346 lines
9.5 KiB
C++
346 lines
9.5 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, Sandia National Laboratories
|
|
LAMMPS development team: developers@lammps.org
|
|
|
|
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 "compute_angle_local.h"
|
|
#include <cmath>
|
|
#include <cstring>
|
|
#include "atom.h"
|
|
#include "atom_vec.h"
|
|
#include "molecule.h"
|
|
#include "update.h"
|
|
#include "domain.h"
|
|
#include "force.h"
|
|
#include "angle.h"
|
|
#include "input.h"
|
|
#include "variable.h"
|
|
#include "math_const.h"
|
|
#include "memory.h"
|
|
#include "error.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace MathConst;
|
|
|
|
#define DELTA 10000
|
|
|
|
enum{THETA,ENG,VARIABLE};
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
|
|
Compute(lmp, narg, arg),
|
|
bstyle(nullptr), vvar(nullptr), tstr(nullptr), vstr(nullptr), vlocal(nullptr), alocal(nullptr)
|
|
{
|
|
if (narg < 4) error->all(FLERR,"Illegal compute angle/local command");
|
|
|
|
if (atom->avec->angles_allow == 0)
|
|
error->all(FLERR,"Compute angle/local used when angles are not allowed");
|
|
|
|
local_flag = 1;
|
|
|
|
// style args
|
|
|
|
nvalues = narg - 3;
|
|
bstyle = new int[nvalues];
|
|
vstr = new char*[nvalues];
|
|
vvar = new int[nvalues];
|
|
|
|
nvalues = 0;
|
|
tflag = 0;
|
|
nvar = 0;
|
|
|
|
int iarg;
|
|
for (iarg = 3; iarg < narg; iarg++) {
|
|
if (strcmp(arg[iarg],"theta") == 0) {
|
|
bstyle[nvalues++] = THETA;
|
|
tflag = 1;
|
|
} else if (strcmp(arg[iarg],"eng") == 0) {
|
|
bstyle[nvalues++] = ENG;
|
|
} else if (strncmp(arg[iarg],"v_",2) == 0) {
|
|
bstyle[nvalues++] = VARIABLE;
|
|
vstr[nvar] = utils::strdup(&arg[iarg][2]);
|
|
nvar++;
|
|
} else break;
|
|
}
|
|
|
|
// optional args
|
|
|
|
setflag = 0;
|
|
tstr = nullptr;
|
|
|
|
while (iarg < narg) {
|
|
if (strcmp(arg[iarg],"set") == 0) {
|
|
setflag = 1;
|
|
if (iarg+3 > narg) error->all(FLERR,"Illegal compute angle/local command");
|
|
if (strcmp(arg[iarg+1],"theta") == 0) {
|
|
delete [] tstr;
|
|
tstr = utils::strdup(arg[iarg+2]);
|
|
tflag = 1;
|
|
} else error->all(FLERR,"Illegal compute angle/local command");
|
|
iarg += 3;
|
|
} else error->all(FLERR,"Illegal compute angle/local command");
|
|
}
|
|
|
|
// error check
|
|
|
|
if (nvar) {
|
|
if (!setflag)
|
|
error->all(FLERR,"Compute angle/local variable requires a set variable");
|
|
for (int i = 0; i < nvar; i++) {
|
|
vvar[i] = input->variable->find(vstr[i]);
|
|
if (vvar[i] < 0)
|
|
error->all(FLERR,"Variable name for copute angle/local does not exist");
|
|
if (!input->variable->equalstyle(vvar[i]))
|
|
error->all(FLERR,"Variable for compute angle/local is invalid style");
|
|
}
|
|
|
|
if (tstr) {
|
|
tvar = input->variable->find(tstr);
|
|
if (tvar < 0)
|
|
error->all(FLERR,"Variable name for compute angle/local does not exist");
|
|
if (!input->variable->internalstyle(tvar))
|
|
error->all(FLERR,"Variable for compute angle/local is invalid style");
|
|
}
|
|
} else if (setflag)
|
|
error->all(FLERR,"Compute angle/local set with no variable");
