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Fix atom sorting

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-04-09 01:19:12 +02:00
parent 1ad981a059
commit b6982d56f5
4 changed files with 30 additions and 14 deletions
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4
Makefile
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@ -30,6 +30,10 @@ ifneq ($(ASM_SYNTAX), ATT)
ASFLAGS += -masm=intel ASFLAGS += -masm=intel
endif endif
ifeq ($(strip $(SORT_ATOMS)),true)
DEFINES += -DSORT_ATOMS
endif
ifeq ($(strip $(EXPLICIT_TYPES)),true) ifeq ($(strip $(EXPLICIT_TYPES)),true)
DEFINES += -DEXPLICIT_TYPES DEFINES += -DEXPLICIT_TYPES
endif endif

5
common/parameter.c
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@ -169,6 +169,11 @@ void printParameter(Parameter *param) {
printf("\tNumber of timesteps: %d\n", param->ntimes); printf("\tNumber of timesteps: %d\n", param->ntimes);
printf("\tReport stats every (timesteps): %d\n", param->nstat); printf("\tReport stats every (timesteps): %d\n", param->nstat);
printf("\tReneighbor every (timesteps): %d\n", param->reneigh_every); printf("\tReneighbor every (timesteps): %d\n", param->reneigh_every);
#ifdef SORT_ATOMS
printf("\tSort atoms when reneighboring: yes\n");
#else
printf("\tSort atoms when reneighboring: no\n");
#endif
printf("\tPrune every (timesteps): %d\n", param->prune_every); printf("\tPrune every (timesteps): %d\n", param->prune_every);
printf("\tOutput positions every (timesteps): %d\n", param->x_out_every); printf("\tOutput positions every (timesteps): %d\n", param->x_out_every);
printf("\tOutput velocities every (timesteps): %d\n", param->v_out_every); printf("\tOutput velocities every (timesteps): %d\n", param->v_out_every);

9
lammps/main.c
View File

@ -63,6 +63,10 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
setupNeighbor(param); setupNeighbor(param);
setupThermo(param, atom->Natoms); setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); } if(param->input_file == NULL) { adjustThermo(param, atom); }
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
setupPbc(atom, param); setupPbc(atom, param);
initDevice(atom, neighbor); initDevice(atom, neighbor);
updatePbc(atom, param, true); updatePbc(atom, param, true);
@ -76,9 +80,12 @@ double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
S = getTimeStamp(); S = getTimeStamp();
LIKWID_MARKER_START("reneighbour"); LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param); updateAtomsPbc(atom, param);
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
setupPbc(atom, param); setupPbc(atom, param);
updatePbc(atom, param, true); updatePbc(atom, param, true);
//sortAtom(atom);
buildNeighbor(atom, neighbor); buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour"); LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp(); E = getTimeStamp();