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make separate find_custom_ghost() and use four separate ghost info arrays

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This commit is contained in:
Shern Tee
2024-01-16 23:35:40 +10:00
parent 89fd9ec531
commit b95706ca64
3 changed files with 60 additions and 13 deletions
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12
src/AMOEBA/pair_amoeba.cpp
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@ -831,17 +831,21 @@ void PairAmoeba::init_style()
"xyzaxis", "polaxe", "pval"};
int const flag_check[6] = {0, 0, 1, 1, 0, 1}; // correct type (0 int, 1 dbl)
int const cols_check[6] = {0, 0, 0, 3, 0, 0}; // xyzaxis 3 cols, all others 0
int const border_check[6] = {1, 0, 0, 0, 0, 0}; // which types need ghost
int flag, cols, border;
int const ghost_check[6] = {1, 0, 0, 0, 0, 0}; // which types need ghost
int flag, cols, ghost;
int index[6];
for (int i = 0; i < 6; i++) {
index[i] = atom->find_custom(names[i], flag, cols, border);
if (ghost_check[i]) {
index[i] = atom->find_custom_ghost(names[i], flag, cols, ghost);
} else {
index[i] = atom->find_custom(names[i], flag, cols);
}
std::string err = "";
if (index[i] < 0) err = "was not defined";
else if (flag_check[i] != flag) err = "has the wrong type";
else if (cols_check[i] != cols) err = "has the wrong number of columns";
else if (border_check[i] && !border) err = "must be set by fix property/atom with ghost yes";
else if (ghost_check[i] && !ghost) err = "must be set by fix property/atom with ghost yes";
if (err != "")
error->all(FLERR,"Pair {} per-atom variable {} {}", mystyle, names[i], err);
}

