Commit 0067a5b0 authored by Donatas Surblys's avatar Donatas Surblys
Browse files

add support for pressatomflag=2 to compute.h and vflag=8 to integrate.cpp and... 

add support for pressatomflag=2 to compute.h and vflag=8 to integrate.cpp and min.cpp to indicate centroid atomic stress computation
parent de7a8c65

src/compute.h

+2 −0
Original line number Diff line number Diff line
@@ -59,6 +59,8 @@ class Compute : protected Pointers { 
  int pressflag;      // 1 if Compute can be used as pressure (uses virial)

                      // must have both compute_scalar, compute_vector

  int pressatomflag;  // 1 if Compute calculates per-atom virial

                      // 2 if Compute calculates per-atom centroid virial

                      // 3 if Compute calculates both

  int peflag;         // 1 if Compute calculates PE (uses Force energies)

  int peatomflag;     // 1 if Compute calculates per-atom PE

  int create_attribute;    // 1 if compute stores attributes that need

src/integrate.cpp

+24 −8
Original line number Diff line number Diff line
@@ -26,7 +26,7 @@ using namespace LAMMPS_NS; 
Integrate::Integrate(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)

{

  elist_global = elist_atom = NULL;

  vlist_global = vlist_atom = NULL;

  vlist_global = vlist_atom = cvlist_atom = NULL;

  external_force_clear = 0;

}
@@ -38,6 +38,7 @@ Integrate::~Integrate() 
  delete [] elist_atom;

  delete [] vlist_global;

  delete [] vlist_atom;

  delete [] cvlist_atom;

}



/* ---------------------------------------------------------------------- */
@@ -72,25 +73,28 @@ void Integrate::ev_setup() 
  delete [] elist_atom;

  delete [] vlist_global;

  delete [] vlist_atom;

  delete [] cvlist_atom;

  elist_global = elist_atom = NULL;

  vlist_global = vlist_atom = NULL;

  vlist_global = vlist_atom = cvlist_atom = NULL;



  nelist_global = nelist_atom = 0;

  nvlist_global = nvlist_atom = 0;

  nvlist_global = nvlist_atom = ncvlist_atom = 0;

  for (int i = 0; i < modify->ncompute; i++) {

    if (modify->compute[i]->peflag) nelist_global++;

    if (modify->compute[i]->peatomflag) nelist_atom++;

    if (modify->compute[i]->pressflag) nvlist_global++;

    if (modify->compute[i]->pressatomflag) nvlist_atom++;

    if (modify->compute[i]->pressatomflag & 1) nvlist_atom++;

    if (modify->compute[i]->pressatomflag & 2) ncvlist_atom++;

  }



  if (nelist_global) elist_global = new Compute*[nelist_global];

  if (nelist_atom) elist_atom = new Compute*[nelist_atom];

  if (nvlist_global) vlist_global = new Compute*[nvlist_global];

  if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];

  if (ncvlist_atom) cvlist_atom = new Compute*[ncvlist_atom];



  nelist_global = nelist_atom = 0;

  nvlist_global = nvlist_atom = 0;

  nvlist_global = nvlist_atom = ncvlist_atom = 0;

  for (int i = 0; i < modify->ncompute; i++) {

    if (modify->compute[i]->peflag)

      elist_global[nelist_global++] = modify->compute[i];
@@ -98,8 +102,10 @@ void Integrate::ev_setup() 
      elist_atom[nelist_atom++] = modify->compute[i];

    if (modify->compute[i]->pressflag)

      vlist_global[nvlist_global++] = modify->compute[i];

    if (modify->compute[i]->pressatomflag)

    if (modify->compute[i]->pressatomflag & 1)

      vlist_atom[nvlist_atom++] = modify->compute[i];

    if (modify->compute[i]->pressatomflag & 2)

      cvlist_atom[ncvlist_atom++] = modify->compute[i];

  }

}
@@ -116,6 +122,10 @@ void Integrate::ev_setup() 
   vflag = 2 = global virial with pair portion via F dot r including ghosts

   vflag = 4 = per-atom virial only

   vflag = 5 or 6 = both global and per-atom virial

   vflag = 8 = per-atom centroid virial only

   vflag = 9 or 10 = both global and per-atom centroid virial

   vflag = 12 = both per-atom virial and per-atom centroid virial

   vflag = 13 or 15 = global, per-atom virial and per-atom centroid virial

------------------------------------------------------------------------- */



void Integrate::ev_set(bigint ntimestep)
@@ -150,7 +160,13 @@ void Integrate::ev_set(bigint ntimestep) 
    if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;

  if (flag) vflag_atom = 4;



  flag = 0;

  int cvflag_atom = 0;

  for (i = 0; i < ncvlist_atom; i++)

    if (cvlist_atom[i]->matchstep(ntimestep)) flag = 1;

  if (flag) cvflag_atom = 8;



  if (vflag_global) update->vflag_global = ntimestep;

  if (vflag_atom) update->vflag_atom = ntimestep;

  vflag = vflag_global + vflag_atom;

  if (vflag_atom || cvflag_atom) update->vflag_atom = ntimestep;

  vflag = vflag_global + vflag_atom + cvflag_atom;

