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lammps/src/RIGID/fix_shake.cpp
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fix_shake.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.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "stdio.h"
#include "fix_shake.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "angle.h"
#include "comm.h"
#include "group.h"
#include "fix_respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
// allocate space for static class variable
FixShake *FixShake::fsptr;
#define BIG 1.0e20
#define MASSDELTA 0.1
/* ---------------------------------------------------------------------- */
FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
virial_flag = 1;
create_attribute = 1;
// error check
molecular = atom->molecular;
if (molecular == 0)
error->all(FLERR,"Cannot use fix shake with non-molecular system");
// perform initial allocation of atom-based arrays
// register with Atom class
shake_flag = NULL;
shake_atom = NULL;
shake_type = NULL;
xshake = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// set comm size needed by this fix
comm_forward = 3;
// parse SHAKE args
if (narg < 8) error->all(FLERR,"Illegal fix shake command");
tolerance = force->numeric(FLERR,arg[3]);
max_iter = force->inumeric(FLERR,arg[4]);
output_every = force->inumeric(FLERR,arg[5]);
// parse SHAKE args for bond and angle types
// will be used by find_clusters
// store args for "b" "a" "t" as flags in (1:n) list for fast access
// store args for "m" in list of length nmass for looping over
// for "m" verify that atom masses have been set
bond_flag = new int[atom->nbondtypes+1];
for (int i = 1; i <= atom->nbondtypes; i++) bond_flag[i] = 0;
angle_flag = new int[atom->nangletypes+1];
for (int i = 1; i <= atom->nangletypes; i++) angle_flag[i] = 0;
type_flag = new int[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) type_flag[i] = 0;
mass_list = new double[atom->ntypes];
nmass = 0;
char mode = '\0';
int next = 6;
while (next < narg) {
if (strcmp(arg[next],"b") == 0) mode = 'b';
else if (strcmp(arg[next],"a") == 0) mode = 'a';
else if (strcmp(arg[next],"t") == 0) mode = 't';
else if (strcmp(arg[next],"m") == 0) {
mode = 'm';
atom->check_mass();
// break if keyword that is not b,a,t,m
} else if (isalpha(arg[next][0])) break;
// read numeric args of b,a,t,m
else if (mode == 'b') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->nbondtypes)
error->all(FLERR,"Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->nangletypes)
error->all(FLERR,"Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->ntypes)
error->all(FLERR,"Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
double massone = force->numeric(FLERR,arg[next]);
if (massone == 0.0) error->all(FLERR,"Invalid atom mass for fix shake");
if (nmass == atom->ntypes)
error->all(FLERR,"Too many masses for fix shake");
mass_list[nmass++] = massone;
} else error->all(FLERR,"Illegal fix shake command");
next++;
}
// parse optional args
onemol = NULL;
int iarg = next;
while (iarg < narg) {
if (strcmp(arg[next],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix shake command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix shake does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix shake has multiple molecules");
onemol = atom->molecules[imol];
iarg += 2;
} else error->all(FLERR,"Illegal fix shake command");
}
// error check for Molecule template
if (onemol && onemol->shakeflag == 0)
error->all(FLERR,"Fix shake molecule template must have shake info");
// allocate bond and angle distance arrays, indexed from 1 to n
bond_distance = new double[atom->nbondtypes+1];
angle_distance = new double[atom->nangletypes+1];
// allocate statistics arrays
if (output_every) {
int nb = atom->nbondtypes + 1;
b_count = new int[nb];
b_count_all = new int[nb];
b_ave = new double[nb];
b_ave_all = new double[nb];
b_max = new double[nb];
b_max_all = new double[nb];
b_min = new double[nb];
b_min_all = new double[nb];
int na = atom->nangletypes + 1;
a_count = new int[na];
a_count_all = new int[na];
a_ave = new double[na];
a_ave_all = new double[na];
a_max = new double[na];
a_max_all = new double[na];
a_min = new double[na];
a_min_all = new double[na];
}
// identify all SHAKE clusters
find_clusters();
// initialize list of SHAKE clusters to constrain
maxlist = 0;
list = NULL;
}
/* ---------------------------------------------------------------------- */
FixShake::~FixShake()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// set bond_type and angle_type back to positive for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
angletype_findset(i,shake_atom[i][1],shake_atom[i][2],1);
} else if (shake_flag[i] == 2) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
} else if (shake_flag[i] == 3) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
} else if (shake_flag[i] == 4) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][3],1);
}
}
// delete locally stored arrays
memory->destroy(shake_flag);
memory->destroy(shake_atom);
memory->destroy(shake_type);
memory->destroy(xshake);
delete [] bond_flag;
delete [] angle_flag;
delete [] type_flag;
delete [] mass_list;
delete [] bond_distance;
delete [] angle_distance;
if (output_every) {
delete [] b_count;
delete [] b_count_all;
delete [] b_ave;
delete [] b_ave_all;
delete [] b_max;
delete [] b_max_all;
delete [] b_min;
delete [] b_min_all;
delete [] a_count;
delete [] a_count_all;
delete [] a_ave;
delete [] a_ave_all;
delete [] a_max;
delete [] a_max_all;
delete [] a_min;
delete [] a_min_all;
}
memory->destroy(list);
}
/* ---------------------------------------------------------------------- */
int FixShake::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
set bond and angle distances
this init must happen after force->bond and force->angle inits
------------------------------------------------------------------------- */
void FixShake::init()
{
int i,m,flag,flag_all,type1,type2,bond1_type,bond2_type;
double rsq,angle;
// error if more than one shake fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0) count++;
if (count > 1) error->all(FLERR,"More than one fix shake");
// cannot use with minimization since SHAKE turns off bonds
// that should contribute to potential energy
if (update->whichflag == 2)
