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

This commit is contained in:
Donatas Surblys 2019-10-04 17:34:15 +09:00
parent de7a8c6559
commit 0067a5b0fe
5 changed files with 54 additions and 18 deletions
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2
src/compute.h
View File

@ -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

32
src/integrate.cpp
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@ -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;
}

3
src/integrate.h
View File

@ -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

32
src/min.cpp
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@ -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;
}
/* ----------------------------------------------------------------------

3
src/min.h
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@ -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;