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threshold scaling and fix possible null pointer deref
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threshold scaling based on found vectors
fix possible null pointer dereference in context
minor fixes
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@mcodev31
mcodev31 committed Nov 9, 2015
1 parent 4adbebf commit 29d7dba
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Showing 8 changed files with 75 additions and 59 deletions.
22 changes: 12 additions & 10 deletions examples/example.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,13 +70,11 @@ int example(const char* in_file, msym_thresholds_t *thresholds){
int length = read_xyz(in_file, &elements);
if(length <= 0) return -1;

//orbitalsl = sizeof(orbitals)/sizeof(char*);
//bfsl = orbitalsl*length;
//bfs = calloc(bfsl, sizeof(msym_basis_function_t));
double (*psalcs)[bfsl] = NULL; //calloc(bfsl, sizeof(*salcs)); // SALCs in matrix form, and input for symmetrization
double *pcmem = NULL; // calloc(bfsl, sizeof(double)); // Some temporary memory
int *pspecies = NULL; // calloc(bfsl, sizeof(*species));
msym_partner_function_t *ppf = NULL; //calloc(bfsl, sizeof(*pf));

double (*psalcs)[bfsl] = NULL; // SALCs in matrix form, and input for symmetrization
double *pcmem = NULL; // Some temporary memory
int *pspecies = NULL;
msym_partner_function_t *ppf = NULL;

/* Create a context */
msym_context ctx = msymCreateContext();
Expand Down Expand Up @@ -306,9 +304,13 @@ int example(const char* in_file, msym_thresholds_t *thresholds){
do{

int sel_ss = 0, sel_salc = 0;
for(int i = 0; i < msrsl;i++) printf("\t [%d] %s (%d SALCs with %d partner functions each)\n",i, mct->s[msrs[i].s].name, msrs[i].salcl, mct->s[msrs[i].s].d);

do {printf("\nChoose subspace [0-%d]:",msrsl-1);} while(scanf(" %d", &sel_ss) <= 0 || sel_ss < 0 || sel_ss >= msrsl);
for(int i = 0; i < msrsl;i++){
if(msrs[i].salcl > 0)
printf("\t [%d] %s (%d SALCs with %d partner functions each)\n",i, mct->s[msrs[i].s].name, msrs[i].salcl, mct->s[msrs[i].s].d);
else
printf("\t [-] %s (no SALCs of this symmetry species)\n",mct->s[msrs[i].s].name);
}
do {printf("\nChoose subspace [0-%d]:",msrsl-1);} while(scanf(" %d", &sel_ss) <= 0 || sel_ss < 0 || sel_ss >= msrsl || msrs[sel_ss].salcl <= 0);

int salcl = msrs[sel_ss].salcl;

Expand Down
53 changes: 27 additions & 26 deletions src/context.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ msym_error_t msymSetThresholds(msym_context ctx, const msym_thresholds_t *thresh

msym_error_t msymGetThresholds(msym_context ctx, const msym_thresholds_t **thresholds){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->thresholds == NULL) ret = MSYM_INVALID_THRESHOLD;
*thresholds = ctx->thresholds;
err:
Expand All @@ -126,7 +126,7 @@ msym_error_t msymGetThresholds(msym_context ctx, const msym_thresholds_t **thres

msym_error_t msymSetElements(msym_context ctx, int length, msym_element_t *elements){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
/* Allow manual setting of point group before elements */
if(NULL != ctx->es) ctxDestroyPointGroup(ctx);
return ctxSetElements(ctx, length, elements);
Expand All @@ -137,7 +137,7 @@ msym_error_t msymSetElements(msym_context ctx, int length, msym_element_t *eleme
msym_error_t msymGetElements(msym_context ctx, int *length, msym_element_t **elements){
msym_error_t ret = MSYM_SUCCESS;
msym_element_t *relements = NULL;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL || ctx->ext.elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}