error->all(FLERR,"Fix shake cannot be used with minimization");
// error if npt,nph fix comes before shake fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
error->all(FLERR,"Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
// could have changed locations in fix list since created
// set ptrs to rRESPA variables
if (strstr(update->integrate_style,"respa")) {
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"RESPA") == 0) ifix_respa = i;
nlevels_respa = ((Respa *) update->integrate)->nlevels;
loop_respa = ((Respa *) update->integrate)->loop;
step_respa = ((Respa *) update->integrate)->step;
}
// set equilibrium bond distances
if (force->bond == NULL)
error->all(FLERR,"Bond potential must be defined for SHAKE");
for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
// set equilibrium angle distances
int nlocal = atom->nlocal;
for (i = 1; i <= atom->nangletypes; i++) {
if (angle_flag[i] == 0) continue;
if (force->angle == NULL)
error->all(FLERR,"Angle potential must be defined for SHAKE");
// scan all atoms for a SHAKE angle cluster
// extract bond types for the 2 bonds in the cluster
// bond types must be same in all clusters of this angle type,
// else set error flag
flag = 0;
bond1_type = bond2_type = 0;
for (m = 0; m < nlocal; m++) {
if (shake_flag[m] != 1) continue;
if (shake_type[m][2] != i) continue;
type1 = MIN(shake_type[m][0],shake_type[m][1]);
type2 = MAX(shake_type[m][0],shake_type[m][1]);
if (bond1_type > 0) {
if (type1 != bond1_type || type2 != bond2_type) {
flag = 1;
break;
}
}
bond1_type = type1;
bond2_type = type2;
}
// error check for any bond types that are not the same
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all(FLERR,"Shake angles have different bond types");
// insure all procs have bond types
MPI_Allreduce(&bond1_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond1_type = flag_all;
MPI_Allreduce(&bond2_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond2_type = flag_all;
// if bond types are 0, no SHAKE angles of this type exist
// just skip this angle
if (bond1_type == 0) {
angle_distance[i] = 0.0;
continue;
}
// compute the angle distance as a function of 2 bond distances
angle = force->angle->equilibrium_angle(i);
rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
(1.0-cos(angle));
angle_distance[i] = sqrt(rsq);
}
}
/* ----------------------------------------------------------------------
SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShake::setup(int vflag)
{
pre_neighbor();
if (output_every) stats();
// setup SHAKE output
bigint ntimestep = update->ntimestep;
if (output_every) {
next_output = ntimestep + output_every;
if (ntimestep % output_every != 0)
next_output = (ntimestep/output_every)*output_every + output_every;
} else next_output = -1;
// half timestep constraint on pre-step, full timestep thereafter
if (strstr(update->integrate_style,"verlet")) {
dtv = update->dt;
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
post_force(vflag);
dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
// apply correction to all rRESPA levels
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
((Respa *) update->integrate)->copy_flevel_f(ilevel);
post_force_respa(vflag,ilevel,loop_respa[ilevel]-1);
((Respa *) update->integrate)->copy_f_flevel(ilevel);
}
dtf_inner = step_respa[0] * force->ftm2v;
}
}
/* ----------------------------------------------------------------------
build list of SHAKE clusters to constrain
if one or more atoms in cluster are on this proc,
this proc lists the cluster exactly once
------------------------------------------------------------------------- */
void FixShake::pre_neighbor()
{
int atom1,atom2,atom3,atom4;
// local copies of atom quantities
// used by SHAKE until next re-neighboring
x = atom->x;
v = atom->v;
f = atom->f;
mass = atom->mass;
rmass = atom->rmass;
type = atom->type;
nlocal = atom->nlocal;
// extend size of SHAKE list if necessary
if (nlocal > maxlist) {
maxlist = nlocal;
memory->destroy(list);
memory->create(list,maxlist,"shake:list");
}
// build list of SHAKE clusters I compute
nlist = 0;
for (int i = 0; i < nlocal; i++)
if (shake_flag[i]) {
if (shake_flag[i] == 2) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
list[nlist++] = i;
}
}
}
/* ----------------------------------------------------------------------
compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShake::post_force(int vflag)
{
if (update->ntimestep == next_output) stats();
// xshake = unconstrained move with current v,f
// communicate results if necessary
unconstrained_update();
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
}
/* ----------------------------------------------------------------------
enforce SHAKE constraints from rRESPA
xshake prediction portion is different than Verlet
------------------------------------------------------------------------- */
void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
{
// call stats only on outermost level
if (ilevel == nlevels_respa-1 && update->ntimestep == next_output) stats();
// might be OK to skip enforcing SHAKE constraings
// on last iteration of inner levels if pressure not requested
// however, leads to slightly different trajectories
//if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1 && !vflag)
// return;
// xshake = unconstrained move with current v,f as function of level
// communicate results if necessary
unconstrained_update_respa(ilevel);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup only needed on last iteration of innermost level
// and if pressure is requested
// virial accumulation happens via evflag at last iteration of each level
if (ilevel == 0 && iloop == loop_respa[ilevel]-1 && vflag) v_setup(vflag);
if (iloop == loop_respa[ilevel]-1) evflag = 1;
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
}
/* ----------------------------------------------------------------------
count # of degrees-of-freedom removed by SHAKE for atoms in igroup
------------------------------------------------------------------------- */
int FixShake::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// count dof in a cluster if and only if
// the central atom is in group and atom i is the central atom
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (shake_flag[i] == 0) continue;
if (shake_atom[i][0] != tag[i]) continue;
