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added functionity to lib interface

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This commit is contained in:
Steve Plimpton
2016-12-13 16:22:17 -07:00
parent fb3f597f41
commit ae5764beac
28 changed files with 386 additions and 160 deletions
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140
src/library.cpp
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@ -129,7 +129,7 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
}
catch(LAMMPSException & e) {
fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
*ptr = (void*) NULL;
*ptr = (void *) NULL;
}
#else
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
@ -309,6 +309,23 @@ void lammps_free(void *ptr)
customize by adding a function here and in library.h header file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
extract a LAMMPS setting as an integer
only use for settings that require return of an int
customize by adding names
------------------------------------------------------------------------- */
int lammps_extract_setting(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
if (strcmp(name,"bigint") == 0) return sizeof(bigint);
if (strcmp(name,"tagint") == 0) return sizeof(tagint);
if (strcmp(name,"imageint") == 0) return sizeof(imageint);
return -1;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS global entity
name = desired quantity, e.g. dt or boxyhi or natoms
@ -325,12 +342,16 @@ void *lammps_extract_global(void *ptr, char *name)
LAMMPS *lmp = (LAMMPS *) ptr;
if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
if (strcmp(name,"boxlo") == 0) return (void *) lmp->domain->boxlo;
if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi;
if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];
if (strcmp(name,"boxyhi") == 0) return (void *) &lmp->domain->boxhi[1];
if (strcmp(name,"boxzlo") == 0) return (void *) &lmp->domain->boxlo[2];
if (strcmp(name,"boxzhi") == 0) return (void *) &lmp->domain->boxhi[2];
if (strcmp(name,"periodicity") == 0) return (void *) lmp->domain->periodicity;
if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
@ -344,7 +365,12 @@ void *lammps_extract_global(void *ptr, char *name)
if (strcmp(name,"nmax") == 0) return (void *) &lmp->atom->nmax;
if (strcmp(name,"ntimestep") == 0) return (void *) &lmp->update->ntimestep;
// update atime can be referenced as a pointer
if (strcmp(name,"units") == 0) return (void *) lmp->update->unit_style;
if (strcmp(name,"triclinic") == 0) return (void *) &lmp->domain->triclinic;
if (strcmp(name,"q_flag") == 0) return (void *) &lmp->atom->q_flag;
// update->atime can be referenced as a pointer
// thermo "timer" data cannot be, since it is computed on request
// lammps_get_thermo() can access all thermo keywords by value
@ -354,6 +380,38 @@ void *lammps_extract_global(void *ptr, char *name)
return NULL;
}
/* ----------------------------------------------------------------------
extract simulation box parameters
see domain.h for definition of these arguments
domain->init() call needed to set box_change
------------------------------------------------------------------------- */
void lammps_extract_box(void *ptr, double *boxlo, double *boxhi,
double *xy, double *yz, double *xz,
int *periodicity, int *box_change)
{
LAMMPS *lmp = (LAMMPS *) ptr;
Domain *domain = lmp->domain;
domain->init();
boxlo[0] = domain->boxlo[0];
boxlo[1] = domain->boxlo[1];
boxlo[2] = domain->boxlo[2];
boxhi[0] = domain->boxhi[0];
boxhi[1] = domain->boxhi[1];
boxhi[2] = domain->boxhi[2];
*xy = domain->xy;
*yz = domain->yz;
*xz = domain->xz;
periodicity[0] = domain->periodicity[0];
periodicity[1] = domain->periodicity[1];
periodicity[2] = domain->periodicity[2];
*box_change = domain->box_change;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS atom-based entity
name = desired quantity, e.g. x or mass
@ -586,6 +644,35 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
return NULL;
}
/* ----------------------------------------------------------------------
reset simulation box parameters
see domain.h for definition of these arguments
assumes domain->set_intiial_box() has been invoked previously
------------------------------------------------------------------------- */
void lammps_reset_box(void *ptr, double *boxlo, double *boxhi,
