ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

reading of bitorsion data file

Browse Source
This commit is contained in:
Steve Plimpton
2022-03-14 18:08:14 -06:00
parent 1dda3055c2
commit 1d86b3e270
6 changed files with 2051 additions and 24 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1884
examples/amoeba/bitorsion.ubiquitin.data Normal file
View File

File diff suppressed because it is too large Load Diff

75
examples/amoeba/data.ubiquitin
View File

@ -14,6 +14,7 @@ LAMMPS data file created from Tinker ubiquitin.xyz and amoeba_ubiquitin.prm file
0 41.91 ylo yhi
0 41.91 zlo zhi
6 pitorsion types
106 bitorsions
106 pitorsions
Masses
@ -26348,6 +26349,80 @@ UreyBradley Coeffs
110 0.0 0.0
111 -7.6 1.5537
BiTorsions
1 1 3 20 21 22 37
2 1 22 37 38 39 56
3 1 39 56 57 58 76
4 1 58 76 77 78 92
5 1 78 92 93 94 114
6 1 94 114 115 116 128
7 1 116 128 129 130 147
8 1 130 147 148 149 161
9 2 149 161 162 163 168
10 1 163 168 169 170 190
11 1 170 190 191 192 204
12 1 192 204 205 206 223
13 1 206 223 224 225 237
14 1 225 237 238 239 256
15 1 239 256 257 258 271
16 1 258 271 272 273 287
17 3 273 287 288 289 302
18 1 304 316 317 318 327
19 1 318 327 328 329 339
20 1 329 339 340 341 353
21 1 341 353 354 355 372
22 1 355 372 373 374 387
23 1 374 387 388 389 401
24 1 389 401 402 403 417
25 1 403 417 418 419 439
26 1 419 439 440 441 449
27 1 441 449 450 451 471
28 1 451 471 472 473 490
29 1 473 490 491 492 507
30 1 492 507 508 509 519
31 1 509 519 520 521 541
32 1 521 541 542 543 556
33 2 543 556 557 558 563
34 3 558 563 564 565 582
35 1 598 610 611 612 622
36 1 612 622 623 624 639
37 1 624 639 640 641 656
38 1 641 656 657 658 680
39 1 658 680 681 682 699
40 1 682 699 700 701 718
41 1 701 718 719 720 738
42 1 720 738 739 740 748
43 2 740 748 749 750 755
44 1 750 755 756 757 777
45 1 757 777 778 779 794
46 1 779 794 795 796 813
47 1 796 813 814 815 828
48 1 815 828 829 830 840
49 2 830 840 841 842 847
50 1 842 847 848 849 871
51 1 849 871 872 873 885
52 1 873 885 886 887 904
53 1 887 904 905 906 915
54 1 906 915 916 917 927
55 1 917 927 928 929 948
56 1 929 948 949 950 962
57 1 950 962 963 964 981
58 1 964 981 982 983 998
59 1 983 998 999 1000 1020
60 1 1000 1020 1021 1022 1035
61 1 1022 1035 1036 1037 1046
62 1 1037 1046 1047 1048 1060
63 1 1048 1060 1061 1062 1079
64 1 1062 1079 1080 1081 1097
65 1 1081 1097 1098 1099 1116
66 1 1099 1116 1117 1118 1132
67 1 1118 1132 1133 1134 1151
68 1 1134 1151 1152 1153 1175
69 1 1153 1175 1176 1177 1194
70 1 1177 1194 1195 1196 1218
71 2 1196 1218 1219 1220 1225
PiTorsions
1 1 2 4 3 20 21 24

4
examples/amoeba/in.ubiquitin
View File

@ -16,6 +16,8 @@ improper_style amoeba
fix amtype all property/atom i_amtype ghost yes
fix pitorsion all pitorsion
fix_modify pitorsion energy yes
fix bitorsion all bitorsion bitorsion.ubiquitin.data
fix_modify bitorsion energy yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
@ -26,7 +28,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pitorsion "pitorsion types" "PiTorsion Coeffs" &
fix pitorsion pitorsions PiTorsions
pair_style amoeba
pair_style amoeba include bitorsion
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes

