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Merge branch 'develop' of github.com:lammps/lammps into Elastic_stress

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This commit is contained in:
Germain Clavier
2022-03-21 10:46:53 +01:00
parent 9742817ba3 649e8a27b3
commit 6f2c09c187
1191 changed files with 217736 additions and 400996 deletions
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288
src/dihedral.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,11 +13,11 @@
#include "dihedral.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "atom_masks.h"
#include "memory.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "suffix.h"
#include "update.h"
@ -29,7 +28,7 @@ using namespace LAMMPS_NS;
DihedralCharmm will override this
------------------------------------------------------------------------- */
Dihedral::Dihedral(LAMMPS *lmp) : Pointers(lmp)
Dihedral::Dihedral(LAMMPS *_lmp) : Pointers(_lmp)
{
energy = 0.0;
writedata = 0;
@ -69,10 +68,9 @@ Dihedral::~Dihedral()
void Dihedral::init()
{
if (!allocated && atom->ndihedraltypes)
error->all(FLERR,"Dihedral coeffs are not set");
if (!allocated && atom->ndihedraltypes) error->all(FLERR, "Dihedral coeffs are not set");
for (int i = 1; i <= atom->ndihedraltypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All dihedral coeffs are not set");
if (setflag[i] == 0) error->all(FLERR, "All dihedral coeffs are not set");
init_style();
}
@ -95,7 +93,7 @@ void Dihedral::init()
void Dihedral::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
int i, n;
evflag = 1;
@ -105,11 +103,9 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR);
vflag_atom = vflag & VIRIAL_ATOM;
if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL)
vflag_atom = 1;
if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) vflag_atom = 1;
cvflag_atom = 0;
if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL)
cvflag_atom = 1;
if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) cvflag_atom = 1;
vflag_either = vflag_global || vflag_atom || cvflag_atom;
// reallocate per-atom arrays if necessary
@ -118,28 +114,29 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
maxeatom = atom->nmax;
if (alloc) {
memory->destroy(eatom);
memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom");
memory->create(eatom, comm->nthreads * maxeatom, "dihedral:eatom");
}
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
if (alloc) {
memory->destroy(vatom);
memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom");
memory->create(vatom, comm->nthreads * maxvatom, 6, "dihedral:vatom");
}
}
if (cvflag_atom && atom->nmax > maxcvatom) {
maxcvatom = atom->nmax;
if (alloc) {
memory->destroy(cvatom);
memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom");
memory->create(cvatom, comm->nthreads * maxcvatom, 9, "dihedral:cvatom");
}
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag_global)
for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
@ -182,20 +179,19 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc)
= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
------------------------------------------------------------------------- */
void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
int nlocal, int newton_bond,
double edihedral, double *f1, double *f3, double *f4,
double vb1x, double vb1y, double vb1z,
double vb2x, double vb2y, double vb2z,
void Dihedral::ev_tally(int i1, int i2, int i3, int i4, int nlocal, int newton_bond,