if (shake_flag[i] == 1) n += 3;
else if (shake_flag[i] == 2) n += 1;
else if (shake_flag[i] == 3) n += 2;
else if (shake_flag[i] == 4) n += 3;
}
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
identify whether each atom is in a SHAKE cluster
only include atoms in fix group and those bonds/angles specified in input
test whether all clusters are valid
set shake_flag, shake_atom, shake_type values
set bond,angle types negative so will be ignored in neighbor lists
------------------------------------------------------------------------- */
void FixShake::find_clusters()
{
int i,j,m,n,imol,iatom;
int flag,flag_all,messtag,loop,nbuf,nbufmax,size;
tagint tagprev;
double massone;
tagint *buf;
MPI_Request request;
MPI_Status status;
if (me == 0 && screen) fprintf(screen,"Finding SHAKE clusters ...\n");
onemols = atom->avec->onemols;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
double *rmass = atom->rmass;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int angles_allow = atom->avec->angles_allow;
// setup ring of procs
int next = me + 1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
// -----------------------------------------------------
// allocate arrays for self (1d) and bond partners (2d)
// max = max # of bond partners for owned atoms = 2nd dim of partner arrays
// npartner[i] = # of bonds attached to atom i
// nshake[i] = # of SHAKE bonds attached to atom i
// partner_tag[i][] = global IDs of each partner
// partner_mask[i][] = mask of each partner
// partner_type[i][] = type of each partner
// partner_massflag[i][] = 1 if partner meets mass criterion, 0 if not
// partner_bondtype[i][] = type of bond attached to each partner
// partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// partner_nshake[i][] = nshake value for each partner
// -----------------------------------------------------
int max = 0;
if (molecular == 1) {
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][0]);
} else {
for (i = 0; i < nlocal; i++) {
imol = molindex[i];
if (imol < 0) continue;
iatom = molatom[i];
max = MAX(max,onemols[imol]->nspecial[iatom][0]);
}
}
int *npartner;
memory->create(npartner,nlocal,"shake:npartner");
memory->create(nshake,nlocal,"shake:nshake");
tagint **partner_tag;
int **partner_mask,**partner_type,**partner_massflag;
int **partner_bondtype,**partner_shake,**partner_nshake;
memory->create(partner_tag,nlocal,max,"shake:partner_tag");
memory->create(partner_mask,nlocal,max,"shake:partner_mask");
memory->create(partner_type,nlocal,max,"shake:partner_type");
memory->create(partner_massflag,nlocal,max,"shake:partner_massflag");
memory->create(partner_bondtype,nlocal,max,"shake:partner_bondtype");
memory->create(partner_shake,nlocal,max,"shake:partner_shake");
memory->create(partner_nshake,nlocal,max,"shake:partner_nshake");
// -----------------------------------------------------
// set npartner and partner_tag from special arrays
// -----------------------------------------------------
if (molecular == 1) {
for (i = 0; i < nlocal; i++) {
npartner[i] = nspecial[i][0];
for (j = 0; j < npartner[i]; j++)
partner_tag[i][j] = special[i][j];
}
} else {
for (i = 0; i < nlocal; i++) {
imol = molindex[i];
if (imol < 0) continue;
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
npartner[i] = onemols[imol]->nspecial[iatom][0];
for (j = 0; j < npartner[i]; j++)
partner_tag[i][j] = onemols[imol]->special[iatom][j] + tagprev;;
}
}
// -----------------------------------------------------
// set partner_mask, partner_type, partner_massflag, partner_bondtype
// for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in mask, type, massflag, bondtype if own bond partner
// info to store in buf for each off-proc bond = nper = 6
// 2 atoms IDs in bond, space for mask, type, massflag, bondtype
// nbufmax = largest buffer needed to hold info from any proc
int nper = 6;
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
partner_mask[i][j] = 0;
partner_type[i][j] = 0;
partner_massflag[i][j] = 0;
partner_bondtype[i][j] = 0;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
partner_mask[i][j] = mask[m];
partner_type[i][j] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
partner_massflag[i][j] = masscheck(massone);
}
n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
if (n) partner_bondtype[i][j] = n;
else {
n = bondtype_findset(m,tag[i],partner_tag[i][j],0);
if (n) partner_bondtype[i][j] = n;
}
} else nbuf += nper;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
buf[size+2] = 0;
buf[size+3] = 0;
buf[size+4] = 0;
n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
if (n) buf[size+5] = n;
else buf[size+5] = 0;
size += nper;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,1,ring_bonds,buf);
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_mask[i][j] = buf[m+2];
partner_type[i][j] = buf[m+3];
partner_massflag[i][j] = buf[m+4];
partner_bondtype[i][j] = buf[m+5];
m += nper;
}
memory->destroy(buf);
// error check for unfilled partner info
// if partner_type not set, is an error
// partner_bondtype may not be set if special list is not consistent
// with bondatom (e.g. due to delete_bonds command)
// this is OK if one or both atoms are not in fix group, since
// bond won't be SHAKEn anyway
// else it's an error
flag = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < npartner[i]; j++) {
if (partner_type[i][j] == 0) flag = 1;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] == 0) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Did not find fix shake partner info");
// -----------------------------------------------------
// identify SHAKEable bonds
// set nshake[i] = # of SHAKE bonds attached to atom i
// set partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// both atoms must be in group, bondtype must be > 0
// check if bondtype is in input bond_flag
// check if type of either atom is in input type_flag
// check if mass of either atom is in input mass_list
// -----------------------------------------------------
int np;
for (i = 0; i < nlocal; i++) {
nshake[i] = 0;
np = npartner[i];
for (j = 0; j < np; j++) {
partner_shake[i][j] = 0;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] <= 0) continue;
if (bond_flag[partner_bondtype[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (nmass) {
