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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15071 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -28,56 +28,9 @@ namespace LAMMPS_NS {
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class FixAveSpatial : public Fix {
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public:
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FixAveSpatial(class LAMMPS *, int, char **);
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~FixAveSpatial();
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int setmask();
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void init();
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void setup(int);
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void end_of_step();
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double compute_array(int,int);
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double memory_usage();
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private:
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int me,nvalues;
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int nrepeat,nfreq,irepeat;
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bigint nvalid,nvalid_last;
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int ndim,normflag,regionflag,overwrite,discard;
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char *tstring,*sstring,*idregion;
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int *which,*argindex,*value2index;
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char **ids;
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FILE *fp;
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class Region *region;
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int ave,nwindow,scaleflag;
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int norm,iwindow,window_limit;
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double xscale,yscale,zscale;
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double bin_volume;
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long filepos;
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int dim[3],originflag[3],nlayers[3];
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double origin[3],delta[3];
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double offset[3],invdelta[3];
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int maxvar;
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double *varatom;
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int maxatom;
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int *bin;
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int nbins,maxbin;
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double **coord;
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double *count_one,*count_many,*count_sum;
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double **values_one,**values_many,**values_sum;
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double *count_total,**count_list;
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double **values_total,***values_list;
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int minflag[3],maxflag[3];
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double minvalue[3],maxvalue[3];
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void setup_bins();
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void atom2bin1d();
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void atom2bin2d();
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void atom2bin3d();
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bigint nextvalid();
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~FixAveSpatial() {}
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int setmask() {}
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void init() {}
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};
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}
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@ -87,106 +40,10 @@ class FixAveSpatial : public Fix {
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/* ERROR/WARNING messages:
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W: The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015
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E: The fix ave/spatial command has been removed from LAMMPS
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Self-explanatory.
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Cannot use fix ave/spatial z for 2 dimensional model
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Self-explanatory.
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E: Same dimension twice in fix ave/spatial
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Self-explanatory.
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E: No input values for fix ave/spatial
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Self-explanatory.
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E: Region ID for fix ave/spatial does not exist
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Self-explanatory.
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E: Cannot open fix ave/spatial file %s
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The specified file cannot be opened. Check that the path and name are
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correct.
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E: Compute ID for fix ave/spatial does not exist
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Self-explanatory.
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E: Fix ave/spatial compute does not calculate per-atom values
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A compute used by fix ave/spatial must generate per-atom values.
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E: Fix ave/spatial compute does not calculate a per-atom vector
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A compute used by fix ave/spatial must generate per-atom values.
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E: Fix ave/spatial compute does not calculate a per-atom array
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Self-explanatory.
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E: Fix ave/spatial compute vector is accessed out-of-range
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The index for the vector is out of bounds.
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E: Fix ID for fix ave/spatial does not exist
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Self-explanatory.
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E: Fix ave/spatial fix does not calculate per-atom values
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A fix used by fix ave/spatial must generate per-atom values.
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E: Fix ave/spatial fix does not calculate a per-atom vector
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A fix used by fix ave/spatial must generate per-atom values.
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E: Fix ave/spatial fix does not calculate a per-atom array
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Self-explanatory.
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E: Fix ave/spatial fix vector is accessed out-of-range
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The index for the vector is out of bounds.
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E: Variable name for fix ave/spatial does not exist
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Self-explanatory.
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E: Fix ave/spatial variable is not atom-style variable
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A variable used by fix ave/spatial must generate per-atom values.
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E: Fix ave/spatial for triclinic boxes requires units reduced
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Self-explanatory.
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E: Fix ave/spatial settings invalid with changing box size
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If the box size changes, only the units reduced option can be
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used.
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E: Fix for fix ave/spatial not computed at compatible time
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Fixes generate their values on specific timesteps. Fix ave/spatial is
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requesting a value on a non-allowed timestep.
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E: Invalid timestep reset for fix ave/spatial
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Resetting the timestep has invalidated the sequence of timesteps this
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fix needs to process.
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E: Invalid bin bounds in fix ave/spatial
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The lo/hi values are inconsistent.
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It has been replaced by the more flexible fix ave/chunk and compute
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chunk/atom commands. All the fix ave/spatial keywords and options are
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available in those two newer commands.
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*/
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@ -63,6 +63,7 @@ void PairTable::compute(int eflag, int vflag)
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int i,j,ii,jj,inum,jnum,itype,jtype,itable;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,factor_lj,fraction,value,a,b;
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char estr[128];
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int *ilist,*jlist,*numneigh,**firstneigh;
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Table *tb;
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@ -109,25 +110,37 @@ 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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if (rsq < tb->innersq) {
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sprintf(estr,"Pair distance < table inner cutoff: "
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"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
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error->one(FLERR,estr);
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}
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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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if (itable >= tlm1) {
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sprintf(estr,"Pair distance > table outer cutoff: "
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"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
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error->one(FLERR,estr);
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}
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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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if (itable >= tlm1) {
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sprintf(estr,"Pair distance > table outer cutoff: "
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"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
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error->one(FLERR,estr);
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}
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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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if (itable >= tlm1) {
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sprintf(estr,"Pair distance > table outer cutoff: "
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"ijtype %d %d dist %g",itype,jtype,sqrt(rsq));
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error->one(FLERR,estr);
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}
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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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