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
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Christoph Scherer
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5756dedfed
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187ccdd222
@ -16,7 +16,7 @@
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scherer@mpip-mainz.mpg.de
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------------------------------------------------------------------------- */
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#include "pair_3b_table.h"
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#include "pair_threebody_table.h"
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#include "atom.h"
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#include "comm.h"
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@ -41,7 +41,7 @@ using MathConst::MY_PI;
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/* ---------------------------------------------------------------------- */
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Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr)
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PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr)
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{
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single_enable = 0;
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restartinfo = 0;
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@ -56,7 +56,7 @@ Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(n
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check if allocated, since class can be destructed when incomplete
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------------------------------------------------------------------------- */
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Pair3BTable::~Pair3BTable()
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PairThreebodyTable::~PairThreebodyTable()
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{
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if (copymode) return;
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@ -73,7 +73,7 @@ Pair3BTable::~Pair3BTable()
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::compute(int eflag, int vflag)
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void PairThreebodyTable::compute(int eflag, int vflag)
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{
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int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
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int itype,jtype,ktype,ijparam,ijkparam;
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@ -202,7 +202,7 @@ void Pair3BTable::compute(int eflag, int vflag)
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::allocate()
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void PairThreebodyTable::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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@ -217,7 +217,7 @@ void Pair3BTable::allocate()
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global settings
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------------------------------------------------------------------------- */
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void Pair3BTable::settings(int narg, char ** /*arg*/)
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void PairThreebodyTable::settings(int narg, char ** /*arg*/)
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{
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if (narg != 0) error->all(FLERR,"Illegal pair_style command");
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}
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@ -226,7 +226,7 @@ void Pair3BTable::settings(int narg, char ** /*arg*/)
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void Pair3BTable::coeff(int narg, char **arg)
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void PairThreebodyTable::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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@ -242,12 +242,12 @@ void Pair3BTable::coeff(int narg, char **arg)
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init specific to this pair style
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------------------------------------------------------------------------- */
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void Pair3BTable::init_style()
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void PairThreebodyTable::init_style()
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{
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if (atom->tag_enable == 0)
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error->all(FLERR,"Pair style 3b/table requires atom IDs");
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error->all(FLERR,"Pair style threebody/table requires atom IDs");
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if (force->newton_pair == 0)
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error->all(FLERR,"Pair style 3b/table requires newton pair on");
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error->all(FLERR,"Pair style threebody/table requires newton pair on");
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// need a full neighbor list
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@ -258,7 +258,7 @@ void Pair3BTable::init_style()
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double Pair3BTable::init_one(int i, int j)
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double PairThreebodyTable::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
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@ -267,7 +267,7 @@ double Pair3BTable::init_one(int i, int j)
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::read_file(char *file)
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void PairThreebodyTable::read_file(char *file)
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{
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memory->sfree(params);
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params = nullptr;
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@ -276,7 +276,7 @@ void Pair3BTable::read_file(char *file)
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// open file on proc 0
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if (comm->me == 0) {
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PotentialFileReader reader(lmp, file, "3b/table", unit_convert_flag);
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PotentialFileReader reader(lmp, file, "threebody", unit_convert_flag);
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char *line;
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while ((line = reader.next_line(NPARAMS_PER_LINE))) {
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@ -339,7 +339,7 @@ void Pair3BTable::read_file(char *file)
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}
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auto tablestyle = values.next_string();
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if (tablestyle != "linear")
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error->all(FLERR,"Unknown table style {} in 3b table", tablestyle);
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error->all(FLERR,"Unknown table style {} in threebody table", tablestyle);
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params[nparams].tablength = values.next_int();
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} catch (TokenizerException &e) {
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@ -347,7 +347,7 @@ void Pair3BTable::read_file(char *file)
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}
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if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0)
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error->one(FLERR,"Illegal 3b/table parameters");
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error->one(FLERR,"Illegal threebody/table parameters");
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nparams++;
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}
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@ -362,7 +362,7 @@ void Pair3BTable::read_file(char *file)
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MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
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// for each set of parameters, broadcast table name and keyword and read 3b table
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// for each set of parameters, broadcast table name and keyword and read threebody table
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for (int m = 0; m < nparams; ++m){
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if (comm->me != 0) {
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memory->create(params[m].tablename, params[m].tablenamelength, "params.tablename");
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@ -373,27 +373,27 @@ void Pair3BTable::read_file(char *file)
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}
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MPI_Bcast(¶ms[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world);
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// initialize 3btable
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memory->create(params[m].mltable,1,"param:3btable");
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// initialize threebodytable
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memory->create(params[m].mltable,1,"param:threebodytable");
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null_table(params[m].mltable);
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//call read_table to read corresponding tabulated 3b file (only called by process 0)
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//call read_table to read corresponding tabulated threebody file (only called by process 0)
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if (comm->me == 0){
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read_table(params[m].mltable,params[m].tablename,params[m].keyword,params[m].symmetric);
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}
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// broadcast read in 3btable to all processes
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// broadcast read in threebodytable to all processes
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bcast_table(params[m].mltable,params[m].symmetric);
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// error check on table parameters
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if (params[m].mltable->ninput <= 1) error->one(FLERR,"Invalid 3b table length");
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if (params[m].mltable->ninput <= 1) error->one(FLERR,"Invalid threebody table length");
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}
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}
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::setup_params()
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void PairThreebodyTable::setup_params()
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{
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int i,j,k,m,n;
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double rtmp;
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@ -446,9 +446,9 @@ void Pair3BTable::setup_params()