*elements = ctx->ext.elements;
Expand All @@ -164,7 +164,7 @@ msym_error_t msymGetEquivalenceSets(msym_context ctx, int *length, const msym_eq

msym_error_t msymGetBasisFunctions(msym_context ctx, int *length, msym_basis_function_t **basis){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->basis == NULL) {
msymSetErrorDetails("Found no basis functions");
ret = MSYM_INVALID_BASIS_FUNCTIONS;
Expand All @@ -179,7 +179,7 @@ msym_error_t msymGetBasisFunctions(msym_context ctx, int *length, msym_basis_fun

msym_error_t msymSetBasisFunctions(msym_context ctx, int length, msym_basis_function_t *basis){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
ctxDestroyBasisFunctions(ctx);
ctx->basis = malloc(sizeof(msym_basis_function_t[length]));
Expand Down Expand Up @@ -229,7 +229,7 @@ msym_error_t msymSetBasisFunctions(msym_context ctx, int length, msym_basis_func

msym_error_t msymGetPointGroupName(msym_context ctx, int l, char buf[l]){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->pg == NULL) {ret = MSYM_INVALID_POINT_GROUP;goto err;}
snprintf(buf, l, "%s",ctx->pg->name);
err:
Expand All @@ -238,7 +238,7 @@ msym_error_t msymGetPointGroupName(msym_context ctx, int l, char buf[l]){

msym_error_t msymGetPointGroupType(msym_context ctx, msym_point_group_type_t *t, int *n){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->pg == NULL) {ret = MSYM_INVALID_POINT_GROUP;goto err;}

*t = ctx->pg->type;
Expand All @@ -254,7 +254,7 @@ msym_error_t msymGetSubgroups(msym_context ctx, int *sgl, const msym_subgroup_t
msym_subgroup_t *gsg = NULL;
int gsgl = 0;

if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->pg == NULL) {ret = MSYM_INVALID_POINT_GROUP;goto err;}
if(ctx->pg->perm == NULL && !(isLinearPointGroup(ctx->pg) && !isLinearSubgroup(ctx->pg))) {
ret = MSYM_INVALID_PERMUTATION;
Expand Down Expand Up @@ -337,7 +337,7 @@ msym_error_t msymGetCharacterTable(msym_context ctx, const msym_character_table_

msym_error_t msymGetCenterOfMass(msym_context ctx, double v[3]){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
vcopy(ctx->cm, v);
err:
Expand All @@ -355,7 +355,7 @@ msym_error_t msymSetCenterOfMass(msym_context ctx, double cm[3]){

msym_error_t msymGetGeometry(msym_context ctx, msym_geometry_t *geometry){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
if(ctx->geometry == MSYM_GEOMETRY_UNKNOWN) {ret = MSYM_INVALID_GEOMETRY;goto err;}
*geometry = ctx->geometry;
Expand All @@ -365,15 +365,15 @@ msym_error_t msymGetGeometry(msym_context ctx, msym_geometry_t *geometry){

msym_error_t msymGetPrincipalMoments(msym_context ctx, double eigval[3]){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
vcopy(ctx->eigval, eigval);
err:
return ret;
}
msym_error_t msymGetPrincipalAxes(msym_context ctx, double eigvec[3][3]){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
mcopy(ctx->eigvec, eigvec);
err:
Expand All @@ -382,9 +382,9 @@ msym_error_t msymGetPrincipalAxes(msym_context ctx, double eigvec[3][3]){

msym_error_t msymGetRadius(msym_context ctx, double *radius){
msym_error_t ret = MSYM_SUCCESS;
double r = 0.0;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
double r = 0.0;
for(int i = 0;i < ctx->elementsl;i++){
double abs = vabs(ctx->elements[i].v);
r = r > abs ? r : abs;
Expand All @@ -398,7 +398,7 @@ msym_error_t msymGetRadius(msym_context ctx, double *radius){
msym_error_t msymGetSymmetryOperations(msym_context ctx, int *sopsl, const msym_symmetry_operation_t **sops){
msym_error_t ret = MSYM_SUCCESS;
msym_symmetry_operation_t *rsops = NULL;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->pg == NULL || ctx->pg->sops == NULL) {ret = MSYM_INVALID_POINT_GROUP;goto err;}