double edihedral, double *f1, double *f3, double *f4, double vb1x,
double vb1y, double vb1z, double vb2x, double vb2y, double vb2z,
double vb3x, double vb3y, double vb3z)
{
double edihedralquarter,v[6];
double edihedralquarter, v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) energy += edihedral;
if (newton_bond)
energy += edihedral;
else {
edihedralquarter = 0.25*edihedral;
edihedralquarter = 0.25 * edihedral;
if (i1 < nlocal) energy += edihedralquarter;
if (i2 < nlocal) energy += edihedralquarter;
if (i3 < nlocal) energy += edihedralquarter;
@ -203,7 +199,7 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
}
}
if (eflag_atom) {
edihedralquarter = 0.25*edihedral;
edihedralquarter = 0.25 * edihedral;
if (newton_bond || i1 < nlocal) eatom[i1] += edihedralquarter;
if (newton_bond || i2 < nlocal) eatom[i2] += edihedralquarter;
if (newton_bond || i3 < nlocal) eatom[i3] += edihedralquarter;
@ -212,12 +208,12 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
}
if (vflag_either) {
v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0];
v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1];
v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2];
v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1];
v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2];
v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2];
v[0] = vb1x * f1[0] + vb2x * f3[0] + (vb3x + vb2x) * f4[0];
v[1] = vb1y * f1[1] + vb2y * f3[1] + (vb3y + vb2y) * f4[1];
v[2] = vb1z * f1[2] + vb2z * f3[2] + (vb3z + vb2z) * f4[2];
v[3] = vb1x * f1[1] + vb2x * f3[1] + (vb3x + vb2x) * f4[1];
v[4] = vb1x * f1[2] + vb2x * f3[2] + (vb3x + vb2x) * f4[2];
v[5] = vb1y * f1[2] + vb2y * f3[2] + (vb3y + vb2y) * f4[2];
if (vflag_global) {
if (newton_bond) {
@ -229,72 +225,72 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
virial[5] += v[5];
} else {
if (i1 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
virial[0] += 0.25 * v[0];
virial[1] += 0.25 * v[1];
virial[2] += 0.25 * v[2];
virial[3] += 0.25 * v[3];
virial[4] += 0.25 * v[4];
virial[5] += 0.25 * v[5];
}
if (i2 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
virial[0] += 0.25 * v[0];
virial[1] += 0.25 * v[1];
virial[2] += 0.25 * v[2];
virial[3] += 0.25 * v[3];
virial[4] += 0.25 * v[4];
virial[5] += 0.25 * v[5];
}
if (i3 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
virial[0] += 0.25 * v[0];
virial[1] += 0.25 * v[1];
virial[2] += 0.25 * v[2];
virial[3] += 0.25 * v[3];
virial[4] += 0.25 * v[4];
virial[5] += 0.25 * v[5];
}
if (i4 < nlocal) {
virial[0] += 0.25*v[0];
virial[1] += 0.25*v[1];
virial[2] += 0.25*v[2];
virial[3] += 0.25*v[3];
virial[4] += 0.25*v[4];
virial[5] += 0.25*v[5];
virial[0] += 0.25 * v[0];
virial[1] += 0.25 * v[1];
virial[2] += 0.25 * v[2];
virial[3] += 0.25 * v[3];
virial[4] += 0.25 * v[4];
virial[5] += 0.25 * v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i1 < nlocal) {
vatom[i1][0] += 0.25*v[0];
vatom[i1][1] += 0.25*v[1];
vatom[i1][2] += 0.25*v[2];
vatom[i1][3] += 0.25*v[3];
vatom[i1][4] += 0.25*v[4];
vatom[i1][5] += 0.25*v[5];
vatom[i1][0] += 0.25 * v[0];
vatom[i1][1] += 0.25 * v[1];
vatom[i1][2] += 0.25 * v[2];
vatom[i1][3] += 0.25 * v[3];
vatom[i1][4] += 0.25 * v[4];
vatom[i1][5] += 0.25 * v[5];
}
if (newton_bond || i2 < nlocal) {
vatom[i2][0] += 0.25*v[0];
vatom[i2][1] += 0.25*v[1];
vatom[i2][2] += 0.25*v[2];
vatom[i2][3] += 0.25*v[3];
vatom[i2][4] += 0.25*v[4];
