enable and process pair style table with clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -18,20 +17,17 @@
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#include "pair_table.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "force.h"
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#include "comm.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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#include "tokenizer.h"
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#include "force.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include "table_file_reader.h"
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#include "tokenizer.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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@ -117,27 +113,27 @@ void PairTable::compute(int eflag, int vflag)
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if (rsq < cutsq[itype][jtype]) {
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tb = &tables[tabindex[itype][jtype]];
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if (rsq < tb->innersq)
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error->one(FLERR,"Pair distance < table inner cutoff: "
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"ijtype {} {} dist {}",itype,jtype,sqrt(rsq));
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error->one(FLERR, "Pair distance < table inner cutoff: ijtype {} {} dist {}", itype,
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jtype, sqrt(rsq));
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if (tabstyle == LOOKUP) {
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itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff: "
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"ijtype {} {} dist {}",itype,jtype,sqrt(rsq));
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error->one(FLERR, "Pair distance > table outer cutoff: ijtype {} {} dist {}", itype,
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jtype, sqrt(rsq));
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fpair = factor_lj * tb->f[itable];
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} else if (tabstyle == LINEAR) {
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itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff: "
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"ijtype {} {} dist {}",itype,jtype,sqrt(rsq));
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error->one(FLERR, "Pair distance > table outer cutoff: ijtype {} {} dist {}", itype,
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jtype, sqrt(rsq));
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fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
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value = tb->f[itable] + fraction * tb->df[itable];
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fpair = factor_lj * value;
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} else if (tabstyle == SPLINE) {
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itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff: "
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"ijtype {} {} dist {}",itype,jtype,sqrt(rsq));
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error->one(FLERR, "Pair distance > table outer cutoff: ijtype {} {} dist {}", itype,
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jtype, sqrt(rsq));
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b = (rsq - tb->rsq[itable]) * tb->invdelta;
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a = 1.0 - b;
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value = a * tb->f[itable] + b * tb->f[itable + 1] +
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@ -174,8 +170,7 @@ void PairTable::compute(int eflag, int vflag)
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
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}
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}
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}
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@ -211,11 +206,16 @@ void PairTable::settings(int narg, char **arg)
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// new settings
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if (strcmp(arg[0],"lookup") == 0) tabstyle = LOOKUP;
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else if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
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else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
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else if (strcmp(arg[0],"bitmap") == 0) tabstyle = BITMAP;
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else error->all(FLERR,"Unknown table style in pair_style command: {}", arg[0]);
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if (strcmp(arg[0], "lookup") == 0)
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tabstyle = LOOKUP;
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else if (strcmp(arg[0], "linear") == 0)
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tabstyle = LINEAR;
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else if (strcmp(arg[0], "spline") == 0)
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tabstyle = SPLINE;
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else if (strcmp(arg[0], "bitmap") == 0)
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tabstyle = BITMAP;
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else
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error->all(FLERR, "Unknown table style in pair_style command: {}", arg[0]);
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tablength = utils::inumeric(FLERR, arg[1], false, lmp);
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if (tablength < 2) error->all(FLERR, "Illegal number of pair table entries");
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@ -225,12 +225,18 @@ void PairTable::settings(int narg, char **arg)
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int iarg = 2;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"ewald") == 0) ewaldflag = 1;
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else if (strcmp(arg[iarg],"pppm") == 0) pppmflag = 1;
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else if (strcmp(arg[iarg],"msm") == 0) msmflag = 1;
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else if (strcmp(arg[iarg],"dispersion") == 0) dispersionflag = 1;
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else if (strcmp(arg[iarg],"tip4p") == 0) tip4pflag = 1;
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else error->all(FLERR,"Illegal pair_style command");
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if (strcmp(arg[iarg], "ewald") == 0)
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ewaldflag = 1;
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else if (strcmp(arg[iarg], "pppm") == 0)
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pppmflag = 1;
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else if (strcmp(arg[iarg], "msm") == 0)
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msmflag = 1;
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else if (strcmp(arg[iarg], "dispersion") == 0)
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dispersionflag = 1;
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else if (strcmp(arg[iarg], "tip4p") == 0)
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tip4pflag = 1;
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else
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error->all(FLERR, "Illegal pair_style command");
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iarg++;
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}
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@ -265,8 +271,7 @@ void PairTable::coeff(int narg, char **arg)
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int me;
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MPI_Comm_rank(world, &me);
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tables = (Table *)
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memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
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tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "pair:tables");
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Table *tb = &tables[ntables];
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null_table(tb);
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if (me == 0) read_table(tb, arg[2], arg[3]);
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@ -274,9 +279,12 @@ void PairTable::coeff(int narg, char **arg)
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// set table cutoff
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if (narg == 5) tb->cut = utils::numeric(FLERR,arg[4],false,lmp);
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else if (tb->rflag) tb->cut = tb->rhi;
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else tb->cut = tb->rfile[tb->ninput-1];
