diff --git a/examples/amoeba/in.ubiquitin b/examples/amoeba/in.ubiquitin index dbf544b402..4d5e341bcd 100644 --- a/examples/amoeba/in.ubiquitin +++ b/examples/amoeba/in.ubiquitin @@ -14,10 +14,10 @@ improper_style amoeba # per-atom properties required by AMOEBA or HIPPO 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 pit all amoeba/pitorsion +fix_modify pit energy yes +fix bit all amoeba/bitorsion bitorsion.ubiquitin.data +fix_modify bit energy yes fix extra all property/atom & i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes @@ -25,9 +25,9 @@ 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" & - fix pitorsion "pitorsion types" "PiTorsion Coeffs" & - fix pitorsion pitorsions PiTorsions & - fix bitorsion bitorsions BiTorsions + fix pit "pitorsion types" "PiTorsion Coeffs" & + fix pit pitorsions PiTorsions & + fix bit bitorsions BiTorsions pair_style amoeba exclude bitorsion pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key diff --git a/src/AMOEBA/fix_bitorsion.cpp b/src/AMOEBA/fix_amoeba_bitorsion.cpp similarity index 92% rename from src/AMOEBA/fix_bitorsion.cpp rename to src/AMOEBA/fix_amoeba_bitorsion.cpp index a1bb149872..e9ff52a0b7 100644 --- a/src/AMOEBA/fix_bitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_bitorsion.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "fix_bitorsion.h" +#include "fix_amoeba_bitorsion.h" #include @@ -78,13 +78,13 @@ void bcuint1(double *ftt, double *ft1, double *ft2, double *ft12, /* ---------------------------------------------------------------------- */ -FixBiTorsion::FixBiTorsion(LAMMPS *lmp, int narg, char **arg) : +FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), bitorsion_list(nullptr), num_bitorsion(nullptr), bitorsion_type(nullptr), bitorsion_atom1(nullptr), bitorsion_atom2(nullptr), bitorsion_atom3(nullptr), bitorsion_atom4(nullptr), bitorsion_atom5(nullptr) { - if (narg != 4) error->all(FLERR,"Illegal fix bitorsion command"); + if (narg != 4) error->all(FLERR,"Illegal fix amoeba/bitorsion command"); restart_global = 1; restart_peratom = 1; @@ -139,7 +139,7 @@ FixBiTorsion::FixBiTorsion(LAMMPS *lmp, int narg, char **arg) : /* --------------------------------------------------------------------- */ -FixBiTorsion::~FixBiTorsion() +FixAmoebaBiTorsion::~FixAmoebaBiTorsion() { // unregister callbacks to this fix from Atom class @@ -171,7 +171,7 @@ FixBiTorsion::~FixBiTorsion() /* ---------------------------------------------------------------------- */ -int FixBiTorsion::setmask() +int FixAmoebaBiTorsion::setmask() { int mask = 0; mask |= PRE_NEIGHBOR; @@ -184,7 +184,7 @@ int FixBiTorsion::setmask() /* ---------------------------------------------------------------------- */ -void FixBiTorsion::init() +void FixAmoebaBiTorsion::init() { if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; @@ -209,7 +209,7 @@ void FixBiTorsion::init() /* --------------------------------------------------------------------- */ -void FixBiTorsion::setup(int vflag) +void FixAmoebaBiTorsion::setup(int vflag) { pre_neighbor(); @@ -224,21 +224,21 @@ void FixBiTorsion::setup(int vflag) /* --------------------------------------------------------------------- */ -void FixBiTorsion::setup_pre_neighbor() +void FixAmoebaBiTorsion::setup_pre_neighbor() { pre_neighbor(); } /* --------------------------------------------------------------------- */ -void FixBiTorsion::setup_pre_reverse(int eflag, int vflag) +void FixAmoebaBiTorsion::setup_pre_reverse(int eflag, int vflag) { pre_reverse(eflag,vflag); } /* --------------------------------------------------------------------- */ -void FixBiTorsion::min_setup(int vflag) +void FixAmoebaBiTorsion::min_setup(int vflag) { pre_neighbor(); post_force(vflag); @@ -250,7 +250,7 @@ void FixBiTorsion::min_setup(int vflag) this proc lists the bitorsion exactly once ------------------------------------------------------------------------- */ -void FixBiTorsion::pre_neighbor() +void FixAmoebaBiTorsion::pre_neighbor() { int i,m,atom1,atom2,atom3,atom4,atom5; @@ -313,14 +313,14 @@ void FixBiTorsion::pre_neighbor() store eflag, so can use it in post_force to tally per-atom energies ------------------------------------------------------------------------- */ -void FixBiTorsion::pre_reverse(int eflag, int /*vflag*/) +void FixAmoebaBiTorsion::pre_reverse(int eflag, int /*vflag*/) { eflag_caller = eflag; } /* ---------------------------------------------------------------------- */ -void FixBiTorsion::post_force(int vflag) +void FixAmoebaBiTorsion::post_force(int vflag) { if (disable) return; @@ -667,14 +667,14 @@ void FixBiTorsion::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixBiTorsion::post_force_respa(int vflag, int ilevel, int /*iloop*/) +void FixAmoebaBiTorsion::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixBiTorsion::min_post_force(int vflag) +void FixAmoebaBiTorsion::min_post_force(int vflag) { post_force(vflag); } @@ -683,7 +683,7 @@ void FixBiTorsion::min_post_force(int vflag) energy of BiTorision term ------------------------------------------------------------------------- */ -double FixBiTorsion::compute_scalar() +double FixAmoebaBiTorsion::compute_scalar() { double all; MPI_Allreduce(&ebitorsion,&all,1,MPI_DOUBLE,MPI_SUM,world); @@ -696,7 +696,7 @@ double FixBiTorsion::compute_scalar() // ---------------------------------------------------------------------- // ---------------------------------------------------------------------- -void FixBiTorsion::read_grid_data(char *bitorsion_file) +void FixAmoebaBiTorsion::read_grid_data(char *bitorsion_file) { char line[MAXLINE]; char *eof; @@ -705,19 +705,20 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file) if (me == 0) { fp = utils::open_potential(bitorsion_file,lmp,nullptr); if (fp == nullptr) - error->one(FLERR,"Cannot open fix bitorsion file {}: {}", + error->one(FLERR,"Cannot open fix amoeba/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"); + if (eof == nullptr) + error->one(FLERR,"Unexpected end of fix amoeba/bitorsion file"); sscanf(line,"%d",&ntypes); } 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 amoeba/bitorsion file has no types"); btgrid = new double***[ntypes+1]; nxgrid = new int[ntypes+1]; @@ -733,7 +734,7 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file) eof = fgets(line,MAXLINE,fp); eof = fgets(line,MAXLINE,fp); if (eof == nullptr) - error->one(FLERR,"Unexpected end of fix bitorsion file"); + error->one(FLERR,"Unexpected end of fix amoeba/bitorsion file"); sscanf(line,"%d %d %d",&tmp,&nx,&ny); } @@ -751,7 +752,7 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file) for (int ix = 0; ix < nx; ix++) { eof = fgets(line,MAXLINE,fp); if (eof == nullptr) - error->one(FLERR,"Unexpected end of fix bitorsion file"); + error->one(FLERR,"Unexpected end of fix amoeba/bitorsion file"); sscanf(line,"%lg %lg %lg",&xgrid,&ygrid,&value); btgrid[itype][ix][iy][0] = xgrid; btgrid[itype][ix][iy][1] = ygrid; @@ -772,11 +773,12 @@ void FixBiTorsion::read_grid_data(char *bitorsion_file) // ---------------------------------------------------------------------- // ---------------------------------------------------------------------- -void FixBiTorsion::read_data_header(char *line) +void FixAmoebaBiTorsion::read_data_header(char *line) { if (strstr(line,"bitorsions")) { sscanf(line,BIGINT_FORMAT,&nbitorsions); - } else error->all(FLERR,"Invalid read data header line for fix bitorsion"); + } else error->all(FLERR, + "Invalid read data header line for fix amoeba/bitorsion"); } /* ---------------------------------------------------------------------- @@ -784,7 +786,7 @@ void FixBiTorsion::read_data_header(char *line) id_offset is applied to atomID fields if multiple data files are read ------------------------------------------------------------------------- */ -void FixBiTorsion::read_data_section(char *keyword, int n, char *buf, +void FixAmoebaBiTorsion::read_data_section(char *keyword, int n, char *buf, tagint id_offset) { int m,tmp,itype; @@ -882,7 +884,7 @@ void FixBiTorsion::read_data_section(char *keyword, int n, char *buf, /* ---------------------------------------------------------------------- */ -bigint FixBiTorsion::read_data_skip_lines(char * /*keyword*/) +bigint FixAmoebaBiTorsion::read_data_skip_lines(char * /*keyword*/) { return nbitorsions; } @@ -892,7 +894,7 @@ bigint FixBiTorsion::read_data_skip_lines(char * /*keyword*/) only called by proc 0 ------------------------------------------------------------------------- */ -void FixBiTorsion::write_data_header(FILE *fp, int /*mth*/) +void FixAmoebaBiTorsion::write_data_header(FILE *fp, int /*mth*/) { fprintf(fp,BIGINT_FORMAT " bitorsions\n",nbitorsions); } @@ -905,7 +907,7 @@ void FixBiTorsion::write_data_header(FILE *fp, int /*mth*/) // ny = 6 columns = type + 5 atom IDs ------------------------------------------------------------------------- */ -void FixBiTorsion::write_data_section_size(int /*mth*/, int &nx, int &ny) +void FixAmoebaBiTorsion::write_data_section_size(int /*mth*/, int &nx, int &ny) { int i,m; @@ -925,7 +927,7 @@ void FixBiTorsion::write_data_section_size(int /*mth*/, int &nx, int &ny) buf allocated by caller as owned BiTorsions by 6 ------------------------------------------------------------------------- */ -void FixBiTorsion::write_data_section_pack(int /*mth*/, double **buf) +void FixAmoebaBiTorsion::write_data_section_pack(int /*mth*/, double **buf) { int i,m; @@ -956,7 +958,7 @@ void FixBiTorsion::write_data_section_pack(int /*mth*/, double **buf) only called by proc 0 ------------------------------------------------------------------------- */ -void FixBiTorsion::write_data_section_keyword(int /*mth*/, FILE *fp) +void FixAmoebaBiTorsion::write_data_section_keyword(int /*mth*/, FILE *fp) { fprintf(fp,"\nBiTorsions\n\n"); } @@ -968,7 +970,7 @@ void FixBiTorsion::write_data_section_keyword(int /*mth*/, FILE *fp) only called by proc 0 ------------------------------------------------------------------------- */ -void FixBiTorsion::write_data_section(int /*mth*/, FILE *fp, +void FixAmoebaBiTorsion::write_data_section(int /*mth*/, FILE *fp, int n, double **buf, int index) { for (int i = 0; i < n; i++) @@ -989,7 +991,7 @@ void FixBiTorsion::write_data_section(int /*mth*/, FILE *fp, pack entire state of Fix into one write ------------------------------------------------------------------------- */ -void FixBiTorsion::write_restart(FILE *fp) +void FixAmoebaBiTorsion::write_restart(FILE *fp) { if (comm->me == 0) { int size = sizeof(bigint); @@ -1002,7 +1004,7 @@ void FixBiTorsion::write_restart(FILE *fp) use state info from restart file to restart the Fix ------------------------------------------------------------------------- */ -void FixBiTorsion::restart(char *buf) +void FixAmoebaBiTorsion::restart(char *buf) { nbitorsions = *((bigint *) buf); } @@ -1011,7 +1013,7 @@ void FixBiTorsion::restart(char *buf) pack values in local atom-based arrays for restart file ------------------------------------------------------------------------- */ -int FixBiTorsion::pack_restart(int i, double *buf) +int FixAmoebaBiTorsion::pack_restart(int i, double *buf) { int n = 1; for (int m = 0; m < num_bitorsion[i]; m++) { @@ -1031,7 +1033,7 @@ int FixBiTorsion::pack_restart(int i, double *buf) unpack values from atom->extra array to restart the fix ------------------------------------------------------------------------- */ -void FixBiTorsion::unpack_restart(int nlocal, int nth) +void FixAmoebaBiTorsion::unpack_restart(int nlocal, int nth) { double **extra = atom->extra; @@ -1058,7 +1060,7 @@ void FixBiTorsion::unpack_restart(int nlocal, int nth) maxsize of any atom's restart data ------------------------------------------------------------------------- */ -int FixBiTorsion::maxsize_restart() +int FixAmoebaBiTorsion::maxsize_restart() { return 1 + BITORSIONMAX*6; } @@ -1067,7 +1069,7 @@ int FixBiTorsion::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixBiTorsion::size_restart(int nlocal) +int FixAmoebaBiTorsion::size_restart(int nlocal) { return 1 + num_bitorsion[nlocal]*6; } @@ -1076,7 +1078,7 @@ int FixBiTorsion::size_restart(int nlocal) allocate atom-based array ------------------------------------------------------------------------- */ -void FixBiTorsion::grow_arrays(int nmax) +void FixAmoebaBiTorsion::grow_arrays(int nmax) { num_bitorsion = memory->grow(num_bitorsion,nmax,"cmap:num_bitorsion"); bitorsion_type = memory->grow(bitorsion_type,nmax,BITORSIONMAX, @@ -1103,7 +1105,7 @@ void FixBiTorsion::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixBiTorsion::copy_arrays(int i, int j, int /*delflag*/) +void FixAmoebaBiTorsion::copy_arrays(int i, int j, int /*delflag*/) { num_bitorsion[j] = num_bitorsion[i]; @@ -1121,7 +1123,7 @@ void FixBiTorsion::copy_arrays(int i, int j, int /*delflag*/) initialize one atom's array values, called when atom is created ------------------------------------------------------------------------- */ -void FixBiTorsion::set_arrays(int i) +void FixAmoebaBiTorsion::set_arrays(int i) { num_bitorsion[i] = 0; } @@ -1130,7 +1132,7 @@ void FixBiTorsion::set_arrays(int i) pack values in local atom-based array for exchange with another proc ------------------------------------------------------------------------- */ -int FixBiTorsion::pack_exchange(int i, double *buf) +int FixAmoebaBiTorsion::pack_exchange(int i, double *buf) { int n = 0; buf[n++] = ubuf(num_bitorsion[i]).d; @@ -1149,7 +1151,7 @@ int FixBiTorsion::pack_exchange(int i, double *buf) unpack values in local atom-based array from exchange with another proc ------------------------------------------------------------------------- */ -int FixBiTorsion::unpack_exchange(int nlocal, double *buf) +int FixAmoebaBiTorsion::unpack_exchange(int nlocal, double *buf) { int n = 0; num_bitorsion[nlocal] = (int) ubuf(buf[n++]).i; @@ -1168,7 +1170,7 @@ int FixBiTorsion::unpack_exchange(int nlocal, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double FixBiTorsion::memory_usage() +double FixAmoebaBiTorsion::memory_usage() { int nmax = atom->nmax; double bytes = (double)nmax * sizeof(int); // num_bitorsion diff --git a/src/AMOEBA/fix_bitorsion.h b/src/AMOEBA/fix_amoeba_bitorsion.h similarity index 92% rename from src/AMOEBA/fix_bitorsion.h rename to src/AMOEBA/fix_amoeba_bitorsion.h index 1bc5fc1012..49af5cc95d 100644 --- a/src/AMOEBA/fix_bitorsion.h +++ b/src/AMOEBA/fix_amoeba_bitorsion.h @@ -13,20 +13,20 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(bitorsion,FixBiTorsion); +FixStyle(amoeba/bitorsion,FixAmoebaBiTorsion); // clang-format on #else -#ifndef LMP_FIX_BITORSION_H -#define LMP_FIX_BITORSION_H +#ifndef LMP_FIX_AMOEBA_BITORSION_H +#define LMP_FIX_AMOEBA_BITORSION_H #include "fix.h" namespace LAMMPS_NS { -class FixBiTorsion : public Fix { +class FixAmoebaBiTorsion : public Fix { public: - FixBiTorsion(class LAMMPS *, int, char **); - ~FixBiTorsion(); + FixAmoebaBiTorsion(class LAMMPS *, int, char **); + ~FixAmoebaBiTorsion(); int setmask(); void init(); void setup(int); diff --git a/src/AMOEBA/fix_pitorsion.cpp b/src/AMOEBA/fix_amoeba_pitorsion.cpp similarity index 93% rename from src/AMOEBA/fix_pitorsion.cpp rename to src/AMOEBA/fix_amoeba_pitorsion.cpp index 689097df99..21f2f957ef 100644 --- a/src/AMOEBA/fix_pitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_pitorsion.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "fix_pitorsion.h" +#include "fix_amoeba_pitorsion.h" #include @@ -36,16 +36,15 @@ using namespace MathConst; #define LISTDELTA 8196 #define LB_FACTOR 1.5 - /* ---------------------------------------------------------------------- */ -FixPiTorsion::FixPiTorsion(LAMMPS *lmp, int narg, char **arg) : +FixAmoebaPiTorsion::FixAmoebaPiTorsion(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), pitorsion_list(nullptr), num_pitorsion(nullptr), pitorsion_type(nullptr), pitorsion_atom1(nullptr), pitorsion_atom2(nullptr), pitorsion_atom3(nullptr), pitorsion_atom4(nullptr), pitorsion_atom5(nullptr), pitorsion_atom6(nullptr) { - if (narg != 3) error->all(FLERR,"Illegal fix pitorsion command"); + if (narg != 3) error->all(FLERR,"Illegal fix amoeba/pitorsion command"); // settings for this fix @@ -103,7 +102,7 @@ FixPiTorsion::FixPiTorsion(LAMMPS *lmp, int narg, char **arg) : /* --------------------------------------------------------------------- */ -FixPiTorsion::~FixPiTorsion() +FixAmoebaPiTorsion::~FixAmoebaPiTorsion() { // unregister callbacks to this fix from Atom class @@ -132,7 +131,7 @@ FixPiTorsion::~FixPiTorsion() /* ---------------------------------------------------------------------- */ -int FixPiTorsion::setmask() +int FixAmoebaPiTorsion::setmask() { int mask = 0; mask |= PRE_NEIGHBOR; @@ -145,7 +144,7 @@ int FixPiTorsion::setmask() /* ---------------------------------------------------------------------- */ -void FixPiTorsion::init() +void FixAmoebaPiTorsion::init() { if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; @@ -170,7 +169,7 @@ void FixPiTorsion::init() /* --------------------------------------------------------------------- */ -void FixPiTorsion::setup(int vflag) +void FixAmoebaPiTorsion::setup(int vflag) { pre_neighbor(); @@ -185,21 +184,21 @@ void FixPiTorsion::setup(int vflag) /* --------------------------------------------------------------------- */ -void FixPiTorsion::setup_pre_neighbor() +void FixAmoebaPiTorsion::setup_pre_neighbor() { pre_neighbor(); } /* --------------------------------------------------------------------- */ -void FixPiTorsion::setup_pre_reverse(int eflag, int vflag) +void FixAmoebaPiTorsion::setup_pre_reverse(int eflag, int vflag) { pre_reverse(eflag,vflag); } /* --------------------------------------------------------------------- */ -void FixPiTorsion::min_setup(int vflag) +void FixAmoebaPiTorsion::min_setup(int vflag) { pre_neighbor(); post_force(vflag); @@ -211,7 +210,7 @@ void FixPiTorsion::min_setup(int vflag) this proc lists the pitorsion exactly once ------------------------------------------------------------------------- */ -void FixPiTorsion::pre_neighbor() +void FixAmoebaPiTorsion::pre_neighbor() { int i,m,atom1,atom2,atom3,atom4,atom5,atom6; @@ -278,7 +277,7 @@ void FixPiTorsion::pre_neighbor() store eflag, so can use it in post_force to tally per-atom energies ------------------------------------------------------------------------- */ -void FixPiTorsion::pre_reverse(int eflag, int /*vflag*/) +void FixAmoebaPiTorsion::pre_reverse(int eflag, int /*vflag*/) { eflag_caller = eflag; } @@ -287,7 +286,7 @@ void FixPiTorsion::pre_reverse(int eflag, int /*vflag*/) compute PiTorsion terms ------------------------------------------------------------------------- */ -void FixPiTorsion::post_force(int vflag) +void FixAmoebaPiTorsion::post_force(int vflag) { if (disable) return; @@ -568,14 +567,14 @@ void FixPiTorsion::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixPiTorsion::post_force_respa(int vflag, int ilevel, int /*iloop*/) +void FixAmoebaPiTorsion::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixPiTorsion::min_post_force(int vflag) +void FixAmoebaPiTorsion::min_post_force(int vflag) { post_force(vflag); } @@ -584,7 +583,7 @@ void FixPiTorsion::min_post_force(int vflag) energy of PiTorsion term ------------------------------------------------------------------------- */ -double FixPiTorsion::compute_scalar() +double FixAmoebaPiTorsion::compute_scalar() { double all; MPI_Allreduce(&epitorsion,&all,1,MPI_DOUBLE,MPI_SUM,world); @@ -597,13 +596,14 @@ double FixPiTorsion::compute_scalar() // ---------------------------------------------------------------------- // ---------------------------------------------------------------------- -void FixPiTorsion::read_data_header(char *line) +void FixAmoebaPiTorsion::read_data_header(char *line) { if (strstr(line,"pitorsions")) { sscanf(line,BIGINT_FORMAT,&npitorsions); } else if (strstr(line,"pitorsion types")) { sscanf(line,"%d",&npitorsion_types); - } else error->all(FLERR,"Invalid read data header line for fix pitorsion"); + } else error->all(FLERR, + "Invalid read data header line for amoeba/fix pitorsion"); } /* ---------------------------------------------------------------------- @@ -611,7 +611,7 @@ void FixPiTorsion::read_data_header(char *line) id_offset is applied to atomID fields if multiple data files are read ------------------------------------------------------------------------- */ -void FixPiTorsion::read_data_section(char *keyword, int n, char *buf, +void FixAmoebaPiTorsion::read_data_section(char *keyword, int n, char *buf, tagint id_offset) { int which; @@ -622,7 +622,7 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf, } else if (strstr(keyword,"PiTorsion Coeffs")) { sscanf(keyword,"%d",&npitorsion_types); which = 1; - } else error->all(FLERR,"Invalid read data section for fix pitorsion"); + } else error->all(FLERR,"Invalid read data section for fix amoeba/pitorsion"); // loop over lines of PiTorsion Coeffs // tokenize the line into values @@ -640,7 +640,7 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf, *next = '\0'; sscanf(buf,"%d %lg",&itype,&value); if (itype <= 0 || itype > npitorsion_types) - error->all(FLERR,"Incorrect args for pitorsion coefficients"); + error->all(FLERR,"Incorrect args for fix amoeba/pitorsion coeffs"); kpit[itype] = value; buf = next + 1; } @@ -763,7 +763,7 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf, /* ---------------------------------------------------------------------- */ -bigint FixPiTorsion::read_data_skip_lines(char *keyword) +bigint FixAmoebaPiTorsion::read_data_skip_lines(char *keyword) { if (strcmp(keyword,"PiTorsions") == 0) return npitorsions; if (strcmp(keyword,"PiTorsion Coeffs") == 0) return (bigint) npitorsion_types; @@ -775,7 +775,7 @@ bigint FixPiTorsion::read_data_skip_lines(char *keyword) only called by proc 0 ------------------------------------------------------------------------- */ -void FixPiTorsion::write_data_header(FILE *fp, int mth) +void FixAmoebaPiTorsion::write_data_header(FILE *fp, int mth) { if (mth == 0) fprintf(fp,BIGINT_FORMAT " pitorsions\n",npitorsions); else if (mth == 1) @@ -787,7 +787,7 @@ void FixPiTorsion::write_data_header(FILE *fp, int mth) # of data sections = 2 for this fix ------------------------------------------------------------------------- */ -void FixPiTorsion::write_data_section_size(int mth, int &nx, int &ny) +void FixAmoebaPiTorsion::write_data_section_size(int mth, int &nx, int &ny) { int i,m; @@ -824,7 +824,7 @@ void FixPiTorsion::write_data_section_size(int mth, int &nx, int &ny) buf allocated by caller as owned PiTorsions by 7 ------------------------------------------------------------------------- */ -void FixPiTorsion::write_data_section_pack(int mth, double **buf) +void FixAmoebaPiTorsion::write_data_section_pack(int mth, double **buf) { int i,m; @@ -875,7 +875,7 @@ void FixPiTorsion::write_data_section_pack(int mth, double **buf) only called by proc 0 ------------------------------------------------------------------------- */ -void FixPiTorsion::write_data_section_keyword(int mth, FILE *fp) +void FixAmoebaPiTorsion::write_data_section_keyword(int mth, FILE *fp) { if (mth == 0) fprintf(fp,"\nPiTorsions\n\n"); else if (mth == 1) fprintf(fp,"\nPiTorsion Coeffs\n\n"); @@ -888,7 +888,7 @@ void FixPiTorsion::write_data_section_keyword(int mth, FILE *fp) only called by proc 0 ------------------------------------------------------------------------- */ -void FixPiTorsion::write_data_section(int mth, FILE *fp, +void FixAmoebaPiTorsion::write_data_section(int mth, FILE *fp, int n, double **buf, int index) { // PiTorsions section @@ -921,7 +921,7 @@ void FixPiTorsion::write_data_section(int mth, FILE *fp, pack entire state of Fix into one write ------------------------------------------------------------------------- */ -void FixPiTorsion::write_restart(FILE *fp) +void FixAmoebaPiTorsion::write_restart(FILE *fp) { if (comm->me == 0) { int size = sizeof(bigint); @@ -934,7 +934,7 @@ void FixPiTorsion::write_restart(FILE *fp) use state info from restart file to restart the Fix ------------------------------------------------------------------------- */ -void FixPiTorsion::restart(char *buf) +void FixAmoebaPiTorsion::restart(char *buf) { npitorsions = *((bigint *) buf); } @@ -943,7 +943,7 @@ void FixPiTorsion::restart(char *buf) pack values in local atom-based arrays for restart file ------------------------------------------------------------------------- */ -int FixPiTorsion::pack_restart(int i, double *buf) +int FixAmoebaPiTorsion::pack_restart(int i, double *buf) { int n = 1; for (int m = 0; m < num_pitorsion[i]; m++) { @@ -964,7 +964,7 @@ int FixPiTorsion::pack_restart(int i, double *buf) unpack values from atom->extra array to restart the fix ------------------------------------------------------------------------- */ -void FixPiTorsion::unpack_restart(int nlocal, int nth) +void FixAmoebaPiTorsion::unpack_restart(int nlocal, int nth) { double **extra = atom->extra; @@ -992,7 +992,7 @@ void FixPiTorsion::unpack_restart(int nlocal, int nth) maxsize of any atom's restart data ------------------------------------------------------------------------- */ -int FixPiTorsion::maxsize_restart() +int