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Merge pull request #1090 from Iximiel/plumed_hCasts
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Removed old-style-cast from Plumed.h
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@GiovanniBussi
GiovanniBussi authored Jul 24, 2024
2 parents 7401ac8 + a517046 commit 3e1bc05
Showing 1 changed file with 77 additions and 57 deletions.
134 changes: 77 additions & 57 deletions src/wrapper/Plumed.h
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Original file line number Diff line number Diff line change
Expand Up @@ -653,6 +653,15 @@

/* The following macros are just to define shortcuts */

/* This is needed to use non c-style cast when working in c++ */
#ifdef __cplusplus
#define __PLUMED_WRAPPER_STATIC_CAST(to,what) static_cast<to>(what)
#define __PLUMED_WRAPPER_REINTERPRET_CAST(to,what) reinterpret_cast<to>(what)
#else
#define __PLUMED_WRAPPER_STATIC_CAST(to,what) ((to) what)
#define __PLUMED_WRAPPER_REINTERPRET_CAST(to,what) __PLUMED_WRAPPER_STATIC_CAST(to,what)
#endif

/* Simplify addition of extern "C" blocks. */
#ifdef __cplusplus
#define __PLUMED_WRAPPER_EXTERN_C_BEGIN extern "C" {
Expand Down Expand Up @@ -988,7 +997,7 @@ __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_merge_with_nested(plumed_error*
}

/* Allocate the new message */
new_buffer=(char*)plumed_malloc(len+1);
new_buffer=__PLUMED_WRAPPER_STATIC_CAST(char*, plumed_malloc(len+1));
if(new_buffer) {
/* If allocation was successful, merge the messages */
new_buffer[0]='\0';
Expand Down Expand Up @@ -1034,12 +1043,12 @@ __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set(void*ptr,int code,const cha
void*const* options;
plumed_error_filesystem_path path;

error=(plumed_error*) ptr;
error=__PLUMED_WRAPPER_STATIC_CAST(plumed_error*, ptr);

error->code=code;
error->error_code=0;
len=__PLUMED_WRAPPER_STD strlen(what);
error->what_buffer=(char*) plumed_malloc(len+1);
error->what_buffer=__PLUMED_WRAPPER_STATIC_CAST(char*, plumed_malloc(len+1));
if(!error->what_buffer) {
plumed_error_set_bad_alloc(error);
return;
Expand All @@ -1050,31 +1059,31 @@ __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set(void*ptr,int code,const cha

/* interpret optional arguments */
if(opt) {
options=(void*const*)opt;
options=__PLUMED_WRAPPER_STATIC_CAST(void*const*, opt);
while(*options) {
/* c: error code */
if(*((const char*)*options)=='c' && *(options+1)) {
error->error_code=*((const int*)*(options+1));
if(*(__PLUMED_WRAPPER_STATIC_CAST(const char*,*options))=='c' && *(options+1)) {
error->error_code=*(__PLUMED_WRAPPER_STATIC_CAST(const int*,*(options+1)));
break;
}
options+=2;
}

options=(void*const*)opt;
options=__PLUMED_WRAPPER_STATIC_CAST(void*const*,opt);
while(*options) {
/* C: error_category */
if(*((const char*)*options)=='C' && *(options+1)) {
error->error_category=*((const int*)*(options+1));
if(*(__PLUMED_WRAPPER_STATIC_CAST(char*, *options))=='C' && *(options+1)) {
error->error_category=*(__PLUMED_WRAPPER_STATIC_CAST(const int*,*(options+1)));
break;
}
options+=2;
}

options=(void*const*)opt;
options=__PLUMED_WRAPPER_STATIC_CAST(void*const*, opt);
while(*options) {
/* path 1 */
if(*((const char*)*options)=='p' && *(options+1)) {
path=*(plumed_error_filesystem_path*)*(options+1);
if(*(__PLUMED_WRAPPER_STATIC_CAST(char*, *options))=='p' && *(options+1)) {
path=*__PLUMED_WRAPPER_STATIC_CAST(plumed_error_filesystem_path*,*(options+1));
error->path1.ptr=plumed_malloc(path.numbytes);
if(!error->path1.ptr) {
plumed_error_set_bad_alloc(error);
Expand All @@ -1087,11 +1096,11 @@ __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set(void*ptr,int code,const cha
options+=2;
}

