From 1d86b3e270b5fe1735c4aecb167000e992d54def Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 14 Mar 2022 18:08:14 -0600 Subject: [PATCH] reading of bitorsion data file --- examples/amoeba/bitorsion.ubiquitin.data | 1884 ++++++++++++++++++++++ examples/amoeba/data.ubiquitin | 75 + examples/amoeba/in.ubiquitin | 4 +- src/AMOEBA/fix_bitorsion.cpp | 102 +- src/AMOEBA/fix_bitorsion.h | 8 +- src/modify.cpp | 2 +- 6 files changed, 2051 insertions(+), 24 deletions(-) create mode 100644 examples/amoeba/bitorsion.ubiquitin.data diff --git a/examples/amoeba/bitorsion.ubiquitin.data b/examples/amoeba/bitorsion.ubiquitin.data new file mode 100644 index 0000000000..5a59e1a16e --- /dev/null +++ b/examples/amoeba/bitorsion.ubiquitin.data @@ -0,0 +1,1884 @@ +Tinker BiTorsion parameter file for fix bitorsion + +3 bitorsion types + +1 25 25 + -180.0 -180.0 0.98936 + -165.0 -180.0 0.76408 + -150.0 -180.0 0.21674 + -135.0 -180.0 -0.182 + -120.0 -180.0 -0.37729 + -105.0 -180.0 -0.47834 + -90.0 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0.0765 + 120.0 165.0 -0.49787 + 135.0 165.0 -0.79017 + 150.0 165.0 -0.50914 + 165.0 165.0 0.18602 + 180.0 165.0 0.76902 + -180.0 180.0 0.98936 + -165.0 180.0 0.76408 + -150.0 180.0 0.21674 + -135.0 180.0 -0.182 + -120.0 180.0 -0.37729 + -105.0 180.0 -0.47834 + -90.0 180.0 -0.59267 + -75.0 180.0 -0.93985 + -60.0 180.0 -1.55558 + -45.0 180.0 -2.01849 + -30.0 180.0 -1.94076 + -15.0 180.0 -1.464 + 0.0 180.0 0.18253 + 15.0 180.0 -0.80364 + 30.0 180.0 -1.32974 + 45.0 180.0 -1.31658 + 60.0 180.0 -0.5014 + 75.0 180.0 0.20431 + 90.0 180.0 0.39356 + 105.0 180.0 0.20356 + 120.0 180.0 -0.16993 + 135.0 180.0 -0.22733 + 150.0 180.0 0.13703 + 165.0 180.0 0.66356 + 180.0 180.0 0.98936 diff --git a/examples/amoeba/data.ubiquitin b/examples/amoeba/data.ubiquitin index 05a0673ce8..2e4836880a 100644 --- a/examples/amoeba/data.ubiquitin +++ b/examples/amoeba/data.ubiquitin @@ -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 diff --git a/examples/amoeba/in.ubiquitin b/examples/amoeba/in.ubiquitin index 8603398ac0..f53a3c87c8 100644 --- a/examples/amoeba/in.ubiquitin +++ b/examples/amoeba/in.ubiquitin @@ -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 diff --git a/src/AMOEBA/fix_bitorsion.cpp b/src/AMOEBA/fix_bitorsion.cpp index 2fe63c08dd..44669cb68e 100644 --- a/src/AMOEBA/fix_bitorsion.cpp +++ b/src/AMOEBA/fix_bitorsion.cpp @@ -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]); + } + } + } } // ---------------------------------------------------------------------- diff --git a/src/AMOEBA/fix_bitorsion.h b/src/AMOEBA/fix_bitorsion.h index 0ed072f37c..1bc5fc1012 100644 --- a/src/AMOEBA/fix_bitorsion.h +++ b/src/AMOEBA/fix_bitorsion.h @@ -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 diff --git a/src/modify.cpp b/src/modify.cpp index ef738ecc67..07d5b8ee9b 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -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;