FixAmoebaPiTorsion::maxsize_restart() { return 1 + PITORSIONMAX*6; } @@ -1001,7 +1001,7 @@ int FixPiTorsion::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixPiTorsion::size_restart(int nlocal) +int FixAmoebaPiTorsion::size_restart(int nlocal) { return 1 + num_pitorsion[nlocal]*7; } @@ -1010,7 +1010,7 @@ int FixPiTorsion::size_restart(int nlocal) allocate atom-based arrays ------------------------------------------------------------------------- */ -void FixPiTorsion::grow_arrays(int nmax) +void FixAmoebaPiTorsion::grow_arrays(int nmax) { num_pitorsion = memory->grow(num_pitorsion,nmax,"pitorsion:num_pitorsion"); pitorsion_type = memory->grow(pitorsion_type,nmax,PITORSIONMAX, @@ -1039,7 +1039,7 @@ void FixPiTorsion::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixPiTorsion::copy_arrays(int i, int j, int /*delflag*/) +void FixAmoebaPiTorsion::copy_arrays(int i, int j, int /*delflag*/) { num_pitorsion[j] = num_pitorsion[i]; @@ -1058,7 +1058,7 @@ void FixPiTorsion::copy_arrays(int i, int j, int /*delflag*/) initialize one atom's array values, called when atom is created ------------------------------------------------------------------------- */ -void FixPiTorsion::set_arrays(int i) +void FixAmoebaPiTorsion::set_arrays(int i) { num_pitorsion[i] = 0; } @@ -1067,7 +1067,7 @@ void FixPiTorsion::set_arrays(int i) pack values in local atom-based array for exchange with another proc ------------------------------------------------------------------------- */ -int FixPiTorsion::pack_exchange(int i, double *buf) +int FixAmoebaPiTorsion::pack_exchange(int i, double *buf) { int n = 0; buf[n++] = ubuf(num_pitorsion[i]).d; @@ -1087,7 +1087,7 @@ int FixPiTorsion::pack_exchange(int i, double *buf) unpack values in local atom-based array from exchange with another proc ------------------------------------------------------------------------- */ -int FixPiTorsion::unpack_exchange(int nlocal, double *buf) +int FixAmoebaPiTorsion::unpack_exchange(int nlocal, double *buf) { int n = 0; num_pitorsion[nlocal] = (int) ubuf(buf[n++]).i; @@ -1107,7 +1107,7 @@ int FixPiTorsion::unpack_exchange(int nlocal, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double FixPiTorsion::memory_usage() +double FixAmoebaPiTorsion::memory_usage() { int nmax = atom->nmax; double bytes = (double)nmax * sizeof(int); // num_pitorsion diff --git a/src/AMOEBA/fix_pitorsion.h b/src/AMOEBA/fix_amoeba_pitorsion.h similarity index 92% rename from src/AMOEBA/fix_pitorsion.h rename to src/AMOEBA/fix_amoeba_pitorsion.h index e335c6efa1..d1404c2580 100644 --- a/src/AMOEBA/fix_pitorsion.h +++ b/src/AMOEBA/fix_amoeba_pitorsion.h @@ -13,20 +13,20 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(pitorsion,FixPiTorsion); +FixStyle(amoeba/pitorsion,FixAmoebaPiTorsion); // clang-format on #else -#ifndef LMP_FIX_PITORSION_H -#define LMP_FIX_PITORSION_H +#ifndef LMP_FIX_AMOEBA_PITORSION_H +#define LMP_FIX_AMOEBA_PITORSION_H #include "fix.h" namespace LAMMPS_NS { -class FixPiTorsion : public Fix { +class FixAmoebaPiTorsion : public Fix { public: - FixPiTorsion(class LAMMPS *, int, char **); - ~FixPiTorsion(); + FixAmoebaPiTorsion(class LAMMPS *, int, char **); + ~FixAmoebaPiTorsion(); int setmask(); void init(); void setup(int); diff --git a/src/modify.cpp b/src/modify.cpp index 07d5b8ee9b..3bb85d55f8 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -810,7 +810,8 @@ 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", "bitorsion", nullptr}; + "deprecated", "STORE/KIM", "amoeba/pitorsion", "amoeba/bitorsion", + nullptr}; if (domain->box_exist == 0) { int m;