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if (narg == 5)
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tb->cut = utils::numeric(FLERR, arg[4], false, lmp);
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else if (tb->rflag)
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tb->cut = tb->rhi;
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else
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tb->cut = tb->rfile[tb->ninput - 1];
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// error check on table parameters
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// insure cutoff is within table
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@ -300,10 +308,10 @@ void PairTable::coeff(int narg, char **arg)
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// for tabstyle SPLINE, always need to build spline tables
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tb->match = 0;
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if (tabstyle == LINEAR && tb->ninput == tablength &&
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tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
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if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
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tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1;
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if (tabstyle == LINEAR && tb->ninput == tablength && tb->rflag == RSQ && tb->rhi == tb->cut)
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tb->match = 1;
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if (tabstyle == BITMAP && tb->ninput == 1 << tablength && tb->rflag == BMP && tb->rhi == tb->cut)
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tb->match = 1;
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if (tb->rflag == BMP && tb->match == 0)
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error->all(FLERR, "Bitmapped table in file does not match requested table");
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@ -354,13 +362,10 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
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// transparently convert units for supported conversions
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int unit_convert = reader.get_unit_convert();
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double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
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unit_convert);
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double conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert);
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char *line = reader.find_section_start(keyword);
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if (!line) {
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error->one(FLERR,"Did not find keyword in table file");
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}
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if (!line) { error->one(FLERR, "Did not find keyword in table file"); }
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// read args on 2nd line of section
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// allocate table arrays for file values
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@ -410,8 +415,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
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if (tb->rflag == RLINEAR)
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rnew = tb->rlo + (tb->rhi - tb->rlo) * i / (tb->ninput - 1);
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else if (tb->rflag == RSQ) {
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rnew = tb->rlo*tb->rlo +
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(tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
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rnew = tb->rlo * tb->rlo + (tb->rhi * tb->rhi - tb->rlo * tb->rlo) * i / (tb->ninput - 1);
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rnew = sqrt(rnew);
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} else if (tb->rflag == BMP) {
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rsq_lookup.i = i << nshiftbits;
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@ -458,21 +462,24 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
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}
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if (ferror)
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error->warning(FLERR,"{} of {} force values in table {} are inconsistent "
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"with -dE/dr.\nWARNING: Should only be flagged at "
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"inflection points",ferror,tb->ninput,keyword);
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error->warning(FLERR,
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"{} of {} force values in table {} are inconsistent with -dE/dr.\n"
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"WARNING: Should only be flagged at inflection points",
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ferror, tb->ninput, keyword);
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// warn if re-computed distance values differ from file values
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if (rerror)
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error->warning(FLERR,"{} of {} distance values in table {} with relative "
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"error\nWARNING: over {} to re-computed values",
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error->warning(FLERR,
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"{} of {} distance values in table {} with relative error\n"
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"WARNING: over {} to re-computed values",
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rerror, tb->ninput, EPSILONR, keyword);
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// warn if data was read incompletely, e.g. columns were missing
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if (cerror)
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error->warning(FLERR,"{} of {} lines in table {} were incomplete\n"
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error->warning(FLERR,
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"{} of {} lines in table {} were incomplete\n"
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"WARNING: or could not be parsed completely",
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cerror, tb->ninput, keyword);
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}
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@ -556,9 +563,12 @@ void PairTable::param_extract(Table *tb, char *line)
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if (word == "N") {
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tb->ninput = values.next_int();
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} else if ((word == "R") || (word == "RSQ") || (word == "BITMAP")) {
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if (word == "R") tb->rflag = RLINEAR;
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else if (word == "RSQ") tb->rflag = RSQ;
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else if (word == "BITMAP") tb->rflag = BMP;
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if (word == "R")
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tb->rflag = RLINEAR;
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else if (word == "RSQ")
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tb->rflag = RSQ;
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else if (word == "BITMAP")
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tb->rflag = BMP;
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tb->rlo = values.next_double();
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tb->rhi = values.next_double();
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} else if (word == "FPRIME") {
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@ -589,8 +599,10 @@ void PairTable::compute_table(Table *tb)
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// delta = table spacing in rsq for N-1 bins
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double inner;
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if (tb->rflag) inner = tb->rlo;
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else inner = tb->rfile[0];
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if (tb->rflag)
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inner = tb->rlo;
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else
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inner = tb->rfile[0];
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tb->innersq = inner * inner;
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tb->delta = (tb->cut * tb->cut - tb->innersq) / tlm1;
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tb->invdelta = 1.0 / tb->delta;
