document latest fix hyper/local diagnostics

doc/src/fix_hyper_local.txt

@@ -345,7 +345,7 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy of the bias potential to the system's potential
 energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 26,
+This fix computes a global scalar and global vector of length 28,
 which can be accessed by various "output commands"_Howto_output.html.
 The scalar is the magnitude of the bias potential (energy units)
 applied on the current timestep, summed over all biased bonds.  The
@@ -368,19 +368,22 @@ vector stores the following quantities:
 14 = max bond length during this run (distance units)
 15 = average bias coeff for all bonds during this run (unitless)
 16 = min bias coeff for any bond during this run (unitless)
-17 = max bias coeff for any bond during this run (unitless)
+17 = max bias coeff for any bond during this run (unitless) :ul
 
 18 = max drift distance of any bond atom during this run (distance units)
 19 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
 20 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
 21 = count of ghost atoms that could not be found on reneighbor steps during this run
-22 = count of bias overlaps (< Dcut) found during this run
+22 = count of bias overlaps (< Dcut) found during this run :ul
 
 23 = cumulative hyper time since fix created (time units)
 24 = cumulative count of event timesteps since fix created
 25 = cumulative count of atoms in events since fix created
 26 = cumulative # of new bonds formed since fix created :ul
 
+27 = average boost for biased bonds on this step (unitless)
+28 = # of bonds with absolute strain >= q on this step
+
 The first quantities 1-9 are for the current timestep.  Quantities
 10-22 are for the current hyper run.  They are reset each time a new
 hyper run is performed.  Quantities 23-26 are cumulative across
@@ -473,6 +476,11 @@ operation.  Bonds between a specific I,J pair of atoms may persist for
 the entire hyperdynamics simulation if neither I or J are involved in
 an event.
 
+Value 27 computes the average boost for biased bonds only on this step.
+
+Value 28 is the count of bonds with an absolute value of strain >= q
+on this step.
+
 The scalar and vector values calculated by this fix are all
 "intensive".
 

src/REPLICA/fix_hyper_local.cpp

@@ -63,7 +63,6 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
   hyperflag = 2;
   scalar_flag = 1;
   vector_flag = 1;
-  // DEBUG - changed 26 to 28
   size_vector = 28;
   local_flag = 1;
   size_local_rows = 0;
@@ -196,7 +195,6 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
   bound_upper = 1.0 + boundfrac;
   lastreset = update->ntimestep;
 
-  // DEBUG - one line
   overcount = 0;
 }
 
@@ -485,7 +483,6 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
 
   double **x = atom->x;
 
-  // DEBUG - one line
   overcount = 0;
 
   m = 0;
@@ -506,7 +503,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
       maxbondlen = MAX(r,maxbondlen);
       r0 = blist[m].r0;
       estrain = fabs(r-r0) / r0;
-      // DEBUG - one line
+      // DEBUG quantity - could remove this line and output option
       if (estrain >= qfactor) overcount++;
       maxstrain[i] = MAX(maxstrain[i],estrain);
       maxstrain[j] = MAX(maxstrain[j],estrain);
@@ -739,6 +736,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
   // delta in boost coeff is function of boost_domain vs target boost
   // boost_domain is function of two maxstrain_domains for I,J
   // NOTE: biascoeff update is now scaled by 1/Vmax
+  //       still need to think about what this means for units
 
   minbiascoeff = BIG;
   maxbiascoeff = 0.0;
@@ -1466,8 +1464,7 @@ double FixHyperLocal::compute_scalar()
 
 double FixHyperLocal::compute_vector(int i)
 {
-  // 26 vector outputs returned for i = 0-25
-  // DEBUG = 28
+  // 28 vector outputs returned for i = 0-27
 
   // i = 0 = average boost for all bonds on this step
   // i = 1 = # of biased bonds on this step
@@ -1502,7 +1499,8 @@ double FixHyperLocal::compute_vector(int i)
   // i = 24 = cumulative # of atoms in events since fix created
   // i = 25 = cumulative # of new bonds formed since fix created
 
-  // i = 26 = average boost for biased bonds on this step (unitless)
+  // these 2 were added for debugging - could be removed at some point
+  // i = 26 = average boost for biased bonds on this step
   // i = 27 = current count of bonds with strain >= q
 
   if (i == 0) {
@@ -1658,7 +1656,7 @@ double FixHyperLocal::compute_vector(int i)
     return (double) allnewbond;
   }
 
-  // DEBUG - added two options
+  // these two options were added for debugging
 
   if (i == 26) {
     double allboost;

src/REPLICA/fix_hyper_local.h

@@ -140,7 +140,7 @@ class FixHyperLocal : public FixHyper {
   };
 
   OneBond *blist;              // list of owned bonds
-  double *biascoeff;           // biasing coefficient Cij for each bond
+  double *biascoeff;           // bias coefficient Cij for each bond
   int nblocal;                 // # of owned bonds
   int maxbond;                 // allocated size of blist