}

src/integrate.h

+2 −1
Original line number Diff line number Diff line
@@ -36,11 +36,12 @@ class Integrate : protected Pointers { 
  int external_force_clear;         // clear forces locally or externally



  int nelist_global,nelist_atom;    // # of PE,virial computes to check

  int nvlist_global,nvlist_atom;

  int nvlist_global,nvlist_atom,ncvlist_atom;

  class Compute **elist_global;     // lists of PE,virial Computes

  class Compute **elist_atom;

  class Compute **vlist_global;

  class Compute **vlist_atom;

  class Compute **cvlist_atom;



  int pair_compute_flag;            // 0 if pair->compute is skipped

  int kspace_compute_flag;          // 0 if kspace->compute is skipped

src/min.cpp

+24 −8
Original line number Diff line number Diff line
@@ -59,7 +59,7 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp) 
  normstyle = TWO;



  elist_global = elist_atom = NULL;

  vlist_global = vlist_atom = NULL;

  vlist_global = vlist_atom = cvlist_atom = NULL;



  nextra_global = 0;

  fextra = NULL;
@@ -83,6 +83,7 @@ Min::~Min() 
  delete [] elist_atom;

  delete [] vlist_global;

  delete [] vlist_atom;

  delete [] cvlist_atom;



  delete [] fextra;
@@ -691,25 +692,28 @@ void Min::ev_setup() 
  delete [] elist_atom;

  delete [] vlist_global;

  delete [] vlist_atom;

  delete [] cvlist_atom;

  elist_global = elist_atom = NULL;

  vlist_global = vlist_atom = NULL;

  vlist_global = vlist_atom = cvlist_atom = NULL;



  nelist_global = nelist_atom = 0;

  nvlist_global = nvlist_atom = 0;

  nvlist_global = nvlist_atom = ncvlist_atom = 0;

  for (int i = 0; i < modify->ncompute; i++) {

    if (modify->compute[i]->peflag) nelist_global++;

    if (modify->compute[i]->peatomflag) nelist_atom++;

    if (modify->compute[i]->pressflag) nvlist_global++;

    if (modify->compute[i]->pressatomflag) nvlist_atom++;

    if (modify->compute[i]->pressatomflag & 1) nvlist_atom++;

    if (modify->compute[i]->pressatomflag & 2) ncvlist_atom++;

  }



  if (nelist_global) elist_global = new Compute*[nelist_global];

  if (nelist_atom) elist_atom = new Compute*[nelist_atom];

  if (nvlist_global) vlist_global = new Compute*[nvlist_global];

  if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];

  if (ncvlist_atom) cvlist_atom = new Compute*[ncvlist_atom];



  nelist_global = nelist_atom = 0;

  nvlist_global = nvlist_atom = 0;

  nvlist_global = nvlist_atom = ncvlist_atom = 0;

  for (int i = 0; i < modify->ncompute; i++) {

    if (modify->compute[i]->peflag)

      elist_global[nelist_global++] = modify->compute[i];
@@ -717,8 +721,10 @@ void Min::ev_setup() 
      elist_atom[nelist_atom++] = modify->compute[i];

    if (modify->compute[i]->pressflag)

      vlist_global[nvlist_global++] = modify->compute[i];

    if (modify->compute[i]->pressatomflag)

    if (modify->compute[i]->pressatomflag & 1)

      vlist_atom[nvlist_atom++] = modify->compute[i];

    if (modify->compute[i]->pressatomflag & 2)

      cvlist_atom[ncvlist_atom++] = modify->compute[i];

  }

}
@@ -736,6 +742,10 @@ void Min::ev_setup() 
   vflag = 2 = global virial with pair portion via F dot r including ghosts

   vflag = 4 = per-atom virial only

   vflag = 5 or 6 = both global and per-atom virial

   vflag = 8 = per-atom centroid virial only

   vflag = 9 or 10 = both global and per-atom centroid virial

   vflag = 12 = both per-atom virial and per-atom centroid virial

   vflag = 13 or 15 = global, per-atom virial and per-atom centroid virial

------------------------------------------------------------------------- */



void Min::ev_set(bigint ntimestep)
@@ -768,9 +778,15 @@ void Min::ev_set(bigint ntimestep) 
    if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;

  if (flag) vflag_atom = 4;



  flag = 0;

  int cvflag_atom = 0;

  for (i = 0; i < ncvlist_atom; i++)

    if (cvlist_atom[i]->matchstep(ntimestep)) flag = 1;

  if (flag) cvflag_atom = 8;



  if (vflag_global) update->vflag_global = update->ntimestep;

  if (vflag_atom) update->vflag_atom = update->ntimestep;

  vflag = vflag_global + vflag_atom;

  if (vflag_atom || cvflag_atom) update->vflag_atom = update->ntimestep;

  vflag = vflag_global + vflag_atom + cvflag_atom;

}



/* ----------------------------------------------------------------------

src/min.h

+2 −1
Original line number Diff line number Diff line
@@ -71,11 +71,12 @@ class Min : protected Pointers { 
  int normstyle;                // TWO, MAX or INF flag for force norm evaluation



  int nelist_global,nelist_atom;    // # of PE,virial computes to check

  int nvlist_global,nvlist_atom;

  int nvlist_global,nvlist_atom,ncvlist_atom;

  class Compute **elist_global;     // lists of PE,virial Computes

  class Compute **elist_atom;

  class Compute **vlist_global;

  class Compute **vlist_atom;

  class Compute **cvlist_atom;



  int triclinic;              // 0 if domain is orthog, 1 if triclinic

  int pairflag;

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