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detect missing initialization and run it instead of crashing with a non-descript segfault

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This commit is contained in:
Axel Kohlmeyer
2018-12-12 16:39:27 -05:00
parent f2f7bcfa5a
commit 5b0c43108d
3 changed files with 82 additions and 48 deletions
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20
src/compute_reduce.cpp
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@ -30,8 +30,8 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ReduceRegion enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduceRegion
enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{UNKNOWN=-1,X,V,F,COMPUTE,FIX,VARIABLE};
enum{PERATOM,LOCAL}; enum{PERATOM,LOCAL};
#define INVOKED_VECTOR 2 #define INVOKED_VECTOR 2
@ -92,6 +92,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
flavor = new int[nargnew]; flavor = new int[nargnew];
ids = new char*[nargnew]; ids = new char*[nargnew];
value2index = new int[nargnew]; value2index = new int[nargnew];
for (int i=0; i < nargnew; ++i) {
which[i] = argindex[i] = flavor[i] = value2index[i] = UNKNOWN;
ids[i] = NULL;
}
nvalues = 0; nvalues = 0;
iarg = 0; iarg = 0;
@ -345,7 +349,7 @@ void ComputeReduce::init()
error->all(FLERR,"Variable name for compute reduce does not exist"); error->all(FLERR,"Variable name for compute reduce does not exist");
value2index[m] = ivariable; value2index[m] = ivariable;
} else value2index[m] = -1; } else value2index[m] = UNKNOWN;
} }
// set index and check validity of region // set index and check validity of region
@ -468,8 +472,16 @@ double ComputeReduce::compute_one(int m, int flag)
index = -1; index = -1;
int vidx = value2index[m]; int vidx = value2index[m];
int aidx = argindex[m];
// initialization in case it has not yet been run, e.g. when
// the compute was invoked right after it has been created
if (vidx == UNKNOWN) {
init();
vidx = value2index[m];
}
int aidx = argindex[m];
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;