55
src/atom.cpp
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@ -234,6 +234,7 @@ Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp), atom_style(nullptr), avec(nullptr), a
darray = nullptr;
icols = dcols = nullptr;
ivname = dvname = ianame = daname = nullptr;
ivghost = dvghost = iaghost = daghost = nullptr;
// initialize atom style and array existence flags
@ -333,6 +334,10 @@ Atom::~Atom()
memory->sfree(darray);
memory->sfree(icols);
memory->sfree(dcols);
memory->destroy(ivghost);
memory->destroy(dvghost);
memory->destroy(iaghost);
memory->destroy(daghost);
// delete user-defined molecules
@ -2599,13 +2604,24 @@ void Atom::update_callback(int ifix)
if (extra_border[i] > ifix) extra_border[i]--;
}
/** \brief Find a custom per-atom property with given name
\verbatim embed:rst
This function returns the list index of a custom per-atom property
with the name "name", also returning by reference its data type and
number of values per atom.
\endverbatim
* \param name Name of the property (w/o a "i_" or "d_" or "i2_" or "d2_" prefix)
* \param &flag Returns data type of property: 0 for int, 1 for double
* \param &cols Returns number of values: 0 for a single value, 1 or more for a vector of values
* \return index of property in the respective list of properties
*/
/* ----------------------------------------------------------------------
find custom per-atom vector with name
return index if found, -1 if not found
lists of names can have NULL entries if previously removed
return flag = 0/1 for int/double
return cols = 0/N for vector/array where N = # of columns
return border = 0/1 if fix property/atom has "ghost" no/yes
------------------------------------------------------------------------- */
int Atom::find_custom(const char *name, int &flag, int &cols)
@ -2643,10 +2659,30 @@ int Atom::find_custom(const char *name, int &flag, int &cols)
return -1;
}
int Atom::find_custom(const char *name, int &flag, int &cols, int &border)
/** \brief Find a custom per-atom property with given name and retrieve ghost property
\verbatim embed:rst
This function returns the list index of a custom per-atom property
with the name "name", also returning by reference its data type,
number of values per atom, and if it is communicated to ghost particles.
Classes rarely need to check on ghost communication and so `find_custom`
is typically preferred to this function. See :doc:`pair amoeba <pair_amoeba>`
for an example where checking ghost communication is necessary.
\endverbatim
* \param name Name of the property (w/o a "i_" or "d_" or "i2_" or "d2_" prefix)
* \param &flag Returns data type of property: 0 for int, 1 for double
* \param &cols Returns number of values: 0 for a single value, 1 or more for a vector of values
* \param &ghost Returns whether property is communicated to ghost atoms: 0 for no, 1 for yes
* \return index of property in the respective list of properties
*/
int Atom::find_custom_ghost(const char *name, int &flag, int &cols, int &ghost)
{
int i = find_custom(name, flag, cols);
if (i != -1) border = custom_border[flag + (cols) ? 2 : 0][i];
if (i == -1) return i;
if ((flag == 0) && (cols == 0)) ghost = ivghost[i];
else if ((flag == 1) && (cols == 0)) ghost = dvghost[i];
else if ((flag == 0) && (cols == 1)) ghost = iaghost[i];
else if ((flag == 1) && (cols == 1)) ghost = daghost[i];
return i;
}
@ -2660,9 +2696,10 @@ This function is called, e.g. from :doc:`fix property/atom <fix_property_atom>`.
* \param name Name of the property (w/o a "i_" or "d_" or "i2_" or "d2_" prefix)
* \param flag Data type of property: 0 for int, 1 for double
* \param cols Number of values: 0 for a single value, 1 or more for a vector of values
* \param ghost Whether property is communicated to ghost atoms: 0 for no, 1 for yes
* \return index of property in the respective list of properties
*/
int Atom::add_custom(const char *name, int flag, int cols, int border)
int Atom::add_custom(const char *name, int flag, int cols, int ghost)
{
int index = -1;
@ -2671,6 +2708,8 @@ int Atom::add_custom(const char *name, int flag, int cols, int border)
nivector++;
ivname = (char **) memory->srealloc(ivname,nivector*sizeof(char *),"atom:ivname");
ivname[index] = utils::strdup(name);
ivghost = (int *) memory->srealloc(ivghost,nivector*sizeof(int),"atom:ivghost");
ivghost[index] = ghost;
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
@ -2679,6 +2718,8 @@ int Atom::add_custom(const char *name, int flag, int cols, int border)
ndvector++;
dvname = (char **) memory->srealloc(dvname,ndvector*sizeof(char *),"atom:dvname");
dvname[index] = utils::strdup(name);
dvghost = (int *) memory->srealloc(dvghost,ndvector*sizeof(int),"atom:dvghost");
dvghost[index] = ghost;
dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),"atom:dvector");
memory->create(dvector[index],nmax,"atom:dvector");
@ -2687,6 +2728,8 @@ int Atom::add_custom(const char *name, int flag, int cols, int border)
niarray++;
ianame = (char **) memory->srealloc(ianame,niarray*sizeof(char *),"atom:ianame");
ianame[index] = utils::strdup(name);
iaghost = (int *) memory->srealloc(iaghost,niarray*sizeof(int),"atom:iaghost");
iaghost[index] = ghost;
iarray = (int ***) memory->srealloc(iarray,niarray*sizeof(int **),"atom:iarray");
memory->create(iarray[index],nmax,cols,"atom:iarray");
icols = (int *) memory->srealloc(icols,niarray*sizeof(int),"atom:icols");
@ -2697,6 +2740,8 @@ int Atom::add_custom(const char *name, int flag, int cols, int border)
ndarray++;
daname = (char **) memory->srealloc(daname,ndarray*sizeof(char *),"atom:daname");
daname[index] = utils::strdup(name);
daghost = (int *) memory->srealloc(daghost,ndarray*sizeof(int),"atom:daghost");
daghost[index] = ghost;
darray = (double ***) memory->srealloc(darray,ndarray*sizeof(double **),"atom:darray");
memory->create(darray[index],nmax,cols,"atom:darray");
dcols = (int *) memory->srealloc(dcols,ndarray*sizeof(int),"atom:dcols");
@ -2705,8 +2750,6 @@ int Atom::add_custom(const char *name, int flag, int cols, int border)
if (index < 0)
error->all(FLERR,"Invalid call to Atom::add_custom()");
else
custom_border[flag + (cols) ? 2 : 0].push_back(border);
return index;
}

6
src/atom.h
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@ -244,7 +244,7 @@ class Atom : protected Pointers {
int *icols, *dcols;
char **ivname, **dvname, **ianame, **daname;
int nivector, ndvector, niarray, ndarray;
std::array<std::vector<int>, 4> custom_border;
int *ivghost, *dvghost, *iaghost, *daghost;
// molecule templates
// each template can be a set of consecutive molecules
@ -366,8 +366,8 @@ class Atom : protected Pointers {
void update_callback(int);
int find_custom(const char *, int &, int &);
int find_custom(const char *, int &, int &, int &);
virtual int add_custom(const char *, int, int, int border = 0);
int find_custom_ghost(const char *, int &, int &, int &);
virtual int add_custom(const char *, int, int, int ghost = 0);
virtual void remove_custom(int, int, int);
void *extract(const char *);