options=(void*const*)opt;
options=__PLUMED_WRAPPER_STATIC_CAST(void*const*, opt);
while(*options) {
/* path 2 */
if(*((const char*)*options)=='q' && *(options+1)) {
path=*(plumed_error_filesystem_path*)*(options+1);
if(*(__PLUMED_WRAPPER_STATIC_CAST(char*, *options))=='q' && *(options+1)) {
path=*__PLUMED_WRAPPER_STATIC_CAST(plumed_error_filesystem_path*,*(options+1));
error->path2.ptr=plumed_malloc(path.numbytes);
if(!error->path2.ptr) {
plumed_error_set_bad_alloc(error);
Expand All @@ -1104,20 +1113,20 @@ __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set(void*ptr,int code,const cha
options+=2;
}

options=(void*const*)opt;
options=__PLUMED_WRAPPER_STATIC_CAST(void*const*, opt);
while(*options) {
/* n: nested exception */
if(*((const char*)*options)=='n' && *(options+1)) {
if(*(__PLUMED_WRAPPER_STATIC_CAST(char*, *options))=='n' && *(options+1)) {
/* notice that once this is allocated it is guaranteed to be deallocated by the recursive destructor */
error->nested=(plumed_error*) plumed_malloc(sizeof(plumed_error));
error->nested=__PLUMED_WRAPPER_STATIC_CAST(plumed_error*, plumed_malloc(sizeof(plumed_error)));
/* this is if malloc fails */
if(!error->nested) {
plumed_error_set_bad_alloc(error);
break;
}
plumed_error_init((plumed_error*)error->nested);
plumed_error_init(__PLUMED_WRAPPER_STATIC_CAST(plumed_error*,error->nested));
/* plumed will make sure to only use this if it is not null */
*(void**)*(options+1)=error->nested;
*__PLUMED_WRAPPER_STATIC_CAST(void**,*(options+1))=error->nested;
break;
}
options+=2;
Expand Down Expand Up @@ -1482,7 +1491,7 @@ __PLUMED_WRAPPER_C_END
plumed_nothrow_handler nothrow; \
safe.ptr=ptr; \
safe.nelem=nelem; \
safe.shape=(const size_t*)shape; \
safe.shape=__PLUMED_WRAPPER_STATIC_CAST(const size_t*, shape); \
safe.flags=flags_; \
safe.opt=NULL; \
if(error) { \
Expand Down Expand Up @@ -1966,17 +1975,23 @@ class Plumed {
*/
f(::std::filesystem::filesystem_error(msg,
::std::filesystem::path(::std::filesystem::path::string_type(
(::std::filesystem::path::value_type*) h.path1.ptr,h.path1.numbytes/sizeof(::std::filesystem::path::value_type)
),::std::filesystem::path::format::native_format),
reinterpret_cast<::std::filesystem::path::value_type*>(h.path1.ptr),
h.path1.numbytes/sizeof(::std::filesystem::path::value_type)
),
::std::filesystem::path::format::native_format),
error_code));
} else {
f(::std::filesystem::filesystem_error(msg,
::std::filesystem::path(::std::filesystem::path::string_type(
(::std::filesystem::path::value_type*) h.path1.ptr,h.path1.numbytes/sizeof(::std::filesystem::path::value_type)
),::std::filesystem::path::format::native_format),
reinterpret_cast<::std::filesystem::path::value_type*>(h.path1.ptr),
h.path1.numbytes/sizeof(::std::filesystem::path::value_type)
),
::std::filesystem::path::format::native_format),
::std::filesystem::path(::std::filesystem::path::string_type(
(::std::filesystem::path::value_type*) h.path2.ptr,h.path2.numbytes/sizeof(::std::filesystem::path::value_type)
),::std::filesystem::path::format::native_format),
reinterpret_cast<::std::filesystem::path::value_type*>(h.path2.ptr),
h.path2.numbytes/sizeof(::std::filesystem::path::value_type)
),
::std::filesystem::path::format::native_format),
error_code));
}
}
Expand Down Expand Up @@ -3766,7 +3781,7 @@ plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmai
void* tmpptr;
if(f) {
if(__PLUMED_GETENV("PLUMED_LOAD_DEBUG")) {
__PLUMED_FPRINTF(stderr,"+++ Ignoring registration at %p (",(const void*)f);
__PLUMED_FPRINTF(stderr,"+++ Ignoring registration at %p (",__PLUMED_WRAPPER_STATIC_CAST(const void*,f));
__PLUMED_CONVERT_FPTR(tmpptr,f->create);
__PLUMED_FPRINTF(stderr,"%p,",tmpptr);
__PLUMED_CONVERT_FPTR(tmpptr,f->cmd);
Expand Down Expand Up @@ -3811,7 +3826,7 @@ void* plumed_attempt_dlopen(const char*path,int mode) {
*/
__PLUMED_FPRINTF(stderr,"+++ An error occurred. Message from dlopen(): %s +++\n",dlerror());
strlenpath=__PLUMED_WRAPPER_STD strlen(path);
