add dump skip option

src/AMOEBA/pair_amoeba.cpp

@@ -2077,6 +2077,16 @@ void *PairAmoeba::extract(const char *str, int &dim)
   if (strcmp(str,"opbend_pentic") == 0) return (void *) &opbend_pentic;
   if (strcmp(str,"opbend_sextic") == 0) return (void *) &opbend_sextic;
 
+  // requests from FixPair
+
+  if (strcmp(str,"uind") == 0) {
+    dim = 3;
+    return (void *) uind;
+  } else if (strcmp(str,"uinp") == 0) {
+    dim = 3;
+    return (void *) uinp;
+  }
+
   return nullptr;
 }
 

src/MANYBODY/pair_eam.cpp

@@ -933,5 +933,16 @@ void *PairEAM::extract(const char *str, int &dim)
 {
   dim = 2;
   if (strcmp(str,"scale") == 0) return (void *) scale;
+
+  // requests from FixPair
+
+  if (strcmp(str,"rho") == 0) {
+    dim = 0;
+    return (void *) rho;
+  } else if (strcmp(str,"fp") == 0) {
+    dim = 0;
+    return (void *) fp;
+  }
+
   return nullptr;
 }

src/dump.cpp

@@ -20,11 +20,13 @@
 #include "error.h"
 #include "fix.h"
 #include "group.h"
+#include "input.h"
 #include "irregular.h"
 #include "memory.h"
 #include "modify.h"
 #include "output.h"
 #include "update.h"
+#include "variable.h"
 
 #include <cstring>
 
@@ -87,6 +89,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   delay_flag = 0;
   write_header_flag = 1;
 
+  skipflag = 0;
+  skipvar = nullptr;
+
   maxfiles = -1;
   numfiles = 0;
   fileidx = 0;
@@ -165,6 +170,8 @@ Dump::~Dump()
 
   delete[] refresh;
 
+  delete[] skipvar;
+
   // format_column_user is deallocated by child classes that use it
 
   memory->destroy(buf);
@@ -298,6 +305,15 @@ void Dump::init()
     else error->all(FLERR,"Dump could not find refresh compute ID");
   }
 
+  // if skipflag, check skip variable
+
+  if (skipflag) {
+    skipindex = input->variable->find(skipvar);
+    if (skipindex < 0) error->all(FLERR,"Dump skip variable not found");
+    if (!input->variable->equalstyle(skipindex)) 
+      error->all(FLERR,"Variable for dump skip is invalid style");
+  }
+
   // preallocation for PBC copies if requested
 
   if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
@@ -359,6 +375,15 @@ void Dump::write()
 
   nme = count();
 
+  // if skip condition is defined and met, just return
+  // do it after count() b/c that invoked computes
+  // NOTE: for multifile, will have already opened file
+
+  if (skipflag) {
+    double value = input->variable->compute_equal(skipindex);
+    if (value != 0.0) return;
+  }
+
   // ntotal = total # of dump lines in snapshot
   // nmax = max # of dump lines on any proc
 
@@ -1044,6 +1069,12 @@ void Dump::modify_params(int narg, char **arg)
       append_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"balance") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (nprocs > 1)
+        balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"buffer") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       buffer_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
@@ -1051,6 +1082,32 @@ void Dump::modify_params(int narg, char **arg)
         error->all(FLERR,"Dump_modify buffer yes not allowed for this style");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"colname") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (strcmp(arg[iarg+1],"default") == 0) {
+        for (auto item : keyword_user) item.clear();
+        iarg += 2;
+      } else {
+        if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
+        int icol = -1;
+        if (utils::is_integer(arg[iarg + 1])) {
+          icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
+          if (icol < 0) icol = keyword_user.size() + icol + 1;
+          icol--;
+        } else {
+          try {
+            icol = key2col.at(arg[iarg + 1]);
+          } catch (std::out_of_range &) {
+            icol = -1;
+          }
+        }
+        if ((icol < 0) || (icol >= (int)keyword_user.size()))
+          error->all(FLERR, "Incorrect dump_modify arguments: {} {} {}",
+                     arg[iarg], arg[iarg+1], arg[iarg+2]);
+        keyword_user[icol] = arg[iarg+2];
+        iarg += 3;
+      }
+
     } else if (strcmp(arg[iarg],"delay") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       delaystep = utils::bnumeric(FLERR,arg[iarg+1],false,lmp);
@@ -1131,31 +1188,6 @@ void Dump::modify_params(int narg, char **arg)
       flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;
 
-    } else if (strcmp(arg[iarg],"colname") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
-      if (strcmp(arg[iarg+1],"default") == 0) {
-        for (auto item : keyword_user) item.clear();
-        iarg += 2;
-      } else {
-        if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
-        int icol = -1;
-        if (utils::is_integer(arg[iarg + 1])) {
-          icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
-          if (icol < 0) icol = keyword_user.size() + icol + 1;
-          icol--;
-        } else {
-          try {
-            icol = key2col.at(arg[iarg + 1]);
-          } catch (std::out_of_range &) {
-            icol = -1;
-          }
-        }
-        if ((icol < 0) || (icol >= (int)keyword_user.size()))
-          error->all(FLERR, "Incorrect dump_modify arguments: {} {} {}",
-                     arg[iarg], arg[iarg+1], arg[iarg+2]);
-        keyword_user[icol] = arg[iarg+2];
-        iarg += 3;
-      }
     } else if (strcmp(arg[iarg],"format") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
 