double xy, double yz, double xz)
{
LAMMPS *lmp = (LAMMPS *) ptr;
Domain *domain = lmp->domain;
domain->boxlo[0] = boxlo[0];
domain->boxlo[1] = boxlo[1];
domain->boxlo[2] = boxlo[2];
domain->boxhi[0] = boxhi[0];
domain->boxhi[1] = boxhi[1];
domain->boxhi[2] = boxhi[2];
domain->xy = xy;
domain->yz = yz;
domain->xz = xz;
domain->set_global_box();
lmp->comm->set_proc_grid();
domain->set_local_box();
}
/* ----------------------------------------------------------------------
set the value of a STRING variable to str
return -1 if variable doesn't exist or not a STRING variable
@ -648,7 +735,7 @@ int lammps_get_natoms(void *ptr)
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
return atom-based values in data, ordered by count, then by atom ID
return atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be pre-allocated by caller to correct length
------------------------------------------------------------------------- */
@ -744,7 +831,7 @@ void lammps_gather_atoms(void *ptr, char *name,
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
data = atom-based values in data, ordered by count, then by atom ID
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
------------------------------------------------------------------------- */
@ -823,16 +910,29 @@ void lammps_scatter_atoms(void *ptr, char *name,
/* ----------------------------------------------------------------------
create N atoms and assign them to procs based on coords
id = atom IDs (optional, NULL if just use 1 to N)
id = atom IDs (optional, NULL will generate 1 to N)
type = N-length vector of atom types (required)
x = 3N-length vector of atom coords (required)
v = 3N-length vector of atom velocities (optional, NULL if just 0.0)
x = 3N-length 1d vector of atom coords (required)
v = 3N-length 1d vector of atom velocities (optional, NULL if just 0.0)
image flags can be treated in two ways:
(a) image = vector of current image flags
each atom will be remapped into periodic box by domain->ownatom()
image flag will be incremented accordingly and stored with atom
(b) image = NULL
each atom will be remapped into periodic box by domain->ownatom()
image flag will be set to 0 by atom->avec->create_atom()
shrinkexceed = 1 allows atoms to be outside a shrinkwrapped boundary
passed to ownatom() which will assign them to boundary proc
important if atoms may be (slightly) outside non-periodic dim
e.g. due to restoring a snapshot from a previous run and previous box
id and image must be 32-bit integers
x,v = ordered by xyz, then by atom
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
------------------------------------------------------------------------- */
void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
double *x, double *v)
double *x, double *v, imageint *image,
int shrinkexceed)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@ -857,14 +957,19 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
Domain *domain = lmp->domain;
int nlocal = atom->nlocal;
int nprev = nlocal;
bigint natoms_prev = atom->natoms;
int nlocal_prev = nlocal;
double xdata[3];
for (int i = 0; i < n; i++) {
xdata[0] = x[3*i];
xdata[1] = x[3*i+1];
xdata[2] = x[3*i+2];
if (!domain->ownatom(xdata)) continue;
if (image) {
if (!domain->ownatom(id[i],xdata,&image[i],shrinkexceed)) continue;
} else {
if (!domain->ownatom(id[i],xdata,NULL,shrinkexceed)) continue;
}
atom->avec->create_atom(type[i],xdata);
if (id) atom->tag[nlocal] = id[i];
@ -874,6 +979,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
atom->v[nlocal][1] = v[3*i+1];
atom->v[nlocal][2] = v[3*i+2];
}
if (image) atom->image[nlocal] = image[i];
nlocal++;
}
@ -885,8 +991,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
// init per-atom fix/compute/variable values for created atoms
atom->data_fix_compute_variable(nprev,nlocal);
atom->data_fix_compute_variable(nlocal_prev,nlocal);
// if global map exists, reset it
// invoke map_init() b/c atom count has grown
@ -894,6 +1000,16 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
lmp->atom->map_init();
lmp->atom->map_set();
}
// warn if new natoms is not correct
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
"invalid total atoms %ld %ld",lmp->atom->natoms,natoms_prev+n);
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,str);
}
}
END_CAPTURE
}