pathcopy=(char*) plumed_malloc(strlenpath+1);
pathcopy=__PLUMED_WRAPPER_STATIC_CAST(char*, plumed_malloc(strlenpath+1));
if(!pathcopy) {
__PLUMED_FPRINTF(stderr,"+++ Allocation error +++\n");
__PLUMED_WRAPPER_STD abort();
Expand All @@ -3836,11 +3851,16 @@ __PLUMED_WRAPPER_INTERNALS_END
/**
Utility to search for a function.
*/
#define __PLUMED_SEARCH_FUNCTION(tmpptr,handle,func,name,debug) \
#ifdef __cplusplus
#define __PLUMED_WRAPPER_SEARCHF_CAST(functype,func,tmpptr) func=reinterpret_cast<functype>(tmpptr)
#else
#define __PLUMED_WRAPPER_SEARCHF_CAST(functype,func,tmpptr) *(void **)&func=tmpptr
#endif
#define __PLUMED_SEARCH_FUNCTION(functype,tmpptr,handle,func,name,debug) \
if(!func) { \
tmpptr=dlsym(handle,name); \
if(tmpptr) { \
*(void **)(&func)=tmpptr; \
__PLUMED_WRAPPER_SEARCHF_CAST(functype,func,tmpptr); \
if(debug) __PLUMED_FPRINTF(stderr,"+++ %s found at %p +++\n",name,tmpptr); \
} else { \
if(debug) __PLUMED_FPRINTF(stderr,"+++ Function %s not found\n",name); \
Expand Down Expand Up @@ -3872,12 +3892,12 @@ void plumed_search_symbols(void* handle, plumed_plumedmain_function_holder* f,pl
unnecessary and might be removed at some point.
*/
debug=__PLUMED_GETENV("PLUMED_LOAD_DEBUG");
table_ptr=(plumed_symbol_table_type*) dlsym(handle,"plumed_symbol_table");
table_ptr=__PLUMED_WRAPPER_STATIC_CAST(plumed_symbol_table_type*, dlsym(handle,"plumed_symbol_table"));
if(table_ptr) functions=table_ptr->functions;
if(debug) {
if(table_ptr) {
__PLUMED_FPRINTF(stderr,"+++ plumed_symbol_table version %i found at %p +++\n",table_ptr->version,(void*)table_ptr);
__PLUMED_FPRINTF(stderr,"+++ plumed_function_pointers found at %p (",(void*)&table_ptr->functions);
__PLUMED_FPRINTF(stderr,"+++ plumed_symbol_table version %i found at %p +++\n",table_ptr->version,__PLUMED_WRAPPER_STATIC_CAST(void*,table_ptr));
__PLUMED_FPRINTF(stderr,"+++ plumed_function_pointers found at %p (",__PLUMED_WRAPPER_STATIC_CAST(void*,&table_ptr->functions));
__PLUMED_CONVERT_FPTR(tmpptr,functions.create);
__PLUMED_FPRINTF(stderr,"%p,",tmpptr);
__PLUMED_CONVERT_FPTR(tmpptr,functions.cmd);
Expand All @@ -3889,12 +3909,12 @@ void plumed_search_symbols(void* handle, plumed_plumedmain_function_holder* f,pl
}
}
/* only searches if they were not found already */
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.create,"plumedmain_create",debug);
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.create,"plumed_plumedmain_create",debug);
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.cmd,"plumedmain_cmd",debug);
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.cmd,"plumed_plumedmain_cmd",debug);
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.finalize,"plumedmain_finalize",debug);
__PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.finalize,"plumed_plumedmain_finalize",debug);
__PLUMED_SEARCH_FUNCTION(plumed_create_pointer,tmpptr,handle,functions.create,"plumedmain_create",debug);
__PLUMED_SEARCH_FUNCTION(plumed_create_pointer,tmpptr,handle,functions.create,"plumed_plumedmain_create",debug);
__PLUMED_SEARCH_FUNCTION(plumed_cmd_pointer,tmpptr,handle,functions.cmd,"plumedmain_cmd",debug);
__PLUMED_SEARCH_FUNCTION(plumed_cmd_pointer,tmpptr,handle,functions.cmd,"plumed_plumedmain_cmd",debug);
__PLUMED_SEARCH_FUNCTION(plumed_finalize_pointer,tmpptr,handle,functions.finalize,"plumedmain_finalize",debug);
__PLUMED_SEARCH_FUNCTION(plumed_finalize_pointer,tmpptr,handle,functions.finalize,"plumed_plumedmain_finalize",debug);
if(functions.create && functions.cmd && functions.finalize) {
if(debug) __PLUMED_FPRINTF(stderr,"+++ PLUMED was loaded correctly +++\n");
*f=functions;
Expand Down Expand Up @@ -4079,7 +4099,7 @@ __PLUMED_WRAPPER_INTERNALS_BEGIN
plumed_implementation* plumed_malloc_pimpl() {
plumed_implementation* pimpl;
/* allocate space for implementation object. this is free-ed in plumed_finalize(). */