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@ -696,23 +708,24 @@ void PairTable::compute_table(Table *tb)
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double fp0, fpn;
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double secant_factor = 0.1;
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if (tb->fpflag) fp0 = (tb->fplo/sqrt(tb->innersq) - tb->f[0]/tb->innersq) /
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(2.0 * sqrt(tb->innersq));
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if (tb->fpflag)
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fp0 = (tb->fplo / sqrt(tb->innersq) - tb->f[0] / tb->innersq) / (2.0 * sqrt(tb->innersq));
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else {
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double rsq1 = tb->innersq;
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double rsq2 = rsq1 + secant_factor * tb->delta;
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fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) /
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sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
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fp0 = (splint(tb->rfile, tb->ffile, tb->f2file, tb->ninput, sqrt(rsq2)) / sqrt(rsq2) -
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tb->f[0] / sqrt(rsq1)) /
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(secant_factor * tb->delta);
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}
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if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn =
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(tb->fphi/tb->cut - tb->f[tlm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut);
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if (tb->fpflag && tb->cut == tb->rfile[tb->ninput - 1])
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fpn = (tb->fphi / tb->cut - tb->f[tlm1] / (tb->cut * tb->cut)) / (2.0 * tb->cut);
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else {
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double rsq2 = tb->cut * tb->cut;
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double rsq1 = rsq2 - secant_factor * tb->delta;
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fpn = (tb->f[tlm1] / sqrt(rsq2) -
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splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
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sqrt(rsq1)) / (secant_factor*tb->delta);
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splint(tb->rfile, tb->ffile, tb->f2file, tb->ninput, sqrt(rsq1)) / sqrt(rsq1)) /
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(secant_factor * tb->delta);
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}
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for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]);
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@ -856,14 +869,14 @@ void PairTable::free_table(Table *tb)
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spline and splint routines modified from Numerical Recipes
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------------------------------------------------------------------------- */
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void PairTable::spline(double *x, double *y, int n,
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double yp1, double ypn, double *y2)
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void PairTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2)
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{
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int i, k;
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double p, qn, sig, un;
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double *u = new double[n];
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if (yp1 > 0.99e30) y2[0] = u[0] = 0.0;
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if (yp1 > 0.99e30)
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y2[0] = u[0] = 0.0;
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else {
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y2[0] = -0.5;
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u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1);
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@ -875,7 +888,8 @@ void PairTable::spline(double *x, double *y, int n,
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u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]);
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u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p;
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}
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if (ypn > 0.99e30) qn = un = 0.0;
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if (ypn > 0.99e30)
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qn = un = 0.0;
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else {
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qn = 0.5;
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un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
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@ -897,8 +911,10 @@ double PairTable::splint(double *xa, double *ya, double *y2a, int n, double x)
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khi = n - 1;
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while (khi - klo > 1) {
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k = (khi + klo) >> 1;
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if (xa[k] > x) khi = k;
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else klo = k;
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if (xa[k] > x)
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khi = k;
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else
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klo = k;
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}
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h = xa[khi] - xa[klo];
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a = (xa[khi] - x) / h;
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@ -969,8 +985,7 @@ void PairTable::read_restart_settings(FILE *fp)
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/* ---------------------------------------------------------------------- */
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double PairTable::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
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double /*factor_coul*/, double factor_lj,
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double &fforce)
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double /*factor_coul*/, double factor_lj, double &fforce)
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{
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int itable;
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double fraction, value, a, b, phi;
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@ -995,8 +1010,7 @@ double PairTable::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
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b = (rsq - tb->rsq[itable]) * tb->invdelta;
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a = 1.0 - b;
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value = a * tb->f[itable] + b * tb->f[itable + 1] +
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((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
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tb->deltasq6;
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((a * a * a - a) * tb->f2[itable] + (b * b * b - b) * tb->f2[itable + 1]) * tb->deltasq6;
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fforce = factor_lj * value;
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} else {
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union_int_float_t rsq_lookup;
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@ -1036,9 +1050,9 @@ void *PairTable::extract(const char *str, int &dim)
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double cut_coul = tables[0].cut;
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for (int m = 1; m < ntables; m++)
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if (tables[m].cut != cut_coul)
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error->all(FLERR,
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"Pair table cutoffs must all be equal to use with KSpace");
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error->all(FLERR, "Pair table cutoffs must all be equal to use with KSpace");
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dim = 0;
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return &tables[0].cut;
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} else return nullptr;
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} else
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return nullptr;
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}
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