102
src/AMOEBA/fix_bitorsion.cpp
View File

@ -35,6 +35,7 @@ using namespace MathConst;
#define BITORSIONMAX 6 // max # of BiTorsion terms stored by one atom
#define LISTDELTA 10000
#define LB_FACTOR 1.5
#define MAXLINE 1024
// NOTE: extra until figure things out
@ -106,7 +107,7 @@ FixBiTorsion::FixBiTorsion(LAMMPS *lmp, int narg, char **arg) :
// read and setup BiTorsion grid data
read_grid_map(arg[3]);
read_grid_data(arg[3]);
// perform initial allocation of atom-based arrays
@ -130,6 +131,12 @@ FixBiTorsion::FixBiTorsion(LAMMPS *lmp, int narg, char **arg) :
nbitorsion_list = 0;
max_bitorsion_list = 0;
bitorsion_list = nullptr;
// BiTorsion grid data
ntypes = 0;
nxgrid,nygrid = nullptr;
btgrid = nullptr;
}
/* --------------------------------------------------------------------- */
@ -154,6 +161,14 @@ FixBiTorsion::~FixBiTorsion()
// local list of bitorsions to compute
memory->destroy(bitorsion_list);
// BiTorsion grid data
delete [] nxgrid;
delete [] nygrid;
for (int itype = 0; itype < ntypes; itype++)
memory->destroy(btgrid[itype]);
delete [] btgrid;
}
/* ---------------------------------------------------------------------- */
@ -679,47 +694,92 @@ double FixBiTorsion::compute_scalar()
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
// methods to read BiTorsion potential file, perform interpolation
// methods to read BiTorsion grid file, perform interpolation
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
void FixBiTorsion::read_grid_map(char *bitorsion_file)
void FixBiTorsion::read_grid_data(char *bitorsion_file)
{
int MAXLINE = 1024;
char linebuf[MAXLINE];
char *chunk,*line;
int i1, i2, i3, i4, i5, i6, j1, j2, j3, j4, j5, j6, counter;
char line[MAXLINE];
char *eof;
FILE *fp = nullptr;
if (me == 0) {
fp = utils::open_potential(bitorsion_file,lmp,nullptr);
if (fp == nullptr)
error->one(FLERR,"Cannot open fix cmap file {}: {}",
error->one(FLERR,"Cannot open fix bitorsion file {}: {}",
bitorsion_file, utils::getsyserror());
eof = fgets(line,MAXLINE,fp);
eof = fgets(line,MAXLINE,fp);
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of fix bitorsion file");
sscanf(line,"%d",&ntypes);
}
int done;
MPI_Bcast(&ntypes,1,MPI_INT,0,world);
if (ntypes == 0) error->all(FLERR,"Fix bitorsion file has no types");
while (!done) {
// only read on rank 0 and broadcast to all other ranks
if (me == 0)
done = (fgets(linebuf,MAXLINE,fp) == nullptr);
btgrid = new double***[ntypes];
nxgrid = new int[ntypes];
nygrid = new int[ntypes];
MPI_Bcast(&done,1,MPI_INT,0,world);
if (done) continue;
// read one array for each BiTorsion type from file
MPI_Bcast(linebuf,MAXLINE,MPI_CHAR,0,world);
int tmp,nx,ny;
double xgrid,ygrid,value;
// remove leading whitespace
line = linebuf;
while (line && (*line == ' ' || *line == '\t' || *line == '\r')) ++line;
for (int itype = 0; itype < ntypes; itype++) {
if (me == 0) {
eof = fgets(line,MAXLINE,fp);
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr)
error->one(FLERR,"Unexpected end of fix bitorsion file");
sscanf(line,"%d %d %d",&tmp,&nx,&ny);
}
// skip if empty line or comment
if (!line || *line =='\n' || *line == '\0' || *line == '#') continue;
MPI_Bcast(&nx,1,MPI_INT,0,world);
MPI_Bcast(&ny,1,MPI_INT,0,world);
nxgrid[itype] = nx;
nygrid[itype] = ny;
memory->create(btgrid[itype],nx,ny,3,"bitorsion:btgrid");
// NOTE: should read this chunk of lines with utils in single read
if (me == 0) {
for (int iy = 0; iy < ny; iy++) {
for (int ix = 0; ix < nx; ix++) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr)
error->one(FLERR,"Unexpected end of fix bitorsion file");
sscanf(line,"%lg %lg %lg",&xgrid,&ygrid,&value);
btgrid[itype][ix][iy][0] = xgrid;
btgrid[itype][ix][iy][1] = ygrid;
btgrid[itype][ix][iy][2] = value;
}
}
}
MPI_Bcast(&btgrid[itype][0][0][0],nx*ny*3,MPI_DOUBLE,0,world);
}
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]);
}
}
}
}
// ----------------------------------------------------------------------

8
src/AMOEBA/fix_bitorsion.h
View File

@ -90,9 +90,15 @@ class FixBiTorsion : public Fix {
int max_bitorsion_list;
int **bitorsion_list;
// BiTorsion grid data
int ntypes;
int *nxgrid,*nygrid;
double ****btgrid;
// read BiTorsion grid data
void read_grid_map(char *);
void read_grid_data(char *);
};
} // namespace LAMMPS_NS

2
src/modify.cpp
View File

@ -810,7 +810,7 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix)
const char *exceptions[] =
{"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx",
"deprecated", "STORE/KIM", "pitorsion", nullptr};
"deprecated", "STORE/KIM", "pitorsion", "bitorsion", nullptr};
if (domain->box_exist == 0) {
int m;