pimpl=(plumed_implementation*) plumed_malloc(sizeof(plumed_implementation));
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, plumed_malloc(sizeof(plumed_implementation)));
if(!pimpl) {
__PLUMED_FPRINTF(stderr,"+++ Allocation error +++\n");
__PLUMED_WRAPPER_STD abort();
Expand All @@ -4090,7 +4110,7 @@ plumed_implementation* plumed_malloc_pimpl() {
pimpl->refcount=1;
#if __PLUMED_WRAPPER_DEBUG_REFCOUNT
/* cppcheck-suppress nullPointerRedundantCheck */
__PLUMED_FPRINTF(stderr,"refcount: new at %p\n",(void*)pimpl);
__PLUMED_FPRINTF(stderr,"refcount: new at %p\n",__PLUMED_WRAPPER_STATIC_CAST(void*,pimpl));
#endif
/* cppcheck-suppress nullPointerRedundantCheck */
pimpl->dlhandle=__PLUMED_WRAPPER_CXX_NULLPTR;
Expand Down Expand Up @@ -4222,7 +4242,7 @@ plumed plumed_create_dlopen2(const char*path,int mode) {
if(dlhandle) {
p=plumed_create_dlsym(dlhandle);
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
/* make sure the handler is closed when plumed is finalized */
pimpl->dlclose=1;
return p;
Expand All @@ -4239,7 +4259,7 @@ __PLUMED_WRAPPER_C_BEGIN
plumed plumed_create_reference(plumed p) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
/* increase reference count */
/* with PLUMED > 2.8, we can use an internal reference counter which is thread safe */
Expand All @@ -4249,7 +4269,7 @@ plumed plumed_create_reference(plumed p) {
pimpl->refcount++;
}
#if __PLUMED_WRAPPER_DEBUG_REFCOUNT
__PLUMED_FPRINTF(stderr,"refcount: increase at %p\n",(void*)pimpl);
__PLUMED_FPRINTF(stderr,"refcount: increase at %p\n",__PLUMED_WRAPPER_STATIC_CAST(void*,pimpl));
#endif
return p;
}
Expand Down Expand Up @@ -4281,7 +4301,7 @@ __PLUMED_WRAPPER_C_BEGIN
void plumed_cmd(plumed p,const char*key,const void*val) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
if(!pimpl->p) {
__PLUMED_FPRINTF(stderr,"+++ ERROR: You are trying to use an invalid plumed object. +++\n");
Expand All @@ -4305,7 +4325,7 @@ void plumed_cmd_safe_nothrow(plumed p,const char*key,plumed_safeptr safe,plumed_
return;
}
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
if(!pimpl->p) {
if(pimpl->used_plumed_kernel) {
Expand Down Expand Up @@ -4341,7 +4361,7 @@ __PLUMED_WRAPPER_C_BEGIN
void plumed_cmd_safe(plumed p,const char*key,plumed_safeptr safe) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
if(!pimpl->p) {
__PLUMED_FPRINTF(stderr,"+++ ERROR: You are trying to use an invalid plumed object. +++\n");
Expand All @@ -4362,10 +4382,10 @@ __PLUMED_WRAPPER_C_BEGIN
void plumed_finalize(plumed p) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
#if __PLUMED_WRAPPER_DEBUG_REFCOUNT
__PLUMED_FPRINTF(stderr,"refcount: decrease at %p\n",(void*)pimpl);
__PLUMED_FPRINTF(stderr,"refcount: decrease at %p\n",__PLUMED_WRAPPER_STATIC_CAST(void*,pimpl));
#endif
/* with PLUMED > 2.8, we can use an internal reference counter which is thread safe */
if(pimpl->p && pimpl->table && pimpl->table->version>3) {
Expand All @@ -4390,7 +4410,7 @@ void plumed_finalize(plumed p) {
}
#endif
#if __PLUMED_WRAPPER_DEBUG_REFCOUNT
__PLUMED_FPRINTF(stderr,"refcount: delete at %p\n",(void*)pimpl);
__PLUMED_FPRINTF(stderr,"refcount: delete at %p\n",__PLUMED_WRAPPER_STATIC_CAST(void*,pimpl));
#endif
/* free pimpl space */
plumed_free(pimpl);
Expand All @@ -4401,7 +4421,7 @@ __PLUMED_WRAPPER_C_BEGIN
int plumed_valid(plumed p) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
if(pimpl->p) return 1;
else return 0;
Expand All @@ -4412,7 +4432,7 @@ __PLUMED_WRAPPER_C_BEGIN
int plumed_use_count(plumed p) {
plumed_implementation* pimpl;
/* obtain pimpl */
pimpl=(plumed_implementation*) p.p;
pimpl=__PLUMED_WRAPPER_STATIC_CAST(plumed_implementation*, p.p);
assert(plumed_check_pimpl(pimpl));
/* with PLUMED > 2.8, we can use an internal reference counter which is thread safe */
if(pimpl->p && pimpl->table && pimpl->table->version>3) {
Expand Down Expand Up @@ -4513,7 +4533,7 @@ void plumed_c2f(plumed p,char*c) {
assert(sizeof(p.p)<=16);

