CFix operator*(const Fix &x, const CFix &y)
{
return CFix(x.get_re() * y.get_re(),
x.get_re() * y.get_im(),
x.get_shift() + y.get_shift(),
0, 0);
}
CFix operator/(const CFix &x, const Fix &y)
{
return CFix(x.get_re() / y.get_re(),
x.get_im() / y.get_re(),
x.get_shift() - y.get_shift(),
0, 0);
}
CFix operator/(const Fix &x, const CFix &y)
{
fixrep denominator = y.get_re() * y.get_re() + y.get_im() * y.get_im();
return CFix(x.get_re() * y.get_re() / denominator,
-x.get_re() * y.get_im() / denominator,
x.get_shift() - y.get_shift(),
0, 0);
}
void ComputeSlice::extract_one(int m, double *vec, int stride)
{
int i,j;
// invoke the appropriate compute if needed
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]];
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = cvector[i-1];
j += stride;
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = carray[i-1][icol];
j += stride;
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
error->all(FLERR,"Fix used in compute slice not computed at compatible time");
Fix *fix = modify->fix[value2index[m]];
if (argindex[m] == 0) {
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_vector(i-1);
j += stride;
}
} else {
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_array(i-1,icol);
j += stride;
}
}
}
}
Constraint::Constraint(ConstraintKind kind, Fix fix,
Type first, Type second, ConstraintLocator *locator,
ArrayRef<TypeVariableType *> typeVars)
: Kind(kind), TheFix(fix.getKind()), FixData(fix.getData()),
HasRestriction(false), HasFix(true),
IsActive(false), RememberChoice(false), IsFavored(false),
NumTypeVariables(typeVars.size()),
Types{ first, second, Identifier() }, Locator(locator)
{
assert(!first.isNull());
assert(!second.isNull());
std::copy(typeVars.begin(), typeVars.end(), getTypeVariablesBuffer().begin());
}
CFix operator-(const Fix &x, const CFix &y)
{
return CFix(x.get_re() - y.get_re(),
-y.get_im(),
assert_shifts(y, x),
0, 0);
}
CFix operator+(const CFix &x, const Fix &y)
{
return CFix(x.get_re() + y.get_re(),
x.get_im(),
assert_shifts(x, y),
0, 0);
}
double Properties::max_radius()
{
const double maxtype = max_type();
double maxRadius = -1.0;
// check local particles
for (int i=0;i<atom->nlocal;i++)
{
const double irad = atom->radius[i];
// maximum
if (irad > maxRadius)
maxRadius = irad;
}
// check all fixes
// such as fix insert, fix change/type, fix wall, fix pour
for(int i=0;i<modify->nfix;i++)
{
// checks
Fix *fix = modify->fix[i];
if(!fix->use_rad_for_cut_neigh_and_ghost())
continue;
// loop over all types since min_rad(int) and max_rad(int) need a type
for (int j=1;j<maxtype+1;j++)
{
const double f_maxrad = fix->max_rad(j);
if(f_maxrad > SMALL && f_maxrad > maxRadius)
maxRadius = f_maxrad;
}
}
//Get min/max from other procs
double maxRadius_all;
MPI_Allreduce(&maxRadius,&maxRadius_all, 1, MPI_DOUBLE, MPI_MAX, world);
maxRadius = maxRadius_all;
//error check
if(maxRadius <= SMALL)
error->all(FLERR,"Atom radius must be bigger than zero for granular simulations");
return maxRadius;
}
void *lammps_extract_fix(void *ptr, char *id, int style, int type,
int i, int j)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
if (style == 0) {
double *dptr = (double *) malloc(sizeof(double));
if (type == 0) {
if (!fix->scalar_flag) return NULL;
*dptr = fix->compute_scalar();
return (void *) dptr;
}
if (type == 1) {
if (!fix->vector_flag) return NULL;
*dptr = fix->compute_vector(i);
return (void *) dptr;
}
if (type == 2) {
if (!fix->array_flag) return NULL;
*dptr = fix->compute_array(i,j);
return (void *) dptr;
}
}
if (style == 1) {
if (!fix->peratom_flag) return NULL;
if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
}
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
return NULL;
}
void FixGrem::init()
{
if (domain->triclinic)
error->all(FLERR,"Triclinic cells are not supported");
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature compute ID for fix grem does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_ke);
if (icompute < 0)
error->all(FLERR,"KE compute ID for fix grem does not exist");
ke = modify->compute[icompute];
icompute = modify->find_compute(id_pe);
if (icompute < 0)