*sops = ctx->pg->sops;
Expand All @@ -413,12 +413,12 @@ msym_error_t msymGetSymmetryOperations(msym_context ctx, int *sopsl, const msym_

msym_error_t msymReleaseContext(msym_context ctx){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
free(ctx->thresholds);
ctxDestroyElements(ctx);
ctxDestroyPointGroup(ctx);
free(ctx);
err:
//err:
return ret;
}

Expand All @@ -433,7 +433,7 @@ msym_error_t msymReleaseContext(msym_context ctx){
msym_error_t ctxSetElements(msym_context ctx, int length, msym_element_t elements[length]){
msym_error_t ret = MSYM_SUCCESS;
msym_thresholds_t *thresholds = NULL;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}

ctxDestroyElements(ctx);

Expand Down Expand Up @@ -466,6 +466,7 @@ msym_error_t ctxSetElements(msym_context ctx, int length, msym_element_t element

return ret;
err:

free(ctx->elements);
free(ctx->pelements);
free(ctx->ext.elements);
Expand All @@ -480,8 +481,8 @@ msym_error_t ctxSetElements(msym_context ctx, int length, msym_element_t element

msym_error_t ctxGetThresholds(msym_context ctx, msym_thresholds_t **thresholds){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx->thresholds == NULL) ret = MSYM_INVALID_THRESHOLD;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->thresholds == NULL) {ret = MSYM_INVALID_THRESHOLD; goto err;}
msym_thresholds_t *t = ctx->thresholds;
if(t->angle < 1.0 && !signbit(t->angle) &&
t->equivalence < 1.0 && !signbit(t->equivalence) &&
Expand All @@ -501,7 +502,7 @@ msym_error_t ctxGetThresholds(msym_context ctx, msym_thresholds_t **thresholds){

msym_error_t ctxGetElements(msym_context ctx, int *l, msym_element_t **elements){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->elements == NULL) {ret = MSYM_INVALID_ELEMENTS; goto err;}
*elements = (msym_element_t *) ctx->elements;
*l = ctx->elementsl;
Expand All @@ -511,7 +512,7 @@ msym_error_t ctxGetElements(msym_context ctx, int *l, msym_element_t **elements)

msym_error_t ctxGetExternalElements(msym_context ctx, int *l, msym_element_t **elements){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->ext.elements == NULL) {ret = MSYM_INVALID_ELEMENTS; goto err;}
*elements = (msym_element_t *) ctx->ext.elements;
*l = ctx->elementsl;
Expand All @@ -537,7 +538,7 @@ msym_error_t ctxUpdateExternalElementCoordinates(msym_context ctx){

msym_error_t ctxGetInternalElement(msym_context ctx, msym_element_t *ext, msym_element_t **element){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->ext.elements == NULL) {ret = MSYM_INVALID_ELEMENTS;goto err;}
if(ext < ctx->ext.elements || ext >= ctx->ext.elements+ctx->elementsl){
msymSetErrorDetails("Element pointer (%p) outside memory block (%p -> %p)", ext, ctx->ext.elements, ctx->ext.elements + ctx->elementsl);
Expand All @@ -551,7 +552,7 @@ msym_error_t ctxGetInternalElement(msym_context ctx, msym_element_t *ext, msym_e

msym_error_t ctxGetSubgroups(msym_context ctx, int *sgl, msym_subgroup_t **sg){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->sg == NULL) {ret = MSYM_INVALID_SUBGROUPS;goto err;}
*sg = ctx->sg;
*sgl = ctx->sgl;
Expand All @@ -561,7 +562,7 @@ msym_error_t ctxGetSubgroups(msym_context ctx, int *sgl, msym_subgroup_t **sg){

