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Merge pull request #3753 from akohlmey/tally-compute-warn

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Add warning message when the callback for a /tally compute was not run
This commit is contained in:
Axel Kohlmeyer
2023-04-26 18:29:40 -04:00
committed by GitHub
parent 4aee151b0e f68603703f
commit 717c3207d6
10 changed files with 76 additions and 28 deletions
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22
doc/src/compute_tally.rst
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@ -187,16 +187,22 @@ Both the scalar and vector values calculated by this compute are
Restrictions
""""""""""""
This compute is part of the TALLY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the TALLY package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as :doc:`Tersoff <pair_tersoff>` and
:doc:`Stillinger-Weber <pair_sw>` cannot be used. :doc:`EAM <pair_eam>`
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.
this compute. For example, 3-body and other many-body potentials, such
as :doc:`Tersoff <pair_tersoff>` and :doc:`Stillinger-Weber <pair_sw>`
cannot be used. :doc:`EAM <pair_eam>` potentials only include the pair
potential portion of the EAM interaction when used by this compute, not
the embedding term. Also bonded or Kspace interactions do not
contribute to this compute.
These computes are not compatible with accelerated pair styles from the
GPU, INTEL, KOKKOS, or OPENMP packages. They will either create an error
or print a warning when required data was not tallied in the required way
and thus the data acquisition functions from these computes not called.
When used with dynamic groups, a :doc:`run 0 <run>` command needs to
be inserted in order to initialize the dynamic groups before accessing

1
doc/utils/sphinx-config/false_positives.txt
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@ -1562,6 +1562,7 @@ invertibility
ionicities
ionizable
ionocovalent
iOS
iostreams
iparam
ipi

16
src/TALLY/compute_force_tally.cpp
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@ -21,6 +21,7 @@
#include "memory.h"
#include "pair.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
@ -29,10 +30,11 @@ using namespace LAMMPS_NS;
ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute force/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute force/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1) error->all(FLERR, "Could not find compute force/tally second group ID");
if (igroup2 == -1)
error->all(FLERR, "Could not find compute force/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
@ -177,7 +179,10 @@ double ComputeForceTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// sum accumulated forces across procs
@ -193,7 +198,10 @@ void ComputeForceTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// collect contributions from ghost atoms

10
src/TALLY/compute_heat_flux_tally.cpp
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@ -29,10 +29,11 @@ using namespace LAMMPS_NS;
ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute heat/flux/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute heat/flux/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1) error->all(FLERR, "Could not find compute heat/flux/tally second group ID");
if (igroup2 == -1)
error->all(FLERR, "Could not find compute heat/flux/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
vector_flag = 1;
@ -204,7 +205,10 @@ void ComputeHeatFluxTally::compute_vector()
{
invoked_vector = update->ntimestep;
if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// collect contributions from ghost atoms

14
src/TALLY/compute_heat_flux_virial_tally.cpp
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@ -29,11 +29,11 @@ using namespace LAMMPS_NS;
ComputeHeatFluxVirialTally::ComputeHeatFluxVirialTally(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute heat/flux/virial/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute heat/flux/virial/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1)
error->all(FLERR, "Could not find compute heat/flux/virial/tally second group ID");
error->all(FLERR, "Could not find compute heat/flux/virial/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
@ -191,7 +191,10 @@ double ComputeHeatFluxVirialTally::compute_scalar()
invoked_scalar = update->ntimestep;
if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// sum heat flux across procs
double hflux = 0.0;
@ -210,7 +213,10 @@ void ComputeHeatFluxVirialTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// collect contributions from ghost atoms

8
src/TALLY/compute_pe_mol_tally.cpp
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@ -27,10 +27,11 @@ using namespace LAMMPS_NS;
ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute pe/mol/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute pe/mol/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1) error->all(FLERR, "Could not find compute pe/mol/tally second group ID");
if (igroup2 == -1)
error->all(FLERR, "Could not find compute pe/mol/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
vector_flag = 1;
@ -127,6 +128,9 @@ void ComputePEMolTally::compute_vector()
if ((did_setup != invoked_vector) || (update->eflag_global != invoked_vector))
error->all(FLERR, "Energy was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Energy was not tallied by pair style");
// sum accumulated energies across procs
MPI_Allreduce(etotal, vector, size_vector, MPI_DOUBLE, MPI_SUM, world);

10
src/TALLY/compute_pe_tally.cpp
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@ -28,10 +28,10 @@ using namespace LAMMPS_NS;
ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute pe/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute pe/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1) error->all(FLERR, "Could not find compute pe/tally second group ID");
if (igroup2 == -1) error->all(FLERR, "Could not find compute pe/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
@ -169,6 +169,9 @@ double ComputePETally::compute_scalar()
if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar))
error->all(FLERR, "Energy was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Energy was not tallied by pair style");
// sum accumulated energies across procs
MPI_Allreduce(etotal, vector, size_peratom_cols, MPI_DOUBLE, MPI_SUM, world);
@ -185,6 +188,9 @@ void ComputePETally::compute_peratom()
if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom))
error->all(FLERR, "Energy was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Energy was not tallied by pair style");
// collect contributions from ghost atoms
if (force->newton_pair) {

15
src/TALLY/compute_stress_tally.cpp
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@ -29,10 +29,11 @@ using namespace LAMMPS_NS;
ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR, "Illegal compute stress/tally command");
if (narg < 4) utils::missing_cmd_args(FLERR, "compute stress/tally", error);
igroup2 = group->find(arg[3]);
if (igroup2 == -1) error->all(FLERR, "Could not find compute stress/tally second group ID");
if (igroup2 == -1)
error->all(FLERR, "Could not find compute stress/tally second group ID {}", arg[3]);
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
@ -201,7 +202,10 @@ double ComputeStressTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
if ((did_setup != invoked_scalar) || (update->eflag_global != invoked_scalar))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// sum accumulated forces across procs
@ -221,7 +225,10 @@ void ComputeStressTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
if ((did_setup != invoked_peratom) || (update->eflag_global != invoked_peratom))
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Stress was not tallied on needed timestep");
if ((comm->me == 0) && !force->pair->did_tally_callback())
error->warning(FLERR, "Stress was not tallied by pair style");
// collect contributions from ghost atoms

5
src/pair.cpp
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@ -109,6 +109,7 @@ Pair::Pair(LAMMPS *lmp) :
maxeatom = maxvatom = maxcvatom = 0;
num_tally_compute = 0;
did_tally_flag = 0;
nelements = nparams = maxparam = 0;
@ -295,6 +296,9 @@ void Pair::init()
utils::logmesg(lmp,"Generated {} of {} mixed pair_coeff terms from {} mixing rule\n",
mixed_count, num_mixed_pairs, mixing_rule_names[mix_flag]);
}
// for monitoring, if Pair::ev_tally() was called.
did_tally_flag = 0;
}
/* ----------------------------------------------------------------------
@ -1095,6 +1099,7 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
}
if (num_tally_compute > 0) {
did_tally_flag = 1;
for (int k=0; k < num_tally_compute; ++k) {
Compute *c = list_tally_compute[k];
c->pair_tally_callback(i, j, nlocal, newton_pair,

3
src/pair.h
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@ -230,12 +230,13 @@ class Pair : protected Pointers {
// management of callbacks to be run from ev_tally()
protected:
int num_tally_compute;
int num_tally_compute, did_tally_flag;
class Compute **list_tally_compute;
public:
virtual void add_tally_callback(class Compute *);
virtual void del_tally_callback(class Compute *);
bool did_tally_callback() const { return did_tally_flag != 0; }
protected:
int instance_me; // which Pair class instantiation I am