if (partner_massflag[i][j]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
} else {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (masscheck(massone)) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
}
}
}
}
// -----------------------------------------------------
// set partner_nshake for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in partner_nshake if own bond partner
// info to store in buf for each off-proc bond =
// 2 atoms IDs in bond, space for nshake value
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) partner_nshake[i][j] = nshake[m];
else nbuf += 3;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
size += 3;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf);
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_nshake[i][j] = buf[m+2];
m += 3;
}
memory->destroy(buf);
// -----------------------------------------------------
// error checks
// no atom with nshake > 3
// no connected atoms which both have nshake > 1
// -----------------------------------------------------
flag = 0;
for (i = 0; i < nlocal; i++) if (nshake[i] > 3) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Shake cluster of more than 4 atoms");
flag = 0;
for (i = 0; i < nlocal; i++) {
if (nshake[i] <= 1) continue;
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j] && partner_nshake[i][j] > 1) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Shake clusters are connected");
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
// zero shake arrays for all owned atoms
// if I am central atom set shake_flag & shake_atom & shake_type
// for 2-atom clusters, I am central atom if my atom ID < partner ID
// for 3-atom clusters, test for angle constraint
// angle will be stored by this atom if it exists
// if angle type matches angle_flag, then it is angle-constrained
// shake_flag[] = 0 if atom not in SHAKE cluster
// 2,3,4 = size of bond-only cluster
// 1 = 3-atom angle cluster
// shake_atom[][] = global IDs of 2,3,4 atoms in cluster
// central atom is 1st
// for 2-atom cluster, lowest ID is 1st
// shake_type[][] = bondtype of each bond in cluster
// for 3-atom angle cluster, 3rd value is angletype
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
shake_flag[i] = 0;
shake_atom[i][0] = 0;
shake_atom[i][1] = 0;
shake_atom[i][2] = 0;
shake_atom[i][3] = 0;
shake_type[i][0] = 0;
shake_type[i][1] = 0;
shake_type[i][2] = 0;
if (nshake[i] == 1) {
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) break;
if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
shake_flag[i] = 2;
shake_atom[i][0] = tag[i];
shake_atom[i][1] = partner_tag[i][j];
shake_type[i][0] = partner_bondtype[i][j];
}
}
if (nshake[i] > 1) {
shake_flag[i] = 1;
shake_atom[i][0] = tag[i];
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) {
m = shake_flag[i];
shake_atom[i][m] = partner_tag[i][j];
shake_type[i][m-1] = partner_bondtype[i][j];
shake_flag[i]++;
}
}
if (nshake[i] == 2 && angles_allow) {
n = angletype_findset(i,shake_atom[i][1],shake_atom[i][2],0);
if (n <= 0) continue;
if (angle_flag[n]) {
shake_flag[i] = 1;
shake_type[i][2] = n;
}
}
}
// -----------------------------------------------------
// set shake_flag,shake_atom,shake_type for non-central atoms
// requires communication for off-proc atoms
// -----------------------------------------------------
// fill in shake arrays for each bond partner I own
// info to store in buf for each off-proc bond =
// all values from shake_flag, shake_atom, shake_type
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = shake_flag[i];
shake_atom[m][0] = shake_atom[i][0];
shake_atom[m][1] = shake_atom[i][1];
shake_atom[m][2] = shake_atom[i][2];
shake_atom[m][3] = shake_atom[i][3];
shake_type[m][0] = shake_type[i][0];
shake_type[m][1] = shake_type[i][1];
shake_type[m][2] = shake_type[i][2];
} else nbuf += 9;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = partner_tag[i][j];
buf[size+1] = shake_flag[i];
buf[size+2] = shake_atom[i][0];
buf[size+3] = shake_atom[i][1];
buf[size+4] = shake_atom[i][2];
buf[size+5] = shake_atom[i][3];
buf[size+6] = shake_type[i][0];
buf[size+7] = shake_type[i][1];
buf[size+8] = shake_type[i][2];
size += 9;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,3,ring_shake,NULL);
memory->destroy(buf);
// -----------------------------------------------------
// free local memory
// -----------------------------------------------------
memory->destroy(npartner);
memory->destroy(nshake);
memory->destroy(partner_tag);
memory->destroy(partner_mask);
memory->destroy(partner_type);
memory->destroy(partner_massflag);
memory->destroy(partner_bondtype);
memory->destroy(partner_shake);
memory->destroy(partner_nshake);
// -----------------------------------------------------
// set bond_type and angle_type negative for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
angletype_findset(i,shake_atom[i][1],shake_atom[i][2],-1);
} else if (shake_flag[i] == 2) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
} else if (shake_flag[i] == 3) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
} else if (shake_flag[i] == 4) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][3],-1);
}
}
// -----------------------------------------------------
// print info on SHAKE clusters
// -----------------------------------------------------
int count1,count2,count3,count4;
count1 = count2 = count3 = count4 = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 1) count1++;
else if (shake_flag[i] == 2) count2++;
else if (shake_flag[i] == 3) count3++;
else if (shake_flag[i] == 4) count4++;
}
int tmp;
tmp = count1;
MPI_Allreduce(&tmp,&count1,1,MPI_INT,MPI_SUM,world);
tmp = count2;
MPI_Allreduce(&tmp,&count2,1,MPI_INT,MPI_SUM,world);
tmp = count3;
MPI_Allreduce(&tmp,&count3,1,MPI_INT,MPI_SUM,world);
tmp = count4;
MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen," %d = # of size 2 clusters\n",count2/2);
fprintf(screen," %d = # of size 3 clusters\n",count3/3);
fprintf(screen," %d = # of size 4 clusters\n",count4/4);
fprintf(screen," %d = # of frozen angles\n",count1/3);
}
if (logfile) {
fprintf(logfile," %d = # of size 2 clusters\n",count2/2);
fprintf(logfile," %d = # of size 3 clusters\n",count3/3);
fprintf(logfile," %d = # of size 4 clusters\n",count4/4);
fprintf(logfile," %d = # of frozen angles\n",count1/3);
}