msym_error_t ctxSetSubgroups(msym_context ctx, int sgl, msym_subgroup_t *sg){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
ctxDestroySubgroups(ctx);
ctx->sg = sg;
ctx->sgl = sgl;
Expand All @@ -572,7 +573,7 @@ msym_error_t ctxSetSubgroups(msym_context ctx, int sgl, msym_subgroup_t *sg){

msym_error_t ctxGetElementPtrs(msym_context ctx, int *l, msym_element_t ***pelements){
msym_error_t ret = MSYM_SUCCESS;
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT;goto err;}
if(ctx == NULL) {ret = MSYM_INVALID_CONTEXT; return ret;}
if(ctx->pelements == NULL) {ret = MSYM_INVALID_ELEMENTS; goto err;}
*pelements = (msym_element_t **) ctx->pelements;
*l = ctx->elementsl;
Expand Down
2 changes: 1 addition & 1 deletion src/context.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
#define DEFAULT_EQUIVALENCE_THRESHOLD 5.0e-4
#define DEFAULT_EIGFACT_THRESHOLD 1.0e-3
#define DEFAULT_PERMUTATION_THRESHOLD 5.0e-3
#define DEFAULT_ORTHOGONALIZATION_THRESHOLD 0.01
#define DEFAULT_ORTHOGONALIZATION_THRESHOLD 1.0e-2


msym_error_t ctxGetThresholds(msym_context ctx, msym_thresholds_t **thresholds);
Expand Down
10 changes: 9 additions & 1 deletion src/equivalence_set.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,13 @@ msym_error_t generateEquivalenceSet(msym_point_group_t *pg, int length, msym_ele
msym_equivalence_set_t *ges = calloc(length,sizeof(msym_equivalence_set_t));
int gel = 0;
int gesl = 0;

if(pg->order <= 0){
ret = MSYM_INVALID_POINT_GROUP;
msymSetErrorDetails("Point group of zero order when determining equivalence set");
goto err;
}

for(int i = 0;i < length;i++){
double ev[3];
vsub(elements[i].v, cm, ev);
Expand Down Expand Up @@ -83,7 +90,7 @@ msym_error_t generateEquivalenceSet(msym_point_group_t *pg, int length, msym_ele
}
}

if(pg->order % aes->length != 0){
if(!aes->length || (pg->order % aes->length != 0)){
msymSetErrorDetails("Equivalence set length (%d) not a divisor of point group order (%d)",pg->order);
ret = MSYM_INVALID_EQUIVALENCE_SET;
goto err;
Expand Down Expand Up @@ -185,6 +192,7 @@ msym_error_t findPointGroupEquivalenceSets(msym_point_group_t *pg, int length, m
free(pelements);
return ret;
err:
free(ges);
free(pelements);
return ret;

Expand Down
3 changes: 3 additions & 0 deletions src/linalg.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -535,6 +535,7 @@ int mgs(int l, const double m[l][l], double o[l][l], int n, double t){
int mgs2(int l, int lm, const double m[l][l], double o[l][l], int n, double t){

int nm = n + lm + MGS_ADD;
double ts = l/(1.0 + l);
for(int i = 0; i < l && n < nm;i++){
if(vlabs(l, m[i]) < t){
continue;
Expand All @@ -550,8 +551,10 @@ int mgs2(int l, int lm, const double m[l][l], double o[l][l], int n, double t){
for(int k = 0;k < l;k++) o[n][k] -= c*o[j][k];
}
if(vlabs(l, o[n]) >= t){
t *= ts;
vlnorm(l, o[n]);
n++;

}
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/point_group.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -793,8 +793,8 @@ msym_error_t transformAxes(msym_point_group_type_t type, int n, msym_symmetry_op
case (MSYM_POINT_GROUP_TYPE_Ih) : {
msym_symmetry_operation_t *dprimary = NULL;
msym_symmetry_operation_t *sop;
double z = -2.0;
for(sop = sops; sop < (sops + sopsl); sop++){
double z = -2.0;
if(sop->type == PROPER_ROTATION && sop->order == 2){
double v[3];
vnorm2(sop->v,v);
Expand Down
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