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lammps/src/USER-FEP/fix_adapt_fep.cpp
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fix_adapt_fep.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_adapt_fep.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "modify.h"
#include "force.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "kspace.h"
#include "fix_store.h"
#include "input.h"
#include "variable.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{PAIR,KSPACE,ATOM};
enum{DIAMETER,CHARGE};
/* ---------------------------------------------------------------------- */
FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix adapt/fep command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt/fep command");
dynamic_group_allow = 1;
create_attribute = 1;
// count # of adaptations
nadapt = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 4;
} else break;
}
if (nadapt == 0) error->all(FLERR,"Illegal fix adapt/fep command");
adapt = new Adapt[nadapt];
// parse keywords
nadapt = 0;
diamflag = 0;
chgflag = 0;
iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
adapt[nadapt].which = PAIR;
int n = strlen(arg[iarg+1]) + 1;
adapt[nadapt].pstyle = new char[n];
strcpy(adapt[nadapt].pstyle,arg[iarg+1]);
n = strlen(arg[iarg+2]) + 1;
adapt[nadapt].pparam = new char[n];
strcpy(adapt[nadapt].pparam,arg[iarg+2]);
force->bounds(FLERR,arg[iarg+3],atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi);
force->bounds(FLERR,arg[iarg+4],atom->ntypes,
adapt[nadapt].jlo,adapt[nadapt].jhi);
if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
n = strlen(&arg[iarg+5][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
} else error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
adapt[nadapt].which = KSPACE;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].aparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt/fep command");
force->bounds(FLERR,arg[iarg+2],atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+3][2]);
} else error->all(FLERR,"Illegal fix adapt/fep command");
nadapt++;
iarg += 4;
} else break;
}
// optional keywords
resetflag = 0;
scaleflag = 0;
afterflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"reset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
if (strcmp(arg[iarg+1],"no") == 0) resetflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) resetflag = 1;
else error->all(FLERR,"Illegal fix adapt/fep command");
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix adapt/fep command");
iarg += 2;
} else if (strcmp(arg[iarg],"after") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt/fep command");
if (strcmp(arg[iarg+1],"no") == 0) afterflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) afterflag = 1;
else error->all(FLERR,"Illegal fix adapt/fep command");
iarg += 2;
} else error->all(FLERR,"Illegal fix adapt/fep command");
}
// allocate pair style arrays
int n = atom->ntypes;
for (int m = 0; m < nadapt; m++)
if (adapt[m].which == PAIR)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
id_fix_diam = id_fix_chg = NULL;
}
/* ---------------------------------------------------------------------- */
FixAdaptFEP::~FixAdaptFEP()
{
for (int m = 0; m < nadapt; m++) {
delete [] adapt[m].var;
if (adapt[m].which == PAIR) {
delete [] adapt[m].pstyle;
delete [] adapt[m].pparam;
memory->destroy(adapt[m].array_orig);
}
}
delete [] adapt;
// check nfix in case all fixes have already been deleted
if (id_fix_diam && modify->nfix) modify->delete_fix(id_fix_diam);
if (id_fix_chg && modify->nfix) modify->delete_fix(id_fix_chg);
delete [] id_fix_diam;
delete [] id_fix_chg;
}
/* ---------------------------------------------------------------------- */
int FixAdaptFEP::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
mask |= POST_RUN;
mask |= PRE_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
if need to restore per-atom quantities, create new fix STORE styles
------------------------------------------------------------------------- */
void FixAdaptFEP::post_constructor()
{
if (!resetflag) return;
if (!diamflag && !chgflag) return;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
// new fix group = group for this fix
id_fix_diam = NULL;
id_fix_chg = NULL;
char **newarg = new char*[6];
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
if (diamflag) {
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
id_fix_diam = new char[n];
strcpy(id_fix_diam,id);
strcat(id_fix_diam,"_FIX_STORE_DIAM");
newarg[0] = id_fix_diam;
modify->add_fix(6,newarg);
fix_diam = (FixStore *) modify->fix[modify->nfix-1];
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = radius[i];