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner:
fill in mask and type and massflag
search for bond with 1st atom and fill in bondtype
------------------------------------------------------------------------- */
void FixShake::ring_bonds(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
int nmass = fsptr->nmass;
tagint *buf = (tagint *) cbuf;
int m,n;
double massone;
for (int i = 0; i < ndatum; i += 6) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) {
buf[i+2] = mask[m];
buf[i+3] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
buf[i+4] = fsptr->masscheck(massone);
}
if (buf[i+5] == 0) {
n = fsptr->bondtype_findset(m,buf[i],buf[i+1],0);
if (n) buf[i+5] = n;
}
}
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner, fill in nshake value
------------------------------------------------------------------------- */
void FixShake::ring_nshake(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
int nlocal = atom->nlocal;
int *nshake = fsptr->nshake;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 3) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) buf[i+2] = nshake[m];
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner, fill in nshake value
------------------------------------------------------------------------- */
void FixShake::ring_shake(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
int nlocal = atom->nlocal;
int *shake_flag = fsptr->shake_flag;
tagint **shake_atom = fsptr->shake_atom;
int **shake_type = fsptr->shake_type;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 9) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = buf[i+1];
shake_atom[m][0] = buf[i+2];
shake_atom[m][1] = buf[i+3];
shake_atom[m][2] = buf[i+4];
shake_atom[m][3] = buf[i+5];
shake_type[m][0] = buf[i+6];
shake_type[m][1] = buf[i+7];
shake_type[m][2] = buf[i+8];
}
}
}
/* ----------------------------------------------------------------------
check if massone is within MASSDELTA of any mass in mass_list
return 1 if yes, 0 if not
------------------------------------------------------------------------- */
int FixShake::masscheck(double massone)
{
for (int i = 0; i < nmass; i++)
if (fabs(mass_list[i]-massone) <= MASSDELTA) return 1;
return 0;
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update()
{
double dtfmsq;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / rmass[i];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / mass[type[i]];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom in a rRESPA step
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update_respa(int ilevel)
{
// xshake = atom coords after next x update in innermost loop
// depends on rRESPA level
// for levels > 0 this includes more than one velocity update
// xshake = predicted position from call to this routine at level N =
// x + dt0 (v + dtN/m fN + 1/2 dt(N-1)/m f(N-1) + ... + 1/2 dt0/m f0)
// also set dtfsq = dt0*dtN so that shake,shake3,etc can use it
double ***f_level = ((FixRespa *) modify->fix[ifix_respa])->f_level;
dtfsq = dtf_inner * step_respa[ilevel];
double invmass,dtfmsq;
int jlevel;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / rmass[i];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / mass[type[i]];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake(int m)
{
int nlist,list[2];
double v[6];
double invmass0,invmass1;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
double bond1 = bond_distance[shake_type[m][0]];
// r01 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
// s01 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
// a,b,c = coeffs in quadratic equation for lamda
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
}
double a = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double b = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double c = s01sq - bond1*bond1;
// error check
double determ = b*b - 4.0*a*c;
if (determ < 0.0) {
error->warning(FLERR,"Shake determinant < 0.0",0);
determ = 0.0;
}
// exact quadratic solution for lamda
double lamda,lamda1,lamda2;
lamda1 = (-b+sqrt(determ)) / (2.0*a);
lamda2 = (-b-sqrt(determ)) / (2.0*a);
if (fabs(lamda1) <= fabs(lamda2)) lamda = lamda1;
else lamda = lamda2;
// update forces if atom is owned by this processor
lamda /= dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda*r01[0];
f[i0][1] += lamda*r01[1];
f[i0][2] += lamda*r01[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda*r01[0];
f[i1][1] -= lamda*r01[1];
f[i1][2] -= lamda*r01[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
v[0] = lamda*r01[0]*r01[0];
v[1] = lamda*r01[1]*r01[1];
v[2] = lamda*r01[2]*r01[2];
v[3] = lamda*r01[0]*r01[1];
v[4] = lamda*r01[0]*r01[2];
v[5] = lamda*r01[1]*r01[2];
v_tally(nlist,list,2.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
// r01,r02 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
// s01,s02 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
// inverse of matrix
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = a22*determinv;
double a12inv = -a12*determinv;
double a21inv = -a21*determinv;
double a22inv = a11*determinv;
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,b1,b2,lamda01_new,lamda02_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
quad1_0102 * lamda01*lamda02;
quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
quad2_0102 * lamda01*lamda02;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
lamda01_new = a11inv*b1 + a12inv*b2;
lamda02_new = a21inv*b1 + a22inv*b2;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0] + lamda02*r02[0]*r02[0];
v[1] = lamda01*r01[1]*r01[1] + lamda02*r02[1]*r02[1];
v[2] = lamda01*r01[2]*r01[2] + lamda02*r02[2]*r02[2];
v[3] = lamda01*r01[0]*r01[1] + lamda02*r02[0]*r02[1];
v[4] = lamda01*r01[0]*r01[2] + lamda02*r02[0]*r02[2];
v[5] = lamda01*r01[1]*r01[2] + lamda02*r02[1]*r02[2];
v_tally(nlist,list,3.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake4(int m)
{
int nlist,list[4];
double v[6];
double invmass0,invmass1,invmass2,invmass3;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
int i3 = atom->map(shake_atom[m][3]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond3 = bond_distance[shake_type[m][2]];
// r01,r02,r03 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r03[3];
r03[0] = x[i0][0] - x[i3][0];
r03[1] = x[i0][1] - x[i3][1];
r03[2] = x[i0][2] - x[i3][2];