error->all(FLERR,"PE compute ID for fix grem does not exist");
pe = modify->compute[icompute];
int ifix = modify->find_fix(id_nh);
if (ifix < 0)
error->all(FLERR,"Fix id for nvt or npt fix does not exist");
Fix *nh = modify->fix[ifix];
double *t_start = (double *)nh->extract("t_start",ifix);
double *t_stop = (double *)nh->extract("t_stop",ifix);
if ((t_start != NULL) && (t_stop != NULL) && (ifix == 0)) {
tbath = *t_start;
if (*t_start != *t_stop)
error->all(FLERR,"Thermostat temperature ramp not allowed");
} else
error->all(FLERR,"Problem extracting target temperature from fix nvt or npt");
pressref = 0.0;
if (pressflag) {
int *p_flag = (int *)nh->extract("p_flag",ifix);
double *p_start = (double *) nh->extract("p_start",ifix);
double *p_stop = (double *) nh->extract("p_stop",ifix);
if ((p_flag != NULL) && (p_start != NULL) && (p_stop != NULL)
&& (ifix == 1)) {
ifix = 0;
pressref = p_start[0];
if ((p_start[0] != p_stop[0]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[1] != p_stop[1]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[2] != p_stop[2]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[0] != p_start[1]) || (p_start[1] != p_start[2])) ++ifix;
if ((p_flag[3] != 0) || (p_flag[4] != 0) || (p_flag[5] != 0)) ++ifix;
if (ifix > 0)
error->all(FLERR,"Unsupported pressure settings in fix npt");
} else
error->all(FLERR,"Problem extracting target pressure from fix npt");
}
}
int Properties::max_type()
{
// loop over all particles to check how many atom types are present
mintype = 100000;
maxtype = 1;
for (int i=0;i<atom->nlocal;i++)
{
if (atom->type[i]<mintype)
mintype=atom->type[i];
if (atom->type[i]>maxtype)
maxtype=atom->type[i];
}
// check all fixes
// such as fix insert, fix change/type, fix wall, fix pour
for(int i=0;i<modify->nfix;i++)
{
// checks
Fix *fix = modify->fix[i];
if(fix->min_type() > 0 && fix->min_type() < mintype)
mintype = fix->min_type();
if(fix->max_type() > 0 && fix->max_type() > maxtype)
maxtype = fix->max_type();
}
//Get min/max from other procs
int mintype_all,maxtype_all;
MPI_Allreduce(&mintype,&mintype_all, 1, MPI_INT, MPI_MIN, world);
MPI_Allreduce(&maxtype,&maxtype_all, 1, MPI_INT, MPI_MAX, world);
mintype = mintype_all;
maxtype = maxtype_all;
//error check
if(mintype != 1)
error->all(FLERR,"Atom types must start from 1 for granular simulations");
if(maxtype > atom->ntypes)
error->all(FLERR,"Please increase the number of atom types in the 'create_box' command to match the number of atom types you use in the simulation");
return maxtype;
}
int FixAppendAtoms::get_spatial()
{
if (update->ntimestep % freq == 0) {
int ifix = modify->find_fix(spatialid);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
Fix *fix = modify->fix[ifix];
int failed = 0;
int count = 0;
while (failed < 2) {
double tmp = fix->compute_vector(2*count);
if (tmp == 0.0) failed++;
else failed = 0;
count++;
}
double *pos = new double[count-2];
double *val = new double[count-2];
for (int loop=0; loop < count-2; loop++) {
pos[loop] = fix->compute_vector(2*loop);
val[loop] = fix->compute_vector(2*loop+1);
}
// always ignore the first and last
double binsize = 2.0;
double min_energy=0.0;
double max_energy=0.0;
int header = static_cast<int> (size / binsize);
advance = 0;
for (int loop=1; loop <= header; loop++) {
max_energy += val[loop];
}
for (int loop=count-2-2*header; loop <=count-3-header; loop++) {
min_energy += val[loop];
}
max_energy /= header;
min_energy /= header;
double shockfront_min = 0.0;
double shockfront_max = 0.0;
double shockfront_loc = 0.0;
int front_found1 = 0;
for (int loop=count-3-header; loop > header; loop--) {
if (front_found1 == 1) continue;
if (val[loop] > min_energy + 0.1*(max_energy - min_energy)) {
shockfront_max = pos[loop];
front_found1=1;
}
}
int front_found2 = 0;
for (int loop=header+1; loop <=count-3-header; loop++) {
if (val[loop] > min_energy + 0.6*(max_energy - min_energy)) {
shockfront_min = pos[loop];
front_found2=1;
}
}
if (front_found1 + front_found2 == 0) shockfront_loc = 0.0;
else if (front_found1 + front_found2 == 1)
shockfront_loc = shockfront_max + shockfront_min;
else if (front_found1 == 1 && front_found2 == 1 &&
shockfront_max-shockfront_min > spatlead/2.0)
