void FixAdapt::init()
{
int i,j;
// allow a dynamic group only if ATOM attribute not used
if (group->dynamic[igroup])
for (int i = 0; i < nadapt; i++)
if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt atom");
// setup and error checks
anypair = 0;
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name for fix adapt does not exist");
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable for fix adapt is invalid style");
if (ad->which == PAIR) {
anypair = 1;
ad->pair = NULL;
// if ad->pstyle has trailing sub-style annotation ":N",
// strip it for pstyle arg to pair_match() and set nsub = N
// this should work for appended suffixes as well
int n = strlen(ad->pstyle) + 1;
char *pstyle = new char[n];
strcpy(pstyle,ad->pstyle);
char *cptr;
int nsub = 0;
if ((cptr = strchr(pstyle,':'))) {
*cptr = '\0';
nsub = force->inumeric(FLERR,cptr+1);
}
if (lmp->suffix_enable) {
int len = 2 + strlen(pstyle) + strlen(lmp->suffix);
char *psuffix = new char[len];
strcpy(psuffix,pstyle);
strcat(psuffix,"/");
strcat(psuffix,lmp->suffix);
ad->pair = force->pair_match(psuffix,1,nsub);
delete[] psuffix;
}
if (ad->pair == NULL) ad->pair = force->pair_match(pstyle,1,nsub);
if (ad->pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL)
error->all(FLERR,"Fix adapt pair style param not supported");
// for pair styles only parameters that are 2-d arrays in atom types or
// scalars are supported
if (ad->pdim != 2 && ad->pdim != 0)
error->all(FLERR,"Fix adapt pair style param is not compatible");
if(ad->pdim == 2) ad->array = (double **) ptr;
if(ad->pdim == 0) ad->scalar = (double *) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,pstyle))
error->all(FLERR,"Fix adapt type pair range is not valid for "
"pair hybrid sub-style");
}
delete [] pstyle;
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
if (ad->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"Fix adapt requires atom attribute charge");
}
}
}
// make copy of original pair array values
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}else if (ad->which == PAIR && ad->pdim == 0){
ad->scalar_orig = *ad->scalar;
}
}
// fixes that store initial per-atom values
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_diam = (FixStore *) modify->fix[ifix];
}
if (id_fix_chg) {
int ifix = modify->find_fix(id_fix_chg);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_chg = (FixStore *) modify->fix[ifix];
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
void FixAdapt::init()
{
int i,j;
// setup and error checks
anypair = 0;
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all("Variable name for fix adapt does not exist");
if (!input->variable->equalstyle(ad->ivar))
error->all("Variable for fix adapt is invalid style");
if (ad->which == PAIR) {
anypair = 1;
Pair *pair = force->pair_match(ad->pstyle,1);
if (pair == NULL) error->all("Fix adapt pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL) error->all("Fix adapt pair style param not supported");
ad->pdim = 2;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
if (ad->pdim == 2) ad->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,ad->pstyle))
error->all("Fix adapt type pair range is not valid for "
"pair hybrid sub-style");
}
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all("Fix adapt is incompatible with KSpace style");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all("Fix adapt requires atom attribute diameter");
}
}
}
// make copy of original pair array values
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}
}
}
void ComputeFEP::init()
{
int i,j;
if (!fepinitflag) // avoid init to run entirely when called by write_data
fepinitflag = 1;
else return;
// setup and error checks
pairflag = 0;
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
pert->ivar = input->variable->find(pert->var);
if (pert->ivar < 0)
error->all(FLERR,"Variable name for compute fep does not exist");
if (!input->variable->equalstyle(pert->ivar))
error->all(FLERR,"Variable for compute fep is of invalid style");
if (force->pair == NULL)
error->all(FLERR,"compute fep pair requires pair interactions");
if (pert->which == PAIR) {
pairflag = 1;
Pair *pair = force->pair_match(pert->pstyle,1);
if (pair == NULL) error->all(FLERR,"compute fep pair style "
"does not exist");
void *ptr = pair->extract(pert->pparam,pert->pdim);
if (ptr == NULL)
error->all(FLERR,"compute fep pair style param not supported");
pert->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if ((strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = pert->ilo; i <= pert->ihi; i++)
for (j = MAX(pert->jlo,i); j <= pert->jhi; j++)
if (!pair->check_ijtype(i,j,pert->pstyle))
error->all(FLERR,"compute fep type pair range is not valid for "
"pair hybrid sub-style");
}
} else if (pert->which == ATOM) {
if (pert->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"compute fep requires atom attribute charge");
}
}
}
if (tailflag) {
if (force->pair->tail_flag == 0)
error->all(FLERR,"Compute fep tail when pair style does not "
"compute tail corrections");
}
// detect if package gpu is present
int ifixgpu = modify->find_fix("package_gpu");
if (ifixgpu >= 0) fixgpu = modify->fix[ifixgpu];
if (comm->me == 0) {
if (screen) {
fprintf(screen, "FEP settings ...\n");
fprintf(screen, " temperature = %f\n", temp_fep);
fprintf(screen, " tail %s\n", (tailflag ? "yes":"no"));
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR)
fprintf(screen, " %s %s %d-%d %d-%d\n", pert->pstyle, pert->pparam,
pert->ilo, pert->ihi, pert->jlo, pert->jhi);
else if (pert->which == ATOM)
fprintf(screen, " %d-%d charge\n", pert->ilo, pert->ihi);
}
}
if (logfile) {
fprintf(logfile, "FEP settings ...\n");
fprintf(logfile, " temperature = %f\n", temp_fep);
fprintf(logfile, " tail %s\n", (tailflag ? "yes":"no"));
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR)
fprintf(logfile, " %s %s %d-%d %d-%d\n", pert->pstyle, pert->pparam,
pert->ilo, pert->ihi, pert->jlo, pert->jhi);
else if (pert->which == ATOM)
fprintf(logfile, " %d-%d charge\n", pert->ilo, pert->ihi);
}
}
}
}
void FixAdaptFEP::init()
{
int i,j;
// setup and error checks
anypair = 0;
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name for fix adapt/fep does not exist");
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable for fix adapt/fep is invalid style");
if (ad->which == PAIR) {
anypair = 1;
Pair *pair = force->pair_match(ad->pstyle,1);
if (pair == NULL) error->all(FLERR,"Fix adapt/fep pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL)
error->all(FLERR,"Fix adapt/fep pair style param not supported");
ad->pdim = 2;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
if (ad->pdim == 2) ad->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,ad->pstyle))
error->all(FLERR,"Fix adapt/fep type pair range is not valid for "
"pair hybrid sub-style");
}
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt/fep kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt/fep requires atom attribute diameter");
}
if (ad->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"Fix adapt/fep requires atom attribute charge");
}
}
}
// make copy of original pair array values
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}
}
#ifdef ADAPT_DEBUG
if (comm->me == 0 && screen) {
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
fprintf(screen, "###ADAPT original %s %s\n", ad->pstyle, ad->pparam);
fprintf(screen, "###ADAPT I J old_param\n");
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
fprintf(screen, "###ADAPT %2d %2d %9.5f\n", i, j,
ad->array_orig[i][j]);
}
}
}
#endif
}