domain->minimum_image(r03);
// s01,s02,s03 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s03[3];
s03[0] = xshake[i0][0] - xshake[i3][0];
s03[1] = xshake[i0][1] - xshake[i3][1];
s03[2] = xshake[i0][2] - xshake[i3][2];
domain->minimum_image(s03);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r03sq = r03[0]*r03[0] + r03[1]*r03[1] + r03[2]*r03[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s03sq = s03[0]*s03[0] + s03[1]*s03[1] + s03[2]*s03[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
invmass3 = 1.0/rmass[i3];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
invmass3 = 1.0/mass[type[i3]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = 2.0 * invmass0 *
(s01[0]*r03[0] + s01[1]*r03[1] + s01[2]*r03[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass0 *
(s02[0]*r03[0] + s02[1]*r03[1] + s02[2]*r03[2]);
double a31 = 2.0 * invmass0 *
(s03[0]*r01[0] + s03[1]*r01[1] + s03[2]*r01[2]);
double a32 = 2.0 * invmass0 *
(s03[0]*r02[0] + s03[1]*r02[1] + s03[2]*r02[2]);
double a33 = 2.0 * (invmass0+invmass3) *
(s03[0]*r03[0] + s03[1]*r03[1] + s03[2]*r03[2]);
// inverse of matrix;
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0103 = (r01[0]*r03[0] + r01[1]*r03[1] + r01[2]*r03[2]);
double r0203 = (r02[0]*r03[0] + r02[1]*r03[1] + r02[2]*r03[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0303 = invmass0*invmass0 * r03sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0103 = 2.0 * (invmass0+invmass1)*invmass0 * r0103;
double quad1_0203 = 2.0 * invmass0*invmass0 * r0203;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0303 = invmass0*invmass0 * r03sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0103 = 2.0 * invmass0*invmass0 * r0103;
double quad2_0203 = 2.0 * (invmass0+invmass2)*invmass0 * r0203;
double quad3_0101 = invmass0*invmass0 * r01sq;
double quad3_0202 = invmass0*invmass0 * r02sq;
double quad3_0303 = (invmass0+invmass3)*(invmass0+invmass3) * r03sq;
double quad3_0102 = 2.0 * invmass0*invmass0 * r0102;
double quad3_0103 = 2.0 * (invmass0+invmass3)*invmass0 * r0103;
double quad3_0203 = 2.0 * (invmass0+invmass3)*invmass0 * r0203;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda03 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_0303 * lamda03*lamda03 +
quad1_0102 * lamda01*lamda02 +
quad1_0103 * lamda01*lamda03 +
quad1_0203 * lamda02*lamda03;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_0303 * lamda03*lamda03 +
quad2_0102 * lamda01*lamda02 +
quad2_0103 * lamda01*lamda03 +
quad2_0203 * lamda02*lamda03;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_0303 * lamda03*lamda03 +
quad3_0102 * lamda01*lamda02 +
quad3_0103 * lamda01*lamda03 +
quad3_0203 * lamda02*lamda03;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond3*bond3 - s03sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda03_new-lamda03) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda03 = lamda03_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda03 = lamda03/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0] + lamda03*r03[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1] + lamda03*r03[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2] + lamda03*r03[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (i3 < nlocal) {
f[i3][0] -= lamda03*r03[0];
f[i3][1] -= lamda03*r03[1];
f[i3][2] -= lamda03*r03[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
if (i3 < nlocal) list[nlist++] = i3;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda03*r03[0]*r03[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda03*r03[1]*r03[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda03*r03[2]*r03[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda03*r03[0]*r03[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda03*r03[0]*r03[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda03*r03[1]*r03[2];
v_tally(nlist,list,4.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3angle(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond12 = angle_distance[shake_type[m][2]];
// r01,r02,r12 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r12[3];
r12[0] = x[i1][0] - x[i2][0];
r12[1] = x[i1][1] - x[i2][1];
r12[2] = x[i1][2] - x[i2][2];
domain->minimum_image(r12);
// s01,s02,s12 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s12[3];
s12[0] = xshake[i1][0] - xshake[i2][0];
s12[1] = xshake[i1][1] - xshake[i2][1];
s12[2] = xshake[i1][2] - xshake[i2][2];
domain->minimum_image(s12);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r12sq = r12[0]*r12[0] + r12[1]*r12[1] + r12[2]*r12[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s12sq = s12[0]*s12[0] + s12[1]*s12[1] + s12[2]*s12[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = - 2.0 * invmass1 *
(s01[0]*r12[0] + s01[1]*r12[1] + s01[2]*r12[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass2 *
(s02[0]*r12[0] + s02[1]*r12[1] + s02[2]*r12[2]);
double a31 = - 2.0 * invmass1 *
(s12[0]*r01[0] + s12[1]*r01[1] + s12[2]*r01[2]);
double a32 = 2.0 * invmass2 *
(s12[0]*r02[0] + s12[1]*r02[1] + s12[2]*r02[2]);
double a33 = 2.0 * (invmass1+invmass2) *
(s12[0]*r12[0] + s12[1]*r12[1] + s12[2]*r12[2]);
// inverse of matrix
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0112 = (r01[0]*r12[0] + r01[1]*r12[1] + r01[2]*r12[2]);
double r0212 = (r02[0]*r12[0] + r02[1]*r12[1] + r02[2]*r12[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_1212 = invmass1*invmass1 * r12sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0112 = - 2.0 * (invmass0+invmass1)*invmass1 * r0112;
double quad1_0212 = - 2.0 * invmass0*invmass1 * r0212;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_1212 = invmass2*invmass2 * r12sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0112 = 2.0 * invmass0*invmass2 * r0112;
double quad2_0212 = 2.0 * (invmass0+invmass2)*invmass2 * r0212;
double quad3_0101 = invmass1*invmass1 * r01sq;
double quad3_0202 = invmass2*invmass2 * r02sq;
double quad3_1212 = (invmass1+invmass2)*(invmass1+invmass2) * r12sq;
double quad3_0102 = - 2.0 * invmass1*invmass2 * r0102;
double quad3_0112 = - 2.0 * (invmass1+invmass2)*invmass1 * r0112;
double quad3_0212 = 2.0 * (invmass1+invmass2)*invmass2 * r0212;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda12 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_1212 * lamda12*lamda12 +
quad1_0102 * lamda01*lamda02 +
