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enable per-atom custom arrays in addition to vectors

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This commit is contained in:
Steve Plimpton
2020-09-04 11:33:49 -06:00
parent d00807ee9a
commit d1442b0538
23 changed files with 1390 additions and 722 deletions
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202
src/atom.cpp
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@ -178,10 +178,13 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// custom atom arrays
nivector = ndvector = 0;
nivector = ndvector = niarray = ndarray = 0;
ivector = NULL;
dvector = NULL;
iname = dname = NULL;
iarray = NULL;
darray = NULL;
icols = dcols = NULL;
ivname = dvname = ianame = daname = NULL;
// initialize atom style and array existence flags
@ -262,20 +265,32 @@ Atom::~Atom()
// delete custom atom arrays
for (int i = 0; i < nivector; i++) {
delete [] iname[i];
delete [] ivname[i];
memory->destroy(ivector[i]);
}
if (dvector != NULL) {
for (int i = 0; i < ndvector; i++) {
delete [] dname[i];
memory->destroy(dvector[i]);
}
for (int i = 0; i < ndvector; i++) {
delete [] dvname[i];
memory->destroy(dvector[i]);
}
for (int i = 0; i < niarray; i++) {
delete [] ianame[i];
memory->destroy(iarray[i]);
}
for (int i = 0; i < ndarray; i++) {
delete [] daname[i];
memory->destroy(darray[i]);
}
memory->sfree(iname);
memory->sfree(dname);
memory->sfree(ivname);
memory->sfree(dvname);
memory->sfree(ianame);
memory->sfree(daname);
memory->sfree(ivector);
memory->sfree(dvector);
memory->sfree(iarray);
memory->sfree(darray);
memory->sfree(icols);
memory->sfree(dcols);
// delete user-defined molecules
@ -2282,23 +2297,41 @@ void Atom::update_callback(int ifix)
/* ----------------------------------------------------------------------
find custom per-atom vector with name
return index if found, and flag = 0/1 for int/double
return -1 if not found
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
------------------------------------------------------------------------- */
int Atom::find_custom(const char *name, int &flag)
int Atom::find_custom(const char *name, int &flag, int &cols)
{
if(name == NULL) return -1;
if (name == NULL) return -1;
for (int i = 0; i < nivector; i++)
if (iname[i] && strcmp(iname[i],name) == 0) {
if (ivname[i] && strcmp(ivname[i],name) == 0) {
flag = 0;
cols = 0;
return i;
}
for (int i = 0; i < ndvector; i++)
if (dname[i] && strcmp(dname[i],name) == 0) {
if (dvname[i] && strcmp(dvname[i],name) == 0) {
flag = 1;
cols = 0;
return i;
}
for (int i = 0; i < niarray; i++)
if (ianame[i] && strcmp(ianame[i],name) == 0) {
flag = 0;
cols = icols[i];
return i;
}
for (int i = 0; i < ndarray; i++)
if (daname[i] && strcmp(daname[i],name) == 0) {
flag = 1;
cols = dcols[i];
return i;
}
@ -2306,60 +2339,107 @@ int Atom::find_custom(const char *name, int &flag)
}
/* ----------------------------------------------------------------------
add a custom variable with name of type flag = 0/1 for int/double
add a custom variable with name
flag = 0/1 for int/double, cols = 0/N for vector/array where N = # of columns
assumes name does not already exist
return index in ivector or dvector of its location
vectors of names and data ptrs are always incremented by one
return index in vector/array lists of its location
------------------------------------------------------------------------- */
int Atom::add_custom(const char *name, int flag)
int Atom::add_custom(const char *name, int flag, int cols)
{
int index;
if (flag == 0) {
if (flag == 0 && cols == 0) {
index = nivector;
nivector++;
iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
"atom:iname");
ivname = (char **) memory->srealloc(ivname,nivector*sizeof(char *),
"atom:ivname");
int n = strlen(name) + 1;
iname[index] = new char[n];
strcpy(iname[index],name);
ivname[index] = new char[n];
strcpy(ivname[index],name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
} else {
} else if (flag == 1 && cols == 0) {
index = ndvector;
ndvector++;
dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
"atom:dname");
dvname = (char **) memory->srealloc(dvname,ndvector*sizeof(char *),
"atom:dvname");
int n = strlen(name) + 1;
dname[index] = new char[n];
strcpy(dname[index],name);
dvname[index] = new char[n];
strcpy(dvname[index],name);
dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
"atom:dvector");
memory->create(dvector[index],nmax,"atom:dvector");
}
} else if (flag == 0 && cols) {
index = niarray;
niarray++;
ianame = (char **) memory->srealloc(ianame,niarray*sizeof(char *),
"atom:ianame");
int n = strlen(name) + 1;
ianame[index] = new char[n];
strcpy(ianame[index],name);
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");
icols[index] = cols;
} else if (flag == 1 && cols) {
index = ndarray;
ndarray++;
daname = (char **) memory->srealloc(daname,ndarray*sizeof(char *),
"atom:daname");
int n = strlen(name) + 1;
daname[index] = new char[n];
strcpy(daname[index],name);
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");
dcols[index] = cols;
}
return index;
}
/* ----------------------------------------------------------------------
remove a custom variable of type flag = 0/1 for int/double at index
free memory for vector and name and set ptrs to NULL
ivector/dvector and iname/dname lists never shrink
remove a custom variable stored at index
flag = 0/1 for int/double, cols = 0/1 for vector/array or N for array columns
free memory for vector/array and name and set ptrs to NULL
vector/array lists and name lists never shrink
------------------------------------------------------------------------- */
void Atom::remove_custom(int flag, int index)
void Atom::remove_custom(int index, int flag, int cols)
{
if (flag == 0) {
if (flag == 0 && cols == 0) {
memory->destroy(ivector[index]);
ivector[index] = NULL;
delete [] iname[index];
iname[index] = NULL;
} else {
delete [] ivname[index];
ivname[index] = NULL;
} else if (flag == 1 && cols == 0) {
memory->destroy(dvector[index]);
dvector[index] = NULL;
delete [] dname[index];
dname[index] = NULL;
delete [] dvname[index];
dvname[index] = NULL;
} else if (flag == 0 && cols) {
memory->destroy(iarray[index]);
iarray[index] = NULL;
delete [] ianame[index];
ianame[index] = NULL;
} else if (flag == 1 && cols) {
memory->destroy(darray[index]);
darray[index] = NULL;
delete [] daname[index];
daname[index] = NULL;
}
}
@ -2372,7 +2452,8 @@ void *Atom::extract(char *name)
{
// --------------------------------------------------------------------
// 4th customization section: customize by adding new variable name
// if new variable is from a package, add package comment
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"id") == 0) return (void *) tag;
@ -2415,10 +2496,30 @@ void *Atom::extract(char *name)
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
// USER-MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
// custom vectors and arrays
if (strstr(name,"i_") == name || strstr(name,"d_") == name ||
strstr(name,"i2_") == name || strstr(name,"d2_") == name) {
int which = 0;
if (name[0] == 'd') which = 1;
int array = 0;
if (name[1] == '2') array = 1;
int index,flag,cols;
if (!array) index = find_custom(&name[2],flag,cols);
else index = find_custom(&name[3],flag,cols);
if (index < 0) return NULL;
if (which != flag) return NULL;
if ((!array && cols) || (array && !cols)) return NULL;
if (!which && !array) return (void *) ivector[index];
if (which && !array) return (void *) dvector[index];
if (!which && array) return (void *) iarray[index];
if (which && array) return (void *) darray[index];
}
// USER-SMD package
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
@ -2429,9 +2530,20 @@ void *Atom::extract(char *name)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
// USER-DPD package
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
// USER-MESO package
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// USER-MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
// end of customization section
// --------------------------------------------------------------------