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Merge branch 'develop' into general-triclinic

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# Conflicts:
#	src/atom.cpp
This commit is contained in:
Axel Kohlmeyer
2024-02-06 19:21:50 -05:00
parent 7905e5d146 b9ec85427d
commit dbdcfc5c97
356 changed files with 8055 additions and 5135 deletions
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58
src/atom.cpp
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@ -50,8 +50,6 @@ using namespace MathConst;
static constexpr int DELTA = 1;
static constexpr double EPSILON = 1.0e-6;
static constexpr double EPS_ZCOORD = 1.0e-12;
static constexpr int MAXLINE = 256;
/* ----------------------------------------------------------------------
one instance per AtomVec style in style_atom.h
@ -236,6 +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
@ -335,6 +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
@ -2647,6 +2650,18 @@ 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
@ -2690,6 +2705,33 @@ int Atom::find_custom(const char *name, int &flag, int &cols)
return -1;
}
/** \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) 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;
}
/** \brief Add a custom per-atom property with the given name and type and size
\verbatim embed:rst
@ -2700,9 +2742,10 @@ 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 Atom::add_custom(const char *name, int flag, int cols, int ghost)
{
int index = -1;
@ -2711,6 +2754,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
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");
@ -2719,6 +2764,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
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");
@ -2727,6 +2774,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
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");
@ -2737,6 +2786,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
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");
@ -2745,6 +2796,7 @@ int Atom::add_custom(const char *name, int flag, int cols)
if (index < 0)
error->all(FLERR,"Invalid call to Atom::add_custom()");
return index;
}