|
|
|
|
// initialize output
|
|
|
|
if (nvalues == 1) size_local_cols = 0;
|
|
else size_local_cols = nvalues;
|
|
|
|
nmax = 0;
|
|
vlocal = nullptr;
|
|
alocal = nullptr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeAngleLocal::~ComputeAngleLocal()
|
|
{
|
|
delete [] bstyle;
|
|
for (int i = 0; i < nvar; i++) delete [] vstr[i];
|
|
delete [] vstr;
|
|
delete [] vvar;
|
|
|
|
delete [] tstr;
|
|
|
|
memory->destroy(vlocal);
|
|
memory->destroy(alocal);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeAngleLocal::init()
|
|
{
|
|
if (force->angle == nullptr)
|
|
error->all(FLERR,"No angle style is defined for compute angle/local");
|
|
|
|
if (nvar) {
|
|
for (int i = 0; i < nvar; i++) {
|
|
vvar[i] = input->variable->find(vstr[i]);
|
|
if (vvar[i] < 0)
|
|
error->all(FLERR,"Variable name for compute angle/local does not exist");
|
|
}
|
|
|
|
if (tstr) {
|
|
tvar = input->variable->find(tstr);
|
|
if (tvar < 0)
|
|
error->all(FLERR,"Variable name for compute angle/local does not exist");
|
|
}
|
|
}
|
|
|
|
// do initial memory allocation so that memory_usage() is correct
|
|
|
|
ncount = compute_angles(0);
|
|
if (ncount > nmax) reallocate(ncount);
|
|
size_local_rows = ncount;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeAngleLocal::compute_local()
|
|
{
|
|
invoked_local = update->ntimestep;
|
|
|
|
// count local entries and compute angle info
|
|
|
|
ncount = compute_angles(0);
|
|
if (ncount > nmax) reallocate(ncount);
|
|
size_local_rows = ncount;
|
|
ncount = compute_angles(1);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
count angles and compute angle info on this proc
|
|
only count if 2nd atom is the one storing the angle
|
|
all atoms in interaction must be in group
|
|
all atoms in interaction must be known to proc
|
|
if angle is deleted (type = 0), do not count
|
|
if angle is turned off (type < 0), still count
|
|
if flag is set, compute requested info about angle
|
|
if angle is turned off (type < 0), energy = 0.0
|
|
------------------------------------------------------------------------- */
|
|
|
|
int ComputeAngleLocal::compute_angles(int flag)
|
|
{
|
|
int i,m,na,atom1,atom2,atom3,imol,iatom,atype,ivar;
|
|
tagint tagprev;
|
|
double delx1,dely1,delz1,delx2,dely2,delz2;
|
|
double rsq1,rsq2,r1,r2,c,theta;
|
|
double *ptr;
|
|
|
|
double **x = atom->x;
|
|
tagint *tag = atom->tag;
|
|
int *num_angle = atom->num_angle;
|
|
tagint **angle_atom1 = atom->angle_atom1;
|
|
tagint **angle_atom2 = atom->angle_atom2;
|
|
tagint **angle_atom3 = atom->angle_atom3;
|
|
int **angle_type = atom->angle_type;
|
|
int *mask = atom->mask;
|
|
|
|
int *molindex = atom->molindex;
|
|
int *molatom = atom->molatom;
|
|
Molecule **onemols = atom->avec->onemols;
|
|
|
|
int nlocal = atom->nlocal;
|
|
int molecular = atom->molecular;
|
|
|
|
// loop over all atoms and their angles
|
|
|
|
Angle *angle = force->angle;
|
|
|
|
m = 0;
|
|
for (atom2 = 0; atom2 < nlocal; atom2++) {
|
|
if (!(mask[atom2] & groupbit)) continue;