vatom[i2][5] += 0.25*v[5];
vatom[i2][0] += 0.25 * v[0];
vatom[i2][1] += 0.25 * v[1];
vatom[i2][2] += 0.25 * v[2];
vatom[i2][3] += 0.25 * v[3];
vatom[i2][4] += 0.25 * v[4];
vatom[i2][5] += 0.25 * v[5];
}
if (newton_bond || i3 < nlocal) {
vatom[i3][0] += 0.25*v[0];
vatom[i3][1] += 0.25*v[1];
vatom[i3][2] += 0.25*v[2];
vatom[i3][3] += 0.25*v[3];
vatom[i3][4] += 0.25*v[4];
vatom[i3][5] += 0.25*v[5];
vatom[i3][0] += 0.25 * v[0];
vatom[i3][1] += 0.25 * v[1];
vatom[i3][2] += 0.25 * v[2];
vatom[i3][3] += 0.25 * v[3];
vatom[i3][4] += 0.25 * v[4];
vatom[i3][5] += 0.25 * v[5];
}
if (newton_bond || i4 < nlocal) {
vatom[i4][0] += 0.25*v[0];
vatom[i4][1] += 0.25*v[1];
vatom[i4][2] += 0.25*v[2];
vatom[i4][3] += 0.25*v[3];
vatom[i4][4] += 0.25*v[4];
vatom[i4][5] += 0.25*v[5];
vatom[i4][0] += 0.25 * v[0];
vatom[i4][1] += 0.25 * v[1];
vatom[i4][2] += 0.25 * v[2];
vatom[i4][3] += 0.25 * v[3];
vatom[i4][4] += 0.25 * v[4];
vatom[i4][5] += 0.25 * v[5];
}
}
}
@ -313,99 +309,97 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4,
double a1[3];
// a1 = r10 = (3*r12 - 2*r32 - r43)/4
a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x);
a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y);
a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z);
a1[0] = 0.25 * (3 * vb1x - 2 * vb2x - vb3x);
a1[1] = 0.25 * (3 * vb1y - 2 * vb2y - vb3y);
a1[2] = 0.25 * (3 * vb1z - 2 * vb2z - vb3z);
cvatom[i1][0] += a1[0]*f1[0];
cvatom[i1][1] += a1[1]*f1[1];
cvatom[i1][2] += a1[2]*f1[2];
cvatom[i1][3] += a1[0]*f1[1];
cvatom[i1][4] += a1[0]*f1[2];
cvatom[i1][5] += a1[1]*f1[2];
cvatom[i1][6] += a1[1]*f1[0];
cvatom[i1][7] += a1[2]*f1[0];
cvatom[i1][8] += a1[2]*f1[1];
cvatom[i1][0] += a1[0] * f1[0];
cvatom[i1][1] += a1[1] * f1[1];
cvatom[i1][2] += a1[2] * f1[2];
cvatom[i1][3] += a1[0] * f1[1];
cvatom[i1][4] += a1[0] * f1[2];
cvatom[i1][5] += a1[1] * f1[2];
cvatom[i1][6] += a1[1] * f1[0];
cvatom[i1][7] += a1[2] * f1[0];
cvatom[i1][8] += a1[2] * f1[1];
}
if (newton_bond || i2 < nlocal) {
double a2[3];
double f2[3];
// a2 = r20 = ( -r12 - 2*r32 - r43)/4
a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x);
a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y);
a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z);
a2[0] = 0.25 * (-vb1x - 2 * vb2x - vb3x);
a2[1] = 0.25 * (-vb1y - 2 * vb2y - vb3y);
a2[2] = 0.25 * (-vb1z - 2 * vb2z - vb3z);
f2[0] = - f1[0] - f3[0] - f4[0];
f2[1] = - f1[1] - f3[1] - f4[1];
f2[2] = - f1[2] - f3[2] - f4[2];
f2[0] = -f1[0] - f3[0] - f4[0];
f2[1] = -f1[1] - f3[1] - f4[1];
f2[2] = -f1[2] - f3[2] - f4[2];
cvatom[i2][0] += a2[0]*f2[0];
cvatom[i2][1] += a2[1]*f2[1];
cvatom[i2][2] += a2[2]*f2[2];
cvatom[i2][3] += a2[0]*f2[1];
cvatom[i2][4] += a2[0]*f2[2];
cvatom[i2][5] += a2[1]*f2[2];
cvatom[i2][6] += a2[1]*f2[0];
cvatom[i2][7] += a2[2]*f2[0];
cvatom[i2][8] += a2[2]*f2[1];
cvatom[i2][0] += a2[0] * f2[0];
cvatom[i2][1] += a2[1] * f2[1];
cvatom[i2][2] += a2[2] * f2[2];
cvatom[i2][3] += a2[0] * f2[1];
cvatom[i2][4] += a2[0] * f2[2];
cvatom[i2][5] += a2[1] * f2[2];
cvatom[i2][6] += a2[1] * f2[0];
cvatom[i2][7] += a2[2] * f2[0];
cvatom[i2][8] += a2[2] * f2[1];
}
if (newton_bond || i3 < nlocal) {
double a3[3];
// a3 = r30 = ( -r12 + 2*r32 - r43)/4
a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x);
a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y);
a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z);
a3[0] = 0.25 * (-vb1x + 2 * vb2x - vb3x);
a3[1] = 0.25 * (-vb1y + 2 * vb2y - vb3y);