shockfront_loc = shockfront_max;
else shockfront_loc = (shockfront_max + shockfront_min) / 2.0;
if (comm->me == 0)
printf("SHOCK: %g %g %g %g %g\n", shockfront_loc, shockfront_min,
shockfront_max, domain->boxlo[2], domain->boxhi[2]);
if (domain->boxhi[2] - shockfront_loc < spatlead) advance = 1;
delete [] pos;
delete [] val;
}
advance_sum = 0;
MPI_Allreduce(&advance,&advance_sum,1,MPI_INT,MPI_SUM,world);
if (advance_sum > 0) return 1;
else return 0;
}
void CreateAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Create_atoms command before simulation box is defined");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot create_atoms after "
"reading restart file with per-atom info");
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");
itype = force->inumeric(FLERR,arg[0]);
if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms command");
int iarg = 0;
if (strcmp(arg[1],"box") == 0) {
style = BOX;
iarg = 2;
} else if (strcmp(arg[1],"region") == 0) {
style = REGION;
if (narg < 3) error->all(FLERR,"Illegal create_atoms command");
nregion = domain->find_region(arg[2]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
xone[0] = force->numeric(FLERR,arg[2]);
xone[1] = force->numeric(FLERR,arg[3]);
xone[2] = force->numeric(FLERR,arg[4]);
iarg = 5;
} else if (strcmp(arg[1],"random") == 0) {
style = RANDOM;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
nrandom = force->inumeric(FLERR,arg[2]);
seed = force->inumeric(FLERR,arg[3]);
if (strcmp(arg[4],"NULL") == 0) nregion = -1;
else {
nregion = domain->find_region(arg[4]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
}
iarg = 5;
} else error->all(FLERR,"Illegal create_atoms command");
// process optional keywords
int scaleflag = 1;
remapflag = 0;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int ibasis = force->inumeric(FLERR,arg[iarg+1]);
itype = force->inumeric(FLERR,arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis ||
itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid basis setting in create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"yes") == 0) remapflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else error->all(FLERR,"Illegal create_atoms command");
}
// error checks
if (style == RANDOM) {
if (nrandom < 0) error->all(FLERR,"Illegal create_atoms command");
if (seed <= 0) error->all(FLERR,"Illegal create_atoms command");
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
if (style == BOX || style == REGION) {
if (nbasis == 0)
error->all(FLERR,"Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
}
// set bounds for my proc in sublo[3] & subhi[3]
// if periodic and style = BOX or REGION, i.e. using lattice:
// should create exactly 1 atom when 2 images are both "on" the boundary
// either image may be slightly inside/outside true box due to round-off
// if I am lo proc, decrement lower bound by EPSILON
// this will insure lo image is created
// if I am hi proc, decrement upper bound by 2.0*EPSILON
// this will insure hi image is not created
// thus insertion box is EPSILON smaller than true box
// and is shifted away from true boundary
// which is where atoms are likely to be generated
triclinic = domain->triclinic;
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (style == BOX || style == REGION) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
}
}
// add atoms in one of 3 ways
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
if (style == SINGLE) add_single();
else if (style == RANDOM) add_random();
else add_lattice();
// invoke set_arrays() for fixes that need initialization of new atoms
int nlocal = atom->nlocal;
for (int m = 0; m < modify->nfix; m++) {
Fix *fix = modify->fix[m];
if (fix->create_attribute)
{
fix->pre_set_arrays();
for (int i = nlocal_previous; i < nlocal; i++)
fix->set_arrays(i);
}
}
// clean up
if (domain->lattice) delete [] basistype;
// new total # of atoms
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
// print status
if (comm->me == 0) {
if (screen)
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
if (logfile)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
// reset simulation now that more atoms are defined