@@ -1212,6 +1244,7 @@ void Dump::modify_params(int narg, char **arg)
         fileidx = 0;
       }
       iarg += 2;
+
     } else if (strcmp(arg[iarg],"nfile") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       if (!multiproc)
@@ -1254,6 +1287,15 @@ void Dump::modify_params(int narg, char **arg)
       pbcflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"skip") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      skipflag = 1;
+      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
+        delete[] skipvar;
+        skipvar = utils::strdup(&arg[iarg+1][2]);
+      } else error->all(FLERR,"Illegal dump_modify command");
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"sort") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
@@ -1274,12 +1316,6 @@ void Dump::modify_params(int narg, char **arg)
       }
       iarg += 2;
 
-    } else if (strcmp(arg[iarg],"balance") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
-      if (nprocs > 1)
-        balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
-      iarg += 2;
-
     } else if (strcmp(arg[iarg],"time") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       time_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);

src/dump.h

@@ -91,6 +91,10 @@ class Dump : protected Pointers {
   char *refresh;      // compute ID to invoke refresh() on
   int irefresh;       // index of compute
 
+  int skipflag;       // 1 if skip condition defined
+  char *skipvar;      // name of variable to check for skip condition
+  int skipindex;      // index of skip variable
+
   char boundstr[9];    // encoding of boundary flags
 