a3[2] = 0.25 * (-vb1z + 2 * vb2z - vb3z);
cvatom[i3][0] += a3[0]*f3[0];
cvatom[i3][1] += a3[1]*f3[1];
cvatom[i3][2] += a3[2]*f3[2];
cvatom[i3][3] += a3[0]*f3[1];
cvatom[i3][4] += a3[0]*f3[2];
cvatom[i3][5] += a3[1]*f3[2];
cvatom[i3][6] += a3[1]*f3[0];
cvatom[i3][7] += a3[2]*f3[0];
cvatom[i3][8] += a3[2]*f3[1];
cvatom[i3][0] += a3[0] * f3[0];
cvatom[i3][1] += a3[1] * f3[1];
cvatom[i3][2] += a3[2] * f3[2];
cvatom[i3][3] += a3[0] * f3[1];
cvatom[i3][4] += a3[0] * f3[2];
cvatom[i3][5] += a3[1] * f3[2];
cvatom[i3][6] += a3[1] * f3[0];
cvatom[i3][7] += a3[2] * f3[0];
cvatom[i3][8] += a3[2] * f3[1];
}
if (newton_bond || i4 < nlocal) {
double a4[3];
// a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x);
a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y);
a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z);
a4[0] = 0.25 * (-vb1x + 2 * vb2x + 3 * vb3x);
a4[1] = 0.25 * (-vb1y + 2 * vb2y + 3 * vb3y);
a4[2] = 0.25 * (-vb1z + 2 * vb2z + 3 * vb3z);
cvatom[i4][0] += a4[0]*f4[0];
cvatom[i4][1] += a4[1]*f4[1];
cvatom[i4][2] += a4[2]*f4[2];
cvatom[i4][3] += a4[0]*f4[1];
cvatom[i4][4] += a4[0]*f4[2];
cvatom[i4][5] += a4[1]*f4[2];
cvatom[i4][6] += a4[1]*f4[0];
cvatom[i4][7] += a4[2]*f4[0];
cvatom[i4][8] += a4[2]*f4[1];
cvatom[i4][0] += a4[0] * f4[0];
cvatom[i4][1] += a4[1] * f4[1];
cvatom[i4][2] += a4[2] * f4[2];
cvatom[i4][3] += a4[0] * f4[1];
cvatom[i4][4] += a4[0] * f4[2];
cvatom[i4][5] += a4[1] * f4[2];
cvatom[i4][6] += a4[1] * f4[0];
cvatom[i4][7] += a4[2] * f4[0];
cvatom[i4][8] += a4[2] * f4[1];
}
}
}
/* ---------------------------------------------------------------------- */
void Dihedral::problem(const char *filename, int lineno,
int i1, int i2, int i3, int i4)
void Dihedral::problem(const char *filename, int lineno, int i1, int i2, int i3, int i4)
{
const auto x = atom->x;
auto warn = fmt::format("Dihedral problem: {} {} {} {} {} {}\n",
comm->me, update->ntimestep, atom->tag[i1],
atom->tag[i2], atom->tag[i3], atom->tag[i4]);
warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n",
comm->me,x[i1][0],x[i1][1],x[i1][2]);
warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n",
comm->me,x[i2][0],x[i2][1],x[i2][2]);
warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n",
comm->me,x[i3][0],x[i3][1],x[i3][2]);
warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}",
comm->me,x[i4][0],x[i4][1],x[i4][2]);
auto warn = fmt::format("Dihedral problem: {} {} {} {} {} {}\n", comm->me, update->ntimestep,
atom->tag[i1], atom->tag[i2], atom->tag[i3], atom->tag[i4]);
warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i1][0], x[i1][1],
x[i1][2]);
warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i2][0], x[i2][1],
x[i2][2]);
warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i3][0], x[i3][1],
x[i3][2]);
warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", comm->me, x[i4][0], x[i4][1],
x[i4][2]);
error->warning(filename, lineno, warn);
}
@ -413,8 +407,8 @@ void Dihedral::problem(const char *filename, int lineno,
double Dihedral::memory_usage()
{
double bytes = (double)comm->nthreads*maxeatom * sizeof(double);
bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double);
bytes += (double)comm->nthreads*maxcvatom*9 * sizeof(double);
double bytes = (double) comm->nthreads * maxeatom * sizeof(double);
bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double);
bytes += (double) comm->nthreads * maxcvatom * 9 * sizeof(double);
return bytes;
}