// add tags for newly created atoms if possible
// if global map exists, reset it
// change these to MAXTAGINT when allow tagint = bigint
if (atom->natoms > MAXSMALLINT) {
if (comm->me == 0)
error->warning(FLERR,"Total atom count exceeds ID limit, "
"atoms will not have individual IDs");
atom->tag_enable = 0;
}
if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// if a molecular system, set nspecial to 0 for new atoms
// NOTE: 31May12, don't think this is needed, avec->create_atom() does it
//if (atom->molecular) {
// int **nspecial = atom->nspecial;
// for (int i = nlocal_previous; i < atom->nlocal; i++) {
// nspecial[i][0] = 0;
// nspecial[i][1] = 0;
// nspecial[i][2] = 0;
// }
//}
// error checks on coarsegraining
if(force->cg_active())
error->cg(FLERR,"create_atoms");
}
FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix grem command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
scale_grem = 1.0;
// tbath - temp of bath, the same as defined in thermostat
lambda = force->numeric(FLERR,arg[3]);
eta = force->numeric(FLERR,arg[4]);
h0 = force->numeric(FLERR,arg[5]);
int n = strlen(arg[6])+1;
id_nh = new char[n];
strcpy(id_nh,arg[6]);
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[5];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "PRESSURE/GREM";
newarg[3] = id_temp;
newarg[4] = id;
modify->add_compute(5,newarg);
delete [] newarg;
// create a new compute ke style
// id = fix-ID + ke
n = strlen(id) + 8;
id_ke = new char[n];
strcpy(id_ke,id);
strcat(id_ke,"_ke");
newarg = new char*[3];
newarg[0] = id_ke;
newarg[1] = (char *) "all";
newarg[2] = (char *) "ke";
modify->add_compute(3,newarg);
delete [] newarg;
// create a new compute pe style
// id = fix-ID + pe
n = strlen(id) + 9;
id_pe = new char[n];
strcpy(id_pe,id);
strcat(id_pe,"_pe");
newarg = new char*[3];
newarg[0] = id_pe;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pe";
modify->add_compute(3,newarg);
delete [] newarg;
int ifix = modify->find_fix(id_nh);
if (ifix < 0)
error->all(FLERR,"Fix id for nvt or npt fix does not exist");
Fix *nh = modify->fix[ifix];
pressflag = 0;
int *p_flag = (int *)nh->extract("p_flag",ifix);
if ((p_flag == NULL) || (ifix != 1) || (p_flag[0] == 0)
|| (p_flag[1] == 0) || (p_flag[2] == 0)) {
pressflag = 0;
} else if ((p_flag[0] == 1) && (p_flag[1] == 1)
&& (p_flag[2] == 1) && (ifix == 1)) {
pressflag = 1;
char *modargs[2];
modargs[0] = (char *) "press";
modargs[1] = id_press;
nh->modify_param(2,modargs);
}
}
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp," %g",array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
void ComputeChunkSpreadAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow local vector_atom or array_atom if necessary
if (atom->nmax > nmax) {
if (nvalues == 1) {
memory->destroy(vector_atom);
nmax = atom->nmax;
memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom");
} else {
memory->destroy(array_atom);
nmax = atom->nmax;
memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom");
}
}
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
int nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
// loop over values, access compute or fix
// loop over atoms, use chunk ID of each atom to store value from compute/fix
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i,m,n,index,nstride;
double *ptr;
for (m = 0; m < nvalues; m++) {
n = value2index[m];
// copy compute/fix values into vector_atom or array_atom
// nstride between values for each atom
if (nvalues == 1) {
ptr = vector_atom;
nstride = 1;
} else {
ptr = &array_atom[0][m];
nstride = nvalues;
}
// invoke compute if not previously invoked
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk) continue;
*ptr = cvector[index];
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
int icol = argindex[m]-1;
double **carray = compute->array;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk) continue;
*ptr = carray[index][icol];
}
}
// access fix data, check if fix frequency is a match
// are assuming the fix global vector/array is per-chunk data
// check if index exceeds fix output length/rows
} else if (which[m] == FIX) {
Fix *fix = modify->fix[n];
