (me == 0) fclose(fp);
// DEBUG
for (int i = 0; i < ntypes; i++) {
printf("ITYPE %d NXY %d %d\n",i+1,nxgrid[i],nygrid[i]);
for (int iy = 0; iy < ny; iy++) {
for (int ix = 0; ix < nx; ix++) {
printf(" IXY %d %d, values %g %g %g\n",ix+1,iy+1,
btgrid[i][ix][iy][0],
btgrid[i][ix][iy][1],
btgrid[i][ix][iy][2]);
}
}
}
} }
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------

4
src/AMOEBA/fix_pitorsion.cpp
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@ -95,6 +95,10 @@ FixPiTorsion::FixPiTorsion(LAMMPS *lmp, int narg, char **arg) :
// pitorsion coeff // pitorsion coeff
kpit = nullptr; kpit = nullptr;
// zero thermo energy
epitorsion = 0.0;
} }
/* --------------------------------------------------------------------- */ /* --------------------------------------------------------------------- */

2
tools/tinker/tinker2lmp.py
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@ -1384,7 +1384,7 @@ if npitorsions:
d.sections["PiTorsions"] = lines d.sections["PiTorsions"] = lines
if nbitorsions: if nbitorsions:
d.headers["bitorsions"] = len(pitorsionlist) d.headers["bitorsions"] = len(bitorsionlist)
# if there are bitorsions, then -bitorsion file must have been specified # if there are bitorsions, then -bitorsion file must have been specified