   char *format;            // format string for the file write

src/fix_pair.cpp

@@ -0,0 +1,271 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_pair.h"
+
+#include "atom.h"
+#include "dump.h"
+#include "error.h"
+#include "force.h"
+#include "fix.h"
+#include "input.h"
+#include "memory.h"
+#include "pair.h"
+#include "output.h"
+#include "variable.h"
+#include "update.h"
+#include "variable.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixPair::FixPair(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg < 7) error->all(FLERR,"Illegal fix pair command");
+
+  nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+  if (nevery < 1) error->all(FLERR,"Illegal fix pair command");
+
+  int n = strlen(arg[4]) + 1;
+  pairname = new char[n];
+  strcpy(pairname,arg[4]);
+  pstyle = force->pair_match(pairname,1,0);
+  if (pstyle == nullptr) error->all(FLERR,"Fix pair pair style not found");
+
+  nfield = (narg-5) / 2;
+  fieldname = new char*[nfield];
+  trigger = new int[nfield];
+
+  nfield = 0;
+  int iarg = 5;
+
+  while (iarg < narg) {
+    if (iarg+2 > narg) error->all(FLERR,"Illegal fix pair command");
+    n = strlen(arg[iarg]) + 1;
+    fieldname[nfield] = new char[n];
+    strcpy(fieldname[nfield],arg[iarg]);
+    int flag = utils::inumeric(FLERR,arg[iarg+1],true,lmp);
+    if (flag == 0) trigger[nfield] = 0;
+    else if (flag == 1) trigger[nfield] = 1;
+    else error->all(FLERR,"Illegal fix pair command");
+    nfield++;
+    iarg += 2;
+  }
+
+  // set trigger names = fieldname + "_flag"
+
+  triggername = new char*[nfield];
+
+  for (int ifield = 0; ifield < nfield; ifield++) {
+    if (trigger[ifield] == 0) triggername[ifield] = nullptr;
+    else {
+      n = strlen(fieldname[ifield]) + 6;
+      triggername[ifield] = new char[n];
+      sprintf(triggername[ifield],"%s_flag",fieldname[ifield]);
+    }
+  }
+
+  // extract all fields just to get number of per-atom values, ptrs may be NULL
+  // also check if triggername can be extracted as a scalar value
+
+  triggerptr = new int*[nfield];
+
+  int columns,dim;
+  ncols = 0;
+
+  for (int ifield = 0; ifield < nfield; ifield++) {
+    void *tmp = pstyle->extract(fieldname[ifield],columns);
+    //if (!tmp) 
+    //  error->all(FLERR,"Fix pair pair style cannot extract {}",fieldname[ifield]);
+    if (columns) ncols += columns;
+    else ncols++;
+    if (trigger[ifield]) {
+      triggerptr[ifield] = (int *) pstyle->extract(triggername[ifield],dim);
+      if (!triggerptr[ifield]) 
+        error->all(FLERR,"Fix pair pair style cannot extract {}",
+                   triggername[ifield]);
+      if (dim) error->all(FLERR,"Fix pair pair style {} is not a scalar",
+                          triggername[ifield]);
+    }
+  }
+
+  // settings
+  // freq = 1 since vector/array always have values
+  // allows user to specify nevery = 0 for a dump
+  //   which this fix outputs whenever it wants
+
+  peratom_flag = 1;
+  if (ncols == 1) size_peratom_cols = 0;
+  else size_peratom_cols = ncols;
+  peratom_freq = nevery;
+
+  // perform initial allocation of atom-based array
+  // register with Atom class
+
+  vector = nullptr;
+  array = nullptr;
+  grow_arrays(atom->nmax);
+  atom->add_callback(Atom::GROW);
+
+  // zero the vector/array since dump may access it on timestep 0
+  // zero the vector/array since a variable may access it before first run
+
+  int nlocal = atom->nlocal;
+
+  if (ncols == 0) {
+    for (int i = 0; i < nlocal; i++)
+      vector[i] = 0.0;
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      for (int m = 0; m < ncols; m++)
+        array[i][m] = 0.0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixPair::~FixPair()
+{
+  // unregister callbacks to this fix from Atom class
+
+  atom->delete_callback(id,Atom::GROW);
+
+  delete [] pairname;
+  for (int ifield = 0; ifield < nfield; ifield++) {
+    delete [] fieldname[ifield];
+    delete [] triggername[ifield];
+  }
+
+  delete [] fieldname;
+  delete [] trigger;
+  delete [] triggername;
+  delete [] triggerptr;
+  
+  if (ncols == 0) memory->destroy(vector);
+  else memory->destroy(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixPair::setmask()
+{
+  int mask = 0;
+  mask |= PRE_FORCE;
+  mask |= POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPair::init()
+{
+  // make sure pair style still exists
+
+  pstyle = force->pair_match(pairname,1,0);
+  if (pstyle == nullptr) error->all(FLERR,"Fix pair pair style not found");
+}
+
+/* ----------------------------------------------------------------------
+   trigger pair style computation on steps which are multiples of Nevery
+------------------------------------------------------------------------- */
+
+void FixPair::pre_force(int /*vflag*/)
+{
+  if (update->ntimestep % nevery) return;
+
+  // set pair style triggers
+
+  for (int ifield = 0; ifield < nfield; ifield++)
+    if (trigger[ifield]) *(triggerptr[ifield]) = 1;
+}
+
+/* ----------------------------------------------------------------------
+   extract results from pair style
+------------------------------------------------------------------------- */
+
+void FixPair::post_force(int /*vflag*/)
+{
+  if (update->ntimestep % nevery) return;
+
+  // extract pair style fields one by one 
+  // store their values in this fix
+
+  int nlocal = atom->nlocal;
+
+  int icol = 0;
+  int columns;
+
+  for (int ifield = 0; ifield < nfield; ifield++) {
+    void *pvoid = pstyle->extract(fieldname[ifield],columns);
+    if (pvoid == nullptr) 
+      error->all(FLERR,"Fix pair pair style cannot extract {}",fieldname[ifield]);
+
+    if (columns == 0) {
+      double *pvector = (double *) pvoid;
+      if (ncols == 0) { 
+        for (int i = 0; i < nlocal; i++)
+          vector[i] = pvector[i];
+      } else {
+        for (int i = 0; i < nlocal; i++)
+          array[i][icol] = pvector[i];
+      }
+      icol++;
+
+    } else {
+      double **parray = (double **) pvoid;
+      for (int i = 0; i < nlocal; i++)
+        for (int m = 0; m < columns; m++) {
+          array[i][icol] = parray[i][m];
+          icol++;
+        }
+    }
+  }
+
+  // unset pair style triggers
+
+  for (int ifield = 0; ifield < nfield; ifield++)
+    if (trigger[ifield]) *(triggerptr[ifield]) = 0;
+}
+
+/* ----------------------------------------------------------------------
+   allocate atom-based vector or array
+------------------------------------------------------------------------- */
+
+void FixPair::grow_arrays(int nmax)
+{
+  if (ncols == 0) {
+    memory->grow(vector,nmax,"store/state:vector");
+    vector_atom = vector;
+  } else {
+    memory->grow(array,nmax,ncols,"store/state:array");
+    array_atom = array;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based vector or array
+------------------------------------------------------------------------- */
+
+double FixPair::memory_usage()
+{
+  double bytes = 0.0;
+  if (ncols == 0) bytes += (double)atom->nmax * sizeof(double);
+  else bytes += (double)atom->nmax*ncols * sizeof(double);
+  return bytes;
+}

src/fix_pair.h

@@ -0,0 +1,54 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(pair,FixPair);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_PAIR_H
+#define LMP_FIX_PAIR_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixPair : public Fix {
+ public:
+  FixPair(class LAMMPS *, int, char **);
+  ~FixPair() override;
+  int setmask() override;
+  void init() override;
+  void pre_force(int) override;
+  void post_force(int) override;
+
+  void grow_arrays(int) override;
+  double memory_usage() override;
+
+ private:
+  int nevery,nfield,ncols;
+  char *pairname;
+  char **fieldname,**triggername;
+  int *trigger;
+  int **triggerptr;
+
+  class Pair *pstyle;
+  double *vector;
+  double **array;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif