From 187ccdd2223bb5cd2101e57789d45c5a8276f0fb Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:03:06 +0200 Subject: [PATCH] Update and rename pair_3b_table.cpp to pair_threebody_table.cpp changed pair 3b/table to pair threebody/table including name of .cpp file --- ..._3b_table.cpp => pair_threebody_table.cpp} | 84 +++++++++---------- 1 file changed, 42 insertions(+), 42 deletions(-) rename src/MANYBODY/{pair_3b_table.cpp => pair_threebody_table.cpp} (90%) diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_threebody_table.cpp similarity index 90% rename from src/MANYBODY/pair_3b_table.cpp rename to src/MANYBODY/pair_threebody_table.cpp index 00af61ee82..201e2a77a2 100644 --- a/src/MANYBODY/pair_3b_table.cpp +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -16,7 +16,7 @@ scherer@mpip-mainz.mpg.de ------------------------------------------------------------------------- */ -#include "pair_3b_table.h" +#include "pair_threebody_table.h" #include "atom.h" #include "comm.h" @@ -41,7 +41,7 @@ using MathConst::MY_PI; /* ---------------------------------------------------------------------- */ -Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) +PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) { single_enable = 0; restartinfo = 0; @@ -56,7 +56,7 @@ Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(n check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -Pair3BTable::~Pair3BTable() +PairThreebodyTable::~PairThreebodyTable() { if (copymode) return; @@ -73,7 +73,7 @@ Pair3BTable::~Pair3BTable() /* ---------------------------------------------------------------------- */ -void Pair3BTable::compute(int eflag, int vflag) +void PairThreebodyTable::compute(int eflag, int vflag) { int i,j,k,ii,jj,kk,inum,jnum,jnumm1; int itype,jtype,ktype,ijparam,ijkparam; @@ -202,7 +202,7 @@ void Pair3BTable::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void Pair3BTable::allocate() +void PairThreebodyTable::allocate() { allocated = 1; int n = atom->ntypes; @@ -217,7 +217,7 @@ void Pair3BTable::allocate() global settings ------------------------------------------------------------------------- */ -void Pair3BTable::settings(int narg, char ** /*arg*/) +void PairThreebodyTable::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -226,7 +226,7 @@ void Pair3BTable::settings(int narg, char ** /*arg*/) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void Pair3BTable::coeff(int narg, char **arg) +void PairThreebodyTable::coeff(int narg, char **arg) { if (!allocated) allocate(); @@ -242,12 +242,12 @@ void Pair3BTable::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void Pair3BTable::init_style() +void PairThreebodyTable::init_style() { if (atom->tag_enable == 0) - error->all(FLERR,"Pair style 3b/table requires atom IDs"); + error->all(FLERR,"Pair style threebody/table requires atom IDs"); if (force->newton_pair == 0) - error->all(FLERR,"Pair style 3b/table requires newton pair on"); + error->all(FLERR,"Pair style threebody/table requires newton pair on"); // need a full neighbor list @@ -258,7 +258,7 @@ void Pair3BTable::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double Pair3BTable::init_one(int i, int j) +double PairThreebodyTable::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); @@ -267,7 +267,7 @@ double Pair3BTable::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -void Pair3BTable::read_file(char *file) +void PairThreebodyTable::read_file(char *file) { memory->sfree(params); params = nullptr; @@ -276,7 +276,7 @@ void Pair3BTable::read_file(char *file) // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "3b/table", unit_convert_flag); + PotentialFileReader reader(lmp, file, "threebody", unit_convert_flag); char *line; while ((line = reader.next_line(NPARAMS_PER_LINE))) { @@ -339,7 +339,7 @@ void Pair3BTable::read_file(char *file) } auto tablestyle = values.next_string(); if (tablestyle != "linear") - error->all(FLERR,"Unknown table style {} in 3b table", tablestyle); + error->all(FLERR,"Unknown table style {} in threebody table", tablestyle); params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -347,7 +347,7 @@ void Pair3BTable::read_file(char *file) } if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0) - error->one(FLERR,"Illegal 3b/table parameters"); + error->one(FLERR,"Illegal threebody/table parameters"); nparams++; } @@ -362,7 +362,7 @@ void Pair3BTable::read_file(char *file) MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); - // for each set of parameters, broadcast table name and keyword and read 3b table + // for each set of parameters, broadcast table name and keyword and read threebody table for (int m = 0; m < nparams; ++m){ if (comm->me != 0) { memory->create(params[m].tablename, params[m].tablenamelength, "params.tablename"); @@ -373,27 +373,27 @@ void Pair3BTable::read_file(char *file) } MPI_Bcast(¶ms[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); - // initialize 3btable - memory->create(params[m].mltable,1,"param:3btable"); + // initialize threebodytable + memory->create(params[m].mltable,1,"param:threebodytable"); null_table(params[m].mltable); - //call read_table to read corresponding tabulated 3b file (only called by process 0) + //call read_table to read corresponding tabulated threebody file (only called by process 0) if (comm->me == 0){ read_table(params[m].mltable,params[m].tablename,params[m].keyword,params[m].symmetric); } - // broadcast read in 3btable to all processes + // broadcast read in threebodytable to all processes bcast_table(params[m].mltable,params[m].symmetric); // error check on table parameters - if (params[m].mltable->ninput <= 1) error->one(FLERR,"Invalid 3b table length"); + if (params[m].mltable->ninput <= 1) error->one(FLERR,"Invalid threebody table length"); } } /* ---------------------------------------------------------------------- */ -void Pair3BTable::setup_params() +void PairThreebodyTable::setup_params() { int i,j,k,m,n; double rtmp; @@ -446,9 +446,9 @@ void Pair3BTable::setup_params() read table file, only called by proc 0 ------------------------------------------------------------------------- */ -void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) +void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) { - TableFileReader reader(lmp, file, "3body"); + TableFileReader reader(lmp, file, "threebodytable"); char *line = reader.find_section_start(keyword); @@ -460,7 +460,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri line = reader.next_line(); param_extract(tb, line); - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ memory->create(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r12file"); memory->create(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r13file"); @@ -488,11 +488,11 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri } - // read 3b table values from file + // read threebody table values from file int cerror = 0; reader.skip_line(); - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ for (int i = 0; i < tb->ninput*tb->ninput*(tb->ninput+1); i++) { line = reader.next_line(11); @@ -551,7 +551,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri only called by read_table, only called by proc 0 ------------------------------------------------------------------------- */ -void Pair3BTable::param_extract(Table *tb, char *line) +void PairThreebodyTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->rmin = 0.0; @@ -577,9 +577,9 @@ void Pair3BTable::param_extract(Table *tb, char *line) error->one(FLERR, e.what()); } - if (tb->ninput == 0) error->one(FLERR, "3body table parameters did not set N"); - if (tb->rmin == 0.0) error->one(FLERR, "3body table parameters did not set rmin"); - if (tb->rmax == 0.0) error->one(FLERR, "3body table parameters did not set rmax"); + if (tb->ninput == 0) error->one(FLERR, "threebodytable parameters did not set N"); + if (tb->rmin == 0.0) error->one(FLERR, "threebodytable parameters did not set rmin"); + if (tb->rmax == 0.0) error->one(FLERR, "threebodytable parameters did not set rmax"); } @@ -589,14 +589,14 @@ void Pair3BTable::param_extract(Table *tb, char *line) ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 ------------------------------------------------------------------------- */ -void Pair3BTable::bcast_table(Table *tb, bool symmetric) +void PairThreebodyTable::bcast_table(Table *tb, bool symmetric) { MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); int me; MPI_Comm_rank(world, &me); if (me > 0) { - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ memory->create(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r12file"); memory->create(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r13file"); @@ -624,7 +624,7 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric) } } - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ MPI_Bcast(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),MPI_DOUBLE,0,world); MPI_Bcast(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),MPI_DOUBLE,0,world); @@ -657,11 +657,11 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric) /* ---------------------------------------------------------------------- */ -void Pair3BTable::free_param(Param *pm) +void PairThreebodyTable::free_param(Param *pm) { - // call free_table to destroy associated 3btable + // call free_table to destroy associated threebodytable free_table(pm->mltable); - // then destroy associated 3btable + // then destroy associated threebodytable memory->sfree(pm->tablename); memory->sfree(pm->keyword); memory->sfree(pm->mltable); @@ -669,7 +669,7 @@ void Pair3BTable::free_param(Param *pm) /* ---------------------------------------------------------------------- */ -void Pair3BTable::free_table(Table *tb) +void PairThreebodyTable::free_table(Table *tb) { memory->destroy(tb->r12file); memory->destroy(tb->r13file); @@ -685,7 +685,7 @@ void Pair3BTable::free_table(Table *tb) /* ---------------------------------------------------------------------- */ -void Pair3BTable::null_table(Table *tb) +void PairThreebodyTable::null_table(Table *tb) { tb->r12file = tb->r13file = tb->thetafile = nullptr; tb->f11file = tb->f12file = nullptr; @@ -698,7 +698,7 @@ void Pair3BTable::null_table(Table *tb) calculate potential u and force f at angle x ------------------------------------------------------------------------- */ -void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12, +void PairThreebodyTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12, double &f21, double &f22, double &f31, double &f32, double &u) { int i,itable,nr12,nr13,ntheta; @@ -708,7 +708,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou //lookup scheme - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (pm->symmetric == true){ nr12 = (r12 - pm->mltable->rmin + 0.5*dr - 0.00000001)/dr; if (r12 == (pm->mltable->rmin - 0.5*dr)){ @@ -761,7 +761,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou /* ---------------------------------------------------------------------- */ -void Pair3BTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, +void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, double *fi, double *fj, double *fk, int eflag, double &eng) { double r12,r13,theta,rinv,cs;