97
src/compute_reduce_chunk.cpp
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@ -28,7 +28,7 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
enum{SUM,MINN,MAXX}; enum{SUM,MINN,MAXX};
enum{COMPUTE,FIX,VARIABLE}; enum{UNKNOWN=-1,COMPUTE,FIX,VARIABLE};
#define INVOKED_PERATOM 8 #define INVOKED_PERATOM 8
@ -74,6 +74,10 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
argindex = new int[nargnew]; argindex = new int[nargnew];
ids = new char*[nargnew]; ids = new char*[nargnew];
value2index = new int[nargnew]; value2index = new int[nargnew];
for (int i=0; i < nargnew; ++i) {
which[i] = argindex[i] = value2index[i] = UNKNOWN;
ids[i] = NULL;
}
nvalues = 0; nvalues = 0;
iarg = 0; iarg = 0;
@ -123,46 +127,46 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) { if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]); int icompute = modify->find_compute(ids[i]);
if (icompute < 0) if (icompute < 0)
error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); error->all(FLERR,"Compute ID for compute reduce/chunk does not exist");
if (!modify->compute[icompute]->peratom_flag) if (!modify->compute[icompute]->peratom_flag)
error->all(FLERR,"Compute reduce/chunk compute does not " error->all(FLERR,"Compute reduce/chunk compute does not "
"calculate per-atom values"); "calculate per-atom values");
if (argindex[i] == 0 && if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0) modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce/chunk compute does not " error->all(FLERR,"Compute reduce/chunk compute does not "
"calculate a per-atom vector"); "calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce/chunk compute does not " error->all(FLERR,"Compute reduce/chunk compute does not "
"calculate a per-atom array"); "calculate a per-atom array");
if (argindex[i] && if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols) argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR, error->all(FLERR,
"Compute reduce/chunk compute array is accessed out-of-range"); "Compute reduce/chunk compute array is accessed out-of-range");
} else if (which[i] == FIX) { } else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]); int ifix = modify->find_fix(ids[i]);
if (ifix < 0) if (ifix < 0)
error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); error->all(FLERR,"Fix ID for compute reduce/chunk does not exist");
if (!modify->fix[ifix]->peratom_flag) if (!modify->fix[ifix]->peratom_flag)
error->all(FLERR,"Compute reduce/chunk fix does not " error->all(FLERR,"Compute reduce/chunk fix does not "
"calculate per-atom values"); "calculate per-atom values");
if (argindex[i] == 0 && if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0) modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce/chunk fix does not " error->all(FLERR,"Compute reduce/chunk fix does not "
"calculate a per-atom vector"); "calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce/chunk fix does not " error->all(FLERR,"Compute reduce/chunk fix does not "
"calculate a per-atom array"); "calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Compute reduce/chunk fix array is " error->all(FLERR,"Compute reduce/chunk fix array is "
"accessed out-of-range"); "accessed out-of-range");
} else if (which[i] == VARIABLE) { } else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]); int ivariable = input->variable->find(ids[i]);
if (ivariable < 0) if (ivariable < 0)
error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); error->all(FLERR,"Variable name for compute reduce/chunk does not exist");
if (input->variable->atomstyle(ivariable) == 0) if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute reduce/chunk variable is " error->all(FLERR,"Compute reduce/chunk variable is "
"not atom-style variable"); "not atom-style variable");
} }
} }
@ -354,10 +358,19 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int index; int index = -1;
int vidx = value2index[m];
// initialization in case it has not yet been run, e.g. when
// the compute was invoked right after it has been created
if (vidx == UNKNOWN) {
init();
vidx = value2index[m];
}
if (which[m] == COMPUTE) { if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]]; Compute *compute = modify->compute[vidx];
if (!(compute->invoked_flag & INVOKED_PERATOM)) { if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom(); compute->compute_peratom();
@ -367,26 +380,26 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
if (argindex[m] == 0) { if (argindex[m] == 0) {
double *vcompute = compute->vector_atom; double *vcompute = compute->vector_atom;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1; index = ichunk[i]-1;
if (index < 0) continue; if (index < 0) continue;
combine(vchunk[index*nstride],vcompute[i]); combine(vchunk[index*nstride],vcompute[i]);
} }
} else { } else {
double **acompute = compute->array_atom; double **acompute = compute->array_atom;
int argindexm1 = argindex[m] - 1; int argindexm1 = argindex[m] - 1;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1; index = ichunk[i]-1;
if (index < 0) continue; if (index < 0) continue;
combine(vchunk[index*nstride],acompute[i][argindexm1]); combine(vchunk[index*nstride],acompute[i][argindexm1]);
} }
} }
// access fix fields, check if fix frequency is a match // access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) { } else if (which[m] == FIX) {
Fix *fix = modify->fix[value2index[m]]; Fix *fix = modify->fix[vidx];
if (update->ntimestep % fix->peratom_freq) if (update->ntimestep % fix->peratom_freq)
error->all(FLERR,"Fix used in compute reduce/chunk not " error->all(FLERR,"Fix used in compute reduce/chunk not "
"computed at compatible time"); "computed at compatible time");
@ -394,19 +407,19 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
if (argindex[m] == 0) { if (argindex[m] == 0) {
double *vfix = fix->vector_atom; double *vfix = fix->vector_atom;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1; index = ichunk[i]-1;
if (index < 0) continue; if (index < 0) continue;
combine(vchunk[index*nstride],vfix[i]); combine(vchunk[index*nstride],vfix[i]);
} }
} else { } else {
double **afix = fix->array_atom; double **afix = fix->array_atom;
int argindexm1 = argindex[m] - 1; int argindexm1 = argindex[m] - 1;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1; index = ichunk[i]-1;
if (index < 0) continue; if (index < 0) continue;
combine(vchunk[index*nstride],afix[i][argindexm1]); combine(vchunk[index*nstride],afix[i][argindexm1]);
} }
} }
@ -419,7 +432,7 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
memory->create(varatom,maxatom,"reduce/chunk:varatom"); memory->create(varatom,maxatom,"reduce/chunk:varatom");
} }
input->variable->compute_atom(value2index[m],igroup,varatom,1,0); input->variable->compute_atom(vidx,igroup,varatom,1,0);
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1; index = ichunk[i]-1;

13
src/compute_reduce_region.cpp
View File

@ -28,8 +28,8 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduce enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduce
enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{UNKNOWN=-1,X,V,F,COMPUTE,FIX,VARIABLE};
enum{PERATOM,LOCAL}; enum{PERATOM,LOCAL};
#define INVOKED_VECTOR 2 #define INVOKED_VECTOR 2
@ -70,6 +70,15 @@ double ComputeReduceRegion::compute_one(int m, int flag)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int n = value2index[m]; int n = value2index[m];
// initialization in case it has not yet been run,
// e.g. when invoked
if (n == UNKNOWN) {
init();
n = value2index[m];
}
int aidx = argindex[m];
int j = argindex[m]; int j = argindex[m];
double one = 0.0; double one = 0.0;