assert(c);
cc=(unsigned char*)&p.p;
cc=__PLUMED_WRAPPER_REINTERPRET_CAST(unsigned char*,&p.p);
for(i=0; i<sizeof(p.p); i++) {
/*
characters will range between '0' (ASCII 48) and 'o' (ASCII 111=48+63)
Expand Down Expand Up @@ -4543,7 +4563,7 @@ plumed plumed_f2c(const char*c) {
needed to avoid cppcheck warning on uninitialized p
*/
p.p=__PLUMED_WRAPPER_CXX_NULLPTR;
cc=(unsigned char*)&p.p;
cc=__PLUMED_WRAPPER_REINTERPRET_CAST(unsigned char*,&p.p);
for(i=0; i<sizeof(p.p); i++) {
assert(c[2*i]>=48 && c[2*i]<48+64);
assert(c[2*i+1]>=48 && c[2*i+1]<48+64);
Expand All @@ -4562,14 +4582,14 @@ __PLUMED_WRAPPER_C_END

__PLUMED_WRAPPER_C_BEGIN
void* plumed_c2v(plumed p) {
assert(plumed_check_pimpl((plumed_implementation*)p.p));
assert(plumed_check_pimpl(__PLUMED_WRAPPER_REINTERPRET_CAST(plumed_implementation*,p.p)));
return p.p;
}
__PLUMED_WRAPPER_C_END

__PLUMED_WRAPPER_C_BEGIN
plumed plumed_v2c(void* v) {
assert(plumed_check_pimpl((plumed_implementation*)v));
assert(plumed_check_pimpl(__PLUMED_WRAPPER_REINTERPRET_CAST(plumed_implementation*,v)));
plumed p;
p.p=v;
return p;
Expand Down

1 comment on commit 3e1bc05

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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/METATENSOR.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.tmp
Found broken examples in automatic/Q3.tmp
Found broken examples in automatic/Q4.tmp
Found broken examples in automatic/Q6.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_LINEAR_PROJ.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_MAHA_DIST.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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