|
|
|
|
if (molecular == Atom::MOLECULAR) na = num_angle[atom2];
|
|
else {
|
|
if (molindex[atom2] < 0) continue;
|
|
imol = molindex[atom2];
|
|
iatom = molatom[atom2];
|
|
na = onemols[imol]->num_angle[iatom];
|
|
}
|
|
|
|
for (i = 0; i < na; i++) {
|
|
if (molecular == Atom::MOLECULAR) {
|
|
if (tag[atom2] != angle_atom2[atom2][i]) continue;
|
|
atype = angle_type[atom2][i];
|
|
atom1 = atom->map(angle_atom1[atom2][i]);
|
|
atom3 = atom->map(angle_atom3[atom2][i]);
|
|
} else {
|
|
if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue;
|
|
atype = onemols[imol]->angle_type[atom2][i];
|
|
tagprev = tag[atom2] - iatom - 1;
|
|
atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i]+tagprev);
|
|
atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i]+tagprev);
|
|
}
|
|
|
|
if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
|
|
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
|
|
if (atype == 0) continue;
|
|
|
|
if (!flag) {
|
|
m++;
|
|
continue;
|
|
}
|
|
|
|
// theta needed by one or more outputs
|
|
|
|
if (tflag) {
|
|
delx1 = x[atom1][0] - x[atom2][0];
|
|
dely1 = x[atom1][1] - x[atom2][1];
|
|
delz1 = x[atom1][2] - x[atom2][2];
|
|
domain->minimum_image(delx1,dely1,delz1);
|
|
|
|
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
|
r1 = sqrt(rsq1);
|
|
|
|
delx2 = x[atom3][0] - x[atom2][0];
|
|
dely2 = x[atom3][1] - x[atom2][1];
|
|
delz2 = x[atom3][2] - x[atom2][2];
|
|
domain->minimum_image(delx2,dely2,delz2);
|
|
|
|
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
|
r2 = sqrt(rsq2);
|
|
|
|
// c = cosine of angle
|
|
// theta = angle in radians
|
|
|
|
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
|
c /= r1*r2;
|
|
if (c > 1.0) c = 1.0;
|
|
if (c < -1.0) c = -1.0;
|
|
theta = acos(c);
|
|
}
|
|
|
|
if (nvalues == 1) ptr = &vlocal[m];
|
|
else ptr = alocal[m];
|
|
|
|
if (nvar) {
|
|
ivar = 0;
|
|
if (tstr) input->variable->internal_set(tvar,theta);
|
|
}
|
|
|
|
for (int n = 0; n < nvalues; n++) {
|
|
switch (bstyle[n]) {
|
|
case THETA:
|
|
ptr[n] = 180.0*theta/MY_PI;
|
|
break;
|
|
case ENG:
|
|
if (atype > 0) ptr[n] = angle->single(atype,atom1,atom2,atom3);
|
|
else ptr[n] = 0.0;
|
|
break;
|
|
case VARIABLE:
|
|
ptr[n] = input->variable->compute_equal(vvar[ivar]);
|
|
ivar++;
|
|
break;
|
|
}
|
|
}
|
|
|
|
m++;
|
|
}
|
|
}
|
|
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeAngleLocal::reallocate(int n)
|
|
{
|
|
// grow vector_local or array_local
|
|
|
|
while (nmax < n) nmax += DELTA;
|
|
|
|
if (nvalues == 1) {
|
|
memory->destroy(vlocal);
|
|
memory->create(vlocal,nmax,"angle/local:vector_local");
|
|
vector_local = vlocal;
|
|
} else {
|
|
memory->destroy(alocal);
|
|
memory->create(alocal,nmax,nvalues,"angle/local:array_local");
|
|
array_local = alocal;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage of local data
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeAngleLocal::memory_usage()
|
|
{
|
|
double bytes = (double)nmax*nvalues * sizeof(double);
|
|
return bytes;
|
|
}
|