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read table file, only called by proc 0
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------------------------------------------------------------------------- */
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void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetric)
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void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool symmetric)
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{
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TableFileReader reader(lmp, file, "3body");
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TableFileReader reader(lmp, file, "threebodytable");
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char *line = reader.find_section_start(keyword);
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@ -460,7 +460,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri
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line = reader.next_line();
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param_extract(tb, line);
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// if it is a symmetric 3body interaction, less table entries are required
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// if it is a symmetric threebody interaction, less table entries are required
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if (symmetric == true){
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memory->create(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r12file");
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memory->create(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r13file");
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@ -488,11 +488,11 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri
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}
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// read 3b table values from file
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// read threebody table values from file
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int cerror = 0;
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reader.skip_line();
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// if it is a symmetric 3body interaction, less table entries are required
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// if it is a symmetric threebody interaction, less table entries are required
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if (symmetric == true){
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for (int i = 0; i < tb->ninput*tb->ninput*(tb->ninput+1); i++) {
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line = reader.next_line(11);
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@ -551,7 +551,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri
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only called by read_table, only called by proc 0
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------------------------------------------------------------------------- */
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void Pair3BTable::param_extract(Table *tb, char *line)
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void PairThreebodyTable::param_extract(Table *tb, char *line)
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{
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tb->ninput = 0;
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tb->rmin = 0.0;
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@ -577,9 +577,9 @@ void Pair3BTable::param_extract(Table *tb, char *line)
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error->one(FLERR, e.what());
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}
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if (tb->ninput == 0) error->one(FLERR, "3body table parameters did not set N");
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if (tb->rmin == 0.0) error->one(FLERR, "3body table parameters did not set rmin");
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if (tb->rmax == 0.0) error->one(FLERR, "3body table parameters did not set rmax");
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if (tb->ninput == 0) error->one(FLERR, "threebodytable parameters did not set N");
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if (tb->rmin == 0.0) error->one(FLERR, "threebodytable parameters did not set rmin");
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if (tb->rmax == 0.0) error->one(FLERR, "threebodytable parameters did not set rmax");
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}
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@ -589,14 +589,14 @@ void Pair3BTable::param_extract(Table *tb, char *line)
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ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0
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------------------------------------------------------------------------- */
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void Pair3BTable::bcast_table(Table *tb, bool symmetric)
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void PairThreebodyTable::bcast_table(Table *tb, bool symmetric)
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{
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MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
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int me;
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MPI_Comm_rank(world, &me);
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if (me > 0) {
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// if it is a symmetric 3body interaction, less table entries are required
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// if it is a symmetric threebody interaction, less table entries are required
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if (symmetric == true){
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memory->create(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r12file");
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memory->create(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r13file");
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@ -624,7 +624,7 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric)
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}
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}
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// if it is a symmetric 3body interaction, less table entries are required
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// if it is a symmetric threebody interaction, less table entries are required
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if (symmetric == true){
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MPI_Bcast(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),MPI_DOUBLE,0,world);
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MPI_Bcast(tb->r13file,tb->ninput*tb->ninput*(tb->ninput+1),MPI_DOUBLE,0,world);
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@ -657,11 +657,11 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric)
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::free_param(Param *pm)
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void PairThreebodyTable::free_param(Param *pm)
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{
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// call free_table to destroy associated 3btable
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// call free_table to destroy associated threebodytable
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free_table(pm->mltable);
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// then destroy associated 3btable
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// then destroy associated threebodytable
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memory->sfree(pm->tablename);
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memory->sfree(pm->keyword);
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memory->sfree(pm->mltable);
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@ -669,7 +669,7 @@ void Pair3BTable::free_param(Param *pm)
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::free_table(Table *tb)
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void PairThreebodyTable::free_table(Table *tb)
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{
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memory->destroy(tb->r12file);
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memory->destroy(tb->r13file);
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@ -685,7 +685,7 @@ void Pair3BTable::free_table(Table *tb)
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::null_table(Table *tb)
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void PairThreebodyTable::null_table(Table *tb)
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{
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tb->r12file = tb->r13file = tb->thetafile = nullptr;
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tb->f11file = tb->f12file = nullptr;
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@ -698,7 +698,7 @@ void Pair3BTable::null_table(Table *tb)
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calculate potential u and force f at angle x
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------------------------------------------------------------------------- */
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void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12,
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void PairThreebodyTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12,
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double &f21, double &f22, double &f31, double &f32, double &u)
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{
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int i,itable,nr12,nr13,ntheta;
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@ -708,7 +708,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou
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//lookup scheme
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// if it is a symmetric 3body interaction, less table entries are required
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// if it is a symmetric threebody interaction, less table entries are required
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if (pm->symmetric == true){
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nr12 = (r12 - pm->mltable->rmin + 0.5*dr - 0.00000001)/dr;
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if (r12 == (pm->mltable->rmin - 0.5*dr)){
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@ -761,7 +761,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou
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/* ---------------------------------------------------------------------- */
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void Pair3BTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2,
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void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2,
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double *fi, double *fj, double *fk, int eflag, double &eng)
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{
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double r12,r13,theta,rinv,cs;
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