quad1_0112 * lamda01*lamda12 +
quad1_0212 * lamda02*lamda12;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_1212 * lamda12*lamda12 +
quad2_0102 * lamda01*lamda02 +
quad2_0112 * lamda01*lamda12 +
quad2_0212 * lamda02*lamda12;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_1212 * lamda12*lamda12 +
quad3_0102 * lamda01*lamda02 +
quad3_0112 * lamda01*lamda12 +
quad3_0212 * lamda02*lamda12;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond12*bond12 - s12sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda12_new-lamda12) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda12 = lamda12_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda12 = lamda12/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0] - lamda12*r12[0];
f[i1][1] -= lamda01*r01[1] - lamda12*r12[1];
f[i1][2] -= lamda01*r01[2] - lamda12*r12[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0] + lamda12*r12[0];
f[i2][1] -= lamda02*r02[1] + lamda12*r12[1];
f[i2][2] -= lamda02*r02[2] + lamda12*r12[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda12*r12[0]*r12[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda12*r12[1]*r12[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda12*r12[2]*r12[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda12*r12[0]*r12[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda12*r12[0]*r12[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda12*r12[1]*r12[2];
v_tally(nlist,list,3.0,v);
}
}
/* ----------------------------------------------------------------------
print-out bond & angle statistics
------------------------------------------------------------------------- */
void FixShake::stats()
{
int i,j,m,n,iatom,jatom,katom;
double delx,dely,delz;
double r,r1,r2,r3,angle;
// zero out accumulators
int nb = atom->nbondtypes + 1;
int na = atom->nangletypes + 1;
for (i = 0; i < nb; i++) {
b_count[i] = 0;
b_ave[i] = b_max[i] = 0.0;
b_min[i] = BIG;
}
for (i = 0; i < na; i++) {
a_count[i] = 0;
a_ave[i] = a_max[i] = 0.0;
a_min[i] = BIG;
}
// log stats for each bond & angle
// OK to double count since are just averaging
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
// bond stats
n = shake_flag[i];
if (n == 1) n = 3;
iatom = atom->map(shake_atom[i][0]);
for (j = 1; j < n; j++) {
jatom = atom->map(shake_atom[i][j]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
m = shake_type[i][j-1];
b_count[m]++;
b_ave[m] += r;
b_max[m] = MAX(b_max[m],r);
b_min[m] = MIN(b_min[m],r);
}
// angle stats
if (shake_flag[i] == 1) {
iatom = atom->map(shake_atom[i][0]);
jatom = atom->map(shake_atom[i][1]);
katom = atom->map(shake_atom[i][2]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r1 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[iatom][0] - x[katom][0];
dely = x[iatom][1] - x[katom][1];
delz = x[iatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r2 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[jatom][0] - x[katom][0];
dely = x[jatom][1] - x[katom][1];
delz = x[jatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r3 = sqrt(delx*delx + dely*dely + delz*delz);
angle = acos((r1*r1 + r2*r2 - r3*r3) / (2.0*r1*r2));
angle *= 180.0/MY_PI;
m = shake_type[i][2];
a_count[m]++;
a_ave[m] += angle;
a_max[m] = MAX(a_max[m],angle);
a_min[m] = MIN(a_min[m],angle);
}
}
// sum across all procs
MPI_Allreduce(b_count,b_count_all,nb,MPI_INT,MPI_SUM,world);
MPI_Allreduce(b_ave,b_ave_all,nb,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(b_max,b_max_all,nb,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(b_min,b_min_all,nb,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(a_count,a_count_all,na,MPI_INT,MPI_SUM,world);
MPI_Allreduce(a_ave,a_ave_all,na,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(a_max,a_max_all,na,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(a_min,a_min_all,na,MPI_DOUBLE,MPI_MIN,world);
// print stats only for non-zero counts
if (me == 0) {
if (screen) {
fprintf(screen,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 1; i < nb; i++)
if (b_count_all[i])
fprintf(screen," %d %g %g %d\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i],
b_count_all[i]);
for (i = 1; i < na; i++)
if (a_count_all[i])
fprintf(screen," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
if (logfile) {
fprintf(logfile,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 0; i < nb; i++)
if (b_count_all[i])
fprintf(logfile," %d %g %g\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
for (i = 0; i < na; i++)
if (a_count_all[i])
fprintf(logfile," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
}
// next timestep for stats
next_output += output_every;
}
/* ----------------------------------------------------------------------
find a bond between global atom IDs n1 and n2 stored with local atom i
if find it:
if setflag = 0, return bond type
if setflag = -1/1, set bond type to negative/positive and return 0
if do not find it, return 0
------------------------------------------------------------------------- */
int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
{
int m,nbonds;
int *btype;
if (molecular == 1) {
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
nbonds = atom->num_bond[i];
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == bond_atom[i][m]) break;
if (n1 == bond_atom[i][m] && n2 == tag[i]) break;
}
} else {
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
tagint *batom = onemols[imol]->bond_atom[iatom];
btype = onemols[imol]->bond_type[iatom];
nbonds = onemols[imol]->num_bond[iatom];
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == batom[m]+tagprev) break;
if (n1 == batom[m]+tagprev && n2 == tag[i]) break;
}
}
if (m < nbonds) {
if (setflag == 0) {
if (molecular == 1) return atom->bond_type[i][m];
else return btype[m];
}
if (molecular == 1) {
if ((setflag < 0 && atom->bond_type[i][m] > 0) ||
(setflag > 0 && atom->bond_type[i][m] < 0))
atom->bond_type[i][m] = -atom->bond_type[i][m];
} else {
if ((setflag < 0 && btype[m] > 0) ||
(setflag > 0 && btype[m] < 0)) btype[m] = -btype[m];
}
}
return 0;
}
/* ----------------------------------------------------------------------
find an angle with global end atom IDs n1 and n2 stored with local atom i
if find it:
if setflag = 0, return angle type
if setflag = -1/1, set angle type to negative/positive and return 0