if (update->ntimestep % fix->global_freq)
error->all(FLERR,"Fix used in compute chunk/spread/atom not "
"computed at compatible time");
if (argindex[m] == 0) {
int nfix = fix->size_vector;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk || index >= nfix) continue;
*ptr = fix->compute_vector(index);
}
} else {
int icol = argindex[m]-1;
int nfix = fix->size_array_rows;
for (i = 0; i < nlocal; i++, ptr += nstride) {
*ptr = 0.0;
if (!(mask[i] & groupbit)) continue;
index = ichunk[i]-1;
if (index < 0 || index >= nchunk || index >= nfix) continue;
*ptr = fix->compute_array(index,icol);
}
}
}
}
}
Fix operator*(const int x, const Fix &y)
{
return Fix(x * y.get_re(),
y.get_shift(),
0, 0);
}
Fix operator/(const int x, const Fix &y)
{
return Fix(x / y.get_re(),
-y.get_shift(),
0, 0);
}
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// first sample within single Nfreq epoch
// zero out arrays that accumulate over many samples, but not across epochs
// invoke setup_chunks() to determine current nchunk
// re-allocate per-chunk arrays if needed
// invoke lock() in two cases:
// if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
// will be unlocked on last repeat of this Nfreq
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
// both nevery and nfreq are future steps,
// since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
if (irepeat == 0) {
if (any_variable_length) {
modify->clearstep_compute();
int nrows_new = column_length(1);
modify->addstep_compute(ntimestep+nevery);
modify->addstep_compute(ntimestep+nfreq);
if (all_variable_length && nrows_new != nrows) {
nrows = nrows_new;
memory->destroy(column);
memory->create(column,nrows,"ave/time:column");
allocate_arrays();
}
bigint ntimestep = update->ntimestep;
int lockforever_flag = 0;
for (i = 0; i < nvalues; i++) {
if (!varlen[i]) continue;
if (nrepeat > 1 && ave == ONE) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
} else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,update->ntimestep,-1);
lockforever_flag = 1;
}
}
if (lockforever_flag) lockforever = 1;
}
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// unlock any variable length computes at end of Nfreq epoch
// do not unlock if ave = RUNNING or WINDOW
if (any_variable_length && nrepeat > 1 && ave == ONE) {
for (i = 0; i < nvalues; i++) {
if (!varlen[i]) continue;
Compute *compute = modify->compute[value2index[i]];
compute->unlock(this);
}
}
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp,format,array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
Fix operator-(const Fix &x, const int y)
{
return Fix(x.get_re() - y,
assert_shifts(x, y),
0, 0);
}
Fix operator/(const Fix &x, const int y)
{
return Fix(x.get_re() / y,
x.get_shift(),
0, 0);
}
Fix operator+(const int x, const Fix &y)
{
return Fix(x + y.get_re(),
assert_shifts(y, x),
0, 0);
}
void FixAveHisto::end_of_step()
{
int i,j,m;
// skip if not step which requires doing something
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
// zero if first step
if (irepeat == 0) {
stats[0] = stats[1] = 0.0;
stats[2] = BIG;
stats[3] = -BIG;
for (i = 0; i < nbins; i++) bin[i] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
j = argindex[i];
// atom attributes
if (which[i] == X)
bin_atoms(&atom->x[0][j],3);
else if (which[i] == V)
bin_atoms(&atom->v[0][j],3);
else if (which[i] == F)
bin_atoms(&atom->f[0][j],3);
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
bin_one(compute->scalar);
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_one(compute->vector[j-1]);
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_vector(compute->size_vector,compute->vector,1);
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
if (compute->array)
bin_vector(compute->size_array_rows,&compute->array[0][j-1],
compute->size_array_cols);
}
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0)
bin_atoms(compute->vector_atom,1);
else if (compute->array_atom)
bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols);
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0)
bin_vector(compute->size_local_rows,compute->vector_local,1);
else if (compute->array_local)
bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