else vec[i] = 0.0;
}
}
}
if (chgflag) {
int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
id_fix_chg = new char[n];
strcpy(id_fix_chg,id);
strcat(id_fix_chg,"_FIX_STORE_CHG");
newarg[0] = id_fix_chg;
modify->add_fix(6,newarg);
fix_chg = (FixStore *) modify->fix[modify->nfix-1];
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = q[i];
else vec[i] = 0.0;
}
}
}
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::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/fep 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/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 = NULL;
if (lmp->suffix_enable) {
char psuffix[128];
strcpy(psuffix,ad->pstyle);
strcat(psuffix,"/");
strcat(psuffix,lmp->suffix);
pair = force->pair_match(psuffix,1);
}
if (pair == NULL) 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];
}
}
// 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 FixAdaptFEP::setup_pre_force(int vflag)
{
change_settings();
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::setup_pre_force_respa(int vflag, int ilevel)
{
if (ilevel < nlevels_respa-1) return;
setup_pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::pre_force(int vflag)
{
if (nevery == 0) return;
if (afterflag) { // update at n+1 (better with fix ave/time)
if (nevery == 1 || update->ntimestep == 0)
change_settings();
else if (update->ntimestep > 1 && !((update->ntimestep - 1) % nevery))
change_settings();
} else { // original version: update at n
if (update->ntimestep % nevery)
return;
change_settings();
}
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::pre_force_respa(int vflag, int ilevel, int)
{
if (ilevel < nlevels_respa-1) return;
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdaptFEP::post_run()
{
if (resetflag) restore_settings();
}
/* ----------------------------------------------------------------------
change pair,kspace,atom parameters based on variable evaluation
------------------------------------------------------------------------- */
void FixAdaptFEP::change_settings()
{
int i,j;
// variable evaluation may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
double value = input->variable->compute_equal(ad->ivar);
// set global scalar or type pair array values
if (ad->which == PAIR) {
if (ad->pdim == 0) {
if (scaleflag) *ad->scalar = value * ad->scalar_orig;
else *ad->scalar = value;
} else if (ad->pdim == 2) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value*ad->array_orig[i][j];
else
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
}
// set kspace scale factor
} else if (ad->which == KSPACE) {
*kspace_scale = value;
// set per atom values, also make changes for ghost atoms
} else if (ad->which == ATOM) {
// reset radius from diameter
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
int mflag = 0;
if (atom->rmass_flag) mflag = 1;
double density;
int *atype = atom->type;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (mflag == 0) {
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
} else if (ad->aparam == CHARGE) {
int *atype = atom->type;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++)
if (atype[i] >= ad->ilo && atype[i] <= ad->ihi)
if (mask[i] & groupbit) q[i] = value;
}
}
}
modify->addstep_compute(update->ntimestep + nevery);
// re-initialize pair styles if any PAIR settings were changed
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections
if (anypair) force->pair->reinit();
// reset KSpace charges if charges have changed
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
restore pair,kspace.atom parameters to original values
------------------------------------------------------------------------- */
void FixAdaptFEP::restore_settings()
{
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR) {
if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
else if (ad->pdim == 2) {
for (int i = ad->ilo; i <= ad->ihi; i++)
for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = ad->array_orig[i][j];
}
} else if (ad->which == KSPACE) {
*kspace_scale = 1.0;
} else if (ad->which == ATOM) {
if (diamflag) {
double density;
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = vec[i];
rmass[i] = 4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i] * density;
}
}
if (chgflag) {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) q[i] = vec[i];
}
}
}
if (anypair) force->pair->reinit();
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void FixAdaptFEP::set_arrays(int i)
{
if (fix_diam) fix_diam->vstore[i] = atom->radius[i];
if (fix_chg) fix_chg->vstore[i] = atom->q[i];
}
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