if do not find it, return 0
------------------------------------------------------------------------- */
int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
{
int m,nangles;
int *atype;
if (molecular == 1) {
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom3 = atom->angle_atom3;
nangles = atom->num_angle[i];
for (m = 0; m < nangles; m++) {
if (n1 == angle_atom1[i][m] && n2 == angle_atom3[i][m]) break;
if (n1 == angle_atom3[i][m] && n2 == angle_atom1[i][m]) break;
}
} else {
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
tagint *aatom1 = onemols[imol]->angle_atom1[iatom];
tagint *aatom3 = onemols[imol]->angle_atom3[iatom];
atype = onemols[imol]->angle_type[iatom];
nangles = onemols[imol]->num_angle[iatom];
for (m = 0; m < nangles; m++) {
if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break;
if (n1 == aatom3[m]+tagprev && n2 == aatom1[m]+tagprev) break;
}
}
if (m < nangles) {
if (setflag == 0) {
if (molecular == 1) return atom->angle_type[i][m];
else return atype[m];
}
if (molecular == 1) {
if ((setflag < 0 && atom->angle_type[i][m] > 0) ||
(setflag > 0 && atom->angle_type[i][m] < 0))
atom->angle_type[i][m] = -atom->angle_type[i][m];
} else {
if ((setflag < 0 && atype[m] > 0) ||
(setflag > 0 && atype[m] < 0)) atype[m] = -atype[m];
}
}
return 0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShake::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*4 * sizeof(int);
bytes += nmax*3 * sizeof(int);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::grow_arrays(int nmax)
{
memory->grow(shake_flag,nmax,"shake:shake_flag");
memory->grow(shake_atom,nmax,4,"shake:shake_atom");
memory->grow(shake_type,nmax,3,"shake:shake_type");
memory->destroy(xshake);
memory->create(xshake,nmax,3,"shake:xshake");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::copy_arrays(int i, int j, int delflag)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
} else if (flag == 2) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_type[j][0] = shake_type[i][0];
} else if (flag == 3) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
} else if (flag == 4) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_atom[j][3] = shake_atom[i][3];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
}
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixShake::set_arrays(int i)
{
shake_flag[i] = 0;
}
/* ----------------------------------------------------------------------
update one atom's array values
called when molecule is created from fix gcmc
------------------------------------------------------------------------- */
void FixShake::update_arrays(int i, int atom_offset)
{
int flag = shake_flag[i];
if (flag == 1) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
} else if (flag == 2) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
} else if (flag == 3) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
} else if (flag == 4) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
shake_atom[i][3] += atom_offset;
}
}
/* ----------------------------------------------------------------------
initialize a molecule inserted by another fix, e.g. deposit or pour
called when molecule is created
nlocalprev = # of atoms on this proc before molecule inserted
tagprev = atom ID previous to new atoms in the molecule
xgeom,vcm,quat ignored
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev,
double *xgeom, double *vcm, double *quat)
{
int m,flag;
int nlocal = atom->nlocal;
if (nlocalprev == nlocal) return;
tagint *tag = atom->tag;
tagint **mol_shake_atom = onemol->shake_atom;
int **mol_shake_type = onemol->shake_type;
for (int i = nlocalprev; i < nlocal; i++) {
m = tag[i] - tagprev-1;
flag = shake_flag[i] = onemol->shake_flag[m];
if (flag == 1) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
shake_type[i][2] = mol_shake_type[m][2];
} else if (flag == 2) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
} else if (flag == 3) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
} else if (flag == 4) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_atom[i][3] = mol_shake_atom[m][3] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
shake_type[i][2] = mol_shake_type[m][2];
}
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShake::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = shake_flag[i];
int flag = shake_flag[i];
if (flag == 1) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
} else if (flag == 2) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_type[i][0];
} else if (flag == 3) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
} else if (flag == 4) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_atom[i][3];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShake::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
int flag = shake_flag[nlocal] = static_cast<int> (buf[m++]);
if (flag == 1) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
} else if (flag == 2) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
} else if (flag == 3) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
} else if (flag == 4) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][3] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
}
return m;
}
/* ---------------------------------------------------------------------- */
int FixShake::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0];
buf[m++] = xshake[j][1];
buf[m++] = xshake[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0] + dx;
buf[m++] = xshake[j][1] + dy;
buf[m++] = xshake[j][2] + dz;
}
}
return 3;
}
/* ---------------------------------------------------------------------- */
void FixShake::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
xshake[i][0] = buf[m++];
xshake[i][1] = buf[m++];
xshake[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void FixShake::reset_dt()
{
if (strstr(update->integrate_style,"verlet")) {
dtv = update->dt;
dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = step_respa[0] * force->ftm2v;
}
}
/* ----------------------------------------------------------------------
extract Molecule ptr
------------------------------------------------------------------------- */
void *FixShake::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"onemol") == 0) {
return onemol;
}
return NULL;
}
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