compute->size_local_cols);
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one(fix->compute_scalar());
else bin_one(fix->compute_vector(j-1));
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
} else {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1));
}
} else if (kind == PERATOM) {
if (j == 0) bin_atoms(fix->vector_atom,1);
else if (fix->array_atom)
bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols);
} else if (kind == LOCAL) {
if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1);
else if (fix->array_local)
bin_vector(fix->size_local_rows,&fix->array_local[0][j-1],
fix->size_local_cols);
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one(input->variable->compute_equal(m));
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
maxatom = atom->nmax;
memory->create(vector,maxatom,"ave/histo:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms(vector,1);
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// merge histogram stats across procs if necessary
if (kind == PERATOM || kind == LOCAL) {
MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world);
stats[0] = stats_all[0];
stats[1] = stats_all[1];
stats[2] = stats_all[2];
stats[3] = stats_all[3];
for (i = 0; i < nbins; i++) bin[i] = bin_all[i];
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
stats_total[0] = stats[0];
stats_total[1] = stats[1];
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (i = 0; i < nbins; i++) bin_total[i] = bin[i];
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (i = 0; i < nbins; i++) bin_total[i] += bin[i];
} else if (ave == WINDOW) {
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
stats_list[iwindow][0] = stats[0];
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
if (window_limit) m = nwindow;
else m = iwindow+1;
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
for (i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
for (i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
for (i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
}
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins,
stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",
i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
}
}
}
int NeighborKokkos::init_lists_kokkos()
{
int i;
for (i = 0; i < nlist_host; i++) delete lists_host[i];
delete [] lists_host;
delete [] pair_build_host;
delete [] stencil_create_host;
nlist_host = 0;
for (i = 0; i < nlist_device; i++) delete lists_device[i];
delete [] lists_device;
delete [] pair_build_device;
delete [] stencil_create_device;
nlist_device = 0;
nlist = 0;
for (i = 0; i < nrequest; i++) {
if (requests[i]->kokkos_device) nlist_device++;
else if (requests[i]->kokkos_host) nlist_host++;
else nlist++;
}
lists_host = new NeighListKokkos<LMPHostType>*[nrequest];
pair_build_host = new PairPtrHost[nrequest];
stencil_create_host = new StencilPtrHost[nrequest];
for (i = 0; i < nrequest; i++) {
lists_host[i] = NULL;
pair_build_host[i] = NULL;
stencil_create_host[i] = NULL;
}
for (i = 0; i < nrequest; i++) {
if (!requests[i]->kokkos_host) continue;
lists_host[i] = new NeighListKokkos<LMPHostType>(lmp);
lists_host[i]->index = i;
lists_host[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists_host[i]);
}
if (requests[i]->fix) {
Fix *fix = (Fix *) requests[i]->requestor;
fix->init_list(requests[i]->id,lists_host[i]);
}
}
lists_device = new NeighListKokkos<LMPDeviceType>*[nrequest];
pair_build_device = new PairPtrDevice[nrequest];
stencil_create_device = new StencilPtrDevice[nrequest];
for (i = 0; i < nrequest; i++) {
lists_device[i] = NULL;
pair_build_device[i] = NULL;
stencil_create_device[i] = NULL;
}
for (i = 0; i < nrequest; i++) {
if (!requests[i]->kokkos_device) continue;
lists_device[i] = new NeighListKokkos<LMPDeviceType>(lmp);
lists_device[i]->index = i;
lists_device[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists_device[i]);
}
if (requests[i]->fix) {
Fix *fix = (Fix *) requests[i]->requestor;
fix->init_list(requests[i]->id,lists_device[i]);
}
}
// 1st time allocation of xhold
if (dist_check)
xhold = DAT::tdual_x_array("neigh:xhold",maxhold);
// return # of non-Kokkos lists
return nlist;
}
