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plug memory leak and avoid accessing uninitialized memory in virial computation and properly handle PPPM/Ewald cases that don't compute a virial

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This commit is contained in:
Axel Kohlmeyer
2018-12-06 18:30:12 -05:00
parent 9ee076e4c7
commit e37436d646
2 changed files with 37 additions and 19 deletions
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4
doc/src/kspace_style.txt
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@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units) smallq = cutoff for charges to be considered (optional) (charge units)
{scafacos} values = method accuracy {scafacos} values = method accuracy
method = fmm or p2nfft or ewald or direct method = fmm or p2nfft or p3m or ewald or direct
accuracy = desired relative error in forces :pre accuracy = desired relative error in forces :pre
:ule :ule
@ -392,6 +392,8 @@ the same bond/angle/dihedral are weighted by the
"special_bonds"_special_bonds.html command. Likewise it does not "special_bonds"_special_bonds.html command. Likewise it does not
support the "TIP4P water style" where a fictitious charge site is support the "TIP4P water style" where a fictitious charge site is
introduced in each water molecule. introduced in each water molecule.
Finally, the methods {p3m} and {ewald} do not support computing the
virial, so this contribution is not included.
[Related commands:] [Related commands:]

40
src/USER-SCAFACOS/scafacos.cpp
View File

@ -100,6 +100,12 @@ void Scafacos::init()
if (logfile && me == 0) fprintf(logfile, if (logfile && me == 0) fprintf(logfile,
"Setting up ScaFaCoS with solver %s ...\n",method); "Setting up ScaFaCoS with solver %s ...\n",method);
if ((strcmp(method,"p3m") == 0) && (me == 0))
error->warning(FLERR,"Virial computation for P3M not available");
if ((strcmp(method,"ewald") == 0) && (me == 0))
error->warning(FLERR,"Virial computation for Ewald not available");
if (!atom->q_flag) if (!atom->q_flag)
error->all(FLERR,"Kspace style requires atom attribute q"); error->all(FLERR,"Kspace style requires atom attribute q");
@ -143,8 +149,7 @@ void Scafacos::init()
double *q = atom->q; double *q = atom->q;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
if (strcmp(method,"fmm") == 0) if (strcmp(method,"fmm") == 0) {
{
if (fmm_tuning_flag == 1) if (fmm_tuning_flag == 1)
fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
else else
@ -152,8 +157,7 @@ void Scafacos::init()
} }
// for the FMM at least one particle is required per process // for the FMM at least one particle is required per process
if (strcmp(method,"fmm") == 0) if (strcmp(method,"fmm") == 0) {
{
int empty = (nlocal==0)?1:0; int empty = (nlocal==0)?1:0;
MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
if (empty > 0) if (empty > 0)
@ -212,11 +216,15 @@ void Scafacos::compute(int eflag, int vflag)
memory->create(efield,maxatom,3,"scafacos:efield"); memory->create(efield,maxatom,3,"scafacos:efield");
} }
if (vflag_global) if (vflag_global) {
{
fcs_set_compute_virial((FCS)fcs,1); // for P3M or Ewald we cannot compute the virial. skip it.
//if (strcmp(method,"p3m") == 0)
// error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); if ((strcmp(method,"p3m") != 0)
&& (strcmp(method,"ewald") != 0)) {
result = fcs_set_compute_virial((FCS)fcs,1);
check_result((void*)&result);
}
} }
// pack coords into xpbc and apply PBC // pack coords into xpbc and apply PBC
@ -230,6 +238,7 @@ void Scafacos::compute(int eflag, int vflag)
j += 3; j += 3;
} }
} }
// if simulation box has changed, call fcs_tune() // if simulation box has changed, call fcs_tune()
if (box_has_changed()) { if (box_has_changed()) {
@ -245,9 +254,15 @@ void Scafacos::compute(int eflag, int vflag)
// extract virial // extract virial
if (vflag_global) if (vflag_global) {
{
fcs_get_virial((FCS)fcs,virial_int); // for P3M or Ewald we cannot compute the virial. skip it.
if ((strcmp(method,"p3m") != 0)
&& (strcmp(method,"ewald") != 0)) {
result = fcs_get_virial((FCS)fcs,virial_int);
check_result((void*)&result);
virial[0] = virial_int[0]; virial[0] = virial_int[0];
virial[1] = virial_int[1]; virial[1] = virial_int[1];
virial[2] = virial_int[2]; virial[2] = virial_int[2];
@ -255,6 +270,7 @@ void Scafacos::compute(int eflag, int vflag)
virial[4] = virial_int[5]; virial[4] = virial_int[5];
virial[5] = virial_int[8]; virial[5] = virial_int[8];
} }
}
// apply Efield to each particle // apply Efield to each particle
// accumulate total energy // accumulate total energy